Refactor JsonFile to include User when processing resources

bbimber · bbimber · commit 0983212a6061 · 2023-11-27T11:39:51.000-08:00
diff --git a/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseService.java b/jbrowse/api-src/org/labkey/api/jbrowse/JBrowseService.java
@@ -8,7 +8,9 @@
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.security.User;
 
+import java.io.File;
 import java.io.IOException;
+import java.util.List;
 
 /**
  * Created by bimber on 11/3/2016.
@@ -38,4 +40,6 @@ static public void setInstance(JBrowseService instance)
     abstract public void registerGroupsProvider(GroupsProvider provider);
 
     abstract public void registerFieldCustomizer(JBrowseFieldCustomizer customizer);
+
+    abstract public void prepareLuceneIndex(File vcf, File indexDir, Logger log, List<String> infoFieldsForFullTextSearch, boolean allowLenientLuceneProcessing) throws PipelineJobException;
 }
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseMaintenanceTask.java b/jbrowse/src/org/labkey/jbrowse/JBrowseMaintenanceTask.java
@@ -286,7 +286,8 @@ private void processContainer(Container c, Logger log) throws IOException
                 {
                     try
                     {
-                        j.prepareResource(log, false, true);
+                        User u = LDKService.get().getBackgroundAdminUser();
+                        j.prepareResource(u, log, false, true);
                     }
                     catch (Exception e)
                     {
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseSchema.java b/jbrowse/src/org/labkey/jbrowse/JBrowseSchema.java
@@ -26,6 +26,7 @@ public class JBrowseSchema
     private static final JBrowseSchema _instance = new JBrowseSchema();
     public static final String NAME = "jbrowse";
 
+    public static final String SEQUENCE_ANALYSIS = "sequenceanalysis";
     public static final String TABLE_DATABASES = "databases";
     public static final String TABLE_DATABASE_MEMBERS = "database_members";
     public static final String TABLE_JSONFILES = "jsonfiles";
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java b/jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java
@@ -17,8 +17,10 @@
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.jbrowse.model.JBrowseSession;
 import org.labkey.jbrowse.model.JsonFile;
+import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob;
 import org.labkey.jbrowse.pipeline.JBrowseSessionPipelineJob;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -60,7 +62,7 @@ public String prepareOutputFile(User u, Logger log, Integer outputFileId, boolea
         {
             try
             {
-                ret.prepareResource(log, false, true);
+                ret.prepareResource(u, log, false, true);
             }
             catch (PipelineJobException e)
             {
@@ -108,6 +110,12 @@ public void registerFieldCustomizer(JBrowseFieldCustomizer customizer)
         _customizers.add(customizer);
     }
 
+    @Override
+    public void prepareLuceneIndex(File vcf, File indexDir, Logger log, List<String> infoFieldsForFullTextSearch, boolean allowLenientLuceneProcessing) throws PipelineJobException
+    {
+        JBrowseLucenePipelineJob.prepareLuceneIndex(vcf, indexDir, log, infoFieldsForFullTextSearch, allowLenientLuceneProcessing);
+    }
+
     public Map<String, Map<String, Object>> resolveSubjects(List<String> subjects, User u, Container c)
     {
         Map<String, Map<String, Object>> ret = new HashMap<>();
diff --git a/jbrowse/src/org/labkey/jbrowse/model/DbBackedJsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/DbBackedJsonFile.java
@@ -114,10 +114,10 @@ public boolean shouldExist()
     abstract protected TableSelector getSelector();
 
