comparison toolfactory/rgToolFactory2.py @ 97:515be7318f2b draft

Uploaded

96:d54976fc996a

                "--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.testdir, stderr=tout, stdout=tout
            )
        tout.close()

    if args.make_Tool == "generate":
        retcode = r.run()
        r.moveRunOutputs()
        r.makeToolTar()
    else:
        retcode = r.planemo_test(genoutputs=True)  # this fails :( - see PR
        r.moveRunOutputs()
        r.makeToolTar()
        retcode = r.planemo_test(genoutputs=False)
        r.moveRunOutputs()
        r.makeToolTar()
        print(f"second planemo_test returned {retcode}")
        if args.make_Tool == "gentestinstall":
            r.shedLoad()
            r.eph_galaxy_load()


if __name__ == "__main__":
    main()

97:515be7318f2b

                "--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.testdir, stderr=tout, stdout=tout
            )
        tout.close()
        return p.returncode


    def gal_test(self, genoutputs=True):
        """
export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \
&& export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox

        """
        tool_test_rep_path = os.path.join(self.repdir,f"{self.tool_name}_galaxy_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 = [
            "mkdir -p ./test","&&","export GALAXY_TEST_SAVE='./test'", "&&", "export GALAXY_TEST_NO_CLEANUP='1'", \
           "&&", "export GALAXY_TEST_TMP_DIR='./test'", "&&", f"sh {self.args.galaxy_root}/run_tests.sh --id {self.args.tool_id} --report_file {tool_test_rep_path} functional.test_toolbox",
            ]
            p = subprocess.run(
                cll,
                shell=False,
                cwd=self.testdir,
                stderr=dummy,
                stdout=dummy,
            )
            # if all went well, tgz is in ./test and down a nest of tmp directories lurk the output files
            outfiles = []
            for p in self.outfiles:
                oname = p[ONAMEPOS]
                outfiles.append(oname)
            paths = []
            for root, dirs, files in os.walk('./test'):
                for f in files:
                    if f in outfiles:
                        paths.append([root,f])
            for p in paths:
                src = os.path.join(p[0],p[1])
                dest = os.path.join(self.testdir,f"{p[1]}_sample")
                shutil.copyfile(src,dest)

        else:
            cll = [
            "mkdir -p ./test","&&","rm -rf ./test/*","&&","export GALAXY_TEST_SAVE='./test'", "&&", "export GALAXY_TEST_NO_CLEANUP=", \
           "&&", "export GALAXY_TEST_TMP_DIR='./test'", "&&", f"sh {self.args.galaxy_root}/run_tests.sh --id {self.args.tool_id} --report_file {tool_test_rep_path} functional.test_toolbox",
            ]
            p = subprocess.run(
                cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout
            )
        tout.close()

    if args.make_Tool == "generate":
        retcode = r.run()
        r.moveRunOutputs()
        r.makeToolTar()
    else:
        r.makeToolTar()
        r.shedLoad()
        r.eph_galaxy_load()
        retcode = r.gal_test(genoutputs=True)  # this fails
        r.makeToolTar()
        retcode = r.gal_test(genoutputs=False)
        r.moveRunOutputs()
        r.makeToolTar()
        print(f"second galaxy_test returned {retcode}")


if __name__ == "__main__":
    main()