Cleanup JBrowseMaintenanceTask code

Author: bbimber

jbrowse/src/org/labkey/jbrowse/JBrowseMaintenanceTask.java

@@ -27,11 +27,13 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
+import java.util.function.Function;
+import java.util.stream.Collectors;
 
 /**
  * User: bimber
@@ -165,7 +167,7 @@ private void processContainer(Container c, Logger log) throws IOException
         filter.addCondition(FieldKey.fromString("sequenceid"), null, CompareType.ISBLANK);
 
         TableSelector ts = new TableSelector(tableJsonFiles, filter, null);
-        List<JsonFile> rows = new ArrayList<>(ts.getArrayList(JsonFile.class));
+        Map<String, JsonFile> rowMap = ts.getArrayList(JsonFile.class).stream().collect(Collectors.toMap(JsonFile::getObjectId, Function.identity()));
 
         // Also check for genomes from this container, and any additional JsonFiles they may have:
         TableInfo tableGenomes = DbSchema.get(JBrowseManager.SEQUENCE_ANALYSIS, DbSchemaType.Module).getTable("reference_libraries");
@@ -184,6 +186,7 @@ private void processContainer(Container c, Logger log) throws IOException
                     JBrowseSession session = JBrowseSession.getGenericGenomeSession(genomeId);
                     for (JsonFile json : session.getJsonFiles(u, true))
                     {
+                        rowMap.put(json.getObjectId(), json);
                         expectedDirs.add(json.getBaseDir());
                         if (!json.getBaseDir().exists())
                         {
@@ -197,7 +200,7 @@ private void processContainer(Container c, Logger log) throws IOException
         if (jbrowseRoot != null && jbrowseRoot.exists())
         {
             log.info("processing container: " + c.getPath());
-            for (JsonFile json : rows)
+            for (JsonFile json : rowMap.values())
             {
                 if (json.getBaseDir() != null)
                 {
@@ -248,7 +251,7 @@ private void processContainer(Container c, Logger log) throws IOException
             }
         }
 
-        for (JsonFile j : rows)
+        for (JsonFile j : rowMap.values())
         {
             if (j.needsProcessing())
             {

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -657,17 +657,17 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
         if (needsGzip() && !isGzipped())
         {
             //need to gzip and tabix index:
-            File finalLocation = getLocationOfProcessedTrack(true);
+            final File finalLocation = getLocationOfProcessedTrack(true);
             if (finalLocation.exists() && !SequencePipelineService.get().hasMinLineCount(finalLocation, 1))
             {
                 log.info("File exists but is zero-length, deleting and re-processing:");
                 forceReprocess = true;
             }
 
+            File idx = new File(finalLocation.getPath() + ".tbi");
             if (finalLocation.exists() && forceReprocess && !targetFile.equals(finalLocation))
             {
                 finalLocation.delete();
-                File idx = new File(finalLocation.getPath() + ".tbi");
                 if (idx.exists())
                 {
                     idx.delete();
@@ -710,7 +710,6 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
                 }
             }
 
-            File idx = new File(finalLocation.getPath() + ".tbi");
             if (forceReprocess || !idx.exists())
             {
                 if (throwIfNotPrepared)