Mercurial > repos > yating-l > hubarchivecreatortest

annotate util/index/TrixIndex.py @ 3:fa990284327b draft default tip

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Mon, 30 Oct 2017 11:58:31 -0400
parents 85195e0d4b71
children
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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
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yating-l
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yating-l
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3 import os
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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
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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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9 class TrixIndex(ExternIndex):
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yating-l
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10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, **args):
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yating-l
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11 self.logger = logging.getLogger(__name__)
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12 self.indexIx = indexIx
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yating-l
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13 self.indexIxx = indexIxx
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yating-l
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14 self.trackName = trackName
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yating-l
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15 self.mySpecieFolderPath = mySpecieFolderPath
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16 self.index_settings = collections.OrderedDict()
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yating-l
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17 if "trixId" in args:
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yating-l
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18 self.trixId = args["trixId"]
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19 else:
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yating-l
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20 self.trixId = None
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22 def setExtLink(self):
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yating-l
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23 self.moveIndexFile()
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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24 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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25 return self.index_settings
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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27 def moveIndexFile(self):
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28 indexFolder = os.path.join(self.mySpecieFolderPath, 'trix')
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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29 self.indexIxName = "".join( ( self.trackName, ".ix") )
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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30 self.indexIxxName = "".join( ( self.trackName, ".ixx") )
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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31 if not os.path.exists(indexFolder):
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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32 os.makedirs(indexFolder)
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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34 # Move index files to the index folder
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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35 self.indexIxPath = os.path.join(indexFolder, self.indexIxName)
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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36 shutil.copyfile(self.indexIx, self.indexIxPath)
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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37 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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38 shutil.copyfile(self.indexIxx, self.indexIxxPath)
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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40 def setSearchIndex(self):
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41 if self.trixId:
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42 set_index = set()
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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43 set_index.add(self.trixId)
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yating-l
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44 set_index.add("name")
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45 search_index = ",".join(set_index)
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46 else:
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47 search_index = "name"
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48 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
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49 self.index_settings["searchIndex"] = search_index
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