Mercurial > repos > rmarenco > hubarchivecreator

annotate TrackDb.py @ 32:6d1f2bb5c1d1 draft default tip

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5a0c39ed61b4408ba65a759aede807df260d097d
author yating-l
date Sun, 26 Aug 2018 16:44:27 -0400
parents e7c4be523cb7
children
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fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
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1 #!/usr/bin/python
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yating-l
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2 import os
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yating-l
parents: 26
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3 import collections
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 26
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4 from util import santitizer
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rmarenco
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6 class TrackDb(object):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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7 """docstring for TrackDb"""
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yating-l
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8 def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", extraSettings=None):
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yating-l
parents: 26
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9 #super(TrackDb, self).__init__()
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 26
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10 not_init_message = "The {0} is not initialized."
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yating-l
parents: 26
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11 if trackName is None:
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yating-l
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12 raise TypeError(not_init_message.format('trackName'))
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 26
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13 if longLabel is None:
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14 raise TypeError(not_init_message.format('longLabel'))
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 26
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15 if trackType is None:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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16 raise TypeError(not_init_message.format('trackType'))
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yating-l
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17 if trackDataURL is None:
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18 raise TypeError(not_init_message.format('trackDataURL'))
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20 self.createTrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extraSettings)
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21
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parents: 26
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22 def createTrackDb(self, track_name, long_label, short_label, file_path, track_type, extraSettings = None):
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24 # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
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25 data_url = "tracks/%s" % os.path.basename(file_path)
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yating-l
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26 if not short_label:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 26
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27 short_label = TrackDb.getShortName(long_label)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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28 # Replace '_' by ' ', to invert the sanitization mecanism
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yating-l
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29 # TODO: Find a better way to manage the sanitization of file path
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yating-l
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30 long_label = long_label.replace("_", " ")
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yating-l
parents: 26
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31 short_label = short_label.replace("_", " ")
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33 #sanitize the track_name
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34 sanitized_name = santitizer.prefixTrackName(track_name)
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35
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36 self.track_db = collections.OrderedDict([("track",sanitized_name),
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37 ("type",track_type),
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38 ("shortLabel",short_label),
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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39 ("longLabel",long_label),
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40 ("bigDataUrl",data_url)]
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41 )
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44 TrackDb.prepareExtraSetting(extraSettings)
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45 self.track_db.update(extraSettings)
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46 #print self.track_db
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47
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48 # TODO: Rename for PEP8
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49 @staticmethod
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50 def getShortName(name_to_shortify):
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51 # Slice to get from Long label the short label
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52 short_label_slice = slice(0, 17)
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53 return name_to_shortify[short_label_slice]
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55 @staticmethod
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56 def getRgb(track_color):
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57 #TODO: Check if rgb or hexa
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58 # Convert hexa to rgb array
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59 hexa_without_sharp = track_color.lstrip('#')
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60 rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
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61 rgb_ucsc = ','.join(map(str, rgb_array))
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62 return rgb_ucsc
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64 @staticmethod
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65 def prepareExtraSetting(extraSettings):
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66 if not extraSettings:
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yating-l
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67 extraSettings = collections.OrderedDict()
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68 if not "color" in extraSettings:
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69 extraSettings["color"] = "#000000"
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70 extraSettings["color"] = TrackDb.getRgb(extraSettings["color"])
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71 if not "group" in extraSettings or not extraSettings["group"]:
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72 extraSettings["group"] = "Default group"
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73 if not "thickDrawItem" in extraSettings:
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74 extraSettings["thickDrawItem"] = "off"
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75
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76 def get(self, item_name):
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77 if item_name in self.track_db:
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78 return self.track_db[item_name]
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79 return None
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