     @Override
-    public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException
+    public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException
     {
         createGtf(log, throwIfNotPrepared, forceReprocess);
-        return super.prepareResource(log, throwIfNotPrepared, forceReprocess);
+        return super.prepareResource(u, log, throwIfNotPrepared, forceReprocess);
     }
 
     public void createGtf(Logger log, boolean throwOnNotFound, boolean forceRecreate) throws PipelineJobException
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java b/jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java
@@ -213,7 +213,7 @@ public void ensureJsonFilesPrepared(User u, Logger log) throws PipelineJobExcept
         {
             try
             {
-                x.prepareResource(log, false, false);
+                x.prepareResource(u, log, false, false);
             }
             catch (Exception e)
             {
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
@@ -51,6 +51,7 @@
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.jbrowse.JBrowseManager;
 import org.labkey.jbrowse.JBrowseSchema;
+import org.labkey.jbrowse.pipeline.IndexVariantsStep;
 import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob;
 import org.labkey.sequenceanalysis.run.util.TabixRunner;
 
@@ -297,7 +298,7 @@ else if (TRACK_TYPES.bam.getFileType().isType(targetFile.getFile()) || TRACK_TYP
         }
         else if (TRACK_TYPES.gff.getFileType().isType(targetFile.getFile()))
         {
-            ret = getGxfTrack(log, targetFile, rg);
+            ret = getGxfTrack(u, log, targetFile, rg);
         }
         else if (TRACK_TYPES.gtf.getFileType().isType(targetFile.getFile()))
         {
@@ -308,7 +309,7 @@ else if (TRACK_TYPES.gtf.getFileType().isType(targetFile.getFile()))
         }
         else if (TRACK_TYPES.bed.getFileType().isType(targetFile.getFile()))
         {
-            ret = getBedTrack(log, targetFile, rg);
+            ret = getBedTrack(u, log, targetFile, rg);
         }
         else if (TRACK_TYPES.bw.getFileType().isType(targetFile.getFile()))
         {
@@ -643,12 +644,12 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
         return ret;
     }
 
-    private JSONObject getBedTrack(Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException
+    private JSONObject getBedTrack(User u, Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException
     {
         String adapterType = "BedTabixAdapter";
         String prefix = "bed";
 
-        return getTabixTrack(log, targetFile, rg, adapterType, prefix);
+        return getTabixTrack(u, log, targetFile, rg, adapterType, prefix);
     }
 
     private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException
@@ -682,12 +683,12 @@ private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenom
         return ret;
     }
 
-    private JSONObject getGxfTrack(Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException
+    private JSONObject getGxfTrack(User u, Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException
     {
         String adapterType = TRACK_TYPES.gff.getFileType().isType(targetFile.getFile()) ? "Gff3TabixAdapter" : "GtfTabixAdapter";
         String prefix = TRACK_TYPES.gff.getFileType().isType(targetFile.getFile()) ? "gff" : "gtf";
 
-        return getTabixTrack(log, targetFile, rg, adapterType, prefix);
+        return getTabixTrack(u, log, targetFile, rg, adapterType, prefix);
     }
 
     public String getTrackType()
@@ -729,7 +730,7 @@ else if (TRACK_TYPES.bw.getFileType().isType(targetFile.getFile()))
         }
     }
 
-    private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome rg, String adapterType, String prefix) throws PipelineJobException
+    private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, ReferenceGenome rg, String adapterType, String prefix) throws PipelineJobException
     {
         JSONObject ret = new JSONObject();
         ret.put("type", getTrackType());
@@ -743,7 +744,7 @@ private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome
         }});
 
         // if not gzipped, we need to process it:
-        File gzipped = prepareResource(log, true, false);
+        File gzipped = prepareResource(u, log, true, false);
         final String url;
         if (!getExpData().getFile().equals(gzipped))
         {
@@ -809,7 +810,7 @@ protected boolean needsGzip()
         return !isGzipped() && (TRACK_TYPES.gff.getFileType().isType(fn) || TRACK_TYPES.gtf.getFileType().isType(fn) || TRACK_TYPES.bed.getFileType().isType(fn));
     }
 
