Mercurial > repos > yating-l > hubarchivecreator

comparison TrackDb.py @ 66:4ca7cbf2d9b8 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
author yating-l
date Tue, 26 Sep 2017 16:44:58 -0400
parents b39dd0b5a166
children 39a32cb31623
comparison
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65:5a4206366b41 66:4ca7cbf2d9b8
1 #!/usr/bin/python 1 #!/usr/bin/python
2 import collections
3 from util import santitizer
2 4
3 class TrackDb(object): 5 class TrackDb(object):
4 """docstring for TrackDb""" 6 """docstring for TrackDb"""
7 def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", extraSettings=None):
8 #super(TrackDb, self).__init__()
9 not_init_message = "The {0} is not initialized."
10 if trackName is None:
11 raise TypeError(not_init_message.format('trackName'))
12 if longLabel is None:
13 raise TypeError(not_init_message.format('longLabel'))
14 if trackType is None:
15 raise TypeError(not_init_message.format('trackType'))
16 if trackDataURL is None:
17 raise TypeError(not_init_message.format('trackDataURL'))
18
19 self.createTrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extraSettings)
5 20
6 def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", visibility="", 21 def createTrackDb(self, track_name, long_label, short_label, file_path, track_type, extraSettings = None):
7 thickDrawItem='off', priority="0", track_color="#000000", group_name="Default", database=""): 22
8 super(TrackDb, self).__init__() 23 # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
24 data_url = "tracks/%s" % track_name
25 if not short_label:
26 short_label = TrackDb.getShortName(long_label)
27 # Replace '_' by ' ', to invert the sanitization mecanism
28 # TODO: Find a better way to manage the sanitization of file path
29 long_label = long_label.replace("_", " ")
30 short_label = short_label.replace("_", " ")
9 31
10 self.trackName = trackName 32 #sanitize the track_name
11 self.longLabel = longLabel 33 sanitized_name = santitizer.prefixTrackName(track_name)
12 self.shortLabel = shortLabel 34
13 self.trackDataURL = trackDataURL 35 self.track_db = collections.OrderedDict([("track",sanitized_name),
14 self.trackType = trackType 36 ("type",track_type),
15 self.visibility = visibility 37 ("shortLabel",short_label),
16 self.thickDrawItem = thickDrawItem 38 ("longLabel",long_label),
17 self.priority = priority 39 ("bigDataUrl",data_url)]
18 self.track_color = track_color 40 )
19 self.group_name = group_name 41
20 self.database = database 42
21 43 TrackDb.prepareExtraSetting(extraSettings)
44 self.track_db.update(extraSettings)
45 #print self.track_db
46
47 # TODO: Rename for PEP8
48 @staticmethod
49 def getShortName(name_to_shortify):
50 # Slice to get from Long label the short label
51 short_label_slice = slice(0, 17)
52 return name_to_shortify[short_label_slice]
53
54 @staticmethod
55 def getRgb(track_color):
56 #TODO: Check if rgb or hexa
57 # Convert hexa to rgb array
58 hexa_without_sharp = track_color.lstrip('#')
59 rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
60 rgb_ucsc = ','.join(map(str, rgb_array))
61 return rgb_ucsc
62
63 @staticmethod
64 def prepareExtraSetting(extraSettings):
65 if not extraSettings:
66 extraSettings = collections.OrderedDict()
67 if not "color" in extraSettings:
68 extraSettings["color"] = "#000000"
69 extraSettings["color"] = TrackDb.getRgb(extraSettings["color"])
70 if not "group" in extraSettings:
71 extraSettings["group"] = "Default group"
72 if not "thickDrawItem" in extraSettings:
73 extraSettings["thickDrawItem"] = "off"
74
75 def get(self, item_name):
76 if item_name in self.track_db:
77 return self.track_db[item_name]
78 return None
79
80