diff tracks/CanvasFeatures.py @ 38:d17f629f5486 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty

--- a/tracks/CanvasFeatures.py	Thu Feb 15 16:54:36 2018 -0500
+++ b/tracks/CanvasFeatures.py	Fri Apr 06 13:44:56 2018 -0400
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import os
 import json
 import logging
 
@@ -11,22 +12,41 @@
         super(CanvasFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
 
     def prepareExtraSetting(self):
-        """ set CanvasFeatures configuration options """
-        extraConfigs = dict()
-        self.extraSettings["clientConfig"] = dict()
-        self.extraSettings["config"] = dict()
+        if 'category' not in self.extraSettings or not self.extraSettings['category']:
+            self.extraSettings['category'] = "Default group"
+        self.extraSettings['style'] = {}
+        self.extraSettings['style']['className'] = 'feature'
         if 'color' not in self.extraSettings or not self.extraSettings['color']:
-            self.extraSettings["clientConfig"]['color'] = "#daa520"
+            self.extraSettings['style']['color'] = "#FFA600"
         else:
-            self.extraSettings["clientConfig"]['color'] = self.extraSettings['color']
-        if 'category' not in self.extraSettings or not self.extraSettings['category']:
-            self.extraSettings["config"]['category'] = "Default group"
-        else:
-            self.extraSettings["config"]['category'] = self.extraSettings['category']
-        if 'glyph' in self.extraSettings:
-            self.extraSettings["config"]['glyph'] = self.extraSettings['glyph']
-        if 'transcriptType' in self.extraSettings:
-            self.extraSettings['config']['transcriptType'] = self.extraSettings['transcriptType']
-        extraConfigs["config"] = json.dumps(self.extraSettings["config"])
-        extraConfigs["clientConfig"] = json.dumps(self.extraSettings["clientConfig"])
-        return extraConfigs
\ No newline at end of file
+            self.extraSettings['style']['color'] = self.extraSettings['color']
+        track = dict()
+        track['type'] = 'JBrowse/View/Track/' + self.trackType
+        track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix'
+        track['urlTemplate'] = os.path.join('tracks', self.trackName)
+        track['label'] = self.trackLabel
+        track['category'] = self.extraSettings['category']
+        track['style'] = self.extraSettings['style']
+        extraConfigs = track
+        return extraConfigs
+
+    # def prepareExtraSetting(self):
+    #     """ set CanvasFeatures configuration options """
+    #     extraConfigs = dict()
+    #     self.extraSettings["clientConfig"] = dict()
+    #     self.extraSettings["config"] = dict()
+    #     if 'color' not in self.extraSettings or not self.extraSettings['color']:
+    #         self.extraSettings["clientConfig"]['color'] = "#daa520"
+    #     else:
+    #         self.extraSettings["clientConfig"]['color'] = self.extraSettings['color']
+    #     if 'category' not in self.extraSettings or not self.extraSettings['category']:
+    #         self.extraSettings["config"]['category'] = "Default group"
+    #     else:
+    #         self.extraSettings["config"]['category'] = self.extraSettings['category']
+    #     if 'glyph' in self.extraSettings:
+    #         self.extraSettings["config"]['glyph'] = self.extraSettings['glyph']
+    #     if 'transcriptType' in self.extraSettings:
+    #         self.extraSettings['config']['transcriptType'] = self.extraSettings['transcriptType']
+    #     extraConfigs["config"] = json.dumps(self.extraSettings["config"])
+    #     extraConfigs["clientConfig"] = json.dumps(self.extraSettings["clientConfig"])
+    #     return extraConfigs
\ No newline at end of file