Merge pull request #119 from LabKey/fb_merge_21.11_to_develop

Merge discvr-21.11 to develop

Author: bbimber

.gitignore

@@ -19,3 +19,6 @@ jbrowse/resources/external/jb-cli/*
 #generated by Gradle
 SequenceAnalysis/resources/credits/jars.txt
 SequenceAnalysis/resources/credits/dependencies.txt
+
+OpenLdapSync/resources/credits/dependencies.txt
+OpenLdapSync/resources/credits/jars.txt

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java

@@ -19,8 +19,8 @@
 import org.apache.commons.io.FileUtils;
 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;
@@ -243,11 +243,11 @@ public void deleteAnalysis(User user, Container container, Collection<Integer> r
             throw new IllegalArgumentException("Unable to find sequenceanalysis user schema");
         }
 
+        TableInfo analysesTable = us.getTable(SequenceAnalysisSchema.TABLE_ANALYSES, null);
         try (DbScope.Transaction transaction = s.getSchema().getScope().ensureTransaction())
         {
             for (int rowId : rowIds)
             {
-
                 new SqlExecutor(s.getSchema()).execute(new SQLFragment("DELETE FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY_JUNCTION + " WHERE analysis_id = ?", rowId));
                 new SqlExecutor(s.getSchema()).execute(new SQLFragment("DELETE FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ALIGNMENT_SUMMARY + " WHERE analysis_id = ?", rowId));
                 cascadeDeleteWithQUS(us, SequenceAnalysisSchema.TABLE_OUTPUTFILES, new SimpleFilter(FieldKey.fromString("analysis_id"), rowId), "rowid");
@@ -258,11 +258,11 @@ public void deleteAnalysis(User user, Container container, Collection<Integer> r
                 new SqlExecutor(s.getSchema()).execute(new SQLFragment("DELETE FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_QUALITY_METRICS + " WHERE analysis_id = ?", rowId));
 
                 List<Map<String, Object>> keysToDelete = new ArrayList<>();
-                keysToDelete.add(new CaseInsensitiveHashMap<Object>(){{put("rowId", rowId);}});
+                keysToDelete.add(new CaseInsensitiveHashMap<>(){{put("rowId", rowId);}});
 
                 Map<String, Object> scriptContext = new HashMap<>();
                 scriptContext.put("deleteFromServer", true);  //a flag to make the trigger script accept this
-                us.getTable(SequenceAnalysisSchema.TABLE_ANALYSES, null).getUpdateService().deleteRows(user, container, keysToDelete, null, scriptContext);
+                analysesTable.getUpdateService().deleteRows(user, container, keysToDelete, null, scriptContext);
             }
             transaction.commit();
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -485,7 +485,16 @@ public static String getVCFLineCount(File vcf, Logger log, boolean passOnly, boo
                 throw new PipelineJobException("bcftools VCF count cannot be used with passOnly");
             }
 
-            return countUsingBcfTools(vcf, log);
+            try
+            {
+                return countUsingBcfTools(vcf, log);
+            }
+            catch (PipelineJobException e)
+            {
+                // ignore and continue:
+                log.error("Cannot count variants using bcftools, this index might have been created using another tool");
+            }
+
         }
 
         String cat = vcf.getName().endsWith(".gz") ? "zcat" : "cat";

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

@@ -37,11 +37,15 @@
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.attribute.PosixFilePermission;
+import java.nio.file.attribute.PosixFilePermissions;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
+import java.util.EnumSet;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
@@ -331,7 +335,19 @@ private void copyTopLevelFiles(PipelineJob job, File sourceWorkspace, File desti
                 dest.delete();
             }
 
+            Set<PosixFilePermission> expected = PosixFilePermissions.fromString("rw-rw----");
+            if (!Files.getPosixFilePermissions(source.toPath()).containsAll(expected))
+            {
+                job.getLogger().debug("Setting POSIX permissions on file: " + source.getPath());
+                Files.setPosixFilePermissions(source.toPath(), expected);
+            }
+
             FileUtils.copyFile(source, dest);
+            if (!Files.getPosixFilePermissions(dest.toPath()).containsAll(expected))
+            {
+                job.getLogger().debug("Setting POSIX permissions on file: " + dest.getPath());
+                Files.setPosixFilePermissions(dest.toPath(), expected);
+            }
         }
 
         File metaDir = new File(sourceWorkspace, "genomicsdb_meta_dir");

jbrowse/package-lock.json

@@ -24,6 +24,7 @@
     "mobx-react": "^6.0.0",
     "mobx-state-tree": "3.14.1",
     "node-polyfill-webpack-plugin": "1.1.0",
+    "jquery": "^3.6.0",
     "path-browserify": "^1.0.1",
     "pkg": "^5.3.2",
     "react-google-charts": "^3.0.15",

jbrowse/package.json

@@ -58,6 +58,7 @@
           "type": "ExtendedVariantDisplay",
           "displayId": "mgap_hg38-ExtendedVariantDisplay",
           "maxDisplayedBpPerPx": 2000,
+          "mouseover": "jexl:'Position: ' + formatWithCommas(get(feature,'POS'))",
           "renderer": {
             "type": "ExtendedVariantRenderer"
           },

jbrowse/resources/external/mGAPSession.json

@@ -24,6 +24,11 @@ const JBrowseFooter = observer(props => {
         viewState.session.view.activateTrackSelector()
     }
 
+    if (!viewState) {
+        return (
+            <></>
+        )
+    }
     return (
         <>
         <Box padding={'5px'}>

jbrowse/resources/web/README.txt

@@ -5,4 +5,9 @@ fieldset.MuiOutlinedInput-notchedOutline > legend {
 
 html {
     font-size: 16px !important;
+}
+
+/* Increase font size for tooltips: */
+div[class^="makeStyles-tooltip-"] {
+    font-size: 12px;
 }