| Previous changeset 97:515be7318f2b (2020-11-21) Next changeset 99:d4d88d393285 (2020-11-23) |
|
Commit message:
Uploaded |
|
modified:
toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| b |
| diff -r 515be7318f2b -r 67628c7dc9f3 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Sat Nov 21 10:11:36 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Nov 22 06:29:33 2020 +0000 |
| [ |
| b'@@ -40,6 +40,8 @@\n \n from bioblend import toolshed\n \n+# import docker\n+\n import galaxyxml.tool as gxt\n import galaxyxml.tool.parameters as gxtp\n \n@@ -183,8 +185,8 @@\n FAKEEXE,\n )\n self.newtarpath = "toolfactory_%s.tgz" % self.tool_name\n- self.tooloutdir = "tfout"\n- self.repdir = "TF_run_report_tempdir"\n+ self.tooloutdir = "./tfout"\n+ self.repdir = "./TF_run_report_tempdir"\n self.testdir = os.path.join(self.tooloutdir, "test-data")\n if not os.path.exists(self.tooloutdir):\n os.mkdir(self.tooloutdir)\n@@ -641,10 +643,10 @@\n "## Executing Toolfactory generated command line = %s\\n" % scl\n )\n sto.flush()\n- p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)\n+ subp = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)\n sto.close()\n ste.close()\n- retval = p.returncode\n+ retval = subp.returncode\n else: # work around special case - stdin and write to stdout\n if len(self.infiles) > 0:\n sti = open(self.infiles[0][IPATHPOS], "rb")\n@@ -654,9 +656,9 @@\n sto = open(self.outfiles[0][ONAMEPOS], "wb")\n else:\n sto = sys.stdout\n- p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)\n+ subp = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)\n sto.write("## Executing Toolfactory generated command line = %s\\n" % scl)\n- retval = p.returncode\n+ retval = subp.returncode\n sto.close()\n sti.close()\n if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:\n@@ -691,14 +693,14 @@\n rnames = [x.get("name", "?") for x in repos]\n rids = [x.get("id", "?") for x in repos]\n sto.write(f"############names={rnames} rids={rids}\\n")\n- cat = "ToolFactory generated tools"\n+ tfcat = "ToolFactory generated tools"\n if self.args.tool_name not in rnames:\n tscat = ts.categories.get_categories()\n- cnames = [x.get("name", "?") for x in tscat]\n+ cnames = [x.get("name", "?").strip() for x in tscat]\n cids = [x.get("id", "?") for x in tscat]\n catID = None\n- if cat in cnames:\n- ci = cnames.index(cat)\n+ if tfcat.strip() in cnames:\n+ ci = cnames.index(tfcat)\n catID = cids[ci]\n res = ts.repositories.create_repository(\n name=self.args.tool_name,\n@@ -744,12 +746,12 @@\n "ToolFactory",\n ]\n tout.write("running\\n%s\\n" % " ".join(cll))\n- p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)\n+ subp = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)\n tout.write(\n- "installed %s - got retcode %d\\n" % (self.args.tool_name, p.returncode)\n+ "installed %s - got retcode %d\\n" % (self.args.tool_name, subp.returncode)\n )\n tout.close()\n- return p.returncode\n+ return subp.returncode\n \n def planemo_shedload(self):\n """\n@@ -790,12 +792,12 @@\n self.args.toolshed_api_key,\n ]\n try:\n- p = subprocess.run(\n+ subp = subprocess.run(\n cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout\n )\n except:\n pass\n- if p.returncode != 0:\n+ if subp.returncode != 0:\n tout.write("Repository %s exists\\n" % self.args.tool_name)\n else:\n tout.write("initiated %s\\n" % self.args.tool_name)\n@@ -813,10 +815,10 @@\n "--tar",\n self.newtarpath,\n ]\n- p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)\n- tout.write("Ran %s got %d\\n" % (" ".joi'..b' stdout=dummy,\n )\n+ dummy.close()\n # if all went well, tgz is in ./test and down a nest of tmp directories lurk the output files\n outfiles = []\n for p in self.outfiles:\n oname = p[ONAMEPOS]\n outfiles.append(oname)\n paths = []\n- for root, dirs, files in os.walk(\'./test\'):\n+ for root, dirs, files in os.walk(testdir):\n for f in files:\n+ tout.write(f"{root} {f}\\n")\n if f in outfiles:\n paths.append([root,f])\n- for p in paths:\n- src = os.path.join(p[0],p[1])\n- dest = os.path.join(self.testdir,f"{p[1]}_sample")\n+ tout.write(f"## found output {f}")\n+\n+ if len(paths) != len(self.outfiles):\n+ tout.write(f"## problem - outfiles not all found")\n+ for path in paths:\n+ fname = path[1]\n+ src = os.path.join(path[0],fname)\n+ dest = os.path.join(self.testdir,f"{fname}_sample")\n shutil.copyfile(src,dest)\n-\n else:\n cll = [\n- "mkdir -p ./test","&&","rm -rf ./test/*","&&","export GALAXY_TEST_SAVE=\'./test\'", "&&", "export GALAXY_TEST_NO_CLEANUP=", \\\n- "&&", "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",\n+ "sh", f"{self.args.galaxy_root}/run_tests.sh", "--id", self.args.tool_name,\n+ "--report_file", tool_test_rep_path, "functional.test_toolbox",\n ]\n- p = subprocess.run(\n- cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout\n+ subp = subprocess.run(\n+ cll, env = ourenv,\n+ shell=False, cwd=self.testdir, stderr=tout, stdout=tout\n )\n tout.close()\n- return p.returncode\n+ return subp.returncode\n+\n \n \n def writeShedyml(self):\n@@ -1111,6 +1128,41 @@\n tf.close()\n shutil.copyfile(self.newtarpath, self.args.new_tool)\n \n+ def fakeToolTar(self):\n+ """move fake outputs into test-data and prepare the tarball"""\n+ excludeme = "tool_test_output"\n+\n+ def exclude_function(tarinfo):\n+ filename = tarinfo.name\n+ return (\n+ None\n+ if filename.startswith(excludeme)\n+ else tarinfo\n+ )\n+\n+ for p in self.outfiles:\n+ oname = p[ONAMEPOS]\n+ src = os.path.join(self.testdir,oname)\n+ if os.path.isfile(src):\n+ dest = os.path.join(self.testdir, "%s_sample" % oname)\n+ shutil.copyfile(src, dest)\n+ dest = os.path.join(self.repdir, "%s.sample" % (oname))\n+ shutil.copyfile(src, dest)\n+ else:\n+ with open(src,\'w\') as fayk:\n+ fayk.write(\'fake!\\n\')\n+ dest = os.path.join(self.testdir, "%s_sample" % oname)\n+ shutil.copyfile(src, dest)\n+ print(\n+ "### problem - output file %s not found in tooloutdir %s so faked"\n+ % (src, self.tooloutdir)\n+ )\n+ tf = tarfile.open(self.newtarpath, "w:gz")\n+ tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)\n+ tf.close()\n+ shutil.copyfile(self.newtarpath, self.args.new_tool)\n+\n+\n def moveRunOutputs(self):\n """need to move planemo or run outputs into toolfactory collection"""\n with os.scandir(self.tooloutdir) as outs:\n@@ -1202,7 +1254,7 @@\n r.moveRunOutputs()\n r.makeToolTar()\n else:\n- r.makeToolTar()\n+ r.fakeToolTar()\n r.shedLoad()\n r.eph_galaxy_load()\n retcode = r.gal_test(genoutputs=True) # this fails\n' |
| b |
| diff -r 515be7318f2b -r 67628c7dc9f3 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Sat Nov 21 10:11:36 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Sun Nov 22 06:29:33 2020 +0000 |
| [ |
| @@ -136,6 +136,7 @@ <requirement type="package" version="0.14.0">bioblend</requirement> <requirement type="package" version="0.10.6">ephemeris</requirement> <requirement type="package" version="0.72.0">planemo</requirement> + <requirement type="package" version="4.3.1">docker-py</requirement> </requirements> <command ><![CDATA[ |