Mercurial > repos > rmarenco > hubarchivecreator
annotate util/index/TrixIndex.py @ 32:6d1f2bb5c1d1 draft default tip
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5a0c39ed61b4408ba65a759aede807df260d097d
| author | yating-l |
|---|---|
| date | Sun, 26 Aug 2018 16:44:27 -0400 |
| parents | 7e8a8b732db3 |
| children |
| rev | line source |
|---|---|
|
29
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
1 #!/usr/bin/python |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
2 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
3 import os |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
4 import collections |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
5 import shutil |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
6 import logging |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
7 from ExternIndex import ExternIndex |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
8 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
9 class TrixIndex(ExternIndex): |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
10 def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args): |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
11 self.logger = logging.getLogger(__name__) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
12 self.indexIx = indexIx |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
13 self.indexIxx = indexIxx |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
14 self.trackName = trackName |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
15 self.mySpecieFolderPath = mySpecieFolderPath |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
16 self.index_settings = collections.OrderedDict() |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
17 self.trixId = trixId.rstrip() |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
18 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
19 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
20 def setExtLink(self): |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
21 self.setSearchIndex() |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
22 self.moveIndexFile() |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
23 self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
24 return self.index_settings |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
25 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
26 def moveIndexFile(self): |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
27 indexFolder = os.path.join(self.mySpecieFolderPath, 'trix') |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
28 self.indexIxName = "".join( ( self.trackName, ".ix") ) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
29 self.indexIxxName = "".join( ( self.trackName, ".ixx") ) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
30 if not os.path.exists(indexFolder): |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
31 os.makedirs(indexFolder) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
32 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
33 # Move index files to the index folder |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
34 self.indexIxPath = os.path.join(indexFolder, self.indexIxName) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
35 shutil.copyfile(self.indexIx, self.indexIxPath) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
36 self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
37 shutil.copyfile(self.indexIxx, self.indexIxxPath) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
38 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
39 def setSearchIndex(self): |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
40 if not self.trixId: |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
41 self.logger.error("Didn't specify Trix Id") |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
42 self.logger.debug("trixId= %s, searchIndex= %s", self.trixId, self.trixId) |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
43 self.index_settings["searchIndex"] = self.trixId |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
44 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
45 |