def object_from_state(state, parms, frag_only, supportsMultipleInput):
inputobj = {}
for inp in parms:
iid = inp["id"]
if frag_only:
iid = shortname(iid)
if "source" in inp:
if isinstance(inp["source"], list) and not supportsMultipleInput:
raise WorkflowException("Workflow contains multiple inbound links to a single parameter but MultipleInputFeatureRequirement is not declared.")
connections = aslist(inp["source"])
for src in connections:
if src in state and state[src] is not None:
if not match_types(inp["type"], state[src], iid, inputobj,
inp.get("linkMerge", ("merge_nested" if len(connections) > 1 else None)),
valueFrom=inp.get("valueFrom")):
raise WorkflowException("Type mismatch between source '%s' (%s) and sink '%s' (%s)" % (src, state[src].parameter["type"], inp["id"], inp["type"]))
elif src not in state:
raise WorkflowException("Connect source '%s' on parameter '%s' does not exist" % (src, inp["id"]))
else:
return None
elif "default" in inp:
inputobj[iid] = inp["default"]
elif "valueFrom" in inp:
inputobj[iid] = None
else:
raise WorkflowException("Value for %s not specified" % (inp["id"]))
return inputobj
def __init__(self, step):
self.step = step
self.tool = step.tool
self.id = step.id
self.submitted = False
self.completed = False
self.name = uniquename("step %s" % shortname(self.id))
def generate_parser(toolparser, tool, namemap):
toolparser.add_argument("job_order", nargs="?", help="Job input json file")
namemap["job_order"] = "job_order"
for inp in tool.tool["inputs"]:
name = shortname(inp["id"])
if len(name) == 1:
flag = "-"
else:
flag = "--"
namemap[name.replace("-", "_")] = name
inptype = inp["type"]
required = True
if isinstance(inptype, list):
if inptype[0] == "null":
required = False
if len(inptype) == 2:
inptype = inptype[1]
else:
_logger.debug("Can't make command line argument from %s",
inptype)
return None
help = inp.get("description", "").replace("%", "%%")
kwargs = {}
if inptype == "File":
kwargs["action"] = FileAction
elif isinstance(inptype, dict) and inptype["type"] == "array":
if inptype["items"] == "File":
kwargs["action"] = FileAppendAction
else:
kwargs["action"] = "append"
if inptype == "string":
kwargs["type"] = str
elif inptype == "int":
kwargs["type"] = int
elif inptype == "float":
kwargs["type"] = float
elif inptype == "boolean":
kwargs["action"] = "store_true"
if "default" in inp:
kwargs["default"] = inp["default"]
required = False
if "type" not in kwargs and "action" not in kwargs:
_logger.debug("Can't make command line argument from %s", inptype)
return None
toolparser.add_argument(flag + name,
required=required,
help=help,
**kwargs)
return toolparser
def collect_output_ports(self, ports, builder, outdir):
try:
ret = {}
custom_output = os.path.join(outdir, "cwl.output.json")
if builder.fs_access.exists(custom_output):
with builder.fs_access.open(custom_output, "r") as f:
ret = yaml.load(f)
_logger.debug("Raw output from %s: %s", custom_output, json.dumps(ret, indent=4))
adjustFileObjs(ret, remove_hostfs)
adjustFileObjs(ret, functools.partial(revmap_file, builder, outdir))
adjustFileObjs(ret, remove_hostfs)
validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
return ret
for port in ports:
fragment = shortname(port["id"])
try:
ret[fragment] = self.collect_output(port, builder, outdir)
except Exception as e:
raise WorkflowException("Error collecting output for parameter '%s': %s" % (shortname(port["id"]), e))
if ret:
adjustFileObjs(ret, remove_hostfs)
validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
return ret if ret is not None else {}
except validate.ValidationException as e:
raise WorkflowException("Error validating output record, " + str(e) + "\n in " + json.dumps(ret, indent=4))
def collect_output_ports(self, ports, builder, outdir):
try:
ret = {}
custom_output = os.path.join(outdir, "cwl.output.json")
if builder.fs_access.exists(custom_output):
with builder.fs_access.open(custom_output, "r") as f:
ret = yaml.load(f)
_logger.debug("Raw output from %s: %s", custom_output, json.dumps(ret, indent=4))
adjustFileObjs(ret, remove_hostfs)
adjustFileObjs(ret, functools.partial(revmap_file, builder, outdir))
adjustFileObjs(ret, remove_hostfs)
validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
return ret
for port in ports:
fragment = shortname(port["id"])
try:
ret[fragment] = self.collect_output(port, builder, outdir)
except Exception as e:
raise WorkflowException("Error collecting output for parameter '%s': %s" % (shortname(port["id"]), e))
if ret:
adjustFileObjs(ret, remove_hostfs)
validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
return ret if ret is not None else {}
except validate.ValidationException as e:
raise WorkflowException("Error validating output record, " + str(e) + "\n in " + json.dumps(ret, indent=4))
def __init__(self, step):
self.step = step
self.tool = step.tool
self.id = step.id
self.submitted = False
self.completed = False
self.name = uniquename("step %s" % shortname(self.id))
def generate_parser(toolparser, tool, namemap):
toolparser.add_argument("job_order", nargs="?", help="Job input json file")
namemap["job_order"] = "job_order"
for inp in tool.tool["inputs"]:
name = shortname(inp["id"])
if len(name) == 1:
