Mercurial > repos > yating-l > hubarchivecreatortest

comparison 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
comparison
equal deleted inserted replaced
2:7486909dfc22 3:fa990284327b
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, trixId, **args): 10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, **args):
11 self.logger = logging.getLogger(__name__)
11 self.indexIx = indexIx 12 self.indexIx = indexIx
12 self.indexIxx = indexIxx 13 self.indexIxx = indexIxx
13 self.trackName = trackName 14 self.trackName = trackName
14 self.mySpecieFolderPath = mySpecieFolderPath 15 self.mySpecieFolderPath = mySpecieFolderPath
15 self.trixId = trixId
16 self.index_settings = collections.OrderedDict() 16 self.index_settings = collections.OrderedDict()
17 if "default_index" in args: 17 if "trixId" in args:
18 self.default_index = args["default_index"] 18 self.trixId = args["trixId"]
19 else: 19 else:
20 self.default_index = None 20 self.trixId = None
21 21
22 def setExtLink(self): 22 def setExtLink(self):
23 self.setSearchIndex()
24 self.moveIndexFile() 23 self.moveIndexFile()
25 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName 24 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
26 return self.index_settings 25 return self.index_settings
27 26
28 def moveIndexFile(self): 27 def moveIndexFile(self):
37 shutil.copyfile(self.indexIx, self.indexIxPath) 36 shutil.copyfile(self.indexIx, self.indexIxPath)
38 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName) 37 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
39 shutil.copyfile(self.indexIxx, self.indexIxxPath) 38 shutil.copyfile(self.indexIxx, self.indexIxxPath)
40 39
41 def setSearchIndex(self): 40 def setSearchIndex(self):
42 if self.default_index: 41 if self.trixId:
43 set_index = set() 42 set_index = set()
44 set_index.add(self.trixId) 43 set_index.add(self.trixId)
45 set_index.add(self.default_index) 44 set_index.add("name")
46 search_index = ",".join(set_index) 45 search_index = ",".join(set_index)
47 else: 46 else:
48 search_index = self.trixId 47 search_index = "name"
49 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index) 48 logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
50 self.index_settings["searchIndex"] = search_index 49 self.index_settings["searchIndex"] = search_index
50
51 51