Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 149:ecd1d283b5a7 draft
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author | fubar |
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date | Tue, 20 Apr 2021 04:36:02 +0000 |
parents | 470d3e309508 |
children |
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148:470d3e309508 | 149:ecd1d283b5a7 |
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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 | 1046 penv = os.environ |
1047 # ourdir = os.getcwd() | 1047 phome = penv['HOME'] |
1048 # print('########## ourdir=',ourdir,'gr=',self.args.galaxy_root) | 1048 isDocker = os.path.exists('/.dockerenv') |
1049 # pconfig = os.path.join(ourdir,'planemo', '.planemo.yml') | 1049 if isDocker: # use the volume if it exists |
1050 # penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig | 1050 phome = '/home/planemo' |
1051 # os.mkdir(os.path.join(ourdir,'planemo')) | 1051 if os.path.exists(phome): # is mounted |
1052 # penv["HOME"] = os.path.join(ourdir,'home') | 1052 home = phome |
1053 # os.mkdir(os.path.join(ourdir,'home')) | 1053 else: |
1054 home = '/tmp/planemo' # this will be brutal but otherwise /home/galaxy | |
1055 os.mkdir('/tmp/planemo') | |
1056 penv["HOME"] = phome | |
1057 path = penv['PATH'] | |
1058 penv['PATH'] = '%s:%s' % (phome,path) | |
1059 print(f"#### set home to {phome} with path={penv['PATH']}") | |
1060 #pconfig = os.path.join(phome,'.planemo.yml') | |
1061 #penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig | |
1054 # self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig) | 1062 # self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig) |
1055 xreal = "%s.xml" % self.tool_name | 1063 xreal = "%s.xml" % self.tool_name |
1056 tool_test_path = os.path.join( | 1064 tool_test_path = os.path.join( |
1057 self.repdir, f"{self.tool_name}_planemo_test_report.html" | 1065 self.repdir, f"{self.tool_name}_planemo_test_report.html" |
1058 ) | 1066 ) |
1067 self.args.python_version, | 1075 self.args.python_version, |
1068 "--test_data", | 1076 "--test_data", |
1069 os.path.abspath(self.testdir), | 1077 os.path.abspath(self.testdir), |
1070 "--test_output", | 1078 "--test_output", |
1071 os.path.abspath(tool_test_path), | 1079 os.path.abspath(tool_test_path), |
1072 "--galaxy_root", | 1080 ## "--galaxy_root", |
1073 self.args.galaxy_root, | 1081 ## self.args.galaxy_root, |
1074 "--update_test_data", | 1082 "--update_test_data", |
1075 os.path.abspath(xreal), | 1083 os.path.abspath(xreal), |
1076 ] | 1084 ] |
1077 p = subprocess.run( | 1085 p = subprocess.run( |
1078 cll, | 1086 cll, |
1087 env = penv, | |
1079 shell=False, | 1088 shell=False, |
1080 env=penv, | |
1081 cwd=self.tooloutdir, | 1089 cwd=self.tooloutdir, |
1082 stderr=tout, | 1090 stderr=tout, |
1083 stdout=tout, | 1091 stdout=tout, |
1084 ) | 1092 ) |
1085 tout.close() | 1093 tout.close() |
1111 #password: "<TODO>" | 1119 #password: "<TODO>" |
1112 """ | 1120 """ |
1113 if not os.path.exists(config_path): | 1121 if not os.path.exists(config_path): |
1114 with open(config_path, "w") as f: | 1122 with open(config_path, "w") as f: |
1115 f.write(CONFIG_TEMPLATE % galaxyroot) | 1123 f.write(CONFIG_TEMPLATE % galaxyroot) |
1116 | |
1117 | 1124 |
1118 | 1125 |
1119 def main(): | 1126 def main(): |
1120 """ | 1127 """ |
1121 This is a Galaxy wrapper. | 1128 This is a Galaxy wrapper. |