flag = "-"
else:
flag = "--"
namemap[name.replace("-", "_")] = name
inptype = inp["type"]
required = True
if isinstance(inptype, list):
if inptype[0] == "null":
required = False
if len(inptype) == 2:
inptype = inptype[1]
else:
_logger.debug("Can't make command line argument from %s", inptype)
return None
help = inp.get("description", "").replace("%", "%%")
kwargs = {}
if inptype == "File":
kwargs["action"] = FileAction
elif isinstance(inptype, dict) and inptype["type"] == "array":
if inptype["items"] == "File":
kwargs["action"] = FileAppendAction
else:
kwargs["action"] = "append"
if inptype == "string":
kwargs["type"] = str
elif inptype == "int":
kwargs["type"] = int
elif inptype == "float":
kwargs["type"] = float
elif inptype == "boolean":
kwargs["action"] = "store_true"
if "default" in inp:
kwargs["default"] = inp["default"]
required = False
if "type" not in kwargs and "action" not in kwargs:
_logger.debug("Can't make command line argument from %s", inptype)
return None
toolparser.add_argument(flag + name, required=required, help=help, **kwargs)
return toolparser
def receive_output(self, output_callback, jobout, processStatus):
#_logger.debug("WorkflowStep output from run is %s", jobout)
output = {}
for i in self.tool["outputs"]:
field = shortname(i["id"])
if field in jobout:
output[i["id"]] = jobout[field]
else:
processStatus = "permanentFail"
output_callback(output, processStatus)
def receive_output(self, output_callback, jobout, processStatus):
#_logger.debug("WorkflowStep output from run is %s", jobout)
output = {}
for i in self.tool["outputs"]:
field = shortname(i["id"])
if field in jobout:
output[i["id"]] = jobout[field]
else:
processStatus = "permanentFail"
output_callback(output, processStatus)
def job(self, joborder, basedir, output_callback, **kwargs):
for i in self.tool["inputs"]:
p = i["id"]
field = shortname(p)
joborder[field] = joborder[i["id"]]
del joborder[i["id"]]
kwargs["requirements"] = kwargs.get("requirements", []) + self.tool.get("requirements", [])
kwargs["hints"] = kwargs.get("hints", []) + self.tool.get("hints", [])
for t in self.embedded_tool.job(joborder, basedir, functools.partial(self.receive_output, output_callback), **kwargs):
yield t
def __init__(self, workflow, **kwargs):
self.workflow = workflow
self.tool = workflow.tool
self.steps = [WorkflowJobStep(s) for s in workflow.steps]
self.id = workflow.tool["id"]
if "outdir" in kwargs:
self.outdir = kwargs["outdir"]
elif "tmp_outdir_prefix" in kwargs:
self.outdir = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"])
else:
# tmp_outdir_prefix defaults to tmp, so this is unlikely to be used
self.outdir = tempfile.mkdtemp()
self.name = uniquename(kwargs.get("name", shortname(self.workflow.tool["id"])))
_logger.debug("[workflow %s] initialized from %s", self.name, self.tool["id"])
def collect_output_ports(self, ports, builder, outdir):
try:
custom_output = os.path.join(outdir, "cwl.output.json")
if builder.fs_access.exists(custom_output):
outputdoc = yaml.load(custom_output)
validate.validate_ex(self.names.get_name("outputs_record_schema", ""), outputdoc)
return outputdoc
ret = {}
for port in ports:
fragment = shortname(port["id"])
ret[fragment] = self.collect_output(port, builder, outdir)
validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
return ret if ret is not None else {}
except validate.ValidationException as e:
raise WorkflowException("Error validating output record, " + str(e) + "\n in " + json.dumps(ret, indent=4))
def job(self, joborder, basedir, output_callback, **kwargs):
for i in self.tool["inputs"]:
p = i["id"]
field = shortname(p)
joborder[field] = joborder[i["id"]]
del joborder[i["id"]]
kwargs["requirements"] = kwargs.get("requirements", []) + self.tool.get("requirements", [])
kwargs["hints"] = kwargs.get("hints", []) + self.tool.get("hints", [])
try:
for t in self.embedded_tool.job(joborder, basedir,
functools.partial(self.receive_output, output_callback),
**kwargs):
yield t
except WorkflowException:
raise
except Exception as e:
_logger.exception("Unexpected exception")
raise WorkflowException(str(e))
def job(self, joborder, basedir, output_callback, **kwargs):
for i in self.tool["inputs"]:
p = i["id"]
field = shortname(p)
joborder[field] = joborder[i["id"]]
del joborder[i["id"]]
kwargs["requirements"] = kwargs.get("requirements", []) + self.tool.get("requirements", [])
kwargs["hints"] = kwargs.get("hints", []) + self.tool.get("hints", [])
try:
for t in self.embedded_tool.job(joborder, basedir,
functools.partial(self.receive_output, output_callback),
**kwargs):
yield t
except WorkflowException:
_logger.error("Exception on step '%s'", kwargs.get("name"))
raise
except Exception as e:
_logger.exception("Unexpected exception")
raise WorkflowException(str(e))
def collect_output_ports(self, ports, builder, outdir):
try:
custom_output = os.path.join(outdir, "cwl.output.json")
if builder.fs_access.exists(custom_output):
outputdoc = yaml.load(custom_output)
validate.validate_ex(
self.names.get_name("outputs_record_schema", ""),
outputdoc)
return outputdoc
ret = {}
for port in ports:
fragment = shortname(port["id"])
ret[fragment] = self.collect_output(port, builder, outdir)
validate.validate_ex(
