| Previous changeset 105:373e1f9cb609 (2020-11-27) Next changeset 107:18e616939a91 (2020-11-28) |
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Commit message:
Uploaded |
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modified:
toolfactory/rgToolFactory2.py |
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| diff -r 373e1f9cb609 -r 6de08f44e551 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Fri Nov 27 23:17:10 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sat Nov 28 00:50:29 2020 +0000 |
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| b'@@ -557,8 +557,10 @@\n scrpt.insert(0, "```\\n")\n if len(scrpt) > 300:\n safertext = (\n- safertext + scrpt[:100] + \\\n- [">500 lines - stuff deleted", "......"] + scrpt[-100:]\n+ safertext\n+ + scrpt[:100]\n+ + [">500 lines - stuff deleted", "......"]\n+ + scrpt[-100:]\n )\n else:\n safertext = safertext + scrpt\n@@ -649,7 +651,9 @@\n "## Executing Toolfactory generated command line = %s\\n" % scl\n )\n sto.flush()\n- subp = subprocess.run(self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste)\n+ subp = subprocess.run(\n+ self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste\n+ )\n sto.close()\n ste.close()\n retval = subp.returncode\n@@ -662,7 +666,9 @@\n sto = open(self.outfiles[0][ONAMEPOS], "wb")\n else:\n sto = sys.stdout\n- subp = subprocess.run(self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti)\n+ subp = subprocess.run(\n+ self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti\n+ )\n sto.write("## Executing Toolfactory generated command line = %s\\n" % scl)\n retval = subp.returncode\n sto.close()\n@@ -676,42 +682,35 @@\n logging.debug("run done")\n return retval\n \n-\n def copy_to_container(self, src, dest, container):\n- """ Recreate the src directory tree at dest - full path included\n- """\n+ """Recreate the src directory tree at dest - full path included"""\n idir = os.getcwd()\n workdir = os.path.dirname(src)\n os.chdir(workdir)\n _, tfname = tempfile.mkstemp(suffix=".tar")\n- tar = tarfile.open(tfname, mode=\'w\')\n+ tar = tarfile.open(tfname, mode="w")\n srcb = os.path.basename(src)\n tar.add(srcb)\n tar.close()\n- data = open(tfname, \'rb\').read()\n+ data = open(tfname, "rb").read()\n container.put_archive(dest, data)\n os.unlink(tfname)\n os.chdir(idir)\n \n-\n def copy_from_container(self, src, dest, container):\n- """ recreate the src directory tree at dest using docker sdk\n- """\n- os.makedirs(dest,exist_ok=True)\n+ """recreate the src directory tree at dest using docker sdk"""\n+ os.makedirs(dest, exist_ok=True)\n _, tfname = tempfile.mkstemp(suffix=".tar")\n- tf = open(tfname,\'wb\')\n+ tf = open(tfname, "wb")\n bits, stat = container.get_archive(src)\n for chunk in bits:\n tf.write(chunk)\n tf.close()\n- tar = tarfile.open(tfname,\'r\')\n+ tar = tarfile.open(tfname, "r")\n tar.extractall(dest)\n tar.close()\n os.unlink(tfname)\n \n-\n-\n-\n def planemo_biodocker_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@@ -720,13 +719,14 @@\n \n \n """\n- def prun(container,tout,cl,user="biodocker"):\n- rlog = container.exec_run(cl,user=user)\n- slogl = str(rlog).split(\'\\\\n\')\n- slog = \'\\n\'.join(slogl)\n+\n+ def prun(container, tout, cl, user="biodocker"):\n+ rlog = container.exec_run(cl, user=user)\n+ slogl = str(rlog).split("\\\\n")\n+ slog = "\\n".join(slogl)\n tout.write(f"## got rlog {slog} from {cl}\\n")\n \n- dgroup = grp.getgrnam(\'docker\')[2]\n+ dgroup = grp.getgrnam("docker")[2]\n if os.path.exists(self.tlog):\n tout = open(self.tlog, "a")\n else:\n@@ -734,25 +734,30 @@\n planemoimage '..b' "test",\n- "--test_data", os.path.self.testdir,\n- "--test_output", os.path.tool_test_path,\n+ "--test_data",\n+ os.path.self.testdir,\n+ "--test_output",\n+ os.path.tool_test_path,\n "--skip_venv",\n "--galaxy_root",\n self.args.galaxy_root,\n xreal,\n ]\n subp = subprocess.run(\n- cll, env=self.ourenv, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout\n+ cll,\n+ env=self.ourenv,\n+ shell=False,\n+ cwd=self.tooloutdir,\n+ stderr=tout,\n+ stdout=tout,\n )\n tout.close()\n return subp.returncode\n \n-\n def writeShedyml(self):\n """for planemo"""\n yuser = self.args.user_email.split("@")[0]\n@@ -1094,17 +1137,13 @@\n \n def exclude_function(tarinfo):\n filename = tarinfo.name\n- return (\n- None\n- if filename.endswith(excludeme)\n- else tarinfo\n- )\n+ return None if filename.endswith(excludeme) else tarinfo\n \n for p in self.outfiles:\n oname = p[ONAMEPOS]\n tdest = os.path.join(self.testdir, "%s_sample" % oname)\n if not os.path.isfile(tdest):\n- src = os.path.join(self.testdir,oname)\n+ src = os.path.join(self.testdir, oname)\n if os.path.isfile(src):\n shutil.copyfile(src, tdest)\n dest = os.path.join(self.repdir, "%s.sample" % (oname))\n@@ -1127,8 +1166,8 @@\n continue\n if "." in entry.name:\n nayme, ext = os.path.splitext(entry.name)\n- if ext in [\'.yml\',\'.xml\',\'.json\',\'.yaml\']:\n- ext = f\'{ext}.txt\'\n+ if ext in [".yml", ".xml", ".json", ".yaml"]:\n+ ext = f"{ext}.txt"\n else:\n ext = ".txt"\n ofn = "%s%s" % (entry.name.replace(".", "_"), ext)\n@@ -1137,7 +1176,11 @@\n shutil.copyfile(src, dest)\n with os.scandir(self.testdir) as outs:\n for entry in outs:\n- if (not entry.is_file()) or entry.name.endswith(\'_sample\') or entry.name.endswith("_planemo_test_report.html"):\n+ if (\n+ (not entry.is_file())\n+ or entry.name.endswith("_sample")\n+ or entry.name.endswith("_planemo_test_report.html")\n+ ):\n continue\n if "." in entry.name:\n nayme, ext = os.path.splitext(entry.name)\n@@ -1149,7 +1192,6 @@\n shutil.copyfile(src, dest)\n \n \n-\n def main():\n """\n This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:\n@@ -1183,8 +1225,7 @@\n a("--tfout", default="./tfout")\n a("--new_tool", default="new_tool")\n a("--galaxy_url", default="http://localhost:8080")\n- a(\n- "--toolshed_url", default="http://localhost:9009")\n+ a("--toolshed_url", default="http://localhost:9009")\n # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails\n a("--toolshed_api_key", default="fakekey")\n a("--galaxy_api_key", default="fakekey")\n@@ -1207,11 +1248,11 @@\n r.writeShedyml()\n r.makeTool()\n if args.make_Tool == "generate":\n- retcode = r.run() # for testing toolfactory itself\n+ retcode = r.run() # for testing toolfactory itself\n r.moveRunOutputs()\n r.makeToolTar()\n else:\n- r.planemo_biodocker_test() # test to make outputs and then test\n+ r.planemo_biodocker_test() # test to make outputs and then test\n r.moveRunOutputs()\n r.makeToolTar()\n if args.make_Tool == "gentestinstall":\n' |