Mercurial > repos > fubar > tool_factory_2
changeset 117:b1a29d3d50d6 draft
Uploaded
author | fubar |
---|---|
date | Sun, 06 Dec 2020 01:21:06 +0000 |
parents | b1ea31ea3f00 |
children | e43c43396a70 |
files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
diffstat | 2 files changed, 17 insertions(+), 6 deletions(-) [+] |
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--- a/toolfactory/rgToolFactory2.py Sat Dec 05 04:34:19 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Dec 06 01:21:06 2020 +0000 @@ -635,7 +635,7 @@ part2 = exml.split("</tests>")[1] fixed = "%s\n%s\n%s" % (part1, self.test_override, part2) exml = fixed - exml = exml.replace('range="1:"', 'range="1000:"') + #exml = exml.replace('range="1:"', 'range="1000:"') xf = open("%s.xml" % self.tool_name, "w") xf.write(exml) xf.write("\n") @@ -756,7 +756,7 @@ tvolname = tvol.name destdir = "/toolfactory/ptest" imrep = os.path.join(destdir, repname) - # need to keep the container running so keep it open with tail -f. + # need to keep the container running so keep it open with sleep # will stop and destroy it when we are done container = client.containers.run( planemoimage, @@ -786,7 +786,8 @@ try: prun(container, tout, cl) except: - pass + e = sys.exc_info()[0] + tout.write(f"#### error: {e} from {ptestcl}\n") testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp", dir=".") self.copy_from_container(destdir, testouts, container) src = os.path.join(testouts, "ptest") @@ -930,6 +931,10 @@ filename = tarinfo.name return None if filename.endswith(excludeme) else tarinfo + if os.path.exists(self.tlog): + tout = open(self.tlog, "a") + else: + tout = open(self.tlog, "w") for p in self.outfiles: oname = p[ONAMEPOS] tdest = os.path.join(self.testdir, "%s_sample" % oname) @@ -940,8 +945,8 @@ dest = os.path.join(self.repdir, "%s.sample" % (oname)) shutil.copyfile(src, dest) else: - print( - "### problem - output file %s not found in testdir %s" + tout.write( + "###Output file %s not found in testdir %s. This is normal during the first Planemo run that generates test outputs" % (tdest, self.testdir) ) tf = tarfile.open(self.newtarpath, "w:gz")
--- a/toolfactory/rgToolFactory2.xml Sat Dec 05 04:34:19 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Sun Dec 06 01:21:06 2020 +0000 @@ -69,7 +69,13 @@ </repeat> <repeat name="history_outputs" title="one or more output file parameters generated by the tool to be added to the user history" help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> - <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help="Argparse will also use this name as --[name]"/> + <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" + help="No spaces! Argparse will also use this name as --[name]"> + <sanitizer invalid_char="_"> + <valid initial="string.letters,string.digits"/> + <add value="_" /> + </sanitizer> + </param> <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> <options from_parameter="tool.app.datatypes_registry.upload_file_formats">