Mercurial > repos > yating-l > hubarchivecreatortest

annotate util/index/TrixIndex.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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children fa990284327b
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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
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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yating-l
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3 import os
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yating-l
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4 import collections
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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5 import shutil
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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6 import logging
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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7 from ExternIndex import ExternIndex
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yating-l
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9 class TrixIndex(ExternIndex):
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yating-l
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10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args):
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yating-l
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11 self.indexIx = indexIx
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12 self.indexIxx = indexIxx
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yating-l
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13 self.trackName = trackName
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14 self.mySpecieFolderPath = mySpecieFolderPath
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yating-l
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15 self.trixId = trixId
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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16 self.index_settings = collections.OrderedDict()
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yating-l
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17 if "default_index" in args:
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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18 self.default_index = args["default_index"]
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yating-l
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19 else:
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yating-l
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20 self.default_index = None
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22 def setExtLink(self):
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23 self.setSearchIndex()
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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24 self.moveIndexFile()
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25 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
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26 return self.index_settings
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28 def moveIndexFile(self):
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29 indexFolder = os.path.join(self.mySpecieFolderPath, 'trix')
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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30 self.indexIxName = "".join( ( self.trackName, ".ix") )
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31 self.indexIxxName = "".join( ( self.trackName, ".ixx") )
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yating-l
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32 if not os.path.exists(indexFolder):
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yating-l
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33 os.makedirs(indexFolder)
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35 # Move index files to the index folder
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36 self.indexIxPath = os.path.join(indexFolder, self.indexIxName)
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37 shutil.copyfile(self.indexIx, self.indexIxPath)
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38 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
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39 shutil.copyfile(self.indexIxx, self.indexIxxPath)
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41 def setSearchIndex(self):
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42 if self.default_index:
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43 set_index = set()
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44 set_index.add(self.trixId)
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45 set_index.add(self.default_index)
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46 search_index = ",".join(set_index)
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47 else:
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48 search_index = self.trixId
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49 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
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50 self.index_settings["searchIndex"] = search_index
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