-    public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException
+    public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException
     {
         ExpData expData = getExpData();
         if (expData == null)
@@ -939,6 +940,13 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
 
         if (shouldHaveFreeTextSearch())
         {
+            // TODO:
+            // Try to find a matching existing index:
+            // Container targetContainer = getContainerObj().isWorkbookOrTab() ? getContainerObj().getParent() : getContainerObj();
+            // TableInfo ti = QueryService.get().getUserSchema(u, targetContainer, JBrowseSchema.SEQUENCE_ANALYSIS).getTable("outputfiles");
+            // SimpleFilter filter = new SimpleFilter(FieldKey.fromString("category"), IndexVariantsStep.CATEGORY);
+            // filter.addCondition(FieldKey.fromString("library_id"), rg)
+
             File luceneDir = getExpectedLocationOfLuceneIndex(throwIfNotPrepared);
             long sizeInGb = targetFile.length() / (1024 * 1024 * 1024);
             log.debug("preparing lucene index, VCF size: " + sizeInGb);
diff --git a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionTask.java
@@ -135,7 +135,7 @@ private void prepareGenome(boolean forceReprocess) throws PipelineJobException
         getJob().getLogger().info("total files to reprocess: " + jsonFiles.size());
         for (JsonFile f : jsonFiles)
         {
-            f.prepareResource(getJob().getLogger(), false, forceReprocess);
+            f.prepareResource(getJob().getUser(), getJob().getLogger(), false, forceReprocess);
         }
     }
 
@@ -152,7 +152,7 @@ private void reprocessResources() throws PipelineJobException
         getJob().getLogger().info("total files to reprocess: " + jsonFiles.size());
         for (JsonFile f : jsonFiles)
         {
-            f.prepareResource(getJob().getLogger(), false, true);
+            f.prepareResource(getJob().getUser(), getJob().getLogger(), false, true);
         }
     }
 
@@ -257,7 +257,7 @@ private void createOrAddToSession() throws PipelineJobException
                     trackRecord = Table.insert(getJob().getUser(), databaseMembers, trackRecord);
                     databaseMemberRecordsCreated.add((Integer)trackRecord.get("rowid"));
 
-                    json.prepareResource(getJob().getLogger(), false, false);
+                    json.prepareResource(getJob().getUser(), getJob().getLogger(), false, false);
                 }
             }
             else
@@ -308,7 +308,7 @@ private void createOrAddToSession() throws PipelineJobException
                     trackRecord = Table.insert(getJob().getUser(), databaseMembers, trackRecord);
                     databaseMemberRecordsCreated.add((Integer) trackRecord.get("rowid"));
 
-                    json.prepareResource(getJob().getLogger(), false, false);
+                    json.prepareResource(getJob().getUser(), getJob().getLogger(), false, false);
                 }
             }
 

