Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 97:515be7318f2b draft

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Uploaded
author fubar
date Sat, 21 Nov 2020 10:11:36 +0000
parents d54976fc996a
children 67628c7dc9f3
comparison
equal deleted inserted replaced
96:d54976fc996a 97:515be7318f2b
989 "--test_output", os.path.abspath(tool_test_path), 989 "--test_output", os.path.abspath(tool_test_path),
990 "--skip_venv", 990 "--skip_venv",
991 "--galaxy_root", 991 "--galaxy_root",
992 self.args.galaxy_root, 992 self.args.galaxy_root,
993 os.path.abspath(xreal), 993 os.path.abspath(xreal),
994 ]
995 p = subprocess.run(
996 cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout
997 )
998 tout.close()
999 return p.returncode
1000
1001
1002 def gal_test(self, genoutputs=True):
1003 """
1004 export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \
1005 && export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
1006
1007 """
1008 tool_test_rep_path = os.path.join(self.repdir,f"{self.tool_name}_galaxy_test_report.html")
1009 if os.path.exists(self.tlog):
1010 tout = open(self.tlog, "a")
1011 else:
1012 tout = open(self.tlog, "w")
1013 if genoutputs:
1014 dummy, tfile = tempfile.mkstemp()
1015 cll = [
1016 "mkdir -p ./test","&&","export GALAXY_TEST_SAVE='./test'", "&&", "export GALAXY_TEST_NO_CLEANUP='1'", \
1017 "&&", "export GALAXY_TEST_TMP_DIR='./test'", "&&", f"sh {self.args.galaxy_root}/run_tests.sh --id {self.args.tool_id} --report_file {tool_test_rep_path} functional.test_toolbox",
1018 ]
1019 p = subprocess.run(
1020 cll,
1021 shell=False,
1022 cwd=self.testdir,
1023 stderr=dummy,
1024 stdout=dummy,
1025 )
1026 # if all went well, tgz is in ./test and down a nest of tmp directories lurk the output files
1027 outfiles = []
1028 for p in self.outfiles:
1029 oname = p[ONAMEPOS]
1030 outfiles.append(oname)
1031 paths = []
1032 for root, dirs, files in os.walk('./test'):
1033 for f in files:
1034 if f in outfiles:
1035 paths.append([root,f])
1036 for p in paths:
1037 src = os.path.join(p[0],p[1])
1038 dest = os.path.join(self.testdir,f"{p[1]}_sample")
1039 shutil.copyfile(src,dest)
1040
1041 else:
1042 cll = [
1043 "mkdir -p ./test","&&","rm -rf ./test/*","&&","export GALAXY_TEST_SAVE='./test'", "&&", "export GALAXY_TEST_NO_CLEANUP=", \
1044 "&&", "export GALAXY_TEST_TMP_DIR='./test'", "&&", f"sh {self.args.galaxy_root}/run_tests.sh --id {self.args.tool_id} --report_file {tool_test_rep_path} functional.test_toolbox",
994 ] 1045 ]
995 p = subprocess.run( 1046 p = subprocess.run(
996 cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout 1047 cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout
997 ) 1048 )
998 tout.close() 1049 tout.close()
1149 if args.make_Tool == "generate": 1200 if args.make_Tool == "generate":
1150 retcode = r.run() 1201 retcode = r.run()
1151 r.moveRunOutputs() 1202 r.moveRunOutputs()
1152 r.makeToolTar() 1203 r.makeToolTar()
1153 else: 1204 else:
1154 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR 1205 r.makeToolTar()
1206 r.shedLoad()
1207 r.eph_galaxy_load()
1208 retcode = r.gal_test(genoutputs=True) # this fails
1209 r.makeToolTar()
1210 retcode = r.gal_test(genoutputs=False)
1155 r.moveRunOutputs() 1211 r.moveRunOutputs()
1156 r.makeToolTar() 1212 r.makeToolTar()
1157 retcode = r.planemo_test(genoutputs=False) 1213 print(f"second galaxy_test returned {retcode}")
1158 r.moveRunOutputs()
1159 r.makeToolTar()
1160 print(f"second planemo_test returned {retcode}")
1161 if args.make_Tool == "gentestinstall":
1162 r.shedLoad()
1163 r.eph_galaxy_load()
1164 1214
1165 1215
1166 if __name__ == "__main__": 1216 if __name__ == "__main__":
1167 main() 1217 main()