Merge discvr-23.3 to develop

LabPurchasing/test/src/org/labkey/test/tests/labpurchasing/LabPurchasingTest.java

@@ -11,16 +11,12 @@
 import org.labkey.test.categories.External;
 import org.labkey.test.categories.LabModule;
 import org.labkey.test.components.ext4.Window;
-import org.labkey.test.util.DataRegion;
 import org.labkey.test.util.DataRegionTable;
 import org.labkey.test.util.Ext4Helper;
-import org.labkey.test.util.LogMethod;
-import org.labkey.test.util.LoggedParam;
 import org.labkey.test.util.ext4cmp.Ext4ComboRef;
 import org.labkey.test.util.ext4cmp.Ext4FieldRef;
 import org.labkey.test.util.ext4cmp.Ext4GridRef;
 import org.openqa.selenium.WebElement;
-import org.openqa.selenium.support.ui.ExpectedConditions;
 
 import java.util.Collections;
 import java.util.List;
@@ -98,7 +94,26 @@ public void testLabPurchasingModule()
 
         // Adding the new vendor should have updated the combo:
         grid.clickTbarButton("Add New");
+        checker().withScreenshot("LabPurchasingBeforeVendor");
         grid.setGridCell(1, "vendorId", "New Vendor 1");
+        try
+        {
+            Assert.assertTrue("Missing vendor cell", isElementPresent(Ext4GridRef.locateExt4GridCell("New Vendor 1")));
+        }
+        catch (AssertionError e)
+        {
+            checker().withScreenshot("LabPurchasingVendor0");
+            WebElement el = grid.startEditing(1, "vendorId");
+            checker().withScreenshot("LabPurchasingVendor1");
+
+            setFormElementJS(el, "");
+            el.sendKeys("New Vendor 1");
+            sleep(1000);
+
+            checker().withScreenshot("LabPurchasingVendor2");
+
+            throw e;
+        }
 
         // Try to save, expect error:
         click(Ext4Helper.Locators.ext4Button("Order Items"));

mGAP/resources/etls/prime-seq.xml

@@ -131,9 +131,10 @@
                 </columnTransforms>
             </destination>
         </transform>
+
         <transform id="step5" type="RemoteQueryTransformStep">
             <description>Copy to local table</description>
-            <source schemaName="mGAP" queryName="variantList" remoteSource="PRIMESEQ">
+            <source schemaName="mGAP" queryName="variantList" remoteSource="PRIMESEQ" sourceTimeout="0">
                 <sourceColumns>
                     <column>releaseId</column>
                     <column>contig</column>

mGAP/resources/queries/mGAP/releaseTracks/.qview.xml

@@ -0,0 +1,23 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <columns>
+        <column name="rowid"/>
+        <column name="trackName"/>
+        <column name="label"/>
+        <column name="source"/>
+        <column name="category"/>
+        <column name="url"/>
+        <column name="vcfId"/>
+        <column name="description"/>
+        <column name="isprimarytrack"/>
+        <column name="mergepriority"/>
+        <column name="skipvalidation"/>
+        <column name="vcfId/container/Name">
+            <properties>
+                <property name="columnTitle" value="Workbook"/>
+            </properties>
+        </column>
+    </columns>
+    <sorts>
+        <sort column="trackName" descending="false"/>
+    </sorts>
+</customView>

mGAP/resources/schemas/mgap.xml

@@ -1076,8 +1076,7 @@
                 <datatype>lsidtype</datatype>
                 <isReadOnly>true</isReadOnly>
                 <isHidden>true</isHidden>
-                <isUserEditable>false</isUserEditable>
-                <isUnselectable>true</isUnselectable>
+                <isUserEditable>false</isUserEditable>                
                 <fk>
                     <fkColumnName>ObjectUri</fkColumnName>
                     <fkTable>Object</fkTable>
@@ -1141,4 +1140,4 @@
             </column>
         </columns>
     </table>
-</tables>
+</tables>

mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java

@@ -75,8 +75,9 @@ public static class Provider extends AbstractVariantProcessingStepProvider<Gener
         public Provider()
         {
             super("GenerateMgapTracksStep", "Generate mGAP Tracks", "GenerateMgapTracksStep", "This will use the set of sample IDs from the table mgap.releaseTrackSubsets to subset the input VCF and produce one VCF per track. It will perform basic validation and also update mgap.releaseTracks.", Arrays.asList(
-                    ToolParameterDescriptor.create("releaseVersion", "mGAP Version", "This is the string that was used to annotate novel variants.", "textfield", new JSONObject(){{
+                    ToolParameterDescriptor.create("releaseVersion", "mGAP Version", "This is the string that was used to annotate novel variants.", "ldk-numberfield", new JSONObject(){{
                         put("allowBlank", false);
+                        put("decimalPrecision", 1);
                         put("doNotIncludeInTemplates", true);
                     }}, null)
             ), null, null);
@@ -174,17 +175,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         }
 
         // Also create the Novel Sites track:
-        String releaseVersion = getProvider().getParameterByName("releaseVersion").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
-        if (releaseVersion.toLowerCase().startsWith("v"))
-        {
-            releaseVersion = releaseVersion.substring(1);
-        }
-
-        if (!NumberUtils.isCreatable(releaseVersion))
-        {
-            throw new IllegalArgumentException("Expected the release version to be numeric: " + releaseVersion);
-        }
-
+        Double releaseVersion = getProvider().getParameterByName("releaseVersion").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Double.class);
         File novelSitesOutput = new File(outputDirectory, "mGAP_v" + releaseVersion + "_NovelSites.vcf.gz");
         if (new File(novelSitesOutput.getPath() + ".tbi").exists())
         {
@@ -240,10 +231,10 @@ private void createOrUpdateTrack(SequenceOutputFile so, PipelineJob job, String
         {
             Container targetContainer = job.getContainer().isWorkbook() ? job.getContainer().getParent() : job.getContainer();
             TableInfo releaseTracks = QueryService.get().getUserSchema(job.getUser(), targetContainer, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_RELEASE_TRACKS);
-            TableSelector ts = new TableSelector(releaseTracks, PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("trackName"), so.getName()), null);
+            TableSelector ts = new TableSelector(releaseTracks, PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("trackName"), trackName), null);
             if (!ts.exists())
             {
-                job.getLogger().debug("Creating new track: " + so.getName());
+                job.getLogger().debug("Creating new track: " + trackName + " / " + so.getName());
                 Map<String, Object> newRow = new CaseInsensitiveHashMap<>();
                 newRow.put("trackName", trackName);
                 newRow.put("label", trackName);
@@ -259,13 +250,15 @@ private void createOrUpdateTrack(SequenceOutputFile so, PipelineJob job, String
             }
             else
             {
-                job.getLogger().debug("Updating existing track: " + so.getName());
+                int rowId = ts.getObject(Integer.class);
+                job.getLogger().debug("Updating existing track: " + so.getName() + " / " + rowId);
+
                 Map<String, Object> toUpdate = new CaseInsensitiveHashMap<>();
-                toUpdate.put("rowId", ts.getObject(Integer.class));
+                toUpdate.put("rowId", rowId);
                 toUpdate.put("vcfId", so.getRowid());
 
                 Map<String, Object> oldKeys = new CaseInsensitiveHashMap<>();
-                toUpdate.put("rowId", ts.getObject(Integer.class));
+                oldKeys.put("rowId", rowId);
 
                 releaseTracks.getUpdateService().updateRows(job.getUser(), targetContainer, Arrays.asList(toUpdate), Arrays.asList(oldKeys), null, null);
             }