Original file line number	Diff line number	Diff line change
`@@ -286,7 +286,8 @@ private void processContainer(Container c, Logger log) throws IOException`
`286`	`286`	`{`
`287`	`287`	`try`
`288`	`288`	`{`
`289`		`- j.prepareResource(log, false, true);`
	`289`	`+ User u = LDKService.get().getBackgroundAdminUser();`
	`290`	`+ j.prepareResource(u, log, false, true);`
`290`	`291`	`}`
`291`	`292`	`catch (Exception e)`
`292`	`293`	`{`
Original file line number	Diff line number	Diff line change
`@@ -17,8 +17,10 @@`
`17`	`17`	`import org.labkey.api.util.logging.LogHelper;`
`18`	`18`	`import org.labkey.jbrowse.model.JBrowseSession;`
`19`	`19`	`import org.labkey.jbrowse.model.JsonFile;`
	`20`	`+import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob;`
`20`	`21`	`import org.labkey.jbrowse.pipeline.JBrowseSessionPipelineJob;`
`21`	`22`
	`23`	`+import java.io.File;`
`22`	`24`	`import java.util.ArrayList;`
`23`	`25`	`import java.util.Collection;`
`24`	`26`	`import java.util.Collections;`
`@@ -60,7 +62,7 @@ public String prepareOutputFile(User u, Logger log, Integer outputFileId, boolea`
`60`	`62`	`{`
`61`	`63`	`try`
`62`	`64`	`{`
`63`		`- ret.prepareResource(log, false, true);`
	`65`	`+ ret.prepareResource(u, log, false, true);`
`64`	`66`	`}`
`65`	`67`	`catch (PipelineJobException e)`
`66`	`68`	`{`
`@@ -108,6 +110,12 @@ public void registerFieldCustomizer(JBrowseFieldCustomizer customizer)`
`108`	`110`	`_customizers.add(customizer);`
`109`	`111`	`}`
`110`	`112`
	`113`	`+ @Override`
	`114`	`+ public void prepareLuceneIndex(File vcf, File indexDir, Logger log, List<String> infoFieldsForFullTextSearch, boolean allowLenientLuceneProcessing) throws PipelineJobException`
	`115`	`+ {`
	`116`	`+ JBrowseLucenePipelineJob.prepareLuceneIndex(vcf, indexDir, log, infoFieldsForFullTextSearch, allowLenientLuceneProcessing);`
	`117`	`+ }`
	`118`	`+`
`111`	`119`	`public Map<String, Map<String, Object>> resolveSubjects(List<String> subjects, User u, Container c)`
`112`	`120`	`{`
`113`	`121`	`Map<String, Map<String, Object>> ret = new HashMap<>();`
Original file line number	Diff line number	Diff line change
`@@ -114,10 +114,10 @@ public boolean shouldExist()`
`114`	`114`	`abstract protected TableSelector getSelector();`
`115`	`115`
`116`	`116`	`@Override`
`117`		`- public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException`
	`117`	`+ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException`
`118`	`118`	`{`
`119`	`119`	`createGtf(log, throwIfNotPrepared, forceReprocess);`
`120`		`- return super.prepareResource(log, throwIfNotPrepared, forceReprocess);`
	`120`	`+ return super.prepareResource(u, log, throwIfNotPrepared, forceReprocess);`
`121`	`121`	`}`
`122`	`122`
`123`	`123`	`public void createGtf(Logger log, boolean throwOnNotFound, boolean forceRecreate) throws PipelineJobException`
Original file line number	Diff line number	Diff line change
`@@ -213,7 +213,7 @@ public void ensureJsonFilesPrepared(User u, Logger log) throws PipelineJobExcept`
`213`	`213`	`{`
`214`	`214`	`try`
`215`	`215`	`{`
`216`		`- x.prepareResource(log, false, false);`
	`216`	`+ x.prepareResource(u, log, false, false);`
`217`	`217`	`}`
`218`	`218`	`catch (Exception e)`
`219`	`219`	`{`
Original file line number	Diff line number	Diff line change
`@@ -51,6 +51,7 @@`
`51`	`51`	`import org.labkey.api.view.UnauthorizedException;`
`52`	`52`	`import org.labkey.jbrowse.JBrowseManager;`
`53`	`53`	`import org.labkey.jbrowse.JBrowseSchema;`
	`54`	`+import org.labkey.jbrowse.pipeline.IndexVariantsStep;`
