comparison toolfactory/rgToolFactory2.py @ 81:6395be766c2e draft

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80:f423a77bc669

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

    def planemo_test(self, genoutputs=True):
        """planemo is a requirement so is available for testing
        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")

        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                "planemo",
                "test",
                "--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),
            ]

        else:
            cll = [
                "planemo",
                "test",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--galaxy_root",
                self.args.galaxy_root,
                os.path.abspath(xreal),
            ]
            p = subprocess.run(

81:6395be766c2e

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

    def planemo_test(self, genoutputs=True):
        """planemo is a requirement so is available for testing
        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  --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml

        Planemo runs:
python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
/export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html
--with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
--structured-data-file
/export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox


        for the planemo-biocontainer,
        planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.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")

        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                "planemo",
                "test",
                "--conda_dependency_resolution",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--skip_venv",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                os.path.abspath(xreal),
            ]

        else:
            cll = [
                "planemo",
                "test",
                "--conda_dependency_resolution",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--skip_venv",
                "--galaxy_root",
                self.args.galaxy_root,
                os.path.abspath(xreal),
            ]
            p = subprocess.run(