comparison toolfactory/rgToolFactory2.py @ 95:6d122fd54cd0 draft

Uploaded

94:e8f35fec0f2f

# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
# No support for automatic HTML file creation from arbitrary outputs
# essential problem is to create two command lines - one for the tool xml and a different
# one to run the executable with the supplied test data and settings
# Be simpler to write the tool, then run it with planemo and soak up the test outputs.


import argparse
import datetime
import json
import logging

        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                "planemo",
                "test",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--skip_venv",

                stdout=dummy,
            )

        else:
            cll = [
                "planemo",
                "test",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--skip_venv",

95:6d122fd54cd0

# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
# No support for automatic HTML file creation from arbitrary outputs
# essential problem is to create two command lines - one for the tool xml and a different
# one to run the executable with the supplied test data and settings
# Be simpler to write the tool, then run it with planemo and soak up the test outputs.
# well well. sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
# does the needful. Use GALAXY_TEST_SAVE /foo to save outputs - only the tar.gz - not the rest sadly
# GALAXY_TEST_NO_CLEANUP GALAXY_TEST_TMP_DIR=wherever

import argparse
import datetime
import json
import logging

        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            dummy, tfile = tempfile.mkstemp()
            cll = [
                ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
                "planemo",
                "test",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--skip_venv",

                stdout=dummy,
            )

        else:
            cll = [
                ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
                "planemo",
                "test",
                "--test_data", os.path.abspath(self.testdir),
                "--test_output", os.path.abspath(tool_test_path),
                "--skip_venv",