`54`	`55`	`import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob;`
`55`	`56`	`import org.labkey.sequenceanalysis.run.util.TabixRunner;`
`56`	`57`
`@@ -297,7 +298,7 @@ else if (TRACK_TYPES.bam.getFileType().isType(targetFile.getFile()) \|\| TRACK_TYP`
`297`	`298`	`}`
`298`	`299`	`else if (TRACK_TYPES.gff.getFileType().isType(targetFile.getFile()))`
`299`	`300`	`{`
`300`		`- ret = getGxfTrack(log, targetFile, rg);`
	`301`	`+ ret = getGxfTrack(u, log, targetFile, rg);`
`301`	`302`	`}`
`302`	`303`	`else if (TRACK_TYPES.gtf.getFileType().isType(targetFile.getFile()))`
`303`	`304`	`{`
`@@ -308,7 +309,7 @@ else if (TRACK_TYPES.gtf.getFileType().isType(targetFile.getFile()))`
`308`	`309`	`}`
`309`	`310`	`else if (TRACK_TYPES.bed.getFileType().isType(targetFile.getFile()))`
`310`	`311`	`{`
`311`		`- ret = getBedTrack(log, targetFile, rg);`
	`312`	`+ ret = getBedTrack(u, log, targetFile, rg);`
`312`	`313`	`}`
`313`	`314`	`else if (TRACK_TYPES.bw.getFileType().isType(targetFile.getFile()))`
`314`	`315`	`{`
`@@ -643,12 +644,12 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe`
`643`	`644`	`return ret;`
`644`	`645`	`}`
`645`	`646`
`646`		`- private JSONObject getBedTrack(Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException`
	`647`	`+ private JSONObject getBedTrack(User u, Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException`
`647`	`648`	`{`
`648`	`649`	`String adapterType = "BedTabixAdapter";`
`649`	`650`	`String prefix = "bed";`
`650`	`651`
`651`		`- return getTabixTrack(log, targetFile, rg, adapterType, prefix);`
	`652`	`+ return getTabixTrack(u, log, targetFile, rg, adapterType, prefix);`
`652`	`653`	`}`
`653`	`654`
`654`	`655`	`private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException`
`@@ -682,12 +683,12 @@ private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenom`
`682`	`683`	`return ret;`
`683`	`684`	`}`
`684`	`685`
`685`		`- private JSONObject getGxfTrack(Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException`
	`686`	`+ private JSONObject getGxfTrack(User u, Logger log, ExpData targetFile, ReferenceGenome rg) throws PipelineJobException`
`686`	`687`	`{`
`687`	`688`	`String adapterType = TRACK_TYPES.gff.getFileType().isType(targetFile.getFile()) ? "Gff3TabixAdapter" : "GtfTabixAdapter";`
`688`	`689`	`String prefix = TRACK_TYPES.gff.getFileType().isType(targetFile.getFile()) ? "gff" : "gtf";`
`689`	`690`
`690`		`- return getTabixTrack(log, targetFile, rg, adapterType, prefix);`
	`691`	`+ return getTabixTrack(u, log, targetFile, rg, adapterType, prefix);`
`691`	`692`	`}`
`692`	`693`
`693`	`694`	`public String getTrackType()`
`@@ -729,7 +730,7 @@ else if (TRACK_TYPES.bw.getFileType().isType(targetFile.getFile()))`
`729`	`730`	`}`
`730`	`731`	`}`
`731`	`732`
`732`		`- private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome rg, String adapterType, String prefix) throws PipelineJobException`
	`733`	`+ private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, ReferenceGenome rg, String adapterType, String prefix) throws PipelineJobException`
`733`	`734`	`{`
`734`	`735`	`JSONObject ret = new JSONObject();`
`735`	`736`	`ret.put("type", getTrackType());`
`@@ -743,7 +744,7 @@ private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome`
`743`	`744`	`}});`
`744`	`745`
`745`	`746`	`// if not gzipped, we need to process it:`
`746`		`- File gzipped = prepareResource(log, true, false);`
	`747`	`+ File gzipped = prepareResource(u, log, true, false);`