self.names.get_name("outputs_record_schema", ""), ret)
return ret if ret is not None else {}
except validate.ValidationException as e:
raise WorkflowException("Error validating output record, " +
str(e) + "\n in " +
json.dumps(ret, indent=4))
def __init__(self, toolpath_object, pos, **kwargs):
if "id" in toolpath_object:
self.id = toolpath_object["id"]
else:
self.id = "#step" + str(pos)
try:
makeTool = kwargs.get("makeTool")
runobj = None
if isinstance(toolpath_object["run"], basestring):
runobj, _ = schema_salad.schema.load_and_validate(kwargs["loader"],
kwargs["avsc_names"],
toolpath_object["run"],
True)
else:
runobj = toolpath_object["run"]
self.embedded_tool = makeTool(runobj, **kwargs)
except validate.ValidationException as v:
raise WorkflowException("Tool definition %s failed validation:\n%s" % (toolpath_object["run"], validate.indent(str(v))))
for field in ("inputs", "outputs"):
for i in toolpath_object[field]:
inputid = i["id"]
p = shortname(inputid)
found = False
for a in self.embedded_tool.tool[field]:
frag = shortname(a["id"])
if frag == p:
i.update(a)
found = True
if not found:
i["type"] = "Any"
#raise WorkflowException("Parameter '%s' of %s in workflow step %s does not correspond to parameter in %s" % (p, field, self.id, self.embedded_tool.tool.get("id")))
i["id"] = inputid
super(WorkflowStep, self).__init__(toolpath_object, **kwargs)
if self.embedded_tool.tool["class"] == "Workflow":
(feature, _) = self.get_requirement("SubworkflowFeatureRequirement")
if not feature:
raise WorkflowException("Workflow contains embedded workflow but SubworkflowFeatureRequirement not in requirements")
if "scatter" in self.tool:
(feature, _) = self.get_requirement("ScatterFeatureRequirement")
if not feature:
raise WorkflowException("Workflow contains scatter but ScatterFeatureRequirement not in requirements")
inputparms = copy.deepcopy(self.tool["inputs"])
outputparms = copy.deepcopy(self.tool["outputs"])
scatter = aslist(self.tool["scatter"])
method = self.tool.get("scatterMethod")
if method is None and len(scatter) != 1:
raise WorkflowException("Must specify scatterMethod when scattering over multiple inputs")
inp_map = {i["id"]: i for i in inputparms}
for s in scatter:
if s not in inp_map:
raise WorkflowException("Invalid Scatter parameter '%s'" % s)
inp_map[s]["type"] = {"type": "array", "items": inp_map[s]["type"]}
if self.tool.get("scatterMethod") == "nested_crossproduct":
nesting = len(scatter)
else:
nesting = 1
for r in xrange(0, nesting):
for i in outputparms:
i["type"] = {"type": "array", "items": i["type"]}
self.tool["inputs"] = inputparms
self.tool["outputs"] = outputparms
def __init__(self, toolpath_object, pos, **kwargs):
if "id" in toolpath_object:
self.id = toolpath_object["id"]
else:
self.id = "#step" + str(pos)
try:
makeTool = kwargs.get("makeTool")
runobj = None
if isinstance(toolpath_object["run"], basestring):
runobj, _ = schema_salad.schema.load_and_validate(
kwargs["loader"], kwargs["avsc_names"],
toolpath_object["run"], True)
else:
runobj = toolpath_object["run"]
self.embedded_tool = makeTool(runobj, **kwargs)
except validate.ValidationException as v:
raise WorkflowException(
"Tool definition %s failed validation:\n%s" %
(toolpath_object["run"], validate.indent(str(v))))
for field in ("inputs", "outputs"):
for i in toolpath_object[field]:
inputid = i["id"]
p = shortname(inputid)
found = False
for a in self.embedded_tool.tool[field]:
frag = shortname(a["id"])
if frag == p:
i.update(a)
found = True
if not found:
i["type"] = "Any"
#raise WorkflowException("Parameter '%s' of %s in workflow step %s does not correspond to parameter in %s" % (p, field, self.id, self.embedded_tool.tool.get("id")))
i["id"] = inputid
super(WorkflowStep, self).__init__(toolpath_object, **kwargs)
if self.embedded_tool.tool["class"] == "Workflow":
(feature,
_) = self.get_requirement("SubworkflowFeatureRequirement")
if not feature:
raise WorkflowException(
"Workflow contains embedded workflow but SubworkflowFeatureRequirement not in requirements"
)
if "scatter" in self.tool:
(feature, _) = self.get_requirement("ScatterFeatureRequirement")
if not feature:
raise WorkflowException(
"Workflow contains scatter but ScatterFeatureRequirement not in requirements"
)
inputparms = copy.deepcopy(self.tool["inputs"])
outputparms = copy.deepcopy(self.tool["outputs"])
scatter = aslist(self.tool["scatter"])
method = self.tool.get("scatterMethod")
if method is None and len(scatter) != 1:
raise WorkflowException(
"Must specify scatterMethod when scattering over multiple inputs"
)
inp_map = {i["id"]: i for i in inputparms}
for s in scatter:
if s not in inp_map:
raise WorkflowException("Invalid Scatter parameter '%s'" %
s)
inp_map[s]["type"] = {
"type": "array",
"items": inp_map[s]["type"]
}
if self.tool.get("scatterMethod") == "nested_crossproduct":
nesting = len(scatter)
else:
nesting = 1
for r in xrange(0, nesting):
for i in outputparms:
i["type"] = {"type": "array", "items": i["type"]}
self.tool["inputs"] = inputparms
self.tool["outputs"] = outputparms
def collect_output(self, schema, builder, outdir):
r = None
if "outputBinding" in schema:
binding = schema["outputBinding"]
globpatterns = []
revmap = functools.partial(revmap_file, builder, outdir)
