diff data_stores/tester.py @ 1:5c5027485f7d draft

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_stores/tester.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,109 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+import optparse
+import sys
+import difflib
+import os
+		
+
+class MyParser(optparse.OptionParser):
+	"""
+	 From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output
+	 Provides a better class for displaying formatted help info in epilog() portion of optParse; allows for carriage returns.
+	"""
+	def format_epilog(self, formatter):
+		return self.epilog
+
+def stop_err( msg ):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(1)
+    
+	
+def __main__(self):
+
+	
+	"""
+	(This is run only in context of command line.)
+	FUTURE: ALLOW GLOB IMPORT OF ALL FILES OF GIVEN SUFFX, each to its own version, initial date taken from file date
+	FUTURE: ALLOW dates of versions to be adjusted.
+	""" 
+	options, args = self.get_command_line()
+	self.options = options
+	
+	if options.test_ids: 
+		return self.test(options.test_ids)
+			
+
+def get_command_line(self):
+	"""
+	*************************** Parse Command Line *****************************
+	
+	"""
+	parser = MyParser(
+		description = 'Tests a program against given input/output files.',
+		usage = 'tester.py [program] [input files] [output files] [parameters]',
+		epilog="""
+		
+		    
+	parser.add_option('-t', '--tests', dest='test_ids', help='Enter "all" or comma-separated id(s) of tests to run.')
+
+	return parser.parse_args()
+
+
+
+def test(self, test_ids):
+	# Future: read this spec from test-data folder itself?
+	tests = {
+		'1': {'input':'a1','outputs':'','options':''}
+	}
+	self.test_suite('keydb.py', test_ids, tests, '/tmp/')
+
+
+def test_suite(self, program, test_ids, tests, output_dir):
+
+	if test_ids == 'all':
+		 test_ids = sorted(tests.keys())
+	else:
+		 test_ids = test_ids.split(',')
+
+	for test_id in test_ids:
+		if test_id in tests:
+			test = tests[test_id]
+			test['program'] = program
+			test['base_dir'] = base_dir = os.path.dirname(__file__)
+			executable = os.path.join(base_dir,program)
+			if not os.path.isfile(executable):
+				stop_err('\n\tUnable to locate ' + executable)
+			# Each output file has to be prefixed with the output (usualy /tmp/) folder 
+			test['tmp_output'] = (' ' + test['outputs']).replace(' ',' ' + output_dir)
+			# Note: output_dir output files don't get cleaned up after each test.  Should they?!
+			params = '%(base_dir)s/%(program)s %(base_dir)s/test-data/%(input)s%(tmp_output)s %(options)s' % test
+			print("Test " + test_id + ': ' + params)
+			print("................")
+			os.system(params)
+			print("................") 
+			for file in test['outputs'].split(' '):
+				try:
+					f1 = open(test['base_dir'] + '/test-data/' + file)
+					f2 = open(output_dir + file)
+				except IOError as details:
+					stop_err('Error in test setup: ' + str(details)+'\n')
+
+				#n=[number of context lines
+				diff = difflib.context_diff(f1.readlines(), f2.readlines(), lineterm='',n=0)
+				# One Galaxy issue: it doesn't convert entities when user downloads file. 
+				# BUT IT appears to when generating directly to command line?
+				print '\nCompare ' + file
+				print '\n'.join(list(diff))     
+					
+		else:
+			stop_err("\nExpecting one or more test ids from " + str(sorted(tests.keys())))
+
+	stop_err("\nTest finished.")
+	
+		
+if __name__ == '__main__':
+
+	keydb = KeyDb()
+	keydb.__main__()
+