comparison toolfactory/rgToolFactory2.py @ 83:48acd0708839 draft

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82:60df9669d01c

               cll, shell=False,  stderr=tout, stdout=tout)
            tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode))
        tout.close()
        return p.returncode

    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:

            p = subprocess.run(
                cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        tout.close()
        return p.returncode

    def writeShedyml(self):
        """for planemo"""
        yuser = self.args.user_email.split("@")[0]
        yfname = os.path.join(self.tooloutdir, ".shed.yml")

83:48acd0708839

               cll, shell=False,  stderr=tout, stdout=tout)
            tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode))
        tout.close()
        return p.returncode

    def planemo_test_biocontainer(self, genoutputs=True):
        """planemo is a requirement so is available for testing but testing in a biocontainer
        requires some fiddling to use the hacked galaxy-central .venv

        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")
        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                ".","/home/biodocker/galaxy-central/.venv/bin/activate &&",
                "planemo",
                "test",
                "--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),
            ]
            p = subprocess.run(
                cll,
                shell=False,
                cwd=self.tooloutdir,
                stderr=dummy,
                stdout=dummy,
            )

        else:
            cll = [
                ".","/home/biodocker/galaxy-central/.venv/bin/activate","&&",
                "planemo",
                "test",
                "--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(
                cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        tout.close()
        return p.returncode

    def planemo_test(self, genoutputs=True):
        """planemo is a requirement so is available for testing but needs a different call if
        in the biocontainer - see above
        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:

            p = subprocess.run(
                cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        tout.close()
        return p.returncode


    def writeShedyml(self):
        """for planemo"""
        yuser = self.args.user_email.split("@")[0]
        yfname = os.path.join(self.tooloutdir, ".shed.yml")