| Previous changeset 146:2961862e2236 (2021-04-18) Next changeset 148:470d3e309508 (2021-04-18) |
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Commit message:
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modified:
toolfactory/rgToolFactory2.py |
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| diff -r 2961862e2236 -r 4e83512cb72c toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Sun Apr 18 05:54:49 2021 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Apr 18 07:59:23 2021 +0000 |
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| @@ -1043,6 +1043,13 @@ 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" @@ -1054,6 +1061,8 @@ cll = [ "planemo", "test", + "--galaxy_python_version", + self.args.python_version, "--test_data", os.path.abspath(self.testdir), "--test_output", @@ -1066,6 +1075,7 @@ p = subprocess.run( cll, shell=False, + env=penv, cwd=self.tooloutdir, stderr=tout, stdout=tout, @@ -1073,6 +1083,37 @@ 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. |