Mercurial > repos > damion > versioned_data

comparison data_stores/vdb_kipper.py @ 1:5c5027485f7d draft

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Uploaded correct file
author damion
date Sun, 09 Aug 2015 16:07:50 -0400
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0:d31a1bd74e63 1:5c5027485f7d
1 #!/usr/bin/python
2 ## ********************************* Kipper *************************************
3 ##
4
5 import vdb_common
6 import vdb_data_stores
7 import subprocess
8 import json
9 import glob
10 import os
11 import sys
12
13 class VDBKipperDataStore(vdb_data_stores.VDBDataStore):
14
15 metadata = None
16 versions = None
17 command = None
18
19 def __init__(self, retrieval_obj, spec_file_id):
20 """
21 Metadata (version list) is expected in "master/" subfolder of data_store_path on server.
22
23 Future: allow for more than one database / .md file in a folder?
24 """
25 super(VDBKipperDataStore, self).__init__(retrieval_obj, spec_file_id)
26 # Ensure we're working with this tool's version of Kipper.
27 self.command = os.path.join(os.path.dirname(sys._getframe().f_code.co_filename),'kipper.py')
28 self.versions = []
29
30 metadata_path = os.path.join(self.data_store_path,'master','*.md')
31 metadata_files = glob.glob(metadata_path)
32
33 if len(metadata_files) == 0:
34 return # Handled by empty list error in versioned_data_form.py
35
36 metadata_file = metadata_files[0]
37
38 with open(metadata_file,'r') as metadata_handle:
39 self.metadata = json.load(metadata_handle)
40 for volume in self.metadata['volumes']:
41 self.versions.extend(volume['versions'])
42
43 if len(self.versions) == 0:
44 print "Error: Unable to locate metadata file: " + metadata_path
45 sys.exit(1)
46
47 self.versions = sorted(self.versions, key=lambda x: x['id'], reverse=True)
48
49
50 def get_version(self, version_name):
51 """
52 Trigger populating of the appropriate version folder.
53 Returns path information to version folder, and its appropriate library label.
54
55 @param version_id string
56 """
57
58 version = self.get_metadata_version(version_name)
59
60 if not version:
61 print 'Error: Galaxy was not able to find the given version id in the %s data store.' % self.version_path
62 sys.exit( 1 )
63
64 version_name = version['name']
65 self.version_path = os.path.join(self.data_store_path, version_name)
66 self.version_label = vdb_common.lightDate(version['created']) + '_v' + version_name
67
68 print self.library_label_path
69 print self.version_label
70
71 self.library_version_path = os.path.join(self.library_label_path, self.version_label)
72
73 if not os.path.exists(self.version_path):
74 try:
75 os.mkdir(self.version_path)
76 except:
77 print 'Error: Galaxy was not able to create data store folder "%s". Check permissions?' % self.version_path
78 sys.exit( 1 )
79
80 # Generate cache if folder is empty (can take a while):
81 if os.listdir(self.version_path) == []:
82
83 db_file = os.path.join(self.data_store_path, 'master', self.metadata["db_file_name"] )
84 command = [self.command, db_file, '-e','-I', version_name, '-o', self.version_path ]
85
86 try:
87 result = subprocess.call(command);
88 except:
89 print 'Error: Galaxy was not able to run the kipper.py program successfully for this job: "%s". Check permissions?' % self.version_path
90 sys.exit( 1 )
91
92
93 def get_metadata_version(self, version_name=''):
94 if version_name == '':
95 return self.versions[0]
96
97 for version in self.versions:
98 if str(version['name']) == version_name:
99 return version
100
101 return False
102