Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/TrackDb.py @ 20:85971ec2a527 draft default tip

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 81d946d4544a4ea7e5b55f90caef971eca6abba0
author sargentl
date Fri, 21 Sep 2018 16:30:54 -0400
parents 3f9971a91096
children
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1 #!/usr/bin/python
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2 """
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3 Super Class of the tracks
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4 """
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5 import os
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6 import abc
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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7 from abc import ABCMeta
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8 import collections
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9 import json
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10 import logging
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11 from util import santitizer
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12
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13 class TrackDb(object):
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14 """docstring for TrackDb"""
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15 __metaclass__ = ABCMeta
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16
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17 def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
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18 #super(TrackDb, self).__init__()
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19
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20 not_init_message = "The {0} is not initialized."
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21 if trackName is None:
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22 raise TypeError(not_init_message.format('trackName'))
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23 if trackLabel is None:
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24 raise TypeError(not_init_message.format('trackLabel'))
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25 if trackType is None:
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26 raise TypeError(not_init_message.format('trackType'))
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27 self.trackName = trackName
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28 self.trackLabel = trackLabel
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29 self.trackDataURL = trackDataURL
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30 self.trackType = trackType
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31 self.dataType = dataType
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32 self.extraSettings = extraSettings
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33 self.logger = logging.getLogger(__name__)
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34 #self.createTrackDb()
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35
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36 def createTrackDb(self):
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37 self.track_db = collections.OrderedDict([("track",self.trackName),
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38 ("trackLabel",self.trackLabel),
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39 ("trackDataURL",self.trackDataURL),
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40 ("dataType", self.dataType),
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41 ("trackType", self.trackType)]
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42 )
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44 self.track_db["nameIndex"] = self.extraSettings['nameIndex']
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45
6
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46 extraConfigs = self.prepareExtraSetting()
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47 self.logger.debug("Generate extraConfigs = %s", json.dumps(extraConfigs))
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48 self.track_db["options"] = extraConfigs
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49 #print self.track_db
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50 self.logger.debug("TrackDb object is created track_db = %s ", json.dumps(self.track_db))
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51
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52 @abc.abstractmethod
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53 def prepareExtraSetting(self):
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54 """ set optional configurations for the track """