Mercurial > repos > yating-l > hubarchivecreator

annotate util/index/TrixIndex.py @ 85:a65e52152476 draft default tip

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Mon, 06 Nov 2017 13:13:01 -0500
parents cb62314a6297
children
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0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
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1 #!/usr/bin/python
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yating-l
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3 import os
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
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4 import collections
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
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5 import shutil
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
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6 import logging
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
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7 from ExternIndex import ExternIndex
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9 class TrixIndex(ExternIndex):
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10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args):
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11 self.logger = logging.getLogger(__name__)
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12 self.indexIx = indexIx
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13 self.indexIxx = indexIxx
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14 self.trackName = trackName
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15 self.mySpecieFolderPath = mySpecieFolderPath
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16 self.index_settings = collections.OrderedDict()
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a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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17 self.trixId = trixId.rstrip()
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20 def setExtLink(self):
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21 self.setSearchIndex()
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22 self.moveIndexFile()
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
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23 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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24 return self.index_settings
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26 def moveIndexFile(self):
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27 indexFolder = os.path.join(self.mySpecieFolderPath, 'trix')
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yating-l
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28 self.indexIxName = "".join( ( self.trackName, ".ix") )
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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29 self.indexIxxName = "".join( ( self.trackName, ".ixx") )
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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30 if not os.path.exists(indexFolder):
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31 os.makedirs(indexFolder)
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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33 # Move index files to the index folder
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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34 self.indexIxPath = os.path.join(indexFolder, self.indexIxName)
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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35 shutil.copyfile(self.indexIx, self.indexIxPath)
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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36 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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37 shutil.copyfile(self.indexIxx, self.indexIxxPath)
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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39 def setSearchIndex(self):
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yating-l
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40 if not self.trixId:
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
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41 self.logger.error("Didn't specify Trix Id")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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42 self.logger.debug("trixId= %s, searchIndex= %s", self.trixId, self.trixId)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
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43 self.index_settings["searchIndex"] = self.trixId
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