diff tracks/IntervalFeatures.py @ 38:d17f629f5486 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tracks/IntervalFeatures.py	Fri Apr 06 13:44:56 2018 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+import json
+import logging
+import collections
+
+from TrackDb import TrackDb
+from util import subtools
+from util import santitizer
+
+class Features(TrackDb):
+    def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
+        super(Features, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
+
+    def prepareExtraSetting(self):
+        if self.trackType == 'HTMLFeatures':
+            self.prepareHTMLExtraSetting()
+        else:
+            self.prepareCanvasExtraSetting()
+
+    def prepareHTMLExtraSetting(self):
+        """ set HTMLFeatures configuration options """
+        extraConfigs = dict()
+        self.extraSettings["clientConfig"] = dict()
+        self.extraSettings["config"] = dict()
+        if 'type' in self.extraSettings:
+            extraConfigs["type"] = self.extraSettings['type']
+        if 'color' in self.extraSettings and self.extraSettings['color']:
+            extraConfigs['feature_color'] = self.extraSettings['color']
+        else:
+            extraConfigs['feature_color'] = "#000000"
+        #self.extraSettings['clientConfig']['color'] = self.extraSettings['color']
+        if 'subfeatureClasses' in self.extraSettings:
+            subfeature_css_class = santitizer.sanitize_name(self.trackLabel + "_" + self.extraSettings['subfeatureClasses'])
+            extraConfigs['subfeatureClasses'] = {self.extraSettings['subfeatureClasses']: subfeature_css_class}
+
+        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']
+
+        extraConfigs['config'] = json.dumps(self.extraSettings["config"])
+        extraConfigs['clientConfig'] = json.dumps(self.extraSettings["clientConfig"])
+        return extraConfigs
+
+    def prepareCanvasExtraSetting(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
+
+    def createTrackDb(self):
+        self.track_db = collections.OrderedDict([("track",self.trackName),
+                                                 ("trackLabel",self.trackLabel),
+                                                 ("trackDataURL",self.trackDataURL),
+                                                 ("dataType", self.dataType),
+                                                 ("trackType", self.trackType)]
+                                                )
+
+
+        htmlExtraConfigs = self.prepareHTMLExtraSetting()
+        self.logger.debug("Generate extraConfigs for htmlFeatures = %s", json.dumps(htmlExtraConfigs))
+        self.track_db["html"]["options"] = htmlExtraConfigs
+        canvasExtraConfigs = self.prepareCanvasExtraSetting()
+        self.logger.debug("Generate extraConfigs for canvasFeatures = %s", json.dumps(canvasExtraConfigs))
+        self.track_db["canvas"]["options"] = canvasExtraConfigs
+        self.logger.debug("TrackDb object is created track_db = %s ", json.dumps(self.track_db))
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