From 9faa3bd3e079dd63b1308a507b58bfdbe5604fe3 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Thu, 8 May 2014 18:30:41 -0400
Subject: [PATCH 01/46] whoops, in ff4cd45 missed file type card #3961

- the highlights were being added to every card type
---
 src/main/webapp/search-include-fragment.xhtml | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml
index c63082dd079..1371abb95bf 100644
--- a/src/main/webapp/search-include-fragment.xhtml
+++ b/src/main/webapp/search-include-fragment.xhtml
@@ -597,17 +597,17 @@
                                             <h:outputText value="... " rendered="#{varStatus.last != true}"/>
                                         </ui:repeat>
                                     </ui:fragment>
-                                </ui:fragment>
-                                <ui:fragment rendered="#{result.highlightsAsList.size() > 0}">
-                                    <div>
-                                        <ui:repeat value="#{result.highlightsAsList}" var="highlight">
-                                            <ui:repeat value="#{highlight.snippets}" var="snippet">
-                                                <h:outputText value="#{highlight.displayName}: "/>
-                                                <h:outputText value="#{snippet}" escape="false"/>
-                                                <br/>
+                                    <ui:fragment rendered="#{result.highlightsAsList.size() > 0}">
+                                        <div>
+                                            <ui:repeat value="#{result.highlightsAsList}" var="highlight">
+                                                <ui:repeat value="#{highlight.snippets}" var="snippet">
+                                                    <h:outputText value="#{highlight.displayName}: "/>
+                                                    <h:outputText value="#{snippet}" escape="false"/>
+                                                    <br/>
+                                                </ui:repeat>
                                             </ui:repeat>
-                                        </ui:repeat>
-                                    </div>
+                                        </div>
+                                    </ui:fragment>
                                 </ui:fragment>
                             </p:column>
                         </p:dataTable>

From 51636d00623d429f74c0e81e952ce7550460119a Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.83.216>
Date: Fri, 9 May 2014 13:20:43 -0400
Subject: [PATCH 02/46] Added "disabled" style class to the pagination
 First/Previous links if you are on the first page of results. Added styling
 for the cursor hand icon, to the search icon in the persistent navbar, to
 show it is a clickable element.

---
 src/main/webapp/resources/css/structure.css   | 1 +
 src/main/webapp/search-include-fragment.xhtml | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/webapp/resources/css/structure.css b/src/main/webapp/resources/css/structure.css
index 1c1a171f593..75122523db8 100644
--- a/src/main/webapp/resources/css/structure.css
+++ b/src/main/webapp/resources/css/structure.css
@@ -16,6 +16,7 @@ body .ui-widget {font-size: inherit;}
 #navbarFixed .navbar-brand {color:#C55B28; padding-left:34px;background: url(/resources/images/logo_dataverse.png) no-repeat left center;background-size:20% auto;}
 #navbarFixed .label.beta {display:block; float:left; margin-top:10px; background:#C55B28; font-size:1.4em; font-weight:normal;}
 
+#navbarFixed #navbar-search-toggle {cursor: pointer; cursor: hand;}
 #navbarFixed .dropdown.accountName .label.label-danger {margin-left:.5em;}
 #navbarFixed .dropdown.accountName .logout form {margin:0; padding:0; width:100%;}
 #navbarFixed .dropdown.accountName .logout a {clear: both; color: #333333; display: block; font-weight: normal; line-height: 1.42857; padding: 3px 20px; white-space: nowrap; text-decoration: none;}
diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml
index 1371abb95bf..636bc430785 100644
--- a/src/main/webapp/search-include-fragment.xhtml
+++ b/src/main/webapp/search-include-fragment.xhtml
@@ -256,7 +256,7 @@
                                         <div class="pagination pull-right">
                                             <ul class="pagination">
                                                 <!--should take you to page 1-->
-                                                <li>
+                                                <li class="#{SearchIncludeFragment.page == '1' ? 'disabled' : ''}">
                                                     <h:outputLink>
                                                         <h:outputText value="&#171;"/>
                                                         <f:param name="id" value="#{SearchIncludeFragment.dataverseId}"/>
@@ -270,7 +270,7 @@
                                                         <f:param name="page" value="1"/>
                                                     </h:outputLink>
                                                 </li>
-                                                <li>
+                                                <li class="#{SearchIncludeFragment.page == '1' ? 'disabled' : ''}">
                                                     <h:outputLink>
                                                         <h:outputText value="&lt; Previous"/>
                                                         <f:param name="id" value="#{SearchIncludeFragment.dataverseId}"/>

From 5e963a3cf90fbffd435b6b8e3f82ecb4ae896d09 Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.83.216>
Date: Fri, 9 May 2014 13:34:07 -0400
Subject: [PATCH 03/46] Also added "disabled" style class to the bottom
 pagination First/Previous links.

---
 src/main/webapp/search-include-fragment.xhtml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml
index 636bc430785..bcd0cef4e28 100644
--- a/src/main/webapp/search-include-fragment.xhtml
+++ b/src/main/webapp/search-include-fragment.xhtml
@@ -619,7 +619,7 @@
                                 <div class="pagination pull-right" >
                                     <ul class="pagination">
                                         <!--should take you to page 1-->
-                                        <li>
+                                        <li class="#{SearchIncludeFragment.page == '1' ? 'disabled' : ''}">
                                             <h:outputLink>
                                                 <h:outputText value="&#171;"/>
                                                 <f:param name="id" value="#{SearchIncludeFragment.dataverseId}"/>
@@ -633,7 +633,7 @@
                                                 <f:param name="page" value="1"/>
                                             </h:outputLink>
                                         </li>
-                                        <li>
+                                        <li class="#{SearchIncludeFragment.page == '1' ? 'disabled' : ''}">
                                             <h:outputLink>
                                                 <h:outputText value="&lt; Previous"/>
                                                 <f:param name="id" value="#{SearchIncludeFragment.dataverseId}"/>

From 373e3d8e3fac6502b5d08e3c001f7ac95c9b3da3 Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.83.216>
Date: Fri, 9 May 2014 14:10:07 -0400
Subject: [PATCH 04/46] Cleaned up the "Add "Replication Data for" to Title"
 button on the edit mode of the dataset pg by applying Bootstrap style
 classes.

---
 src/main/webapp/datasetFieldForEditFragment.xhtml | 2 +-
 src/main/webapp/resources/css/structure.css       | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/webapp/datasetFieldForEditFragment.xhtml b/src/main/webapp/datasetFieldForEditFragment.xhtml
index 1fc4d97ecda..4aa8e3d70b7 100644
--- a/src/main/webapp/datasetFieldForEditFragment.xhtml
+++ b/src/main/webapp/datasetFieldForEditFragment.xhtml
@@ -37,7 +37,7 @@
 
     <!-- This button / script is for replication data for the title field and is client side only -->                         
     <ui:fragment rendered="#{dsfv.datasetField.datasetFieldType.name == 'title' and DatasetPage.editMode == 'CREATE' }">
-        <input type="button" id="replicationDataButton" value="Add 'Replication Data for' to Title" onclick="replicationFor();
+        <input type="button" id="replicationDataButton" class="btn btn-default" value="Add &#34;Replication Data for&#34; to Title" onclick="replicationFor();
                 return false;"/>
 
         <script type="text/javascript">
diff --git a/src/main/webapp/resources/css/structure.css b/src/main/webapp/resources/css/structure.css
index 75122523db8..046e3137add 100644
--- a/src/main/webapp/resources/css/structure.css
+++ b/src/main/webapp/resources/css/structure.css
@@ -179,6 +179,8 @@ div[id$='resultsTable'].resultsNone .ui-datatable-tablewrapper table tfoot {disp
 .panelgridLayoutTable.titleCitationBlock tr.ui-widget-content td {border:0;}
 
 span[id$='editDataSet'] .ui-button-text {white-space: nowrap;}
+
+#replicationDataButton {margin-top:5px;}
                                     
 #title {/*display:block;*/font-size:1.5em;font-weight:bold; /*margin-bottom:.5em;*/}
 #author, #contact {display:block; margin-bottom:.5em;}

From 269412f0a9d2a109de014c57840976ae31e8c4ae Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Fri, 9 May 2014 15:28:00 -0400
Subject: [PATCH 05/46] split out docs for Data Deposit and Data Sharing APIs
 #3385

- also link to https://redmine.hmdc.harvard.edu/issues/3385 where work
  will be done to connect these APIs
---
 doc/Sphinx/source/API/data-deposit.rst        |  8 +++++++
 .../{dataverse-apis.rst => data-sharing.rst}  | 24 +------------------
 doc/Sphinx/source/API/index.rst               | 10 ++++++--
 3 files changed, 17 insertions(+), 25 deletions(-)
 create mode 100644 doc/Sphinx/source/API/data-deposit.rst
 rename doc/Sphinx/source/API/{dataverse-apis.rst => data-sharing.rst} (91%)

diff --git a/doc/Sphinx/source/API/data-deposit.rst b/doc/Sphinx/source/API/data-deposit.rst
new file mode 100644
index 00000000000..aed5456ed0d
--- /dev/null
+++ b/doc/Sphinx/source/API/data-deposit.rst
@@ -0,0 +1,8 @@
+Data Deposit API
+================
+
+Please note that while Dataverse Network (DVN) 3.6 and higher support a
+new Data Deposit API documented at
+http://thedata.harvard.edu/guides/dataverse-api-main.html#data-deposit-api
+the API has not yet been added Dataverse 4.0 Beta.  That work will be
+completed in https://redmine.hmdc.harvard.edu/issues/3385 
diff --git a/doc/Sphinx/source/API/dataverse-apis.rst b/doc/Sphinx/source/API/data-sharing.rst
similarity index 91%
rename from doc/Sphinx/source/API/dataverse-apis.rst
rename to doc/Sphinx/source/API/data-sharing.rst
index ebd485bdc73..6e93cc438cf 100644
--- a/doc/Sphinx/source/API/dataverse-apis.rst
+++ b/doc/Sphinx/source/API/data-sharing.rst
@@ -1,13 +1,5 @@
-Dataverse Network APIs
-++++++++++++++++++++++++
-
-We strongly encourage anyone interested in building tools to
-interoperate with the Dataverse Network to utilize our open source
-APIs. Please visit our `website <http://thedata.org/book/apps>`__  for
-examples of external apps that have been built to work with our APIs.
-
 Data Sharing API
-==================
+================
 
 As of version 3.0, a new API for programmatic access to the DVN data and
 metadata has been added. The API allows a remote, non-DVN
@@ -307,17 +299,3 @@ type, file name and such)
 | Authorization header supplied, but the authenticated user is not
 | authorized to directly access the object protected by Access
 | Permissions and/or Access Restrictions (“Terms of Use”).
-
-
-Data Deposit API
-===========
-
-As of version 3.6, a new API for programmatic deposit of data and metadata to the Dataverse Network will be added. The API will allow a remote, non-Dataverse Network archive/application to deposit files and metadata to a Dataverse Network installation.
-
-The latest information on this plugin is available here:
-`https://redmine.hmdc.harvard.edu/issues/3108 <https://redmine.hmdc.harvard.edu/issues/3108>`__
-
-
-
-
-
diff --git a/doc/Sphinx/source/API/index.rst b/doc/Sphinx/source/API/index.rst
index ad9a2913a80..ff372eb2e18 100644
--- a/doc/Sphinx/source/API/index.rst
+++ b/doc/Sphinx/source/API/index.rst
@@ -4,11 +4,17 @@
    contain the root `toctree` directive.
 
 API Guide
-=======================================================
+=========
+
+We strongly encourage anyone interested in building tools to
+interoperate with the Dataverse Network to utilize our open source
+APIs. Please visit http://datascience.iq.harvard.edu/collaborations for
+examples of external apps that have been built to work with our APIs.
 
 Contents:
 
 .. toctree::
    :maxdepth: 2
 
-  dataverse-apis
+  data-sharing
+  data-deposit

From f4412588213cf108f488438bb53bb2393906dcc9 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Fri, 9 May 2014 16:01:48 -0400
Subject: [PATCH 06/46] explain how to set up PageKite

---
 doc/Sphinx/source/Developers/index.rst |  1 +
 doc/Sphinx/source/Developers/tools.rst | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 doc/Sphinx/source/Developers/tools.rst

diff --git a/doc/Sphinx/source/Developers/index.rst b/doc/Sphinx/source/Developers/index.rst
index 501f3aadfec..9e547cd547d 100644
--- a/doc/Sphinx/source/Developers/index.rst
+++ b/doc/Sphinx/source/Developers/index.rst
@@ -12,5 +12,6 @@ Contents:
    :maxdepth: 2
 
   dev-main
+  tools
 
 
diff --git a/doc/Sphinx/source/Developers/tools.rst b/doc/Sphinx/source/Developers/tools.rst
new file mode 100644
index 00000000000..9d245e38d76
--- /dev/null
+++ b/doc/Sphinx/source/Developers/tools.rst
@@ -0,0 +1,20 @@
+=====
+Tools
+=====
+
+PageKite
+++++++++
+
+PageKite is a fantastic service that can be used to share your
+local development environment over the Internet on a public IP address.
+
+With PageKite running on your laptop, the world can access a URL such as
+http://pdurbin.pagekite.me to see what you see at http://localhost:8080
+
+Sign up at https://pagekite.net and follow the installation instructions or simply download https://pagekite.net/pk/pagekite.py
+
+The first time you run ``./pagekite.py`` a file at ``~/.pagekite.rc`` will be
+created. You can edit this file to configure PageKite to serve up port 8080
+(the default GlassFish HTTP port) or the port of your choosing.
+
+According to https://pagekite.net/support/free-for-foss/ PageKite (very generously!) offers free accounts to developers writing software the meets http://opensource.org/docs/definition.php such as Dataverse.

From bd54c4d60b8af2f070a926c7b768e60239a7f203 Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.85.140>
Date: Mon, 12 May 2014 15:26:10 -0400
Subject: [PATCH 07/46] Minor layout improvements for spacing and font-size to
 Draft/Unpublished/Beta lables, and the background color for citation blocks.

---
 src/main/webapp/dataset.xhtml                 |  6 +++---
 src/main/webapp/resources/css/structure.css   | 12 +++++++-----
 src/main/webapp/search-include-fragment.xhtml |  2 +-
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml
index 0b480d68345..90600942812 100644
--- a/src/main/webapp/dataset.xhtml
+++ b/src/main/webapp/dataset.xhtml
@@ -154,11 +154,11 @@
                                 <div id="datasetVersionBlock">
                                     <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.title.value}">
                                         <span id="title">#{DatasetPage.datasetVersionUI.title.value}</span>
-                                        <h:outputText value="Draft" styleClass="label label-warning" style="margin-left:1em;vertical-align:text-top;" rendered="#{DatasetPage.displayVersion.draft}"/>
-                                        <h:outputText value="Unpublished" styleClass="label label-danger" style="margin-left:1em;vertical-align:text-top;" rendered="#{!DatasetPage.dataset.released}"/>
+                                        <h:outputText value="Draft" styleClass="label label-warning" rendered="#{DatasetPage.displayVersion.draft}"/>
+                                        <h:outputText value="Unpublished" styleClass="label label-danger" rendered="#{!DatasetPage.dataset.released}"/>
                                     </ui:fragment>
                                     <ui:fragment rendered="#{!empty DatasetPage.displayCitation}">
-                                        <div id="citation">
+                                        <div id="citation" class="bg-info">
                                             <span>#{DatasetPage.displayCitation}</span> 
                                             <ui:fragment rendered="#{!DatasetPage.dataset.released}">
                                                 <span class="glyphicon glyphicon-question-sign text-primary" style="cursor:pointer; cursor:hand;" data-toggle="tooltip" data-trigger="hover" data-placement="top" data-original-title="DRAFT VERSION will be replaced in the citation with V1 once the dataset has been published."></span>
diff --git a/src/main/webapp/resources/css/structure.css b/src/main/webapp/resources/css/structure.css
index 046e3137add..5f9fdd658b3 100644
--- a/src/main/webapp/resources/css/structure.css
+++ b/src/main/webapp/resources/css/structure.css
@@ -14,10 +14,10 @@ body .ui-widget {font-size: inherit;}
     z-index: 930;
 }
 #navbarFixed .navbar-brand {color:#C55B28; padding-left:34px;background: url(/resources/images/logo_dataverse.png) no-repeat left center;background-size:20% auto;}
-#navbarFixed .label.beta {display:block; float:left; margin-top:10px; background:#C55B28; font-size:1.4em; font-weight:normal;}
+#navbarFixed .label.beta {display:block; float:left; margin-top:12px; background:#C55B28; font-size:18px; font-weight:normal;}
 
 #navbarFixed #navbar-search-toggle {cursor: pointer; cursor: hand;}
-#navbarFixed .dropdown.accountName .label.label-danger {margin-left:.5em;}
+#navbarFixed .dropdown.accountName .label.label-danger {margin-left:.5em; line-height:normal; vertical-align:text-top;}
 #navbarFixed .dropdown.accountName .logout form {margin:0; padding:0; width:100%;}
 #navbarFixed .dropdown.accountName .logout a {clear: both; color: #333333; display: block; font-weight: normal; line-height: 1.42857; padding: 3px 20px; white-space: nowrap; text-decoration: none;}
 #navbarFixed .dropdown.accountName .logout a:hover, #navbarFixed .dropdown.accountName .logout a:focus {background-color: #E8E8E8; background-image: linear-gradient(to bottom, #F5F5F5 0px, #E8E8E8 100%); background-repeat: repeat-x; color: #262626; outline: 0; text-decoration: none;}
@@ -110,8 +110,8 @@ table.ui-selectmanycheckbox.metadata-blocks-select label.ui-state-disabled {back
 
 span.search-term-match {font-weight: bold;}
 div[id$='resultsTable'] div.ui-datatable-tablewrapper table td > div {clear:left; margin-bottom: .5em;}
-div[id$='resultsTable'] div.ui-datatable-tablewrapper table td > div > span.label {vertical-align:text-top; line-height: normal; margin-left:.5em;}
-div[id$='resultsTable'] .resultDatasetCitationBlock {display:block;margin:4px 0 .5em 60px;background:#FCFCE2;padding:4px;}
+div[id$='resultsTable'] div.ui-datatable-tablewrapper table td > div > span.label {vertical-align:text-bottom; line-height: normal; margin-left:.5em;}
+div[id$='resultsTable'] .resultDatasetCitationBlock {display:block;margin:4px 0 .5em 60px;padding:4px;}
 div[id$='resultsTable'] .resultDatasetCitationBlock span.search-term-match {font-weight: normal;}
 
 form[id$='facetType'] > div.clearfix {margin-bottom:4px;}
@@ -178,13 +178,15 @@ div[id$='resultsTable'].resultsNone .ui-datatable-tablewrapper table tfoot {disp
 .panelgridLayoutTable.titleCitationBlock tr.ui-widget-content, 
 .panelgridLayoutTable.titleCitationBlock tr.ui-widget-content td {border:0;}
 
+#datasetVersionBlock span.label {vertical-align:text-top; line-height:normal; margin-left: 1em;}
+
 span[id$='editDataSet'] .ui-button-text {white-space: nowrap;}
 
 #replicationDataButton {margin-top:5px;}
                                     
 #title {/*display:block;*/font-size:1.5em;font-weight:bold; /*margin-bottom:.5em;*/}
 #author, #contact {display:block; margin-bottom:.5em;}
-#citation {background-color: #FCFCE2; padding:.5em; margin-bottom:.5em;}
+#citation {padding:.5em; margin-bottom:.5em;}
 #description {display:block; margin-bottom:.5em;}
 #keywords, #subject, #note, #publication {display:block; margin-bottom:.5em;}
 #keywords {}
diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml
index bcd0cef4e28..2117b8e8295 100644
--- a/src/main/webapp/search-include-fragment.xhtml
+++ b/src/main/webapp/search-include-fragment.xhtml
@@ -530,7 +530,7 @@
                                         <h:outputText value="#{result.parent.get('name')} Dataverse"/>
                                     </h:outputLink>
 
-                                    <h:outputText value="#{result.citation}" styleClass="resultDatasetCitationBlock"/>
+                                    <h:outputText value="#{result.citation}" styleClass="resultDatasetCitationBlock bg-info"/>
 
                                     <h:outputText value="#{Strings:abbreviate(result.descriptionNoSnippet, descriptionAbbreviationThreshold)}" rendered="#{result.descriptionSnippets.size() eq 0}"/>
                                     <ui:fragment rendered="#{result.descriptionSnippets.size() gt 0}">

From 5a3c8d338a0515b20ab3ba27f5cdfed072c71262 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Mon, 12 May 2014 10:52:42 -0400
Subject: [PATCH 08/46] re-format file with Netbeans #3433

---
 src/main/webapp/WEB-INF/web.xml | 50 ++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
index 4840ef547b2..a15812b8d16 100644
--- a/src/main/webapp/WEB-INF/web.xml
+++ b/src/main/webapp/WEB-INF/web.xml
@@ -33,8 +33,8 @@
         <load-on-startup>1</load-on-startup>
     </servlet>
     <servlet>
-      <servlet-name>Push Servlet</servlet-name>
-      <servlet-class>org.primefaces.push.PushServlet</servlet-class>
+        <servlet-name>Push Servlet</servlet-name>
+        <servlet-class>org.primefaces.push.PushServlet</servlet-class>
     </servlet>
  
     <!-- Map these files with JSF -->
@@ -55,30 +55,30 @@
         <url-pattern>*.xhtml</url-pattern>
     </servlet-mapping>
     <servlet-mapping>
-      <servlet-name>Push Servlet</servlet-name>
-      <url-pattern>/primepush/*</url-pattern>
+        <servlet-name>Push Servlet</servlet-name>
+        <url-pattern>/primepush/*</url-pattern>
     </servlet-mapping>
 	
 	
-	<!-- web fonts -->
-	<mime-mapping>
-		<extension>eot</extension>
-		<mime-type>application/vnd.ms-fontobject</mime-type>
-	</mime-mapping>
-	<mime-mapping>  
-		<extension>otf</extension>  
-		<mime-type>font/opentype</mime-type>  
-	</mime-mapping>      
-	<mime-mapping>  
-		<extension>ttf</extension>  
-		<mime-type>application/x-font-ttf</mime-type>  
-	</mime-mapping>      
-	<mime-mapping>  
-		<extension>woff</extension>  
-		<mime-type>application/x-font-woff</mime-type>  
-	</mime-mapping>
-	<mime-mapping>  
-		<extension>svg</extension>  
-		<mime-type>image/svg+xml</mime-type>  
-	</mime-mapping>
+    <!-- web fonts -->
+    <mime-mapping>
+        <extension>eot</extension>
+        <mime-type>application/vnd.ms-fontobject</mime-type>
+    </mime-mapping>
+    <mime-mapping>  
+        <extension>otf</extension>  
+        <mime-type>font/opentype</mime-type>  
+    </mime-mapping>      
+    <mime-mapping>  
+        <extension>ttf</extension>  
+        <mime-type>application/x-font-ttf</mime-type>  
+    </mime-mapping>      
+    <mime-mapping>  
+        <extension>woff</extension>  
+        <mime-type>application/x-font-woff</mime-type>  
+    </mime-mapping>
+    <mime-mapping>  
+        <extension>svg</extension>  
+        <mime-type>image/svg+xml</mime-type>  
+    </mime-mapping>
 </web-app>

From 20a8bdee0ca368d8911f059ea16f759e7b67a339 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Mon, 12 May 2014 18:56:10 -0400
Subject: [PATCH 09/46] start adding SWORD (service document with many todo's)
 #3385

---
 pom.xml                                       |  40 ++++-
 scripts/api/data-deposit/service-document     |   2 +
 scripts/installer/glassfish-setup.sh          |   2 +
 .../SWORDv2ServiceDocumentServlet.java        |  28 +++
 .../ServiceDocumentManagerImpl.java           |  86 +++++++++
 .../dataverse/api/datadeposit/SwordAuth.java  |  87 +++++++++
 .../datadeposit/SwordConfigurationImpl.java   | 107 +++++++++++
 .../dataverse/api/datadeposit/UrlManager.java | 167 ++++++++++++++++++
 src/main/webapp/WEB-INF/web.xml               |  17 +-
 9 files changed, 534 insertions(+), 2 deletions(-)
 create mode 100755 scripts/api/data-deposit/service-document
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/UrlManager.java

diff --git a/pom.xml b/pom.xml
index dfda62dd6ff..295c3163ee6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -61,7 +61,45 @@
             <version>3.0.1</version>
             <type>jar</type>
         </dependency>
-	<dependency>
+        <!-- BEGIN Data Deposit API v1 (SWORD v2) -->
+        <dependency>
+            <groupId>org.swordapp.server</groupId>
+            <artifactId>sword2-server</artifactId>
+            <version>1.0-classes</version>
+            <type>jar</type>
+        </dependency>
+        <dependency>
+            <!-- required by org.swordapp.server.sword2-server -->
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+            <version>1.2.17</version>
+        </dependency>
+        <dependency>
+            <!-- required by org.swordapp.server.sword2-server -->
+            <groupId>org.apache.abdera</groupId>
+            <artifactId>abdera-core</artifactId>
+            <version>1.1.3</version>
+        </dependency>
+        <dependency>
+            <!-- required by org.swordapp.server.sword2-server -->
+            <groupId>org.apache.abdera</groupId>
+            <artifactId>abdera-parser</artifactId>
+            <version>1.1.3</version>
+        </dependency>
+        <dependency>
+            <!-- required by org.swordapp.server.sword2-server -->
+            <groupId>commons-fileupload</groupId>
+            <artifactId>commons-fileupload</artifactId>
+            <version>1.3.1</version>
+        </dependency>
+        <dependency>
+            <!-- required by org.swordapp.server.sword2-server -->
+            <groupId>xom</groupId>
+            <artifactId>xom</artifactId>
+            <version>1.1</version>
+        </dependency>
+        <!-- END Data Deposit API v1 (SWORD v2) -->
+        <dependency>
             <groupId>javax</groupId>
             <artifactId>javaee-api</artifactId>
             <version>7.0</version>
diff --git a/scripts/api/data-deposit/service-document b/scripts/api/data-deposit/service-document
new file mode 100755
index 00000000000..6af8c9e2ef8
--- /dev/null
+++ b/scripts/api/data-deposit/service-document
@@ -0,0 +1,2 @@
+#!/bin/bash
+curl --insecure https://pete:FIXME@localhost:8181/dvn/api/data-deposit/v1/swordv2/service-document | xmllint -format -
diff --git a/scripts/installer/glassfish-setup.sh b/scripts/installer/glassfish-setup.sh
index 513b329f275..7551f7acbb1 100755
--- a/scripts/installer/glassfish-setup.sh
+++ b/scripts/installer/glassfish-setup.sh
@@ -202,6 +202,8 @@ fi
 ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.rserve.port=${RSERVE_PORT}"
 ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.rserve.user=${RSERVE_USER}"
 ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.rserve.password=${RSERVE_PASS}"
+# Data Deposit API options
+./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddataverse.datadeposit.hostname=${HOST_ADDRESS}"
 
 # enable comet support
 ./asadmin $ASADMIN_OPTS set server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled="true"
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java
new file mode 100644
index 00000000000..5304c60480f
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java
@@ -0,0 +1,28 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.io.IOException;
+import javax.inject.Inject;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import org.swordapp.server.ServiceDocumentAPI;
+import org.swordapp.server.servlets.SwordServlet;
+
+public class SWORDv2ServiceDocumentServlet extends SwordServlet {
+
+    @Inject
+    ServiceDocumentManagerImpl serviceDocumentManagerImpl;
+    protected ServiceDocumentAPI api;
+
+    public void init() throws ServletException {
+        super.init();
+        this.api = new ServiceDocumentAPI(serviceDocumentManagerImpl, this.config);
+    }
+
+    @Override
+    protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.get(req, resp);
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java
new file mode 100644
index 00000000000..4f5d22795b5
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java
@@ -0,0 +1,86 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseServiceBean;
+import edu.harvard.iq.dataverse.DataverseUser;
+import java.util.List;
+import java.util.logging.Logger;
+import javax.ejb.EJB;
+import javax.inject.Inject;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.ServiceDocument;
+import org.swordapp.server.ServiceDocumentManager;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordCollection;
+import org.swordapp.server.SwordConfiguration;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+import org.swordapp.server.SwordWorkspace;
+import org.swordapp.server.UriRegistry;
+
+public class ServiceDocumentManagerImpl implements ServiceDocumentManager {
+
+    private static final Logger logger = Logger.getLogger(ServiceDocumentManagerImpl.class.getCanonicalName());
+    @EJB
+    DataverseServiceBean dataverseService;
+    @Inject
+    SwordAuth swordAuth;
+    @Inject
+    UrlManager urlManager;
+
+    @Override
+    public ServiceDocument getServiceDocument(String sdUri, AuthCredentials authCredentials, SwordConfiguration config)
+            throws SwordError, SwordServerException, SwordAuthException {
+
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        urlManager.processUrl(sdUri);
+        ServiceDocument service = new ServiceDocument();
+        SwordWorkspace swordWorkspace = new SwordWorkspace();
+        Dataverse rootDataverse = dataverseService.findRootDataverse();
+        if (rootDataverse != null) {
+            String name = rootDataverse.getName();
+            if (name != null) {
+                swordWorkspace.setTitle(name);
+            }
+        }
+        service.setMaxUploadSize(config.getMaxUploadSize());
+        String hostnamePlusBaseUrl = urlManager.getHostnamePlusBaseUrlPath(sdUri);
+        if (hostnamePlusBaseUrl == null) {
+            ServiceDocument serviceDocument = new ServiceDocument();
+            return serviceDocument;
+        }
+        /**
+         * @todo All dataverses? listing all dataverse here is horribly
+         * inefficient. We need the equivalent of this from 3.x:
+         *
+         * List<VDC> vdcList = vdcService.getUserVDCs(vdcUser.getId());
+         */
+        List<Dataverse> allDataverses = dataverseService.findAll();
+        for (Dataverse dataverse : allDataverses) {
+            if (swordAuth.hasAccessToModifyDataverse(vdcUser, dataverse)) {
+                String dvAlias = dataverse.getAlias();
+                if (dvAlias != null && !dvAlias.isEmpty()) {
+                    SwordCollection swordCollection = new SwordCollection();
+                    swordCollection.setTitle(dataverse.getName());
+                    swordCollection.setHref(hostnamePlusBaseUrl + "/collection/dataverse/" + dvAlias);
+                    swordCollection.addAcceptPackaging(UriRegistry.PACKAGE_SIMPLE_ZIP);
+                    /**
+                     * @todo for backwards-compatibility with DVN 3.x, display
+                     * terms of uses for root dataverse and the dataverse we
+                     * are iterating over. What if the root dataverse is not the
+                     * direct parent of the dataverse we're iterating over? Show
+                     * the terms of use each generation back to the root?
+                     *
+                     * See also https://redmine.hmdc.harvard.edu/issues/3967
+                     */
+                    // swordCollection.setCollectionPolicy(dvnNetworkName + " deposit terms of use: " + vdcNetworkService.findRootNetwork().getDepositTermsOfUse() + "\n---\n" + dataverse.getName() + " deposit terms of use: " + dataverse.getDepositTermsOfUse());
+                    swordWorkspace.addCollection(swordCollection);
+                }
+            }
+        }
+        service.addWorkspace(swordWorkspace);
+
+        return service;
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java
new file mode 100644
index 00000000000..4d4b16f99e9
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java
@@ -0,0 +1,87 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseUser;
+import edu.harvard.iq.dataverse.DataverseUserServiceBean;
+import java.util.logging.Logger;
+import javax.ejb.EJB;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+
+public class SwordAuth {
+
+    private static final Logger logger = Logger.getLogger(SwordAuth.class.getCanonicalName());
+    @EJB
+    DataverseUserServiceBean dataverseUserService;
+
+    public DataverseUser auth(AuthCredentials authCredentials) throws SwordAuthException, SwordServerException {
+
+        if (authCredentials != null) {
+            String username = authCredentials.getUsername();
+            String password = authCredentials.getPassword();
+            logger.fine("Checking username " + username + " ...");
+            DataverseUser dataverseUser = dataverseUserService.findByUserName(username);
+            if (dataverseUser != null) {
+                /**
+                 * @todo actually check the user's password! Can't use
+                 * validateMethod on LoginPage.java since it's a backing bean...
+                 */
+//                if (dataverseUserService.validatePassword(username, password)) {
+                return dataverseUser;
+//                } else {
+//                    logger.info("wrong password");
+//                    throw new SwordAuthException();
+//                }
+            } else {
+                logger.info("could not find username: " + username);
+                throw new SwordAuthException();
+            }
+        } else {
+            // in DVN 3.x at least, it seems this was never reached... eaten somewhere by way of ServiceDocumentServletDefault -> ServiceDocumentAPI -> SwordAPIEndpoint
+            logger.info("no credentials provided");
+            throw new SwordAuthException();
+        }
+    }
+
+    boolean hasAccessToModifyDataverse(DataverseUser dataverseUser, Dataverse dataverse) throws SwordError {
+        boolean authorized = false;
+
+        /**
+         * @todo use actual roles
+         */
+//        VDCRole role = vdcUser.getVDCRole(dv);
+//        String roleString = null;
+//        if (role != null) {
+//            roleString = role.getRole().getName();
+//            if ("admin".equals(roleString)) {
+//                authorized = true;
+//            } else if ("contributor".equals(roleString) || "curator".equals(roleString) || "privileged viewer".equals(roleString)) {
+//                authorized = false;
+//                 return early to avoid throwing exception when getting Service Document
+//                return authorized;
+//            } else {
+//                authorized = false;
+//            }
+//        }
+//
+        if (dataverse.getCreator().equals(dataverseUser)) {
+            authorized = true;
+            return authorized;
+        } else {
+            authorized = false;
+            return authorized;
+        }
+
+        /**
+         * @todo: for backwards compatibility with DVN 3.x do we need to throw
+         * this SWORD error?
+         */
+//        if (!authorized) {
+//            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + dataverseUser.getUserName() + " with role of " + roleString + " is not authorized to modify dataverse " + dataverse.getAlias());
+//        } else {
+//            return authorized;
+//        }
+    }
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
new file mode 100644
index 00000000000..734af9a8468
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
@@ -0,0 +1,107 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.io.File;
+import java.util.logging.Logger;
+import org.swordapp.server.SwordConfiguration;
+
+public class SwordConfigurationImpl implements SwordConfiguration {
+
+    private static final Logger logger = Logger.getLogger(SwordConfigurationImpl.class.getCanonicalName());
+
+    String getBaseUrlPath() {
+        return "/dvn/api/data-deposit/v1/swordv2";
+    }
+
+    @Override
+    public boolean returnDepositReceipt() {
+        return true;
+    }
+
+    @Override
+    public boolean returnStackTraceInError() {
+        return true;
+    }
+
+    @Override
+    public boolean returnErrorBody() {
+        return true;
+    }
+
+    @Override
+    public String generator() {
+        return "http://www.swordapp.org/";
+    }
+
+    @Override
+    public String generatorVersion() {
+        return "2.0";
+    }
+
+    @Override
+    public String administratorEmail() {
+        return null;
+    }
+
+    @Override
+    public String getAuthType() {
+        // using "Basic" here to match what's in SwordAPIEndpoint
+        return "Basic";
+    }
+
+    @Override
+    public boolean storeAndCheckBinary() {
+        return true;
+    }
+
+    @Override
+    public String getTempDirectory() {
+        /**
+         * @todo is it safe to use dataverse.files.directory for this?
+         */
+        String tmpFileDir = System.getProperty("vdc.temp.file.dir");
+        if (tmpFileDir != null) {
+            return tmpFileDir + File.separator + "sword";
+        } else {
+            return null;
+        }
+    }
+
+    @Override
+    public int getMaxUploadSize() {
+        int unlimited = -1;
+        /**
+         * @todo rename this from dvn to dataverse?
+         */
+        String jvmOption = "dvn.dataDeposit.maxUploadInBytes";
+        String maxUploadInBytes = System.getProperty(jvmOption);
+        if (maxUploadInBytes != null) {
+            try {
+                int maxUploadSizeInBytes = Integer.parseInt(maxUploadInBytes);
+                return maxUploadSizeInBytes;
+            } catch (NumberFormatException ex) {
+                logger.fine("Could not convert " + maxUploadInBytes + " from JVM option " + jvmOption + " to int. Setting Data Deposit APU max upload size limit to unlimited.");
+                return unlimited;
+            }
+        } else {
+            logger.fine("JVM option " + jvmOption + " is undefined. Setting Data Deposit APU max upload size limit to unlimited.");
+            return unlimited;
+
+        }
+    }
+
+    @Override
+    public String getAlternateUrl() {
+        return null;
+    }
+
+    @Override
+    public String getAlternateUrlContentType() {
+        return null;
+    }
+
+    @Override
+    public boolean allowUnauthenticatedMediaAccess() {
+        return false;
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/UrlManager.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/UrlManager.java
new file mode 100644
index 00000000000..2c960d54ea9
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/UrlManager.java
@@ -0,0 +1,167 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.logging.Logger;
+import org.apache.commons.lang.StringUtils;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.UriRegistry;
+
+public class UrlManager {
+
+    private static final Logger logger = Logger.getLogger(UrlManager.class.getCanonicalName());
+    String originalUrl;
+    SwordConfigurationImpl swordConfiguration = new SwordConfigurationImpl();
+    String servlet;
+    String targetType;
+    String targetIdentifier;
+    int port;
+
+    void processUrl(String url) throws SwordError {
+        logger.fine("URL was: " + url);
+        this.originalUrl = url;
+        URI javaNetUri;
+        try {
+            javaNetUri = new URI(url);
+        } catch (URISyntaxException ex) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid URL syntax: " + url);
+        }
+        if (!"https".equals(javaNetUri.getScheme())) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "https is required but protocol was " + javaNetUri.getScheme());
+        }
+        this.port = javaNetUri.getPort();
+        String[] urlPartsArray = javaNetUri.getPath().split("/");
+        List<String> urlParts = Arrays.asList(urlPartsArray);
+        String dataDepositApiBasePath;
+        try {
+            List<String> dataDepositApiBasePathParts;
+            //             1 2   3   4            5  6       7          8         9
+            // for example: /dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword
+            dataDepositApiBasePathParts = urlParts.subList(0, 6);
+            dataDepositApiBasePath = StringUtils.join(dataDepositApiBasePathParts, "/");
+        } catch (IndexOutOfBoundsException ex) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Error processing URL: " + url);
+        }
+        if (!dataDepositApiBasePath.equals(swordConfiguration.getBaseUrlPath())) {
+            throw new SwordError(dataDepositApiBasePath + " found but " + swordConfiguration.getBaseUrlPath() + " expected");
+        }
+        try {
+            this.servlet = urlParts.get(6);
+        } catch (ArrayIndexOutOfBoundsException ex) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine servlet path from URL: " + url);
+        }
+        if (!servlet.equals("service-document")) {
+            List<String> targetTypeAndIdentifier;
+            try {
+                //               6          7         8
+                // for example: /collection/dataverse/sword
+                targetTypeAndIdentifier = urlParts.subList(7, urlParts.size());
+            } catch (IndexOutOfBoundsException ex) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No target components specified in URL: " + url);
+            }
+            this.targetType = targetTypeAndIdentifier.get(0);
+            if (targetType != null) {
+                if (targetType.equals("dataverse")) {
+                    String dvAlias;
+                    try {
+                        dvAlias = targetTypeAndIdentifier.get(1);
+                    } catch (IndexOutOfBoundsException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No dataverse alias provided in URL: " + url);
+                    }
+                    this.targetIdentifier = dvAlias;
+                } else if (targetType.equals("study")) {
+                    String globalId;
+                    try {
+                        List<String> globalIdParts = targetTypeAndIdentifier.subList(1, targetTypeAndIdentifier.size());
+                        globalId = StringUtils.join(globalIdParts, "/");
+                    } catch (IndexOutOfBoundsException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid study global id provided in URL: " + url);
+                    }
+                    this.targetIdentifier = globalId;
+                } else if (targetType.equals("file")) {
+                    String fileIdString;
+                    try {
+                        // a user might reasonably pass in a filename as well [.get(2)] since
+                        // we expose it in the statement of a study but we ignore it here
+                        fileIdString = targetTypeAndIdentifier.get(1);
+                    } catch (IndexOutOfBoundsException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No file id provided in URL: " + url);
+                    }
+                    this.targetIdentifier = fileIdString;
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "unsupported target type: " + targetType);
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine target type from URL: " + url);
+            }
+            logger.fine("target type: " + targetType);
+            logger.fine("target identifier: " + targetIdentifier);
+        }
+    }
+
+    String getHostnamePlusBaseUrlPath(String url) throws SwordError {
+        String optionalPort = "";
+        URI u;
+        try {
+            u = new URI(url);
+            int port = u.getPort();
+            if (port != -1) {
+                // https often runs on port 8181 in dev
+                optionalPort = ":" + port;
+            }
+        } catch (URISyntaxException ex) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "unable to part URL");
+        }
+        /**
+         * @todo do we need the equivalent of dvn.inetAddress in 4.0?
+         */
+        String hostName = System.getProperty("dataverse.datadeposit.hostname");
+        if (hostName == null) {
+            hostName = "localhost";
+        }
+        return "https://" + hostName + optionalPort + swordConfiguration.getBaseUrlPath();
+    }
+
+    public String getOriginalUrl() {
+        return originalUrl;
+    }
+
+    public void setOriginalUrl(String originalUrl) {
+        this.originalUrl = originalUrl;
+    }
+
+    public String getServlet() {
+        return servlet;
+    }
+
+    public void setServlet(String servlet) {
+        this.servlet = servlet;
+    }
+
+    public String getTargetIdentifier() {
+        return targetIdentifier;
+    }
+
+    public void setTargetIdentifier(String targetIdentifier) {
+        this.targetIdentifier = targetIdentifier;
+    }
+
+    public String getTargetType() {
+        return targetType;
+    }
+
+    public void setTargetType(String targetType) {
+        this.targetType = targetType;
+    }
+
+    public int getPort() {
+        return port;
+    }
+
+    public void setPort(int port) {
+        this.port = port;
+    }
+
+}
diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
index a15812b8d16..a0f9202cbe9 100644
--- a/src/main/webapp/WEB-INF/web.xml
+++ b/src/main/webapp/WEB-INF/web.xml
@@ -7,7 +7,6 @@
          id="WebApp_ID" version="2.5">
  
