Make MDC DataCite URl configurable

conf/docker-aio/configure_doi.bash

@@ -17,3 +17,8 @@ if [ ! -z "${doi_baseurl}" ]; then
         doi_baseurl_esc=`echo ${doi_baseurl} | sed -e 's/:/\\:/'`
         bin/asadmin create-jvm-options "\"-Ddoi.baseurlstring=${doi_baseurl_esc}\""
 fi
+if [ ! -z "${doi_mdcbaseurl}" ]; then
+        bin/asadmin delete-jvm-options "-Ddoi.mdcbaseurlstring=https\://api.test.datacite.org"
+        doi_mdcbaseurl_esc=`echo ${doi_mdcbaseurl} | sed -e 's/:/\\:/'`
+        bin/asadmin create-jvm-options "\"-Ddoi.mdcbaseurlstring=${doi_mdcbaseurl_esc}\""
+fi

doc/sphinx-guides/source/admin/make-data-count.rst

@@ -63,10 +63,12 @@ Enable Logging for Make Data Count
 
 To make Dataverse log dataset usage (views and downloads) for Make Data Count, you must set the ``:MDCLogPath`` database setting. See :ref:`MDCLogPath` for details.
 
+If you wish to start logging in advance of setting up other components, or wish to log without display MDC metrics for any other reason, you can set the optional ``:DisplayMDCMetrics`` database setting to false. See :ref:`DisplayMDCMetrics` for details.
+
 After you have your first day of logs, you can process them the next day.
 
 Enable or Disable Display of Make Data Count Metrics
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 By default, when MDC logging is enabled (when ``:MDCLogPath`` is set), Dataverse will display MDC metrics instead of it's internal (legacy) metrics. You can avoid this (e.g. to collect MDC metrics for some period of time before starting to display them) by setting ``:DisplayMDCMetrics`` to false.
 
@@ -133,11 +135,15 @@ Once you are satisfied with your testing, you should contact support@datacite.or
 - Views ("investigations" in COUNTER)
 - Downloads ("requests" in COUNTER)
 
+.. _MDC-updateCitationsForDataset:
+
 Configuring Dataverse for Make Data Count Citations
 ---------------------------------------------------
 
 Please note: as explained in the note above about limitations, this feature is not available to installations of Dataverse that use Handles.
 
+To configure Dataverse to pull citations from the test vs. production DataCite server see :ref:`doi.mdcbaseurlstring` in the Installation Guide.
+
 Please note that in the curl example, Bash environment variables are used with the idea that you can set a few environment variables and copy and paste the examples as is. For example, "$DOI" could become "doi:10.5072/FK2/BL2IBM" by issuing the following export command from Bash:
 
 ``export DOI="doi:10.5072/FK2/BL2IBM"``

doc/sphinx-guides/source/admin/troubleshooting.rst

@@ -32,12 +32,28 @@ A User Needs Their Account to Be Converted From Institutional (Shibboleth), ORCI
 
 See :ref:`converting-shibboleth-users-to-local` and :ref:`converting-oauth-users-to-local`.
 
+.. _troubleshooting-glassfish:
+
 Glassfish
 ---------
 
-``server.log`` is the main place to look when you encounter problems. Hopefully an error message has been logged. If there's a stack trace, it may be of interest to developers, especially they can trace line numbers back to a tagged version.
+.. _glassfish-log:
+
+Finding the Glassfish Log File
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+``/usr/local/glassfish4/glassfish/domains/domain1/logs/server.log`` is the main place to look when you encounter problems (assuming you installed Glassfish in the default directory). Hopefully an error message has been logged. If there's a stack trace, it may be of interest to developers, especially they can trace line numbers back to a tagged version or commit. Send more of the stack trace (the entire file if possible) to developers who can help (see "Getting Help", below) and be sure to say which version of Dataverse you are running.
+
+.. _increase-glassfish-logging:
+
+Increasing Glassfish Logging
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-For debugging purposes, you may find it helpful to increase logging levels as mentioned in the :doc:`/developers/debugging` section of the Developer Guide.
+For debugging purposes, you may find it helpful to temporarily increase logging levels. Here's an example of increasing logging for the Java class behind the "datasets" API endpoints:
+
+``./asadmin set-log-levels edu.harvard.iq.dataverse.api.Datasets=FINE``
+
+For more on setting log levels, see the :doc:`/developers/debugging` section of the Developer Guide.
 
 Our guides focus on using the command line to manage Glassfish but you might be interested in an admin GUI at http://localhost:4848
 
@@ -100,3 +116,8 @@ Many Files with a File Type of "Unknown", "Application", or "Binary"
 --------------------------------------------------------------------
 
 From the home page of a Dataverse installation you can get a count of files by file type by clicking "Files" and then scrolling down to "File Type". If you see a lot of files that are "Unknown", "Application", or "Binary" you can have Dataverse attempt to redetect the file type by using the :ref:`Redetect File Type <redetect-file-type>` API endpoint.
+
+Getting Help
+------------
+
+If the troubleshooting advice above didn't help, contact any of the support channels mentioned in the :ref:`support` section of the Installation Guide.

doc/sphinx-guides/source/installation/config.rst

@@ -142,6 +142,7 @@ Here are the configuration options for DOIs:
 - :ref:`doi.baseurlstring`
 - :ref:`doi.username`
 - :ref:`doi.password`
+- :ref:`doi.mdcbaseurlstring`
 
 **Database Settings:**
 
@@ -956,6 +957,30 @@ See also these related database settings below:
 - :ref:`:Authority`
 - :ref:`:Shoulder`
 
