Merge discvr-26.3 to develop

GenotypeAssays/resources/views/sbtReview.html

@@ -159,11 +159,9 @@
                             //sort: '-percent',
                             containerPath: Laboratory.Utils.getQueryContainerPath(),
                             removeableFilters: [
-                                LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE)
+                                LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE),
+                                LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUALS)
                             ],
-                            parameters: {
-                                AnalysisId: analysisId
-                            },
                             scope: this,
                             success: this.onDataRegionLoad
                         })
@@ -180,12 +178,10 @@
                             containerPath: Laboratory.Utils.getQueryContainerPath(),
                             removeableFilters: [
                                 LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE),
-                                LABKEY.Filter.create('total_reads', 5, LABKEY.Filter.Types.GT),
-                                LABKEY.Filter.create('totalLineages', 1, LABKEY.Filter.Types.EQUAL)
+                                LABKEY.Filter.create('total_reads_from_locus', 5, LABKEY.Filter.Types.GT),
+                                LABKEY.Filter.create('totalLineages', 1, LABKEY.Filter.Types.EQUAL),
+                                LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)
                             ],
-                            parameters: {
-                                AnalysisId: analysisId
-                            },
                             scope: this,
                             success: this.onDataRegionLoad
                         })
@@ -195,7 +191,7 @@
                         title: 'Haplotype Matches',
                         items: [{
                             xtype: 'genotypeassays-haplotypepanel',
-                            analysisId: [analysisId]
+                            analysisIds: [analysisId]
                         }]
                     },{
                         xtype: 'ldk-querypanel',

GenotypeAssays/resources/web/genotypeassays/buttons.js

@@ -28,7 +28,7 @@ GenotypeAssays.buttons = new function(){
 
             var newForm = Ext4.DomHelper.append(document.getElementsByTagName('body')[0],
                     '<form method="POST" action="' + LABKEY.ActionURL.buildURL("genotypeassays", "bulkHaplotype", null) + '">' +
-                    '<input type="hidden" name="analysisId" value="' + Ext4.htmlEncode(checked[0]) + '" />' +
+                    '<input type="hidden" name="analysisIds" value="' + Ext4.htmlEncode(checked.join(';')) + '" />' +
                     '</form>');
             newForm.submit();
         }

GenotypeAssays/resources/web/genotypeassays/panel/HaplotypePanel.js

@@ -1,7 +1,7 @@
 Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
     extend: 'Ext.panel.Panel',
     alias: 'widget.genotypeassays-haplotypepanel',
-    analysisId: null,
+    analysisIds: null,
     showCheckBoxes: false,
 
     initComponent: function(){
@@ -461,13 +461,11 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
             schemaName: 'sequenceanalysis',
             queryName: 'alignment_summary_by_lineage',
             columns: 'analysis_id,analysis_id/readset,analysis_id/readset/subjectId,lineages,loci,total,total_reads,percent,total_reads_from_locus,percent_from_locus',
-            parameters: {
-                AnalysisId: this.analysisId
-            },
             apiVersion: 13.2,
             scope: this,
             filterArray: [
-                LABKEY.Filter.create('percent_from_locus', minPct || 0, LABKEY.Filter.Types.GTE)
+                LABKEY.Filter.create('percent_from_locus', minPct || 0, LABKEY.Filter.Types.GTE),
+                LABKEY.Filter.create('analysis_id', this.analysisIds, LABKEY.Filter.Types.IN)
             ],
             failure: LDK.Utils.getErrorCallback(),
             success: function(results){
@@ -501,13 +499,13 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
             schemaName: 'sequenceanalysis',
             queryName: 'alignment_summary_grouped',
             columns: 'analysis_id,lineages,loci,alleles,total_reads,percent,total_reads_from_locus,percent_from_locus',
+            filterArray: [
+                LABKEY.Filter.create('analysis_id', this.analysisIds, LABKEY.Filter.Types.IN)
+            ],
             // This is designed to remove the view-level sorts:
             sort: 'analysis_id',
             apiVersion: 13.2,
             scope: this,
-            parameters: {
-                AnalysisId: this.analysisId
-            },
             failure: LDK.Utils.getErrorCallback(),
             success: function(results){
                 this.lineageToAlleleMap = {};

GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js

@@ -11,17 +11,8 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
                 return;
             }
 
-            const analysisId = dr.getParameters()?.AnalysisId;
-            if (!analysisId) {
-                Ext4.Msg.alert('Error', 'Error: unable to find analysisId. This should not occur.');
-                LDK.Assert.assertNotEmpty('Unable to find AnalysisId parameter from the DataRegion in PublishResultsWindow');
-
-                return;
-            }
-
             Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
                 dataRegionName: dataRegionName,
-                analysisId: analysisId,
                 actionName: 'cacheAnalyses'
             }).show();
         }
@@ -116,7 +107,6 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
             scope: this,
             jsonData: {
                 alleleNames: alleleNames,
-                analysisId: this.analysisId,
                 json: Ext4.encode(this.json),
                 protocolId: protocol
             },

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java

@@ -24,13 +24,15 @@
 import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.SpringActionController;
 import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbSchemaType;
 import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.HtmlView;
@@ -53,7 +55,7 @@ public GenotypeAssaysController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class MigrateLegacySSPAction extends ConfirmAction<Object>
+    public static class MigrateLegacySSPAction extends ConfirmAction<Object>
     {
         @Override
         public void validateCommand(Object form, Errors errors)
@@ -64,19 +66,19 @@ public void validateCommand(Object form, Errors errors)
         @Override
         public ModelAndView getConfirmView(Object form, BindException errors) throws Exception
         {
-            DbSchema schema = DbSchema.get("SSP_Assay");
+            DbSchema schema = DbSchema.get("SSP_Assay", DbSchemaType.Module);
             if (schema == null)
-                return new HtmlView("Either the legacy SSP module has not been installed, or it has already been removed");
+                return new HtmlView(HtmlString.of("Either the legacy SSP module has not been installed, or it has already been removed"));
             else
-                return new HtmlView("This allows an admin to copy any primers stored in the original SSP Assay module into the new genotyping module.  Any data has already been copied.  Do you want to continue?");
+                return new HtmlView(HtmlString.of("This allows an admin to copy any primers stored in the original SSP Assay module into the new genotyping module.  Any data has already been copied.  Do you want to continue?"));
         }
 
         @Override
         public boolean handlePost(Object form, BindException errors) throws Exception
         {
             try
             {
-                DbSchema schema = DbSchema.get("SSP_Assay");
+                DbSchema schema = DbSchema.get("SSP_Assay", DbSchemaType.Module);
                 if (schema == null)
                     return true; //module not installed
 
@@ -113,7 +115,7 @@ public URLHelper getSuccessURL(Object form)
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class CacheAnalysesAction extends MutatingApiAction<CacheAnalysesForm>
+    public static class CacheAnalysesAction extends MutatingApiAction<CacheAnalysesForm>
     {
         @Override
         public ApiResponse execute(CacheAnalysesForm form, BindException errors)
@@ -133,7 +135,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)
                     }
 
                     String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
-                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), form.getAnalysisId(), protocol, alleleNames);
+                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
                     resultProperties.put("runsCreated", ret.first);
                     resultProperties.put("runsDeleted", ret.second);
                 }
@@ -159,7 +161,6 @@ public static class CacheAnalysesForm
     {
         private String[] _alleleNames;
         private String _json;
-        private int _analysisId;
         private int _protocolId;
 
         public String[] getAlleleNames()
@@ -191,20 +192,10 @@ public void setJson(String json)
         {
             _json = json;
         }
-
-        public int getAnalysisId()
-        {
-            return _analysisId;
-        }
-
-        public void setAnalysisId(int analysisId)
-        {
-            _analysisId = analysisId;
-        }
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class CacheHaplotypesAction extends MutatingApiAction<CacheAnalysesForm>
+    public static class CacheHaplotypesAction extends MutatingApiAction<CacheAnalysesForm>
     {
         @Override
         public ApiResponse execute(CacheAnalysesForm form, BindException errors)

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -90,7 +90,7 @@ public static GenotypeAssaysManager get()
         return _instance;
     }
 
-    public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final int analysisId, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
+    public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
     {
         final User u = ctx.getUser();
         final List<Long> runsCreated = new ArrayList<>();
@@ -125,7 +125,6 @@ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final i
 
