Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 96:d54976fc996a draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 20 Nov 2020 09:06:25 +0000 |
| parents | 6d122fd54cd0 |
| children | 515be7318f2b |
comparison
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| 95:6d122fd54cd0 | 96:d54976fc996a |
|---|---|
| 965 if genoutputs: | 965 if genoutputs: |
| 966 dummy, tfile = tempfile.mkstemp() | 966 dummy, tfile = tempfile.mkstemp() |
| 967 cll = [ | 967 cll = [ |
| 968 "planemo", | 968 "planemo", |
| 969 "test", | 969 "test", |
| 970 "--test_data", os.path.abspath(self.testdir), | |
| 971 "--test_output", os.path.abspath(tool_test_path), | |
| 972 "--skip_venv", | 970 "--skip_venv", |
| 973 "--galaxy_root", | 971 "--galaxy_root", |
| 974 self.args.galaxy_root, | 972 self.args.galaxy_root, |
| 975 "--update_test_data", | 973 "--update_test_data", |
| 976 os.path.abspath(xreal), | 974 os.path.abspath(xreal), |
| 977 ] | 975 ] |
| 978 p = subprocess.run( | 976 p = subprocess.run( |
| 979 cll, | 977 cll, |
| 980 shell=False, | 978 shell=False, |
| 981 cwd=self.tooloutdir, | 979 cwd=self.testdir, |
| 982 stderr=dummy, | 980 stderr=dummy, |
| 983 stdout=dummy, | 981 stdout=dummy, |
| 984 ) | 982 ) |
| 985 | 983 |
| 986 else: | 984 else: |
| 993 "--galaxy_root", | 991 "--galaxy_root", |
| 994 self.args.galaxy_root, | 992 self.args.galaxy_root, |
| 995 os.path.abspath(xreal), | 993 os.path.abspath(xreal), |
| 996 ] | 994 ] |
| 997 p = subprocess.run( | 995 p = subprocess.run( |
| 998 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout | 996 cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout |
| 999 ) | 997 ) |
| 1000 tout.close() | 998 tout.close() |
| 1001 return p.returncode | 999 return p.returncode |
| 1002 | 1000 |
| 1003 | 1001 |
| 1043 if filename.startswith(excludeme) | 1041 if filename.startswith(excludeme) |
| 1044 else tarinfo | 1042 else tarinfo |
| 1045 ) | 1043 ) |
| 1046 | 1044 |
| 1047 for p in self.outfiles: | 1045 for p in self.outfiles: |
| 1048 src = p[ONAMEPOS] | 1046 oname = p[ONAMEPOS] |
| 1047 src = os.path.join(self.testdir,oname) | |
| 1049 if os.path.isfile(src): | 1048 if os.path.isfile(src): |
| 1050 dest = os.path.join(self.testdir, "%s_sample" % src) | 1049 dest = os.path.join(self.testdir, "%s_sample" % oname) |
| 1051 shutil.copyfile(src, dest) | 1050 shutil.copyfile(src, dest) |
| 1052 dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS])) | 1051 dest = os.path.join(self.repdir, "%s.sample" % (oname)) |
| 1053 shutil.copyfile(src, dest) | 1052 shutil.copyfile(src, dest) |
| 1054 else: | 1053 else: |
| 1055 print( | 1054 print( |
| 1056 "### problem - output file %s not found in tooloutdir %s" | 1055 "### problem - output file %s not found in tooloutdir %s" |
| 1057 % (src, self.tooloutdir) | 1056 % (src, self.tooloutdir) |