comparison toolfactory/rgToolFactory2.py @ 137:63d15caea378 draft

Uploaded

136:94f5560de46d

        """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
        """
        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):

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


def main():
    """
    This is a Galaxy wrapper.

137:63d15caea378

        """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
        """
        penv = os.environ
        pconfig = os.path.join(self.args.tool_dir,'.planemo.yml')
        penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig
        self.set_planemo_galaxy_root(self.args.galaxy_root,config_path=pconfig)
        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):

            os.path.abspath(xreal),
        ]
        p = subprocess.run(
            cll,
            shell=False,
            env = penv,
            cwd=self.tooloutdir,
            stderr=tout,
            stdout=tout,
        )
        tout.close()
        return p.returncode

    def set_planemo_galaxy_root(self, galaxyroot='/galaxy-central', config_path=".planemo.yml"):
        # bug in planemo - bogus '--dev-wheels' passed to run_tests.sh as at april 2021 - need a fiddled copy so it is ignored until fixed
        CONFIG_TEMPLATE = f"""## Planemo Global Configuration File.
## Everything in this file is completely optional - these values can all be
## configured via command line options for the corresponding commands.

## Specify a default galaxy_root for test and server commands here.
galaxy_root: %s
## Username used with toolshed(s).
#shed_username: "<TODO>"
sheds:
  # For each tool shed you wish to target, uncomment key or both email and
  # password.
  toolshed:
    #key: "<TODO>"
    #email: "<TODO>"
    #password: "<TODO>"
  testtoolshed:
    #key: "<TODO>"
    #email: "<TODO>"
    #password: "<TODO>"
  local:
    #key: "<TODO>"
    #email: "<TODO>"
    #password: "<TODO>"
"""
        if not os.path.exists(config_path):
            with open(config_path, "w") as f:
                f.write(CONFIG_TEMPLATE % galaxyroot)


def main():
    """
    This is a Galaxy wrapper.