Mercurial > repos > yating-l > hubarchivecreatortest

annotate TrackDb.py @ 1:85195e0d4b71 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
author yating-l
date Fri, 29 Sep 2017 13:32:23 -0400
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85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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1 #!/usr/bin/python
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yating-l
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2 import collections
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3 from util import santitizer
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5 class TrackDb(object):
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6 """docstring for TrackDb"""
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7 def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", extraSettings=None):
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8 #super(TrackDb, self).__init__()
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9 not_init_message = "The {0} is not initialized."
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10 if trackName is None:
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11 raise TypeError(not_init_message.format('trackName'))
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12 if longLabel is None:
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13 raise TypeError(not_init_message.format('longLabel'))
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14 if trackType is None:
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15 raise TypeError(not_init_message.format('trackType'))
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16 if trackDataURL is None:
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17 raise TypeError(not_init_message.format('trackDataURL'))
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19 self.createTrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extraSettings)
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21 def createTrackDb(self, track_name, long_label, short_label, file_path, track_type, extraSettings = None):
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23 # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
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24 data_url = "tracks/%s" % track_name
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25 if not short_label:
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26 short_label = TrackDb.getShortName(long_label)
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27 # Replace '_' by ' ', to invert the sanitization mecanism
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28 # TODO: Find a better way to manage the sanitization of file path
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29 long_label = long_label.replace("_", " ")
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30 short_label = short_label.replace("_", " ")
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32 #sanitize the track_name
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33 sanitized_name = santitizer.prefixTrackName(track_name)
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35 self.track_db = collections.OrderedDict([("track",sanitized_name),
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36 ("type",track_type),
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37 ("shortLabel",short_label),
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38 ("longLabel",long_label),
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39 ("bigDataUrl",data_url)]
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40 )
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43 TrackDb.prepareExtraSetting(extraSettings)
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44 self.track_db.update(extraSettings)
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45 #print self.track_db
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47 # TODO: Rename for PEP8
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48 @staticmethod
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49 def getShortName(name_to_shortify):
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50 # Slice to get from Long label the short label
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51 short_label_slice = slice(0, 17)
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52 return name_to_shortify[short_label_slice]
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54 @staticmethod
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55 def getRgb(track_color):
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56 #TODO: Check if rgb or hexa
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57 # Convert hexa to rgb array
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58 hexa_without_sharp = track_color.lstrip('#')
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59 rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
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60 rgb_ucsc = ','.join(map(str, rgb_array))
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61 return rgb_ucsc
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63 @staticmethod
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64 def prepareExtraSetting(extraSettings):
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65 if not extraSettings:
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66 extraSettings = collections.OrderedDict()
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67 if not "color" in extraSettings:
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68 extraSettings["color"] = "#000000"
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69 extraSettings["color"] = TrackDb.getRgb(extraSettings["color"])
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70 if not "group" in extraSettings or not extraSettings["group"]:
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71 extraSettings["group"] = "Default group"
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72 if not "thickDrawItem" in extraSettings:
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73 extraSettings["thickDrawItem"] = "off"
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74
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75 def get(self, item_name):
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76 if item_name in self.track_db:
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77 return self.track_db[item_name]
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78 return None
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