Merge remote-tracking branch 'origin/develop' into fb_gradle_9.0.0

Author: labkey-susanh

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java

@@ -91,6 +91,7 @@ public List<String> getBaseArgs(@Nullable String toolName)
         args.add(SequencePipelineService.get().getJavaFilepath());
         args.addAll(SequencePipelineService.get().getJavaOpts(_maxRamOverride));
         args.add("-DGATK_STACKTRACE_ON_USER_EXCEPTION=true");
+        args.add("-Dsamjdk.optimistic_vcf_4_4=true");
         args.add("-jar");
         args.add(getJAR().getPath());
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -17,16 +17,16 @@
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.pipeline.PipelineJobService;
-import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.DirectoryResource;
+import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.settings.AppProps;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -115,6 +115,10 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs.add("--max-alleles");
         plinkArgs.add("2");
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        plinkArgs.add("--vcf-half-call");
+        plinkArgs.add("missing");
+
         Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
         if (threads != null)
         {

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -227,6 +227,10 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
             args.add(String.valueOf(maxRam));
         }
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        args.add("--vcf-half-call");
+        args.add("missing");
+
         args.addAll(getClientCommandArgs());
 
         getWrapper().execute(args);

Studies/resources/queries/studies/studies/.qview.xml

@@ -0,0 +1,13 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="rowId"/>
+        <column name="studyName"/>
+        <column name="label"/>
+        <column name="category"/>
+        <column name="description"/>
+        <column name="cohorts"/>
+    </columns>
+    <sorts>
+        <sort column="studyName" descending="false"/>
+    </sorts>
+</customView>

Studies/resources/schemas/studies.xml

@@ -132,6 +132,7 @@
         <auditLogging>DETAILED</auditLogging>
         <columns>
             <column columnName="rowid">
+                <columnTitle>Study Id</columnTitle>
                 <isAutoInc>true</isAutoInc>
                 <shownInUpdateView>false</shownInUpdateView>
                 <shownInInsertView>false</shownInInsertView>

Studies/resources/views/studiesOverview.html

@@ -12,7 +12,7 @@
                 name: 'query',
                 schemaName: 'studies',
                 queryName: 'studies',
-                maxRows: 20
+                maxRows: 10
             }).render(webpart.wrapperDivId + '-studies');
 
             // LABKEY.Query.selectRows({
@@ -62,4 +62,5 @@
 }(jQuery, LABKEY));
 
 </script>
+<div style="padding-bottom: 20px;">Below is a list of the studies tracked in this folder. Please use the <a href="<%=contextPath%>/project/<%=containerPath%>/begin.view?pageId=dataBrowser">Data Browser</a> tab to browse the dataset tracked in this project.</div>
 

Studies/src/org/labkey/studies/query/LookupSetTable.java

@@ -22,7 +22,6 @@
 import org.labkey.api.ldk.LDKService;
 import org.labkey.api.ldk.table.AbstractDataDefinedTable;
 import org.labkey.api.query.QueryUpdateService;
-import org.labkey.api.query.SimpleUserSchema;
 
 import java.util.Map;
 
@@ -101,15 +100,7 @@ public LookupSetTable init()
     @Override
     public QueryUpdateService getUpdateService()
     {
-        return new EHRLookupsUpdateService(this);
-    }
-
-    protected class EHRLookupsUpdateService extends UpdateService
-    {
-        public EHRLookupsUpdateService(SimpleUserSchema.SimpleTable<StudiesUserSchema> ti)
-        {
-            super(ti);
-        }
+        return new UpdateService(this);
     }
 }
 

Studies/src/org/labkey/studies/query/StudiesUserSchema.java

@@ -1,18 +1,22 @@
 package org.labkey.studies.query;
 
+import com.google.gwt.user.client.ui.TabBar;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.collections.CaseInsensitiveTreeSet;
 import org.labkey.api.data.AbstractTableInfo;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SchemaTableInfo;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.ldk.table.ContainerScopedTable;
 import org.labkey.api.ldk.table.CustomPermissionsTable;
+import org.labkey.api.query.ExprColumn;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryDefinition;
 import org.labkey.api.query.QueryException;
@@ -134,7 +138,7 @@ else if (TABLE_LOOKUPS.equalsIgnoreCase(name))
         }
         else if (TABLE_STUDIES.equalsIgnoreCase(name))
         {
-            return createStudyDesignTable(name, cf, false);
+            return createStudiesTable(name, cf, false);
         }
         else if (TABLE_COHORTS.equalsIgnoreCase(name))
         {
@@ -165,7 +169,22 @@ else if (TABLE_EVENT_TYPES.equalsIgnoreCase(name))
         return super.createTable(name, cf);
     }
 
-    private TableInfo createStudyDesignTable(String name, ContainerFilter cf, boolean addTriggers)
+    private TableInfo createStudiesTable(String name, ContainerFilter cf, boolean addTriggers)
+    {
+        CustomPermissionsTable<?> ret = createStudyDesignTable(name, cf, addTriggers);
+
+        final String chr = ret.getSqlDialect().isPostgreSQL() ? "chr" : "char";
+        SQLFragment sql1 = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("c.label"), true, true, new SQLFragment(chr + "(10)"))).append(" as expr FROM " + StudiesSchema.NAME + "." + TABLE_COHORTS + " c WHERE c.studyId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");
+        ExprColumn col1 = new ExprColumn(ret, "cohorts", sql1, JdbcType.VARCHAR, ret.getColumn("rowid"));
+        col1.setLabel("Cohort(s)");
+        col1.setDescription("This column lists the cohort labels for this study");
+
+        ret.addColumn(col1);
+
+        return ret;
+    }
+
+    private CustomPermissionsTable<?> createStudyDesignTable(String name, ContainerFilter cf, boolean addTriggers)
     {
         CustomPermissionsTable<SimpleUserSchema> ret = new CustomPermissionsTable<>(this, createSourceTable(name), cf);
         ret.addPermissionMapping(InsertPermission.class, StudiesDataAdminPermission.class);

jbrowse/build.gradle

@@ -30,7 +30,7 @@ dependencies {
 	external "org.apache.lucene:lucene-backward-codecs:${luceneVersion}"
 }
 
-def jbPkgTask = project.tasks.named("npm_run_jb-pkg")
+def jbPkgTask = project.tasks.named("npm_run_jb-sea")
 
 jbPkgTask.configure {
     outputs.cacheIf {false}