diff versioned_data.py @ 1:5c5027485f7d draft

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/versioned_data.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,149 @@
+#!/usr/bin/python
+import os
+import optparse
+import sys
+import time
+import re
+
+import vdb_common 
+import vdb_retrieval
+
+class MyParser(optparse.OptionParser):
+	"""
+	 From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output
+	 Provides a better display of formatted help info in epilog() portion of optParse.
+	"""
+	def format_epilog(self, formatter):
+		return self.epilog
+
+
+def stop_err( msg ):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(1)
+
+
+class ReportEngine(object):
+
+	def __init__(self): pass
+
+	def __main__(self):
+
+		options, args = self.get_command_line()
+		retrieval_obj = vdb_retrieval.VDBRetrieval()
+		retrieval_obj.set_api(options.api_info_path)
+		
+		retrievals=[]
+				
+		for retrieval in options.retrievals.strip().strip('|').split('|'):
+			# Normally xml form supplies "spec_file_id, [version list], [workflow_list]"
+			params = retrieval.strip().split(',')
+			
+			spec_file_id = params[0]
+			
+			if spec_file_id == 'none':
+				print 'Error: Form was selected without requesting a data store to retrieve!'
+				sys.exit( 1 )
+				
+			# STEP 1:  Determine data store type and location
+			data_store_spec = retrieval_obj.user_api.libraries.show_folder(retrieval_obj.library_id, spec_file_id)
+			data_store_type = retrieval_obj.test_data_store_type(data_store_spec['name'])
+			base_folder_id = data_store_spec['folder_id']			
+		
+			if not data_store_type:
+				print 'Error: unrecognized data store type [' + data_store_type + ']'
+				sys.exit( 1 )
+	
+			ds_obj = retrieval_obj.get_data_store_gateway(data_store_type, spec_file_id)
+
+			if len(params) > 1 and len(params[1].strip()) > 0:			
+				_versionList = params[1].strip()
+				version_id = _versionList.split()[0] # VersionList SHOULD just have 1 id
+			else:
+				# User didn't select version_id via "Add new retrieval"
+				if options.globalRetrievalDate:
+					_retrieval_date = vdb_common.parse_date(options.globalRetrievalDate)
+					version_id = ds_obj.get_version_options(global_retrieval_date=_retrieval_date, selection=True)
+					
+				else:
+					version_id = ''
+			
+			# Reestablishes file(s) if they don't exist on disk. Do data library links to it as well.
+			ds_obj.get_version(version_id)
+			if ds_obj.version_path == None:
+			
+					print "Error: unable to retrieve version [%s] from %s archive [%s].  Archive doesn't contain this version id?" % (version_id, data_store_type, ds_obj.library_version_path)
+					sys.exit( 1 )
+		
+			# Version data file(s) are sitting in [ds_obj.version_path] ready for retrieval.
+			library_dataset_ids = retrieval_obj.get_library_version_datasets(ds_obj.library_version_path, base_folder_id, ds_obj.version_label, ds_obj.version_path)
+			
+			# The only thing that doesn't have cache lookup is "folder" data that isn't linked in.
+			# In that case try lookup directly.	
+			if len(library_dataset_ids) == 0 and data_store_type == 'folder':
+				library_version_datasets = retrieval_obj.get_library_folder_datasets(ds_obj.library_version_path)
+				library_dataset_ids = [item['id'] for item in library_version_datasets]
+				
+			if len(library_dataset_ids) == 0:
+			
+					print 'Error: unable to retrieve version [%s] from %s archive [%s] ' % (version_id, data_store_type, ds_obj.library_version_path)
+					sys.exit( 1 )
+			
+			# At this point we have references to the galaxy ids of the requested versioned dataset, after regeneration
+			versioned_datasets = retrieval_obj.update_history(library_dataset_ids, ds_obj.library_version_path, version_id)
+
+			if len(params) > 2:
+
+				workflow_list = params[2].strip() 
+			
+				if len(workflow_list) > 0:
+					# We have workflow run via admin_api and admin_api history.	
+					retrieval_obj.get_workflow_data(workflow_list, versioned_datasets, version_id)
+				
+		
+		result=retrievals
+		
+		# Output file needs to exist.  Otherwise Galaxy doesn't generate a placeholder file name for the output, and so we can't do things like check for [placeholder name]_files folder.  Add something to report on?
+		with open(options.output,'w') as fw:
+			fw.writelines(result)
+
+
+	def get_command_line(self):
+		## *************************** Parse Command Line *****************************
+		parser = MyParser(
+			description = 'This Galaxy tool retrieves versions of prepared data sources and places them in a galaxy "Versioned Data" library',
+			usage = 'python versioned_data.py [options]',
+			epilog="""Details:
+
+			This tool retrieves links to current or past versions of fasta (or other key-value text) databases from a cache kept in the data library called "Fasta Databases". It then places them into the current history so that subsequent tools can work with that data.
+		""")
+
+		parser.add_option('-r', '--retrievals', type='string', dest='retrievals',
+			help='List of datasources and their versions and galaxy workflows to return')
+			
+		parser.add_option('-o', '--output', type='string', dest='output', 
+			help='Path of output log file to create')
+
+		parser.add_option('-O', '--output_id', type='string', dest='output_id', 
+			help='Output identifier')
+			
+		parser.add_option('-d', '--date', type='string', dest='globalRetrievalDate', 
+			help='Provide date/time for data recall.  Defaults to now.')
+		
+		parser.add_option('-v', '--version', dest='version', default=False, action='store_true', 
+			help='Version number of this program.')
+			
+		parser.add_option('-s', '--api_info_path', type='string', dest='api_info_path', help='Galaxy user api key/path.')	
+			
+		return parser.parse_args()
+			
+
+
+if __name__ == '__main__':
+
+	time_start = time.time()
+
+	reportEngine = ReportEngine()
+	reportEngine.__main__()
+	
+	print('Execution time (seconds): ' + str(int(time.time()-time_start)))
+