annotate versioned_data.py @ 1:5c5027485f7d draft

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1 #!/usr/bin/python
2 import os
3 import optparse
4 import sys
5 import time
6 import re
7 
8 import vdb_common 
9 import vdb_retrieval
10 
11 class MyParser(optparse.OptionParser):
12 	"""
13 	 From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output
14 	 Provides a better display of formatted help info in epilog() portion of optParse.
15 	"""
16 	def format_epilog(self, formatter):
17 		return self.epilog
18 
19 
20 def stop_err( msg ):
21     sys.stderr.write("%s\n" % msg)
22     sys.exit(1)
23 
24 
25 class ReportEngine(object):
26 
27 	def __init__(self): pass
28 
29 	def __main__(self):
30 
31 		options, args = self.get_command_line()
32 		retrieval_obj = vdb_retrieval.VDBRetrieval()
33 		retrieval_obj.set_api(options.api_info_path)
34 		
35 		retrievals=[]
36 				
37 		for retrieval in options.retrievals.strip().strip('|').split('|'):
38 			# Normally xml form supplies "spec_file_id, [version list], [workflow_list]"
39 			params = retrieval.strip().split(',')
40 			
41 			spec_file_id = params[0]
42 			
43 			if spec_file_id == 'none':
44 				print 'Error: Form was selected without requesting a data store to retrieve!'
45 				sys.exit( 1 )
46 				
47 			# STEP 1:  Determine data store type and location
48 			data_store_spec = retrieval_obj.user_api.libraries.show_folder(retrieval_obj.library_id, spec_file_id)
49 			data_store_type = retrieval_obj.test_data_store_type(data_store_spec['name'])
50 			base_folder_id = data_store_spec['folder_id']			
51 		
52 			if not data_store_type:
53 				print 'Error: unrecognized data store type [' + data_store_type + ']'
54 				sys.exit( 1 )
55 	
56 			ds_obj = retrieval_obj.get_data_store_gateway(data_store_type, spec_file_id)
57 
58 			if len(params) > 1 and len(params[1].strip()) > 0:			
59 				_versionList = params[1].strip()
60 				version_id = _versionList.split()[0] # VersionList SHOULD just have 1 id
61 			else:
62 				# User didn't select version_id via "Add new retrieval"
63 				if options.globalRetrievalDate:
64 					_retrieval_date = vdb_common.parse_date(options.globalRetrievalDate)
65 					version_id = ds_obj.get_version_options(global_retrieval_date=_retrieval_date, selection=True)
66 					
67 				else:
68 					version_id = ''
69 			
70 			# Reestablishes file(s) if they don't exist on disk. Do data library links to it as well.
71 			ds_obj.get_version(version_id)
72 			if ds_obj.version_path == None:
73 			
74 					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)
75 					sys.exit( 1 )
76 		
77 			# Version data file(s) are sitting in [ds_obj.version_path] ready for retrieval.
78 			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)
79 			
80 			# The only thing that doesn't have cache lookup is "folder" data that isn't linked in.
81 			# In that case try lookup directly.	
82 			if len(library_dataset_ids) == 0 and data_store_type == 'folder':
83 				library_version_datasets = retrieval_obj.get_library_folder_datasets(ds_obj.library_version_path)
84 				library_dataset_ids = [item['id'] for item in library_version_datasets]
85 				
86 			if len(library_dataset_ids) == 0:
87 			
88 					print 'Error: unable to retrieve version [%s] from %s archive [%s] ' % (version_id, data_store_type, ds_obj.library_version_path)
89 					sys.exit( 1 )
90 			
91 			# At this point we have references to the galaxy ids of the requested versioned dataset, after regeneration
92 			versioned_datasets = retrieval_obj.update_history(library_dataset_ids, ds_obj.library_version_path, version_id)
93 
94 			if len(params) > 2:
95 
96 				workflow_list = params[2].strip() 
97 			
98 				if len(workflow_list) > 0:
99 					# We have workflow run via admin_api and admin_api history.	
00 					retrieval_obj.get_workflow_data(workflow_list, versioned_datasets, version_id)
01 				
02 		
03 		result=retrievals
04 		
05 		# 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?
06 		with open(options.output,'w') as fw:
07 			fw.writelines(result)
08 
09 
10 	def get_command_line(self):
11 		## *************************** Parse Command Line *****************************
12 		parser = MyParser(
13 			description = 'This Galaxy tool retrieves versions of prepared data sources and places them in a galaxy "Versioned Data" library',
14 			usage = 'python versioned_data.py [options]',
15 			epilog="""Details:
16 
17 			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.
18 		""")
19 
20 		parser.add_option('-r', '--retrievals', type='string', dest='retrievals',
21 			help='List of datasources and their versions and galaxy workflows to return')
22 			
23 		parser.add_option('-o', '--output', type='string', dest='output', 
24 			help='Path of output log file to create')
25 
26 		parser.add_option('-O', '--output_id', type='string', dest='output_id', 
27 			help='Output identifier')
28 			
29 		parser.add_option('-d', '--date', type='string', dest='globalRetrievalDate', 
30 			help='Provide date/time for data recall.  Defaults to now.')
31 		
32 		parser.add_option('-v', '--version', dest='version', default=False, action='store_true', 
33 			help='Version number of this program.')
34 			
35 		parser.add_option('-s', '--api_info_path', type='string', dest='api_info_path', help='Galaxy user api key/path.')	
36 			
37 		return parser.parse_args()
38 			
39 
40 
41 if __name__ == '__main__':
42 
43 	time_start = time.time()
44 
45 	reportEngine = ReportEngine()
46 	reportEngine.__main__()
47 	
48 	print('Execution time (seconds): ' + str(int(time.time()-time_start)))
49