if "glob" in binding:
r = []
for gb in aslist(binding["glob"]):
gb = builder.do_eval(gb)
if gb:
globpatterns.extend(aslist(gb))
for gb in globpatterns:
if gb.startswith("/"):
raise WorkflowError("glob patterns must not start with '/'")
try:
r.extend([{"path": g, "class": "File", "hostfs": True}
for g in builder.fs_access.glob(os.path.join(outdir, gb))])
except (OSError, IOError) as e:
_logger.warn(str(e))
for files in r:
checksum = hashlib.sha1()
with builder.fs_access.open(files["path"], "rb") as f:
contents = f.read(CONTENT_LIMIT)
if binding.get("loadContents"):
files["contents"] = contents
filesize = 0
while contents != "":
checksum.update(contents)
filesize += len(contents)
contents = f.read(1024*1024)
files["checksum"] = "sha1$%s" % checksum.hexdigest()
files["size"] = filesize
if "format" in schema:
files["format"] = builder.do_eval(schema["format"], context=files)
optional = False
singlefile = False
if isinstance(schema["type"], list):
if "null" in schema["type"]:
optional = True
if "File" in schema["type"]:
singlefile = True
elif schema["type"] == "File":
singlefile = True
if "outputEval" in binding:
r = builder.do_eval(binding["outputEval"], context=r)
if singlefile:
# Handle single file outputs not wrapped in a list
if r is not None and not isinstance(r, (list, tuple)):
r = [r]
if optional and r is None:
pass
elif (r is None or len(r) != 1 or not isinstance(r[0], dict) or "path" not in r[0]):
raise WorkflowException("Expression must return a file object for %s." % schema["id"])
if singlefile:
if not r and not optional:
raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
elif not r and optional:
pass
elif isinstance(r, list):
if len(r) > 1:
raise WorkflowException("Multiple matches for output item that is a single file.")
else:
r = r[0]
# Ensure files point to local references outside of the run environment
adjustFileObjs(r, revmap)
if "secondaryFiles" in schema:
for primary in aslist(r):
if isinstance(primary, dict):
primary["secondaryFiles"] = []
for sf in aslist(schema["secondaryFiles"]):
if isinstance(sf, dict) or "$(" in sf or "${" in sf:
sfpath = builder.do_eval(sf, context=r)
if isinstance(sfpath, basestring):
sfpath = revmap({"path": sfpath, "class": "File"})
else:
sfpath = {"path": substitute(primary["path"], sf), "class": "File", "hostfs": True}
for sfitem in aslist(sfpath):
if builder.fs_access.exists(sfitem["path"]):
primary["secondaryFiles"].append(sfitem)
if not r and optional:
r = None
if not r and isinstance(schema["type"], dict) and schema["type"]["type"] == "record":
r = {}
for f in schema["type"]["fields"]:
r[shortname(f["name"])] = self.collect_output(f, builder, outdir)
return r
def try_make_job(self, step, basedir, **kwargs):
inputparms = step.tool["inputs"]
outputparms = step.tool["outputs"]
supportsMultipleInput = bool(
self.workflow.get_requirement("MultipleInputFeatureRequirement")
[0])
try:
inputobj = object_from_state(self.state, inputparms, False,
supportsMultipleInput)
if inputobj is None:
_logger.debug("[workflow %s] job step %s not ready", self.name,
step.id)
return
_logger.debug("[step %s] starting job step %s of workflow %s",
id(step), step.id, id(self))
if step.submitted:
return
callback = functools.partial(self.receive_output, step,
outputparms)
valueFrom = {
i["id"]: i["valueFrom"]
for i in step.tool["inputs"] if "valueFrom" in i
}
if len(valueFrom) > 0 and not bool(
self.workflow.get_requirement(
"StepInputExpressionRequirement")[0]):
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):
if k in valueFrom:
return expression.do_eval(valueFrom[k],
vfinputs,
self.workflow.requirements,
None,
None, {},
context=v)
else:
return v
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"
)
if "valueFrom" not in kwargs:
kwargs["valueFrom"] = valueFromFunc
if method == "dotproduct" or method is None:
jobs = dotproduct_scatter(step, inputobj, basedir, scatter,
callback, **kwargs)
elif method == "nested_crossproduct":
jobs = nested_crossproduct_scatter(step, inputobj, basedir,
scatter, callback,
**kwargs)
elif method == "flat_crossproduct":
jobs = flat_crossproduct_scatter(step, inputobj, basedir,
scatter, callback, 0,
**kwargs)
else:
_logger.debug("[workflow %s] Job is input %s", self.name,
json.dumps(inputobj, indent=4))
inputobj = {
k: valueFromFunc(k, v)
for k, v in inputobj.items()
}
_logger.debug("[workflow %s] Evaluated job input to %s",
self.name, json.dumps(inputobj, indent=4))
jobs = step.job(inputobj, basedir, callback, **kwargs)
step.submitted = True
for j in jobs:
yield j
except WorkflowException:
raise
except Exception as e:
_logger.exception("Unhandled exception")
self.processStatus = "permanentFail"
step.completed = True
def job(self,
joborder,
basedir,
output_callback,
move_outputs=True,
**kwargs):
self.state = {}
self.processStatus = "success"
if "outdir" in kwargs:
del kwargs["outdir"]
for i in self.tool["inputs"]:
iid = shortname(i["id"])
if iid in joborder:
self.state[i["id"]] = WorkflowStateItem(
i, copy.deepcopy(joborder[iid]))
elif "default" in i:
self.state[i["id"]] = WorkflowStateItem(
i, copy.deepcopy(i["default"]))
else:
raise WorkflowException(
"Input '%s' not in input object and does not have a default value."
