comparison toolfactory/rgToolFactory2.py @ 147:4e83512cb72c draft

Uploaded

146:2961862e2236

        """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):

        else:
            tout = open(self.tlog, "w")
        cll = [
            "planemo",
            "test",
            "--test_data",
            os.path.abspath(self.testdir),
            "--test_output",
            os.path.abspath(tool_test_path),
            "--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 main():
    """
    This is a Galaxy wrapper.
    It expects to be called by a special purpose tool.xml

147:4e83512cb72c

        """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
        # ourdir = os.getcwd()
        # print('########## ourdir=',ourdir,'gr=',self.args.galaxy_root)
        # pconfig = os.path.join(ourdir,'planemo', '.planemo.yml')
        # penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig
        # penv["HOME"] = ourdir
        # # 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):

        else:
            tout = open(self.tlog, "w")
        cll = [
            "planemo",
            "test",
            "--galaxy_python_version",
            self.args.python_version,
            "--test_data",
            os.path.abspath(self.testdir),
            "--test_output",
            os.path.abspath(tool_test_path),
            "--galaxy_root",

            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, config_path=".planemo.yml"):
        # planemo tries to write to ~/.planemo - trying to convince it otherwise
        CONFIG_TEMPLATE = """## 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.
    It expects to be called by a special purpose tool.xml