Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/IntervalFeatures.py @ 38:d17f629f5486 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
author yating-l
date Fri, 06 Apr 2018 13:44:56 -0400
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38
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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1 #!/usr/bin/env python
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2 import json
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3 import logging
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4 import collections
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5
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6 from TrackDb import TrackDb
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7 from util import subtools
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8 from util import santitizer
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9
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10 class Features(TrackDb):
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11 def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
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12 super(Features, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
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13
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14 def prepareExtraSetting(self):
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15 if self.trackType == 'HTMLFeatures':
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16 self.prepareHTMLExtraSetting()
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17 else:
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18 self.prepareCanvasExtraSetting()
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19
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20 def prepareHTMLExtraSetting(self):
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21 """ set HTMLFeatures configuration options """
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22 extraConfigs = dict()
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23 self.extraSettings["clientConfig"] = dict()
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24 self.extraSettings["config"] = dict()
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25 if 'type' in self.extraSettings:
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26 extraConfigs["type"] = self.extraSettings['type']
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27 if 'color' in self.extraSettings and self.extraSettings['color']:
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28 extraConfigs['feature_color'] = self.extraSettings['color']
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29 else:
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30 extraConfigs['feature_color'] = "#000000"
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31 #self.extraSettings['clientConfig']['color'] = self.extraSettings['color']
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32 if 'subfeatureClasses' in self.extraSettings:
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33 subfeature_css_class = santitizer.sanitize_name(self.trackLabel + "_" + self.extraSettings['subfeatureClasses'])
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34 extraConfigs['subfeatureClasses'] = {self.extraSettings['subfeatureClasses']: subfeature_css_class}
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35
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36 if 'category' not in self.extraSettings or not self.extraSettings['category']:
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37 self.extraSettings['config']['category'] = "Default group"
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38 else:
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39 self.extraSettings['config']['category'] = self.extraSettings['category']
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40
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41 extraConfigs['config'] = json.dumps(self.extraSettings["config"])
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42 extraConfigs['clientConfig'] = json.dumps(self.extraSettings["clientConfig"])
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43 return extraConfigs
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44
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45 def prepareCanvasExtraSetting(self):
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46 """ set CanvasFeatures configuration options """
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47 extraConfigs = dict()
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48 self.extraSettings["clientConfig"] = dict()
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49 self.extraSettings["config"] = dict()
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50 if 'color' not in self.extraSettings or not self.extraSettings['color']:
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51 self.extraSettings["clientConfig"]['color'] = "#daa520"
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52 else:
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53 self.extraSettings["clientConfig"]['color'] = self.extraSettings['color']
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54 if 'category' not in self.extraSettings or not self.extraSettings['category']:
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55 self.extraSettings["config"]['category'] = "Default group"
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56 else:
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57 self.extraSettings["config"]['category'] = self.extraSettings['category']
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58 if 'glyph' in self.extraSettings:
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59 self.extraSettings["config"]['glyph'] = self.extraSettings['glyph']
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60 if 'transcriptType' in self.extraSettings:
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61 self.extraSettings['config']['transcriptType'] = self.extraSettings['transcriptType']
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62 extraConfigs["config"] = json.dumps(self.extraSettings["config"])
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63 extraConfigs["clientConfig"] = json.dumps(self.extraSettings["clientConfig"])
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64 return extraConfigs
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65
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66 def createTrackDb(self):
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67 self.track_db = collections.OrderedDict([("track",self.trackName),
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68 ("trackLabel",self.trackLabel),
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69 ("trackDataURL",self.trackDataURL),
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70 ("dataType", self.dataType),
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71 ("trackType", self.trackType)]
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72 )
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73
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74
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75 htmlExtraConfigs = self.prepareHTMLExtraSetting()
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76 self.logger.debug("Generate extraConfigs for htmlFeatures = %s", json.dumps(htmlExtraConfigs))
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77 self.track_db["html"]["options"] = htmlExtraConfigs
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78 canvasExtraConfigs = self.prepareCanvasExtraSetting()
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79 self.logger.debug("Generate extraConfigs for canvasFeatures = %s", json.dumps(canvasExtraConfigs))
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80 self.track_db["canvas"]["options"] = canvasExtraConfigs
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81 self.logger.debug("TrackDb object is created track_db = %s ", json.dumps(self.track_db))