| Previous changeset 96:d54976fc996a (2020-11-20) Next changeset 98:67628c7dc9f3 (2020-11-22) |
|
Commit message:
Uploaded |
|
modified:
toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| b |
| diff -r d54976fc996a -r 515be7318f2b toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Fri Nov 20 09:06:25 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sat Nov 21 10:11:36 2020 +0000 |
| [ |
| @@ -999,6 +999,57 @@ return p.returncode + def gal_test(self, genoutputs=True): + """ +export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \ +&& export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox + + """ + tool_test_rep_path = os.path.join(self.repdir,f"{self.tool_name}_galaxy_test_report.html") + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") + if genoutputs: + dummy, tfile = tempfile.mkstemp() + cll = [ + "mkdir -p ./test","&&","export GALAXY_TEST_SAVE='./test'", "&&", "export GALAXY_TEST_NO_CLEANUP='1'", \ + "&&", "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", + ] + p = subprocess.run( + cll, + shell=False, + cwd=self.testdir, + stderr=dummy, + stdout=dummy, + ) + # if all went well, tgz is in ./test and down a nest of tmp directories lurk the output files + outfiles = [] + for p in self.outfiles: + oname = p[ONAMEPOS] + outfiles.append(oname) + paths = [] + for root, dirs, files in os.walk('./test'): + for f in files: + if f in outfiles: + paths.append([root,f]) + for p in paths: + src = os.path.join(p[0],p[1]) + dest = os.path.join(self.testdir,f"{p[1]}_sample") + shutil.copyfile(src,dest) + + else: + cll = [ + "mkdir -p ./test","&&","rm -rf ./test/*","&&","export GALAXY_TEST_SAVE='./test'", "&&", "export GALAXY_TEST_NO_CLEANUP=", \ + "&&", "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", + ] + p = subprocess.run( + cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout + ) + tout.close() + return p.returncode + + def writeShedyml(self): """for planemo""" yuser = self.args.user_email.split("@")[0] @@ -1151,16 +1202,15 @@ r.moveRunOutputs() r.makeToolTar() else: - retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR + r.makeToolTar() + r.shedLoad() + r.eph_galaxy_load() + retcode = r.gal_test(genoutputs=True) # this fails + r.makeToolTar() + retcode = r.gal_test(genoutputs=False) r.moveRunOutputs() r.makeToolTar() - retcode = r.planemo_test(genoutputs=False) - r.moveRunOutputs() - r.makeToolTar() - print(f"second planemo_test returned {retcode}") - if args.make_Tool == "gentestinstall": - r.shedLoad() - r.eph_galaxy_load() + print(f"second galaxy_test returned {retcode}") if __name__ == "__main__": |
| b |
| diff -r d54976fc996a -r 515be7318f2b toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Fri Nov 20 09:06:25 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Sat Nov 21 10:11:36 2020 +0000 |
| b |
| @@ -411,8 +411,6 @@ <param name="choosescript" value="yes" /> <param name="script_path" value="$runme"/> <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" /> - <output name="output2" file="output2_sample" compare="diff" /> - </test> </tests> <help> |