Mercurial > repos > yating-l > hubarchivecreator

comparison util/index/TrixIndex.py @ 84:cb62314a6297 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Fri, 03 Nov 2017 17:08:19 -0400
parents 0bc486356e2a
children a65e52152476
comparison
equal deleted inserted replaced
83:0bc486356e2a 84:cb62314a6297
5 import shutil 5 import shutil
6 import logging 6 import logging
7 from ExternIndex import ExternIndex 7 from ExternIndex import ExternIndex
8 8
9 class TrixIndex(ExternIndex): 9 class TrixIndex(ExternIndex):
10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, **args): 10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args):
11 self.logger = logging.getLogger(__name__) 11 self.logger = logging.getLogger(__name__)
12 self.indexIx = indexIx 12 self.indexIx = indexIx
13 self.indexIxx = indexIxx 13 self.indexIxx = indexIxx
14 self.trackName = trackName 14 self.trackName = trackName
15 self.mySpecieFolderPath = mySpecieFolderPath 15 self.mySpecieFolderPath = mySpecieFolderPath
16 self.index_settings = collections.OrderedDict() 16 self.index_settings = collections.OrderedDict()
17 if "trixId" in args: 17 self.trixId = trixId
18 self.trixId = args["trixId"] 18
19 else:
20 self.trixId = None
21 19
22 def setExtLink(self): 20 def setExtLink(self):
21 self.setSearchIndex()
23 self.moveIndexFile() 22 self.moveIndexFile()
24 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName 23 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
25 return self.index_settings 24 return self.index_settings
26 25
27 def moveIndexFile(self): 26 def moveIndexFile(self):
36 shutil.copyfile(self.indexIx, self.indexIxPath) 35 shutil.copyfile(self.indexIx, self.indexIxPath)
37 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName) 36 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
38 shutil.copyfile(self.indexIxx, self.indexIxxPath) 37 shutil.copyfile(self.indexIxx, self.indexIxxPath)
39 38
40 def setSearchIndex(self): 39 def setSearchIndex(self):
41 if self.trixId: 40 if not self.trixId:
42 set_index = set() 41 self.logger.error("Didn't specify Trix Id")
43 set_index.add(self.trixId) 42 self.logger.debug("trixId= %s, searchIndex= %s", self.trixId, self.trixId)
44 set_index.add("name") 43 self.index_settings["searchIndex"] = self.trixId
45 search_index = ",".join(set_index)
46 else:
47 search_index = "name"
48 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
49 self.index_settings["searchIndex"] = search_index
50 44
51 45