Mercurial > repos > rmarenco > hubarchivecreator
view TrackDb.py @ 30:e7c4be523cb7 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 2f1b3cc8c9cb463e460f7f79efe99ed472700ecf
author | yating-l |
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date | Tue, 19 Jun 2018 13:02:32 -0400 |
parents | 7e8a8b732db3 |
children |
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#!/usr/bin/python import os import collections from util import santitizer class TrackDb(object): """docstring for TrackDb""" def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", extraSettings=None): #super(TrackDb, self).__init__() not_init_message = "The {0} is not initialized." if trackName is None: raise TypeError(not_init_message.format('trackName')) if longLabel is None: raise TypeError(not_init_message.format('longLabel')) if trackType is None: raise TypeError(not_init_message.format('trackType')) if trackDataURL is None: raise TypeError(not_init_message.format('trackDataURL')) self.createTrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extraSettings) def createTrackDb(self, track_name, long_label, short_label, file_path, track_type, extraSettings = None): # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath data_url = "tracks/%s" % os.path.basename(file_path) if not short_label: short_label = TrackDb.getShortName(long_label) # Replace '_' by ' ', to invert the sanitization mecanism # TODO: Find a better way to manage the sanitization of file path long_label = long_label.replace("_", " ") short_label = short_label.replace("_", " ") #sanitize the track_name sanitized_name = santitizer.prefixTrackName(track_name) self.track_db = collections.OrderedDict([("track",sanitized_name), ("type",track_type), ("shortLabel",short_label), ("longLabel",long_label), ("bigDataUrl",data_url)] ) TrackDb.prepareExtraSetting(extraSettings) self.track_db.update(extraSettings) #print self.track_db # TODO: Rename for PEP8 @staticmethod def getShortName(name_to_shortify): # Slice to get from Long label the short label short_label_slice = slice(0, 17) return name_to_shortify[short_label_slice] @staticmethod def getRgb(track_color): #TODO: Check if rgb or hexa # Convert hexa to rgb array hexa_without_sharp = track_color.lstrip('#') rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)] rgb_ucsc = ','.join(map(str, rgb_array)) return rgb_ucsc @staticmethod def prepareExtraSetting(extraSettings): if not extraSettings: extraSettings = collections.OrderedDict() if not "color" in extraSettings: extraSettings["color"] = "#000000" extraSettings["color"] = TrackDb.getRgb(extraSettings["color"]) if not "group" in extraSettings or not extraSettings["group"]: extraSettings["group"] = "Default group" if not "thickDrawItem" in extraSettings: extraSettings["thickDrawItem"] = "off" def get(self, item_name): if item_name in self.track_db: return self.track_db[item_name] return None