Mercurial > repos > fubar > tool_factory_2

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Sun, 18 Apr 2021 07:59:23 +0000
parents 351d479e4a86
children 470d3e309508
comparison
equal deleted inserted replaced
146:2961862e2236 147:4e83512cb72c
1041 """planemo is a requirement so is available for testing but needs a 1041 """planemo is a requirement so is available for testing but needs a
1042 different call if in the biocontainer - see above 1042 different call if in the biocontainer - see above
1043 and for generating test outputs if command or test overrides are 1043 and for generating test outputs if command or test overrides are
1044 supplied test outputs are sent to repdir for display 1044 supplied test outputs are sent to repdir for display
1045 """ 1045 """
1046 penv = os.environ
1047 # ourdir = os.getcwd()
1048 # print('########## ourdir=',ourdir,'gr=',self.args.galaxy_root)
1049 # pconfig = os.path.join(ourdir,'planemo', '.planemo.yml')
1050 # penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig
1051 # penv["HOME"] = ourdir
1052 # # self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig)
1046 xreal = "%s.xml" % self.tool_name 1053 xreal = "%s.xml" % self.tool_name
1047 tool_test_path = os.path.join( 1054 tool_test_path = os.path.join(
1048 self.repdir, f"{self.tool_name}_planemo_test_report.html" 1055 self.repdir, f"{self.tool_name}_planemo_test_report.html"
1049 ) 1056 )
1050 if os.path.exists(self.tlog): 1057 if os.path.exists(self.tlog):
1052 else: 1059 else:
1053 tout = open(self.tlog, "w") 1060 tout = open(self.tlog, "w")
1054 cll = [ 1061 cll = [
1055 "planemo", 1062 "planemo",
1056 "test", 1063 "test",
1064 "--galaxy_python_version",
1065 self.args.python_version,
1057 "--test_data", 1066 "--test_data",
1058 os.path.abspath(self.testdir), 1067 os.path.abspath(self.testdir),
1059 "--test_output", 1068 "--test_output",
1060 os.path.abspath(tool_test_path), 1069 os.path.abspath(tool_test_path),
1061 "--galaxy_root", 1070 "--galaxy_root",
1064 os.path.abspath(xreal), 1073 os.path.abspath(xreal),
1065 ] 1074 ]
1066 p = subprocess.run( 1075 p = subprocess.run(
1067 cll, 1076 cll,
1068 shell=False, 1077 shell=False,
1078 env=penv,
1069 cwd=self.tooloutdir, 1079 cwd=self.tooloutdir,
1070 stderr=tout, 1080 stderr=tout,
1071 stdout=tout, 1081 stdout=tout,
1072 ) 1082 )
1073 tout.close() 1083 tout.close()
1074 return p.returncode 1084 return p.returncode
1085
1086 def set_planemo_galaxy_root(self, galaxyroot, config_path=".planemo.yml"):
1087 # planemo tries to write to ~/.planemo - trying to convince it otherwise
1088 CONFIG_TEMPLATE = """## Planemo Global Configuration File.
1089 ## Everything in this file is completely optional - these values can all be
1090 ## configured via command line options for the corresponding commands.
1091 ## Specify a default galaxy_root for test and server commands here.
1092 galaxy_root: %s
1093 ## Username used with toolshed(s).
1094 #shed_username: "<TODO>"
1095 sheds:
1096 # For each tool shed you wish to target, uncomment key or both email and
1097 # password.
1098 toolshed:
1099 #key: "<TODO>"
1100 #email: "<TODO>"
1101 #password: "<TODO>"
1102 testtoolshed:
1103 #key: "<TODO>"
1104 #email: "<TODO>"
1105 #password: "<TODO>"
1106 local:
1107 #key: "<TODO>"
1108 #email: "<TODO>"
1109 #password: "<TODO>"
1110 """
1111 if not os.path.exists(config_path):
1112 with open(config_path, "w") as f:
1113 f.write(CONFIG_TEMPLATE % galaxyroot)
1114
1115
1075 1116
1076 def main(): 1117 def main():
1077 """ 1118 """
1078 This is a Galaxy wrapper. 1119 This is a Galaxy wrapper.
1079 It expects to be called by a special purpose tool.xml 1120 It expects to be called by a special purpose tool.xml