diff versioned_data_form.py @ 1:5c5027485f7d draft

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/versioned_data_form.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,149 @@
+#!/usr/bin/python
+#
+import os
+import sys
+
+# Extra step enables this script to locate vdb_common and vdb_retrieval 
+# From http://code.activestate.com/recipes/66062-determining-current-function-name/
+_self_dir = os.path.dirname(sys._getframe().f_code.co_filename)
+sys.path.append(_self_dir)
+
+import vdb_common
+import vdb_retrieval
+
+retrieval_obj = None # Global used here to manage user's currently selected retrieval info.
+
+
+def vdb_init_tool_user(trans):
+	"""
+	Retrieves a user's api key if they have one, otherwise lets them know they need one
+	This function is automatically called from versioned_data.xml form on presentation to user
+	Note that this is how self.api_url gets back into form, for passage back to 2nd call via versioned_data.py
+	self.api_key is passed via secure <configfile> construct. 
+	ALSO: squeezing history_id in this way since no other way to pass it.
+	"trans" is provided only by tool form presentation via <code file="...">
+	BUT NOW SEE John Chilton's: https://gist.github.com/jmchilton/27c5bb05e155a611294d
+  	 See galaxy source code at https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/web/framework.html, 
+	 See http://dev.list.galaxyproject.org/error-using-get-user-id-in-xml-file-in-new-Galaxy-td4665274.html
+	 See http://dev.list.galaxyproject.org/hg-galaxy-2780-Real-Job-tm-support-for-the-library-upload-to-td4133384.html
+	 master api key, set in galaxy config: #self.master_api_key = trans.app.config.master_api_key
+	"""
+	global retrieval_obj
+
+	api_url = trans.request.application_url + '/api'
+	history_id = str(trans.security.encode_id(trans.history.id))
+	user_api_key = None
+	#master_api_key = trans.app.config.master_api_key
+	
+	if trans.user:
+
+		user_name = trans.user.username
+
+		if trans.user.api_keys and len(trans.user.api_keys) > 0:
+			user_api_key = trans.user.api_keys[0].key #First key is always the active one?
+			items = [ { 'name': user_name, 'value': api_url + '-' + history_id, 'options':[], 'selected': True } ]
+
+		else: 
+			items = [ { 'name': user_name + ' - Note: you need a key (see "User" menu)!', 'value': '0', 'options':[], 'selected': False } ]
+	
+	else:
+		items = [ { 'name': 'You need to be logged in to use this tool!', 'value': '1', 'options':[], 'selected': False } ]
+	
+	retrieval_obj = vdb_retrieval.VDBRetrieval()
+	retrieval_obj.set_trans(api_url, history_id, user_api_key) #, master_api_key
+
+	return items
+
+
+def vdb_get_databases():
+	"""
+	Called by Tool Form, retrieves list of versioned databases from galaxy library called "Versioned Data"
+	
+		@return [name,value,selected] array
+	"""
+	global retrieval_obj
+	items = retrieval_obj.get_library_data_store_list()
+	
+	if len(items) == 0:
+		# Not great: Communicating library problem by text in form select pulldown input.
+		items = [[vdb_retrieval.VDB_DATA_LIBRARY_FOLDER_ERROR, None, False]]
+	
+	return items
+
+
+def vdb_get_versions(spec_file_id, global_retrieval_date): 
+	"""
+	  Retrieve applicable versions of given database.
+	  Unfortunately this is only refreshed when form screen is refreshed
+	
+	@param dbKey [folder_id]
+	
+	@return [name,value,selected] array
+	"""
+	global retrieval_obj
+
+	items = []
+	if spec_file_id:
+
+		data_store_spec = retrieval_obj.user_api.libraries.show_folder(retrieval_obj.library_id, spec_file_id)
+
+		if data_store_spec: #OTHERWISE DOES THIS MEAN USER DOESN'T HAVE PERMISSIONS?  VALIDATE
+
+			file_name = data_store_spec['name']  # Short (no path), original file name, not galaxy-assigned file_name
+			data_store_type = retrieval_obj.test_data_store_type(file_name)
+			library_label_path = retrieval_obj.get_library_label_path(spec_file_id)
+
+			if not data_store_type or not library_label_path:
+				# Cludgy method of sending message to user
+				items.append([vdb_retrieval.VDB_DATA_LIBRARY_FOLDER_ERROR, None, False])
+				items.append([vdb_retrieval.VDB_DATA_LIBRARY_CONFIG_ERROR + '"' + vdb_retrieval.VDB_DATA_LIBRARY + '/' + str(library_label_path) + '/' + file_name + '"', None, False])
+				return items
+			
+			_retrieval_date = vdb_common.parse_date(global_retrieval_date)
+
+			# Loads interface for appropriate data source retrieval
+			ds_obj = retrieval_obj.get_data_store_gateway(data_store_type, spec_file_id)
+			items = ds_obj.get_version_options(global_retrieval_date=_retrieval_date)
+
+		else:
+			items.append(['Unable to find' + spec_file_id + ':Check permissions?','',False])
+
+	return items
+
+
+def vdb_get_workflows(dbKey): 
+	"""
+	List appropriate workflows for database.  These are indicated by prefix "Versioning:" in name.
+	Currently can see ALL workflows that are published; admin_api() receives this in all galaxy versions.
+	Seems like only some galaxy versions allow user_api() to also see published workflows.
+	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.
+	
+	Future: Sensitivity: Some workflows apply only to some kinds of database
+	
+		@param dbKey [data_spec_id]
+		@return [name,value,selected] array
+	"""
+	global retrieval_obj
+		
+	data = []
+	try:
+		workflows = retrieval_obj.admin_api.workflows.get_workflows(published=True)
+		
+	except Exception as err: 
+		if err.message[-21:] == 'HTTP status code: 403':
+			data.append(['Error: User does not have permissions to see workflows (or they need to be published).' , 0, False])
+		else:
+			data.append(['Error: In getting workflows: %s' % err.message , 0, False])
+		return data
+
+	oldName = ""
+	for workflow in workflows:
+		name = workflow['name']
+		if name[0:11].lower() == "versioning:" and name != oldName:
+			# 	Interface Bug: If an item is published and is also shared personally with a user, it is shown twice.
+			data.append([name, workflow['id'], False])
+		oldName = name
+
+	return data
+
+