diff tracks/TrackStyles.py @ 6:237707a6b74d draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tracks/TrackStyles.py	Thu Feb 15 17:05:05 2018 -0500
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+import os
+import json
+import logging
+from mako.lookup import TemplateLookup
+
+class TrackStyles(object):
+    def __init__(self, tool_directory, species_folder, trackListFile, cssFolderName="css", cssFileName="custom_track_styles.css"):
+        self.logger = logging.getLogger(__name__)
+        self.tool_directory = tool_directory
+        self.species_folder = species_folder
+        self.trackList = trackListFile
+        self.cssFolderName = cssFolderName
+        self.cssFileName = cssFileName
+        self.cssFilePath = self._createCssFile()
+        self.cssTemplate = self._getCssTemplate()
+        self._addCssToTrackList()
+        
+
+    def addCustomColor(self, feature_class_name, feature_color):
+        with open(self.cssFilePath, 'a+') as css:
+            htmlMakoRendered = self.cssTemplate.render(
+            label = feature_class_name,
+            color = feature_color
+        )
+            css.write(htmlMakoRendered)
+        self.logger.debug("create customized track css class: cssFilePath= %s", self.cssFilePath)
+   
+
+    def _createCssFile(self):
+        cssFolderPath = os.path.join(self.species_folder, self.cssFolderName)
+        cssFilePath = os.path.join(cssFolderPath, self.cssFileName)
+        if not os.path.exists(cssFilePath):
+            if not os.path.exists(cssFolderPath):
+                os.mkdir(cssFolderPath)
+            os.mknod(cssFilePath)   
+            os.chmod(cssFilePath, 0o755)
+        return cssFilePath
+
+    def _getCssTemplate(self):
+        mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
+                                  output_encoding='utf-8', encoding_errors='replace')
+        cssTemplate = mylookup.get_template("custom_track_styles.css")
+        return cssTemplate
+
+    
+    def _addCssToTrackList(self):
+        with open(self.trackList, 'r+') as track:
+            data = json.load(track)
+            css_path = os.path.join('data', self.cssFolderName, self.cssFileName)
+            data['css'] = {'url': css_path}
+            json_string = json.dumps(data, indent=4, separators=(',', ': '))
+            track.seek(0)
+            track.write(json_string)
+            track.truncate()
+        self.logger.debug("added customized css url to trackList.json")
+        
+
+    
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