             AtomicInteger records = new AtomicInteger();
             TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);
-            tsAlignments.setNamedParameters(Map.of("AnalysisId", analysisId));
 
             tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()
             {

SivStudies/resources/queries/study/demographics/Expanded Vaccine Detail.qview.xml

@@ -14,6 +14,7 @@
         <column name="interventions/allInterventions"/>
         <column name="interventions/firstInterventionDPI"/>
         <column name="pvlInfo/numPVL"/>
+        <column name="pvlInfo/lastPvlWPI"/>
     </columns>
     <sorts>
         <sort column="Id" descending="false"/>

SivStudies/src/org/labkey/sivstudies/etl/PerformManualIdrStepsTask.java

@@ -294,7 +294,7 @@ public void setContainerUser(ContainerUser containerUser)
 
     private void updateJS46() throws PipelineJobException
     {
-        updateTreatmentRecords("JS46", new SimpleFilter(FieldKey.fromString("treatment"), "SIV - Unknown"), Map.of("treatment", "SIVmac239", "route", "IV"));
+        updateTreatmentRecords("JS46", new SimpleFilter(FieldKey.fromString("treatment"), "SIV - Unknown"), Map.of("treatment", "SIVmac239", "route", "Rectal", "amount", 1500, "amount_units", "TCID50"));
     }
 
     private void updateTreatmentRecords(String cohortName, SimpleFilter treatmentFilter, final Map<String, Object> additionalProps) throws PipelineJobException

SivStudies/src/org/labkey/sivstudies/query/SivStudiesCustomizer.java

@@ -464,9 +464,11 @@ public TableInfo getLookupTableInfo()
                 qd.setSql("SELECT\n" +
                         "min(tr.date) as artInitiation,\n" +
                         "CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY', CAST(min(tr.date) AS DATE), CAST(c." + dateColName + " AS DATE)), INTEGER) as daysPostArtInitiation,\n" +
+                        "CONVERT(TIMESTAMPDIFF('SQL_TSI_DAY', CAST(min(tr.date) AS DATE), CAST(c." + dateColName + " AS DATE)) / 7, INTEGER) as weeksPostArtInitiation,\n" +
                         "CONVERT(age_in_months(CAST(min(tr.date) AS DATE), CAST(c." + dateColName + " AS DATE)), FLOAT) as monthsPostArtInitiation,\n" +
                         "max(tr.enddate) as artRelease,\n" +
                         "CONVERT(CASE WHEN max(tr.enddate) IS NULL THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_DAY', CAST(max(tr.enddate) AS DATE), CAST(c." + dateColName + " AS DATE)) END, INTEGER) as daysPostArtRelease,\n" +
+                        "CONVERT(CASE WHEN max(tr.enddate) IS NULL THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_DAY', CAST(max(tr.enddate) AS DATE), CAST(c." + dateColName + " AS DATE)) END  / 7, INTEGER) as weeksPostArtRelease,\n" +
                         "CONVERT(CASE WHEN max(tr.enddate) IS NULL THEN NULL ELSE age_in_months(CAST(max(tr.enddate) AS DATE), CAST(c." + dateColName + " AS DATE)) END, FLOAT) as monthsPostArtRelease,\n" +
                         "CAST(CASE WHEN CAST(min(tr.date) AS DATE) <= CAST(c." + dateCol.getFieldKey().toString()  + " AS DATE) AND CAST(max(coalesce(tr.enddate, now())) AS DATE) >= CAST(c." + dateCol.getFieldKey().toString() + " AS DATE) THEN 'Y' ELSE null END as VARCHAR) as onArt,\n" +
                         "GROUP_CONCAT(DISTINCT tr.treatment) AS artTreatment,\n" +
@@ -499,9 +501,11 @@ public TableInfo getLookupTableInfo()
                     ((BaseColumnInfo)ti.getColumn("artRelease")).setLabel("ART Release");
 
                     ((BaseColumnInfo)ti.getColumn("daysPostArtInitiation")).setLabel("Days Post-ART Initiation");
+                    ((BaseColumnInfo)ti.getColumn("weeksPostArtInitiation")).setLabel("Weeks Post-ART Initiation");
                     ((BaseColumnInfo)ti.getColumn("monthsPostArtInitiation")).setLabel("Months Post-ART Initiation");
 