     <display-name>Dataverse</display-name>
- 
 
     <!-- Welcome page -->
     <welcome-file-list>
@@ -81,4 +80,20 @@
         <extension>svg</extension>  
         <mime-type>image/svg+xml</mime-type>  
     </mime-mapping>
+
+    <!-- BEGIN Data Deposit API v1 (SWORD v2) -->
+    <context-param>
+        <param-name>config-impl</param-name>
+        <param-value>edu.harvard.iq.dataverse.api.datadeposit.SwordConfigurationImpl</param-value>
+    </context-param>
+    <servlet>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ServiceDocumentServlet</servlet-name>
+        <servlet-class>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ServiceDocumentServlet</servlet-class>
+    </servlet>
+    <servlet-mapping>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ServiceDocumentServlet</servlet-name>
+        <url-pattern>/dvn/api/data-deposit/v1/swordv2/service-document/*</url-pattern>
+    </servlet-mapping>
+    <!-- END Data Deposit API v1 (SWORD v2) -->
+
 </web-app>

From 5b380104ff3b314682ab29eb39d70f8e0a0b5a65 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 13 May 2014 11:18:57 -0400
Subject: [PATCH 10/46] stub out SWORD dataset creation (many todo's) #3385

---
 scripts/api/data-deposit/create-dataset       |   7 +
 .../data-deposit/data/atom-entry-study.xml    |  41 ++++
 .../CollectionDepositManagerImpl.java         | 211 ++++++++++++++++++
 .../CollectionListManagerImpl.java            |  79 +++++++
 .../api/datadeposit/ReceiptGenerator.java     |  44 ++++
 .../datadeposit/SWORDv2CollectionServlet.java |  37 +++
 .../datadeposit/SwordConfigurationImpl.java   |   3 +-
 src/main/webapp/WEB-INF/web.xml               |  18 ++
 8 files changed, 439 insertions(+), 1 deletion(-)
 create mode 100755 scripts/api/data-deposit/create-dataset
 create mode 100644 scripts/api/data-deposit/data/atom-entry-study.xml
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java

diff --git a/scripts/api/data-deposit/create-dataset b/scripts/api/data-deposit/create-dataset
new file mode 100755
index 00000000000..52096569541
--- /dev/null
+++ b/scripts/api/data-deposit/create-dataset
@@ -0,0 +1,7 @@
+#!/bin/bash
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+DATAVERSE_ALIAS=peteTop
+curl --insecure --data-binary "@scripts/api/data-deposit/data/atom-entry-study.xml" -H "Content-Type: application/atom+xml" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS \
+| xmllint -format -
diff --git a/scripts/api/data-deposit/data/atom-entry-study.xml b/scripts/api/data-deposit/data/atom-entry-study.xml
new file mode 100644
index 00000000000..8adfb574188
--- /dev/null
+++ b/scripts/api/data-deposit/data/atom-entry-study.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<!--
+modified from http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html#protocoloperations_editingcontent_metadata
+
+comments at https://docs.google.com/document/d/1Rn70XItfA6_mJ4JA3I7m4em0spfdXIIHhwkrgCl40uE/edit?usp=sharing
+
+see also https://redmine.hmdc.harvard.edu/issues/3246
+-->
+<entry xmlns="http://www.w3.org/2005/Atom"
+       xmlns:dcterms="http://purl.org/dc/terms/">
+   <!-- some embedded metadata -->
+   <dcterms:title>Roasting at Home</dcterms:title>
+   <dcterms:creator>Peets, John</dcterms:creator>
+   <dcterms:creator>Stumptown, Jane</dcterms:creator>
+   <!-- Producer with financial or admin responsibility of the data -->
+   <dcterms:publisher>Coffee Bean State University</dcterms:publisher>
+   <!-- related publications -->
+   <dcterms:isReferencedBy holdingsURI="http://dx.doi.org/10.1038/dvn333" agency="DOI" IDNo="10.1038/dvn333">Peets, J., &amp; Stumptown, J. (2013). Roasting at Home. New England Journal of Coffee, 3(1), 22-34.</dcterms:isReferencedBy>
+   <!-- production date -->
+   <dcterms:date>2013-07-11</dcterms:date>
+   <!-- Other Identifier for the data in this study (or potentially global id if unused) -->
+   <!--
+   <dcterms:identifier>hdl:1XXZY.1/XYXZ</dcterms:identifier>
+   -->
+   <dcterms:description>Considerations before you start roasting your own coffee at home.</dcterms:description>
+   <!-- keywords -->
+   <dcterms:subject>coffee</dcterms:subject>
+   <dcterms:subject>beverage</dcterms:subject>
+   <dcterms:subject>caffeine</dcterms:subject>
+   <!-- geographic coverage -->
+   <dcterms:coverage>United States</dcterms:coverage>
+   <dcterms:coverage>Canada</dcterms:coverage>
+   <!-- kind of data -->
+   <dcterms:type>aggregate data</dcterms:type>
+   <!-- List of sources of the data collection-->
+   <dcterms:source>Stumptown, Jane. 2011. Home Roasting. Coffeemill Press.</dcterms:source>
+   <!-- restrictions -->
+   <dcterms:rights>Creative Commons CC-BY 3.0 (unported) http://creativecommons.org/licenses/by/3.0/</dcterms:rights>
+   <!-- related materials -->
+   <dcterms:relation>Peets, John. 2010. Roasting Coffee at the Coffee Shop. Coffeemill Press</dcterms:relation>
+</entry>
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
new file mode 100644
index 00000000000..48851690a5e
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
@@ -0,0 +1,211 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.DatasetField;
+import edu.harvard.iq.dataverse.DatasetFieldType;
+import edu.harvard.iq.dataverse.DatasetFieldValidator;
+import edu.harvard.iq.dataverse.DatasetFieldValue;
+import edu.harvard.iq.dataverse.DatasetVersion;
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseServiceBean;
+import edu.harvard.iq.dataverse.DataverseUser;
+import edu.harvard.iq.dataverse.EjbDataverseEngine;
+import edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Logger;
+import javax.ejb.EJB;
+import javax.inject.Inject;
+import javax.validation.ConstraintViolation;
+import javax.validation.ConstraintViolationException;
+import org.apache.commons.io.FileUtils;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.CollectionDepositManager;
+import org.swordapp.server.Deposit;
+import org.swordapp.server.DepositReceipt;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordConfiguration;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+import org.swordapp.server.UriRegistry;
+
+public class CollectionDepositManagerImpl implements CollectionDepositManager {
+
+    private static final Logger logger = Logger.getLogger(CollectionDepositManagerImpl.class.getCanonicalName());
+    @EJB
+    DataverseServiceBean dataverseService;
+    @Inject
+    SwordAuth swordAuth;
+    @Inject
+    UrlManager urlManager;
+    @EJB
+    EjbDataverseEngine engineSvc;
+
+    @Override
+    public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration config)
+            throws SwordError, SwordServerException, SwordAuthException {
+
+        DataverseUser dataverseUser = swordAuth.auth(authCredentials);
+
+        urlManager.processUrl(collectionUri);
+        String dvAlias = urlManager.getTargetIdentifier();
+        if (urlManager.getTargetType().equals("dataverse") && dvAlias != null) {
+
+            logger.fine("attempting deposit into this dataverse alias: " + dvAlias);
+
+            Dataverse dvThatWillOwnDataset = dataverseService.findByAlias(dvAlias);
+
+            if (dvThatWillOwnDataset != null) {
+
+                if (swordAuth.hasAccessToModifyDataverse(dataverseUser, dvThatWillOwnDataset)) {
+
+                    logger.fine("multipart: " + deposit.isMultipart());
+                    logger.fine("binary only: " + deposit.isBinaryOnly());
+                    logger.fine("entry only: " + deposit.isEntryOnly());
+                    logger.fine("in progress: " + deposit.isInProgress());
+                    logger.fine("metadata relevant: " + deposit.isMetadataRelevant());
+
+                    if (deposit.isEntryOnly()) {
+                        logger.fine("deposit XML received by createNew():\n" + deposit.getSwordEntry());
+                        // require title *and* exercise the SWORD jar a bit
+                        Map<String, List<String>> dublinCore = deposit.getSwordEntry().getDublinCore();
+                        if (dublinCore.get("title") == null || dublinCore.get("title").get(0) == null || dublinCore.get("title").get(0).isEmpty()) {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "title field is required");
+                        }
+
+                        if (dublinCore.get("date") != null) {
+                            String date = dublinCore.get("date").get(0);
+                            if (date != null) {
+                                /**
+                                 * @todo re-enable this. use
+                                 * datasetFieldValidator.isValid?
+                                 */
+//                                boolean isValid = DateUtil.validateDate(date);
+//                                if (!isValid) {
+//                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid date: '" + date + "'.  Valid formats are YYYY-MM-DD, YYYY-MM, or YYYY.");
+//                                }
+                            }
+                        }
+
+                        /**
+                         * @todo think about the implications of no longer using
+                         * importStudy(), such as the comment below... do we
+                         * really need to write the XML to disk?
+                         */
+                        // instead of writing a tmp file, maybe importStudy() could accept an InputStream?
+                        String tmpDirectory = config.getTempDirectory();
+                        if (tmpDirectory == null) {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine temp directory");
+                        }
+                        String uploadDirPath = tmpDirectory + File.separator + "import" + File.separator + dvThatWillOwnDataset.getId();
+                        File uploadDir = new File(uploadDirPath);
+                        if (!uploadDir.exists()) {
+                            if (!uploadDir.mkdirs()) {
+                                logger.info("couldn't create directory: " + uploadDir.getAbsolutePath());
+                                throw new SwordServerException("Couldn't create upload directory.");
+                            }
+                        }
+                        String tmpFilePath = uploadDirPath + File.separator + "newStudyViaSwordv2.xml";
+                        File tmpFile = new File(tmpFilePath);
+                        try {
+                            FileUtils.writeStringToFile(tmpFile, deposit.getSwordEntry().getEntry().toString());
+                        } catch (IOException ex) {
+                            logger.info("couldn't write temporary file: " + tmpFile.getAbsolutePath());
+                            throw new SwordServerException("Couldn't write temporary file");
+                        } finally {
+                            uploadDir.delete();
+                        }
+
+                        /**
+                         * @todo properly create a dataset and datasetVersion
+                         */
+                        Dataset dataset = new Dataset();
+                        dataset.setOwner(dvThatWillOwnDataset);
+                        dataset.setIdentifier("myIdentifier");
+                        dataset.setProtocol("myProtocol");
+
+                        DatasetVersion newDatasetVersion = new DatasetVersion();
+                        newDatasetVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
+
+                        List<DatasetField> datasetFields = new ArrayList<>();
+                        DatasetField titleDatasetField = new DatasetField();
+                        DatasetFieldType titleDatasetFieldType = new DatasetFieldType("title", "text", false);
+                        titleDatasetField.setDatasetFieldType(titleDatasetFieldType);
+                        List<DatasetFieldValue> datasetFieldValues = new ArrayList<>();
+                        DatasetFieldValue titleDatasetFieldValue = new DatasetFieldValue(titleDatasetField, "fooTitle");
+                        datasetFieldValues.add(titleDatasetFieldValue);
+                        titleDatasetField.setDatasetFieldValues(datasetFieldValues);
+                        datasetFields.add(titleDatasetField);
+
+                        newDatasetVersion.setDatasetFields(datasetFields);
+
+                        newDatasetVersion.setDataset(dataset);
+                        dataset.getVersions().add(newDatasetVersion);
+                        try {
+                            // there is no importStudy method in 4.0 :(
+                            // study = studyService.importStudy(tmpFile, dcmiTermsFormatId, dvThatWillOwnStudy.getId(), vdcUser.getId());
+                            engineSvc.submit(new CreateDatasetCommand(dataset, dataverseUser));
+                        } catch (Exception ex) {
+//                            StringWriter stringWriter = new StringWriter();
+//                            ex.printStackTrace(new PrintWriter(stringWriter));
+//                            String stackTrace = stringWriter.toString();
+                            /**
+                             * @todo in DVN 3.x we printed the whole stack trace
+                             * here. Is that really necessary?
+                             */
+//                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't import study: " + stackTrace);
+
+                            Throwable cause = ex;
+                            StringBuilder sb = new StringBuilder();
+                            sb.append(ex.getLocalizedMessage());
+                            while (cause.getCause() != null) {
+                                cause = cause.getCause();
+                                if (cause instanceof ConstraintViolationException) {
+                                    ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
+                                    for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
+                                        sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ")
+                                                .append(violation.getPropertyPath()).append(" at ")
+                                                .append(violation.getLeafBean()).append(" - ")
+                                                .append(violation.getMessage());
+                                    }
+                                }
+                            }
+                            logger.info(sb.toString());
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't create dataset: " + sb.toString());
+                        } finally {
+                            tmpFile.delete();
+                            uploadDir.delete();
+                        }
+                        ReceiptGenerator receiptGenerator = new ReceiptGenerator();
+                        String baseUrl = urlManager.getHostnamePlusBaseUrlPath(collectionUri);
+                        DepositReceipt depositReceipt = receiptGenerator.createReceipt(baseUrl, dataset);
+                        return depositReceipt;
+                    } else if (deposit.isBinaryOnly()) {
+                        // get here with this:
+                        // curl --insecure -s --data-binary "@example.zip" -H "Content-Disposition: filename=example.zip" -H "Content-Type: application/zip" https://sword:sword@localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword/
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Binary deposit to the collection IRI via POST is not supported. Please POST an Atom entry instead.");
+                    } else if (deposit.isMultipart()) {
+                        // get here with this:
+                        // wget https://raw.github.com/swordapp/Simple-Sword-Server/master/tests/resources/multipart.dat
+                        // curl --insecure --data-binary "@multipart.dat" -H 'Content-Type: multipart/related; boundary="===============0670350989=="' -H "MIME-Version: 1.0" https://sword:sword@localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword/hdl:1902.1/12345
+                        // but...
+                        // "Yeah, multipart is critically broken across all implementations" -- http://www.mail-archive.com/sword-app-tech@lists.sourceforge.net/msg00327.html
+                        throw new UnsupportedOperationException("Not yet implemented");
+                    } else {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "expected deposit types are isEntryOnly, isBinaryOnly, and isMultiPart");
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + dataverseUser.getUserName() + " is not authorized to modify dataset");
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse: " + dvAlias);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine target type or identifier from URL: " + collectionUri);
+        }
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
new file mode 100644
index 00000000000..97594314c8b
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
@@ -0,0 +1,79 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseServiceBean;
+import edu.harvard.iq.dataverse.DataverseUser;
+import java.util.Collection;
+import java.util.logging.Logger;
+import javax.ejb.EJB;
+import javax.inject.Inject;
+import javax.xml.namespace.QName;
+import org.apache.abdera.Abdera;
+import org.apache.abdera.i18n.iri.IRI;
+import org.apache.abdera.model.Entry;
+import org.apache.abdera.model.Feed;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.CollectionListManager;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordConfiguration;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+import org.swordapp.server.UriRegistry;
+
+public class CollectionListManagerImpl implements CollectionListManager {
+
+    private static final Logger logger = Logger.getLogger(CollectionListManagerImpl.class.getCanonicalName());
+    @EJB
+    DataverseServiceBean dataverseService;
+    @Inject
+    SwordAuth swordAuth;
+    @Inject
+    UrlManager urlManager;
+
+    @Override
+    public Feed listCollectionContents(IRI iri, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordAuthException, SwordError {
+        DataverseUser dataverseUser = swordAuth.auth(authCredentials);
+
+        urlManager.processUrl(iri.toString());
+        String dvAlias = urlManager.getTargetIdentifier();
+        if (urlManager.getTargetType().equals("dataverse") && dvAlias != null) {
+
+            Dataverse dv = dataverseService.findByAlias(dvAlias);
+
+            if (dv != null) {
+                if (swordAuth.hasAccessToModifyDataverse(dataverseUser, dv)) {
+                    Abdera abdera = new Abdera();
+                    Feed feed = abdera.newFeed();
+                    feed.setTitle(dv.getName());
+                    /**
+                     * @todo how do I get a list of datasets belonging to a
+                     * user?
+                     */
+//                    Collection<Study> studies = dv.getOwnedStudies();
+//                    String baseUrl = urlManager.getHostnamePlusBaseUrlPath(iri.toString());
+//                    for (Study study : studies) {
+//                        String editUri = baseUrl + "/edit/study/" + study.getGlobalId();
+//                        String editMediaUri = baseUrl + "/edit-media/study/" + study.getGlobalId();
+//                        Entry entry = feed.addEntry();
+//                        entry.setId(editUri);
+//                        entry.setTitle(study.getLatestVersion().getMetadata().getTitle());
+//                        entry.setBaseUri(new IRI(editUri));
+//                        entry.addLink(editMediaUri, "edit-media");
+//                        feed.addEntry(entry);
+//                    }
+                    Boolean dvHasBeenReleased = dv.isReleased();
+                    feed.addSimpleExtension(new QName(UriRegistry.SWORD_STATE, "dataverseHasBeenReleased"), dvHasBeenReleased.toString());
+                    return feed;
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + dataverseUser.getUserName() + " is not authorized to list datasets in dataverse " + dv.getAlias());
+                }
+
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse: " + dvAlias);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't determine target type or identifer from URL: " + iri);
+        }
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
new file mode 100644
index 00000000000..ab7107dd799
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
@@ -0,0 +1,44 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.Dataset;
+import java.util.logging.Logger;
+import org.apache.abdera.i18n.iri.IRI;
+import org.swordapp.server.DepositReceipt;
+
+public class ReceiptGenerator {
+
+    private static final Logger logger = Logger.getLogger(ReceiptGenerator.class.getCanonicalName());
+
+    DepositReceipt createReceipt(String baseUrl, Dataset dataset) {
+        logger.fine("baseUrl was: " + baseUrl);
+        DepositReceipt depositReceipt = new DepositReceipt();
+        /**
+         * @todo is this same as globalId?
+         */
+        String globalId = dataset.getIdentifier();
+        /**
+         * @todo should these URLs continue to have "study" in them? Do we need
+         * to keep it as "study" for backwards compatibility or it ok to use
+         * "dataset"?
+         */
+        String editIri = baseUrl + "/edit/study/" + globalId;
+        depositReceipt.setEditIRI(new IRI(editIri));
+        /**
+         * @todo: should setLocation depend on if an atom entry or a zip file
+         * was deposited?
+         */
+        depositReceipt.setLocation(new IRI(editIri));
+        depositReceipt.setEditMediaIRI(new IRI(baseUrl + "/edit-media/study/" + globalId));
+        depositReceipt.setStatementURI("application/atom+xml;type=feed", baseUrl + "/statement/study/" + globalId);
+        /**
+         * @todo re-enable bibliographicCitation
+         */
+//        depositReceipt.addDublinCore("bibliographicCitation", study.getLatestVersion().getMetadata().getCitation(false));
+        /**
+         * @todo re-enable this
+         */
+//        depositReceipt.setSplashUri(study.getPersistentURL());
+        return depositReceipt;
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java
new file mode 100644
index 00000000000..6d9605a553e
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java
@@ -0,0 +1,37 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.io.IOException;
+import java.rmi.ServerException;
+import javax.inject.Inject;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import org.swordapp.server.CollectionAPI;
+import org.swordapp.server.servlets.SwordServlet;
+
+public class SWORDv2CollectionServlet extends SwordServlet {
+
+    @Inject
+    CollectionDepositManagerImpl collectionDepositManagerImpl;
+    @Inject
+    CollectionListManagerImpl collectionListManagerImpl;
+    protected CollectionAPI api;
+
+    public void init() throws ServletException {
+        super.init();
+        this.api = new CollectionAPI(collectionListManagerImpl, collectionDepositManagerImpl, this.config);
+    }
+
+    @Override
+    protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.get(req, resp);
+    }
+
+    @Override
+    protected void doPost(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.post(req, resp);
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
index 734af9a8468..3a579dbad3d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
@@ -58,7 +58,8 @@ public String getTempDirectory() {
         /**
          * @todo is it safe to use dataverse.files.directory for this?
          */
-        String tmpFileDir = System.getProperty("vdc.temp.file.dir");
+//        String tmpFileDir = System.getProperty("vdc.temp.file.dir");
+        String tmpFileDir = System.getProperty("dataverse.files.directory");
         if (tmpFileDir != null) {
             return tmpFileDir + File.separator + "sword";
         } else {
diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
index a0f9202cbe9..5b877737b6e 100644
--- a/src/main/webapp/WEB-INF/web.xml
+++ b/src/main/webapp/WEB-INF/web.xml
@@ -94,6 +94,24 @@
         <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ServiceDocumentServlet</servlet-name>
         <url-pattern>/dvn/api/data-deposit/v1/swordv2/service-document/*</url-pattern>
     </servlet-mapping>
+
+    <context-param>
+        <param-name>collection-deposit-impl</param-name>
+        <param-value>edu.harvard.iq.dataverse.api.datadeposit.CollectionDepositManagerImpl</param-value>
+    </context-param>
+    <context-param>
+        <param-name>collection-list-impl</param-name>
+        <param-value>edu.harvard.iq.dataverse.api.datadeposit.CollectionListManagerImpl</param-value>
+    </context-param>
+    <servlet>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet</servlet-name>
+        <servlet-class>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet</servlet-class>
+    </servlet>
+    <servlet-mapping>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet</servlet-name>
+        <url-pattern>/dvn/api/data-deposit/v1/swordv2/collection/*</url-pattern>
+    </servlet-mapping>
+
     <!-- END Data Deposit API v1 (SWORD v2) -->
 
 </web-app>

From 9f3ec0d090b259ddc627da66930349dc161ebb96 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 13 May 2014 15:20:14 -0400
Subject: [PATCH 11/46] fix minimum semi-viable sword dataset creation #3385

---
 .../api/datadeposit/CollectionDepositManagerImpl.java | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
index 48851690a5e..6175456e15f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
@@ -2,6 +2,7 @@
 
 import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.DatasetField;
+import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
 import edu.harvard.iq.dataverse.DatasetFieldType;
 import edu.harvard.iq.dataverse.DatasetFieldValidator;
 import edu.harvard.iq.dataverse.DatasetFieldValue;
@@ -43,6 +44,8 @@ public class CollectionDepositManagerImpl implements CollectionDepositManager {
     UrlManager urlManager;
     @EJB
     EjbDataverseEngine engineSvc;
+    @EJB
+    DatasetFieldServiceBean datasetFieldService;
 
     @Override
     public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration config)
@@ -127,23 +130,21 @@ public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCrede
                         dataset.setIdentifier("myIdentifier");
                         dataset.setProtocol("myProtocol");
 
-                        DatasetVersion newDatasetVersion = new DatasetVersion();
+                        DatasetVersion newDatasetVersion = dataset.getVersions().get(0);
                         newDatasetVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
 
                         List<DatasetField> datasetFields = new ArrayList<>();
                         DatasetField titleDatasetField = new DatasetField();
-                        DatasetFieldType titleDatasetFieldType = new DatasetFieldType("title", "text", false);
+                        DatasetFieldType titleDatasetFieldType = datasetFieldService.findByName("title");
                         titleDatasetField.setDatasetFieldType(titleDatasetFieldType);
                         List<DatasetFieldValue> datasetFieldValues = new ArrayList<>();
-                        DatasetFieldValue titleDatasetFieldValue = new DatasetFieldValue(titleDatasetField, "fooTitle");
+                        DatasetFieldValue titleDatasetFieldValue = new DatasetFieldValue(titleDatasetField, dublinCore.get("title").get(0));
                         datasetFieldValues.add(titleDatasetFieldValue);
                         titleDatasetField.setDatasetFieldValues(datasetFieldValues);
                         datasetFields.add(titleDatasetField);
 
                         newDatasetVersion.setDatasetFields(datasetFields);
 
-                        newDatasetVersion.setDataset(dataset);
-                        dataset.getVersions().add(newDatasetVersion);
                         try {
                             // there is no importStudy method in 4.0 :(
                             // study = studyService.importStudy(tmpFile, dcmiTermsFormatId, dvThatWillOwnStudy.getId(), vdcUser.getId());

From 60b37eb691a860e8093bcf30d0851d696a238187 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 13 May 2014 15:43:59 -0400
Subject: [PATCH 12/46] use pom config from
 https://github.com/swordapp/JavaServer2.0 #3385

---
 pom.xml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 295c3163ee6..09288df8a11 100644
--- a/pom.xml
+++ b/pom.xml
@@ -63,10 +63,17 @@
         </dependency>
         <!-- BEGIN Data Deposit API v1 (SWORD v2) -->
         <dependency>
-            <groupId>org.swordapp.server</groupId>
+            <groupId>org.swordapp</groupId>
             <artifactId>sword2-server</artifactId>
-            <version>1.0-classes</version>
+            <version>1.0</version>
             <type>jar</type>
+            <classifier>classes</classifier>
+        </dependency>
+        <dependency>
+            <groupId>org.swordapp</groupId>
+            <artifactId>sword2-server</artifactId>
+            <version>1.0</version>
+            <type>war</type>
         </dependency>
         <dependency>
             <!-- required by org.swordapp.server.sword2-server -->

From c98655dbc3ce908db37d546f90162450c46b400d Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.80.247>
Date: Tue, 13 May 2014 16:01:55 -0400
Subject: [PATCH 13/46] Layout improvements for the dataset summary section
 (above-the-tabs metadata) to be more consistent with the layout of the
 metadata in the tab. Removed repetitive metadata lables for multivalue
 fields. Fixed layout issue with the select dropdown menus.

