annotate versioned_data_form.py @ 2:269d246ce6d0 draft default tip

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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])
00 				return items
01 			
02 			_retrieval_date = vdb_common.parse_date(global_retrieval_date)
03 
04 			# Loads interface for appropriate data source retrieval
05 			ds_obj = retrieval_obj.get_data_store_gateway(data_store_type, spec_file_id)
06 			items = ds_obj.get_version_options(global_retrieval_date=_retrieval_date)
07 
08 		else:
09 			items.append(['Unable to find' + spec_file_id + ':Check permissions?','',False])
10 
11 	return items
12 
13 
14 def vdb_get_workflows(dbKey): 
15 	"""
16 	List appropriate workflows for database.  These are indicated by prefix "Versioning:" in name.
17 	Currently can see ALL workflows that are published; admin_api() receives this in all galaxy versions.
18 	Seems like only some galaxy versions allow user_api() to also see published workflows.
19 	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.
20 	
21 	Future: Sensitivity: Some workflows apply only to some kinds of database
22 	
23 		@param dbKey [data_spec_id]
24 		@return [name,value,selected] array
25 	"""
26 	global retrieval_obj
27 		
28 	data = []
29 	try:
30 		workflows = retrieval_obj.admin_api.workflows.get_workflows(published=True)
31 		
32 	except Exception as err: 
33 		if err.message[-21:] == 'HTTP status code: 403':
34 			data.append(['Error: User does not have permissions to see workflows (or they need to be published).' , 0, False])
35 		else:
36 			data.append(['Error: In getting workflows: %s' % err.message , 0, False])
37 		return data
38 
39 	oldName = ""
40 	for workflow in workflows:
41 		name = workflow['name']
42 		if name[0:11].lower() == "versioning:" and name != oldName:
43 			# 	Interface Bug: If an item is published and is also shared personally with a user, it is shown twice.
44 			data.append([name, workflow['id'], False])
45 		oldName = name
46 
47 	return data
48 
49