Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 78:89aca6c67405 draft

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author fubar
date Tue, 17 Nov 2020 06:04:40 +0000
parents 46db8143adb7
children f423a77bc669
comparison
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77:1fa49a9a4ec5 78:89aca6c67405
1 #!/usr/bin/python3 1
2 # rgToolFactory.py 2 # rgToolFactory.py
3 # see https://github.com/fubar2/toolfactory 3 # see https://github.com/fubar2/toolfactory
4 # 4 #
5 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 5 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
6 # 6 #
880 and for generating test outputs if command or test overrides are supplied 880 and for generating test outputs if command or test overrides are supplied
881 test outputs are sent to repdir for display 881 test outputs are sent to repdir for display
882 planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml 882 planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
883 """ 883 """
884 xreal = "%s.xml" % self.tool_name 884 xreal = "%s.xml" % self.tool_name
885 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
885 if os.path.exists(self.tlog): 886 if os.path.exists(self.tlog):
886 tout = open(self.tlog, "a") 887 tout = open(self.tlog, "a")
887 else: 888 else:
888 tout = open(self.tlog, "w") 889 tout = open(self.tlog, "w")
889 if genoutputs: 890 if genoutputs:
890 dummy, tfile = tempfile.mkstemp() 891 dummy, tfile = tempfile.mkstemp()
891 cll = [ 892 cll = [
892 "planemo", 893 "planemo",
893 "test", 894 "test",
895 "--test_output_xunit",os.path.join(self.repdir,f"{self.tool_name}_xunit.xml")
896 "--test_data", os.path.abspath(self.testdir),
897 "--test_output", os.path.abspath(tool_test_path),
894 "--galaxy_root", 898 "--galaxy_root",
895 self.args.galaxy_root, 899 self.args.galaxy_root,
896 "--update_test_data", 900 "--update_test_data",
897 xreal, 901 os.path.abspath(xreal),
898 ] 902 ]
899 p = subprocess.run( 903 p = subprocess.run(
900 cll, 904 cll,
901 shell=False, 905 shell=False,
902 cwd=self.tooloutdir, 906 cwd=self.tooloutdir,
903 stderr=dummy, 907 stderr=tout,
904 stdout=dummy, 908 stdout=tout,
905 ) 909 )
906 else: 910 else:
907 cll = [ 911 cll = [
908 "planemo", 912 "planemo",
909 "test", 913 "test",
914 "--test_data", self.testdir,
915 "--test_output", tool_test_path,
910 "--galaxy_root", 916 "--galaxy_root",
911 self.args.galaxy_root, 917 self.args.galaxy_root,
912 xreal, 918 os.path.abspath(xreal),
913 ] 919 ]
914 p = subprocess.run( 920 p = subprocess.run(
915 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout 921 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
916 ) 922 )
917 tout.close() 923 tout.close()