---
 src/main/webapp/dataset.xhtml               |  37 ++-
 src/main/webapp/metadataFragment.xhtml      | 318 ++++++++++----------
 src/main/webapp/resources/css/structure.css |   8 +-
 3 files changed, 184 insertions(+), 179 deletions(-)

diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml
index 90600942812..66f8a483936 100644
--- a/src/main/webapp/dataset.xhtml
+++ b/src/main/webapp/dataset.xhtml
@@ -172,29 +172,38 @@
                                         <span id="description">#{DatasetPage.datasetVersionUI.description.value}</span>
                                     </ui:fragment>
                                     <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.keyword.value or !empty DatasetPage.datasetVersionUI.subject.value or !empty DatasetPage.datasetVersionUI.relPublicationCitation or !empty DatasetPage.datasetVersionUI.notes.value}">
-                                        <div class="panel panel-default" style="margin-top:1em;">
-                                            <div class="panel-body">
+                                        <div id="" class="panel panel-default" style="margin-top:1em;">
+                                            <div class="panel-body" style="padding:12px 0;">
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.keyword.value}">
-                                                    <span id="keywords">
-                                                        <a href="#" data-toggle="tooltip" data-placement="auto top" class="tooltiplabel right" data-original-title="#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.description}" title="" style="margin-right:1em;">Keyword(s)</a>
-                                                        #{DatasetPage.datasetVersionUI.keyword.displayValue}
+                                                    <span id="keywords" class="form-group">
+                                                        <label class="col-sm-3 control-label">
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.name}</a>
+                                                        </label>
+                                                        <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.keyword.displayValue}</span>
                                                     </span>
                                                 </ui:fragment>
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.subject.value}">
-                                                    <span id="subject">
-                                                        <a href="#" data-toggle="tooltip" data-placement="auto top" class="tooltiplabel right" data-original-title="#{DatasetPage.datasetVersionUI.subject.datasetFieldType.description}" title="" style="margin-right:1em;">Subject(s)</a>
-                                                        #{DatasetPage.datasetVersionUI.subject.displayValue}
+                                                    <span id="subject" class="form-group">
+                                                        <label class="col-sm-3 control-label">
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.subject.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.subject.datasetFieldType.name}</a>
+                                                        </label>
+                                                        <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.subject.displayValue}</span>
                                                     </span>
                                                 </ui:fragment>
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.relPublicationCitation}">
-                                                    <span id="publication">Related Publication: #{DatasetPage.datasetVersionUI.relPublicationCitation} #{DatasetPage.datasetVersionUI.relPublicationId}  <a href="#{DatasetPage.datasetVersionUI.relPublicationUrl}" target="_blank">#{DatasetPage.datasetVersionUI.relPublicationUrl}</a></span>
+                                                    <span id="publication" class="form-group">
+                                                        <label class="col-sm-3 control-label">
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="STATIC" title="">Related Publication (STATIC)</a>
+                                                        </label>
+                                                        <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.relPublicationCitation}  <a href="#{DatasetPage.datasetVersionUI.relPublicationUrl}" title="#{DatasetPage.datasetVersionUI.relPublicationUrl}" target="_blank">#{DatasetPage.datasetVersionUI.relPublicationId}</a></span>
+                                                    </span>
                                                 </ui:fragment>
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.notes.value}">
-                                                    <span id="note">
-                                                        <a href="#" data-toggle="tooltip" data-placement="auto top" class="tooltiplabel right" data-original-title="#{DatasetPage.datasetVersionUI.notes.datasetFieldType.description}" title="" style="margin-right:1em;">Notes</a>
-                                                        <div>
-                                                            #{DatasetPage.datasetVersionUI.notes.value}
-                                                        </div>
+                                                    <span id="note" class="form-group">
+                                                        <label class="col-sm-3 control-label">
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.notes.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.notes.datasetFieldType.name}</a>
+                                                        </label>
+                                                        <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.notes.value}</span>
                                                     </span>
                                                 </ui:fragment>
                                             </div>
diff --git a/src/main/webapp/metadataFragment.xhtml b/src/main/webapp/metadataFragment.xhtml
index a85d3b02d44..5df97a5208e 100644
--- a/src/main/webapp/metadataFragment.xhtml
+++ b/src/main/webapp/metadataFragment.xhtml
@@ -17,50 +17,45 @@
                     <div id="collapse#{block.index}" class="collapse #{block.first?'in':''}">
                         <div class="panel-body">
                             <ui:repeat value="#{metadataBlockVal.value}" var="dsf">
-                                <!-- Primitive datasetFields -->
-                                <ui:fragment rendered="#{dsf.datasetFieldType.primitive}">
-                                    <div class="form-group">
-                                        <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
-                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}" title="">
-                                                #{dsf.datasetFieldType.title}
-                                            </a>
-                                        </label>                  
+                                <div class="form-group">
+                                    <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
+                                        <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}" title="">
+                                            #{dsf.datasetFieldType.title}
+                                        </a>
+                                    </label>
+                                    <!-- Primitive datasetFields -->
+                                    <ui:fragment rendered="#{dsf.datasetFieldType.primitive}">
                                         <div class="col-sm-9">
                                             <h:outputText value="#{dsf.value}" rendered="#{!dsf.datasetFieldType.allowMultiples}"/>
                                             <ui:repeat value="#{dsf.values}" var="value" varStatus="loop" rendered="#{dsf.datasetFieldType.allowMultiples}">
                                                 <h:outputText value="#{loop.first?'':'; '}#{value}"/>
-                                            </ui:repeat>                                                 
-                                        </div>                                        
-                                    </div>
-                                </ui:fragment>  
-                                <!-- Compound datasetFields -->
-                                <ui:fragment rendered="#{dsf.datasetFieldType.compound}">
-                                    <ui:repeat value="#{dsf.datasetFieldCompoundValues}" var="compoundValues">
-                                        <div class="form-group">
-                                            <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
-                                                <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}" title="">
-                                                    #{dsf.datasetFieldType.title}
-                                                </a>
-                                            </label>                  
-                                            <div class="col-sm-9">
-                                                <!-- Sub fields -->
-                                                <ui:repeat value="#{compoundValues.childDatasetFields}" var="subdsf">                                                              
-                                                    <div class="col-sm-6">
-                                                        <label class="control-label" for="metadata_BLANK">
-                                                            <a class="tooltiplabel right" data-original-title="#{subdsf.datasetFieldType.description}" data-placement="auto right" data-toggle="tooltip" href="#">#{subdsf.datasetFieldType.title}</a>                                                        
-                                                        </label>
-                                                        <div>
-                                                            <h:outputText value="#{subdsf.value}" rendered="#{!subdsf.datasetFieldType.allowMultiples}"/>
-                                                            <ui:repeat value="#{subdsf.values}" var="value" varStatus="loop" rendered="#{subdsf.datasetFieldType.allowMultiples}">
-                                                                <h:outputText value="#{loop.first?'':'; '}#{value}"/>
-                                                            </ui:repeat>
+                                            </ui:repeat>
+                                        </div>
+                                    </ui:fragment>
+                                    <!-- Compound datasetFields -->
+                                    <ui:fragment rendered="#{dsf.datasetFieldType.compound}">
+                                        <div class="form-col-container col-sm-9">
+                                            <ui:repeat value="#{dsf.datasetFieldCompoundValues}" var="compoundValues">
+                                                <div class="form-group">
+                                                    <!-- Sub fields -->
+                                                    <ui:repeat value="#{compoundValues.childDatasetFields}" var="subdsf">
+                                                        <div class="form-col-container col-sm-6">
+                                                            <label class="control-label" for="metadata_#{subdsf.datasetFieldType.name}">
+                                                                <a class="tooltiplabel right" data-original-title="#{subdsf.datasetFieldType.description}" data-placement="auto right" data-toggle="tooltip" href="#">#{subdsf.datasetFieldType.title}</a>
+                                                            </label>
+                                                            <div>
+                                                                <h:outputText value="#{subdsf.value}" rendered="#{!subdsf.datasetFieldType.allowMultiples}"/>
+                                                                <ui:repeat value="#{subdsf.values}" var="value" varStatus="loop" rendered="#{subdsf.datasetFieldType.allowMultiples}">
+                                                                    <h:outputText value="#{loop.first?'':'; '}#{value}"/>
+                                                                </ui:repeat>
+                                                            </div>
                                                         </div>
-                                                    </div>
-                                                </ui:repeat>
-                                            </div>
+                                                    </ui:repeat>
+                                                </div>
+                                            </ui:repeat>
                                         </div>
-                                    </ui:repeat> 
-                                </ui:fragment>                               
+                                    </ui:fragment>
+                                </div>
                             </ui:repeat>
                         </div>
                     </div>
@@ -82,148 +77,145 @@
                         <div id="collapse#{block.index}" class="collapse #{block.first || DatasetPage.editMode == 'CREATE'?'in':''}">
                             <div class="panel-body">
                                 <ui:repeat value="#{metadataBlockVal.value}" var="dsf">
-                                    <ui:fragment rendered="#{(DatasetPage.editMode == 'METADATA' or dsf.datasetFieldType.displayOnCreate)}">
 
-                                        <!-- Primitive fields -->    
-                                        <p:fragment autoUpdate="true" rendered="#{dsf.datasetFieldType.primitive}">
-                                            <div class="form-group">
-                                                <div class="col-sm-3">
-                                                    <label for="metadata_#{dsf.datasetFieldType.name}" class="control-label">
-                                                        <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}">
-                                                            #{dsf.datasetFieldType.title}
-                                                        </a>
-                                                        <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{dsf.datasetFieldType.required}" /> 
-                                                    </label> 
-                                                </div>
-                                                <ui:remove><!-- There is an issue with the dynamic +/- and the primefaces autoupdate where they are not working
-                                                    well together for the primitive fields, but are for the compound fields. So as a workaround for the primitive,
-                                                    we wrap them in a ui:repeat that iterates on a single list. Note: dummyVar is never used--></ui:remove>
-                                                <ui:repeat value="#{Collections:singletonList('')}" var="dummyVar">
-                                                    <div class="form-group col-sm-9">
-                                                        <ui:repeat value="#{dsf.datasetFieldValues}" var="dsfv" varStatus="valCount" >
-                                                            <div class="form-group">
-                                                                <div class="col-sm-9">
-                                                                    <ui:include src="datasetFieldForEditFragment.xhtml">
-                                                                        <ui:param name="dsfv" value="#{dsfv}"/>
-                                                                        <ui:param name="dsfvIndex" value="#{valCount.index}"/>
-                                                                    </ui:include>
+                                    <div class="form-group">
+                                        <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
+                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}">
+                                                #{dsf.datasetFieldType.title}
+                                            </a>
+                                            <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{dsf.datasetFieldType.required}" />
+                                        </label>
+
+                                        <ui:fragment rendered="#{(DatasetPage.editMode == 'METADATA' or dsf.datasetFieldType.displayOnCreate)}">
+                                            <!-- Primitive fields -->
+                                            <p:fragment autoUpdate="true" rendered="#{dsf.datasetFieldType.primitive}">
+                                                <div class="form-group">
+                                                    <ui:remove><!-- There is an issue with the dynamic +/- and the primefaces autoupdate where they are not working
+                                                        well together for the primitive fields, but are for the compound fields. So as a workaround for the primitive,
+                                                        we wrap them in a ui:repeat that iterates on a single list. Note: dummyVar is never used--></ui:remove>
+                                                    <ui:repeat value="#{Collections:singletonList('')}" var="dummyVar">
+                                                        <div class="form-col-container col-sm-12">
+                                                            <ui:repeat value="#{dsf.datasetFieldValues}" var="dsfv" varStatus="valCount" >
+                                                                <div class="form-group">
+                                                                    <div class="form-col-container col-sm-9">
+                                                                        <ui:include src="datasetFieldForEditFragment.xhtml">
+                                                                            <ui:param name="dsfv" value="#{dsfv}"/>
+                                                                            <ui:param name="dsfvIndex" value="#{valCount.index}"/>
+                                                                        </ui:include>
+                                                                    </div>
+                                                                    <!-- Add / Remove buttons -->
+                                                                    <ui:fragment rendered="#{dsf.datasetFieldType.allowMultiples and !dsf.datasetFieldType.controlledVocabulary}">
+                                                                        <div class="col-xs-3">
+                                                                            <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin:1.8em 1em 0 0;' : 'margin:0 1em 0 0;'}"
+                                                                                             title="Add Record" value="&lt;span class='glyphicon glyphicon-plus'&gt;&lt;/span&gt;" escape="false"
+                                                                                             actionListener="#{dsf.addDatasetFieldValue(valCount.index + 1)}">
+                                                                            </p:commandButton>
+                                                                            <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin-top:1.8em;' : ''}"
+                                                                                             title="Delete Record" value="&lt;span class='glyphicon glyphicon-minus'&gt;&lt;/span&gt;" escape="false"
+                                                                                             rendered="#{dsf.datasetFieldValues.size() > 1}"
+                                                                                             actionListener="#{dsf.removeDatasetFieldValue(valCount.index)}">
+                                                                            </p:commandButton>
+                                                                        </div>
+                                                                    </ui:fragment>
                                                                 </div>
-                                                                <!-- Add / Remove buttons -->
-                                                                <ui:fragment rendered="#{dsf.datasetFieldType.allowMultiples and !dsf.datasetFieldType.controlledVocabulary}">
-                                                                    <div class="col-xs-3">
-                                                                        <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin:1.8em 1em 0 0;' : 'margin:0 1em 0 0;'}"  
-                                                                                         title="Add Record" value="&lt;span class='glyphicon glyphicon-plus'&gt;&lt;/span&gt;" escape="false" 
-                                                                                         actionListener="#{dsf.addDatasetFieldValue(valCount.index + 1)}">
-                                                                        </p:commandButton>
-                                                                        <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin-top:1.8em;' : ''}"  
-                                                                                         title="Delete Record" value="&lt;span class='glyphicon glyphicon-minus'&gt;&lt;/span&gt;" escape="false" 
-                                                                                         rendered="#{dsf.datasetFieldValues.size() > 1}"
-                                                                                         actionListener="#{dsf.removeDatasetFieldValue(valCount.index)}">
-                                                                        </p:commandButton>
+                                                            </ui:repeat>
+                                                            <ui:fragment rendered="#{dsf.datasetFieldType.controlledVocabulary}">
+                                                                <p:selectOneMenu value="#{dsf.singleControlledVocabularyValue}" converter="controlledVocabularyValueConverter" styleClass="form-control"
+                                                                                 rendered="#{!dsf.datasetFieldType.allowMultiples}">
+                                                                    <f:selectItems value="#{dsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />
+                                                                </p:selectOneMenu>
+                                                                <ui:fragment rendered="#{dsf.datasetFieldType.allowMultiples}">
+                                                                    <div class="ui-inputfield form-control select-scroll-block">
+                                                                        <p:selectManyCheckbox value="#{dsf.controlledVocabularyValues}" converter="controlledVocabularyValueConverter"
+                                                                                              layout="pageDirection">
+                                                                            <f:selectItem itemLabel="Select..." itemValue="" noSelectionOption="true"/>
+                                                                            <f:selectItems value="#{dsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />
+                                                                        </p:selectManyCheckbox>
                                                                     </div>
                                                                 </ui:fragment>
-                                                            </div>
-                                                        </ui:repeat>
-                                                        <ui:fragment rendered="#{dsf.datasetFieldType.controlledVocabulary}">
-                                                            <p:selectOneMenu value="#{dsf.singleControlledVocabularyValue}" converter="controlledVocabularyValueConverter" styleClass="form-control"
-                                                                             rendered="#{!dsf.datasetFieldType.allowMultiples}">
-                                                                <f:selectItems value="#{dsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />                                                         
-                                                            </p:selectOneMenu>
-                                                            <ui:fragment rendered="#{dsf.datasetFieldType.allowMultiples}">
-                                                                <div class="ui-inputfield form-control select-scroll-block">
-                                                                    <p:selectManyCheckbox value="#{dsf.controlledVocabularyValues}" converter="controlledVocabularyValueConverter" 
-                                                                                          layout="pageDirection">
-                                                                        <f:selectItem itemLabel="Select One" itemValue="" noSelectionOption="true"/>
-                                                                        <f:selectItems value="#{dsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />                                                         
-                                                                    </p:selectManyCheckbox> 
-                                                                </div>
-                                                            </ui:fragment>
-                                                            <ui:fragment rendered="#{!empty dsf.validationMessage}">
-                                                                <div class="alert-danger">
-                                                                    <strong>#{dsf.validationMessage}</strong>
-                                                                </div>
-                                                            </ui:fragment>                                                             
-                                                        </ui:fragment>
-                                                    </div>
-                                                </ui:repeat>
-                                            </div>                                                    
-                                        </p:fragment>
-
-                                        <!-- Compound fields -->
-                                        <p:fragment autoUpdate="true" rendered="#{dsf.datasetFieldType.compound}">
-                                            <ui:repeat value="#{dsf.datasetFieldCompoundValues}" var="compoundValue" varStatus="valCount">
-                                                <div class="form-group">
-                                                    <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
-                                                        <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}">
-                                                            #{dsf.datasetFieldType.title}
-                                                        </a>
-                                                        <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{dsf.datasetFieldType.required}" /> 
-                                                    </label>                  
-
-                                                    <div class="form-group col-sm-7">
-                                                        <!-- Sub Fields -->
-                                                        <ui:repeat value="#{compoundValue.childDatasetFields}" var="subdsf">
-                                                            <div class="#{(subdsf.datasetFieldType.fieldType == 'textbox') ? 'col-sm-12' : 'col-sm-6'}">
-                                                                <ui:fragment>
-                                                                    <label class="control-label" for="metadata_BLANK">
-                                                                        <a class="tooltiplabel right" data-original-title="#{subdsf.datasetFieldType.description}" data-placement="auto right" data-toggle="tooltip" href="#">#{subdsf.datasetFieldType.title}</a>
-                                                                        <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{subdsf.datasetFieldType.required}" /> 
-                                                                    </label>   
+                                                                <ui:fragment rendered="#{!empty dsf.validationMessage}">
+                                                                    <div class="alert-danger">
+                                                                        <strong>#{dsf.validationMessage}</strong>
+                                                                    </div>
                                                                 </ui:fragment>
+                                                            </ui:fragment>
+                                                        </div>
+                                                    </ui:repeat>
+                                                </div>
+                                            </p:fragment>
 
-                                                                <ui:include src="datasetFieldForEditFragment.xhtml" rendered="#{!subdsf.datasetFieldType.controlledVocabulary}">
-                                                                    <ui:param name="dsfv" value="#{subdsf.singleValue}"/>
-                                                                    <ui:param name="dsfvIndex" value="0"/>
-                                                                </ui:include>
+                                            <!-- Compound fields -->
+                                            <p:fragment autoUpdate="true" rendered="#{dsf.datasetFieldType.compound}">
+                                                <div class="form-group form-col-container col-sm-9">
+                                                    <ui:repeat value="#{dsf.datasetFieldCompoundValues}" var="compoundValue" varStatus="valCount">
+                                                        <div class="form-group form-col-container col-sm-9">
+                                                            <!-- Sub Fields -->
+                                                            <ui:repeat value="#{compoundValue.childDatasetFields}" var="subdsf">
+                                                                <div class="form-col-container #{(subdsf.datasetFieldType.fieldType == 'textbox') ? 'col-sm-12' : 'col-sm-6'}">
+                                                                    <ui:fragment>
+                                                                        <label class="control-label" for="metadata_#{subdsf.datasetFieldType.name}">
+                                                                            <a class="tooltiplabel right" data-original-title="#{subdsf.datasetFieldType.description}" data-placement="auto right" data-toggle="tooltip" href="#">#{subdsf.datasetFieldType.title}</a>
+                                                                            <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{subdsf.datasetFieldType.required}" />
+                                                                        </label>
+                                                                    </ui:fragment>
+                                                                    <ui:fragment rendered="#{!subdsf.datasetFieldType.controlledVocabulary}">
+                                                                        <ui:include src="datasetFieldForEditFragment.xhtml">
+                                                                            <ui:param name="dsfv" value="#{subdsf.singleValue}"/>
+                                                                            <ui:param name="dsfvIndex" value="0"/>
+                                                                        </ui:include>
+                                                                    </ui:fragment>
 
-                                                                <!-- MOVED SELECT ONE TO dataFieldForEdit -->
-                                                                <ui:fragment rendered="#{subdsf.datasetFieldType.controlledVocabulary}">
-                                                                    <p:selectOneMenu value="#{subdsf.singleControlledVocabularyValue}" converter="controlledVocabularyValueConverter" styleClass="form-control"
-                                                                                     rendered="#{!subdsf.datasetFieldType.allowMultiples}">
-                                                                        <f:selectItem itemLabel="Select One" itemValue="" noSelectionOption="true"/>
-                                                                        <f:selectItems value="#{subdsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />                                                         
-                                                                    </p:selectOneMenu>
-                                                                    <ui:fragment rendered="#{subdsf.datasetFieldType.allowMultiples}">
-                                                                        <div class="ui-inputfield form-control select-scroll-block">
-                                                                            <p:selectManyCheckbox value="#{subdsf.controlledVocabularyValues}" converter="controlledVocabularyValueConverter"
-                                                                                                  layout="pageDirection">
-                                                                                <f:selectItems value="#{subdsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />                                                         
-                                                                            </p:selectManyCheckbox>
+                                                                    <!-- MOVED SELECT ONE TO dataFieldForEdit -->
+                                                                    <ui:fragment rendered="#{subdsf.datasetFieldType.controlledVocabulary}">
+                                                                        <div>
+                                                                            <p:selectOneMenu value="#{subdsf.singleControlledVocabularyValue}" converter="controlledVocabularyValueConverter" 
+                                                                                             rendered="#{!subdsf.datasetFieldType.allowMultiples}">
+                                                                                <f:selectItem itemLabel="Select..." itemValue="" noSelectionOption="true"/>
+                                                                                <f:selectItems value="#{subdsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />
+                                                                            </p:selectOneMenu>
+                                                                            <ui:fragment rendered="#{subdsf.datasetFieldType.allowMultiples}">
+                                                                                <div class="ui-inputfield form-control select-scroll-block">
+                                                                                    <p:selectManyCheckbox value="#{subdsf.controlledVocabularyValues}" converter="controlledVocabularyValueConverter"
+                                                                                                          layout="pageDirection">
+                                                                                        <f:selectItems value="#{subdsf.datasetFieldType.controlledVocabularyValues}" var="cvv" itemLabel="#{cvv.strValue}" itemValue="#{cvv}" />
+                                                                                    </p:selectManyCheckbox>
+                                                                                </div>
+                                                                                <ui:fragment rendered="#{!empty subdsf.validationMessage}">
+                                                                                    <div class="alert-danger">
+                                                                                        <strong>#{subdsf.validationMessage}</strong>
+                                                                                    </div>
+                                                                                </ui:fragment>
+                                                                            </ui:fragment>
                                                                         </div>
-                                                                        <ui:fragment rendered="#{!empty subdsf.validationMessage}">
-                                                                            <div class="alert-danger">
-                                                                                <strong>#{subdsf.validationMessage}</strong>
-                                                                            </div>
-                                                                        </ui:fragment>                             
                                                                     </ui:fragment>
-                                                                </ui:fragment>
-                                                            </div>
-                                                        </ui:repeat>
-                                                    </div>
-                                                    <ui:fragment rendered="#{dsf.datasetFieldType.allowMultiples and !dsf.datasetFieldType.controlledVocabulary}">
-                                                        <div class="col-xs-2">
-                                                            <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin:1.8em 1em 0 0;' : 'margin:0 1em 0 0;'}"  
-                                                                             title="Add Record" value="&lt;span class='glyphicon glyphicon-plus'&gt;&lt;/span&gt;" escape="false" 
-                                                                             actionListener="#{dsf.addDatasetFieldCompoundValue(valCount.index + 1)}">
-                                                            </p:commandButton>
-                                                            <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin-top:1.8em;' : ''}"  
-                                                                             title="Delete Record" value="&lt;span class='glyphicon glyphicon-minus'&gt;&lt;/span&gt;" escape="false" 
-                                                                             rendered="#{dsf.datasetFieldCompoundValues.size() > 1}"
-                                                                             actionListener="#{dsf.removeDatasetFieldCompoundValue(valCount.index)}">
-                                                            </p:commandButton>
+                                                                </div>
+                                                            </ui:repeat>
                                                         </div>
-                                                    </ui:fragment>                                                    
+                                                        <ui:fragment rendered="#{dsf.datasetFieldType.allowMultiples and !dsf.datasetFieldType.controlledVocabulary}">
+                                                            <div class="col-sm-3">
+                                                                <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin:1.8em 1em 0 0;' : 'margin:0 1em 0 0;'}"
+                                                                                 title="Add Record" value="&lt;span class='glyphicon glyphicon-plus'&gt;&lt;/span&gt;" escape="false"
+                                                                                 actionListener="#{dsf.addDatasetFieldCompoundValue(valCount.index + 1)}">
+                                                                </p:commandButton>
+                                                                <p:commandButton styleClass="btn btn-default btn-sm" style="#{dsf.datasetFieldType.compound ? 'margin-top:1.8em;' : ''}"
+                                                                                 title="Delete Record" value="&lt;span class='glyphicon glyphicon-minus'&gt;&lt;/span&gt;" escape="false"
+                                                                                 rendered="#{dsf.datasetFieldCompoundValues.size() > 1}"
+                                                                                 actionListener="#{dsf.removeDatasetFieldCompoundValue(valCount.index)}">
+                                                                </p:commandButton>
+                                                            </div>
+                                                        </ui:fragment>
+                                                    </ui:repeat>
                                                 </div>
-                                            </ui:repeat>
-                                        </p:fragment>                                        
-                                    </ui:fragment>
+                                            </p:fragment>
+                                        </ui:fragment>
+                                    </div>
                                 </ui:repeat>
                             </div>
                         </div>
                     </div>
                 </ui:fragment>
             </ui:repeat>
-        </div>    
+        </div>
     </ui:fragment>
 
 </div>
\ No newline at end of file
diff --git a/src/main/webapp/resources/css/structure.css b/src/main/webapp/resources/css/structure.css
index 5f9fdd658b3..6f668812573 100644
--- a/src/main/webapp/resources/css/structure.css
+++ b/src/main/webapp/resources/css/structure.css
@@ -193,9 +193,13 @@ span[id$='editDataSet'] .ui-button-text {white-space: nowrap;}
 
 div.form-group .glyphicon.glyphicon-asterisk {font-size:.5em; vertical-align:text-top;}
 #datasetForm .form-group {overflow: hidden;}
-#datasetForm .form-group .col-sm-9 .col-sm-9, #datasetForm .form-group .col-sm-7 .col-sm-6, #datasetForm .form-group .col-sm-7 .col-sm-12 {padding-left:0;}
+#datasetForm .form-col-container .form-col-container {padding-left:0;}
+#datasetForm .form-col-container .form-col-container .ui-selectonemenu {display:block;}
 
-#datasetForm div.ui-selectonemenu.form-control {padding:1px;}
+#datasetForm div.ui-selectonemenu.form-control {padding:0px;} /* Primefaces vs Bootstrap selectOneMenu fix */
+#datasetForm .form-col-container .form-col-container .ui-selectonemenu .ui-selectonemenu-label {padding:6px 4px;}
+#datasetForm .form-col-container .form-col-container .ui-selectonemenu .ui-selectonemenu-trigger {border-radius:0; width:24px;}
+#datasetForm .form-col-container .form-col-container .ui-selectonemenu .ui-selectonemenu-trigger .ui-icon {margin-top:6px;}
 
 #datasetForm .select-scroll-block {height:auto; max-height:120px; overflow-y:scroll; padding: 6px 12px;}
 #datasetForm .select-scroll-block table.ui-selectmanycheckbox label {margin-left:5px; margin-top:0; font-weight:normal;}

From 7a6dc0337af8e3027701563ee8f395f84d62a915 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 13 May 2014 16:38:40 -0400
Subject: [PATCH 14/46] added sword list-studies script #3385

---
 scripts/api/data-deposit/list-studies         |  7 ++++
 .../CollectionListManagerImpl.java            | 42 +++++++++++++------
 2 files changed, 37 insertions(+), 12 deletions(-)
 create mode 100755 scripts/api/data-deposit/list-studies

diff --git a/scripts/api/data-deposit/list-studies b/scripts/api/data-deposit/list-studies
new file mode 100755
index 00000000000..91fb9dc4f8d
--- /dev/null
+++ b/scripts/api/data-deposit/list-studies
@@ -0,0 +1,7 @@
+#!/bin/bash
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+DATAVERSE_ALIAS=peteTop
+curl --insecure https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS \
+| xmllint -format -
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
index 97594314c8b..ebcd67b4be0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
@@ -1,9 +1,12 @@
 package edu.harvard.iq.dataverse.api.datadeposit;
 
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.DatasetServiceBean;
 import edu.harvard.iq.dataverse.Dataverse;
 import edu.harvard.iq.dataverse.DataverseServiceBean;
 import edu.harvard.iq.dataverse.DataverseUser;
-import java.util.Collection;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.inject.Inject;
@@ -25,6 +28,8 @@ public class CollectionListManagerImpl implements CollectionListManager {
     private static final Logger logger = Logger.getLogger(CollectionListManagerImpl.class.getCanonicalName());
     @EJB
     DataverseServiceBean dataverseService;
+    @EJB
+    DatasetServiceBean datasetService;
     @Inject
     SwordAuth swordAuth;
     @Inject
@@ -50,17 +55,30 @@ public Feed listCollectionContents(IRI iri, AuthCredentials authCredentials, Swo
                      * user?
                      */
 //                    Collection<Study> studies = dv.getOwnedStudies();
-//                    String baseUrl = urlManager.getHostnamePlusBaseUrlPath(iri.toString());
-//                    for (Study study : studies) {
-//                        String editUri = baseUrl + "/edit/study/" + study.getGlobalId();
-//                        String editMediaUri = baseUrl + "/edit-media/study/" + study.getGlobalId();
-//                        Entry entry = feed.addEntry();
-//                        entry.setId(editUri);
-//                        entry.setTitle(study.getLatestVersion().getMetadata().getTitle());
-//                        entry.setBaseUri(new IRI(editUri));
-//                        entry.addLink(editMediaUri, "edit-media");
-//                        feed.addEntry(entry);
-//                    }
+                    List childDvObjects = dataverseService.findByOwnerId(dv.getId());
+                    childDvObjects.addAll(datasetService.findByOwnerId(dv.getId()));
+                    List<Dataset> studies = new ArrayList<>();
+                    for (Object object : childDvObjects) {
+                        if (object instanceof Dataset) {
+                            studies.add((Dataset) object);
+                        }
+                    }
+                    String baseUrl = urlManager.getHostnamePlusBaseUrlPath(iri.toString());
+                    for (Dataset study : studies) {
+                        /**
+                         * @todo is globalId the same as identifier?
+                         */
+                        // String editUri = baseUrl + "/edit/study/" + study.getGlobalId();
+                        String editUri = baseUrl + "/edit/study/" + study.getIdentifier();
+                        // String editMediaUri = baseUrl + "/edit-media/study/" + study.getGlobalId();
+                        String editMediaUri = baseUrl + "/edit-media/study/" + study.getIdentifier();
+                        Entry entry = feed.addEntry();
+                        entry.setId(editUri);
+                        entry.setTitle(study.getLatestVersion().getTitle());
+                        entry.setBaseUri(new IRI(editUri));
+                        entry.addLink(editMediaUri, "edit-media");
+                        feed.addEntry(entry);
+                    }
                     Boolean dvHasBeenReleased = dv.isReleased();
                     feed.addSimpleExtension(new QName(UriRegistry.SWORD_STATE, "dataverseHasBeenReleased"), dvHasBeenReleased.toString());
                     return feed;

From 5e1275fabbca40343cbf9dfb36181338737584e1 Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.80.247>
Date: Tue, 13 May 2014 16:47:25 -0400
Subject: [PATCH 15/46] Changed the link URL for About in the header.

---
 src/main/webapp/dataverse_header.xhtml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/webapp/dataverse_header.xhtml b/src/main/webapp/dataverse_header.xhtml
index 927867d7413..526e35b2e28 100644
--- a/src/main/webapp/dataverse_header.xhtml
+++ b/src/main/webapp/dataverse_header.xhtml
@@ -40,7 +40,7 @@
                         </button>
                     </form>
                     <li>
-                        <h:outputLink value="http://datascience.iq.harvard.edu/dataverse/harvarddataverse" target="_blank">
+                        <h:outputLink value="http://datascience.iq.harvard.edu/blog/dataverse-40-beta" target="_blank">
                             About
                         </h:outputLink>
                     </li>

From 8867b13077d8b827c708c6a8d1c0bff881d31d5b Mon Sep 17 00:00:00 2001
From: Michael Heppler <mheppler@hmdc.harvard.edu>
Date: Wed, 14 May 2014 11:47:29 -0400
Subject: [PATCH 16/46] Updated footer copyright to be consistent with the
 copyright in the guides footer.

