Package list ctdconverter / ef0b785
Refresh patches. Debian Janitor 2 years ago
4 changed file(s) with 21 addition(s) and 14 deletion(s). Raw diff Collapse all Expand all
00 From: Michael R. Crusoe <michael.crusoe@gmail.com>
11 Subject: Add setup.py
22 Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40
3 Index: ctdconverter/convert.py
4 ===================================================================
35 --- ctdconverter.orig/convert.py
46 +++ ctdconverter/convert.py
5 @@ -8,7 +8,7 @@
7 @@ -8,7 +8,7 @@ from argparse import RawDescriptionHelpF
68 from common.exceptions import ApplicationException, ModelError
79
810 __all__ = []
1113 __date__ = '2014-09-17'
1214 __updated__ = '2017-08-09'
1315
14 @@ -269,4 +269,4 @@
16 @@ -269,4 +269,4 @@ def validate_and_prepare_common_argument
1517
1618
1719 if __name__ == "__main__":
1820 - sys.exit(main())
1921 \ No newline at end of file
2022 + sys.exit(main())
23 Index: ctdconverter/setup.py
24 ===================================================================
2125 --- /dev/null
2226 +++ ctdconverter/setup.py
2327 @@ -0,0 +1,170 @@
00 From: Michael R. Crusoe <michael.crusoe@gmail.com>
11 Subject: unify script name reporting
2 Index: ctdconverter/convert.py
3 ===================================================================
24 --- ctdconverter.orig/convert.py
35 +++ ctdconverter/convert.py
4 @@ -17,10 +17,11 @@
6 @@ -17,10 +17,11 @@ program_build_date = str(__updated__)
57 program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date)
68 program_short_description = "CTDConverter - A project from the WorkflowConversion family " \
79 "(https://github.com/WorkflowConversion/CTDConverter)"
1416
1517 FORMAT can be either one of the supported output formats: cwl, galaxy.
1618
17 @@ -30,12 +31,12 @@
19 @@ -30,12 +31,12 @@ documentation for each of the converters
1820
1921 I - Parsing a single CTD file and convert it:
2022
2931
3032
3133 III - Hardcoding parameters
32 @@ -141,7 +142,7 @@
34 @@ -141,7 +142,7 @@ III - Hardcoding parameters
3335
3436 There are, for now, no CWL-specific parameters or options.
3537
3840
3941 program_license = '''%(short_description)s
4042
41 @@ -174,7 +175,8 @@
43 @@ -174,7 +175,8 @@ def main(argv=None):
4244 # converter will register its own parameters after we've registered the basic ones... we have to do it old school
4345 if len(argv) < 2:
4446 utils.error("Not enough arguments provided")
00 From: Michael R. Crusoe <michael.crusoe@gmail.com>
11 Subject: use `open` instead of `file`
2 Index: ctdconverter/cwl/converter.py
3 ===================================================================
24 --- ctdconverter.orig/cwl/converter.py
35 +++ ctdconverter/cwl/converter.py
4 @@ -72,7 +72,7 @@
6 @@ -72,7 +72,7 @@ def convert_models(args, parsed_ctds):
57
68 logger.info("Writing to %s" % utils.get_filename(output_file), 1)
79
1012 stream.write(CWL_SHEBANG + '\n\n')
1113 stream.write("# This CWL file was automatically generated using CTDConverter.\n")
1214 stream.write("# Visit https://github.com/WorkflowConversion/CTDConverter for more information.\n\n")
13 @@ -103,6 +103,8 @@
15 @@ -103,6 +103,8 @@ def convert_to_cwl(ctd_model, args):
1416 param_name = utils.extract_param_name(param)
1517 cwl_fixed_param_name = fix_param_name(param_name)
1618 hardcoded_value = args.parameter_hardcoder.get_hardcoded_value(param_name, ctd_model.name)
00 From: Michael R. Crusoe <michael.crusoe@gmail.com>
11 Subject: Upgrade deprecated using of string.strip()
2 Index: ctdconverter/common/utils.py
3 ===================================================================
24 --- ctdconverter.orig/common/utils.py
35 +++ ctdconverter/common/utils.py
4 @@ -4,8 +4,7 @@
6 @@ -4,7 +4,6 @@ import ntpath
57 import os
68
79 from lxml import etree
810 -from string import strip
9 -from logger import info, error, warning
10 +from logger import info, error, warning
11 from logger import info, error, warning
1112
1213 from common.exceptions import ApplicationException
13 from CTDopts.CTDopts import CTDModel, ParameterGroup
14 @@ -73,9 +72,9 @@
14 @@ -73,9 +72,9 @@ def validate_argument_is_valid_path(args
1515 if member_value is not None:
1616 if isinstance(member_value, list):
1717 for file_name in member_value:
2323
2424 for path_to_check in paths_to_check:
2525 validate_path_exists(path_to_check)
26