% (i["id"]))
for s in self.steps:
for out in s.tool["outputs"]:
self.state[out["id"]] = None
output_dirs = set()
completed = 0
while completed < len(self.steps) and self.processStatus == "success":
made_progress = False
completed = 0
for step in self.steps:
if step.completed:
completed += 1
else:
for newjob in self.try_make_job(step, basedir, **kwargs):
if newjob:
made_progress = True
if newjob.outdir:
output_dirs.add(newjob.outdir)
yield newjob
if not made_progress and completed < len(self.steps):
yield None
supportsMultipleInput = bool(
self.workflow.get_requirement("MultipleInputFeatureRequirement")
[0])
wo = object_from_state(self.state, self.tool["outputs"], True,
supportsMultipleInput)
if wo is None:
raise WorkflowException("Output for workflow not available")
if move_outputs:
targets = set()
conflicts = set()
outfiles = findfiles(wo)
for f in outfiles:
for a in output_dirs:
if f["path"].startswith(a):
src = f["path"]
dst = os.path.join(self.outdir, src[len(a) + 1:])
if dst in targets:
conflicts.add(dst)
else:
targets.add(dst)
for f in outfiles:
for a in output_dirs:
if f["path"].startswith(a):
src = f["path"]
dst = os.path.join(self.outdir, src[len(a) + 1:])
if dst in conflicts:
sp = os.path.splitext(dst)
dst = "%s-%s%s" % (
sp[0], str(random.randint(1,
1000000000)), sp[1])
dirname = os.path.dirname(dst)
if not os.path.exists(dirname):
os.makedirs(dirname)
_logger.debug("[workflow %s] Moving '%s' to '%s'",
self.name, src, dst)
shutil.move(src, dst)
f["path"] = dst
for a in output_dirs:
if os.path.exists(a) and empty_subtree(a):
if kwargs.get("rm_tmpdir", True):
_logger.debug(
"[workflow %s] Removing intermediate output directory %s",
self.name, a)
shutil.rmtree(a, True)
_logger.info("[workflow %s] outdir is %s", self.name, self.outdir)
output_callback(wo, self.processStatus)
def load_tool(argsworkflow, updateonly, strict, makeTool, debug,
print_pre=False,
print_rdf=False,
print_dot=False,
print_deps=False,
relative_deps=False,
rdf_serializer=None,
stdout=sys.stdout,
urifrag=None):
(document_loader, avsc_names, schema_metadata) = process.get_schema()
if isinstance(avsc_names, Exception):
raise avsc_names
jobobj = None
if isinstance(argsworkflow, basestring):
split = urlparse.urlsplit(argsworkflow)
if split.scheme:
uri = argsworkflow
else:
uri = "file://" + os.path.abspath(argsworkflow)
fileuri, urifrag = urlparse.urldefrag(uri)
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
workflowobj = argsworkflow
uri = urifrag
fileuri = "#"
else:
raise schema_salad.validate.ValidationException("Must be URI or dict")
if "cwl:tool" in workflowobj:
jobobj = workflowobj
uri = urlparse.urljoin(uri, jobobj["cwl:tool"])
fileuri, urifrag = urlparse.urldefrag(uri)
workflowobj = document_loader.fetch(fileuri)
del jobobj["cwl:tool"]
if isinstance(workflowobj, list):
# bare list without a version must be treated as draft-2
workflowobj = {"cwlVersion": "https://w3id.org/cwl/cwl#draft-2",
"id": fileuri,
"@graph": workflowobj}
workflowobj = update.update(workflowobj, document_loader, fileuri)
document_loader.idx.clear()
if updateonly:
stdout.write(json.dumps(workflowobj, indent=4))
return 0
if print_deps:
printdeps(workflowobj, document_loader, stdout, relative_deps)
return 0
try:
processobj, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, workflowobj, strict)
except (schema_salad.validate.ValidationException, RuntimeError) as e:
_logger.error("Tool definition failed validation:\n%s", e, exc_info=(e if debug else False))
return 1
if print_pre:
stdout.write(json.dumps(processobj, indent=4))
return 0
if print_rdf:
printrdf(argsworkflow, processobj, document_loader.ctx, rdf_serializer, stdout)
return 0
if print_dot:
printdot(argsworkflow, processobj, document_loader.ctx, stdout)
return 0
if urifrag:
processobj, _ = document_loader.resolve_ref(uri)
elif isinstance(processobj, list):
if 1 == len(processobj):
processobj = processobj[0]
else:
_logger.error("Tool file contains graph of multiple objects, must specify one of #%s",
", #".join(urlparse.urldefrag(i["id"])[1]
for i in processobj if "id" in i))
return 1
try:
t = makeTool(processobj, strict=strict, makeTool=makeTool, loader=document_loader, avsc_names=avsc_names)
except (schema_salad.validate.ValidationException) as e:
_logger.error("Tool definition failed validation:\n%s", e, exc_info=(e if debug else False))
return 1
except (RuntimeError, workflow.WorkflowException) as e:
_logger.error("Tool definition failed initialization:\n%s", e, exc_info=(e if debug else False))
return 1
if jobobj:
for inp in t.tool["inputs"]:
if shortname(inp["id"]) in jobobj:
inp["default"] = jobobj[shortname(inp["id"])]
if metadata:
t.metadata = metadata
else:
t.metadata = {"$namespaces": t.tool.get("$namespaces", {}), "$schemas": t.tool.get("$schemas", [])}
return t
def job(self, joborder, basedir, output_callback, **kwargs):
kwargs["part_of"] = self.name
kwargs["name"] = shortname(self.id)