---
 src/main/webapp/dataverse_template.xhtml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/webapp/dataverse_template.xhtml b/src/main/webapp/dataverse_template.xhtml
index 570fedf8065..b257960b5a3 100644
--- a/src/main/webapp/dataverse_template.xhtml
+++ b/src/main/webapp/dataverse_template.xhtml
@@ -33,7 +33,7 @@
             <ui:insert name="body">Default Body</ui:insert>
         </div>
         <div class="container" id="footer" style="margin-top:3em;">
-            &#169; 2014 The President and Fellows of Harvard College <!-- | <a href="#">Privacy</a> -->
+            &#169; Copyright 1997-2014, President &#38; Fellows Harvard University. <!-- | <a href="#">Privacy</a> -->
         </div>
         <p:ajaxStatus style="width:31px;height:31px;position:fixed;right:50%;bottom:50%;" id="ajaxStatusPanel">
             <f:facet name="start">

From 80a39ac8ac6828ea3e2504c9b1e69d59b22c8483 Mon Sep 17 00:00:00 2001
From: Raman Prasad <raman_prasad@harvard.edu>
Date: Wed, 14 May 2014 12:47:52 -0400
Subject: [PATCH 17/46] adding a python wrapper for the api

bari related testing
---
 .gitignore                                  |   1 +
 scripts/api/py_api_wrapper/dataverse_api.py | 207 ++++++++++++++++++++
 scripts/api/py_api_wrapper/msg_util.py      |   4 +
 scripts/api/py_api_wrapper/readme.md        |  83 ++++++++
 4 files changed, 295 insertions(+)
 create mode 100644 scripts/api/py_api_wrapper/dataverse_api.py
 create mode 100644 scripts/api/py_api_wrapper/msg_util.py
 create mode 100644 scripts/api/py_api_wrapper/readme.md

diff --git a/.gitignore b/.gitignore
index 36a8cec089b..ab378a6f94c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,4 @@ michael-local
 ehthumbs.db
 Thumbs.db
 .vagrant
+*.pyc
diff --git a/scripts/api/py_api_wrapper/dataverse_api.py b/scripts/api/py_api_wrapper/dataverse_api.py
new file mode 100644
index 00000000000..3701d50e4af
--- /dev/null
+++ b/scripts/api/py_api_wrapper/dataverse_api.py
@@ -0,0 +1,207 @@
+"""
+Use APIs from: 
+https://github.com/IQSS/dataverse/tree/master/scripts/api
+
+5/8/2013 - scratch work, examining API
+"""
+import urllib 
+import urllib2
+import json
+from msg_util import *
+
+class DataverseAPILink:
+    """Used to test the Dataverse API described in github:
+        https://github.com/IQSS/dataverse/tree/master/scripts/api 
+    """
+    RETURN_MODE_STR = 'RETURN_MODE_STR'
+    RETURN_MODE_PYTHON = 'RETURN_MODE_PYTHON'
+    HTTP_GET = 'GET'
+    HTTP_POST = 'POST'
+    HTTP_DELETE = 'DELETE'
+    HTTP_METHODS = [HTTP_GET, HTTP_POST, HTTP_DELETE]
+    
+    def __init__(self, server_name, use_https, apikey=None):
+        """
+        :param  server_name: e.g. dataverse.org, dvn-build.hmdc.harvard.edu, etc.
+        :type   server_name: str
+        :param  use_https: Use https for api calls?
+        :type   use_https: boolean
+        """
+        self.server_name = server_name
+        self.use_https = use_https
+        self.apikey = apikey
+        self.update_server_name()
+        self.return_mode = self.RETURN_MODE_STR
+        
+    def set_return_mode_python(self):
+        """API calls return JSON text response as a Python object
+        Uses json.loads(json_str)
+        """
+        self.return_mode = self.RETURN_MODE_PYTHON
+    
+    def set_return_mode_string(self):
+        """API calls return JSON responses as a string"""
+        self.return_mode = self.RETURN_MODE_STR
+    
+        
+    def update_server_name(self):
+        if self.server_name is None:
+            raise Exception('Server name is None!')
+            
+        if self.server_name.endswith('/'):  # cut trailing slash
+            self.server_name = self.server_name[-1]
+
+        server_name_pieces = self.server_name.split('//')
+        if len(server_name_pieces) > 1:
+            self.server_name = server_name_pieces[1]
+        
+    def get_server_name(self):
+        
+        if self.use_https:
+            return 'https://' + self.server_name
+        return 'http://' + self.server_name
+        
+    
+    def make_api_call(self, url_str, method, kwargs=None):
+        msg('url_str: [%s]  method:[%s] kwargs:[%s]' % (url_str, method, kwargs))
+        if url_str is None:
+            return None
+        if not method in self.HTTP_METHODS:
+            msgt('Error: Method not found: %s' % method)
+
+        request = urllib2.Request(url_str)
+        request.get_method = lambda:method  # GET, POST, DELETE
+        if kwargs:
+            request.add_data(urllib.urlencode(kwargs))
+
+        response = urllib2.urlopen(request)
+
+        print response.info()
+
+        if self.return_mode == self.RETURN_MODE_PYTHON:
+            json_response = json.loads(response.read())
+            response.close()  
+            return json_response
+
+        json_str = response.read()
+        response.close()  
+        return json_str
+        
+       
+    def get_dataverse_metadata(self, dv_id=None):
+        """List all dataverses using GET http://{{SERVER}}/api/dvs
+        :param dv_id: dataverse id or None.  None lists all dataverses
+        :type dv_id: int, None, ':root' 
+        :return: JSON, dataverses metadata
+        """
+        msgt('get_dataverse_metadata: [%s]' % dv_id)    
+        url_str = self.get_server_name() + '/api/dvs'
+        if dv_id is not None:
+            url_str += '/%s' % dv_id
+        return self.make_api_call(url_str, self.HTTP_GET)
+
+    def list_dataverses(self):
+        msgt('list_dataverses')    
+        return self.get_dataverse_metadata()
+        
+    def get_root_dataverse_metadata(self):
+        msgt('get_root_dataverse_metadata')    
+        return self.get_dataverse_metadata(':root')
+        
+    
+    def get_dataset_metadata(self, dataset_id, dataset_version=None):
+        """List all dataverses using GET http://{{SERVER}}/api/datasets/?key={{apikey}}
+        @return: JSON, list of dataverses
+        """
+        msgt('get_dataset_metadata')    
+        if not self.apikey:
+            msg('Sorry!  You need an api key!')
+            return
+        url_str = self.get_server_name() + '/api/datasets/%s' % dataset_id
+        if dataset_version:
+            url_str = self.get_server_name() + '/api/datasets/%s/versions/%s/metadata' % (dataset_id, dataset_version)
+        else:
+            url_str = self.get_server_name() + '/api/datasets/%s' % (dataset_id)    
+
+        url_str = '%s?key=%s' % (url_str, self.apikey)
+        
+        return self.make_api_call(url_str, self.HTTP_GET)
+        
+
+    def list_datasets(self):
+        """List all datadryd using GET http://{{SERVER}}/api/datasets?key={{apikey}}
+        @return: JSON, list of dataverses
+        """
+        msgt('list_datasets')    
+        if not self.apikey:
+            msg('Sorry!  You need an api key!')
+            return
+        url_str = self.get_server_name() + '/api/datasets/?key=%s' % self.apikey
+        return self.make_api_call(url_str, self.HTTP_GET)
+    
+    
+
+    def delete_dataverse_by_id(self, id_val):        
+        msgt('delete_dataverse_by_id: %s' % id_val)    
+        url_str = self.get_server_name() + '/api/dvs/%s' % id_val
+        kwargs = { 'key': self.apikey }
+        return self.make_api_call(url_str, self.HTTP_DELETE, kwargs)
+
+        
+    '''
+    def make_dataverse(self, username, dvn_info_as_dict, dv_id=None):
+        """Make a dataverse
+        POST http://{{SERVER}}/api/dvs?key={{username}}
+        """
+        msgt('make_dataverse: [username:%s]  [dv_id:%s]' % (username, dv_id))
+        url_str = self.get_server_name() + '/api/dvs?key=%s' % username 
+        #kwargs = {'key': username}
+        return self.make_api_call(url_str, self.HTTP_POST, dvn_info_as_dict)
+    '''   
+def write_to_file(content, fname):
+    open(fname, 'w').write(content)
+    print 'file written: %s' % fname
+
+def save_current_metadata(server_name):
+    dat = DataverseAPILink(server_name, use_https=False, apikey='admin')
+
+    dv_json = dat.list_dataverses()
+    write_to_file(dv_json, '../demo-beta/2014_0513_dataverses.json')
+    
+    dataset_ids = """113:41 121:42 91:30 87:29 84:28 83:27 61:22 71:33 62:23 35:21
+                    56:19 53:44 49:45 46:18 40:36 22:13 32:20 26:10 29:38""".split()
+                    
+    geo_list = []
+    for ds in dataset_ids:
+        did, vid = ds.split(':')
+        geo_meta = dat.get_dataset_metadata(did,':latest')
+        geo_list.append(geo_meta.strip())
+    geo_content = '\n'.join(geo_list)
+    write_to_file(geo_content, '../demo-beta/2014_0513_datasets.json')
+    
+if __name__=='__main__':
+    
+    server_with_api = 'dvn-build.hmdc.harvard.edu'
+    #server_with_api = 'dataverse-demo.iq.harvard.edu'
+    
+    #save_current_metadata(server_with_api)
+    
+    dat = DataverseAPILink(server_with_api, use_https=False, apikey='admin')
+    json_text = dat.list_dataverses()
+    print json_text
+    
+    dat.set_return_mode_python()
+    d = dat.list_dataverses()   # python dictionary {}
+    print d.keys()
+    dv_names = [dv_info.get('name', '?') for dv_info in d['data']]
+    print dv_names
+    #dat.set_return_mode_python()
+    
+    
+    #print dat.get_root_dataverse_metadata()
+    #print dat.get_dataverse_metadata(':root')
+    #print dat.list_datasets()
+    #print dat.get_dataset_metadata(113,':latest')
+    #print dat.make_dataverse('pete')
+    #print dat.delete_dataverse_by_id()
+    
\ No newline at end of file
diff --git a/scripts/api/py_api_wrapper/msg_util.py b/scripts/api/py_api_wrapper/msg_util.py
new file mode 100644
index 00000000000..78606dff4cc
--- /dev/null
+++ b/scripts/api/py_api_wrapper/msg_util.py
@@ -0,0 +1,4 @@
+def msg(s): print s
+def dashes(): msg(40*'-')
+def msgt(s): dashes(); msg(s); dashes()
+
diff --git a/scripts/api/py_api_wrapper/readme.md b/scripts/api/py_api_wrapper/readme.md
new file mode 100644
index 00000000000..826386345b4
--- /dev/null
+++ b/scripts/api/py_api_wrapper/readme.md
@@ -0,0 +1,83 @@
+# Python API Wrapper Guide
+
+(in progress)
+
+This a python class "DataverseAPILink" which may be used to make the API calls described in the dataverse/scripts/api/readme.md
+Results of API calls may by returned as JSON (string format) or as python dictionaries.
+
+Given a DVN server name and optional apikey, the class uses python's basic urllib2 to make the API calls.
+Generate the infamous _Pete_,_Uma_ and _Gabbi_. 
+
+	setup-dvs.sh
+
+Generates root dataverse and some other dataverses for Pete and Uma.
+
+## Quick example
+
+List the dataverses
+	
+	server_with_api = 'dataverse-demo.iq.harvard.edu'
+	dal = DataverseAPILink(server_with_api, use_https=False, apikey='admin')
+    json_text = dal.list_dataverses()
+    print json_text
+
+Output: 
+
+{
+    "status":"OK",
+    "data":[
+        {
+            "id":93,
+            "alias":"b",
+            "name":"b",
+            "affiliation":"b",
+            "contactEmail":"b@b",
+            "permissionRoot":false,
+            "creator":{
+                "id":13,
+                "firstName":"b",
+                "lastName":"b",
+                "userName":"b",
+                "affiliation":"b",
+                "position":"b",
+                "email":"b@b"
+            },
+            "description":"b",
+            "ownerId":1,
+            "creationDate":"2014-05-12 02:38:36 -04"
+        },
+        {
+            "id":77,
+            "alias":"bc",
+            "name":"Beta Candidate",
+            "affiliation":"Top",
+            "contactEmail":"pete@malinator.com",
+            "permissionRoot":false,
+            "creator":{
+                "id":1,
+                "firstName":"Pete",
+                "lastName":"Privileged",
+                "userName":"pete",
+                "affiliation":"Top ",
+                "position":"The Boss",
+                "email":"pete@malinator.com"
+            },
+            "description":"This is a test",
+            "ownerId":1,
+            "creationDate":"2014-05-08 04:06:58 -04"
+        },
+		(etc, etc)
+	
+Return the same list as a python object
+
+	dat.set_return_mode_python()
+	d = dat.list_dataverses()   # python dictionary {}
+	print d.keys()
+	dv_names = [dv_info.get('name', '?') for dv_info in d['data']]
+	print dv_names
+
+Output:
+
+	[u'status', u'data']
+	[u'b', u'Beta Candidate', u'kc58', u'Kevin Smoke Test 5/8', u'Penultimate Smoke Test', u"Pete's public place", u"Pete's restricted data", u"Pete's secrets", u'Root', u'smoke 5/7', u'testadd', u'testauthor', u'Test Cliosed', u'Test Open', u'testpete', u'Top dataverse of Pete', u'Top dataverse of Uma', u"Uma's first", u"Uma's restricted"]
+

From b1279db67dcf83ff677ae20a0f6e499a69f5d653 Mon Sep 17 00:00:00 2001
From: Raman Prasad <raman_prasad@harvard.edu>
Date: Wed, 14 May 2014 12:48:39 -0400
Subject: [PATCH 18/46] indent output for .md file

---
 scripts/api/py_api_wrapper/readme.md | 88 ++++++++++++++--------------
 1 file changed, 44 insertions(+), 44 deletions(-)

diff --git a/scripts/api/py_api_wrapper/readme.md b/scripts/api/py_api_wrapper/readme.md
index 826386345b4..ea012578fd4 100644
--- a/scripts/api/py_api_wrapper/readme.md
+++ b/scripts/api/py_api_wrapper/readme.md
@@ -23,50 +23,50 @@ List the dataverses
 
 Output: 
 
-{
-    "status":"OK",
-    "data":[
-        {
-            "id":93,
-            "alias":"b",
-            "name":"b",
-            "affiliation":"b",
-            "contactEmail":"b@b",
-            "permissionRoot":false,
-            "creator":{
-                "id":13,
-                "firstName":"b",
-                "lastName":"b",
-                "userName":"b",
-                "affiliation":"b",
-                "position":"b",
-                "email":"b@b"
-            },
-            "description":"b",
-            "ownerId":1,
-            "creationDate":"2014-05-12 02:38:36 -04"
-        },
-        {
-            "id":77,
-            "alias":"bc",
-            "name":"Beta Candidate",
-            "affiliation":"Top",
-            "contactEmail":"pete@malinator.com",
-            "permissionRoot":false,
-            "creator":{
-                "id":1,
-                "firstName":"Pete",
-                "lastName":"Privileged",
-                "userName":"pete",
-                "affiliation":"Top ",
-                "position":"The Boss",
-                "email":"pete@malinator.com"
-            },
-            "description":"This is a test",
-            "ownerId":1,
-            "creationDate":"2014-05-08 04:06:58 -04"
-        },
-		(etc, etc)
+	{
+	    "status":"OK",
+	    "data":[
+	        {
+	            "id":93,
+	            "alias":"b",
+	            "name":"b",
+	            "affiliation":"b",
+	            "contactEmail":"b@b",
+	            "permissionRoot":false,
+	            "creator":{
+	                "id":13,
+	                "firstName":"b",
+	                "lastName":"b",
+	                "userName":"b",
+	                "affiliation":"b",
+	                "position":"b",
+	                "email":"b@b"
+	            },
+	            "description":"b",
+	            "ownerId":1,
+	            "creationDate":"2014-05-12 02:38:36 -04"
+	        },
+	        {
+	            "id":77,
+	            "alias":"bc",
+	            "name":"Beta Candidate",
+	            "affiliation":"Top",
+	            "contactEmail":"pete@malinator.com",
+	            "permissionRoot":false,
+	            "creator":{
+	                "id":1,
+	                "firstName":"Pete",
+	                "lastName":"Privileged",
+	                "userName":"pete",
+	                "affiliation":"Top ",
+	                "position":"The Boss",
+	                "email":"pete@malinator.com"
+	            },
+	            "description":"This is a test",
+	            "ownerId":1,
+	            "creationDate":"2014-05-08 04:06:58 -04"
+	        },
+			(etc, etc)
 	
 Return the same list as a python object
 

From 39c97708843fa20db20ca51c7e26bdb31dd13471 Mon Sep 17 00:00:00 2001
From: Raman Prasad <raman_prasad@harvard.edu>
Date: Wed, 14 May 2014 12:49:50 -0400
Subject: [PATCH 19/46] another readme update

---
 scripts/api/py_api_wrapper/readme.md | 26 ++------------------------
 1 file changed, 2 insertions(+), 24 deletions(-)

diff --git a/scripts/api/py_api_wrapper/readme.md b/scripts/api/py_api_wrapper/readme.md
index ea012578fd4..a48b8dd980b 100644
--- a/scripts/api/py_api_wrapper/readme.md
+++ b/scripts/api/py_api_wrapper/readme.md
@@ -8,9 +8,6 @@ Results of API calls may by returned as JSON (string format) or as python dictio
 Given a DVN server name and optional apikey, the class uses python's basic urllib2 to make the API calls.
 Generate the infamous _Pete_,_Uma_ and _Gabbi_. 
 
-	setup-dvs.sh
-
-Generates root dataverse and some other dataverses for Pete and Uma.
 
 ## Quick example
 
@@ -46,26 +43,7 @@ Output:
 	            "ownerId":1,
 	            "creationDate":"2014-05-12 02:38:36 -04"
 	        },
-	        {
-	            "id":77,
-	            "alias":"bc",
-	            "name":"Beta Candidate",
-	            "affiliation":"Top",
-	            "contactEmail":"pete@malinator.com",
-	            "permissionRoot":false,
-	            "creator":{
-	                "id":1,
-	                "firstName":"Pete",
-	                "lastName":"Privileged",
-	                "userName":"pete",
-	                "affiliation":"Top ",
-	                "position":"The Boss",
-	                "email":"pete@malinator.com"
-	            },
-	            "description":"This is a test",
-	            "ownerId":1,
-	            "creationDate":"2014-05-08 04:06:58 -04"
-	        },
+	       
 			(etc, etc)
 	
 Return the same list as a python object
@@ -73,7 +51,7 @@ Return the same list as a python object
 	dat.set_return_mode_python()
 	d = dat.list_dataverses()   # python dictionary {}
 	print d.keys()
-	dv_names = [dv_info.get('name', '?') for dv_info in d['data']]
+	dv_names = [dv_info.get('name', '?no name?') for dv_info in d['data']]
 	print dv_names
 
 Output:

From f7d412b00ade23b134ffb8e48d29fd1bb356b534 Mon Sep 17 00:00:00 2001
From: Raman Prasad <raman_prasad@harvard.edu>
Date: Wed, 14 May 2014 13:54:02 -0400
Subject: [PATCH 20/46] Need to troubleshoot why list datasets api throws

Null pointer exception
---
 .gitignore                                  |  1 +
 scripts/api/py_api_wrapper/dataverse_api.py | 56 +++++++++++++++++----
 scripts/api/py_api_wrapper/readme.md        | 14 ++++++
 3 files changed, 60 insertions(+), 11 deletions(-)

diff --git a/.gitignore b/.gitignore
index ab378a6f94c..b734f6da787 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@ ehthumbs.db
 Thumbs.db
 .vagrant
 *.pyc
+scripts/api/py_api_wrapper/demo-data/*
\ No newline at end of file
diff --git a/scripts/api/py_api_wrapper/dataverse_api.py b/scripts/api/py_api_wrapper/dataverse_api.py
index 3701d50e4af..3ac375aeb24 100644
--- a/scripts/api/py_api_wrapper/dataverse_api.py
+++ b/scripts/api/py_api_wrapper/dataverse_api.py
@@ -136,7 +136,7 @@ def list_datasets(self):
         if not self.apikey:
             msg('Sorry!  You need an api key!')
             return
-        url_str = self.get_server_name() + '/api/datasets/?key=%s' % self.apikey
+        url_str = self.get_server_name() + '/api/datasets?key=%s' % self.apikey
         return self.make_api_call(url_str, self.HTTP_GET)
     
     
@@ -147,6 +147,24 @@ def delete_dataverse_by_id(self, id_val):
         kwargs = { 'key': self.apikey }
         return self.make_api_call(url_str, self.HTTP_DELETE, kwargs)
 
+    def get_user_data(self, uid_or_username=None):
+        """Get metadata for a specific user
+        GET http://{{SERVER}}/api/users/{{uid}}
+        """
+        msgt('get_user_data: %s' % uid_or_username)    
+        url_str = self.get_server_name() + '/api/users/%s' % uid_or_username 
+        return self.make_api_call(url_str, self.HTTP_GET)
+
+    # USERS
+    def list_users(self):
+        """List users
+        GET http://{{SERVER}}/api/users
+        """
+        msgt('list_users')    
+        
+        url_str = self.get_server_name() + '/api/users'
+        return self.make_api_call(url_str, self.HTTP_GET)
+        
         
     '''
     def make_dataverse(self, username, dvn_info_as_dict, dv_id=None):
@@ -165,8 +183,12 @@ def write_to_file(content, fname):
 def save_current_metadata(server_name):
     dat = DataverseAPILink(server_name, use_https=False, apikey='admin')
 
+    output_dir = 'demo-data'
+
     dv_json = dat.list_dataverses()
-    write_to_file(dv_json, '../demo-beta/2014_0513_dataverses.json')
+    write_to_file(dv_json, '%s/2014_0513_dataverses.json' % output_dir)
+    
+    # Currently, troubleshooting list datasets api which is giving a null pointer exception
     
     dataset_ids = """113:41 121:42 91:30 87:29 84:28 83:27 61:22 71:33 62:23 35:21
                     56:19 53:44 49:45 46:18 40:36 22:13 32:20 26:10 29:38""".split()
@@ -176,28 +198,40 @@ def save_current_metadata(server_name):
         did, vid = ds.split(':')
         geo_meta = dat.get_dataset_metadata(did,':latest')
         geo_list.append(geo_meta.strip())
-    geo_content = '\n'.join(geo_list)
-    write_to_file(geo_content, '../demo-beta/2014_0513_datasets.json')
+        write_to_file(geo_meta, '%s/2014_0513_dataset_id_%s.json' % (output_dir, did))
+    #geo_content = '\n'.join(geo_list)
     
-if __name__=='__main__':
     
-    server_with_api = 'dvn-build.hmdc.harvard.edu'
-    #server_with_api = 'dataverse-demo.iq.harvard.edu'
+if __name__=='__main__':
     
-    #save_current_metadata(server_with_api)
+    #server_with_api = 'dvn-build.hmdc.harvard.edu'
+    server_with_api = 'dataverse-demo.iq.harvard.edu'
     
-    dat = DataverseAPILink(server_with_api, use_https=False, apikey='admin')
+    save_current_metadata(server_with_api)
+    """
+    dat = DataverseAPILink(server_with_api, use_https=False, apikey='pete')
     json_text = dat.list_dataverses()
     print json_text
     
+    print dat.list_datasets()
+    """
+    """
+    
     dat.set_return_mode_python()
     d = dat.list_dataverses()   # python dictionary {}
     print d.keys()
     dv_names = [dv_info.get('name', '?') for dv_info in d['data']]
     print dv_names
-    #dat.set_return_mode_python()
-    
+    """
     
+    """
+    dat.set_return_mode_python()
+    user_info = dat.list_users()
+    user_ids = [info['id'] for info in user_info['data'] if info['id'] is not None]
+    for uid in user_ids:
+        print dat.get_user_data(uid)
+    """    
+        
     #print dat.get_root_dataverse_metadata()
     #print dat.get_dataverse_metadata(':root')
     #print dat.list_datasets()
diff --git a/scripts/api/py_api_wrapper/readme.md b/scripts/api/py_api_wrapper/readme.md
index a48b8dd980b..b708fad2020 100644
--- a/scripts/api/py_api_wrapper/readme.md
+++ b/scripts/api/py_api_wrapper/readme.md
@@ -59,3 +59,17 @@ Output:
 	[u'status', u'data']
 	[u'b', u'Beta Candidate', u'kc58', u'Kevin Smoke Test 5/8', u'Penultimate Smoke Test', u"Pete's public place", u"Pete's restricted data", u"Pete's secrets", u'Root', u'smoke 5/7', u'testadd', u'testauthor', u'Test Cliosed', u'Test Open', u'testpete', u'Top dataverse of Pete', u'Top dataverse of Uma', u"Uma's first", u"Uma's restricted"]
 
+### Users
+
+List Users:
+
+	dat.set_return_mode_python()
+	user_info = dat.list_users()
+	print user_info
+	
+Iterate through each user and pull the same data by 'id'
+
+	user_ids = [info['id'] for info in user_info['data'] if info['id'] is not None]
+	for uid in user_ids:
+    	print dat.get_user_data(uid)
+

From 66a3ba4a6b11a6ec481305852655d94531f01ea2 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Wed, 14 May 2014 14:31:25 -0400
Subject: [PATCH 21/46] s/DVN/Dataverse/

---
 scripts/api/py_api_wrapper/readme.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/api/py_api_wrapper/readme.md b/scripts/api/py_api_wrapper/readme.md
index b708fad2020..ac2fc5cc86a 100644
--- a/scripts/api/py_api_wrapper/readme.md
+++ b/scripts/api/py_api_wrapper/readme.md
@@ -5,7 +5,7 @@
 This a python class "DataverseAPILink" which may be used to make the API calls described in the dataverse/scripts/api/readme.md
 Results of API calls may by returned as JSON (string format) or as python dictionaries.
 
-Given a DVN server name and optional apikey, the class uses python's basic urllib2 to make the API calls.
+Given a Dataverse server name and optional apikey, the class uses python's basic urllib2 to make the API calls.
 Generate the infamous _Pete_,_Uma_ and _Gabbi_. 
 
 

From b0c70800f0f55b19fb94413011b5dcedb54a2a2b Mon Sep 17 00:00:00 2001
From: xyang02 <xyang02@hmdc.harvard.edu>
Date: Wed, 14 May 2014 15:54:17 -0400
Subject: [PATCH 22/46] Added logo alignment drop down menu and logo background
 color field to dataverse page and dataverse class. (#3526)

---
 src/main/webapp/dataverse.xhtml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/main/webapp/dataverse.xhtml b/src/main/webapp/dataverse.xhtml
index 6bfaa10d6f8..ee4195cb080 100644
--- a/src/main/webapp/dataverse.xhtml
+++ b/src/main/webapp/dataverse.xhtml
@@ -275,6 +275,18 @@
                                 <f:selectItem itemLabel="RECTANGLE" itemValue="RECTANGLE"/>
                             </p:selectOneRadio>
                             <p:message for="logoFormat"/>
+                            
+                            <h:outputLabel value="Logo Alignment"/>
+                            <p:selectOneMenu id="logoAlignment" value="#{DataversePage.dataverse.logoAlignment}">
+                                <f:selectItem id="left" itemLabel="LEFT" itemValue="LEFT" />
+                                <f:selectItem id="center" itemLabel="CENTER" itemValue="CENTER" />
+                                <f:selectItem id="right" itemLabel="RIGHT" itemValue="RIGHT" />
+                            </p:selectOneMenu>
+                            <p:message for="logoFormat"/>
+                            
+                            <h:outputLabel value="Logo Background Color"/>
+                            <p:inputText id="logoBackgroundColor" value="#{DataversePage.dataverse.logoBackgroundColor}"/>
+                            <p:message for="logoBackgroundColor"/>
 
                             <h:outputLabel value="Tagline"/>
                             <p:inputText id="tagline" value="#{DataversePage.dataverse.tagline}"/>

From 078c3e9caf91824a2d6ad8902da0327349cadcb7 Mon Sep 17 00:00:00 2001
From: xyang02 <xyang02@hmdc.harvard.edu>
Date: Wed, 14 May 2014 15:54:42 -0400
Subject: [PATCH 23/46] Added logo alignment drop down menu and logo background
 color field to dataverse page and dataverse class. (#3526)

---
 .../edu/harvard/iq/dataverse/Dataverse.java   | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
index 1e54d97faac..84f6e8ef967 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
@@ -82,6 +82,11 @@ public enum ImageFormat { SQUARE, RECTANGLE }
 
     @Enumerated(EnumType.STRING)
     private ImageFormat logoFormat;
+    
+    public enum Alignment { LEFT, CENTER, RIGHT }
+    @Enumerated(EnumType.STRING)
+    private Alignment logoAlignment;
+    private String logoBackgroundColor;
     private String logo;
     private String tagline;
     private String linkUrl;
@@ -198,6 +203,22 @@ public void setLogoFormat(ImageFormat logoFormat) {
         this.logoFormat = logoFormat;
     }
 
+    public Alignment getLogoAlignment() {
+        return logoAlignment;
+    }
+
+    public void setLogoAlignment(Alignment logoAlignment) {
+        this.logoAlignment = logoAlignment;
+    }
+
+    public String getLogoBackgroundColor() {
+        return logoBackgroundColor;
+    }
+
+    public void setLogoBackgroundColor(String logoBackgroundColor) {
+        this.logoBackgroundColor = logoBackgroundColor;
+    }
+    
     public String getLogo() {
         return logo;
     }

From bba4e6e026f4aa07acfd8bfc049a973e4c001221 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Wed, 14 May 2014 16:37:14 -0400
Subject: [PATCH 24/46] stub out SWORD file upload (many todo's) #3385

---
 scripts/api/data-deposit/data/example.zip     | Bin 0 -> 820 bytes
 scripts/api/data-deposit/upload-file          |   7 +
 .../datadeposit/MediaResourceManagerImpl.java | 517 ++++++++++++++++++
 .../SWORDv2MediaResourceServlet.java          |  53 ++
 src/main/webapp/WEB-INF/web.xml               |  14 +
 5 files changed, 591 insertions(+)
 create mode 100644 scripts/api/data-deposit/data/example.zip
 create mode 100755 scripts/api/data-deposit/upload-file
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java

