Merge 23.11 to develop

MccColony/resources/queries/study/demographics/.qview.xml

@@ -27,6 +27,46 @@
         <column name="Id/MostRecentWeight/MostRecentWeightDate"/>
         <column name="alternateIds"/>
         <column name="excludeFromCensus"/>
+        <column name="Id/mostRecentObservations/availability::observation">
+            <properties>
+                <property name="columnTitle" value="Availability"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/current_housing_status::observation">
+            <properties>
+                <property name="columnTitle" value="Housing Status"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/infant_history::observation">
+            <properties>
+                <property name="columnTitle" value="Infant History"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/fertility_status::observation">
+            <properties>
+                <property name="columnTitle" value="Fertility Status"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/medical_history::observation">
+            <properties>
+                <property name="columnTitle" value="Medical History"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/usage_current::observation">
+            <properties>
+                <property name="columnTitle" value="Usage (Current)"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/usage_future::observation">
+            <properties>
+                <property name="columnTitle" value="Usage (Future)"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/date_of_observations">
+            <properties>
+                <property name="columnTitle" value="Date of Observations"/>
+            </properties>
+        </column>
     </columns>
     <sorts>
         <sort column="Id" descending="false"/>

MccColony/resources/queries/study/kinship/.qview.xml

@@ -0,0 +1,15 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All Flags">
+    <columns>
+        <column name="Id"/>
+        <column name="Id2"/>
+        <column name="kinship"/>
+        <column name="relationship"/>
+        <column name="Id/mccAlias/externalAlias"/>
+        <column name="Id2MccAlias/externalAlias">
+            <properties>
+                <property name="columnTitle" value="Id2 MCC Alias"/>
+            </properties>
+        </column>
+    </columns>
+
+</customView>

hivrc/build.gradle

@@ -0,0 +1,17 @@
+import org.labkey.gradle.util.BuildUtils
+import org.labkey.gradle.util.ExternalDependency
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "published", depExtension: "module")
+}

hivrc/module.properties

@@ -0,0 +1,6 @@
+ModuleClass: org.labkey.hivrc.HivrcModule
+Label: BMGF HIVRC
+Description: This is designed to manage analyses and data collected as part of the BMGF HIVRC
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+ManageVersion: false

hivrc/resources/folderTypes/HIVRC Analysis.folderType.xml

@@ -0,0 +1,34 @@
+<folderType xmlns="http://labkey.org/data/xml/folderType">
+    <name>HIVRC Analyses</name>
+    <description>Workbook template for HIVRC analyses</description>
+    <requiredWebParts>
+        <webPart>
+            <name>HIVRC Analysis Header</name>
+            <location>body</location>
+        </webPart>
+    </requiredWebParts>
+    <preferredWebParts>
+        <webPart>
+            <name>Pipeline Files</name>
+            <location>body</location>
+            <property name="title" value="Files" />
+        </webPart>
+        <webPart>
+            <name>Messages</name>
+            <location>body</location>
+            <property name="boardName" value="Discussion" />
+            <property name="conversationName" value="Comment" />
+        </webPart>
+    </preferredWebParts>
+    <modules>
+        <moduleName>HIVRC</moduleName>
+        <moduleName>laboratory</moduleName>
+        <moduleName>Pipeline</moduleName>
+        <moduleName>Experiment</moduleName>
+        <moduleName>Query</moduleName>
+        <moduleName>Core</moduleName>
+    </modules>
+    <defaultModule>Core</defaultModule>
+    <workbookType>true</workbookType>
+    <forceAssayUploadIntoWorkbooks>true</forceAssayUploadIntoWorkbooks>
+</folderType>

hivrc/resources/folderTypes/HIVRC.folderType.xml

@@ -0,0 +1,59 @@
+<ft:folderType xmlns:ft="http://labkey.org/data/xml/folderType">
+    <ft:name>HIVRC Overview</ft:name>
+    <ft:description>The default folder layout for an HIVRC project</ft:description>
+    <ft:folderTabs>
+        <ft:folderTab>
+            <ft:name>overview</ft:name>
+            <ft:caption>Overview</ft:caption>
+            <ft:selectors>
+            </ft:selectors>
+            <ft:requiredWebParts>
+            </ft:requiredWebParts>
+            <ft:preferredWebParts>
+                <ft:webPart>
+                    <ft:name>HIVRC Data and Analyses</ft:name>
+                    <ft:location>body</ft:location>
+                </ft:webPart>
+            </ft:preferredWebParts>
+        </ft:folderTab>
+        <ft:folderTab>
+            <ft:name>datasets</ft:name>
+            <ft:caption>Datasets</ft:caption>
+            <ft:selectors>
+                <ft:selector>
+                    <ft:view>datasets</ft:view>
+                </ft:selector>
+            </ft:selectors>
+            <ft:requiredWebParts>
+            </ft:requiredWebParts>
+            <ft:preferredWebParts>
+                <ft:webPart>
+                    <ft:name>HIVRC Datasets</ft:name>
+                    <ft:location>body</ft:location>
+                </ft:webPart>
+            </ft:preferredWebParts>
+        </ft:folderTab>
+        <ft:folderTab>
+            <ft:name>analyses</ft:name>
+            <ft:caption>Analyses</ft:caption>
+            <ft:selectors>
+                <ft:selector>
+                    <ft:view>analyses</ft:view>
+                </ft:selector>
+            </ft:selectors>
+            <ft:requiredWebParts>
+            </ft:requiredWebParts>
+            <ft:preferredWebParts>
+                <ft:webPart>
+                    <ft:name>HIVRC Analyses</ft:name>
+                    <ft:location>body</ft:location>
+                </ft:webPart>
+            </ft:preferredWebParts>
+        </ft:folderTab>
+    </ft:folderTabs>
+    <ft:modules>
+        <ft:moduleName>hivrc</ft:moduleName>
+    </ft:modules>
+    <ft:defaultModule>hivrc</ft:defaultModule>
+    <ft:forceAssayUploadIntoWorkbooks>true</ft:forceAssayUploadIntoWorkbooks>
+</ft:folderType>

