comparison toolfactory/rgToolFactory2.py @ 3:c4f192ec521c draft

Uploaded

2:b65ec4f387b9

        """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",
            self.args.galaxy_root,
            "--update_test_data",
            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

3:c4f192ec521c

        """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
        phome = penv['HOME']
        isDocker = os.path.exists('/.dockerenv')
        if isDocker: # use the volume if it exists
            phome = '/home/planemo'
            if os.path.exists(phome): # is mounted
                home = phome
            else:
                home = '/tmp/planemo' # this will be brutal but otherwise /home/galaxy
                os.mkdir('/tmp/planemo')
        penv["HOME"] = phome
        path = penv['PATH']
        penv['PATH'] = '%s:%s' % (phome,path)
        print(f"#### set home to {phome} with path={penv['PATH']}")
        #pconfig = os.path.join(phome,'.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):

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

    def set_planemo_galaxy_root(self, galaxyroot, config_path):
        # 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