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

Uploaded

77:1fa49a9a4ec5

#!/usr/bin/python3
# rgToolFactory.py
# see https://github.com/fubar2/toolfactory
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#

        and for generating test outputs if command or test overrides are supplied
        test outputs are sent to repdir for display
        planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
        """
        xreal = "%s.xml" % self.tool_name
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                xreal,
            ]
            p = subprocess.run(
                cll,
                shell=False,
                cwd=self.tooloutdir,
                stderr=dummy,
                stdout=dummy,
            )
        else:
            cll = [
                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                xreal,
            ]
            p = subprocess.run(
                cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        tout.close()

78:89aca6c67405

# rgToolFactory.py
# see https://github.com/fubar2/toolfactory
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#

        and for generating test outputs if command or test overrides are supplied
        test outputs are sent to repdir for display
        planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
        """
        xreal = "%s.xml" % self.tool_name
        tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                "planemo",
                "test",
                "--test_output_xunit",os.path.join(self.repdir,f"{self.tool_name}_xunit.xml")
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                os.path.abspath(xreal),
            ]
            p = subprocess.run(
                cll,
                shell=False,
                cwd=self.tooloutdir,
                stderr=tout,
                stdout=tout,
            )
        else:
            cll = [
                "planemo",
                "test",
                "--test_data", self.testdir,
                "--test_output", tool_test_path,
                "--galaxy_root",
                self.args.galaxy_root,
                os.path.abspath(xreal),
            ]
            p = subprocess.run(
                cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        tout.close()