changeset 0:417f332cf4ef draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/refinery_test_tool.py	Thu May 09 00:42:19 2013 -0400
@@ -0,0 +1,127 @@
+#!/usr/bin/env python
+
+'''
+Test tool for running Galaxy workflows from Refinery
+
+@author: Ilya Sytchev
+
+Input: one or more text files
+Output: concatenated input file(s) plus annotation
+
+Requires Python v2.7
+
+'''
+
+
+import argparse
+import random
+import sys
+import time
+
+
+def main(args):
+    time.sleep(args.seconds)
+
+    if check_fail(args.p_fail):
+        cleanup(args)
+        quit("Processing failed by request", args)
+
+    input = read_files(args.input_files)
+    try:
+        for out_file in args.output_files:
+            out_file.write('\n' + "Output file name: " + out_file.name + '\n')
+            out_file.write(input)
+    except IOError as e:
+        cleanup(args)
+        parser.error(e)
+    else:
+        cleanup(args)
+
+
+def check_fail(p_fail):
+    '''Determine success/failure state given a probability of failure
+
+    '''
+    random.seed()
+    if random.random() < p_fail:
+        return True
+    else:
+        return False
+
+
+def read_files(file_list):
+    '''Read files from disk into a string
+
+    '''
+    str = ''
+    for in_file in file_list:
+        str += "Input file name: " + in_file.name + '\n'
+        str += in_file.read()
+    return str
+
+
+def cleanup(args):
+    '''Close all open file handles
+
+    '''
+    file_list = []
+    if args.input_files:
+        file_list.extend(args.input_files)
+    if args.output_files:
+        file_list.extend(args.output_files)
+    for fh in file_list:
+        try:
+            fh.close()
+        except AttributeError:
+            continue
+
+
+def quit(message, args):
+    '''Exit and optionally write to stdout and/or stderr
+
+    '''
+    if args.stdout:
+        sys.stdout.write(message + '\n')
+    if args.stderr:
+        sys.stderr.write(message + '\n')
+    sys.exit(args.exit_code)
+
+
+if __name__ == '__main__':
+    version = "%(prog)s 0.1"
+    description = "Test tool for running workflows on Galaxy platform from Refinery"
+    parser = argparse.ArgumentParser(description=description, version=version)
+
+    parser.add_argument('-i', '--in-file', dest='input_files', nargs='+',
+                        type=file, metavar='INPUT_FILE', required=True,
+                        help='name of the input file')
+    parser.add_argument('-o', '--out-file', dest='output_files', nargs='+',
+                        type=argparse.FileType('w'), metavar='OUTPUT_FILE',
+                        required=True, help='name of the output file')
+    parser.add_argument('-e', '--exit_code', type=int, default=0,
+                        help='code to return on exit, default: %(default)s')
+    parser.add_argument('--stdout', action='store_true',
+                        help='write a message to stdout')
+    parser.add_argument('--stderr', action='store_true',
+                        help='write a message to stderr')
+    parser.add_argument('-p', '--p-fail', type=float, default=0.0,
+                        help='probability of execution failure, default: %(default)s')
+    parser.add_argument('-s', '--sleep', dest='seconds', type=int, default=0,
+                        metavar='SECONDS',
+                        help='number of seconds to sleep, default: %(default)s')
+
+    # check argument values for errors
+    try:
+        args = parser.parse_args()
+    except IOError as e:
+        parser.error(e)
+
+    if args.exit_code < 0 or args.exit_code > 255:
+        cleanup(args)
+        parser.error("Exit code value must be between 0 and 255")
+
+    if args.p_fail < 0.0 or args.p_fail > 1.0:
+        cleanup(args)
+        parser.error("Probability value must be between 0.0 and 1.0 inclusive")
+
+    main(args)