Refresh patches.
Debian Janitor
3 years ago
| 0 | 0 | From: Michael R. Crusoe <michael.crusoe@gmail.com> |
| 1 | 1 | Subject: Add setup.py |
| 2 | 2 | Forwarded: https://github.com/WorkflowConversion/CTDConverter/pull/40 |
| 3 | Index: ctdconverter/convert.py | |
| 4 | =================================================================== | |
| 3 | 5 | --- ctdconverter.orig/convert.py |
| 4 | 6 | +++ ctdconverter/convert.py |
| 5 | @@ -8,7 +8,7 @@ | |
| 7 | @@ -8,7 +8,7 @@ from argparse import RawDescriptionHelpF | |
| 6 | 8 | from common.exceptions import ApplicationException, ModelError |
| 7 | 9 | |
| 8 | 10 | __all__ = [] |
| 11 | 13 | __date__ = '2014-09-17' |
| 12 | 14 | __updated__ = '2017-08-09' |
| 13 | 15 | |
| 14 | @@ -269,4 +269,4 @@ | |
| 16 | @@ -269,4 +269,4 @@ def validate_and_prepare_common_argument | |
| 15 | 17 | |
| 16 | 18 | |
| 17 | 19 | if __name__ == "__main__": |
| 18 | 20 | - sys.exit(main()) |
| 19 | 21 | \ No newline at end of file |
| 20 | 22 | + sys.exit(main()) |
| 23 | Index: ctdconverter/setup.py | |
| 24 | =================================================================== | |
| 21 | 25 | --- /dev/null |
| 22 | 26 | +++ ctdconverter/setup.py |
| 23 | 27 | @@ -0,0 +1,170 @@ |
| 0 | 0 | From: Michael R. Crusoe <michael.crusoe@gmail.com> |
| 1 | 1 | Subject: unify script name reporting |
| 2 | Index: ctdconverter/convert.py | |
| 3 | =================================================================== | |
| 2 | 4 | --- ctdconverter.orig/convert.py |
| 3 | 5 | +++ ctdconverter/convert.py |
| 4 | @@ -17,10 +17,11 @@ | |
| 6 | @@ -17,10 +17,11 @@ program_build_date = str(__updated__) | |
| 5 | 7 | program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date) |
| 6 | 8 | program_short_description = "CTDConverter - A project from the WorkflowConversion family " \ |
| 7 | 9 | "(https://github.com/WorkflowConversion/CTDConverter)" |
| 14 | 16 | |
| 15 | 17 | FORMAT can be either one of the supported output formats: cwl, galaxy. |
| 16 | 18 | |
| 17 | @@ -30,12 +31,12 @@ | |
| 19 | @@ -30,12 +31,12 @@ documentation for each of the converters | |
| 18 | 20 | |
| 19 | 21 | I - Parsing a single CTD file and convert it: |
| 20 | 22 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | 33 | III - Hardcoding parameters |
| 32 | @@ -141,7 +142,7 @@ | |
| 34 | @@ -141,7 +142,7 @@ III - Hardcoding parameters | |
| 33 | 35 | |
| 34 | 36 | There are, for now, no CWL-specific parameters or options. |
| 35 | 37 | |
| 38 | 40 | |
| 39 | 41 | program_license = '''%(short_description)s |
| 40 | 42 | |
| 41 | @@ -174,7 +175,8 @@ | |
| 43 | @@ -174,7 +175,8 @@ def main(argv=None): | |
| 42 | 44 | # converter will register its own parameters after we've registered the basic ones... we have to do it old school |
| 43 | 45 | if len(argv) < 2: |
| 44 | 46 | utils.error("Not enough arguments provided") |
| 0 | 0 | From: Michael R. Crusoe <michael.crusoe@gmail.com> |
| 1 | 1 | Subject: use `open` instead of `file` |
| 2 | Index: ctdconverter/cwl/converter.py | |
| 3 | =================================================================== | |
| 2 | 4 | --- ctdconverter.orig/cwl/converter.py |
| 3 | 5 | +++ ctdconverter/cwl/converter.py |
| 4 | @@ -72,7 +72,7 @@ | |
| 6 | @@ -72,7 +72,7 @@ def convert_models(args, parsed_ctds): | |
| 5 | 7 | |
| 6 | 8 | logger.info("Writing to %s" % utils.get_filename(output_file), 1) |
| 7 | 9 | |
| 10 | 12 | stream.write(CWL_SHEBANG + '\n\n') |
| 11 | 13 | stream.write("# This CWL file was automatically generated using CTDConverter.\n") |
| 12 | 14 | 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): | |
| 14 | 16 | param_name = utils.extract_param_name(param) |
| 15 | 17 | cwl_fixed_param_name = fix_param_name(param_name) |
| 16 | 18 | hardcoded_value = args.parameter_hardcoder.get_hardcoded_value(param_name, ctd_model.name) |
| 0 | 0 | From: Michael R. Crusoe <michael.crusoe@gmail.com> |
| 1 | 1 | Subject: Upgrade deprecated using of string.strip() |
| 2 | Index: ctdconverter/common/utils.py | |
| 3 | =================================================================== | |
| 2 | 4 | --- ctdconverter.orig/common/utils.py |
| 3 | 5 | +++ ctdconverter/common/utils.py |
| 4 | @@ -4,8 +4,7 @@ | |
| 6 | @@ -4,7 +4,6 @@ import ntpath | |
| 5 | 7 | import os |
| 6 | 8 | |
| 7 | 9 | from lxml import etree |
| 8 | 10 | -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 | |
| 11 | 12 | |
| 12 | 13 | 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 | |
| 15 | 15 | if member_value is not None: |
| 16 | 16 | if isinstance(member_value, list): |
| 17 | 17 | for file_name in member_value: |
| 23 | 23 | |
| 24 | 24 | for path_to_check in paths_to_check: |
| 25 | 25 | validate_path_exists(path_to_check) |
| 26 | ||