`747`	`748`	`final String url;`
`748`	`749`	`if (!getExpData().getFile().equals(gzipped))`
`749`	`750`	`{`
`@@ -809,7 +810,7 @@ protected boolean needsGzip()`
`809`	`810`	`return !isGzipped() && (TRACK_TYPES.gff.getFileType().isType(fn) \|\| TRACK_TYPES.gtf.getFileType().isType(fn) \|\| TRACK_TYPES.bed.getFileType().isType(fn));`
`810`	`811`	`}`
`811`	`812`
`812`		`- public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException`
	`813`	`+ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, boolean forceReprocess) throws PipelineJobException`
`813`	`814`	`{`
`814`	`815`	`ExpData expData = getExpData();`
`815`	`816`	`if (expData == null)`
`@@ -939,6 +940,13 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc`
`939`	`940`
`940`	`941`	`if (shouldHaveFreeTextSearch())`
`941`	`942`	`{`
	`943`	`+ // TODO:`
	`944`	`+ // Try to find a matching existing index:`
	`945`	`+ // Container targetContainer = getContainerObj().isWorkbookOrTab() ? getContainerObj().getParent() : getContainerObj();`
	`946`	`+ // TableInfo ti = QueryService.get().getUserSchema(u, targetContainer, JBrowseSchema.SEQUENCE_ANALYSIS).getTable("outputfiles");`
	`947`	`+ // SimpleFilter filter = new SimpleFilter(FieldKey.fromString("category"), IndexVariantsStep.CATEGORY);`
	`948`	`+ // filter.addCondition(FieldKey.fromString("library_id"), rg)`
	`949`	`+`
`942`	`950`	`File luceneDir = getExpectedLocationOfLuceneIndex(throwIfNotPrepared);`
`943`	`951`	`long sizeInGb = targetFile.length() / (1024 * 1024 * 1024);`
`944`	`952`	`log.debug("preparing lucene index, VCF size: " + sizeInGb);`
Original file line number	Diff line number	Diff line change
`@@ -135,7 +135,7 @@ private void prepareGenome(boolean forceReprocess) throws PipelineJobException`
`135`	`135`	`getJob().getLogger().info("total files to reprocess: " + jsonFiles.size());`
`136`	`136`	`for (JsonFile f : jsonFiles)`
`137`	`137`	`{`
`138`		`- f.prepareResource(getJob().getLogger(), false, forceReprocess);`
	`138`	`+ f.prepareResource(getJob().getUser(), getJob().getLogger(), false, forceReprocess);`
`139`	`139`	`}`
`140`	`140`	`}`
`141`	`141`
`@@ -152,7 +152,7 @@ private void reprocessResources() throws PipelineJobException`
`152`	`152`	`getJob().getLogger().info("total files to reprocess: " + jsonFiles.size());`
`153`	`153`	`for (JsonFile f : jsonFiles)`
`154`	`154`	`{`
`155`		`- f.prepareResource(getJob().getLogger(), false, true);`
	`155`	`+ f.prepareResource(getJob().getUser(), getJob().getLogger(), false, true);`
`156`	`156`	`}`
`157`	`157`	`}`
`158`	`158`
`@@ -257,7 +257,7 @@ private void createOrAddToSession() throws PipelineJobException`
`257`	`257`	`trackRecord = Table.insert(getJob().getUser(), databaseMembers, trackRecord);`
`258`	`258`	`databaseMemberRecordsCreated.add((Integer)trackRecord.get("rowid"));`
`259`	`259`
`260`		`- json.prepareResource(getJob().getLogger(), false, false);`
	`260`	`+ json.prepareResource(getJob().getUser(), getJob().getLogger(), false, false);`
`261`	`261`	`}`
`262`	`262`	`}`
`263`	`263`	`else`
`@@ -308,7 +308,7 @@ private void createOrAddToSession() throws PipelineJobException`
`308`	`308`	`trackRecord = Table.insert(getJob().getUser(), databaseMembers, trackRecord);`
`309`	`309`	`databaseMemberRecordsCreated.add((Integer) trackRecord.get("rowid"));`
`310`	`310`
`311`		`- json.prepareResource(getJob().getLogger(), false, false);`
	`311`	`+ json.prepareResource(getJob().getUser(), getJob().getLogger(), false, false);`
`312`	`312`	`}`
`313`	`313`	`}`
`314`	`314`