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java

@@ -99,8 +99,10 @@ public class mGapReleaseGenerator extends AbstractParameterizedOutputHandler<Seq
     public mGapReleaseGenerator()
     {
         super(ModuleLoader.getInstance().getModule(mGAPModule.class), "Create mGAP Release", "This will prepare an input VCF for use as an mGAP public release.  This will optionally include: removing excess annotations and program records, limiting to SNVs (optional) and removing genotype data (optional).  If genotypes are retained, the subject names will be checked for mGAP aliases and replaced as needed.", new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeFileSelectorField.js")), Arrays.asList(
-                ToolParameterDescriptor.create("releaseVersion", "Version", "This string will be used as the version when published.", "textfield", new JSONObject(){{
+                ToolParameterDescriptor.create("releaseVersion", "Version", "This value will be used as the version when published.", "ldk-numberfield", new JSONObject(){{
                     put("allowBlank", false);
+                    put("decimalPrecision", 1);
+                    put("doNotIncludeInTemplates", true);
                 }}, null),
                 ToolParameterDescriptor.createExpDataParam("gtfFile", "GTF File", "The gene file used to create these annotations.", "sequenceanalysis-genomefileselectorfield", new JSONObject()
                 {{

mcc/resources/etls/snprc-datasets.xml

@@ -7,7 +7,7 @@
     <transforms>
         <transform type="RemoteQueryTransformStep" id="demographics">
             <description>Copy to target</description>
-            <source remoteSource="SNPRC" schemaName="study" queryName="Demographics">
+            <source remoteSource="SNPRC" schemaName="study" queryName="Demographics" sourceTimeout="0">
                 <sourceColumns>
                     <column>AnimalId</column>
                     <column>date</column>

mcc/resources/queries/mcc/aggregatedDemographics.query.xml

@@ -0,0 +1,29 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="" tableDbType="TABLE">
+                <tableTitle>MCC Aggregated Demographics</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <columnTitle>MCC ID</columnTitle>
+                    </column>
+                    <column columnName="originalId">
+                        <columnTitle>Center Id</columnTitle>
+                    </column>
+                    <column columnName="dam">
+                        <columnTitle>Dam MCC Id</columnTitle>
+                    </column>
+                    <column columnName="originalDam">
+                        <columnTitle>Dam Center Id</columnTitle>
+                    </column>
+                    <column columnName="originalSire">
+                        <columnTitle>Sire Center Id</columnTitle>
+                    </column>
+                    <column columnName="sire">
+                        <columnTitle>Sire MCC Id</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

mcc/resources/queries/mcc/aggregatedDemographics.sql

@@ -7,6 +7,7 @@ SELECT
   d.birth,
   d.death,
   d.colony,
+  d.source,
   d.damMccAlias.externalAlias as dam,
   d.sireMccAlias.externalAlias as sire,
   d.dam as originalDam,
@@ -18,6 +19,7 @@ SELECT
     WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/SNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
     ELSE false
   END as u24_status,
+  d.Id.mostRecentDeparture.mostRecentDeparture,
   o.availability,
   o.current_housing_status,
   o.infant_history,
@@ -50,6 +52,7 @@ SELECT
   d.birth,
   d.death,
   d.colony,
+  d.source,
   d.damMccAlias.externalAlias as dam,
   d.sireMccAlias.externalAlias as sire,
   d.dam as originalDam,
@@ -61,6 +64,7 @@ SELECT
     WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/WNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
     ELSE false
   END as u24_status,
+  d.Id.mostRecentDeparture.mostRecentDeparture,
   o.availability,
   o.current_housing_status,
   o.infant_history,
@@ -93,6 +97,7 @@ SELECT
     d.birth,
     d.death,
     d.colony,
+    d.source,
     d.damMccAlias.externalAlias as dam,
     d.sireMccAlias.externalAlias as sire,
     d.dam as originalDam,
@@ -101,6 +106,7 @@ SELECT
     d.objectid,
     d.calculated_status,
     d.u24_status,
+    d.Id.mostRecentDeparture.mostRecentDeparture,
     o.availability,
     o.current_housing_status,
     o.infant_history,
@@ -133,6 +139,7 @@ SELECT
     d.birth,
     d.death,
     d.colony,
+    d.source,
     d.damMccAlias.externalAlias as dam,
     d.sireMccAlias.externalAlias as sire,
     d.dam as originalDam,
@@ -141,6 +148,7 @@ SELECT
     d.objectid,
     d.calculated_status,
     d.u24_status,
+    d.Id.mostRecentDeparture.mostRecentDeparture,
     o.availability,
     o.current_housing_status,
     o.infant_history,

