| Previous changeset 102:c632db66f8c0 (2020-11-26) Next changeset 104:05cb28bf2bbc (2020-11-27) |
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Commit message:
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modified:
toolfactory/rgToolFactory2.py |
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| diff -r c632db66f8c0 -r 2ca51677d6d1 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Thu Nov 26 06:26:28 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Fri Nov 27 22:38:43 2020 +0000 |
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| @@ -28,6 +28,7 @@ import argparse import copy import datetime +import grp import json import logging import os @@ -710,6 +711,7 @@ + def planemo_biodocker_test(self): """planemo currently leaks dependencies if used in the same container and gets unhappy after a first successful run. https://github.com/galaxyproject/planemo/issues/1078#issuecomment-731476930 @@ -718,53 +720,67 @@ """ + def prun(container,tout,cl,user="biodocker"): + rlog = container.exec_run(cl,user=user) + slogl = str(rlog).split('\\n') + slog = '\n'.join(slogl) + tout.write(f"## got rlog {slog} from {cl}\n") + + dgroup = grp.getgrnam('docker')[2] if os.path.exists(self.tlog): tout = open(self.tlog, "a") else: tout = open(self.tlog, "w") planemoimage = "quay.io/fubar2/planemo-biocontainer" xreal = "%s.xml" % self.tool_name - destdir = "/tmp/tfout" repname = f"{self.tool_name}_planemo_test_report.html" - imrep = os.path.join(destdir,repname) ptestrep_path = os.path.join(self.repdir,repname) tool_name = self.tool_name client = docker.from_env() - container = client.containers.run(planemoimage,'sleep 10000m', detach=True) - rlog = container.exec_run(f"mkdir -p {destdir}") - slogl = str(rlog).split('\\n') - slog = '\n'.join(slogl) - tout.write(f"## got rlog {slog} from mkdir {destdir}") - ptestpath = os.path.join(destdir,xreal) - self.copy_to_container(self.tooloutdir,'/tmp',container) + tvol = client.volumes.create() + tvolname = tvol.name + destdir = "/toolfactory/ptest" + imrep = os.path.join(destdir,repname) + container = client.containers.run(planemoimage,'sleep 10000m', detach=True, user="biodocker", + network="host", volumes={f"{tvolname}": {'bind': '/toolfactory', 'mode': 'rw'}}) + cl = f"groupmod -g {dgroup} docker" + prun(container, tout, cl, user="root") + cl = f"mkdir -p {destdir}" + prun(container, tout, cl, user="root") + cl = f"rm -rf {destdir}/*" + prun(container, tout, cl, user="root") + ptestpath = os.path.join(destdir,'tfout',xreal) + self.copy_to_container(self.tooloutdir,destdir,container) + cl ='chmod -R a+rwx /toolfactory' + prun(container, tout, cl, user="root") rlog = container.exec_run(f"ls -la {destdir}") - ptestcl = f"planemo test --update_test_data --galaxy_root /home/biodocker/galaxy-central {ptestpath}" + ptestcl = f"planemo test --update_test_data --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}" try: rlog = container.exec_run(ptestcl) except: e = sys.exc_info()[0] - tout.write(f"#### error: {e} from {ptestcl}") + tout.write(f"#### error: {e} from {ptestcl}\n") # fails - used to generate test outputs - ptestcl = f"planemo test --test_output {imrep} --galaxy_root /home/biodocker/galaxy-central {ptestpath}" + cl = f"planemo test --test_output {imrep} --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}" try: - rlog = container.exec_run(ptestcl) + prun(container,tout,cl) except: pass - slogl = str(rlog).split('\\n') - slog = '\n'.join(slogl) - tout.write(f"## got rlog {slog} from mkdir {destdir}") testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp",dir=".") self.copy_from_container(destdir,testouts,container) - try: - shutil.rmtree(os.path.join(testouts,self.tooloutdir,'test-data','test-data')) - except: - e = sys.exc_info()[0] - tout.write(f"#### error: {e} from {ptestcl}") - shutil.copytree(os.path.join(testouts,self.tooloutdir), self.tooloutdir, dirs_exist_ok=True) + src = os.path.join(testouts,'ptest') + if os.path.isdir(src): + shutil.copytree(src, '.', dirs_exist_ok=True) + src = repname + if os.path.isfile(repname): + shutil.copyfile(src,ptestrep_path) + else: + tout.write(f"No output from run to shutil.copytree in {src}\n") tout.close() container.stop() container.remove() - shutil.rmtree(testouts) + tvol.remove() + #shutil.rmtree(testouts) def shedLoad(self): """ |