Add code to ensure the trackId in trix indexes matches the ID used in JBrowse

Author: bbimber

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

@@ -32,6 +32,7 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
+import org.labkey.api.reader.Readers;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
@@ -46,13 +47,16 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
 import org.labkey.api.view.UnauthorizedException;
+import org.labkey.api.writer.PrintWriters;
 import org.labkey.jbrowse.JBrowseManager;
 import org.labkey.jbrowse.JBrowseSchema;
 import org.labkey.sequenceanalysis.run.util.TabixRunner;
 
 import javax.annotation.Nullable;
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.sql.SQLException;
 import java.util.Arrays;
 import java.util.Collections;
@@ -836,6 +840,40 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
                 {
                     throw new PipelineJobException("Unable to find expected index file: " + ixx.getPath());
                 }
+
+                // See here: https://github.com/GMOD/jbrowse-components/issues/2344
+                // for background. this hackery is needed to ensure the trackId listed in the ix matches the GUID, not the filename:
+                log.info("Updating trackId in trix ix file");
+                File ix = getExpectedLocationOfIndexFile(".ix", false);
+                if (!ix.exists())
+                {
+                    throw new PipelineJobException("Unable to find file: " + ix.getPath());
+                }
+
+                File ixCopy = new File(ix.getPath() + ".tmp");
+                try (PrintWriter writer = PrintWriters.getPrintWriter(ixCopy); BufferedReader reader = Readers.getReader(ix))
+                {
+                    String line;
+                    while ((line = reader.readLine()) != null)
+                    {
+                        line = line.replaceAll("\"" + targetFile.getName() + "\"", "\"" + getObjectId() + "\"");
+                        writer.println(line);
+                    }
+                }
+                catch (IOException e)
+                {
+                    throw new PipelineJobException(e);
+                }
+
+                try
+                {
+                    ix.delete();
+                    FileUtils.moveFile(ixCopy, ix);
+                }
+                catch (IOException e)
+                {
+                    throw new PipelineJobException(e);
+                }
             }
         }