Mercurial > repos > damion > versioned_data

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

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author damion
date Sun, 09 Aug 2015 16:07:50 -0400
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0:d31a1bd74e63 1:5c5027485f7d
1 #!/usr/bin/python
2 ## ******************************* FILE FOLDER *********************************
3 ##
4
5 import re
6 import os
7 import vdb_common
8 import vdb_data_stores
9
10 class VDBFolderDataStore(vdb_data_stores.VDBDataStore):
11
12 versions = None
13 library = None
14
15 def __init__(self, retrieval_obj, spec_file_id):
16 """
17 Provides list of available versions where each version is indicated by the
18 existence of a folder that contains its content. This content can be directly
19 in the galaxy Versioned Data folder tree, OR it can be linked to another folder
20 on the server. In the latter case, galaxy will treat the Versioned Data folders as caches.
21 View of versions filters out any folders that are used for derivative data caching.
22 """
23 super(VDBFolderDataStore, self).__init__(retrieval_obj, spec_file_id)
24
25 self.library = retrieval_obj.library
26
27 versions = []
28
29 # If data source spec file has no content, use the library folder directly.
30 # Name of EACH subfolder should be a label for each version, including date/time and version id.
31 if self.data_store_path == '':
32 try:
33 lib_label_len = len(self.library_label_path) +1
34
35 for item in self.library:
36 # If item is under library_label_path ...
37 if item['name'][0:lib_label_len] == self.library_label_path + '/':
38 item_name = item['name'][lib_label_len:len(item['name'])]
39 if item_name.find('/') == -1 and item_name.find('_') != -1:
40 (item_date, item_version) = item_name.split('_',1)
41 created = vdb_common.parse_date(item_date)
42 versions.append({'name':item_name, 'id':item_name, 'created': created})
43
44 except Exception as err:
45 # This is the first call to api so api url or authentication erro can happen here.
46 versions.append({
47 'name':'Software Error: Unable to get version list: ' + err.message,
48 'id':'',
49 'created':''
50 })
51
52 else:
53
54 base_file_path = self.data_store_path
55 #base_file_path = os.path.dirname(self.base_file_name)
56 #Here we need to get directory listing of linked file location.
57 for item_name in os.listdir(base_file_path): # Includes files and folders
58 # Only interested in folders
59 if os.path.isdir( os.path.join(base_file_path, item_name)) and item_name.find('_') != -1:
60 (item_date, item_version) = item_name.split('_',1)
61 created = vdb_common.parse_date(item_date)
62 versions.append({'name':item_name, 'id':item_name, 'created': created})
63
64
65 self.versions = sorted(versions, key=lambda x: x['name'], reverse=True)
66
67 def get_version(self, version_name):
68 """
69 Return server path of requested version info - BUT ONLY IF IT IS LINKED.
70 IF NOT LINKED, returns None for self.version_path
71
72 QUESTION: DOES GALAXY AUTOMATICALLY HANDLE tar.gz/zip decompression?
73
74 @uses library_label_path string Full hierarchic label of a library file or folder, PARENT of version id folder.
75 @uses base_file_name string Server absolute path to data_store spec file
76
77 @param version_name alphaneumeric string (git tag)
78 """
79 self.version_label = version_name
80 self.library_version_path = os.path.join(self.library_label_path, self.version_label)
81
82 if self.data_store_path == '':
83 # In this case version content is held in library directly;
84 self.version_path = self.base_file_name
85
86 else:
87
88 #linked to some other folder, spec is location of base_file_name
89 self.version_path = os.path.join(self.data_store_path, version_name)
90