Merge b007a85 into 9b35abf

GMOD · Feb 26, 2019 · 8094bcf · 8094bcf
2 parents 9b35abf + b007a85
commit 8094bcf
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Showing 21 changed files with 1,037 additions and 120 deletions.
diff --git a/client/apollo/js/JSONUtils.js b/client/apollo/js/JSONUtils.js
@@ -362,10 +362,6 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
         afeature.type.name = typename;
     }
 
-    // if (useName && name) {
-    //     afeature.name = name;
-    // }
-
     var id = jfeature.get('id');
     var name = jfeature.get('name');
     if (useName) {

diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/client/apollo/js/View/Track/AnnotTrack.js
@@ -330,7 +330,11 @@ define([
                         filteredTrack.type = trackConfig.type;
                         filteredTrack.category = trackConfig.category;
                         filteredTrack.urlTemplate = trackConfig.urlTemplate;
+                        filteredTrack.storeClass = trackConfig.storeClass;
                         filteredTrack.visible = visible;
+                        if(trackConfig.apollo){
+                            filteredTrack.apollo = trackConfig.apollo;
+                        }
                         filteredTrackList.push(filteredTrack);
                     }
 

diff --git a/grails-app/conf/Config.groovy b/grails-app/conf/Config.groovy
@@ -400,7 +400,7 @@ auditLog {
 jbrowse {
     git {
         url = "https://github.com/gmod/jbrowse"
-        branch = "1.16.2-release"
+        branch = "1.16.3-release"
 //        branch = "dev"
 //        tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
         alwaysPull = true

diff --git a/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy b/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy
@@ -1,12 +1,11 @@
 package org.bbop.apollo
 
 import grails.converters.JSON
-import grails.transaction.NotTransactional
 import liquibase.util.file.FilenameUtils
 import org.apache.shiro.SecurityUtils
 import org.bbop.apollo.gwt.shared.ClientTokenGenerator
 import org.bbop.apollo.gwt.shared.FeatureStringEnum
-import org.bbop.apollo.sequence.Range
+import org.bbop.apollo.sequence.Range // this line is needed, even if hte import doesn't show it
 import org.codehaus.groovy.grails.web.json.JSONArray
 import org.codehaus.groovy.grails.web.json.JSONObject
 
@@ -16,7 +15,6 @@ import java.text.SimpleDateFormat
 
 import static org.springframework.http.HttpStatus.NOT_FOUND
 
-//@CompileStatic
 class JbrowseController {
 
     private static final int DEFAULT_BUFFER_SIZE = 10240; // ..bytes = 10KB.
@@ -395,7 +393,6 @@ class JbrowseController {
 
      * @param tracksArray
      */
-    @NotTransactional
     def pruneTracks(JSONArray tracksArray){
         JSONArray returnArray = new JSONArray()
 

diff --git a/grails-app/controllers/org/bbop/apollo/OrganismController.groovy b/grails-app/controllers/org/bbop/apollo/OrganismController.groovy
diff --git a/grails-app/services/org/bbop/apollo/FileService.groovy b/grails-app/services/org/bbop/apollo/FileService.groovy
@@ -147,9 +147,9 @@ class FileService {
                 continue;
             }
 
-            FileOutputStream fos = new FileOutputStream(outputFile);
-            IOUtils.copy(tais, fos);
-            fos.close();
+            FileOutputStream fos = new FileOutputStream(outputFile)
+            IOUtils.copy(tais, fos)
+            fos.close()
         }
 
         if (tempDir) {
@@ -170,6 +170,32 @@ class FileService {
         }
     }
 
+    def storeWithNewName(CommonsMultipartFile file, String path, String directoryName,String newName ) {
+        File pathFile = new File(path)
+        if (!pathFile.exists()) {
+            pathFile.mkdirs()
+        }
+        int suffixIndex = newName.indexOf(".")
+        if(suffixIndex<1){
+            throw new RuntimeException("Invalid filename, must have a suffix: [" +newName+"]")
+        }
+        String suffix = newName.substring(suffixIndex)
+        String updatedName = directoryName.replaceAll(" ","_") + suffix
+//        /opt/temporary/apollo/6503-nf_test3/raw || test2 || volvox-sorted.bam
+//        /opt/temporary/apollo/6503-nf_test3/raw || test2 .bam
+        String destinationFileName = path + File.separator + updatedName
+        File destinationFile = new File(destinationFileName)
+        try {
+            println  "NEW NAME transferring track file to ${destinationFileName}"
+            file.transferTo(destinationFile)
+//            destinationFile.renameTo(new File())
+            println  "NEW NAME DONE transferringfile to ${destinationFileName.size()}"
+
+        } catch (Exception e) {
+            println e.message
+        }
+    }
+
 
     def store(CommonsMultipartFile file, String path, String directoryName = null, boolean tempDir = false) {
         File pathFile = new File(path)
@@ -182,10 +208,12 @@ class FileService {
 
         File destinationFile = new File(destinationFileName)
         try {
-            log.debug "transferring track file to ${destinationFileName}"
+            println  "transferring track file to ${destinationFileName}"
             file.transferTo(destinationFile)
+            println  "DONE transferringfile to ${destinationFileName.size()}"
+
         } catch (Exception e) {
-            log.error e.message
+            println e.message
         }
     }
 

diff --git a/grails-app/services/org/bbop/apollo/TrackService.groovy b/grails-app/services/org/bbop/apollo/TrackService.groovy
@@ -483,6 +483,26 @@ class TrackService {
         return null
     }
 
+    /**
+     *
+     * @param tracksArray
+     * @param trackName
+     * @return
+     */
+    @NotTransactional
+    def removeTrackFromArray(JSONArray tracksArray, String trackName) {
+        JSONArray returnArray = new JSONArray()
+        for (int i = 0; i < tracksArray.size(); i++) {
+            JSONObject obj = tracksArray.getJSONObject(i)
+            println "obj ${obj.label} vs ${trackName}"
+            if (obj.getString("label") != trackName) {
+                returnArray.add(obj)
+            }
+        }
+
+        return returnArray
+    }
+
     /**
      * Removes plugins included in annot.json (which is just WebApollo)
      * @param pluginsArray

diff --git a/install_jbrowse.sh b/install_jbrowse.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-./apollo install-tools
+./apollo jbrowse-tools
 
 #done_message () {
 #    if [ $? == 0 ]; then

diff --git a/sample-h2-apollo-config.groovy b/sample-h2-apollo-config.groovy
@@ -77,7 +77,7 @@ environments {
 //jbrowse {
 //    git {
 //        url= "https://github.com/GMOD/jbrowse"
-//        tag = "1.16.2-release"
+//        tag = "1.16.3-release"
 ////        branch = "dev"
 ////        hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
 //        alwaysPull = true

diff --git a/sample-mysql-apollo-config.groovy b/sample-mysql-apollo-config.groovy
@@ -76,7 +76,7 @@ environments {
 //jbrowse {
 //    git {
 //        url= "https://github.com/GMOD/jbrowse"
-//         tag = "1.16.2-release"
+//         tag = "1.16.3-release"
 ////        branch = "dev"
 ////        hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
 //        alwaysPull = true

diff --git a/sample-postgres-apollo-config.groovy b/sample-postgres-apollo-config.groovy
@@ -121,7 +121,7 @@ environments {
 //jbrowse {
 //    git {
 //        url= "https://github.com/GMOD/jbrowse"
-//         tag = "1.16.2-release"
+//         tag = "1.16.3-release"
 ////        branch = "dev"
 ////        hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
 //        alwaysPull = true