| Previous changeset 101:557d5f06f213 (2020-11-26) Next changeset 103:2ca51677d6d1 (2020-11-27) |
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Commit message:
Uploaded |
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modified:
toolfactory/rgToolFactory2.py |
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| diff -r 557d5f06f213 -r c632db66f8c0 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Thu Nov 26 06:17:12 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Thu Nov 26 06:26:28 2020 +0000 |
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| b'@@ -766,191 +766,6 @@\n container.remove()\n shutil.rmtree(testouts)\n \n-\n- def planemo_biodocker_vol_test(self):\n- """planemo currently leaks dependencies if used in the same container and gets unhappy after a\n- first successful run. https://github.com/galaxyproject/planemo/issues/1078#issuecomment-731476930\n-\n- Docker biocontainer has planemo with caches filled to save repeated downloads\n- Cannot get volumes to work right in this version\n-\n- """\n- if os.path.exists(self.tlog):\n- tout = open(self.tlog, "a")\n- else:\n- tout = open(self.tlog, "w")\n- planemoimage = "quay.io/fubar2/planemo-biocontainer"\n- xreal = "%s.xml" % self.tool_name\n- repname = f"{self.tool_name}_planemo_test_report.html"\n- ptestrep_path = os.path.join(self.repdir,repname)\n- tool_name = self.tool_name\n- workdir = "export"\n- aworkdir = os.path.abspath(workdir)\n- os.makedirs(workdir, exist_ok=True)\n- os.chmod(workdir,0o777)\n- imworkdir = "/export"\n- # must be mounted as a volume\n- tooldir = os.path.join(workdir,self.tool_name)\n- testdir = os.path.join(tooldir,\'test-data\')\n- imtooldir = os.path.join(imworkdir,self.tool_name)\n- imtestdir = os.path.join(imtooldir,\'test-data\')\n- for d in [tooldir,testdir]:\n- if not os.path.exists(d):\n- os.mkdir(d)\n- with os.scandir(self.testdir) as outs:\n- for entry in outs:\n- if not entry.is_file():\n- continue\n- src = os.path.join(self.testdir, entry.name)\n- dest = os.path.join(testdir, entry.name)\n- shutil.copyfile(src, dest)\n- shutil.copyfile(xreal,os.path.join(tooldir,xreal))\n- client = docker.from_env()\n- # mnt = docker.types.Mount(source=\'workdir\', target=imworkdir) # mounts=[mnt],)\n- atestcl = "ls -lt /export"\n- container = client.containers.run(planemoimage,atestcl,\n- volumes={aworkdir:{\'bind\':\'/export\',\'mode\':\'rw\'}}, )\n- tout.write(f"## Ran {atestcl} and got {container}")\n- ptestpath = os.path.join(imtooldir,xreal)\n- ptestcll = f"planemo test --job_output_files {imtooldir} --update_test_data --test_data {imtestdir} --galaxy_root /home/biodocker/galaxy-central {ptestpath}"\n- try:\n- container = client.containers.run(planemoimage,ptestcl,\n- volumes={aworkdir:{\'bind\':\'/export\',\'mode\':\'rw\'}}, )\n- except:\n- pass\n- tout.write(f"## Ran {ptestcl}")\n- with os.scandir(testdir) as outs:\n- for entry in outs:\n- if not entry.is_file():\n- continue\n- src = os.path.join(testdir, entry.name)\n- dest = os.path.join(self.testdir, entry.name)\n- shutil.copyfile(src, dest)\n- imrep_path = os.path.join(imtooldir,repname)\n- ptestcl = f"planemo test --job_output_files {imtooldir} --test_output {imrep_path} --test_data {imtestdir} --galaxy_root /home/biodocker/galaxy-central {ptestpath}"\n- try:\n- container = client.containers.run(planemoimage,ptestcl,\n- volumes={aworkdir:{\'bind\':\'/export\',\'mode\':\'rw\'}}, )\n- except:\n- pass\n- tout.write(f"## Ran {ptestcl}")\n- if os.path.isfile(imrep_path):\n- shutil.copyfile(imrep_path,ptestrep_path)\n- else:\n- tout.write(f"## planemo_biodocker_test - no test report {imrep_path} found")\n- tout.close()\n- #shutil.rmtree(workdir)\n-\n-\n-\n- def gal_tool_test(self):\n- """\n- On path should be a handy script writes test outputs even if they don\'t exist\n-\n- galaxy-tool-test -u http://localhost:8080 -a 3c9afe09f1b7892449d266109639c104 -o /tmp/foo -t hello -j /tmp/foo/hello.json --verbose\n-\n- leaves outputs in -o !