diff --git a/scripts/api/data-deposit/data/example.zip b/scripts/api/data-deposit/data/example.zip
new file mode 100644
index 0000000000000000000000000000000000000000..8870dd7d8c7e97dd18c37ececc0b01e70e2290a8
GIT binary patch
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diff --git a/scripts/api/data-deposit/upload-file b/scripts/api/data-deposit/upload-file
new file mode 100755
index 00000000000..72c8b86304a
--- /dev/null
+++ b/scripts/api/data-deposit/upload-file
@@ -0,0 +1,7 @@
+#!/bin/sh
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+GLOBAL_ID=myIdentifier
+curl -s --insecure --data-binary @scripts/api/data-deposit/data/example.zip -H "Content-Disposition: filename=example.zip" -H "Content-Type: application/zip" -H "Packaging: http://purl.org/net/sword/package/SimpleZip" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit-media/study/$GLOBAL_ID \
+| xmllint -format -
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
new file mode 100644
index 00000000000..95dc092576e
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
@@ -0,0 +1,517 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.DataFile;
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.DatasetServiceBean;
+import edu.harvard.iq.dataverse.DatasetVersion;
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseUser;
+import edu.harvard.iq.dataverse.EjbDataverseEngine;
+import edu.harvard.iq.dataverse.FileMetadata;
+import edu.harvard.iq.dataverse.engine.command.Command;
+import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
+import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetCommand;
+import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Logger;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+import javax.ejb.EJB;
+import javax.ejb.EJBException;
+import javax.inject.Inject;
+import javax.naming.Context;
+import javax.naming.InitialContext;
+import javax.naming.NamingException;
+import javax.validation.ConstraintViolation;
+import javax.validation.ConstraintViolationException;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.Deposit;
+import org.swordapp.server.DepositReceipt;
+import org.swordapp.server.MediaResource;
+import org.swordapp.server.MediaResourceManager;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordConfiguration;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+import org.swordapp.server.UriRegistry;
+
+public class MediaResourceManagerImpl implements MediaResourceManager {
+
+    private static final Logger logger = Logger.getLogger(MediaResourceManagerImpl.class.getCanonicalName());
+    @EJB
+    EjbDataverseEngine commandEngine;
+    @EJB
+    DatasetServiceBean datasetService;
+    @EJB
+    IngestServiceBean ingestService;
+    @Inject
+    SwordAuth swordAuth;
+    @Inject
+    UrlManager urlManager;
+
+    @Override
+    public MediaResource getMediaResourceRepresentation(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        urlManager.processUrl(uri);
+        String globalId = urlManager.getTargetIdentifier();
+        if (urlManager.getTargetType().equals("study") && globalId != null) {
+//            EditStudyService editStudyService;
+            Context ctx;
+            try {
+                ctx = new InitialContext();
+//                editStudyService = (EditStudyService) ctx.lookup("java:comp/env/editStudy");
+            } catch (NamingException ex) {
+                logger.info("problem looking up editStudyService");
+                throw new SwordServerException("problem looking up editStudyService");
+            }
+            logger.fine("looking up study with globalId " + globalId);
+//            Study study = editStudyService.getStudyByGlobalId(globalId);
+            Dataset study = null;
+            if (study != null) {
+                /**
+                 * @todo: support this
+                 */
+                boolean getMediaResourceRepresentationSupported = false;
+                if (getMediaResourceRepresentationSupported) {
+                    Dataverse dvThatOwnsStudy = study.getOwner();
+                    if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
+                        InputStream fixmeInputStream = new ByteArrayInputStream("FIXME: replace with zip of all study files".getBytes());
+                        String contentType = "application/zip";
+                        String packaging = UriRegistry.PACKAGE_SIMPLE_ZIP;
+                        boolean isPackaged = true;
+                        MediaResource mediaResource = new MediaResource(fixmeInputStream, contentType, packaging, isPackaged);
+                        return mediaResource;
+                    } else {
+//                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to get a media resource representation of the study with global ID " + study.getGlobalId());
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to get a media resource representation of the dataset with identifier " + study.getIdentifier());
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Please use the Dataverse Network Data Sharing API instead");
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "couldn't find study with global ID of " + globalId);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't dermine target type or identifier from URL: " + uri);
+        }
+    }
+
+    @Override
+    public DepositReceipt replaceMediaResource(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+        /**
+         * @todo: Perhaps create a new version of a study here?
+         *
+         * "The server MUST effectively replace all the existing content in the
+         * item, although implementations may choose to provide versioning or
+         * some other mechanism for retaining the overwritten content." --
+         * http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html#protocoloperations_editingcontent_binary
+         *
+         * Also, if you enable this method, think about the SwordError currently
+         * being returned by replaceOrAddFiles with shouldReplace set to true
+         * and an empty zip uploaded. If no files are unzipped the user will see
+         * a error about this but the files will still be deleted!
+         */
+        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Replacing the files of a study is not supported. Please delete and add files separately instead.");
+    }
+
+    @Override
+    public void deleteMediaResource(String uri, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        urlManager.processUrl(uri);
+        String targetType = urlManager.getTargetType();
+        String fileId = urlManager.getTargetIdentifier();
+        if (targetType != null && fileId != null) {
+            if ("file".equals(targetType)) {
+                String fileIdString = urlManager.getTargetIdentifier();
+                if (fileIdString != null) {
+                    Long fileIdLong;
+                    try {
+                        fileIdLong = Long.valueOf(fileIdString);
+                    } catch (NumberFormatException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "File id must be a number, not '" + fileIdString + "'. URL was: " + uri);
+                    }
+                    if (fileIdLong != null) {
+                        logger.fine("preparing to delete file id " + fileIdLong);
+//                        StudyFile fileToDelete;
+                        try {
+//                            fileToDelete = studyFileService.getStudyFile(fileIdLong);
+                        } catch (EJBException ex) {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id " + fileIdLong);
+                        }
+//                        if (fileToDelete != null) {
+//                            Study study = fileToDelete.getStudy();
+//                            StudyLock studyLock = study.getStudyLock();
+//                            if (studyLock != null) {
+//                                String message = Util.getStudyLockMessage(studyLock, study.getGlobalId());
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, message);
+//                            }
+//                            String globalId = study.getGlobalId();
+//                            VDC dvThatOwnsFile = fileToDelete.getStudy().getOwner();
+//                            if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsFile)) {
+//                                EditStudyFilesService editStudyFilesService;
+//                                try {
+//                                    Context ctx = new InitialContext();
+//                                    editStudyFilesService = (EditStudyFilesService) ctx.lookup("java:comp/env/editStudyFiles");
+//                                } catch (NamingException ex) {
+//                                    logger.info("problem looking up editStudyFilesService");
+//                                    throw new SwordServerException("problem looking up editStudyFilesService");
+//                                }
+//                                editStudyFilesService.setStudyVersionByGlobalId(globalId);
+//                                // editStudyFilesService.findStudyFileEditBeanById() would be nice
+//                                List studyFileEditBeans = editStudyFilesService.getCurrentFiles();
+//                                for (Iterator it = studyFileEditBeans.iterator(); it.hasNext();) {
+//                                    StudyFileEditBean studyFileEditBean = (StudyFileEditBean) it.next();
+//                                    if (studyFileEditBean.getStudyFile().getId().equals(fileToDelete.getId())) {
+//                                        logger.fine("marked for deletion: " + studyFileEditBean.getStudyFile().getFileName());
+//                                        studyFileEditBean.setDeleteFlag(true);
+//                                    } else {
+//                                        logger.fine("not marked for deletion: " + studyFileEditBean.getStudyFile().getFileName());
+//                                    }
+//                                }
+//                                editStudyFilesService.save(dvThatOwnsFile.getId(), vdcUser.getId());
+//                            } else {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + vdcUser.getUserName() + " is not authorized to modify " + dvThatOwnsFile.getAlias());
+//                            }
+//                        } else {
+//                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id " + fileIdLong + " from URL: " + uri);
+//                        }
+                    } else {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find file id in URL: " + uri);
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not file file to delete in URL: " + uri);
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported file type found in URL: " + uri);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target or identifer not specified in URL: " + uri);
+        }
+    }
+
+    @Override
+    public DepositReceipt addResource(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+        boolean shouldReplace = false;
+        return replaceOrAddFiles(uri, deposit, authCredentials, swordConfiguration, shouldReplace);
+    }
+
+    DepositReceipt replaceOrAddFiles(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration, boolean shouldReplace) throws SwordError, SwordAuthException, SwordServerException {
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+
+        urlManager.processUrl(uri);
+        String globalId = urlManager.getTargetIdentifier();
+        if (urlManager.getTargetType().equals("study") && globalId != null) {
+//            EditStudyService editStudyService;
+            Context ctx;
+            try {
+                ctx = new InitialContext();
+//                editStudyService = (EditStudyService) ctx.lookup("java:comp/env/editStudy");
+            } catch (NamingException ex) {
+                logger.info("problem looking up editStudyService");
+                throw new SwordServerException("problem looking up editStudyService");
+            }
+            logger.fine("looking up study with globalId " + globalId);
+            /**
+             * @todo don't hard code this, obviously. In DVN 3.x we had a method
+             * for editStudyService.getStudyByGlobalId(globalId)
+             */
+//            Study study = editStudyService.getStudyByGlobalId(globalId);
+            long databaseIdForRoastingAtHomeDataset = 10;
+            Dataset study = datasetService.find(databaseIdForRoastingAtHomeDataset);
+            if (study == null) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study with global ID of " + globalId);
+            }
+//            StudyLock studyLock = study.getStudyLock();
+//            if (studyLock != null) {
+//                String message = Util.getStudyLockMessage(studyLock, study.getGlobalId());
+//                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, message);
+//            }
+            Long studyId;
+            try {
+                studyId = study.getId();
+            } catch (NullPointerException ex) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "couldn't find study with global ID of " + globalId);
+            }
+            Dataverse dvThatOwnsStudy = study.getOwner();
+            if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
+//                editStudyService.setStudyVersion(studyId);
+//                editStudyService.save(dvThatOwnsStudy.getId(), vdcUser.getId());
+//
+//                EditStudyFilesService editStudyFilesService;
+//                try {
+//                    editStudyFilesService = (EditStudyFilesService) ctx.lookup("java:comp/env/editStudyFiles");
+//                } catch (NamingException ex) {
+//                    logger.info("problem looking up editStudyFilesService");
+//                    throw new SwordServerException("problem looking up editStudyFilesService");
+//                }
+//                editStudyFilesService.setStudyVersionByGlobalId(globalId);
+//                List studyFileEditBeans = editStudyFilesService.getCurrentFiles();
+                List<String> exisitingFilenames = new ArrayList<String>();
+//                for (Iterator it = studyFileEditBeans.iterator(); it.hasNext();) {
+//                    StudyFileEditBean studyFileEditBean = (StudyFileEditBean) it.next();
+                if (shouldReplace) {
+//                        studyFileEditBean.setDeleteFlag(true);
+//                        logger.fine("marked for deletion: " + studyFileEditBean.getStudyFile().getFileName());
+                } else {
+//                        String filename = studyFileEditBean.getStudyFile().getFileName();
+//                        exisitingFilenames.add(filename);
+                }
+            }
+//                editStudyFilesService.save(dvThatOwnsStudy.getId(), vdcUser.getId());
+
+            if (!deposit.getPackaging().equals(UriRegistry.PACKAGE_SIMPLE_ZIP)) {
+                throw new SwordError(UriRegistry.ERROR_CONTENT, 415, "Package format " + UriRegistry.PACKAGE_SIMPLE_ZIP + " is required but format specified in 'Packaging' HTTP header was " + deposit.getPackaging());
+            }
+
+            // Right now we are only supporting UriRegistry.PACKAGE_SIMPLE_ZIP but
+            // in the future maybe we'll support other formats? Rdata files? Stata files?
+            // That's what the uploadDir was going to be for, but for now it's commented out
+            //
+            String importDirString;
+            File importDir;
+            String swordTempDirString = swordConfiguration.getTempDirectory();
+            if (swordTempDirString == null) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine temp directory");
+            } else {
+                importDirString = swordTempDirString + File.separator + "import" + File.separator + study.getId().toString();
+                importDir = new File(importDirString);
+                if (!importDir.exists()) {
+                    if (!importDir.mkdirs()) {
+                        logger.info("couldn't create directory: " + importDir.getAbsolutePath());
+                        throw new SwordServerException("couldn't create import directory");
+                    }
+                }
+            }
+
+            if (true) {
+                DataFile dFile = new DataFile("application/octet-stream");
+                dFile.setOwner(study);
+                datasetService.generateFileSystemName(dFile);
+//                if (true) {
+//                    throw returnEarly("dataFile.getFileSystemName(): " + dFile.getFileSystemName());
+//                }
+                InputStream depositInputStream = deposit.getInputStream();
+                try {
+                    Files.copy(depositInputStream, Paths.get(importDirString, dFile.getFileSystemName()), StandardCopyOption.REPLACE_EXISTING);
+                } catch (IOException ex) {
+                    throw new SwordError("problem running Files.copy");
+                }
+                study.getFiles().add(dFile);
+
+                DatasetVersion editVersion = study.getEditVersion();
+//                boolean metadataExtracted = false;
+//                try {
+//                    metadataExtracted = ingestService.extractIndexableMetadata(importDir.getAbsolutePath() + File.separator + dFile.getFileSystemName(), dFile, editVersion);
+//                } catch (IOException ex) {
+//                    throw returnEarly("couldn't extract metadata" + ex);
+//                }
+                FileMetadata fmd = new FileMetadata();
+                fmd.setDataFile(dFile);
+                fmd.setLabel("myLabel");
+                fmd.setDatasetVersion(editVersion);
+                dFile.getFileMetadatas().add(fmd);
+
+                Command<Dataset> cmd;
+                cmd = new UpdateDatasetCommand(study, vdcUser);
+                try {
+                    /**
+                     * @todo at update time indexing is run but the file is not
+                     * indexed. Why? Manually re-indexing later finds it. Fix
+                     * this. Related to
+                     * https://redmine.hmdc.harvard.edu/issues/3809 ?
+                     */
+                    study = commandEngine.submit(cmd);
+                } catch (CommandException ex) {
+                    throw returnEarly("couldn't update dataset");
+                } catch (EJBException ex) {
+                    Throwable cause = ex;
+                    StringBuilder sb = new StringBuilder();
+                    sb.append(ex.getLocalizedMessage());
+                    while (cause.getCause() != null) {
+                        cause = cause.getCause();
+                        sb.append(cause + " ");
+                        if (cause instanceof ConstraintViolationException) {
+                            ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
+                            for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
+                                sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ")
+                                        .append(violation.getPropertyPath()).append(" at ")
+                                        .append(violation.getLeafBean()).append(" - ")
+                                        .append(violation.getMessage());
+                            }
+                        }
+                    }
+                    throw returnEarly("EJBException: " + sb.toString());
+                }
+
+            }
+
+            /**
+             * @todo remove this comment after confirming that the upstream jar
+             * now has our bugfix
+             */
+            // the first character of the filename is truncated with the official jar
+            // so we use include the bug fix at https://github.com/IQSS/swordv2-java-server-library/commit/aeaef83
+            // and use this jar: https://build.hmdc.harvard.edu:8443/job/swordv2-java-server-library-iqss/2/
+            String uploadedZipFilename = deposit.getFilename();
+            ZipInputStream ziStream = new ZipInputStream(deposit.getInputStream());
+            ZipEntry zEntry;
+            FileOutputStream tempOutStream = null;
+//                List<StudyFileEditBean> fbList = new ArrayList<StudyFileEditBean>();
+
+            try {
+                // copied from createStudyFilesFromZip in AddFilesPage
+                while ((zEntry = ziStream.getNextEntry()) != null) {
+                    // Note that some zip entries may be directories - we 
+                    // simply skip them:
+                    if (!zEntry.isDirectory()) {
+
+                        String fileEntryName = zEntry.getName();
+                        logger.fine("file found: " + fileEntryName);
+
+                        String dirName = null;
+                        String finalFileName = null;
+
+                        int ind = fileEntryName.lastIndexOf('/');
+
+                        if (ind > -1) {
+                            finalFileName = fileEntryName.substring(ind + 1);
+                            if (ind > 0) {
+                                dirName = fileEntryName.substring(0, ind);
+                                dirName = dirName.replace('/', '-');
+                            }
+                        } else {
+                            finalFileName = fileEntryName;
+                        }
+
+                        if (".DS_Store".equals(finalFileName)) {
+                            continue;
+                        }
+
+                        // http://superuser.com/questions/212896/is-there-any-way-to-prevent-a-mac-from-creating-dot-underscore-files
+                        if (finalFileName.startsWith("._")) {
+                            continue;
+                        }
+
+                        File tempUploadedFile = new File(importDir, finalFileName);
+                        tempOutStream = new FileOutputStream(tempUploadedFile);
+
+                        byte[] dataBuffer = new byte[8192];
+                        int i = 0;
+
+                        while ((i = ziStream.read(dataBuffer)) > 0) {
+                            tempOutStream.write(dataBuffer, 0, i);
+                            tempOutStream.flush();
+                        }
+
+                        tempOutStream.close();
+
+                        // We now have the unzipped file saved in the upload directory;
+                        // zero-length dta files (for example) are skipped during zip
+                        // upload in the GUI, so we'll skip them here as well
+                        if (tempUploadedFile.length() != 0) {
+
+                            if (true) {
+//                                tempUploadedFile;
+//                                UploadedFile uFile = tempUploadedFile;
+//                                DataFile dataFile = new DataFile();
+//                                throw new SwordError("let's create a file");
+                            }
+//                                StudyFileEditBean tempFileBean = new StudyFileEditBean(tempUploadedFile, studyService.generateFileSystemNameSequence(), study);
+//                                tempFileBean.setSizeFormatted(tempUploadedFile.length());
+                            String finalFileNameAfterReplace = finalFileName;
+//                                if (tempFileBean.getStudyFile() instanceof TabularDataFile) {
+                            // predict what the tabular file name will be
+//                                    finalFileNameAfterReplace = FileUtil.replaceExtension(finalFileName);
+//                                }
+
+//                                validateFileName(exisitingFilenames, finalFileNameAfterReplace, study);
+                            // And, if this file was in a legit (non-null) directory, 
+                            // we'll use its name as the file category: 
+                            if (dirName != null) {
+//                                    tempFileBean.getFileMetadata().setCategory(dirName);
+                            }
+
+//                                fbList.add(tempFileBean);
+                        }
+                    } else {
+                        logger.fine("directory found: " + zEntry.getName());
+                    }
+                }
+            } catch (IOException ex) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Problem with file: " + uploadedZipFilename);
+            } finally {
+                /**
+                 * @todo shouldn't we delete this uploadDir? Commented out in
+                 * DVN 3.x
+                 */
+//                    if (!uploadDir.delete()) {
+//                        logger.fine("Unable to delete " + uploadDir.getAbsolutePath());
+//                    }
+            }
+//                if (fbList.size() > 0) {
+//                    StudyFileServiceLocal studyFileService;
+//                    try {
+//                        studyFileService = (StudyFileServiceLocal) ctx.lookup("java:comp/env/studyFileService");
+//                    } catch (NamingException ex) {
+//                        logger.info("problem looking up studyFileService");
+//                        throw new SwordServerException("problem looking up studyFileService");
+//                    }
+            try {
+//                        studyFileService.addFiles(study.getLatestVersion(), fbList, vdcUser);
+            } catch (EJBException ex) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to add file(s) to study: " + ex.getMessage());
+            }
+            ReceiptGenerator receiptGenerator = new ReceiptGenerator();
+            String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
+            DepositReceipt depositReceipt = receiptGenerator.createReceipt(baseUrl, study);
+            return depositReceipt;
+        } else {
+//                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Problem with zip file '" + uploadedZipFilename + "'. Number of files unzipped: " + fbList.size());
+        }
+//            } else {
+//                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to modify study with global ID " + study.getGlobalId());
+        return new DepositReceipt(); // added just to get this to compile 2014-05-14
+    }
+//        } else {
+//            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine target type or identifier from URL: " + uri);
+//        }
+//    }
+
+    // copied from AddFilesPage
+//    private void validateFileName(List<String> existingFilenames, String fileName, Study study) throws SwordError {
+//        if (fileName.contains("\\")
+//                || fileName.contains("/")
+//                || fileName.contains(":")
+//                || fileName.contains("*")
+//                || fileName.contains("?")
+//                || fileName.contains("\"")
+//                || fileName.contains("<")
+//                || fileName.contains(">")
+//                || fileName.contains("|")
+//                || fileName.contains(";")
+//                || fileName.contains("#")) {
+//            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid File Name - cannot contain any of the following characters: \\ / : * ? \" < > | ; . Filename was '" + fileName + "'");
+//        }
+//        if (existingFilenames.contains(fileName)) {
+//            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Filename " + fileName + " already exists in study " + study.getGlobalId());
+//        }
+//    }
+    private SwordError returnEarly(String error) {
+        SwordError swordError = new SwordError(error);
+        StackTraceElement[] emptyStackTrace = new StackTraceElement[0];
+        swordError.setStackTrace(emptyStackTrace);
+        return swordError;
+
+    }
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java
new file mode 100644
index 00000000000..dd44278ccef
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java
@@ -0,0 +1,53 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.io.IOException;
+import javax.inject.Inject;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import org.swordapp.server.MediaResourceAPI;
+import org.swordapp.server.servlets.SwordServlet;
+
+public class SWORDv2MediaResourceServlet extends SwordServlet {
+
+    @Inject
+    MediaResourceManagerImpl mediaResourceManagerImpl;
+    protected MediaResourceAPI api;
+
+    public void init() throws ServletException {
+        super.init();
+
+        // load the api
+        this.api = new MediaResourceAPI(mediaResourceManagerImpl, this.config);
+    }
+
+    @Override
+    protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.get(req, resp);
+    }
+
+    @Override
+    protected void doHead(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.head(req, resp);
+    }
+
+    @Override
+    protected void doPost(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.post(req, resp);
+    }
+
+    @Override
+    protected void doPut(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.put(req, resp);
+    }
+
+    @Override
+    protected void doDelete(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.delete(req, resp);
+    }
+}
diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
index 5b877737b6e..c19afc4ff3e 100644
--- a/src/main/webapp/WEB-INF/web.xml
+++ b/src/main/webapp/WEB-INF/web.xml
@@ -112,6 +112,20 @@
         <url-pattern>/dvn/api/data-deposit/v1/swordv2/collection/*</url-pattern>
     </servlet-mapping>
 
+    <context-param>
+        <param-name>media-resource-impl</param-name>
+        <param-value>edu.harvard.iq.dataverse.api.datadeposit.MediaResourceManagerImpl</param-value>
+    </context-param>
+    <servlet>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2MediaResourceServlet</servlet-name>
+        <servlet-class>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2MediaResourceServlet</servlet-class>
+    </servlet>
+    <servlet-mapping>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2MediaResourceServlet</servlet-name>
+        <url-pattern>/dvn/api/data-deposit/v1/swordv2/edit-media/*</url-pattern>
+    </servlet-mapping>
+
+
     <!-- END Data Deposit API v1 (SWORD v2) -->
 
 </web-app>

From e86e52854cdb7ac8afe65baead345a5147e63959 Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.80.247>
Date: Wed, 14 May 2014 17:21:40 -0400
Subject: [PATCH 25/46] Fixed a bug on create mode of dataset pg where labels
 were displaying without input that didn't belong on the page in that mode.

---
 src/main/webapp/metadataFragment.xhtml | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/main/webapp/metadataFragment.xhtml b/src/main/webapp/metadataFragment.xhtml
index 5df97a5208e..024632a6eed 100644
--- a/src/main/webapp/metadataFragment.xhtml
+++ b/src/main/webapp/metadataFragment.xhtml
@@ -77,16 +77,18 @@
                         <div id="collapse#{block.index}" class="collapse #{block.first || DatasetPage.editMode == 'CREATE'?'in':''}">
                             <div class="panel-body">
                                 <ui:repeat value="#{metadataBlockVal.value}" var="dsf">
+                                    
+                                    <ui:fragment rendered="#{(DatasetPage.editMode == 'METADATA' or dsf.datasetFieldType.displayOnCreate)}">
 
-                                    <div class="form-group">
-                                        <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
-                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}">
-                                                #{dsf.datasetFieldType.title}
-                                            </a>
-                                            <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{dsf.datasetFieldType.required}" />
-                                        </label>
+                                        <div class="form-group">
+                                            <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
+                                                <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}">
+                                                    #{dsf.datasetFieldType.title}
+                                                </a>
+                                                <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{dsf.datasetFieldType.required}" />
+                                            </label>
 
-                                        <ui:fragment rendered="#{(DatasetPage.editMode == 'METADATA' or dsf.datasetFieldType.displayOnCreate)}">
+                                        
                                             <!-- Primitive fields -->
                                             <p:fragment autoUpdate="true" rendered="#{dsf.datasetFieldType.primitive}">
                                                 <div class="form-group">
@@ -207,8 +209,11 @@
                                                     </ui:repeat>
                                                 </div>
                                             </p:fragment>
-                                        </ui:fragment>
-                                    </div>
+                                        
+                                        </div>
+                                    
+                                    </ui:fragment>
+                                    
                                 </ui:repeat>
                             </div>
                         </div>

From 59f37f22f7d116b38944254e4308e0d74a2d48e9 Mon Sep 17 00:00:00 2001
From: sekmiller <skraffmiller@hmdc.harvard.edu>
Date: Wed, 14 May 2014 17:59:37 -0400
Subject: [PATCH 26/46] Hide Email from metadata display

Fix Related Publication display title and tooltip.
---
 .../iq/dataverse/DatasetRelPublication.java   | 29 ++++++---
 .../iq/dataverse/DatasetVersionUI.java        |  2 +
 src/main/webapp/dataset.xhtml                 |  8 +--
 src/main/webapp/metadataFragment.xhtml        | 60 ++++++++++---------
 4 files changed, 58 insertions(+), 41 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetRelPublication.java b/src/main/java/edu/harvard/iq/dataverse/DatasetRelPublication.java
index 8c02352af5d..6bf55445d57 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetRelPublication.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetRelPublication.java
@@ -6,14 +6,6 @@
 
 package edu.harvard.iq.dataverse;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Version;
 
 /**
  *
@@ -22,11 +14,13 @@
 
 public class DatasetRelPublication {
 
-    @Column(columnDefinition = "TEXT")
+
     private String text;
     private String idType;
     private String idNumber;
     private String url;
+    private String title;
+    private String description;
     private boolean replicationData;
     private int displayOrder;
 
@@ -68,6 +62,23 @@ public String getUrl() {
     public void setUrl(String url) {
         this.url = url;
     }
+    
+    
+    public String getTitle() {
+        return title;
+    }
+
+    public void setTitle(String title) {
+        this.title = title;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public void setDescription(String description) {
+        this.description = description;
+    }
 
      public boolean isEmpty() {
         return ((text==null || text.trim().equals(""))
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java
index 9e715dd2ce8..9e2cf22a108 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java
@@ -85,6 +85,8 @@ public DatasetVersionUI(DatasetVersion datasetVersion) {
                 if (this.datasetRelPublications.isEmpty()) {
                     for (DatasetFieldCompoundValue relPubVal : dsf.getDatasetFieldCompoundValues()) {
                         DatasetRelPublication datasetRelPublication = new DatasetRelPublication();
+                        datasetRelPublication.setTitle(dsf.getDatasetFieldType().getTitle());
+                        datasetRelPublication.setDescription(dsf.getDatasetFieldType().getDescription());
                         for (DatasetField subField : relPubVal.getChildDatasetFields()) {
                             if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.publicationCitation)) {
                                 datasetRelPublication.setText(subField.getValue());
diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml
index 66f8a483936..47c8cc12164 100644
--- a/src/main/webapp/dataset.xhtml
+++ b/src/main/webapp/dataset.xhtml
@@ -177,7 +177,7 @@
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.keyword.value}">
                                                     <span id="keywords" class="form-group">
                                                         <label class="col-sm-3 control-label">
-                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.name}</a>
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.keyword.datasetFieldType.title}</a>
                                                         </label>
                                                         <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.keyword.displayValue}</span>
                                                     </span>
@@ -185,7 +185,7 @@
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.subject.value}">
                                                     <span id="subject" class="form-group">
                                                         <label class="col-sm-3 control-label">
-                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.subject.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.subject.datasetFieldType.name}</a>
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.subject.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.subject.datasetFieldType.title}</a>
                                                         </label>
                                                         <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.subject.displayValue}</span>
                                                     </span>
@@ -193,7 +193,7 @@
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.relPublicationCitation}">
                                                     <span id="publication" class="form-group">
                                                         <label class="col-sm-3 control-label">
-                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="STATIC" title="">Related Publication (STATIC)</a>
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.datasetRelPublications.get(0).description}" title="">#{DatasetPage.datasetVersionUI.datasetRelPublications.get(0).title} </a>
                                                         </label>
                                                         <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.relPublicationCitation}  <a href="#{DatasetPage.datasetVersionUI.relPublicationUrl}" title="#{DatasetPage.datasetVersionUI.relPublicationUrl}" target="_blank">#{DatasetPage.datasetVersionUI.relPublicationId}</a></span>
                                                     </span>
@@ -201,7 +201,7 @@
                                                 <ui:fragment rendered="#{!empty DatasetPage.datasetVersionUI.notes.value}">
                                                     <span id="note" class="form-group">
                                                         <label class="col-sm-3 control-label">
-                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.notes.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.notes.datasetFieldType.name}</a>
+                                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel" data-original-title="#{DatasetPage.datasetVersionUI.notes.datasetFieldType.description}" title="">#{DatasetPage.datasetVersionUI.notes.datasetFieldType.title}</a>
                                                         </label>
                                                         <span class="col-sm-8" style="padding-left:0; padding-right:0;">#{DatasetPage.datasetVersionUI.notes.value}</span>
                                                     </span>
diff --git a/src/main/webapp/metadataFragment.xhtml b/src/main/webapp/metadataFragment.xhtml
index 024632a6eed..e6e2a3a65a4 100644
--- a/src/main/webapp/metadataFragment.xhtml
+++ b/src/main/webapp/metadataFragment.xhtml
@@ -18,19 +18,21 @@
                         <div class="panel-body">
                             <ui:repeat value="#{metadataBlockVal.value}" var="dsf">
                                 <div class="form-group">
-                                    <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
-                                        <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}" title="">
-                                            #{dsf.datasetFieldType.title}
-                                        </a>
-                                    </label>
-                                    <!-- Primitive datasetFields -->
-                                    <ui:fragment rendered="#{dsf.datasetFieldType.primitive}">
-                                        <div class="col-sm-9">
-                                            <h:outputText value="#{dsf.value}" rendered="#{!dsf.datasetFieldType.allowMultiples}"/>
-                                            <ui:repeat value="#{dsf.values}" var="value" varStatus="loop" rendered="#{dsf.datasetFieldType.allowMultiples}">
-                                                <h:outputText value="#{loop.first?'':'; '}#{value}"/>
-                                            </ui:repeat>
-                                        </div>
+                                    <ui:fragment rendered="#{!(dsf.datasetFieldType.fieldType == 'email') }">
+                                        <label for="metadata_#{dsf.datasetFieldType.name}" class="col-sm-3 control-label">
+                                            <a href="#" data-toggle="tooltip" data-placement="auto right" class="tooltiplabel right" data-original-title="#{dsf.datasetFieldType.description}" title="">
+                                                #{dsf.datasetFieldType.title}
+                                            </a>
+                                        </label>
+                                        <!-- Primitive datasetFields -->
+                                        <ui:fragment rendered="#{dsf.datasetFieldType.primitive}">
+                                            <div class="col-sm-9">
+                                                <h:outputText value="#{dsf.value}" rendered="#{!dsf.datasetFieldType.allowMultiples}"/>
+                                                <ui:repeat value="#{dsf.values}" var="value" varStatus="loop" rendered="#{dsf.datasetFieldType.allowMultiples}">
+                                                    <h:outputText value="#{loop.first?'':'; '}#{value}"/>
+                                                </ui:repeat>
+                                            </div>
+                                        </ui:fragment>
                                     </ui:fragment>
                                     <!-- Compound datasetFields -->
                                     <ui:fragment rendered="#{dsf.datasetFieldType.compound}">
@@ -39,17 +41,19 @@
                                                 <div class="form-group">
                                                     <!-- Sub fields -->
                                                     <ui:repeat value="#{compoundValues.childDatasetFields}" var="subdsf">
-                                                        <div class="form-col-container col-sm-6">
-                                                            <label class="control-label" for="metadata_#{subdsf.datasetFieldType.name}">
-                                                                <a class="tooltiplabel right" data-original-title="#{subdsf.datasetFieldType.description}" data-placement="auto right" data-toggle="tooltip" href="#">#{subdsf.datasetFieldType.title}</a>
-                                                            </label>
-                                                            <div>
-                                                                <h:outputText value="#{subdsf.value}" rendered="#{!subdsf.datasetFieldType.allowMultiples}"/>
-                                                                <ui:repeat value="#{subdsf.values}" var="value" varStatus="loop" rendered="#{subdsf.datasetFieldType.allowMultiples}">
-                                                                    <h:outputText value="#{loop.first?'':'; '}#{value}"/>
-                                                                </ui:repeat>
+                                                        <ui:fragment rendered="#{!(subdsf.datasetFieldType.fieldType == 'email') }">
+                                                            <div class="form-col-container col-sm-6">
+                                                                <label class="control-label" for="metadata_#{subdsf.datasetFieldType.name}">
+                                                                    <a class="tooltiplabel right" data-original-title="#{subdsf.datasetFieldType.description}" data-placement="auto right" data-toggle="tooltip" href="#">#{subdsf.datasetFieldType.title}</a>
+                                                                </label>
+                                                                <div>
+                                                                    <h:outputText value="#{subdsf.value}" rendered="#{!subdsf.datasetFieldType.allowMultiples}"/>
+                                                                    <ui:repeat value="#{subdsf.values}" var="value" varStatus="loop" rendered="#{subdsf.datasetFieldType.allowMultiples}">
+                                                                        <h:outputText value="#{loop.first?'':'; '}#{value}"/>
+                                                                    </ui:repeat>
+                                                                </div>
                                                             </div>
-                                                        </div>
+                                                        </ui:fragment>
                                                     </ui:repeat>
                                                 </div>
                                             </ui:repeat>
@@ -77,7 +81,7 @@
                         <div id="collapse#{block.index}" class="collapse #{block.first || DatasetPage.editMode == 'CREATE'?'in':''}">
                             <div class="panel-body">
                                 <ui:repeat value="#{metadataBlockVal.value}" var="dsf">
-                                    
+
                                     <ui:fragment rendered="#{(DatasetPage.editMode == 'METADATA' or dsf.datasetFieldType.displayOnCreate)}">
 
                                         <div class="form-group">
@@ -88,7 +92,7 @@
                                                 <h:outputText styleClass="glyphicon glyphicon-asterisk text-danger" value="" rendered="#{dsf.datasetFieldType.required}" />
                                             </label>
 
-                                        
+
                                             <!-- Primitive fields -->
                                             <p:fragment autoUpdate="true" rendered="#{dsf.datasetFieldType.primitive}">
                                                 <div class="form-group">
@@ -209,11 +213,11 @@
                                                     </ui:repeat>
                                                 </div>
                                             </p:fragment>
-                                        
+
                                         </div>
-                                    
+
                                     </ui:fragment>
-                                    
+
                                 </ui:repeat>
                             </div>
                         </div>

From 7e187b451239c4d5809b6529be8067a9cba060ec Mon Sep 17 00:00:00 2001
From: posixeleni <ecastro@fas.harvard.edu>
Date: Thu, 15 May 2014 10:23:38 -0400
Subject: [PATCH 27/46] Update appendix.rst

---
 doc/Sphinx/source/User/appendix.rst | 29 -----------------------------
 1 file changed, 29 deletions(-)

diff --git a/doc/Sphinx/source/User/appendix.rst b/doc/Sphinx/source/User/appendix.rst
index 8c16e9bcd2f..a867fc5ea40 100644
--- a/doc/Sphinx/source/User/appendix.rst
+++ b/doc/Sphinx/source/User/appendix.rst
@@ -20,35 +20,6 @@ currently proposed metadata fields for 4.0 (per metadata block):
 - `Biomedical Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodExsRTB2SEpVWWd1Qmx6M09HSkExd3c&usp=sharing>`__ 
   (based on `ISA-Tab <http://isatab.sourceforge.net/format.html>`__ and `Stem Cell Commons <http://stemcellcommons.org/>`__)
 
-DDI 2.5
---------
 
-The Dataverse metadata is compliant with the `DDI schema
-version 2.5 <http://www.ddialliance.org/>`__. The Metadata fields in the Citation and Social Science blocks
-associated with each Dataset contain most of the fields
-in the study description section of the DDI. That way the Dataverse
-metadata can be mapped easily to a DDI, and be exported into XML
-format for preservation and interoperability.
-
-DataCite Schema 3.0
---------------------
-
-Dataverse metadata is compliant with the `DataCite Metadata Schema v.3.0 <http://schema.datacite.org/meta/kernel-3/index.html>`__ requirements. That way the Dataverse
-metadata can be mapped easily to a DataCite, and be exported into XML
-format for preservation and interoperability.
-
-DCMI Terms
------------
-
-Dataverse metadata is compliant with `Dublin Core Metadata Initiative Terms <http://dublincore.org/documents/dcmi-terms/>`__ (DCMI Terms) requirements. That way the Dataverse
-metadata can be mapped easily to DCMI Terms, and be exported into XML
-format for preservation and interoperability.
-
-
-FGDC/CSDGM (imports)
----------------------
-
-For imports only, Dataverse data is compliant with the `Content Standard
-for Digital Geospatial Metadata (CSDGM), Vers. 2 (FGDC-STD-001-1998) <http://www.fgdc.gov/metadata>`__ (FGDC).
 
 

From d713334024e97cb31079158a01c95ae09ab53b29 Mon Sep 17 00:00:00 2001
From: posixeleni <ecastro@fas.harvard.edu>
Date: Thu, 15 May 2014 10:28:49 -0400
Subject: [PATCH 28/46] Update appendix.rst

---
 doc/Sphinx/source/User/appendix.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/Sphinx/source/User/appendix.rst b/doc/Sphinx/source/User/appendix.rst
index a867fc5ea40..5b3577c3aaf 100644
--- a/doc/Sphinx/source/User/appendix.rst
+++ b/doc/Sphinx/source/User/appendix.rst
@@ -16,7 +16,8 @@ currently proposed metadata fields for 4.0 (per metadata block):
 - `Citation Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodDBaYTFPakhGaEpoa3hqZUJTOWZtclE&usp=sharing>`__ (compliant with `DDI 2.5 <http://www.ddialliance.org/>`__ and `DataCite 3.0 <http://schema.datacite.org/meta/kernel-3/index.html>`__) 
 - `Social Science & Humanities Metadata (DDI 2.5 compliant) <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodEppcTFHT1NnajNLV0tacE10NEdmUnc&usp=sharing>`__
 - `Astronomy and Astrophysics Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodEp4Qmp0QURkUWo1S0t4X3hia0FnZUE&usp=sharing>`__
-  : These metadata elements can be mapped/exported to the International Virtual Observatory Alliance’s (IVOA) Resource Metadata for the Virtual Observatory (VOResource Schema format) and based on `Virtual Observatory (VO) Discovery and Provenance Metadata <http://www.wf4ever-project.org/wiki/download/attachments/1179927/DPmetadata.pdf?version=1&modificationDate=1337186963000>`__) 
+  : These metadata elements can be mapped/exported to the International Virtual Observatory Alliance’s (IVOA) 
+  `VOResource Schema format <http://www.ivoa.net/documents/latest/RM.html>`_ and based on `Virtual Observatory (VO) Discovery and Provenance Metadata <http://www.wf4ever-project.org/wiki/download/attachments/1179927/DPmetadata.pdf?version=1&modificationDate=1337186963000>`__) 
 - `Biomedical Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodExsRTB2SEpVWWd1Qmx6M09HSkExd3c&usp=sharing>`__ 
   (based on `ISA-Tab <http://isatab.sourceforge.net/format.html>`__ and `Stem Cell Commons <http://stemcellcommons.org/>`__)
 

From 03b45071896af423918123737149e2970eec78db Mon Sep 17 00:00:00 2001
From: posixeleni <ecastro@fas.harvard.edu>
Date: Thu, 15 May 2014 10:29:23 -0400
Subject: [PATCH 29/46] Update appendix.rst

---
 doc/Sphinx/source/User/appendix.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/Sphinx/source/User/appendix.rst b/doc/Sphinx/source/User/appendix.rst
index 5b3577c3aaf..bb0b57b30f3 100644
--- a/doc/Sphinx/source/User/appendix.rst
+++ b/doc/Sphinx/source/User/appendix.rst
@@ -17,7 +17,7 @@ currently proposed metadata fields for 4.0 (per metadata block):
 - `Social Science & Humanities Metadata (DDI 2.5 compliant) <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodEppcTFHT1NnajNLV0tacE10NEdmUnc&usp=sharing>`__
 - `Astronomy and Astrophysics Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodEp4Qmp0QURkUWo1S0t4X3hia0FnZUE&usp=sharing>`__
   : These metadata elements can be mapped/exported to the International Virtual Observatory Alliance’s (IVOA) 
-  `VOResource Schema format <http://www.ivoa.net/documents/latest/RM.html>`_ and based on `Virtual Observatory (VO) Discovery and Provenance Metadata <http://www.wf4ever-project.org/wiki/download/attachments/1179927/DPmetadata.pdf?version=1&modificationDate=1337186963000>`__) 
+  `VOResource Schema format <http://www.ivoa.net/documents/latest/RM.html>`_ and is based on `Virtual Observatory (VO) Discovery and Provenance Metadata <http://www.wf4ever-project.org/wiki/download/attachments/1179927/DPmetadata.pdf?version=1&modificationDate=1337186963000>`__) 
 - `Biomedical Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodExsRTB2SEpVWWd1Qmx6M09HSkExd3c&usp=sharing>`__ 
   (based on `ISA-Tab <http://isatab.sourceforge.net/format.html>`__ and `Stem Cell Commons <http://stemcellcommons.org/>`__)
 

From e9128cccaca72137691c059f1c7afccd805fd982 Mon Sep 17 00:00:00 2001
From: posixeleni <ecastro@fas.harvard.edu>
Date: Thu, 15 May 2014 10:30:20 -0400
Subject: [PATCH 30/46] Update appendix.rst

---
 doc/Sphinx/source/User/appendix.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/Sphinx/source/User/appendix.rst b/doc/Sphinx/source/User/appendix.rst
index bb0b57b30f3..eabc8c3fdf2 100644
--- a/doc/Sphinx/source/User/appendix.rst
+++ b/doc/Sphinx/source/User/appendix.rst
@@ -17,7 +17,8 @@ currently proposed metadata fields for 4.0 (per metadata block):
 - `Social Science & Humanities Metadata (DDI 2.5 compliant) <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodEppcTFHT1NnajNLV0tacE10NEdmUnc&usp=sharing>`__
 - `Astronomy and Astrophysics Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodEp4Qmp0QURkUWo1S0t4X3hia0FnZUE&usp=sharing>`__
   : These metadata elements can be mapped/exported to the International Virtual Observatory Alliance’s (IVOA) 
-  `VOResource Schema format <http://www.ivoa.net/documents/latest/RM.html>`_ and is based on `Virtual Observatory (VO) Discovery and Provenance Metadata <http://www.wf4ever-project.org/wiki/download/attachments/1179927/DPmetadata.pdf?version=1&modificationDate=1337186963000>`__) 
+  `VOResource Schema format <http://www.ivoa.net/documents/latest/RM.html>`__ and is based on 
+  `Virtual Observatory (VO) Discovery and Provenance Metadata <http://www.wf4ever-project.org/wiki/download/attachments/1179927/DPmetadata.pdf?version=1&modificationDate=1337186963000>`__
 - `Biomedical Metadata <https://docs.google.com/spreadsheet/ccc?key=0AjeLxEN77UZodExsRTB2SEpVWWd1Qmx6M09HSkExd3c&usp=sharing>`__ 
   (based on `ISA-Tab <http://isatab.sourceforge.net/format.html>`__ and `Stem Cell Commons <http://stemcellcommons.org/>`__)
 

From abfb004a9895e2d170df40af7f4a9ebb5e5709e2 Mon Sep 17 00:00:00 2001
From: mheppler <mheppler@10.251.80.247>
Date: Thu, 15 May 2014 12:49:50 -0400
Subject: [PATCH 31/46] Applied new customization settings for positioning a
 rectangle logo, and the background color behind the logo. Also fixed a bug
 where the link feature wasn't being displayed in the customization header.

