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comparison versioned_data_form.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 #
3 import os
4 import sys
5
6 # Extra step enables this script to locate vdb_common and vdb_retrieval
7 # From http://code.activestate.com/recipes/66062-determining-current-function-name/
8 _self_dir = os.path.dirname(sys._getframe().f_code.co_filename)
9 sys.path.append(_self_dir)
10
11 import vdb_common
12 import vdb_retrieval
13
14 retrieval_obj = None # Global used here to manage user's currently selected retrieval info.
15
16
17 def vdb_init_tool_user(trans):
18 """
19 Retrieves a user's api key if they have one, otherwise lets them know they need one
20 This function is automatically called from versioned_data.xml form on presentation to user
21 Note that this is how self.api_url gets back into form, for passage back to 2nd call via versioned_data.py
22 self.api_key is passed via secure <configfile> construct.
23 ALSO: squeezing history_id in this way since no other way to pass it.
24 "trans" is provided only by tool form presentation via <code file="...">
25 BUT NOW SEE John Chilton's: https://gist.github.com/jmchilton/27c5bb05e155a611294d
26 See galaxy source code at https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/web/framework.html,
27 See http://dev.list.galaxyproject.org/error-using-get-user-id-in-xml-file-in-new-Galaxy-td4665274.html
28 See http://dev.list.galaxyproject.org/hg-galaxy-2780-Real-Job-tm-support-for-the-library-upload-to-td4133384.html
29 master api key, set in galaxy config: #self.master_api_key = trans.app.config.master_api_key
30 """
31 global retrieval_obj
32
33 api_url = trans.request.application_url + '/api'
34 history_id = str(trans.security.encode_id(trans.history.id))
35 user_api_key = None
36 #master_api_key = trans.app.config.master_api_key
37
38 if trans.user:
39
40 user_name = trans.user.username
41
42 if trans.user.api_keys and len(trans.user.api_keys) > 0:
43 user_api_key = trans.user.api_keys[0].key #First key is always the active one?
44 items = [ { 'name': user_name, 'value': api_url + '-' + history_id, 'options':[], 'selected': True } ]
45
46 else:
47 items = [ { 'name': user_name + ' - Note: you need a key (see "User" menu)!', 'value': '0', 'options':[], 'selected': False } ]
48
49 else:
50 items = [ { 'name': 'You need to be logged in to use this tool!', 'value': '1', 'options':[], 'selected': False } ]
51
52 retrieval_obj = vdb_retrieval.VDBRetrieval()
53 retrieval_obj.set_trans(api_url, history_id, user_api_key) #, master_api_key
54
55 return items
56
57
58 def vdb_get_databases():
59 """
60 Called by Tool Form, retrieves list of versioned databases from galaxy library called "Versioned Data"
61
62 @return [name,value,selected] array
63 """
64 global retrieval_obj
65 items = retrieval_obj.get_library_data_store_list()
66
67 if len(items) == 0:
68 # Not great: Communicating library problem by text in form select pulldown input.
69 items = [[vdb_retrieval.VDB_DATA_LIBRARY_FOLDER_ERROR, None, False]]
70
71 return items
72
73
74 def vdb_get_versions(spec_file_id, global_retrieval_date):
75 """
76 Retrieve applicable versions of given database.
77 Unfortunately this is only refreshed when form screen is refreshed
78
79 @param dbKey [folder_id]
80
81 @return [name,value,selected] array
82 """
83 global retrieval_obj
84
85 items = []
86 if spec_file_id:
87
88 data_store_spec = retrieval_obj.user_api.libraries.show_folder(retrieval_obj.library_id, spec_file_id)
89
90 if data_store_spec: #OTHERWISE DOES THIS MEAN USER DOESN'T HAVE PERMISSIONS? VALIDATE
91
92 file_name = data_store_spec['name'] # Short (no path), original file name, not galaxy-assigned file_name
93 data_store_type = retrieval_obj.test_data_store_type(file_name)
94 library_label_path = retrieval_obj.get_library_label_path(spec_file_id)
95
96 if not data_store_type or not library_label_path:
97 # Cludgy method of sending message to user
98 items.append([vdb_retrieval.VDB_DATA_LIBRARY_FOLDER_ERROR, None, False])
99 items.append([vdb_retrieval.VDB_DATA_LIBRARY_CONFIG_ERROR + '"' + vdb_retrieval.VDB_DATA_LIBRARY + '/' + str(library_label_path) + '/' + file_name + '"', None, False])
100 return items
101
102 _retrieval_date = vdb_common.parse_date(global_retrieval_date)
103
104 # Loads interface for appropriate data source retrieval
105 ds_obj = retrieval_obj.get_data_store_gateway(data_store_type, spec_file_id)
106 items = ds_obj.get_version_options(global_retrieval_date=_retrieval_date)
107
108 else:
109 items.append(['Unable to find' + spec_file_id + ':Check permissions?','',False])
110
111 return items
112
113
114 def vdb_get_workflows(dbKey):
115 """
116 List appropriate workflows for database. These are indicated by prefix "Versioning:" in name.
117 Currently can see ALL workflows that are published; admin_api() receives this in all galaxy versions.
118 Seems like only some galaxy versions allow user_api() to also see published workflows.
119 Only alternative is to list only individual workflows that current user can see - ones they created, and published workflows; but versioneddata user needs to have permissions on these too.
120
121 Future: Sensitivity: Some workflows apply only to some kinds of database
122
123 @param dbKey [data_spec_id]
124 @return [name,value,selected] array
125 """
126 global retrieval_obj
127
128 data = []
129 try:
130 workflows = retrieval_obj.admin_api.workflows.get_workflows(published=True)
131
132 except Exception as err:
133 if err.message[-21:] == 'HTTP status code: 403':
134 data.append(['Error: User does not have permissions to see workflows (or they need to be published).' , 0, False])
135 else:
136 data.append(['Error: In getting workflows: %s' % err.message , 0, False])
137 return data
138
139 oldName = ""
140 for workflow in workflows:
141 name = workflow['name']
142 if name[0:11].lower() == "versioning:" and name != oldName:
143 # Interface Bug: If an item is published and is also shared personally with a user, it is shown twice.
144 data.append([name, workflow['id'], False])
145 oldName = name
146
147 return data
148
149