\n- """\n- gttscript = f""'..b'galaxy tool tester run_test.sh\n-\n- export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \\\n- && export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox\n-\n- """\n- testdir = tempfile.mkdtemp(suffix=None, prefix="tftemp",dir="/tmp")\n- tool_test_rep = f"{self.tool_name}_galaxy_test_report_html.html"\n- if os.path.exists(self.tlog):\n- tout = open(self.tlog, "a")\n- else:\n- tout = open(self.tlog, "w")\n-\n- fakeenv = copy.copy(os.environ)\n- fakeenv["GALAXY_TEST_SAVE"] = testdir\n- fakeenv["GALAXY_TEST_NO_CLEANUP"] = "1"\n- fakeenv["GALAXY_TEST_TMP_DIR"] = testdir\n- galaxy_lib = os.path.join(self.args.galaxy_root,\'lib\')\n-\n- cll = [\n- "sh", f"{self.args.galaxy_root}/run_tests.sh", "--id", self.tool_name,\n- "--report_file", os.path.join(testdir,tool_test_rep), "functional.test_toolbox",\n- ]\n- subp = subprocess.run(\n- cll, env = fakeenv ,\n- shell=False, cwd=galaxy_lib, stderr=tout, stdout=tout\n- )\n- src = os.path.join(testdir, tool_test_rep)\n- if os.path.isfile(src):\n- dest = os.path.join(self.repdir, tool_test_rep)\n- shutil.copyfile(src, dest)\n- else:\n- tout.write(f"### {src} not found\\n")\n- tout.close()\n- return subp.returncode\n-\n-\n def shedLoad(self):\n """\n {\'deleted\': False,\n@@ -1224,66 +1039,6 @@\n tout.close()\n return subp.returncode\n \n- def planemo_test(self, genoutputs=True):\n- """planemo is a requirement so is available for testing but needs a different call if\n- in the biocontainer - see above\n- and for generating test outputs if command or test overrides are supplied\n- test outputs are sent to repdir for display\n- planemo test --engine docker_galaxy --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml\n-\n- Planemo runs:\n-python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file\n-/export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html\n---with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata\n---structured-data-file\n-/export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox\n-\n-\n- for the planemo-biocontainer,\n- planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml\n-\n- """\n- xreal = "%s.xml" % self.tool_name\n- tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")\n- if os.path.exists(self.tlog):\n- tout = open(self.tlog, "a")\n- else:\n- tout = open(self.tlog, "w")\n- if genoutputs:\n- dummy, tfile = tempfile.mkstemp()\n- cll = [\n- "planemo",\n- "test",\n- "--galaxy_root",\n- self.args.galaxy_root,\n- "--update_test_data",\n- xreal,\n- ]\n- subp = subprocess.run(\n- cll,\n- env=self.ourenv,\n- shell=False,\n- cwd=self.testdir,\n- stderr=dummy,\n- stdout=dummy,\n- )\n-\n- else:\n- cll = [\n- "planemo",\n- "test",\n- "--test_data", self.testdir,\n- "--test_output",tool_test_path,\n- "--galaxy_root",\n- self.args.galaxy_root,\n- xreal,\n- ]\n- subp = subprocess.run(\n- cll, env=self.ourenv, shell=False, cwd=self.testdir, stderr=tout, stdout=tout\n- )\n- tout.close()\n- return subp.returncode\n-\n \n def writeShedyml(self):\n """for planemo"""\n' |