---
 src/main/webapp/dataverse_header.xhtml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/webapp/dataverse_header.xhtml b/src/main/webapp/dataverse_header.xhtml
index 526e35b2e28..f84feabb533 100644
--- a/src/main/webapp/dataverse_header.xhtml
+++ b/src/main/webapp/dataverse_header.xhtml
@@ -115,7 +115,7 @@
     <ui:fragment rendered="#{showDataverseHeader}">
         <div id="dataverseHeader" class="container" style="background:#{!empty dataverse.backgroundColor ? dataverse.backgroundColor : '#F5F5F5'};">
             <ui:fragment rendered="#{!empty dataverse.logo and dataverse.logoFormat == 'RECTANGLE'}">
-                <div class="dataverseHeaderLogo">
+                <div class="dataverseHeaderLogo" style="text-align:#{!empty dataverse.logoAlignment ? dataverse.logoAlignment : 'center'};; background:#{!empty dataverse.logoBackgroundColor ? dataverse.logoBackgroundColor : 'inherit'};">
                     <image src="/logos/#{dataverse.logo}" style="max-width:900px;max-height:120px"/>
                 </div>
             </ui:fragment>
@@ -142,10 +142,10 @@
                         <h:outputText escape="false" style="color:#{!empty dataverse.textColor ? dataverse.textColor : '#888'};" value="#{dataverse.tagline}" />
                     </div>
                 </ui:fragment>
-                <ui:fragment rendered="#{!empty dataverse.tagline}">
+                <ui:fragment rendered="#{!empty dataverse.linkUrl}">
                     <div class="dataverseHeaderCell dataverseHeaderLink">
-                        <h:outputLink value="#{dataverse.linkUrl}" target="_blank">
-                            <h:outputText style="color:#{!empty dataverse.linkColor ? dataverse.linkColor : 'inheret'};" value="#{dataverse.linkText}" />
+                        <h:outputLink value="#{dataverse.linkUrl}" style="color:#{!empty dataverse.linkColor ? dataverse.linkColor : 'inheret'};" target="_blank">
+                            <h:outputText value="#{dataverse.linkText}" escape="false"/>
                         </h:outputLink>
                     </div>
                 </ui:fragment>

From 84a69e7a9171ed4689b28852a300c1fad082bcef Mon Sep 17 00:00:00 2001
From: Gustavo Durand <gdurand@iq.harvard.edu>
Date: Thu, 15 May 2014 13:29:38 -0400
Subject: [PATCH 32/46] removed log4j from pom.xml

---
 pom.xml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/pom.xml b/pom.xml
index 09288df8a11..82d3ddc7250 100644
--- a/pom.xml
+++ b/pom.xml
@@ -75,12 +75,6 @@
             <version>1.0</version>
             <type>war</type>
         </dependency>
-        <dependency>
-            <!-- required by org.swordapp.server.sword2-server -->
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-            <version>1.2.17</version>
-        </dependency>
         <dependency>
             <!-- required by org.swordapp.server.sword2-server -->
             <groupId>org.apache.abdera</groupId>

From 9cdedf1f89011bcac90495451631913e96d35c99 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Thu, 15 May 2014 16:07:35 -0400
Subject: [PATCH 33/46] stub out SWORD statement (lots of todo's) #3385

---
 scripts/api/data-deposit/show-files           |   3 +
 scripts/api/data-deposit/show-statement       |   8 +
 scripts/search/files                          |   3 +
 .../datadeposit/SWORDv2StatementServlet.java  |  35 ++++
 .../api/datadeposit/StatementManagerImpl.java | 161 ++++++++++++++++++
 src/main/webapp/WEB-INF/web.xml               |  12 ++
 6 files changed, 222 insertions(+)
 create mode 100755 scripts/api/data-deposit/show-files
 create mode 100755 scripts/api/data-deposit/show-statement
 create mode 100755 scripts/search/files
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java

diff --git a/scripts/api/data-deposit/show-files b/scripts/api/data-deposit/show-files
new file mode 100755
index 00000000000..42dd477b434
--- /dev/null
+++ b/scripts/api/data-deposit/show-files
@@ -0,0 +1,3 @@
+#!/bin/sh
+#scripts/api/data-deposit/show-statement | xpath "//entry/content/@*[name()='type' or name()='src']"
+scripts/api/data-deposit/show-statement | xpath '//entry/id/text()' | cut -d'/' -f11,12
diff --git a/scripts/api/data-deposit/show-statement b/scripts/api/data-deposit/show-statement
new file mode 100755
index 00000000000..40167f231e5
--- /dev/null
+++ b/scripts/api/data-deposit/show-statement
@@ -0,0 +1,8 @@
+#!/bin/sh
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+GLOBAL_ID=myIdentifier
+curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/statement/study/$GLOBAL_ID \
+| xmllint -format - \
+#| xpath '//entry/title'
diff --git a/scripts/search/files b/scripts/search/files
new file mode 100755
index 00000000000..361c9843458
--- /dev/null
+++ b/scripts/search/files
@@ -0,0 +1,3 @@
+#!/bin/sh
+curl http://localhost:8080/api/index
+curl -s 'http://localhost:8983/solr/collection1/select?rows=100&wt=json&indent=true&q=*&fq=dvtype:files' | jq '.response.docs[] | {name_sort, id, parentid}'
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java
new file mode 100644
index 00000000000..b413309886c
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java
@@ -0,0 +1,35 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.io.IOException;
+import javax.inject.Inject;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import org.swordapp.server.StatementAPI;
+import org.swordapp.server.StatementManager;
+import org.swordapp.server.servlets.SwordServlet;
+
+public class SWORDv2StatementServlet extends SwordServlet {
+
+    @Inject
+    StatementManagerImpl statementManagerImpl;
+    private StatementManager sm;
+    private StatementAPI statementApi;
+
+    public void init() throws ServletException {
+        super.init();
+
+        // load the container manager implementation
+        this.sm = statementManagerImpl;
+
+        // initialise the underlying servlet processor
+        this.statementApi = new StatementAPI(this.sm, this.config);
+    }
+
+    @Override
+    protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.statementApi.get(req, resp);
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
new file mode 100644
index 00000000000..15f35864128
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
@@ -0,0 +1,161 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.DataFile;
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.DatasetServiceBean;
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseUser;
+import edu.harvard.iq.dataverse.FileMetadata;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Logger;
+import javax.ejb.EJB;
+import javax.inject.Inject;
+import org.apache.abdera.i18n.iri.IRI;
+import org.apache.abdera.i18n.iri.IRISyntaxException;
+import org.apache.abdera.model.AtomDate;
+import org.swordapp.server.AtomStatement;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.ResourcePart;
+import org.swordapp.server.Statement;
+import org.swordapp.server.StatementManager;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordConfiguration;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+import org.swordapp.server.UriRegistry;
+
+public class StatementManagerImpl implements StatementManager {
+
+    private static final Logger logger = Logger.getLogger(StatementManagerImpl.class.getCanonicalName());
+
+    @EJB
+    DatasetServiceBean datasetService;
+    @Inject
+    SwordAuth swordAuth;
+    @Inject
+    UrlManager urlManager;
+    SwordConfigurationImpl swordConfiguration = new SwordConfigurationImpl();
+
+    @Override
+    public Statement getStatement(String editUri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordError, SwordAuthException {
+        this.swordConfiguration = (SwordConfigurationImpl) swordConfiguration;
+        swordConfiguration = (SwordConfigurationImpl) swordConfiguration;
+        if (authCredentials == null) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "auth credentials are null");
+        }
+        if (swordAuth == null) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "swordAuth is null");
+        }
+
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        urlManager.processUrl(editUri);
+        String globalId = urlManager.getTargetIdentifier();
+        if (urlManager.getTargetType().equals("study") && globalId != null) {
+
+            logger.fine("request for sword statement by user " + vdcUser.getUserName());
+
+//            Study study = null;
+            /**
+             * @todo don't hard code this, obviously. In DVN 3.x we had a method
+             * for editStudyService.getStudyByGlobalId(globalId)
+             */
+//            Study study = editStudyService.getStudyByGlobalId(globalId);
+            long databaseIdForRoastingAtHomeDataset = 10;
+            Dataset study = datasetService.find(databaseIdForRoastingAtHomeDataset);
+//            try {
+//                study = studyService.getStudyByGlobalId(globalId);
+//            } catch (EJBException ex) {
+//                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + editUri);
+//            }
+            Long studyId;
+            try {
+                studyId = study.getId();
+            } catch (NullPointerException ex) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "couldn't find study with global ID of " + globalId);
+            }
+
+            Dataverse dvThatOwnsStudy = study.getOwner();
+            if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
+                /**
+                 * @todo getIdentifier is equivalent to getGlobalId, right?
+                 */
+//                String feedUri = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit/study/" + study.getGlobalId();
+                String feedUri = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit/study/" + study.getIdentifier();
+                /**
+                 * @todo is it safe to use this?
+                 */
+                String author = study.getLatestVersion().getAuthorsStr();
+                String title = study.getLatestVersion().getTitle();
+                Date lastUpdated = study.getLatestVersion().getLastUpdateTime();
+                if (lastUpdated == null) {
+                    /**
+                     * @todo why is this date null?
+                     */
+                    logger.info("why is lastUpdated null?");
+                    lastUpdated = new Date();
+                }
+                AtomDate atomDate = new AtomDate(lastUpdated);
+//                AtomDate atomDate = new AtomDate(study.getLatestVersion().getLastUpdateTime());
+                String datedUpdated = atomDate.toString();
+                Statement statement = new AtomStatement(feedUri, author, title, datedUpdated);
+                Map<String, String> states = new HashMap<String, String>();
+                states.put("latestVersionState", study.getLatestVersion().getVersionState().toString());
+                /**
+                 * @todo DVN 3.x had a studyLock. What's the equivalent in 4.0?
+                 */
+//                StudyLock lock = study.getStudyLock();
+//                if (lock != null) {
+//                    states.put("locked", "true");
+//                    states.put("lockedDetail", lock.getDetail());
+//                    states.put("lockedStartTime", lock.getStartTime().toString());
+//                } else {
+//                    states.put("locked", "false");
+//                }
+                statement.setStates(states);
+                List<FileMetadata> fileMetadatas = study.getLatestVersion().getFileMetadatas();
+                for (FileMetadata fileMetadata : fileMetadatas) {
+                    DataFile studyFile = fileMetadata.getDataFile();
+                    // We are exposing the filename for informational purposes. The file id is what you
+                    // actually operate on to delete a file, etc.
+                    //
+                    // Replace spaces to avoid IRISyntaxException
+                    String fileNameFinal = fileMetadata.getLabel().replace(' ', '_');
+                    String studyFileUrlString = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit-media/file/" + studyFile.getId() + "/" + fileNameFinal;
+                    IRI studyFileUrl;
+                    try {
+                        studyFileUrl = new IRI(studyFileUrlString);
+                    } catch (IRISyntaxException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid URL for file ( " + studyFileUrlString + " ) resulted in " + ex.getMessage());
+                    }
+                    ResourcePart resourcePart = new ResourcePart(studyFileUrl.toString());
+                    /**
+                     * @todo get this working. show the actual file type
+                     */
+//                    resourcePart.setMediaType(studyFile.getOriginalFileFormat());
+                    resourcePart.setMediaType("application/octet-stream");
+                    /**
+                     * @todo: Why are properties set on a ResourcePart not
+                     * exposed when you GET a Statement?
+                     */
+//                    Map<String, String> properties = new HashMap<String, String>();
+//                    properties.put("filename", studyFile.getFileName());
+//                    properties.put("category", studyFile.getLatestCategory());
+//                    properties.put("originalFileType", studyFile.getOriginalFileType());
+//                    properties.put("id", studyFile.getId().toString());
+//                    properties.put("UNF", studyFile.getUnf());
+//                    resourcePart.setProperties(properties);
+                    statement.addResource(resourcePart);
+                }
+                return statement;
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to view study with global ID " + globalId);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine target type or identifier from URL: " + editUri);
+        }
+    }
+
+}
diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
index c19afc4ff3e..14aeaa873a4 100644
--- a/src/main/webapp/WEB-INF/web.xml
+++ b/src/main/webapp/WEB-INF/web.xml
@@ -125,6 +125,18 @@
         <url-pattern>/dvn/api/data-deposit/v1/swordv2/edit-media/*</url-pattern>
     </servlet-mapping>
 
+    <context-param>
+        <param-name>statement-impl</param-name>
+        <param-value>edu.harvard.iq.dataverse.api.datadeposit.StatementManagerImpl</param-value>
+    </context-param>
+    <servlet>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2StatementServlet</servlet-name>
+        <servlet-class>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2StatementServlet</servlet-class>
+    </servlet>
+    <servlet-mapping>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2StatementServlet</servlet-name>
+        <url-pattern>/dvn/api/data-deposit/v1/swordv2/statement/*</url-pattern>
+    </servlet-mapping>
 
     <!-- END Data Deposit API v1 (SWORD v2) -->
 

From 8752cdb6245c5dbca696a4414cbb8d00df5484f3 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Fri, 16 May 2014 12:30:42 -0400
Subject: [PATCH 34/46] stub out SWORD delete-dataset and show-atom-entry #3385

---
 scripts/api/data-deposit/delete-dataset       |   9 +
 scripts/api/data-deposit/show-atom-entry      |   8 +
 .../api/datadeposit/ContainerManagerImpl.java | 536 ++++++++++++++++++
 .../datadeposit/SWORDv2ContainerServlet.java  |  66 +++
 src/main/webapp/WEB-INF/web.xml               |  13 +
 5 files changed, 632 insertions(+)
 create mode 100755 scripts/api/data-deposit/delete-dataset
 create mode 100755 scripts/api/data-deposit/show-atom-entry
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
 create mode 100644 src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java

diff --git a/scripts/api/data-deposit/delete-dataset b/scripts/api/data-deposit/delete-dataset
new file mode 100755
index 00000000000..531b85ab649
--- /dev/null
+++ b/scripts/api/data-deposit/delete-dataset
@@ -0,0 +1,9 @@
+#!/bin/bash -x
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+GLOBAL_ID=hdl:TEST/12345
+DATABASE_ID=$1
+#curl --insecure -X DELETE https://$DVN_SERVER/api/datasets/$DATABASE_ID?key=$USERNAME
+curl --insecure -i -X DELETE https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID
+#| xmllint -format -
diff --git a/scripts/api/data-deposit/show-atom-entry b/scripts/api/data-deposit/show-atom-entry
new file mode 100755
index 00000000000..d98a8b64f30
--- /dev/null
+++ b/scripts/api/data-deposit/show-atom-entry
@@ -0,0 +1,8 @@
+#!/bin/sh
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+GLOBAL_ID=hdl:TEST/12345
+DATABASE_ID=$1
+curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID \
+| xmllint -format -
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
new file mode 100644
index 00000000000..fb1402a039e
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
@@ -0,0 +1,536 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.DatasetServiceBean;
+import edu.harvard.iq.dataverse.DatasetVersion;
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.DataverseUser;
+import edu.harvard.iq.dataverse.EjbDataverseEngine;
+import edu.harvard.iq.dataverse.IndexServiceBean;
+import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
+import edu.harvard.iq.dataverse.engine.command.exception.CommandExecutionException;
+import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetCommand;
+import edu.harvard.iq.dataverse.export.DDIExportServiceBean;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Logger;
+import javax.ejb.EJB;
+import javax.ejb.EJBException;
+import javax.inject.Inject;
+import javax.naming.Context;
+import javax.naming.InitialContext;
+import javax.naming.NamingException;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import org.swordapp.server.AuthCredentials;
+import org.swordapp.server.ContainerManager;
+import org.swordapp.server.Deposit;
+import org.swordapp.server.DepositReceipt;
+import org.swordapp.server.SwordAuthException;
+import org.swordapp.server.SwordConfiguration;
+import org.swordapp.server.SwordError;
+import org.swordapp.server.SwordServerException;
+import org.swordapp.server.UriRegistry;
+
+public class ContainerManagerImpl implements ContainerManager {
+
+    private static final Logger logger = Logger.getLogger(ContainerManagerImpl.class.getCanonicalName());
+
+    @EJB
+    protected EjbDataverseEngine engineSvc;
+    @EJB
+    DatasetServiceBean datasetService;
+    @EJB
+    IndexServiceBean indexService;
+    @PersistenceContext(unitName = "VDCNet-ejbPU")
+    EntityManager em;
+    @EJB
+    DDIExportServiceBean ddiService;
+    @Inject
+    SwordAuth swordAuth;
+    @Inject
+    UrlManager urlManager;
+//    SwordConfigurationImpl swordConfiguration = new SwordConfigurationImpl();
+
+    @Override
+    public DepositReceipt getEntry(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordError, SwordAuthException {
+        DataverseUser dataverseUser = swordAuth.auth(authCredentials);
+        logger.fine("getEntry called with url: " + uri);
+        urlManager.processUrl(uri);
+        String targetType = urlManager.getTargetType();
+        if (!targetType.isEmpty()) {
+            logger.fine("operating on target type: " + urlManager.getTargetType());
+            if ("study".equals(targetType)) {
+                String globalId = urlManager.getTargetIdentifier();
+                Dataset dataset = null;
+                try {
+                    /**
+                     * @todo don't hard code this, obviously. In DVN 3.x we had
+                     * a method for studyService.getStudyByGlobalId(globalId)
+                     */
+//                    study = studyService.getStudyByGlobalId(globalId);
+                    long databaseIdForRoastingAtHomeDataset = 10;
+                    dataset = datasetService.find(databaseIdForRoastingAtHomeDataset);
+                } catch (EJBException ex) {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
+                }
+                if (dataset != null) {
+                    Dataverse dvThatOwnsStudy = dataset.getOwner();
+                    if (swordAuth.hasAccessToModifyDataverse(dataverseUser, dvThatOwnsStudy)) {
+                        ReceiptGenerator receiptGenerator = new ReceiptGenerator();
+                        String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
+                        DepositReceipt depositReceipt = receiptGenerator.createReceipt(baseUrl, dataset);
+                        if (depositReceipt != null) {
+                            return depositReceipt;
+                        } else {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not generate deposit receipt.");
+                        }
+                    } else {
+                        /**
+                         * @todo need study.getGlobalId() from DVN 3.x
+                         */
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + dataverseUser.getUserName() + " is not authorized to retrieve entry for " + dataset.getIdentifier());
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on URL: " + uri);
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported target type (" + targetType + ") in URL: " + uri);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine target type from URL: " + uri);
+        }
+    }
+
+    @Override
+    public DepositReceipt replaceMetadata(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        logger.fine("replaceMetadata called with url: " + uri);
+        urlManager.processUrl(uri);
+        String targetType = urlManager.getTargetType();
+        if (!targetType.isEmpty()) {
+            logger.fine("operating on target type: " + urlManager.getTargetType());
+            if ("dataverse".equals(targetType)) {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Metadata replace of dataverse is not supported.");
+            } else if ("study".equals(targetType)) {
+                logger.fine("replacing metadata for study");
+                logger.fine("deposit XML received by replaceMetadata():\n" + deposit.getSwordEntry());
+
+                String globalId = urlManager.getTargetIdentifier();
+
+//                EditStudyService editStudyService;
+                Context ctx;
+                try {
+                    ctx = new InitialContext();
+//                    editStudyService = (EditStudyService) ctx.lookup("java:comp/env/editStudy");
+                } catch (NamingException ex) {
+                    logger.info("problem looking up editStudyService");
+                    throw new SwordServerException("problem looking up editStudyService");
+                }
+//                StudyServiceLocal studyService;
+                try {
+                    ctx = new InitialContext();
+//                    studyService = (StudyServiceLocal) ctx.lookup("java:comp/env/studyService");
+                } catch (NamingException ex) {
+                    logger.info("problem looking up studyService");
+                    throw new SwordServerException("problem looking up studyService");
+                }
+//                Study studyToLookup;
+                Dataset studyToLookup = null;
+                try {
+                    /**
+                     * @todo: why doesn't
+                     * editStudyService.setStudyVersionByGlobalId(globalId)
+                     * work?
+                     */
+//                    studyToLookup = studyService.getStudyByGlobalId(globalId);
+                } catch (EJBException ex) {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
+                }
+                if (studyToLookup != null) {
+//                    StudyLock lockOnStudyLookedup = studyToLookup.getStudyLock();
+//                    if (lockOnStudyLookedup != null) {
+//                        String message = Util.getStudyLockMessage(lockOnStudyLookedup, studyToLookup.getGlobalId());
+//                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, message);
+//                    }
+//                    editStudyService.setStudyVersion(studyToLookup.getId());
+//                    Study studyToEdit = editStudyService.getStudyVersion().getStudy();
+                    Dataset studyToEdit = null;
+                    Dataverse dvThatOwnsStudy = studyToEdit.getOwner();
+                    if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
+                        Map<String, List<String>> dublinCore = deposit.getSwordEntry().getDublinCore();
+                        if (dublinCore.get("title") == null || dublinCore.get("title").get(0) == null || dublinCore.get("title").get(0).isEmpty()) {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "title field is required");
+                        }
+                        if (dublinCore.get("date") != null) {
+                            String date = dublinCore.get("date").get(0);
+                            if (date != null) {
+//                                boolean isValid = DateUtil.validateDate(date);
+//                                if (!isValid) {
+//                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Invalid date: '" + date + "'.  Valid formats are YYYY-MM-DD, YYYY-MM, or YYYY.");
+//                                }
+                            }
+                        }
+                        String tmpDirectory = swordConfiguration.getTempDirectory();
+                        if (tmpDirectory == null) {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not determine temp directory");
+                        }
+                        String uploadDirPath = tmpDirectory + File.separator + "import" + File.separator + studyToEdit.getId();
+                        Long dcmiTermsHarvetsFormatId = new Long(4);
+//                        HarvestFormatType dcmiTermsHarvestFormatType = em.find(HarvestFormatType.class, dcmiTermsHarvetsFormatId);
+                        String xmlAtomEntry = deposit.getSwordEntry().getEntry().toString();
+//                        File ddiFile = studyService.transformToDDI(xmlAtomEntry, dcmiTermsHarvestFormatType.getStylesheetFileName(), uploadDirPath);
+                        // erase all metadata before running ddiService.mapDDI() because
+                        // for multivalued fields (such as author) that function appends
+                        // values rather than replacing them
+                        /**
+                         * @todo how best to replace metadata on a dataset in
+                         * 4.0?
+                         */
+//                        studyToEdit.getLatestVersion().setMetadata(new Metadata());
+//                        ddiService.mapDDI(ddiFile, studyToEdit.getLatestVersion(), true);
+                        try {
+//                            editStudyService.save(dvThatOwnsStudy.getId(), vdcUser.getId());
+                        } catch (EJBException ex) {
+                            // OptimisticLockException
+//                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to replace cataloging information for study " + studyToEdit.getGlobalId() + " (may be locked). Please try again later.");
+                        }
+                        ReceiptGenerator receiptGenerator = new ReceiptGenerator();
+                        String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
+                        DepositReceipt depositReceipt = receiptGenerator.createReceipt(baseUrl, studyToEdit);
+                        return depositReceipt;
+                    } else {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + vdcUser.getUserName() + " is not authorized to modify dataverse " + dvThatOwnsStudy.getAlias());
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unknown target type specified on which to replace metadata: " + uri);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No target specified on which to replace metadata: " + uri);
+        }
+    }
+
+    @Override
+    public DepositReceipt replaceMetadataAndMediaResource(String string, Deposit dpst, AuthCredentials ac, SwordConfiguration sc) throws SwordError, SwordServerException, SwordAuthException {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
+    @Override
+    public DepositReceipt addMetadataAndResources(String string, Deposit dpst, AuthCredentials ac, SwordConfiguration sc) throws SwordError, SwordServerException, SwordAuthException {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
+    @Override
+    public DepositReceipt addMetadata(String string, Deposit dpst, AuthCredentials ac, SwordConfiguration sc) throws SwordError, SwordServerException, SwordAuthException {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
+    @Override
+    public DepositReceipt addResources(String string, Deposit dpst, AuthCredentials ac, SwordConfiguration sc) throws SwordError, SwordServerException, SwordAuthException {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
+    @Override
+    public void deleteContainer(String uri, AuthCredentials authCredentials, SwordConfiguration sc) throws SwordError, SwordServerException, SwordAuthException {
+//        swordConfiguration = (SwordConfigurationImpl) sc;
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        logger.fine("deleteContainer called with url: " + uri);
+        urlManager.processUrl(uri);
+        logger.fine("original url: " + urlManager.getOriginalUrl());
+        if (!"edit".equals(urlManager.getServlet())) {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "edit servlet expected, not " + urlManager.getServlet());
+        }
+        String targetType = urlManager.getTargetType();
+        if (!targetType.isEmpty()) {
+            logger.fine("operating on target type: " + urlManager.getTargetType());
+
+//            StudyServiceLocal studyService;
+            Context ctx;
+            try {
+                ctx = new InitialContext();
+//                studyService = (StudyServiceLocal) ctx.lookup("java:comp/env/studyService");
+            } catch (NamingException ex) {
+                logger.info("problem looking up studyService");
+                throw new SwordServerException("problem looking up studyService");
+            }
+
+            if ("dataverse".equals(targetType)) {
+                /**
+                 * @todo throw SWORD error recommending use of 4.0 "native" API
+                 * to delete dataverses
+                 */
+//                String dvAlias = urlManager.getTargetIdentifier();
+//                List<VDC> userVDCs = vdcService.getUserVDCs(vdcUser.getId());
+//                VDC dataverseToEmpty = vdcService.findByAlias(dvAlias);
+//                if (dataverseToEmpty != null) {
+//                    if ("Admin".equals(vdcUser.getNetworkRole().getName())) {
+//                        if (swordConfiguration.allowNetworkAdminDeleteAllStudies()) {
+//
+//                            /**
+//                             * @todo: this is the deleteContainer method...
+//                             * should move this to some sort of "emptyContainer"
+//                             * method
+//                             */
+//                            // curl --insecure -s -X DELETE https://sword:sword@localhost:8181/dvn/api/data-deposit/v1/swordv2/edit/dataverse/sword 
+//                            Collection<Study> studies = dataverseToEmpty.getOwnedStudies();
+//                            for (Study study : studies) {
+//                                logger.info("In dataverse " + dataverseToEmpty.getAlias() + " about to delete study id " + study.getId());
+//                                studyService.deleteStudy(study.getId());
+//                            }
+//                        } else {
+//                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "DELETE on a dataverse is not supported");
+//                        }
+
+//                    } else {
+//                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Role was " + vdcUser.getNetworkRole().getName() + " but admin required.");
+//                    }
+//                } else {
+//                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't find dataverse to delete from URL: " + uri);
+//                }
+            } else if ("study".equals(targetType)) {
+                String globalId = urlManager.getTargetIdentifier();
+                logger.info("globalId: " + globalId);
+                if (globalId != null) {
+                    Dataset study = null;
+                    try {
+
+                        /**
+                         * @todo don't hard code this, obviously. In DVN 3.x we
+                         * had a method for
+                         * studyService.getStudyByGlobalId(globalId)
+                         */
+//                        study = studyService.getStudyByGlobalId(globalId);
+                        long databaseIdForRoastingAtHomeDataset = 10;
+                        study = datasetService.find(databaseIdForRoastingAtHomeDataset);
+                    } catch (EJBException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
+                    }
+                    if (study != null) {
+                        Dataverse dvThatOwnsStudy = study.getOwner();
+                        if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
+                            DatasetVersion.VersionState studyState = study.getLatestVersion().getVersionState();
+                            if (studyState.equals(DatasetVersion.VersionState.DRAFT)) {
+                                /**
+                                 * @todo use getGlobalId when it's available
+                                 */
+                                logger.info("destroying working copy version of study " + study.getIdentifier());
+                                /**
+                                 * @todo in DVN 3.x we had a convenient
+                                 * destroyWorkingCopyVersion method but the
+                                 * DeleteDatasetCommand is pretty scary... what
+                                 * if a released study has a new draft version?
+                                 * What we need is a
+                                 * DeleteDatasetVersionCommand, I suppose...
+                                 */
+//                                studyService.destroyWorkingCopyVersion(study.getLatestVersion().getId());
+                                try {
+                                    engineSvc.submit(new DeleteDatasetCommand(study, vdcUser));
+                                    /**
+                                     * @todo re-index after deletion
+                                     * https://redmine.hmdc.harvard.edu/issues/3544#note-21
+                                     */
+                                    logger.info("dataset deleted");
+                                } catch (CommandExecutionException ex) {
+                                    // internal error
+                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can't delete dataset: " + ex.getMessage());
+                                } catch (CommandException ex) {
+                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Can't delete dataset: " + ex.getMessage());
+                                }
+                                /**
+                                 * @todo think about how to handle non-drafts
+                                 */
+                            } else if (studyState.equals(DatasetVersion.VersionState.RELEASED)) {
+//                                logger.fine("deaccessioning latest version of study " + study.getGlobalId());
+//                                studyService.deaccessionStudy(study.getLatestVersion());
+                            } else if (studyState.equals(DatasetVersion.VersionState.DEACCESSIONED)) {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Lastest version of study " + study.getGlobalId() + " has already been deaccessioned.");
+                            } else if (studyState.equals(DatasetVersion.VersionState.ARCHIVED)) {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Lastest version of study " + study.getGlobalId() + " has been archived and can not be deleted or deaccessioned.");
+                            } else if (studyState.equals(DatasetVersion.VersionState.IN_REVIEW)) {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Lastest version of study " + study.getGlobalId() + " is in review and can not be deleted or deaccessioned.");
+                            } else {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Operation not valid for study " + study.getGlobalId() + " in state " + studyState);
+                            }
+                        } else {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + vdcUser.getUserName() + " is not authorized to modify " + dvThatOwnsStudy.getAlias());
+                        }
+                    } else {
+                        throw new SwordError(404);
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study to delete from URL: " + uri);
+                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported delete target in URL:" + uri);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "No target for deletion specified");
+        }
+    }
+
+    @Override
+    public DepositReceipt useHeaders(String uri, Deposit deposit, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+        logger.fine("uri was " + uri);
+        logger.fine("isInProgress:" + deposit.isInProgress());
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        urlManager.processUrl(uri);
+        String targetType = urlManager.getTargetType();
+        if (!targetType.isEmpty()) {
+            logger.fine("operating on target type: " + urlManager.getTargetType());
+            if ("study".equals(targetType)) {
+                String globalId = urlManager.getTargetIdentifier();
+                if (globalId != null) {
+                    Dataset studyToRelease = null;
+                    try {
+//                        studyToRelease = studyService.getStudyByGlobalId(globalId);
+                    } catch (EJBException ex) {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
+                    }
+                    if (studyToRelease != null) {
+                        Dataverse dvThatOwnsStudy = studyToRelease.getOwner();
+                        if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
+                            if (!deposit.isInProgress()) {
+                                /**
+                                 * We are considering a draft version of a study
+                                 * to be incomplete and are saying that sending
+                                 * isInProgress=false means the study version is
+                                 * complete and can be released.
+                                 *
+                                 * 9.2. Deposit Incomplete
+                                 *
+                                 * "If In-Progress is true, the server SHOULD
+                                 * expect the client to provide further updates
+                                 * to the item some undetermined time in the
+                                 * future. Details of how this is implemented is
+                                 * dependent on the server's purpose. For
+                                 * example, a repository system may hold items
+                                 * which are marked In-Progress in a workspace
+                                 * until such time as a client request indicates
+                                 * that the deposit is complete." --
+                                 * http://swordapp.github.io/SWORDv2-Profile/SWORDProfile.html#continueddeposit_incomplete
+                                 */
+                                if (!studyToRelease.getLatestVersion().getVersionState().equals(DatasetVersion.VersionState.RELEASED)) {
+                                    /**
+                                     * @todo DVN 3.x had
+                                     * studyService.setReleased... what should
+                                     * we do in 4.0?
+                                     */
+//                                    studyService.setReleased(studyToRelease.getId());
+                                    ReceiptGenerator receiptGenerator = new ReceiptGenerator();
+                                    String baseUrl = urlManager.getHostnamePlusBaseUrlPath(uri);
+                                    DepositReceipt depositReceipt = receiptGenerator.createReceipt(baseUrl, studyToRelease);
+                                    return depositReceipt;
+                                } else {
+                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Latest version of dataset " + globalId + " has already been released.");
+                                }
+                            } else {
+                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Pass 'In-Progress: false' header to release a study.");
+                            }
+                        } else {
+                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + vdcUser.getUserName() + " is not authorized to modify dataverse " + dvThatOwnsStudy.getAlias());
+                        }
+                    } else {
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study using globalId " + globalId);
+                    }
+                } else {
+                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find globalId for study in URL:" + uri);
+                }
+            } else if ("dataverse".equals(targetType)) {
+                /**
+                 * @todo support releasing of dataverses via SWORD
+                 */
+//                String dvAlias = urlManager.getTargetIdentifier();
+//                if (dvAlias != null) {
+//                    VDC dvToRelease = vdcService.findByAlias(dvAlias);
+//                    if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvToRelease)) {
+//                        if (dvToRelease != null) {
+//                            String optionalPort = "";
+//                            URI u;
+//                            try {
+//                                u = new URI(uri);
+//                                int port = u.getPort();
+//                                if (port != -1) {
+//                                    // https often runs on port 8181 in dev
+//                                    optionalPort = ":" + port;
+//                                }
+//                            } catch (URISyntaxException ex) {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "unable to part URL");
+//                            }
+//                            String hostName = System.getProperty("dvn.inetAddress");
+//                            String dvHomePage = "https://" + hostName + optionalPort + "/dvn/dv/" + dvToRelease.getAlias();
+//                            if (deposit.isInProgress()) {
+//                                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Changing a dataverse to 'not released' is not supported. Please change to 'not released' from the web interface: " + dvHomePage);
+//                            } else {
+//                                try {
+//                                    getVDCRequestBean().setVdcNetwork(dvToRelease.getVdcNetwork());
+//                                } catch (ContextNotActiveException ex) {
+//                                    /**
+//                                     * todo: observe same rules about dataverse
+//                                     * release via web interface such as a study
+//                                     * or a collection must be release:
+//                                     * https://redmine.hmdc.harvard.edu/issues/3225
+//                                     */
+//                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Releasing a dataverse is not yet supported. Please release from the web interface: " + dvHomePage);
+//                                }
+//                                OptionsPage optionsPage = new OptionsPage();
+//                                if (optionsPage.isReleasable()) {
+//                                    if (dvToRelease.isRestricted()) {
+//                                        logger.fine("releasing dataverse via SWORD: " + dvAlias);
+//                                        /**
+//                                         * @todo: tweet and send email about
+//                                         * release
+//                                         */
+//                                        dvToRelease.setReleaseDate(DateUtil.getTimestamp());
+//                                        dvToRelease.setRestricted(false);
+//                                        vdcService.edit(dvToRelease);
+                DepositReceipt fakeDepositReceipt = new DepositReceipt();
+//                                        IRI fakeIri = new IRI("fakeIriDvWasJustReleased");
+//                                        fakeDepositReceipt.setEditIRI(fakeIri);
+//                                        fakeDepositReceipt.setVerboseDescription("Dataverse alias: " + dvAlias);
+                return fakeDepositReceipt;
+//                                    } else {
+//                                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Dataverse has already been released: " + dvAlias);
+//                                    }
+//                                } else {
+//                                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "dataverse is not releaseable");
+//                                }
+//                            }
+//                        } else {
+//                            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse based on alias in URL: " + uri);
+//                        }
+//                    } else {
+//                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + vdcUser.getUserName() + " is not authorized to modify dataverse " + dvAlias);
+//                    }
+//                } else {
+//                    throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to find dataverse alias in URL: " + uri);
+//                }
+            } else {
+                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "unsupported target type (" + targetType + ") in URL:" + uri);
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target type missing from URL: " + uri);
+        }
+    }
+
+    @Override
+    public boolean isStatementRequest(String uri, Map<String, String> map, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordError, SwordServerException, SwordAuthException {
+        DataverseUser vdcUser = swordAuth.auth(authCredentials);
+        urlManager.processUrl(uri);
+        String servlet = urlManager.getServlet();
+        if (servlet != null) {
+            if (servlet.equals("statement")) {
+                return true;
+            } else {
+                return false;
+            }
+        } else {
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to determine requested IRI from URL: " + uri);
+        }
+
+    }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java
new file mode 100644
index 00000000000..5973b190981
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java
@@ -0,0 +1,66 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import java.io.IOException;
+import javax.inject.Inject;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import org.swordapp.server.ContainerAPI;
+import org.swordapp.server.ContainerManager;
+import org.swordapp.server.StatementManager;
+import org.swordapp.server.servlets.SwordServlet;
+
+public class SWORDv2ContainerServlet extends SwordServlet {
+
+    @Inject
+    ContainerManagerImpl containerManagerImpl;
+    @Inject
+    StatementManagerImpl statementManagerImpl;
+    private ContainerManager cm;
+    private ContainerAPI api;
+    private StatementManager sm;
+
+    public void init() throws ServletException {
+        super.init();
+
+        // load the container manager implementation
+        this.cm = containerManagerImpl;
+
+        // load the statement manager implementation
+        this.sm = statementManagerImpl;
+
+        // initialise the underlying servlet processor
+        this.api = new ContainerAPI(this.cm, this.sm, this.config);
+    }
+
+    @Override
+    protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.get(req, resp);
+    }
+
+    @Override
+    protected void doHead(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.head(req, resp);
+    }
+
+    @Override
+    protected void doPut(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.put(req, resp);
+    }
+
+    @Override
+    protected void doPost(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.post(req, resp);
+    }
+
+    @Override
+    protected void doDelete(HttpServletRequest req, HttpServletResponse resp)
+            throws ServletException, IOException {
+        this.api.delete(req, resp);
+    }
+
+}
diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
index 14aeaa873a4..f2668fc79e0 100644
--- a/src/main/webapp/WEB-INF/web.xml
+++ b/src/main/webapp/WEB-INF/web.xml
@@ -138,6 +138,19 @@
         <url-pattern>/dvn/api/data-deposit/v1/swordv2/statement/*</url-pattern>
     </servlet-mapping>
 
+    <context-param>
+        <param-name>container-impl</param-name>
+        <param-value>edu.harvard.iq.dataverse.api.datadeposit.ContainerManagerImpl</param-value>
+    </context-param>
+    <servlet>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet</servlet-name>
+        <servlet-class>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet</servlet-class>
+    </servlet>
+    <servlet-mapping>
+        <servlet-name>edu.harvard.iq.dataverse.api.datadeposit.SWORDv2ContainerServlet</servlet-name>
+        <url-pattern>/dvn/api/data-deposit/v1/swordv2/edit/*</url-pattern>
+    </servlet-mapping>
+
     <!-- END Data Deposit API v1 (SWORD v2) -->
 
 </web-app>

From 97639c5b6d7def5e0aa0a98415b3b29d8a46e76e Mon Sep 17 00:00:00 2001
From: Michael Heppler <mheppler@hmdc.harvard.edu>
Date: Fri, 16 May 2014 12:58:23 -0400
Subject: [PATCH 35/46] Removed help text block from top of page and added new
 help text block to the bottom, just above the save/cancel buttons.