                     ((BaseColumnInfo)ti.getColumn("daysPostArtRelease")).setLabel("Days Post-ART Release");
+                    ((BaseColumnInfo)ti.getColumn("weeksPostArtRelease")).setLabel("Weeks Post-ART Release");
                     ((BaseColumnInfo)ti.getColumn("monthsPostArtRelease")).setLabel("Months Post-ART Release");
 
                     ((BaseColumnInfo)ti.getColumn("artTreatment")).setLabel("ART Treatment(s)");

mGAP/src/org/labkey/mgap/mGAPModule.java

@@ -110,7 +110,7 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
 
         ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Connection, "https://code.jquery.com", "https://*.fontawesome.com");
         ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Style, "https://code.jquery.com", "https://www.gstatic.com");
-        ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Font, "https://*.fontawesome.com");
+        ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Font, "https://*.fontawesome.com", "https://fonts.googleapis.com");
         ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Connection, "https://oss.maxcdn.com");
 
         new PipelineStartup();

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

@@ -86,6 +86,7 @@ public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<Sequ
                 continue;
             }
 
+            getPipelineCtx().getLogger().info("Storing results in database:");
             List<Map<String, Object>> toInsert = new ArrayList<>();
             try (CSVReader reader = new CSVReader(Readers.getReader(so.getFile()), '\t'))
             {
@@ -120,6 +121,10 @@ public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<Sequ
                     throw new PipelineJobException(e);
                 }
             }
+            else
+            {
+                getPipelineCtx().getLogger().info("No records to insert");
+            }
         }
     }
 

mcc/resources/etls/mcc.xml

@@ -45,6 +45,12 @@
                 </alternateKeys>
             </destination>
         </transform>
+        <transform id="cacheDemographics" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.mcc.etl.CacheDemographicsStep">
+                <settings>
+                </settings>
+            </taskref>
+        </transform>
         <transform type="SimpleQueryTransformStep" id="kinship">
             <description>Copy to target</description>
             <source schemaName="mcc" queryName="aggregatedKinship" >
@@ -149,7 +155,7 @@
                     <column>objectid</column>
                 </sourceColumns>
             </source>
-            <destination schemaName="study" queryName="clinical_observations" targetOption="truncate" bulkLoad="true" batchSize="1000">
+            <destination schemaName="study" queryName="clinical_observations" targetOption="truncate" bulkLoad="true" batchSize="2500">
                 <alternateKeys>
                     <column name="objectid"/>
                 </alternateKeys>

mcc/resources/queries/study/demographicsMostRecentDeparture.query.xml

@@ -14,6 +14,9 @@
                             query.sort=-Date&
                         </url>
                     </column>
+                    <column columnName="destination">
+                        <columnTitle>Destination(s)</columnTitle>
+                    </column>
                     <column columnName="mccRequestId">
                         <columnTitle>MCC Request Id(s)</columnTitle>
                     </column>

mcc/resources/queries/study/demographicsMostRecentDeparture.sql

@@ -2,6 +2,7 @@ select
 
     T1.Id,
     max(T1.date) as MostRecentDeparture,
+    group_concat(distinct t1.destination) as destination,
     group_concat(distinct t1.mccRequestId) as mccRequestId
 
 FROM study.departure T1

mcc/resources/views/mccDataImport.view.xml

@@ -19,12 +19,5 @@
         <!--<dependency path="https://cdn.datatables.net/buttons/1.5.1/js/dataTables.buttons.min.js" mode="production"/>-->
         <!--<dependency path="https://cdn.datatables.net/buttons/1.5.1/css/buttons.dataTables.min.css" mode="production"/>-->
 
-        <dependency path="https://cdn.datatables.net/buttons/1.5.1/js/buttons.flash.min.js"/>
-        <dependency path="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"/>
-        <dependency path="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.32/pdfmake.min.js"/>
-        <dependency path="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.32/vfs_fonts.js"/>
-        <dependency path="https://cdn.datatables.net/buttons/1.5.1/js/buttons.html5.min.js"/>
-        <dependency path="https://cdn.datatables.net/buttons/1.5.1/js/buttons.print.min.js"/>
-
     </dependencies>
 </view>