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Check for $( or ${ in string to eval before calling interpolate. #548

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Merged
merged 2 commits into from
Sep 28, 2017
Merged

Check for $( or ${ in string to eval before calling interpolate. #548

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84d1585
Check for $( or ${ in string to eval before calling interpolate.
Sep 28, 2017
ae9e080
Improve error logged in collect_output_ports.
Sep 28, 2017
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19 changes: 7 additions & 12 deletions cwltool/draft2tool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -519,19 +519,14 @@ def collect_output_ports(self, ports, builder, outdir, compute_checksum=True, jo
_logger.debug(u"Raw output from %s: %s", custom_output, json.dumps(ret, indent=4))
else:
for i, port in enumerate(ports):
with SourceLine(ports, i, WorkflowException, debug):
fragment = shortname(port["id"])
try:
ret[fragment] = self.collect_output(port, builder, outdir, fs_access,
compute_checksum=compute_checksum)
except Exception as e:
_logger.debug(
u"Error collecting output for parameter '%s'"
% shortname(port["id"]), exc_info=True)
raise WorkflowException(
def makeWorkflowException(msg):
return WorkflowException(
u"Error collecting output for parameter '%s':\n%s"
% (shortname(port["id"]), indent(u(str(e)))))

% (shortname(port["id"]), msg))
with SourceLine(ports, i, makeWorkflowException, debug):
fragment = shortname(port["id"])
ret[fragment] = self.collect_output(port, builder, outdir, fs_access,
compute_checksum=compute_checksum)
if ret:
revmap = partial(revmap_file, builder, outdir)
adjustDirObjs(ret, trim_listing)
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2 changes: 1 addition & 1 deletion cwltool/expression.py
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Expand Up @@ -214,7 +214,7 @@ def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,
u"self": context,
u"runtime": runtime}

if isinstance(ex, (str, Text)):
if isinstance(ex, (str, Text)) and ("$(" in ex or "${" in ex):
fullJS = False
jslib = u""
for r in reversed(requirements):
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