Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 83:48acd0708839 draft
Uploaded
| author | fubar |
|---|---|
| date | Thu, 19 Nov 2020 01:04:45 +0000 |
| parents | 6395be766c2e |
| children | 5304cda01f60 |
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| 82:60df9669d01c | 83:48acd0708839 |
|---|---|
| 871 cll, shell=False, stderr=tout, stdout=tout) | 871 cll, shell=False, stderr=tout, stdout=tout) |
| 872 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode)) | 872 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode)) |
| 873 tout.close() | 873 tout.close() |
| 874 return p.returncode | 874 return p.returncode |
| 875 | 875 |
| 876 def planemo_test_biocontainer(self, genoutputs=True): | |
| 877 """planemo is a requirement so is available for testing but testing in a biocontainer | |
| 878 requires some fiddling to use the hacked galaxy-central .venv | |
| 879 | |
| 880 Planemo runs: | |
| 881 python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file | |
| 882 /export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html | |
| 883 --with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata | |
| 884 --structured-data-file | |
| 885 /export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox | |
| 886 | |
| 887 | |
| 888 for the planemo-biocontainer, | |
| 889 planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml | |
| 890 | |
| 891 """ | |
| 892 xreal = "%s.xml" % self.tool_name | |
| 893 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html") | |
| 894 if os.path.exists(self.tlog): | |
| 895 tout = open(self.tlog, "a") | |
| 896 else: | |
| 897 tout = open(self.tlog, "w") | |
| 898 if genoutputs: | |
| 899 dummy, tfile = tempfile.mkstemp() | |
| 900 cll = [ | |
| 901 ".","/home/biodocker/galaxy-central/.venv/bin/activate &&", | |
| 902 "planemo", | |
| 903 "test", | |
| 904 "--test_data", os.path.abspath(self.testdir), | |
| 905 "--test_output", os.path.abspath(tool_test_path), | |
| 906 "--skip_venv", | |
| 907 "--galaxy_root", | |
| 908 self.args.galaxy_root, | |
| 909 "--update_test_data", | |
| 910 os.path.abspath(xreal), | |
| 911 ] | |
| 912 p = subprocess.run( | |
| 913 cll, | |
| 914 shell=False, | |
| 915 cwd=self.tooloutdir, | |
| 916 stderr=dummy, | |
| 917 stdout=dummy, | |
| 918 ) | |
| 919 | |
| 920 else: | |
| 921 cll = [ | |
| 922 ".","/home/biodocker/galaxy-central/.venv/bin/activate","&&", | |
| 923 "planemo", | |
| 924 "test", | |
| 925 "--test_data", os.path.abspath(self.testdir), | |
| 926 "--test_output", os.path.abspath(tool_test_path), | |
| 927 "--skip_venv", | |
| 928 "--galaxy_root", | |
| 929 self.args.galaxy_root, | |
| 930 os.path.abspath(xreal), | |
| 931 ] | |
| 932 p = subprocess.run( | |
| 933 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout | |
| 934 ) | |
| 935 tout.close() | |
| 936 return p.returncode | |
| 937 | |
| 876 def planemo_test(self, genoutputs=True): | 938 def planemo_test(self, genoutputs=True): |
| 877 """planemo is a requirement so is available for testing | 939 """planemo is a requirement so is available for testing but needs a different call if |
| 940 in the biocontainer - see above | |
| 878 and for generating test outputs if command or test overrides are supplied | 941 and for generating test outputs if command or test overrides are supplied |
| 879 test outputs are sent to repdir for display | 942 test outputs are sent to repdir for display |
| 880 planemo test --engine docker_galaxy --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml | 943 planemo test --engine docker_galaxy --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml |
| 881 | 944 |
| 882 Planemo runs: | 945 Planemo runs: |
| 934 p = subprocess.run( | 997 p = subprocess.run( |
| 935 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout | 998 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout |
| 936 ) | 999 ) |
| 937 tout.close() | 1000 tout.close() |
| 938 return p.returncode | 1001 return p.returncode |
| 1002 | |
| 939 | 1003 |
| 940 def writeShedyml(self): | 1004 def writeShedyml(self): |
| 941 """for planemo""" | 1005 """for planemo""" |
| 942 yuser = self.args.user_email.split("@")[0] | 1006 yuser = self.args.user_email.split("@")[0] |
| 943 yfname = os.path.join(self.tooloutdir, ".shed.yml") | 1007 yfname = os.path.join(self.tooloutdir, ".shed.yml") |