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Evaluate valueFrom after scattering. #107

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Jun 30, 2016
Merged

Evaluate valueFrom after scattering. #107

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34 changes: 19 additions & 15 deletions cwltool/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,23 +242,23 @@ def try_make_job(self, step, **kwargs):
raise WorkflowException("Workflow step contains valueFrom but StepInputExpressionRequirement not in requirements")

vfinputs = {shortname(k): v for k,v in inputobj.iteritems()}
def valueFromFunc(k, v): # type: (Any, Any) -> Any
if k in valueFrom:
return expression.do_eval(
valueFrom[k], vfinputs, self.workflow.requirements,
None, None, {}, context=v)
else:
return v
def postScatterEval(io):
shortio = {shortname(k): v for k,v in io.iteritems()}
def valueFromFunc(k, v): # type: (Any, Any) -> Any
if k in valueFrom:
return expression.do_eval(
valueFrom[k], shortio, self.workflow.requirements,
None, None, {}, context=v)
else:
return v
return {k: valueFromFunc(k, v) for k,v in io.items()}

if "scatter" in step.tool:
scatter = aslist(step.tool["scatter"])
method = step.tool.get("scatterMethod")
if method is None and len(scatter) != 1:
raise WorkflowException("Must specify scatterMethod when scattering over multiple inputs")
kwargs["valueFrom"] = valueFromFunc

inputobj = {k: valueFromFunc(k, v) if k not in scatter else v
for k,v in inputobj.items()}
kwargs["postScatterEval"] = postScatterEval

if method == "dotproduct" or method is None:
jobs = dotproduct_scatter(step, inputobj, scatter,
Expand All @@ -280,7 +280,7 @@ def valueFromFunc(k, v): # type: (Any, Any) -> Any
callback), 0, **kwargs)
else:
_logger.debug(u"[job %s] job input %s", step.name, json.dumps(inputobj, indent=4))
inputobj = {k: valueFromFunc(k, v) for k,v in inputobj.items()}
inputobj = postScatterEval(inputobj)
_logger.debug(u"[job %s] evaluated job input to %s", step.name, json.dumps(inputobj, indent=4))
jobs = step.job(inputobj, callback, **kwargs)

Expand Down Expand Up @@ -592,7 +592,9 @@ def dotproduct_scatter(process, joborder, scatter_keys, output_callback, **kwarg
for n in range(0, l):
jo = copy.copy(joborder)
for s in scatter_keys:
jo[s] = kwargs["valueFrom"](s, joborder[s][n])
jo[s] = joborder[s][n]

jo = kwargs["postScatterEval"](jo)

for j in process.job(jo, functools.partial(rc.receive_scatter_output, n), **kwargs):
yield j
Expand All @@ -612,9 +614,10 @@ def nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback

for n in range(0, l):
jo = copy.copy(joborder)
jo[scatter_key] = kwargs["valueFrom"](scatter_key, joborder[scatter_key][n])
jo[scatter_key] = joborder[scatter_key][n]

if len(scatter_keys) == 1:
jo = kwargs["postScatterEval"](jo)
for j in process.job(jo, functools.partial(rc.receive_scatter_output, n), **kwargs):
yield j
else:
Expand Down Expand Up @@ -661,9 +664,10 @@ def flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback,
put = startindex
for n in range(0, l):
jo = copy.copy(joborder)
jo[scatter_key] = kwargs["valueFrom"](scatter_key, joborder[scatter_key][n])
jo[scatter_key] = joborder[scatter_key][n]

if len(scatter_keys) == 1:
jo = kwargs["postScatterEval"](jo)
for j in process.job(jo, functools.partial(rc.receive_scatter_output, put), **kwargs):
yield j
put += 1
Expand Down