+.. _doi.mdcbaseurlstring:
+
+doi.mdcbaseurlstring
+++++++++++++++++++++
+
+This configuration option affects the ``updateCitationsForDataset`` API endpoint documented under :ref:`MDC-updateCitationsForDataset` in the Admin Guide.
+
+As of this writing, "https://api.datacite.org" (DataCite) and "https://api.test.datacite.org" (DataCite Testing) are the main valid values.
+
+Out of the box, Dataverse is configured to use a test DataCite MDC base URL string. You can delete it like this:
+
+``./asadmin delete-jvm-options '-Ddoi.mdcbaseurlstring=https\://api.test.datacite.org'``
+
+Then, to switch to production DataCite, you can issue the following command:
+
+``./asadmin create-jvm-options '-Ddoi.mdcbaseurlstring=https\://api.datacite.org'``
+
+For backward compatibility, if this option is not defined, the default used is "https\://api.datacite.org:.
+
+See also these related database settings below:
+
+- :ref:`:MDCLogPath`
+- :ref:`:DisplayMDCMetrics`
+
 .. _doi.username:
 
 doi.username

scripts/installer/glassfish-setup.sh

@@ -28,6 +28,7 @@
 # DOI_USERNAME
 # DOI_PASSWORD
 # DOI_BASEURL
+# DOI_MDCBASEURL
 #
 # other local configuration:
 # HOST_ADDRESS
@@ -88,6 +89,10 @@ function preliminary_setup()
   ./asadmin $ASADMIN_OPTS create-jvm-options '\-Ddoi.password=${ALIAS=doi_password_alias}'
   ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddoi.baseurlstring=$DOI_BASEURL_ESC"
 
+  # jvm-options use colons as separators, escape as literal
+  DOI_MDCBASEURL_ESC=`echo $DOI_MDCBASEURL | sed -e 's/:/\\\:/'`
+  ./asadmin $ASADMIN_OPTS create-jvm-options "\-Ddoi.mdcbaseurlstring=$DOI_MDCBASEURL_ESC"
+
   ./asadmin $ASADMIN_OPTS create-jvm-options "-Ddataverse.timerServer=true"
   # enable comet support
   ./asadmin $ASADMIN_OPTS set server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled="true"

scripts/installer/install

@@ -84,7 +84,8 @@ else
 
 	'DOI_USERNAME',
 	'DOI_PASSWORD',
-	'DOI_BASEURL'
+	'DOI_BASEURL',
+	'DOI_MDCBASEURL'
 
 	);
 }
@@ -114,6 +115,7 @@ my %CONFIG_DEFAULTS = (
     'DOI_USERNAME',    'dataciteuser',
     'DOI_PASSWORD',    'datacitepassword',
     'DOI_BASEURL',     'https://mds.test.datacite.org',
+    'DOI_MDCBASEURL',  'https://api.test.datacite.org',
 
 );
 
@@ -140,7 +142,8 @@ my %CONFIG_PROMPTS = (
 
     'DOI_USERNAME',    'Datacite username',
     'DOI_PASSWORD',    'Datacite password',
-    'DOI_BASEURL',    'Datacite URL'
+    'DOI_BASEURL',    'Datacite URL',
+    'DOI_MDCBASEURL', 'Datacite MakeDataCount URL'
 
 );
 
@@ -168,7 +171,8 @@ my %CONFIG_COMMENTS = (
 
     'DOI_USERNAME',    'DataCite or EZID username. Only necessary for publishing / minting DOIs.',
     'DOI_PASSWORD',    'DataCite or EZID account password.',
-    'DOI_BASEURL',    'DataCite or EZID URL. Probably https://mds.datacite.org'
+    'DOI_BASEURL',    'DataCite or EZID URL. Probably https://mds.datacite.org',
+    'DOI_MDCBASEURL',    'DataCite Make Data Count API base URL. Probably https://api.datacite.org'
 
 );
 
@@ -1097,7 +1101,9 @@ sub run_asadmin_script {
     $ENV{'RSERVE_PORT'} = $CONFIG_DEFAULTS{'RSERVE_PORT'};
     $ENV{'RSERVE_USER'} = $CONFIG_DEFAULTS{'RSERVE_USER'};
     $ENV{'RSERVE_PASS'} = $CONFIG_DEFAULTS{'RSERVE_PASSWORD'};
-
+    $ENV{'DOI_BASEURL'} = $CONFIG_DEFAULTS{'DOI_BASEURL'};
+    $ENV{'DOI_MDCBASEURL'} = $CONFIG_DEFAULTS{'DOI_MDCBASEURL'};
+
     $ENV{'HOST_ADDRESS'} = $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'};
 
     my ($mail_server_host, $mail_server_port) = split (":", $CONFIG_DEFAULTS{'MAIL_SERVER'});

src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java

@@ -139,7 +139,13 @@ public Response updateCitationsForDataset(@PathParam("id") String id) throws Mal
             // DataCite wants "doi=", not "doi:".
             String authorityPlusIdentifier = persistentId.replaceFirst("doi:", "");
             // curl https://api.datacite.org/events?doi=10.7910/dvn/hqzoob&source=crossref
-            URL url = new URL("https://api.datacite.org/events?doi=" + authorityPlusIdentifier + "&source=crossref");
+            String baseUrl = System.getProperty("doi.mdcbaseurlstring");
+            if(null==baseUrl) {
+            	//Backward compatible default to the production server
+            	baseUrl="https://api.datacite.org";
+            }
+            URL url = new URL(baseUrl + "/events?doi=" + authorityPlusIdentifier + "&source=crossref");
+            logger.fine("Requesting citations from " + url);
             HttpURLConnection connection = (HttpURLConnection) url.openConnection();
             connection.setRequestMethod("GET");
             int status = connection.getResponseCode();