---
 src/main/java/edu/harvard/iq/dataverse/DatasetPage.java | 2 +-
 src/main/webapp/dataset.xhtml                           | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
index 600013712cc..9fb7fbbafcf 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -264,7 +264,7 @@ public void init() {
                     }
                 }
             }
-            FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_INFO, "Add New Dataset", " - Enter metadata to create the dataset's citation. You can add more metadata about this dataset after it's created."));
+            // FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_INFO, "Add New Dataset", " - Enter metadata to create the dataset's citation. You can add more metadata about this dataset after it's created."));
             displayVersion = editVersion;
         } else {
             throw new RuntimeException("On Dataset page without id or ownerid."); // improve error handling
diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml
index 47c8cc12164..b1080045ad7 100644
--- a/src/main/webapp/dataset.xhtml
+++ b/src/main/webapp/dataset.xhtml
@@ -442,6 +442,12 @@
                             </p:tabView>
                         </div>
                     </ui:fragment>
+                    
+                    <ui:fragment rendered="#{DatasetPage.editMode == 'CREATE'}">
+                        <div class="alert alert-info" style="margin-top:.5em;">
+                            Tip: You can add more metadata about this dataset after it's created.
+                        </div>
+                    </ui:fragment>
 
                     <!-- Create/Save Dataset Button Panel -->
                     <p:panel styleClass="panelLayoutButtonBlock" rendered="#{!empty DatasetPage.editMode}">

From a6d263edca5ca7d23822f3199e0f73cc77a7b56a Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Fri, 16 May 2014 15:26:17 -0400
Subject: [PATCH 36/46] stub out dataset lookup by globalId #3988

---
 scripts/api/data-deposit/delete-dataset       |  4 +--
 scripts/api/data-deposit/show-atom-entry      |  4 +--
 .../edu/harvard/iq/dataverse/Dataset.java     |  4 +++
 .../iq/dataverse/DatasetServiceBean.java      | 20 +++++++++++--
 .../CollectionDepositManagerImpl.java         |  4 ++-
 .../CollectionListManagerImpl.java            |  9 ++----
 .../api/datadeposit/ContainerManagerImpl.java | 28 +++----------------
 .../datadeposit/MediaResourceManagerImpl.java | 11 ++------
 .../api/datadeposit/ReceiptGenerator.java     |  5 +---
 .../api/datadeposit/StatementManagerImpl.java | 16 ++---------
 10 files changed, 40 insertions(+), 65 deletions(-)

diff --git a/scripts/api/data-deposit/delete-dataset b/scripts/api/data-deposit/delete-dataset
index 531b85ab649..13948758b7b 100755
--- a/scripts/api/data-deposit/delete-dataset
+++ b/scripts/api/data-deposit/delete-dataset
@@ -2,8 +2,8 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-GLOBAL_ID=hdl:TEST/12345
-DATABASE_ID=$1
+#GLOBAL_ID=hdl:TEST/12345
+GLOBAL_ID=`scripts/api/data-deposit/list-studies | xpath '//id/text()' | cut -d'/' -f11,12`
 #curl --insecure -X DELETE https://$DVN_SERVER/api/datasets/$DATABASE_ID?key=$USERNAME
 curl --insecure -i -X DELETE https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID
 #| xmllint -format -
diff --git a/scripts/api/data-deposit/show-atom-entry b/scripts/api/data-deposit/show-atom-entry
index d98a8b64f30..b1cc4cec006 100755
--- a/scripts/api/data-deposit/show-atom-entry
+++ b/scripts/api/data-deposit/show-atom-entry
@@ -2,7 +2,7 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-GLOBAL_ID=hdl:TEST/12345
-DATABASE_ID=$1
+#GLOBAL_ID=hdl:TEST/12345
+GLOBAL_ID=$1
 curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID \
 | xmllint -format -
diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataset.java b/src/main/java/edu/harvard/iq/dataverse/Dataset.java
index ee47d9d9c13..69b84f62c73 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Dataset.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Dataset.java
@@ -211,4 +211,8 @@ public <T> T accept(Visitor<T> v) {
         return v.visit(this);
     }
 
+    public String getGlobalId() {
+        return protocol + ":" + authority + "/" + getIdentifier();
+    }
+
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
index ac843229ec3..5ffff921859 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -49,7 +49,23 @@ public void generateFileSystemName(DataFile dataFile) {
         dataFile.setFileSystemName(result.toString());
 
     }
-    
-    
+
+    /**
+     * @todo write this method for real. Don't just iterate through every single
+     * dataset! See https://redmine.hmdc.harvard.edu/issues/3988
+     */
+    public Dataset findByGlobalId(String globalId) {
+        Dataset foundDataset = null;
+        if (globalId != null) {
+            Query query = em.createQuery("select object(o) from Dataset as o order by o.id");
+            List<Dataset> datasets = query.getResultList();
+            for (Dataset dataset : datasets) {
+                if (globalId.equals(dataset.getGlobalId())) {
+                    foundDataset = dataset;
+                }
+            }
+        }
+        return foundDataset;
+    }
 
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
index 6175456e15f..129e42b788b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
@@ -17,6 +17,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
+import java.util.UUID;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.inject.Inject;
@@ -127,8 +128,9 @@ public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCrede
                          */
                         Dataset dataset = new Dataset();
                         dataset.setOwner(dvThatWillOwnDataset);
-                        dataset.setIdentifier("myIdentifier");
                         dataset.setProtocol("myProtocol");
+                        dataset.setAuthority("myAuthority");
+                        dataset.setIdentifier(UUID.randomUUID().toString());
 
                         DatasetVersion newDatasetVersion = dataset.getVersions().get(0);
                         newDatasetVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
index ebcd67b4be0..c6b43f9ed19 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
@@ -65,13 +65,8 @@ public Feed listCollectionContents(IRI iri, AuthCredentials authCredentials, Swo
                     }
                     String baseUrl = urlManager.getHostnamePlusBaseUrlPath(iri.toString());
                     for (Dataset study : studies) {
-                        /**
-                         * @todo is globalId the same as identifier?
-                         */
-                        // String editUri = baseUrl + "/edit/study/" + study.getGlobalId();
-                        String editUri = baseUrl + "/edit/study/" + study.getIdentifier();
-                        // String editMediaUri = baseUrl + "/edit-media/study/" + study.getGlobalId();
-                        String editMediaUri = baseUrl + "/edit-media/study/" + study.getIdentifier();
+                        String editUri = baseUrl + "/edit/study/" + study.getGlobalId();
+                        String editMediaUri = baseUrl + "/edit-media/study/" + study.getGlobalId();
                         Entry entry = feed.addEntry();
                         entry.setId(editUri);
                         entry.setTitle(study.getLatestVersion().getTitle());
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
index fb1402a039e..cf1ee53e852 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
@@ -65,13 +65,7 @@ public DepositReceipt getEntry(String uri, Map<String, String> map, AuthCredenti
                 String globalId = urlManager.getTargetIdentifier();
                 Dataset dataset = null;
                 try {
-                    /**
-                     * @todo don't hard code this, obviously. In DVN 3.x we had
-                     * a method for studyService.getStudyByGlobalId(globalId)
-                     */
-//                    study = studyService.getStudyByGlobalId(globalId);
-                    long databaseIdForRoastingAtHomeDataset = 10;
-                    dataset = datasetService.find(databaseIdForRoastingAtHomeDataset);
+                    dataset = datasetService.findByGlobalId(globalId);
                 } catch (EJBException ex) {
                     throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
                 }
@@ -87,10 +81,7 @@ public DepositReceipt getEntry(String uri, Map<String, String> map, AuthCredenti
                             throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not generate deposit receipt.");
                         }
                     } else {
-                        /**
-                         * @todo need study.getGlobalId() from DVN 3.x
-                         */
-                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + dataverseUser.getUserName() + " is not authorized to retrieve entry for " + dataset.getIdentifier());
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "User " + dataverseUser.getUserName() + " is not authorized to retrieve entry for " + dataset.getGlobalId());
                     }
                 } else {
                     throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on URL: " + uri);
@@ -297,15 +288,7 @@ public void deleteContainer(String uri, AuthCredentials authCredentials, SwordCo
                 if (globalId != null) {
                     Dataset study = null;
                     try {
-
-                        /**
-                         * @todo don't hard code this, obviously. In DVN 3.x we
-                         * had a method for
-                         * studyService.getStudyByGlobalId(globalId)
-                         */
-//                        study = studyService.getStudyByGlobalId(globalId);
-                        long databaseIdForRoastingAtHomeDataset = 10;
-                        study = datasetService.find(databaseIdForRoastingAtHomeDataset);
+                        study = datasetService.findByGlobalId(globalId);
                     } catch (EJBException ex) {
                         throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study based on global id (" + globalId + ") in URL: " + uri);
                     }
@@ -314,10 +297,7 @@ public void deleteContainer(String uri, AuthCredentials authCredentials, SwordCo
                         if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
                             DatasetVersion.VersionState studyState = study.getLatestVersion().getVersionState();
                             if (studyState.equals(DatasetVersion.VersionState.DRAFT)) {
-                                /**
-                                 * @todo use getGlobalId when it's available
-                                 */
-                                logger.info("destroying working copy version of study " + study.getIdentifier());
+                                logger.info("destroying working copy version of study " + study.getGlobalId());
                                 /**
                                  * @todo in DVN 3.x we had a convenient
                                  * destroyWorkingCopyVersion method but the
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
index 95dc092576e..bef7b3e2261 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
@@ -93,8 +93,7 @@ public MediaResource getMediaResourceRepresentation(String uri, Map<String, Stri
                         MediaResource mediaResource = new MediaResource(fixmeInputStream, contentType, packaging, isPackaged);
                         return mediaResource;
                     } else {
-//                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to get a media resource representation of the study with global ID " + study.getGlobalId());
-                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to get a media resource representation of the dataset with identifier " + study.getIdentifier());
+                        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + vdcUser.getUserName() + " is not authorized to get a media resource representation of the dataset with global ID " + study.getGlobalId());
                     }
                 } else {
                     throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Please use the Dataverse Network Data Sharing API instead");
@@ -222,13 +221,7 @@ DepositReceipt replaceOrAddFiles(String uri, Deposit deposit, AuthCredentials au
                 throw new SwordServerException("problem looking up editStudyService");
             }
             logger.fine("looking up study with globalId " + globalId);
-            /**
-             * @todo don't hard code this, obviously. In DVN 3.x we had a method
-             * for editStudyService.getStudyByGlobalId(globalId)
-             */
-//            Study study = editStudyService.getStudyByGlobalId(globalId);
-            long databaseIdForRoastingAtHomeDataset = 10;
-            Dataset study = datasetService.find(databaseIdForRoastingAtHomeDataset);
+            Dataset study = datasetService.findByGlobalId(globalId);
             if (study == null) {
                 throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find study with global ID of " + globalId);
             }
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
index ab7107dd799..9ec1765efed 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
@@ -12,10 +12,7 @@ public class ReceiptGenerator {
     DepositReceipt createReceipt(String baseUrl, Dataset dataset) {
         logger.fine("baseUrl was: " + baseUrl);
         DepositReceipt depositReceipt = new DepositReceipt();
-        /**
-         * @todo is this same as globalId?
-         */
-        String globalId = dataset.getIdentifier();
+        String globalId = dataset.getGlobalId();
         /**
          * @todo should these URLs continue to have "study" in them? Do we need
          * to keep it as "study" for backwards compatibility or it ok to use
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
index 15f35864128..320c27298a2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
@@ -56,15 +56,7 @@ public Statement getStatement(String editUri, Map<String, String> map, AuthCrede
         if (urlManager.getTargetType().equals("study") && globalId != null) {
 
             logger.fine("request for sword statement by user " + vdcUser.getUserName());
-
-//            Study study = null;
-            /**
-             * @todo don't hard code this, obviously. In DVN 3.x we had a method
-             * for editStudyService.getStudyByGlobalId(globalId)
-             */
-//            Study study = editStudyService.getStudyByGlobalId(globalId);
-            long databaseIdForRoastingAtHomeDataset = 10;
-            Dataset study = datasetService.find(databaseIdForRoastingAtHomeDataset);
+            Dataset study = datasetService.findByGlobalId(globalId);
 //            try {
 //                study = studyService.getStudyByGlobalId(globalId);
 //            } catch (EJBException ex) {
@@ -79,11 +71,7 @@ public Statement getStatement(String editUri, Map<String, String> map, AuthCrede
 
             Dataverse dvThatOwnsStudy = study.getOwner();
             if (swordAuth.hasAccessToModifyDataverse(vdcUser, dvThatOwnsStudy)) {
-                /**
-                 * @todo getIdentifier is equivalent to getGlobalId, right?
-                 */
-//                String feedUri = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit/study/" + study.getGlobalId();
-                String feedUri = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit/study/" + study.getIdentifier();
+                String feedUri = urlManager.getHostnamePlusBaseUrlPath(editUri) + "/edit/study/" + study.getGlobalId();
                 /**
                  * @todo is it safe to use this?
                  */

From 7229e6442b5e945f1ed0ff27b3bb229f241fb50f Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Mon, 19 May 2014 08:56:30 -0400
Subject: [PATCH 37/46] rename list-studies script to list-datasets

---
 scripts/api/data-deposit/delete-dataset                  | 2 +-
 scripts/api/data-deposit/{list-studies => list-datasets} | 0
 scripts/api/data-deposit/show-statement                  | 2 +-
 scripts/api/data-deposit/upload-file                     | 2 +-
 4 files changed, 3 insertions(+), 3 deletions(-)
 rename scripts/api/data-deposit/{list-studies => list-datasets} (100%)

diff --git a/scripts/api/data-deposit/delete-dataset b/scripts/api/data-deposit/delete-dataset
index 13948758b7b..bcbee607f5f 100755
--- a/scripts/api/data-deposit/delete-dataset
+++ b/scripts/api/data-deposit/delete-dataset
@@ -3,7 +3,7 @@ USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
 #GLOBAL_ID=hdl:TEST/12345
-GLOBAL_ID=`scripts/api/data-deposit/list-studies | xpath '//id/text()' | cut -d'/' -f11,12`
+GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
 #curl --insecure -X DELETE https://$DVN_SERVER/api/datasets/$DATABASE_ID?key=$USERNAME
 curl --insecure -i -X DELETE https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID
 #| xmllint -format -
diff --git a/scripts/api/data-deposit/list-studies b/scripts/api/data-deposit/list-datasets
similarity index 100%
rename from scripts/api/data-deposit/list-studies
rename to scripts/api/data-deposit/list-datasets
diff --git a/scripts/api/data-deposit/show-statement b/scripts/api/data-deposit/show-statement
index 40167f231e5..9648c18df9b 100755
--- a/scripts/api/data-deposit/show-statement
+++ b/scripts/api/data-deposit/show-statement
@@ -2,7 +2,7 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-GLOBAL_ID=myIdentifier
+GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
 curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/statement/study/$GLOBAL_ID \
 | xmllint -format - \
 #| xpath '//entry/title'
diff --git a/scripts/api/data-deposit/upload-file b/scripts/api/data-deposit/upload-file
index 72c8b86304a..935f8a82fcd 100755
--- a/scripts/api/data-deposit/upload-file
+++ b/scripts/api/data-deposit/upload-file
@@ -2,6 +2,6 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-GLOBAL_ID=myIdentifier
+GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
 curl -s --insecure --data-binary @scripts/api/data-deposit/data/example.zip -H "Content-Disposition: filename=example.zip" -H "Content-Type: application/zip" -H "Packaging: http://purl.org/net/sword/package/SimpleZip" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit-media/study/$GLOBAL_ID \
 | xmllint -format -

From 5954c746873cf4770edaafbeab9c2d264500e678 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Mon, 19 May 2014 12:20:18 -0400
Subject: [PATCH 38/46] validate passwords via SWORD #3385

---
 scripts/api/data-deposit/service-document     |  2 +-
 .../dataverse/api/datadeposit/SwordAuth.java  | 20 +++++++++----------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/scripts/api/data-deposit/service-document b/scripts/api/data-deposit/service-document
index 6af8c9e2ef8..87ccdf8c18d 100755
--- a/scripts/api/data-deposit/service-document
+++ b/scripts/api/data-deposit/service-document
@@ -1,2 +1,2 @@
 #!/bin/bash
-curl --insecure https://pete:FIXME@localhost:8181/dvn/api/data-deposit/v1/swordv2/service-document | xmllint -format -
+curl --insecure https://pete:pete@localhost:8181/dvn/api/data-deposit/v1/swordv2/service-document | xmllint -format -
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java
index 4d4b16f99e9..849ea4b4e05 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordAuth.java
@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.Dataverse;
 import edu.harvard.iq.dataverse.DataverseUser;
 import edu.harvard.iq.dataverse.DataverseUserServiceBean;
+import edu.harvard.iq.dataverse.PasswordEncryption;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import org.swordapp.server.AuthCredentials;
@@ -24,18 +25,15 @@ public DataverseUser auth(AuthCredentials authCredentials) throws SwordAuthExcep
             logger.fine("Checking username " + username + " ...");
             DataverseUser dataverseUser = dataverseUserService.findByUserName(username);
             if (dataverseUser != null) {
-                /**
-                 * @todo actually check the user's password! Can't use
-                 * validateMethod on LoginPage.java since it's a backing bean...
-                 */
-//                if (dataverseUserService.validatePassword(username, password)) {
-                return dataverseUser;
-//                } else {
-//                    logger.info("wrong password");
-//                    throw new SwordAuthException();
-//                }
+                String encryptedPassword = PasswordEncryption.getInstance().encrypt(password);
+                if (encryptedPassword.equals(dataverseUser.getEncryptedPassword())) {
+                    return dataverseUser;
+                } else {
+                    logger.fine("wrong password");
+                    throw new SwordAuthException();
+                }
             } else {
-                logger.info("could not find username: " + username);
+                logger.fine("could not find username: " + username);
                 throw new SwordAuthException();
             }
         } else {

From 67214135d546bfec1663d2b9e2a106d118202c7d Mon Sep 17 00:00:00 2001
From: Leonid Andreev <leonid@hmdc.harvard.edu>
Date: Mon, 19 May 2014 15:38:09 -0400
Subject: [PATCH 39/46] log4.properties file - an attempt to get atmosphere
 runtime to shut up.

---
 src/main/java/log4j.properties | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 src/main/java/log4j.properties

diff --git a/src/main/java/log4j.properties b/src/main/java/log4j.properties
new file mode 100644
index 00000000000..9c08addaf9e
--- /dev/null
+++ b/src/main/java/log4j.properties
@@ -0,0 +1,23 @@
+log4j.rootLogger=FATAL, stderr
+
+# Base of all Jena classes
+log4j.logger.org.atmosphere=FATAL
+
+# Example of switching on debug level logging for part of tree
+# log4j.logger.com.hp.hpl.jena.graph.test=debug
+# log4j.logger.com.hp.hpl.jena.reasoner=debug
+# log4j.logger.com.hp.hpl.jena.reasoner.test=debug
+
+# Log format to standard out
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+# Pattern to output the caller's file name and line number.
+log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) - %m%n
+
+# Log format to standard error
+log4j.appender.stderr=org.apache.log4j.ConsoleAppender
+log4j.appender.stderr.target=System.err
+log4j.appender.stderr.layout=org.apache.log4j.PatternLayout
+# Pattern to output the caller's file name and line number.
+log4j.appender.stderr.layout.ConversionPattern=%5p [%t] (%F:%L) - %m%n
+

From 5dc1855abe957e0802892f1c0d48cb2c55560ed9 Mon Sep 17 00:00:00 2001
From: Michael Bar-Sinai <mich.barsinai@gmail.com>
Date: Tue, 20 May 2014 00:56:34 -0400
Subject: [PATCH 40/46] Round-trip json tests for DatasetFields PASSING

---
 scripts/api/data/dataset-sample1.json         | 182 ++++++++++++---
 .../iq/dataverse/util/DatasetFieldWalker.java |   8 +-
 .../iq/dataverse/util/json/JsonParser.java    |   9 +-
 .../iq/dataverse/util/json/JsonPrinter.java   |  16 +-
 .../dataverse/util/json/JsonParserTest.java   | 221 +++++-------------
 5 files changed, 231 insertions(+), 205 deletions(-)

diff --git a/scripts/api/data/dataset-sample1.json b/scripts/api/data/dataset-sample1.json
index 79d35126ab2..dd43fe4c394 100644
--- a/scripts/api/data/dataset-sample1.json
+++ b/scripts/api/data/dataset-sample1.json
@@ -1,48 +1,44 @@
 {
-  "authority": "anAuthority",
-  "identifier": "dataset-one",
-  "protocol": "chadham-house-rule",
-  "initialVersion": {
-    "authors": [
-      {
-        "displayOrder": 0,
-        "affiliation": {
-          "value": "IQSS"
-        },
-        "name": {
-          "value": "Castro, Eleni"
-        }
-      }
-    ],
-    "UNF": "UNF",
-    "title": "Replication Data for: Building a Bridge Between Journal Articles and Research Data",
-    "distributionDate": "Distribution Date",
-    "productionDate": "Production Date",
+  "data": {
     "metadataBlocks": {
       "citation": {
         "fields": [
           {
-            "value": "Replication Data for: Building a Bridge Between Journal Articles and Research Data",
+            "value": "sample dataset",
             "typeClass": "primitive",
             "multiple": false,
             "typeName": "title"
           },
           {
             "value": [
-              [
-                {
-                  "value": "Castro, Eleni",
+              {
+                "authorAffiliation": {
+                  "value": "Top",
                   "typeClass": "primitive",
                   "multiple": false,
-                  "typeName": "authorName"
+                  "typeName": "authorAffiliation"
                 },
-                {
-                  "value": "IQSS",
+                "authorName": {
+                  "value": "Privileged, Pete",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "authorName"
+                }
+              },
+              {
+                "authorAffiliation": {
+                  "value": "Coca-cola co",
                   "typeClass": "primitive",
                   "multiple": false,
                   "typeName": "authorAffiliation"
+                },
+                "authorName": {
+                  "value": "Borrator, Colla",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "authorName"
                 }
-              ]
+              }
             ],
             "typeClass": "compound",
             "multiple": true,
@@ -50,21 +46,23 @@
           },
           {
             "value": [
-              "ecastro@fas.harvard.edu"
+              "pete@malinator.com"
             ],
             "typeClass": "primitive",
             "multiple": true,
             "typeName": "distributorContact"
           },
           {
-            "value": "Research dataset for my publication on connecting journal articles and their underlying research data. Includes an analysis of current data publication practices.",
+            "value": "description description description description description description description description description ",
             "typeClass": "primitive",
             "multiple": false,
-            "typeName": "description"
+            "typeName": "dsDescription"
           },
           {
             "value": [
-              "data publication"
+              "Keyword1",
+              "KeywordTwo",
+              "TheThirdKeyWord"
             ],
             "typeClass": "primitive",
             "multiple": true,
@@ -78,6 +76,80 @@
             "multiple": true,
             "typeName": "subject"
           },
+          {
+            "value": "notes notes notes notes notes notes notes notes notes notes notes ",
+            "typeClass": "primitive",
+            "multiple": false,
+            "typeName": "notesText"
+          },
+          {
+            "value": [
+              {
+                "otherIdAgency": {
+                  "value": "otheridAgency",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "otherIdAgency"
+                },
+                "otherIdValue": {
+                  "value": "otherid",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "otherIdValue"
+                }
+              }
+            ],
+            "typeClass": "compound",
+            "multiple": true,
+            "typeName": "otherId"
+          },
+          {
+            "value": "2014-04-01",
+            "typeClass": "primitive",
+            "multiple": false,
+            "typeName": "productionDate"
+          },
+          {
+            "value": "2014-04-01",
+            "typeClass": "primitive",
+            "multiple": false,
+            "typeName": "productionPlace"
+          },
+          {
+            "value": [
+              {
+                "grantNumberAgency": {
+                  "value": "NSF",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "grantNumberAgency"
+                },
+                "grantNumberValue": {
+                  "value": "NSF12345",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "grantNumberValue"
+                }
+              },
+              {
+                "grantNumberAgency": {
+                  "value": "NIH",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "grantNumberAgency"
+                },
+                "grantNumberValue": {
+                  "value": "NIH99999",
+                  "typeClass": "primitive",
+                  "multiple": false,
+                  "typeName": "grantNumberValue"
+                }
+              }
+            ],
+            "typeClass": "compound",
+            "multiple": true,
+            "typeName": "grantNumber"
+          },
           {
             "value": "Privileged, Pete",
             "typeClass": "primitive",
@@ -85,14 +157,54 @@
             "typeName": "depositor"
           },
           {
-            "value": "2014-05-01",
+            "value": "2014-05-06",
             "typeClass": "primitive",
             "multiple": false,
             "typeName": "dateOfDeposit"
+          },
+          {
+            "value": [
+              "Other reference number one",
+              "Other reference number two"
+            ],
+            "typeClass": "primitive",
+            "multiple": true,
+            "typeName": "otherReferences"
           }
         ],
         "displayName": "Citation Metadata"
       }
-    }
-  }
-}
\ No newline at end of file
+    },
+    "authors": [
+      {
+        "displayOrder": 0,
+        "affiliation": {
+          "value": null
+        },
+        "name": {
+          "value": null
+        }
+      },
+      {
+        "displayOrder": 0,
+        "affiliation": {
+          "value": null
+        },
+        "name": {
+          "value": null
+        }
+      }
+    ],
+    "createTime": "2014-05-06 01:38:01 -04",
+    "UNF": "UNF",
+    "id": 4,
+    "version": 1,
+    "versionNumber": 1,
+    "versionMinorNumber": 0,
+    "versionState": "DRAFT",
+    "title": "sample dataset",
+    "distributionDate": "Distribution Date",
+    "productionDate": "Production Date"
+  },
+  "status": "OK"
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java b/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java
index 6e592a0532c..b437aa37d6e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java
@@ -5,6 +5,8 @@
 import edu.harvard.iq.dataverse.DatasetFieldCompoundValue;
 import edu.harvard.iq.dataverse.DatasetFieldType;
 import edu.harvard.iq.dataverse.DatasetFieldValue;
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 import java.util.SortedSet;
@@ -97,9 +99,9 @@ public void setL(Listener l) {
     }
     
     static private <T> Iterable<T> sort( List<T> list, Comparator<T> cmp ) {
-        SortedSet<T> ret = new TreeSet<>(cmp);
-        ret.addAll( list );
-        return ret;
+        ArrayList<T> tbs = new ArrayList<>(list);
+        Collections.sort(tbs, cmp);
+        return tbs;
     }
     
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
index b43aec1f42f..453c22c0471 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
@@ -165,10 +165,11 @@ public List<DatasetFieldCompoundValue> parseCompoundValue( DatasetFieldType comp
         if ( json.getBoolean("multiple") ) {
             List<DatasetFieldCompoundValue> vals = new LinkedList<>();
             
-            for ( JsonArray arr : json.getJsonArray("value").getValuesAs(JsonArray.class) ) {
+            for ( JsonObject obj : json.getJsonArray("value").getValuesAs(JsonObject.class) ) {
                 DatasetFieldCompoundValue cv = new DatasetFieldCompoundValue();
                 List<DatasetField> fields = new LinkedList<>();
-                for ( JsonObject childFieldJson : arr.getValuesAs(JsonObject.class) ) {
+                for ( String fieldName: obj.keySet() ) {
+                    JsonObject childFieldJson = obj.getJsonObject(fieldName);
                     DatasetField f = parseField( childFieldJson );
                     f.setParentDatasetFieldCompoundValue(cv);
                     fields.add( f );
@@ -183,7 +184,9 @@ public List<DatasetFieldCompoundValue> parseCompoundValue( DatasetFieldType comp
             
             DatasetFieldCompoundValue cv = new DatasetFieldCompoundValue();
             List<DatasetField> fields = new LinkedList<>();
-            for ( JsonObject childFieldJson : json.getJsonArray("value").getValuesAs(JsonObject.class) ) {
+            JsonObject value = json.getJsonObject("value");
+            for ( String key : value.keySet()  ) {
+                JsonObject childFieldJson = value.getJsonObject(key);
                 DatasetField f = parseField( childFieldJson );
                 f.setParentDatasetFieldCompoundValue(cv);
                 fields.add( f );
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
index e9309ee481b..27d370740e4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
@@ -30,11 +30,13 @@
 import java.util.TreeSet;
 
 import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
+import java.math.BigDecimal;
 import java.util.Deque;
 import java.util.LinkedList;
 import java.util.Map;
 import javax.json.JsonArray;
 import javax.json.JsonObject;
+import javax.json.JsonValue;
 
 /**
  * Convert objects to Json.
@@ -225,17 +227,15 @@ public static String typeClassString( DatasetFieldType typ ) {
         return "primitive";
     }
     
-	public static JsonObjectBuilder json( DatasetField dfv ) {
-		JsonObjectBuilder bld = jsonObjectBuilder();
+    public static JsonObject json( DatasetField dfv ) {
 		if ( dfv.isEmpty() ) {
-			bld.addNull("value");
-		} else {
+			return null;
+        } else {
             JsonArrayBuilder fieldArray = Json.createArrayBuilder();
             DatasetFieldWalker.walk(dfv, new DatasetFieldsToJson(fieldArray));
-            bld.add( "value", fieldArray.build().getJsonObject(0) );
+            JsonArray out = fieldArray.build();
+            return out.getJsonObject(0);
 		}
-		
-		return bld;
 	}
 	
 	public static JsonObjectBuilder json( MetadataBlock blk ) {
@@ -325,6 +325,8 @@ private static class DatasetFieldsToJson implements DatasetFieldWalker.Listener
 
         Deque<JsonObjectBuilder> objectStack = new LinkedList<>();
         Deque<JsonArrayBuilder>  valueArrStack = new LinkedList<>();
+        JsonObjectBuilder result = null;
+        
         
         DatasetFieldsToJson( JsonArrayBuilder result ) {
             valueArrStack.push(result);
diff --git a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java
index 0431c65ae04..605516dd206 100644
--- a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java
+++ b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java
@@ -6,7 +6,6 @@
 
 import edu.harvard.iq.dataverse.ControlledVocabularyValue;
 import edu.harvard.iq.dataverse.DatasetField;
-import edu.harvard.iq.dataverse.DatasetFieldCompoundValue;
 import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
 import edu.harvard.iq.dataverse.DatasetFieldType;
 import edu.harvard.iq.dataverse.DatasetFieldValue;
@@ -15,17 +14,17 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import javax.json.Json;
 import javax.json.JsonObject;
-import org.junit.After;
+import javax.json.JsonObjectBuilder;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 /**
  *
@@ -33,7 +32,7 @@
  */
 public class JsonParserTest {
     
-    MockDatasetFieldSvc mockDatasetFieldSvc = null;
+    MockDatasetFieldSvc datasetFieldSvc = null;
     DatasetFieldType keywordType;
     DatasetFieldType descriptionType;
     DatasetFieldType subjectType;
@@ -53,12 +52,12 @@ public static void tearDownClass() {
     
