diff TrackDb.py @ 1:85195e0d4b71 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TrackDb.py	Fri Sep 29 13:32:23 2017 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/python
+import collections
+from util import santitizer
+
+class TrackDb(object):
+    """docstring for TrackDb"""
+    def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", extraSettings=None):
+        #super(TrackDb, self).__init__()
+        not_init_message = "The {0} is not initialized." 
+        if trackName is None:
+            raise TypeError(not_init_message.format('trackName'))
+        if longLabel is None:
+            raise TypeError(not_init_message.format('longLabel'))
+        if trackType is None:
+            raise TypeError(not_init_message.format('trackType'))
+        if trackDataURL is None:
+            raise TypeError(not_init_message.format('trackDataURL'))
+            
+        self.createTrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extraSettings)
+
+    def createTrackDb(self, track_name, long_label, short_label, file_path, track_type, extraSettings = None):
+    
+        # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
+        data_url = "tracks/%s" % track_name
+        if not short_label:
+            short_label = TrackDb.getShortName(long_label)
+        # Replace '_' by ' ', to invert the sanitization mecanism
+        # TODO: Find a better way to manage the sanitization of file path
+        long_label = long_label.replace("_", " ")
+        short_label = short_label.replace("_", " ")
+
+        #sanitize the track_name
+        sanitized_name = santitizer.prefixTrackName(track_name)
+
+        self.track_db = collections.OrderedDict([("track",sanitized_name),
+                ("type",track_type),
+                ("shortLabel",short_label),
+                ("longLabel",long_label),
+                ("bigDataUrl",data_url)]
+                )
+        
+        
+        TrackDb.prepareExtraSetting(extraSettings)
+        self.track_db.update(extraSettings)
+        #print self.track_db
+
+    # TODO: Rename for PEP8
+    @staticmethod
+    def getShortName(name_to_shortify):
+        # Slice to get from Long label the short label
+        short_label_slice = slice(0, 17)
+        return name_to_shortify[short_label_slice]
+
+    @staticmethod
+    def getRgb(track_color):
+        #TODO: Check if rgb or hexa
+        # Convert hexa to rgb array
+        hexa_without_sharp = track_color.lstrip('#')
+        rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
+        rgb_ucsc = ','.join(map(str, rgb_array))
+        return rgb_ucsc
+
+    @staticmethod
+    def prepareExtraSetting(extraSettings):
+        if not extraSettings:
+            extraSettings = collections.OrderedDict()
+        if not "color" in extraSettings:
+            extraSettings["color"] = "#000000"
+        extraSettings["color"] = TrackDb.getRgb(extraSettings["color"])
+        if not "group" in extraSettings or not extraSettings["group"]:
+            extraSettings["group"] = "Default group"
+        if not "thickDrawItem" in extraSettings:
+            extraSettings["thickDrawItem"] = "off"
+    
+    def get(self, item_name):
+        if item_name in self.track_db:
+            return self.track_db[item_name]
+        return None
+
+    
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