allow overlap filter to be configurable (#2585)

* allow overlap filter to be configurable * updated config * updated jbrowse track for pruning
GMOD · Feb 22, 2021 · 20caebb · 20caebb
1 parent b9c8e2d
commit 20caebb
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Showing 3 changed files with 22 additions and 17 deletions.
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -8,6 +8,7 @@ Features
 - Added system info web service [2557](https://github.com/GMOD/Apollo/pull/2557).
 - Add "merged from" comment to merged in transcript and gene [2567](https://github.com/GMOD/Apollo/issues/2567).
 - Added support for "obsolete", and partials in the interface for GFF3s [2573](https://github.com/GMOD/Apollo/pull/2573).
+- Allow overlap filter to be configurable [2582](https://github.com/GMOD/Apollo/issues/2582).
 
 Bug Fixes:
 

diff --git a/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy b/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy
@@ -25,7 +25,6 @@ class JbrowseController {
     def preferenceService
     def jbrowseService
     def servletContext
-    def configWrapperService
     def trackService
 
     def chooseOrganismForJbrowse() {
@@ -62,7 +61,6 @@ class JbrowseController {
 
         // case 3 - validated login (just read from preferences, then
         if (permissionService.currentUser && clientToken) {
-//            Organism organism = preferenceService.getOrganismForToken(clientToken)
             Organism organism = preferenceService.getOrganismForTokenInDB(clientToken)
             if(organism){
                 // we need to generate a client_token and do a redirection
@@ -393,7 +391,7 @@ class JbrowseController {
 
      * @param tracksArray
      */
-    def pruneTracks(JSONArray tracksArray){
+    private JSONArray pruneTracks(JSONArray tracksArray){
         JSONArray returnArray = new JSONArray()
 
         for(track in tracksArray){
@@ -523,14 +521,18 @@ class JbrowseController {
         response.outputStream.close()
     }
 
-    private static boolean isCacheableFile(String fileName) {
-        if (fileName.endsWith(".txt") || fileName.endsWith("txtz") || fileName.endsWith("csv")) {
-            return true;
-        }
-        if (fileName.endsWith(".json") || fileName.endsWith("jsonz")) {
-            String[] names = fileName.split("\\/");
-            String requestName = names[names.length - 1];
-            return requestName.startsWith("lf-");
+    private boolean isCacheableFile(String fileName) {
+        try {
+            if (fileName.endsWith(".txt") || fileName.endsWith("txtz") || fileName.endsWith("csv")) {
+                return true;
+            }
+            if (fileName.endsWith(".json") || fileName.endsWith("jsonz")) {
+                String[] names = fileName.split("\\/");
+                String requestName = names[names.length - 1];
+                return requestName.startsWith("lf-");
+            }
+        } catch (e) {
+            log.warn "Problem trying to cache file ${fileName}: ${e}"
         }
 
         return false;
@@ -592,13 +594,13 @@ class JbrowseController {
 
         String mimeType = getServletContext().getMimeType(fileName);
 
-        String eTag = createHashFromFile(file);
-        String dateString = formatLastModifiedDate(file);
 
-//        if (isCacheableFile(fileName)) {
+        if (isCacheableFile(fileName)) {
+            String eTag = createHashFromFile(file);
+            String dateString = formatLastModifiedDate(file);
             response.setHeader("ETag", eTag);
             response.setHeader("Last-Modified", dateString);
-//        }
+        }
 
         response.setContentType(mimeType);
         // Set content size

diff --git a/grails-app/controllers/org/bbop/apollo/TrackController.groovy b/grails-app/controllers/org/bbop/apollo/TrackController.groovy
@@ -22,7 +22,7 @@ class TrackController {
     def trackService
     def svgService
 
-  final double OVERLAP_FILTER = 10.0
+  final double DEFAULT_OVERLAP_FILTER = 20.0
 
   def beforeInterceptor = {
         if (params.action == "featuresByName"
@@ -196,6 +196,7 @@ class TrackController {
             , @RestApiParam(name = "ignoreCache", type = "boolean", paramType = RestApiParamType.QUERY, description = "(default false).  Use cache for request if available.")
             , @RestApiParam(name = "flatten", type = "string", paramType = RestApiParamType.QUERY, description = "Brings nested top-level components to the root level.  If not provided or 'false' it will not flatten.  Default is 'gene'.")
             , @RestApiParam(name = "type", type = "string", paramType = RestApiParamType.QUERY, description = ".json or .svg")
+            , @RestApiParam(name = "overlapFilter", type = "double", paramType = RestApiParamType.QUERY, description = "(default 20).  The widget of overlapping genes to display.  1 would be only features directly overlapping.  Double_max would be any gene that overlaps, even if it overlaps the entire chromosome.")
     ])
     @Transactional
     def featuresByLocation(String organismString, String trackName, String sequence, Long fmin, Long fmax, String type) {
@@ -206,6 +207,7 @@ class TrackController {
         String flatten = params.flatten != null ? params.flatten : 'gene'
         flatten = flatten == 'false' ? '' : flatten
         Boolean ignoreCache = params.ignoreCache != null ? Boolean.valueOf(params.ignoreCache) : false
+        double overlapFilter = params.overlapFilter != null ? Double.valueOf(params.overlapFilter) : DEFAULT_OVERLAP_FILTER
         Map paramMap = new TreeMap<>()
         paramMap.put("type", type)
         if (nameSet) {
@@ -267,7 +269,7 @@ class TrackController {
 
         renderedArray = renderedArray.unique{  it.name } as JSONArray
         renderedArray = renderedArray.findAll{  it ->
-          return (it.fmax - it.fmin) < (OVERLAP_FILTER*(fmax - fmin))
+          return (it.fmax - it.fmin) < (overlapFilter*(fmax - fmin))
         } as JSONArray
 
       if (type == "json") {