for j in self.step.job(joborder, basedir, output_callback, **kwargs):
yield j
def load_tool(argsworkflow,
updateonly,
strict,
makeTool,
debug,
print_pre=False,
print_rdf=False,
print_dot=False,
print_deps=False,
relative_deps=False,
rdf_serializer=None,
stdout=sys.stdout,
urifrag=None):
(document_loader, avsc_names, schema_metadata) = process.get_schema()
if isinstance(avsc_names, Exception):
raise avsc_names
jobobj = None
if isinstance(argsworkflow, basestring):
split = urlparse.urlsplit(argsworkflow)
if split.scheme:
uri = argsworkflow
else:
uri = "file://" + os.path.abspath(argsworkflow)
fileuri, urifrag = urlparse.urldefrag(uri)
workflowobj = document_loader.fetch(fileuri)
if isinstance(workflowobj, list):
# bare list without a version must be treated as draft-2
workflowobj = {
"cwlVersion": "https://w3id.org/cwl/cwl#draft-2",
"id": fileuri,
"@graph": workflowobj
}
elif isinstance(argsworkflow, dict):
workflowobj = argsworkflow
uri = urifrag
fileuri = ""
else:
raise schema_salad.validate.ValidationException("Must be URI or dict")
if "cwl:tool" in workflowobj:
jobobj = workflowobj
workflowobj = document_loader.fetch(
urlparse.urljoin(uri, workflowobj["cwl:tool"]))
workflowobj = update.update(workflowobj, document_loader, fileuri)
document_loader.idx.clear()
if updateonly:
stdout.write(json.dumps(workflowobj, indent=4))
return 0
if print_deps:
printdeps(workflowobj, document_loader, stdout, relative_deps)
return 0
try:
processobj, metadata = schema_salad.schema.load_and_validate(
document_loader, avsc_names, workflowobj, strict)
except (schema_salad.validate.ValidationException, RuntimeError) as e:
_logger.error("Tool definition failed validation:\n%s",
e,
exc_info=(e if debug else False))
return 1
if print_pre:
stdout.write(json.dumps(processobj, indent=4))
return 0
if print_rdf:
printrdf(argsworkflow, processobj, document_loader.ctx, rdf_serializer,
stdout)
return 0
if print_dot:
printdot(argsworkflow, processobj, document_loader.ctx, stdout)
return 0
if urifrag:
processobj, _ = document_loader.resolve_ref(uri)
elif isinstance(processobj, list):
if 1 == len(processobj):
processobj = processobj[0]
else:
_logger.error(
"Tool file contains graph of multiple objects, must specify one of #%s",
", #".join(
urlparse.urldefrag(i["id"])[1] for i in processobj
if "id" in i))
return 1
try:
t = makeTool(processobj,
strict=strict,
makeTool=makeTool,
loader=document_loader,
avsc_names=avsc_names)
except (schema_salad.validate.ValidationException) as e:
_logger.error("Tool definition failed validation:\n%s",
e,
exc_info=(e if debug else False))
return 1
except (RuntimeError, workflow.WorkflowException) as e:
_logger.error("Tool definition failed initialization:\n%s",
e,
exc_info=(e if debug else False))
return 1
if jobobj:
for inp in t.tool["inputs"]:
if shortname(inp["id"]) in jobobj:
inp["default"] = jobobj[shortname(inp["id"])]
if metadata:
t.metadata = metadata
else:
t.metadata = {
"$namespaces": t.tool.get("$namespaces", {}),
"$schemas": t.tool.get("$schemas", [])
}
return t
def load_job_order(args,
t,
parser,
stdin,
print_input_deps=False,
relative_deps=False,
stdout=sys.stdout):
job_order_object = None
if args.conformance_test:
loader = Loader({})
else:
jobloaderctx = {
"path": {
"@type": "@id"
},
"format": {
"@type": "@id"
},
"id": "@id"
}
jobloaderctx.update(t.metadata.get("$namespaces", {}))
loader = Loader(jobloaderctx)
if len(args.job_order) == 1 and args.job_order[0][0] != "-":
job_order_file = args.job_order[0]
elif len(args.job_order) == 1 and args.job_order[0] == "-":
job_order_object = yaml.load(stdin)
job_order_object, _ = loader.resolve_all(job_order_object, "")
else:
job_order_file = None
if job_order_object:
input_basedir = args.basedir if args.basedir else os.getcwd()
elif job_order_file:
input_basedir = args.basedir if args.basedir else os.path.abspath(
os.path.dirname(job_order_file))
try:
job_order_object, _ = loader.resolve_ref(job_order_file)
except Exception as e:
_logger.error(e, exc_info=(e if args.debug else False))
return 1
toolparser = None
else:
input_basedir = args.basedir if args.basedir else os.getcwd()
namemap = {}
toolparser = generate_parser(
argparse.ArgumentParser(prog=args.workflow), t, namemap)
if toolparser:
if args.tool_help:
toolparser.print_help()
return 0
cmd_line = vars(toolparser.parse_args(args.job_order))
if cmd_line["job_order"]:
try:
input_basedir = args.basedir if args.basedir else os.path.abspath(
os.path.dirname(cmd_line["job_order"]))
job_order_object = loader.resolve_ref(
cmd_line["job_order"])
except Exception as e:
_logger.error(e, exc_info=(e if args.debug else False))
return 1
else:
job_order_object = {"id": args.workflow}
job_order_object.update(
{namemap[k]: v
for k, v in cmd_line.items()})
_logger.debug("Parsed job order from command line: %s",
json.dumps(job_order_object, indent=4))
else:
job_order_object = None
for inp in t.tool["inputs"]:
if "default" in inp and (not job_order_object or shortname(inp["id"])
not in job_order_object):
if not job_order_object:
job_order_object = {}
job_order_object[shortname(inp["id"])] = inp["default"]
if not job_order_object and len(t.tool["inputs"]) > 0:
parser.print_help()
if toolparser:
print "\nOptions for %s " % args.workflow
toolparser.print_help()
_logger.error("")
_logger.error("Input object required")
return 1
if print_input_deps:
printdeps(job_order_object,
loader,
stdout,
relative_deps,
basedir="file://%s/" % input_basedir)
return 0
return (job_order_object, input_basedir)
def load_job_order(args, t, parser, stdin, print_input_deps=False, relative_deps=False, stdout=sys.stdout):
job_order_object = None
if args.conformance_test:
loader = Loader({})
else:
jobloaderctx = {"path": {"@type": "@id"}, "format": {"@type": "@id"}, "id": "@id"}
jobloaderctx.update(t.metadata.get("$namespaces", {}))
loader = Loader(jobloaderctx)
if len(args.job_order) == 1 and args.job_order[0][0] != "-":
job_order_file = args.job_order[0]
elif len(args.job_order) == 1 and args.job_order[0] == "-":
job_order_object = yaml.load(stdin)
job_order_object, _ = loader.resolve_all(job_order_object, "")
else:
job_order_file = None
if job_order_object:
input_basedir = args.basedir if args.basedir else os.getcwd()
elif job_order_file:
input_basedir = args.basedir if args.basedir else os.path.abspath(os.path.dirname(job_order_file))
try:
job_order_object, _ = loader.resolve_ref(job_order_file)
except Exception as e:
_logger.error(e, exc_info=(e if args.debug else False))
return 1
toolparser = None
else:
input_basedir = args.basedir if args.basedir else os.getcwd()
namemap = {}
toolparser = generate_parser(argparse.ArgumentParser(prog=args.workflow), t, namemap)
if toolparser:
if args.tool_help:
toolparser.print_help()
return 0
cmd_line = vars(toolparser.parse_args(args.job_order))
if cmd_line["job_order"]:
try:
input_basedir = args.basedir if args.basedir else os.path.abspath(os.path.dirname(cmd_line["job_order"]))
job_order_object = loader.resolve_ref(cmd_line["job_order"])
except Exception as e:
_logger.error(e, exc_info=(e if args.debug else False))
return 1
else:
job_order_object = {"id": args.workflow}
job_order_object.update({namemap[k]: v for k,v in cmd_line.items()})
_logger.debug("Parsed job order from command line: %s", json.dumps(job_order_object, indent=4))
else:
job_order_object = None
for inp in t.tool["inputs"]:
if "default" in inp and (not job_order_object or shortname(inp["id"]) not in job_order_object):
if not job_order_object:
job_order_object = {}
job_order_object[shortname(inp["id"])] = inp["default"]
if not job_order_object and len(t.tool["inputs"]) > 0:
parser.print_help()
if toolparser:
print "\nOptions for %s " % args.workflow
toolparser.print_help()
_logger.error("")
_logger.error("Input object required")
return 1
if print_input_deps:
printdeps(job_order_object, loader, stdout, relative_deps,
basedir="file://%s/" % input_basedir)
return 0
if "cwl:tool" in job_order_object:
del job_order_object["cwl:tool"]
if "id" in job_order_object:
del job_order_object["id"]
return (job_order_object, input_basedir)
def collect_output(self, schema, builder, outdir):
r = None
if "outputBinding" in schema:
binding = schema["outputBinding"]
globpatterns = []
if "glob" in binding:
r = []
for gb in aslist(binding["glob"]):
try:
gb = builder.do_eval(gb)
globpatterns.append(gb)
if gb:
r.extend([{"path": g, "class": "File"} for g in builder.fs_access.glob(os.path.join(outdir, gb))])
except (OSError, IOError) as e:
_logger.warn(str(e))
for files in r:
checksum = hashlib.sha1()
with builder.fs_access.open(files["path"], "rb") as f:
contents = f.read(CONTENT_LIMIT)
if binding.get("loadContents"):
files["contents"] = contents
filesize = 0
while contents != "":
checksum.update(contents)
filesize += len(contents)
contents = f.read(1024*1024)
files["checksum"] = "sha1$%s" % checksum.hexdigest()
files["size"] = filesize
if "format" in schema:
files["format"] = builder.do_eval(schema["format"], context=files)
optional = False
singlefile = False
if isinstance(schema["type"], list):
if "null" in schema["type"]:
optional = True
if "File" in schema["type"]:
singlefile = True
elif schema["type"] == "File":
singlefile = True
if "outputEval" in binding:
r = builder.do_eval(binding["outputEval"], context=r)
if singlefile:
# Handle single file outputs not wrapped in a list
if r is not None and not isinstance(r, (list, tuple)):
r = [r]
if optional and r is None:
pass
elif (r is None or len(r) != 1 or not isinstance(r[0], dict) or "path" not in r[0]):
raise WorkflowException("Expression must return a file object for %s." % schema["id"])
if singlefile:
if not r and not optional:
raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
elif not r and optional:
pass
elif isinstance(r, list):
if len(r) > 1:
raise WorkflowException("Multiple matches for output item that is a single file.")
