# HG changeset patch
# User fubar
# Date 1605953496 0
# Node ID 515be7318f2b3d768e5eb0354041152785039ed8
# Parent d54976fc996a581ecbc2270628c34a16e642e319
Uploaded
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__":
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
@@ -411,8 +411,6 @@
-
-