hivrc/resources/queries/laboratory/workbooks.query.xml

@@ -0,0 +1,15 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="workbooks" tableDbType="TABLE" useColumnOrder="true">
+                <tableTitle>HIVRC Analyses</tableTitle>
+                <titleColumn>workbookId</titleColumn>
+                <columns>
+                    <column columnName="workbookId">
+                        <columnTitle>Analysis #</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

hivrc/resources/schemas/dbscripts/postgresql/hivrc-0.00-23.000.sql

@@ -0,0 +1 @@
+CREATE SCHEMA hivrc;

hivrc/resources/schemas/dbscripts/postgresql/hivrc-23.000-23.001.sql

@@ -0,0 +1,17 @@
+CREATE TABLE hivrc.datasets (
+    rowid SERIAL,
+    label varchar(1000),
+    description varchar(4000),
+
+    datatype varchar(1000),
+    dataowner varchar(1000),
+    fileid int,
+
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    constraint PK_datasets PRIMARY KEY (rowid)
+);

hivrc/resources/schemas/dbscripts/sqlserver/hivrc-0.00-23.000.sql

@@ -0,0 +1,2 @@
+CREATE SCHEMA hivrc;
+GO

hivrc/resources/schemas/dbscripts/sqlserver/hivrc-23.000-23.001.sql

@@ -0,0 +1,17 @@
+CREATE TABLE hivrc.datasets (
+    rowid int IDENTITY(1,1),
+    label varchar(1000),
+    description varchar(4000),
+
+    datatype varchar(1000),
+    dataowner varchar(1000),
+    fileid int,
+
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    constraint PK_datasets PRIMARY KEY (rowid)
+);

hivrc/resources/schemas/hivrc.xml

@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tables xsi:schemaLocation="http://labkey.org/data/xml ..\..\..\..\schemas\tableInfo.xsd"
+        xmlns="http://labkey.org/data/xml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <table tableName="datasets" tableDbType="TABLE" useColumnOrder="true">
+        <tableTitle>Subjects</tableTitle>
+        <javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
+        <auditLogging>DETAILED</auditLogging>
+        <columns>
+            <column columnName="rowid">
+                <isAutoInc>true</isAutoInc>
+                <shownInInsertView>false</shownInInsertView>
+                <shownInUpdateView>false</shownInUpdateView>
+                <isUserEditable>false</isUserEditable>
+                <columnTitle>Row Id</columnTitle>
+            </column>
+            <column columnName="label">
+                <columnTitle>Label</columnTitle>
+            </column>
+            <column columnName="description">
+                <columnTitle>Description</columnTitle>
+            </column>
+            <column columnName="datatype">
+                <columnTitle>Data Type</columnTitle>
+            </column>
+            <column columnName="dataowner">
+                <columnTitle>Data Owner</columnTitle>
+            </column>
+            <column columnName="fileid">
+                <columnTitle>File ID</columnTitle>
+                <fk>
+                    <fkDbSchema>exp</fkDbSchema>
+                    <fkTable>data</fkTable>
+                    <fkColumnName>RowId</fkColumnName>
+                </fk>
+            </column>
+            <column columnName="container">
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="createdby">
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="created">
+                <isUserEditable>false</isUserEditable>
+                <shownInInsertView>false</shownInInsertView>
+                <shownInUpdateView>false</shownInUpdateView>
+                <nullable>true</nullable>
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="modifiedby">
+                <isHidden>true</isHidden>
+            </column>
+            <column columnName="modified">
+                <isUserEditable>false</isUserEditable>
+                <shownInInsertView>false</shownInInsertView>
+                <shownInUpdateView>false</shownInUpdateView>
+                <nullable>true</nullable>
+                <isHidden>true</isHidden>
+            </column>
+        </columns>
+    </table>
+</tables>

hivrc/resources/views/begin.html

@@ -0,0 +1,9 @@
+This is a prototype for a web-based system to manage BMGF datasets and analyses. Currently, the system is primarily designed to facilitate the work of informaticians/analysts,
+aiding in discoverability of data, access to data, and documentation/sharing of analyses. There are two components to this system:
+<br>
+<br>
+<ol>
+    <li>This system will contain a registry for input datasets. This provides a central table of inputs, each of which can be identified by ID.</li>
+
+    <li>The system also tracks analyses. Each analysis is loosely defined as one unit of work, such as validation of a given biomarker candidate in one cohort. Creating an analysis provides a folder to save any relevant files. The minimum requirement for an analysis is to upload a document (such as a markdown file) that serves to document the details of what was performed.</li>
+</ol>

hivrc/resources/views/begin.view.xml

@@ -0,0 +1,5 @@
+<view xmlns="http://labkey.org/data/xml/view" title="HIVRC Data and Analyses">
+    <dependencies>
+        <dependency path="laboratory.context" />
+    </dependencies>
+</view>

hivrc/resources/views/begin.webpart.xml

@@ -0,0 +1,3 @@
+<webpart xmlns="http://labkey.org/data/xml/webpart" title="HIVRC Data and Analyses">
+   <view name="begin"/>
+</webpart>