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Merged
merged 2 commits into from Nov 25, 2015
Merged

Allow output type: ["null", File] #22

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187e032
Allow output type: ["null", File]
portah Nov 24, 2015
11bb383
Merge remote-tracking branch 'upstream/master'
portah Nov 24, 2015
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16 changes: 12 additions & 4 deletions cwltool/draft2tool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,6 +185,7 @@ def collect_output_ports(self, ports, builder, outdir):
return outputdoc

ret = {}

for port in ports:
fragment = shortname(port["id"])
ret[fragment] = self.collect_output(port, builder, outdir)
Expand All @@ -195,6 +196,7 @@ def collect_output_ports(self, ports, builder, outdir):

def collect_output(self, schema, builder, outdir):
r = None
_type = None
if "outputBinding" in schema:
binding = schema["outputBinding"]
if "glob" in binding:
Expand All @@ -219,19 +221,26 @@ def collect_output(self, schema, builder, outdir):
files["checksum"] = "sha1$%s" % checksum.hexdigest()
files["size"] = filesize

if isinstance(schema["type"], list):
for t in schema["type"]:
if t == "null" and (not r or len(r) == 0):
return None
if t == "File" and len(r) == 1:
_type = "File"

if "outputEval" in binding:
r = builder.do_eval(binding["outputEval"], context=r)
if schema["type"] == "File" and (not isinstance(r, dict) or "path" not in r):
if (schema["type"] == "File" or _type == "File") and (not isinstance(r, dict) or "path" not in r):
raise WorkflowException("Expression must return a file object.")

if schema["type"] == "File":
if schema["type"] == "File" or _type == "File":
if not r:
raise WorkflowException("No matches for output file with glob: '{}'".format(bg))
if len(r) > 1:
raise WorkflowException("Multiple matches for output item that is a single file.")
r = r[0]

if schema["type"] == "File" and "secondaryFiles" in binding:
if (schema["type"] == "File" or _type == "File") and "secondaryFiles" in binding:
r["secondaryFiles"] = []
for sf in aslist(binding["secondaryFiles"]):
if isinstance(sf, dict) or "$(" in sf or "${" in sf:
Expand All @@ -247,7 +256,6 @@ def collect_output(self, schema, builder, outdir):
if not builder.fs_access.exists(sf["path"]):
raise WorkflowException("Missing secondary file of '%s' of primary file '%s'" % (sf["path"], r["path"]))


if not r and schema["type"] == "record":
r = {}
for f in schema["fields"]:
Expand Down
2 changes: 1 addition & 1 deletion cwltool/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,5 +193,5 @@ def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True,
shutil.rmtree(self.tmpdir, True)

if move_outputs and empty_subtree(self.outdir):
_logger.debug("[job %s] Removing empty output directory %s", id(self), self.tmpdir)
_logger.debug("[job %s] Removing empty output directory %s", id(self), self.outdir)
shutil.rmtree(self.outdir, True)