mcc/resources/queries/mcc/aggregatedDemographics/.qview.xml

@@ -0,0 +1,29 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="false">
+    <columns>
+        <column name="Id"/>
+        <column name="originalId"/>
+        <column name="species"/>
+        <column name="gender"/>
+        <column name="birth"/>
+        <column name="death"/>
+        <column name="colony"/>
+        <column name="source"/>
+        <column name="dam"/>
+        <column name="originalDam"/>
+        <column name="sire"/>
+        <column name="originalSire"/>
+        <column name="mostRecentWeight"/>
+        <column name="calculated_status"/>
+        <column name="u24_status"/>
+        <column name="mostRecentDeparture"/>
+        <column name="availability"/>
+        <column name="current_housing_status"/>
+        <column name="infant_history"/>
+        <column name="fertility_status"/>
+        <column name="medical_history"/>
+        <column name="date_of_observations"/>
+    </columns>
+    <sorts>
+        <sort column="Id" descending="true"/>
+    </sorts>
+</customView>

mcc/resources/queries/mcc/aggregatedDemographics/Transfers.qview.xml

@@ -0,0 +1,29 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="false" label="MCC Transfers">
+    <columns>
+        <column name="Id"/>
+        <column name="originalId"/>
+        <column name="species"/>
+        <column name="colony"/>
+        <column name="mostRecentDeparture"/>
+        <column name="source"/>
+        <column name="gender"/>
+        <column name="birth"/>
+        <column name="death"/>
+        <column name="mostRecentWeight"/>
+        <column name="calculated_status"/>
+        <column name="u24_status"/>
+        <column name="date_of_observations"/>
+        <column name="medical_history"/>
+        <column name="availability"/>
+        <column name="current_housing_status"/>
+        <column name="infant_history"/>
+        <column name="fertility_status"/>
+    </columns>
+    <sorts>
+        <sort column="Id" descending="true"/>
+    </sorts>
+    <filters>
+        <filter column="mostRecentDeparture" operator="isnonblank" value=""/>
+        <filter column="source" operator="isnonblank" value=""/>
+    </filters>
+</customView>

mcc/resources/queries/mcc/animalRequests.js

@@ -121,10 +121,11 @@ function calculatePreliminaryScore(row, oldRow) {
         console.error('Unknown MCC institutiontype: ' + row.institutiontype)
     }
 
-    if (['nih', 'other-federal', 'start-up', 'foundation'].indexOf(row.fundingsource) !== -1) {
+    var fs = row.fundingsource ? row.fundingsource.split(',') : []
+    if (fs.indexOf('nih') !== -1 || fs.indexOf('other-federal') !== -1 || fs.indexOf('start-up') !== -1 || fs.indexOf('foundation') !== -1) {
         score += 1;
     }
-    else if (row.fundingsource === 'private' || row.fundingsource === 'no-funding') {
+    else if (fs.indexOf('private') !== -1 || fs.indexOf('no-funding') !== -1) {
         // no score change
     }
     else {

mcc/resources/queries/mcc/animalRequests/Non-Draft.qview.xml

@@ -1,6 +1,8 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="false">
     <filters>
         <filter column="status" operator="neqornull" value="draft" />
+        <filter column="status" operator="neqornull" value="withdrawn" />
+        <filter column="status" operator="neqornull" value="fulfilled" />
     </filters>
     <sorts>
         <sort column="rowid" descending="true"/>

mcc/resources/queries/mcc/requestScores/Pending Requests.qview.xml

@@ -1,6 +1,7 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView" label="Pending Requests" canOverride="false">
     <filters>
-        <filter column="requestId/status" operator="neqornull" value="Approved"/>
+        <filter column="requestId/status" operator="neqornull" value="Withdrawn"/>
+        <filter column="requestId/status" operator="neqornull" value="Fulfilled"/>
     </filters>
     <sorts>
         <sort column="requestId/rowid" descending="true"/>