Workaround for more strict jbrowse enforcement of trackId vs trix index (#163)

Author: bbimber

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.js

@@ -1,7 +1,7 @@
-import {FIELD_NAME_MAP, INFO_FIELD_GROUPS, IGNORED_INFO_FIELDS} from "./fields";
-import {ActionURL} from "@labkey/api";
+import {FIELD_NAME_MAP, IGNORED_INFO_FIELDS, INFO_FIELD_GROUPS} from "./fields";
 import {Chart} from "react-google-charts";
 import {style as styles} from "./style";
+import {getGenotypeURL} from "../../../../utils";
 
 export default jbrowse => {
     const {
@@ -245,8 +245,7 @@ export default jbrowse => {
             const start = feat["POS"];
             const end = feat["end"];
 
-            const link = ActionURL.buildURL("jbrowse", "genotypeTable.view", null, {trackId: trackId, chr: contig, start: start, stop: end})
-            const href = <a href={link} target="_blank">Click here to view sample-level genotypes</a>
+            const href = <a href={getGenotypeURL(trackId, contig, start, end)} target="_blank">Click here to view sample-level genotypes</a>
 
             setState(
                     <div>

jbrowse/src/client/JBrowse/utils.ts

@@ -133,7 +133,7 @@ export async function fetchSession(queryParam, sessionId, nativePlugins, refThem
             }
         },
         failure: function(res){
-            handleFailure("There was an error: " + res.status, sessionId, trackId, isTable)
+            handleFailure("There was an error: " + res.status, sessionId, trackId, isTable, false)
         },
         params: {session: sessionId, activeTracks: activeTracks ? activeTracks.join(',') : undefined}
     });
@@ -244,10 +244,10 @@ function serializeInfoFilters(track) {
     return track.configuration.trackId + ":" + encodeURIComponent(track.configuration.displays[0].renderer.infoFilters.valueJSON)
 }
 
-function handleFailure(error, sessionId?, trackId?, isTable?) {
+function handleFailure(error, sessionId?, trackId?, isTable?, reloadOnFailure = true) {
     alert(error)
 
-    if (sessionId && trackId) {
+    if (reloadOnFailure && sessionId && trackId) {
         if (isTable) {
             navigateToTable(sessionId, "", trackId)
         } else {
@@ -257,5 +257,12 @@ function handleFailure(error, sessionId?, trackId?, isTable?) {
 }
 
 export function getGenotypeURL(trackId, contig, start, end) {
+    // NOTE: due to jbrowse/trix behavior, the trackId that gets serialized into the trix index is the actual trackGUID plus the filename.
+    // Since this action expects the GUID alone, detect long filenames and subset.
+    // TODO: once this behavior is fixed in jbrowse, remove this logic
+    if (trackId.length > 36) {
+        trackId = trackId.substr(0,36)
+    }
+
     return ActionURL.buildURL("jbrowse", "genotypeTable.view", null, {trackId: trackId, chr: contig, start: start, stop: end})
 }

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

@@ -501,7 +501,9 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
     {
         JSONObject ret = new JSONObject();
         ret.put("type", getTrackType());
-        ret.put("trackId", getObjectId());
+        final File finalLocation = getLocationOfProcessedTrack(false);
+        ret.put("trackId", finalLocation == null ? null : finalLocation.getName());
+        ret.put("trackGUID", getObjectId());
         ret.put("name", getLabel());
         ret.put("assemblyNames", new JSONArray(){{
             put(JBrowseSession.getAssemblyName(rg));
@@ -567,7 +569,9 @@ private JSONObject getBamTrack(Logger log, ExpData targetFile, ReferenceGenome r
     {
         JSONObject ret = new JSONObject();
         ret.put("type", getTrackType());
-        ret.put("trackId", getObjectId());
+        final File finalLocation = getLocationOfProcessedTrack(false);
+        ret.put("trackId", finalLocation == null ? null : finalLocation.getName());
+        ret.put("trackGUID", getObjectId());
         ret.put("name", getLabel());
         ret.put("category", new JSONArray(){{
             put(getCategory());
@@ -651,7 +655,9 @@ private JSONObject getTabixTrack(Logger log, ExpData targetFile, ReferenceGenome
     {
         JSONObject ret = new JSONObject();
         ret.put("type", getTrackType());
-        ret.put("trackId", getObjectId());
+        final File finalLocation = getLocationOfProcessedTrack(false);
+        ret.put("trackId", finalLocation == null ? null : finalLocation.getName());
+        ret.put("trackGUID", getObjectId());
         ret.put("name", getLabel());
         ret.put("category", new JSONArray(){{
             put(getCategory());
@@ -833,8 +839,6 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
                 wrapper.setWorkingDir(targetFile.getParentFile());
                 wrapper.setThrowNonZeroExits(true);
 
-                //TODO: eventually remove this. see: https://github.com/GMOD/jbrowse-components/issues/2354#issuecomment-926320747
-                wrapper.addToEnvironment("DEBUG", "*");
                 wrapper.execute(Arrays.asList(exe.getPath(), "text-index", "--force", "--quiet", "--attributes", StringUtils.join(attributes, ","), "--prefixSize", "5", "--file", targetFile.getPath()));
                 if (!ixx.exists())
                 {
@@ -849,31 +853,6 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
                 {
                     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);
-                }
             }
         }