     @Before
     public void setUp() {
-        mockDatasetFieldSvc = new MockDatasetFieldSvc();
+        datasetFieldSvc = new MockDatasetFieldSvc();
 
-        keywordType = mockDatasetFieldSvc.add(new DatasetFieldType("keyword", "primitive", true));
-        descriptionType = mockDatasetFieldSvc.add( new DatasetFieldType("description", "primitive", false) );
+        keywordType = datasetFieldSvc.add(new DatasetFieldType("keyword", "primitive", true));
+        descriptionType = datasetFieldSvc.add( new DatasetFieldType("description", "primitive", false) );
         
-        subjectType = mockDatasetFieldSvc.add(new DatasetFieldType("subject", "controlledVocabulary", true));
+        subjectType = datasetFieldSvc.add(new DatasetFieldType("subject", "controlledVocabulary", true));
         subjectType.setAllowControlledVocabulary(true);
         subjectType.setControlledVocabularyValues( Arrays.asList( 
                 new ControlledVocabularyValue(1l, "mgmt", subjectType),
@@ -66,7 +65,7 @@ public void setUp() {
                 new ControlledVocabularyValue(3l, "cs", subjectType)
         ));
         
-        pubIdType = mockDatasetFieldSvc.add(new DatasetFieldType("publicationIdType", "controlledVocabulary", false));
+        pubIdType = datasetFieldSvc.add(new DatasetFieldType("publicationIdType", "controlledVocabulary", false));
         pubIdType.setAllowControlledVocabulary(true);
         pubIdType.setControlledVocabularyValues( Arrays.asList( 
                 new ControlledVocabularyValue(1l, "ark", pubIdType),
@@ -74,10 +73,10 @@ public void setUp() {
                 new ControlledVocabularyValue(3l, "url", pubIdType)
         ));
         
-        compoundSingleType = mockDatasetFieldSvc.add(new DatasetFieldType("coordinate", "compound", false));
+        compoundSingleType = datasetFieldSvc.add(new DatasetFieldType("coordinate", "compound", false));
         Set<DatasetFieldType> childTypes = new HashSet<>();
-        childTypes.add( mockDatasetFieldSvc.add(new DatasetFieldType("lat", "primitive", false)) );
-        childTypes.add( mockDatasetFieldSvc.add(new DatasetFieldType("lon", "primitive", false)) );
+        childTypes.add( datasetFieldSvc.add(new DatasetFieldType("lat", "primitive", false)) );
+        childTypes.add( datasetFieldSvc.add(new DatasetFieldType("lon", "primitive", false)) );
         
         for ( DatasetFieldType t : childTypes ) {
             t.setParentDatasetFieldType(compoundSingleType);
@@ -86,165 +85,68 @@ public void setUp() {
         
     }
     
-    @After
-    public void tearDown() {
-    }
-    /*
     @Test
-    public void testParseField_compound_single() throws JsonParseException {
-        JsonObject json = json("{\n" +
-                "  \"value\": [\n" +
-                "  {\n" +
-                "    \"value\": \"500.3\",\n" +
-                "    \"typeClass\": \"primitive\",\n" +
-                "    \"multiple\": false,\n" +
-                "    \"typeName\": \"lon\"\n" +
-                "    },\n" +
-                "    {\n" +
-                "      \"value\": \"300.3\",\n" +
-                "      \"typeClass\": \"primitive\",\n" +
-                "      \"multiple\": false,\n" +
-                "      \"typeName\": \"lat\"\n" +
-                "    }\n" +
-                "    ],\n" +
-                "    \"typeClass\": \"compound\",\n" +
-                "    \"multiple\": false,\n" +
-                "    \"typeName\": \"coordinate\"\n" +
-                "}");
-        
-        JsonParser instance = new JsonParser( mockDatasetFieldSvc, null );
-        
-        DatasetField result = instance.parseField(json);
-        
-        assertEquals( compoundSingleType, result.getDatasetFieldType() );
-        DatasetFieldCompoundValue val = result.getDatasetFieldCompoundValues().get(0);
-        DatasetField lon = new DatasetField();
-        lon.setDatasetFieldType( mockDatasetFieldSvc.findByName("lon"));
-        lon.setDatasetFieldValues( Collections.singletonList(new DatasetFieldValue(lon, "500.3")) );
-
-        DatasetField lat = new DatasetField();
-        lat.setDatasetFieldType( mockDatasetFieldSvc.findByName("lat"));
-        lat.setDatasetFieldValues( Collections.singletonList(new DatasetFieldValue(lat, "300.3")) );
-        
-        List<DatasetField> actual = val.getChildDatasetFields();
-        assertEquals( lon, actual.get(0) );
-        assertEquals( lat, actual.get(1) );
+    public void testPrimitiveNoRepeatesFieldRoundTrip() throws JsonParseException {
+        DatasetField expected = new DatasetField();
+        expected.setDatasetFieldType( datasetFieldSvc.findByName("description") );
+        expected.setDatasetFieldValues( Collections.singletonList(new DatasetFieldValue(expected, "This is a description value")) );
+        JsonObject json = JsonPrinter.json(expected);
+        JsonParser sut = new JsonParser(datasetFieldSvc, null);
+        System.out.println("json = " + json);
+        DatasetField actual = sut.parseField(json);
+        
+        assertFieldsEqual(actual, expected);
     }
     
     @Test
-    public void testParseField_controlled_single() throws JsonParseException {
-        JsonObject json = json("{\n" +
-"            \"value\": \"ark\",\n" +
-"            \"typeClass\": \"controlledVocabulary\",\n" +
-"            \"multiple\": false,\n" +
-"            \"typeName\": \"publicationIdType\"\n" +
-"          }");
-        
-        JsonParser instance = new JsonParser( mockDatasetFieldSvc, null );
-        
-        DatasetField result = instance.parseField(json);
-        
-        assertEquals( pubIdType, result.getDatasetFieldType() );
-        assertEquals( pubIdType.getControlledVocabularyValue("ark"), result.getSingleControlledVocabularyValue() );
-        
-    }
-
-    @Test
-    public void testParseField_controlled_multi() throws JsonParseException {
-        JsonObject json = json("{\n" +
-"            \"value\": [\n" +
-"              \"mgmt\",\n" +
-"              \"cs\"\n" +
-"            ],\n" +
-"            \"typeClass\": \"controlledVocabulary\",\n" +
-"            \"multiple\": true,\n" +
-"            \"typeName\": \"subject\"\n" +
-"          }");
-        
-        JsonParser instance = new JsonParser( mockDatasetFieldSvc, null );
-        
-        DatasetField result = instance.parseField(json);
-        
-        assertEquals( subjectType, result.getDatasetFieldType() );
-        assertEquals( Arrays.asList( subjectType.getControlledVocabularyValue("mgmt"),
-                                     subjectType.getControlledVocabularyValue("cs")),
-                      result.getControlledVocabularyValues()
-        );
-        
-    }
-
-    */
-    /**
-     * Test of parsePrimitiveField method, of class JsonParser.
-     */
-    /*
-    @Test
-    public void testParseField_primitive_multi() throws JsonParseException {
-        JsonObject json = json("{\n" +
-"            \"value\": [\n" +
-"              \"data\",\n" +
-"              \"set\",\n" +
-"              \"sample\"\n" +
-"            ],\n" +
-"            \"typeClass\": \"primitive\",\n" +
-"            \"multiple\": true,\n" +
-"            \"typeName\": \"keyword\"\n" +
-"          }");
-        
-        JsonParser instance = new JsonParser( mockDatasetFieldSvc, null );
-        
-        DatasetField result = instance.parseField(json);
-        
-        assertEquals( keywordType, result.getDatasetFieldType() );
-        assertEquals( Arrays.asList("data","set","sample"), result.getValues() );
+    public void testPrimitiveRepeatesFieldRoundTrip() throws JsonParseException {
+        DatasetField expected = new DatasetField();
+        expected.setDatasetFieldType( datasetFieldSvc.findByName("keyword") );
+        expected.setDatasetFieldValues( Arrays.asList(new DatasetFieldValue(expected, "kw1"),
+                new DatasetFieldValue(expected, "kw2"),
+                new DatasetFieldValue(expected, "kw3")) );
+        JsonObject json = JsonPrinter.json(expected);
+        JsonParser sut = new JsonParser(datasetFieldSvc, null);
+        System.out.println("json = " + json);
+        DatasetField actual = sut.parseField(json);
+        
+        assertFieldsEqual(actual, expected);
     }
     
-    @Test
-    public void testParseField_primitive_single() throws JsonParseException {
-        JsonObject json = json("{\n" +
-"            \"value\": \"data\",\n" +
-"            \"typeClass\": \"primitive\",\n" +
-"            \"multiple\": false,\n" +
-"            \"typeName\": \"description\"\n" +
-"          }");
-        
-        JsonParser instance = new JsonParser( mockDatasetFieldSvc, null );
-        
-        DatasetField result = instance.parseField(json);
-        
-        assertEquals( descriptionType, result.getDatasetFieldType() );
-        assertEquals( "data", result.getValue() );
-        
-    }
-    
-    @Test(expected=JsonParseException.class)
-    public void testParseField_primitive_NEType() throws JsonParseException {
-        JsonObject json = json("{\n" +
-"            \"value\": \"data\",\n" +
-"            \"typeClass\": \"primitive\",\n" +
-"            \"multiple\": false,\n" +
-"            \"typeName\": \"no-such-type\"\n" +
-"          }");
-        
-        JsonParser instance = new JsonParser( mockDatasetFieldSvc, null );
-        
-        DatasetField result = instance.parseField(json);
-        
-        assertEquals( descriptionType, result.getDatasetFieldType() );
-        assertEquals( "data", result.getValue() );
-        
-    }
-    */
-    
     JsonObject json( String s ) {
         return Json.createReader( new StringReader(s) ).readObject();
     }
     
+    public boolean assertFieldsEqual( DatasetField ex, DatasetField act ) {
+        if ( ex == act ) return true;
+        if ( (ex == null) ^ (act==null) ) return false;
+        
+        // type
+        if ( ! ex.getDatasetFieldType().equals(act.getDatasetFieldType()) ) return false;
+        if ( ex.getDatasetFieldType().isPrimitive() ) {
+            List<DatasetFieldValue> exVals = ex.getDatasetFieldValues();
+            List<DatasetFieldValue> actVals = act.getDatasetFieldValues();
+            if ( exVals.size() != actVals.size() ) return false;
+            Iterator<DatasetFieldValue> exItr = exVals.iterator();
+            for ( DatasetFieldValue actVal : actVals ) {
+                DatasetFieldValue exVal = exItr.next();
+                if ( ! exVal.getValue().equals(actVal.getValue()) ) {
+                    return false;
+                }
+            }
+            return true;
+        }
+        return false; // not implemented, really.
+    }
+    
     static class MockDatasetFieldSvc extends DatasetFieldServiceBean {
         
         Map<String, DatasetFieldType> fieldTypes = new HashMap<>();
-        
+        long nextId = 1;
         public DatasetFieldType add( DatasetFieldType t ) {
+            if ( t.getId()==null ) {
+                t.setId( nextId++ );
+            }
             fieldTypes.put( t.getName(), t);
             return t;
         }
@@ -253,5 +155,10 @@ public DatasetFieldType add( DatasetFieldType t ) {
         public DatasetFieldType findByName( String name ) {
             return fieldTypes.get(name);
         }
+        
+        @Override
+        public DatasetFieldType findByNameOpt( String name ) {
+            return findByName( name );
+        }
     }
 }

From 40160f50e34a3e681479a4592e8643c14cf080c9 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 20 May 2014 08:55:14 -0400
Subject: [PATCH 41/46] get globalId automatically

---
 scripts/api/data-deposit/show-atom-entry | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/api/data-deposit/show-atom-entry b/scripts/api/data-deposit/show-atom-entry
index b1cc4cec006..bd0c588213d 100755
--- a/scripts/api/data-deposit/show-atom-entry
+++ b/scripts/api/data-deposit/show-atom-entry
@@ -3,6 +3,6 @@ USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
 #GLOBAL_ID=hdl:TEST/12345
-GLOBAL_ID=$1
+GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
 curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID \
 | xmllint -format -

From 4db2f8f25d1ef2d2c420ff72d475360279d226e5 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 20 May 2014 11:17:43 -0400
Subject: [PATCH 42/46] enable citation and persistent URL in deposit receipt
 #3385

---
 .../datadeposit/CollectionDepositManagerImpl.java |  8 +++++++-
 .../api/datadeposit/ReceiptGenerator.java         | 15 +++++++--------
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
index 129e42b788b..6348d16e875 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
@@ -128,7 +128,13 @@ public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCrede
                          */
                         Dataset dataset = new Dataset();
                         dataset.setOwner(dvThatWillOwnDataset);
-                        dataset.setProtocol("myProtocol");
+                        /**
+                         * @todo don't hard code these! See also saving a
+                         * dataset in GUI changes globalId to hard coded value
+                         * (doi:10.5072/FK2/5555)
+                         * https://redmine.hmdc.harvard.edu/issues/3993
+                         */
+                        dataset.setProtocol("doi");
                         dataset.setAuthority("myAuthority");
                         dataset.setIdentifier(UUID.randomUUID().toString());
 
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
index 9ec1765efed..6f55b594adc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ReceiptGenerator.java
@@ -16,25 +16,24 @@ DepositReceipt createReceipt(String baseUrl, Dataset dataset) {
         /**
          * @todo should these URLs continue to have "study" in them? Do we need
          * to keep it as "study" for backwards compatibility or it ok to use
-         * "dataset"?
+         * "dataset"? http://irclog.iq.harvard.edu/dvn/2014-05-14#i_9404
          */
         String editIri = baseUrl + "/edit/study/" + globalId;
         depositReceipt.setEditIRI(new IRI(editIri));
         /**
          * @todo: should setLocation depend on if an atom entry or a zip file
-         * was deposited?
+         * was deposited? (This @todo has been carried over from the DVN 3.x
+         * version.)
          */
         depositReceipt.setLocation(new IRI(editIri));
         depositReceipt.setEditMediaIRI(new IRI(baseUrl + "/edit-media/study/" + globalId));
         depositReceipt.setStatementURI("application/atom+xml;type=feed", baseUrl + "/statement/study/" + globalId);
+        depositReceipt.addDublinCore("bibliographicCitation", dataset.getLatestVersion().getCitation());
         /**
-         * @todo re-enable bibliographicCitation
+         * @todo is this still returning the database id?
+         * https://redmine.hmdc.harvard.edu/issues/3397 ?
          */
-//        depositReceipt.addDublinCore("bibliographicCitation", study.getLatestVersion().getMetadata().getCitation(false));
-        /**
-         * @todo re-enable this
-         */
-//        depositReceipt.setSplashUri(study.getPersistentURL());
+        depositReceipt.setSplashUri(dataset.getPersistentURL());
         return depositReceipt;
     }
 

From 5d7a99a66738b4c14e586a81afb722635af7c553 Mon Sep 17 00:00:00 2001
From: Michael Bar-Sinai <mich.barsinai@gmail.com>
Date: Tue, 20 May 2014 11:35:19 -0400
Subject: [PATCH 43/46] DatasetField i/o unit tests passing

---
 .../dataverse/util/json/JsonParserTest.java   | 123 +++++++++++++++---
 1 file changed, 106 insertions(+), 17 deletions(-)

diff --git a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java
index 605516dd206..c72bff41333 100644
--- a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java
+++ b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonParserTest.java
@@ -6,6 +6,7 @@
 
 import edu.harvard.iq.dataverse.ControlledVocabularyValue;
 import edu.harvard.iq.dataverse.DatasetField;
+import edu.harvard.iq.dataverse.DatasetFieldCompoundValue;
 import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
 import edu.harvard.iq.dataverse.DatasetFieldType;
 import edu.harvard.iq.dataverse.DatasetFieldValue;
@@ -15,12 +16,12 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import javax.json.Json;
 import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -32,12 +33,13 @@
  */
 public class JsonParserTest {
     
-    MockDatasetFieldSvc datasetFieldSvc = null;
+    MockDatasetFieldSvc datasetFieldTypeSvc = null;
     DatasetFieldType keywordType;
     DatasetFieldType descriptionType;
     DatasetFieldType subjectType;
     DatasetFieldType pubIdType;
     DatasetFieldType compoundSingleType;
+    JsonParser sut;
     
     public JsonParserTest() {
     }
@@ -52,12 +54,12 @@ public static void tearDownClass() {
     
     @Before
     public void setUp() {
-        datasetFieldSvc = new MockDatasetFieldSvc();
+        datasetFieldTypeSvc = new MockDatasetFieldSvc();
 
-        keywordType = datasetFieldSvc.add(new DatasetFieldType("keyword", "primitive", true));
-        descriptionType = datasetFieldSvc.add( new DatasetFieldType("description", "primitive", false) );
+        keywordType = datasetFieldTypeSvc.add(new DatasetFieldType("keyword", "primitive", true));
+        descriptionType = datasetFieldTypeSvc.add( new DatasetFieldType("description", "primitive", false) );
         
-        subjectType = datasetFieldSvc.add(new DatasetFieldType("subject", "controlledVocabulary", true));
+        subjectType = datasetFieldTypeSvc.add(new DatasetFieldType("subject", "controlledVocabulary", true));
         subjectType.setAllowControlledVocabulary(true);
         subjectType.setControlledVocabularyValues( Arrays.asList( 
                 new ControlledVocabularyValue(1l, "mgmt", subjectType),
@@ -65,7 +67,7 @@ public void setUp() {
                 new ControlledVocabularyValue(3l, "cs", subjectType)
         ));
         
-        pubIdType = datasetFieldSvc.add(new DatasetFieldType("publicationIdType", "controlledVocabulary", false));
+        pubIdType = datasetFieldTypeSvc.add(new DatasetFieldType("publicationIdType", "controlledVocabulary", false));
         pubIdType.setAllowControlledVocabulary(true);
         pubIdType.setControlledVocabularyValues( Arrays.asList( 
                 new ControlledVocabularyValue(1l, "ark", pubIdType),
@@ -73,26 +75,83 @@ public void setUp() {
                 new ControlledVocabularyValue(3l, "url", pubIdType)
         ));
         
-        compoundSingleType = datasetFieldSvc.add(new DatasetFieldType("coordinate", "compound", false));
+        compoundSingleType = datasetFieldTypeSvc.add(new DatasetFieldType("coordinate", "compound", true));
         Set<DatasetFieldType> childTypes = new HashSet<>();
-        childTypes.add( datasetFieldSvc.add(new DatasetFieldType("lat", "primitive", false)) );
-        childTypes.add( datasetFieldSvc.add(new DatasetFieldType("lon", "primitive", false)) );
+        childTypes.add( datasetFieldTypeSvc.add(new DatasetFieldType("lat", "primitive", false)) );
+        childTypes.add( datasetFieldTypeSvc.add(new DatasetFieldType("lon", "primitive", false)) );
         
         for ( DatasetFieldType t : childTypes ) {
             t.setParentDatasetFieldType(compoundSingleType);
         }
         compoundSingleType.setChildDatasetFieldTypes(childTypes);
+        sut = new JsonParser(datasetFieldTypeSvc, null);
+    }
+    
+    @Test
+    public void testCompoundRepeatsRoundtrip() throws JsonParseException {
+        DatasetField expected = new DatasetField();
+        expected.setDatasetFieldType( datasetFieldTypeSvc.findByName("coordinate") );
+        List<DatasetFieldCompoundValue> vals = new LinkedList<>();
+        for ( int i=0; i<5; i++ ) {
+            DatasetFieldCompoundValue val = new DatasetFieldCompoundValue();
+            val.setParentDatasetField(expected);
+            val.setChildDatasetFields( Arrays.asList(latLonField("lat", Integer.toString(i*10)), latLonField("lon", Integer.toString(3+i*10))));
+            vals.add( val );
+        }
+        expected.setDatasetFieldCompoundValues(vals);
+        
+        JsonObject json = JsonPrinter.json(expected);
+        
+        System.out.println("json = " + json);
+        
+        DatasetField actual = sut.parseField(json);
         
+        assertFieldsEqual(expected, actual);
     }
     
+    DatasetField latLonField( String latLon, String value ) {
+        DatasetField retVal = new DatasetField();
+        retVal.setDatasetFieldType( datasetFieldTypeSvc.findByName(latLon));
+        retVal.setDatasetFieldValues( Collections.singletonList( new DatasetFieldValue(retVal, value)));
+        return retVal;
+    }
+    
+    @Test 
+    public void testControlledVocalNoRepeatsRoundTrip() throws JsonParseException {
+        DatasetField expected = new DatasetField();
+        DatasetFieldType fieldType = datasetFieldTypeSvc.findByName("publicationIdType");
+        expected.setDatasetFieldType( fieldType );
+        expected.setControlledVocabularyValues( Collections.singletonList( fieldType.getControlledVocabularyValue("ark")));
+        JsonObject json = JsonPrinter.json(expected);
+        
+        DatasetField actual = sut.parseField(json);
+        assertFieldsEqual(expected, actual);
+        
+    }
+    
+    @Test 
+    public void testControlledVocalRepeatsRoundTrip() throws JsonParseException {
+        DatasetField expected = new DatasetField();
+        DatasetFieldType fieldType = datasetFieldTypeSvc.findByName("subject");
+        expected.setDatasetFieldType( fieldType );
+        expected.setControlledVocabularyValues( Arrays.asList( fieldType.getControlledVocabularyValue("mgmt"),
+                 fieldType.getControlledVocabularyValue("law"),
+                 fieldType.getControlledVocabularyValue("cs")));
+        
+        JsonObject json = JsonPrinter.json(expected);
+        DatasetField actual = sut.parseField(json);
+        assertFieldsEqual(expected, actual);
+        
+    }
+    
+    
     @Test
     public void testPrimitiveNoRepeatesFieldRoundTrip() throws JsonParseException {
         DatasetField expected = new DatasetField();
-        expected.setDatasetFieldType( datasetFieldSvc.findByName("description") );
+        expected.setDatasetFieldType( datasetFieldTypeSvc.findByName("description") );
         expected.setDatasetFieldValues( Collections.singletonList(new DatasetFieldValue(expected, "This is a description value")) );
         JsonObject json = JsonPrinter.json(expected);
-        JsonParser sut = new JsonParser(datasetFieldSvc, null);
-        System.out.println("json = " + json);
+        
         DatasetField actual = sut.parseField(json);
         
         assertFieldsEqual(actual, expected);
@@ -101,13 +160,12 @@ public void testPrimitiveNoRepeatesFieldRoundTrip() throws JsonParseException {
     @Test
     public void testPrimitiveRepeatesFieldRoundTrip() throws JsonParseException {
         DatasetField expected = new DatasetField();
-        expected.setDatasetFieldType( datasetFieldSvc.findByName("keyword") );
+        expected.setDatasetFieldType( datasetFieldTypeSvc.findByName("keyword") );
         expected.setDatasetFieldValues( Arrays.asList(new DatasetFieldValue(expected, "kw1"),
                 new DatasetFieldValue(expected, "kw2"),
                 new DatasetFieldValue(expected, "kw3")) );
         JsonObject json = JsonPrinter.json(expected);
-        JsonParser sut = new JsonParser(datasetFieldSvc, null);
-        System.out.println("json = " + json);
+        
         DatasetField actual = sut.parseField(json);
         
         assertFieldsEqual(actual, expected);
@@ -123,6 +181,7 @@ public boolean assertFieldsEqual( DatasetField ex, DatasetField act ) {
         
         // type
         if ( ! ex.getDatasetFieldType().equals(act.getDatasetFieldType()) ) return false;
+        
         if ( ex.getDatasetFieldType().isPrimitive() ) {
             List<DatasetFieldValue> exVals = ex.getDatasetFieldValues();
             List<DatasetFieldValue> actVals = act.getDatasetFieldValues();
@@ -135,8 +194,38 @@ public boolean assertFieldsEqual( DatasetField ex, DatasetField act ) {
                 }
             }
             return true;
+            
+        } else if ( ex.getDatasetFieldType().isControlledVocabulary() ) {
+            List<ControlledVocabularyValue> exVals = ex.getControlledVocabularyValues();
+            List<ControlledVocabularyValue> actVals = act.getControlledVocabularyValues();
+            if ( exVals.size() != actVals.size() ) return false;
+            Iterator<ControlledVocabularyValue> exItr = exVals.iterator();
+            for ( ControlledVocabularyValue actVal : actVals ) {
+                ControlledVocabularyValue exVal = exItr.next();
+                if ( ! exVal.getId().equals(actVal.getId()) ) {
+                    return false;
+                }
+            }
+            return true;
+            
+        } else if ( ex.getDatasetFieldType().isCompound() ) {
+            List<DatasetFieldCompoundValue> exVals = ex.getDatasetFieldCompoundValues();
+            List<DatasetFieldCompoundValue> actVals = act.getDatasetFieldCompoundValues();
+            if ( exVals.size() != actVals.size() ) return false;
+            Iterator<DatasetFieldCompoundValue> exItr = exVals.iterator();
+            for ( DatasetFieldCompoundValue actVal : actVals ) {
+                DatasetFieldCompoundValue exVal = exItr.next();
+                Iterator<DatasetField> exChildItr = exVal.getChildDatasetFields().iterator();
+                Iterator<DatasetField> actChildItr = actVal.getChildDatasetFields().iterator();
+                while( exChildItr.hasNext() ) {
+                    assertFieldsEqual(exChildItr.next(), actChildItr.next());
+                }
+            }
+            return true;
+            
         }
-        return false; // not implemented, really.
+        
+        throw new IllegalArgumentException("Unknown dataset field type '" + ex.getDatasetFieldType() + "'");
     }
     
     static class MockDatasetFieldSvc extends DatasetFieldServiceBean {

From 3aa80d484eb564c14ca4a8d210eccfc6c6cd17b3 Mon Sep 17 00:00:00 2001
From: Philip Durbin <philip_durbin@harvard.edu>
Date: Tue, 20 May 2014 12:20:58 -0400
Subject: [PATCH 44/46] lastupdatetime is always null. fall back to
 alternatives #3385

---
 .../api/datadeposit/StatementManagerImpl.java | 26 ++++++++++++++-----
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
index 320c27298a2..8b7eeed0658 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
@@ -77,16 +77,28 @@ public Statement getStatement(String editUri, Map<String, String> map, AuthCrede
                  */
                 String author = study.getLatestVersion().getAuthorsStr();
                 String title = study.getLatestVersion().getTitle();
-                Date lastUpdated = study.getLatestVersion().getLastUpdateTime();
-                if (lastUpdated == null) {
+                // in the statement, the element is called "updated"
+                Date lastUpdatedFinal = new Date();
+                Date lastUpdateTime = study.getLatestVersion().getLastUpdateTime();
+                if (lastUpdateTime != null) {
+                    lastUpdatedFinal = lastUpdateTime;
+                } else {
                     /**
-                     * @todo why is this date null?
+                     * @todo In DVN 3.x lastUpdated was set on the service bean:
+                     * https://github.com/IQSS/dvn/blob/8ca34aded90511730c35ca32ace844770c24c68e/DVN-root/DVN-web/src/main/java/edu/harvard/iq/dvn/core/study/StudyServiceBean.java#L1803
+                     *
+                     * In 4.0, lastUpdateTime is always null.
                      */
-                    logger.info("why is lastUpdated null?");
-                    lastUpdated = new Date();
+                    logger.info("lastUpdateTime was null, trying createtime");
+                    Date createtime = study.getLatestVersion().getCreateTime();
+                    if (createtime != null) {
+                        lastUpdatedFinal = createtime;
+                    } else {
+                        logger.info("creatime was null, using \"now\"");
+                        lastUpdatedFinal = new Date();
+                    }
                 }
-                AtomDate atomDate = new AtomDate(lastUpdated);
-//                AtomDate atomDate = new AtomDate(study.getLatestVersion().getLastUpdateTime());
+                AtomDate atomDate = new AtomDate(lastUpdatedFinal);
                 String datedUpdated = atomDate.toString();
                 Statement statement = new AtomStatement(feedUri, author, title, datedUpdated);
                 Map<String, String> states = new HashMap<String, String>();

From cce8ae2fd46365eb6eeb34586b04080eb08416f9 Mon Sep 17 00:00:00 2001
From: Gustavo Durand <gdurand@iq.harvard.edu>
Date: Tue, 20 May 2014 14:11:37 -0400
Subject: [PATCH 45/46] added Add data button for when you are not logged in

---
 src/main/webapp/search-include-fragment.xhtml | 59 +++++++++++++------
 1 file changed, 41 insertions(+), 18 deletions(-)

diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml
index 2117b8e8295..a2568f6ca62 100644
--- a/src/main/webapp/search-include-fragment.xhtml
+++ b/src/main/webapp/search-include-fragment.xhtml
@@ -26,27 +26,50 @@
                     </h:outputLink>
                 </h:form>
             </ui:fragment>
-
-            <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand')
-                                     or permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand')  }">
-                <h:form id="shareForm">
-                    <div class="btn-group">
-                        <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
+            
+                <ui:fragment rendered="#{dataverseSession.user.guest and (dataverse.owner == null or dataverse.alias.endsWith('_open'))}">
+                    <div style="float:right;">
+                        <button type="button" class="btn btn-default" onclick="addData_popup.show()">
                             <span class="glyphicon glyphicon-plus"/> Add Data <span class="caret"></span>
                         </button>
-                        <ul class="dropdown-menu pull-right text-left" role="menu">
-                            <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand') }">
-                                <li><a href="/dataverse.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataverse</a></li>
-                            </ui:fragment>
-                            <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand') }">
-                                <li><a href="/dataset.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataset</a></li>
-                            </ui:fragment>
-                            <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataverse</a></li>-->
-                            <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataset</a></li>-->
-                        </ul>
                     </div>
-                </h:form>
-            </ui:fragment>
+                    <p:confirmDialog message="You must be logged in to create a dataverse or add a dataset."  header="Add data" widgetVar="addData_popup">                                           
+                        <ul>
+                            <li>
+                                <h:outputLink value="/dataverseuser.xhtml?editMode=CREATE">
+                                    Sign Up
+                                </h:outputLink>
+                            </li>
+                            <li>
+                                <h:outputLink value="/loginpage.xhtml">
+                                    Log In
+                                </h:outputLink>
+                            </li>
+                        </ul>
+
+                    </p:confirmDialog>  
+                </ui:fragment>
+
+                <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand')
+                                         or permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand')  }">
+                    <h:form id="shareForm">
+                        <div class="btn-group">
+                            <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
+                                <span class="glyphicon glyphicon-plus"/> Add Data <span class="caret"></span>
+                            </button>
+                            <ul class="dropdown-menu pull-right text-left" role="menu">
+                                <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand') }">
+                                    <li><a href="/dataverse.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataverse</a></li>
+                                </ui:fragment>
+                                <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand') }">
+                                    <li><a href="/dataset.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataset</a></li>
+                                </ui:fragment>
+                                <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataverse</a></li>-->
+                                <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataset</a></li>-->
+                            </ul>
+                        </div>
+                    </h:form>
+                </ui:fragment>
         </p:panelGrid>
     </p:panel>
     <!-- Search Results -->

From c6204f41784cff54aa9befbc01089c6e8d65b1c2 Mon Sep 17 00:00:00 2001
From: Gustavo Durand <gdurand@iq.harvard.edu>
Date: Tue, 20 May 2014 15:50:12 -0400
Subject: [PATCH 46/46] Cleaned up text in Add Data popup

---
 src/main/webapp/search-include-fragment.xhtml | 73 ++++++++-----------
 1 file changed, 32 insertions(+), 41 deletions(-)

diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml
index a2568f6ca62..f857f565ff1 100644
--- a/src/main/webapp/search-include-fragment.xhtml
+++ b/src/main/webapp/search-include-fragment.xhtml
@@ -26,50 +26,41 @@
                     </h:outputLink>
                 </h:form>
             </ui:fragment>
-            
-                <ui:fragment rendered="#{dataverseSession.user.guest and (dataverse.owner == null or dataverse.alias.endsWith('_open'))}">
-                    <div style="float:right;">
-                        <button type="button" class="btn btn-default" onclick="addData_popup.show()">
+
+            <ui:fragment rendered="#{dataverseSession.user.guest and (dataverse.owner == null or dataverse.alias.endsWith('_open'))}">
+                <div style="float:right;">
+                    <button type="button" class="btn btn-default" onclick="addData_popup.show()">
+                        <span class="glyphicon glyphicon-plus"/> Add Data <span class="caret"></span>
+                    </button>
+                </div>
+                <p:confirmDialog header="Add Data" widgetVar="addData_popup">                                           
+                    <f:facet name="message">
+                        You need to <a href="/dataverseuser.xhtml?editMode=CREATE">Sign Up</a>
+                        or <a href="/loginpage.xhtml">Log In</a> to create a dataverse or add a dataset.
+                    </f:facet>
+                </p:confirmDialog>  
+            </ui:fragment>
+
+            <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand')
+                                     or permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand')  }">
+                <h:form id="shareForm">
+                    <div class="btn-group">
+                        <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
                             <span class="glyphicon glyphicon-plus"/> Add Data <span class="caret"></span>
                         </button>
-                    </div>
-                    <p:confirmDialog message="You must be logged in to create a dataverse or add a dataset."  header="Add data" widgetVar="addData_popup">                                           
-                        <ul>
-                            <li>
-                                <h:outputLink value="/dataverseuser.xhtml?editMode=CREATE">
-                                    Sign Up
-                                </h:outputLink>
-                            </li>
-                            <li>
-                                <h:outputLink value="/loginpage.xhtml">
-                                    Log In
-                                </h:outputLink>
-                            </li>
+                        <ul class="dropdown-menu pull-right text-left" role="menu">
+                            <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand') }">
+                                <li><a href="/dataverse.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataverse</a></li>
+                            </ui:fragment>
+                            <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand') }">
+                                <li><a href="/dataset.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataset</a></li>
+                            </ui:fragment>
+                            <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataverse</a></li>-->
+                            <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataset</a></li>-->
                         </ul>
-
-                    </p:confirmDialog>  
-                </ui:fragment>
-
-                <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand')
-                                         or permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand')  }">
-                    <h:form id="shareForm">
-                        <div class="btn-group">
-                            <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
-                                <span class="glyphicon glyphicon-plus"/> Add Data <span class="caret"></span>
-                            </button>
-                            <ul class="dropdown-menu pull-right text-left" role="menu">
-                                <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDataverseCommand') }">
-                                    <li><a href="/dataverse.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataverse</a></li>
-                                </ui:fragment>
-                                <ui:fragment rendered="#{permissionServiceBean.on(SearchIncludeFragment.dataverse).canIssueCommand('CreateDatasetCommand') }">
-                                    <li><a href="/dataset.xhtml?ownerId=#{SearchIncludeFragment.dataverse.id}">New Dataset</a></li>
-                                </ui:fragment>
-                                <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataverse</a></li>-->
-                                <!--<li><a href="#" style="pointer-events: none; color: grey;">Existing Dataset</a></li>-->
-                            </ul>
-                        </div>
-                    </h:form>
-                </ui:fragment>
+                    </div>
+                </h:form>
+            </ui:fragment>
         </p:panelGrid>
     </p:panel>
     <!-- Search Results -->