else:
r = r[0]
if "secondaryFiles" in schema:
for primary in aslist(r):
if isinstance(primary, dict):
primary["secondaryFiles"] = []
for sf in aslist(schema["secondaryFiles"]):
if isinstance(sf, dict) or "$(" in sf or "${" in sf:
sfpath = builder.do_eval(sf, context=r)
if isinstance(sfpath, basestring):
sfpath = {"path": sfpath, "class": "File"}
else:
sfpath = {"path": substitute(primary["path"], sf), "class": "File"}
for sfitem in aslist(sfpath):
if builder.fs_access.exists(sfitem["path"]):
primary["secondaryFiles"].append(sfitem)
if not r and optional:
r = None
if not r and isinstance(schema["type"], dict) and schema["type"]["type"] == "record":
r = {}
for f in schema["type"]["fields"]:
r[shortname(f["name"])] = self.collect_output(f, builder, outdir)
return r
def job(self, joborder, basedir, output_callback, **kwargs):
kwargs["part_of"] = self.name
kwargs["name"] = shortname(self.id)
for j in self.step.job(joborder, basedir, output_callback, **kwargs):
yield j
def try_make_job(self, step, basedir, **kwargs):
inputparms = step.tool["inputs"]
outputparms = step.tool["outputs"]
supportsMultipleInput = bool(self.workflow.get_requirement("MultipleInputFeatureRequirement")[0])
try:
inputobj = object_from_state(self.state, inputparms, False, supportsMultipleInput)
if inputobj is None:
_logger.debug("[workflow %s] job step %s not ready", self.name, step.id)
return
_logger.debug("[step %s] starting job step %s of workflow %s", id(step), step.id, id(self))
if step.submitted:
return
callback = functools.partial(self.receive_output, step, outputparms)
valueFrom = {i["id"]: i["valueFrom"] for i in step.tool["inputs"] if "valueFrom" in i}
if len(valueFrom) > 0 and not bool(self.workflow.get_requirement("StepInputExpressionRequirement")[0]):
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):
if k in valueFrom:
return expression.do_eval(valueFrom[k], vfinputs, self.workflow.requirements,
None, None, {}, context=v)
else:
return v
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")
if "valueFrom" not in kwargs:
kwargs["valueFrom"] = valueFromFunc
if method == "dotproduct" or method is None:
jobs = dotproduct_scatter(step, inputobj, basedir, scatter,
callback, **kwargs)
elif method == "nested_crossproduct":
jobs = nested_crossproduct_scatter(step, inputobj,
basedir, scatter, callback, **kwargs)
elif method == "flat_crossproduct":
jobs = flat_crossproduct_scatter(step, inputobj, basedir,
scatter, callback, 0, **kwargs)
else:
_logger.debug("[workflow %s] Job is input %s", self.name, json.dumps(inputobj, indent=4))
inputobj = {k: valueFromFunc(k, v) for k,v in inputobj.items()}
_logger.debug("[workflow %s] Evaluated job input to %s", self.name, json.dumps(inputobj, indent=4))
jobs = step.job(inputobj, basedir, callback, **kwargs)
step.submitted = True
for j in jobs:
yield j
except WorkflowException:
raise
except Exception as e:
_logger.exception("Unhandled exception")
self.processStatus = "permanentFail"
step.completed = True
def job(self, joborder, basedir, output_callback, move_outputs=True, **kwargs):
self.state = {}
self.processStatus = "success"
if "outdir" in kwargs:
del kwargs["outdir"]
for i in self.tool["inputs"]:
iid = shortname(i["id"])
if iid in joborder:
self.state[i["id"]] = WorkflowStateItem(i, copy.deepcopy(joborder[iid]))
elif "default" in i:
self.state[i["id"]] = WorkflowStateItem(i, copy.deepcopy(i["default"]))
else:
raise WorkflowException("Input '%s' not in input object and does not have a default value." % (i["id"]))
for s in self.steps:
for out in s.tool["outputs"]:
self.state[out["id"]] = None
output_dirs = set()
completed = 0
iterables = []
while completed < len(self.steps) and self.processStatus == "success":
made_progress = False
for step in self.steps:
if not step.submitted:
step.iterable = self.try_make_job(step, basedir, **kwargs)
if step.iterable:
for newjob in step.iterable:
if newjob:
made_progress = True
if newjob.outdir:
output_dirs.add(newjob.outdir)
yield newjob
else:
break
completed = sum(1 for s in self.steps if s.completed)
if not made_progress and completed < len(self.steps):
yield None
supportsMultipleInput = bool(self.workflow.get_requirement("MultipleInputFeatureRequirement")[0])
wo = object_from_state(self.state, self.tool["outputs"], True, supportsMultipleInput)
if wo is None:
raise WorkflowException("Output for workflow not available")
if move_outputs:
targets = set()
conflicts = set()
outfiles = findfiles(wo)
for f in outfiles:
for a in output_dirs:
if f["path"].startswith(a):
src = f["path"]
dst = os.path.join(self.outdir, src[len(a)+1:])
if dst in targets:
conflicts.add(dst)
else:
targets.add(dst)
for f in outfiles:
for a in output_dirs:
if f["path"].startswith(a):
src = f["path"]
dst = os.path.join(self.outdir, src[len(a)+1:])
if dst in conflicts:
sp = os.path.splitext(dst)
dst = "%s-%s%s" % (sp[0], str(random.randint(1, 1000000000)), sp[1])
dirname = os.path.dirname(dst)
if not os.path.exists(dirname):
os.makedirs(dirname)
_logger.debug("[workflow %s] Moving '%s' to '%s'", self.name, src, dst)
shutil.move(src, dst)
f["path"] = dst
for a in output_dirs:
if os.path.exists(a) and empty_subtree(a):
if kwargs.get("rm_tmpdir", True):
_logger.debug("[workflow %s] Removing intermediate output directory %s", self.name, a)
shutil.rmtree(a, True)
_logger.info("[workflow %s] outdir is %s", self.name, self.outdir)
output_callback(wo, self.processStatus)
