def visit(self, srcobj, uploadfiles):
src = srcobj["location"]
if "#" in src:
src = src[:src.index("#")]
if isinstance(src,
basestring) and ArvPathMapper.pdh_dirpath.match(src):
self._pathmap[src] = MapperEnt(
src, self.collection_pattern % urllib.parse.unquote(src[5:]),
srcobj["class"], True)
if arvados_cwl.util.collectionUUID in srcobj:
self.pdh_to_uuid[src.split(
"/", 1)[0][5:]] = srcobj[arvados_cwl.util.collectionUUID]
debug = logger.isEnabledFor(logging.DEBUG)
if src not in self._pathmap:
if src.startswith("file:"):
# Local FS ref, may need to be uploaded or may be on keep
# mount.
ab = abspath(src, self.input_basedir)
st = arvados.commands.run.statfile("",
ab,
fnPattern="keep:%s/%s",
dirPattern="keep:%s/%s",
raiseOSError=True)
with SourceLine(srcobj, "location", WorkflowException, debug):
if isinstance(st, arvados.commands.run.UploadFile):
uploadfiles.add((src, ab, st))
elif isinstance(st, arvados.commands.run.ArvFile):
self._pathmap[src] = MapperEnt(
st.fn, self.collection_pattern %
urllib.parse.unquote(st.fn[5:]), "File", True)
else:
raise WorkflowException(
"Input file path '%s' is invalid" % st)
elif src.startswith("_:"):
if srcobj["class"] == "File" and "contents" not in srcobj:
raise WorkflowException(
"File literal '%s' is missing `contents`" % src)
if srcobj["class"] == "Directory" and "listing" not in srcobj:
raise WorkflowException(
"Directory literal '%s' is missing `listing`" % src)
elif src.startswith("http:") or src.startswith("https:"):
keepref = http_to_keep(self.arvrunner.api,
self.arvrunner.project_uuid, src)
logger.info("%s is %s", src, keepref)
self._pathmap[src] = MapperEnt(keepref, keepref,
srcobj["class"], True)
else:
self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True)
with SourceLine(srcobj, "secondaryFiles", WorkflowException, debug):
for l in srcobj.get("secondaryFiles", []):
self.visit(l, uploadfiles)
with SourceLine(srcobj, "listing", WorkflowException, debug):
for l in srcobj.get("listing", []):
self.visit(l, uploadfiles)
def keepmount(obj):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
if obj["location"].startswith("keep:"):
obj["location"] = "/keep/" + obj["location"][5:]
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
del obj["location"]
else:
raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
def keepmount(obj):
remove_redundant_fields(obj)
with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
del obj["location"]
else:
raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
def get_overall_res_req(res_reqs):
"""Take the overall of a list of ResourceRequirement,
i.e., the max of coresMin, coresMax, ramMin, ramMax, tmpdirMin, tmpdirMax
and the sum of outdirMin, outdirMax."""
all_res_req = {}
exception_msgs = []
for a in max_res_pars + sum_res_pars:
all_res_req[a] = []
for res_req in res_reqs:
if a in res_req:
if isinstance(res_req[a], int): # integer check
all_res_req[a].append(res_req[a])
else:
msg = SourceLine(res_req, a).makeError(
"Non-top-level ResourceRequirement in single container cannot have expressions")
exception_msgs.append(msg)
if exception_msgs:
raise WorkflowException("\n".join(exception_msgs))
else:
overall_res_req = {}
for a in all_res_req:
if all_res_req[a]:
if a in max_res_pars:
overall_res_req[a] = max(all_res_req[a])
elif a in sum_res_pars:
overall_res_req[a] = sum(all_res_req[a])
if overall_res_req:
overall_res_req["class"] = "ResourceRequirement"
return cmap(overall_res_req)
def visit(item):
if "requirements" in item:
item["requirements"] = [
i for i in item["requirements"]
if i["class"] != "DockerRequirement"
]
for t in ("hints", "requirements"):
if t not in item:
continue
for req in item[t]:
if req["class"] == "ResourceRequirement":
dyn = False
for k in max_res_pars + sum_res_pars:
if k in req:
if isinstance(req[k], basestring):
if item["id"] == "#main":
# only the top-level requirements/hints may contain expressions
self.dynamic_resource_req.append(
req)
dyn = True
break
else:
with SourceLine(
req, k,
WorkflowException):
raise WorkflowException(
"Non-top-level ResourceRequirement in single container cannot have expressions"
)
if not dyn:
self.static_resource_req.append(req)
def visit(self, srcobj, uploadfiles):
src = srcobj["location"]
if srcobj["class"] == "File":
if "#" in src:
src = src[:src.index("#")]
if isinstance(src,
basestring) and ArvPathMapper.pdh_path.match(src):
self._pathmap[src] = MapperEnt(
src, self.collection_pattern % src[5:], "File")
if src not in self._pathmap:
# Local FS ref, may need to be uploaded or may be on keep
# mount.
ab = abspath(src, self.input_basedir)
st = arvados.commands.run.statfile("",
ab,
fnPattern=self.file_pattern)
if isinstance(st, arvados.commands.run.UploadFile):
uploadfiles.add((src, ab, st))
elif isinstance(st, arvados.commands.run.ArvFile):
self._pathmap[src] = MapperEnt(ab, st.fn, "File")
elif src.startswith("_:") and "contents" in srcobj:
pass
else:
raise WorkflowException("Input file path '%s' is invalid" %
st)
if "secondaryFiles" in srcobj:
for l in srcobj["secondaryFiles"]:
self.visit(l, uploadfiles)
elif srcobj["class"] == "Directory":
if isinstance(src,
basestring) and ArvPathMapper.pdh_dirpath.match(src):
self._pathmap[src] = MapperEnt(
src, self.collection_pattern % src[5:], "Directory")
for l in srcobj["listing"]:
self.visit(l, uploadfiles)
def visit(self, srcobj, uploadfiles):
src = srcobj["location"]
if "#" in src:
src = src[:src.index("#")]
if isinstance(src,
basestring) and ArvPathMapper.pdh_dirpath.match(src):
self._pathmap[src] = MapperEnt(
src, self.collection_pattern % urllib.unquote(src[5:]),
srcobj["class"], True)
if src not in self._pathmap:
if src.startswith("file:"):
# Local FS ref, may need to be uploaded or may be on keep
# mount.
ab = abspath(src, self.input_basedir)
st = arvados.commands.run.statfile("",
ab,
fnPattern="keep:%s/%s",
dirPattern="keep:%s/%s",
raiseOSError=True)
with SourceLine(srcobj, "location", WorkflowException):
if isinstance(st, arvados.commands.run.UploadFile):
uploadfiles.add((src, ab, st))
elif isinstance(st, arvados.commands.run.ArvFile):
self._pathmap[src] = MapperEnt(
st.fn, self.collection_pattern %
urllib.unquote(st.fn[5:]), "File", True)
else:
raise WorkflowException(
"Input file path '%s' is invalid" % st)
elif src.startswith("_:"):
if srcobj["class"] == "File" and "contents" not in srcobj:
raise WorkflowException(
"File literal '%s' is missing `contents`" % src)
if srcobj["class"] == "Directory" and "listing" not in srcobj:
raise WorkflowException(
"Directory literal '%s' is missing `listing`" % src)
else:
self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True)
with SourceLine(srcobj, "secondaryFiles", WorkflowException):
for l in srcobj.get("secondaryFiles", []):
self.visit(l, uploadfiles)
with SourceLine(srcobj, "listing", WorkflowException):
for l in srcobj.get("listing", []):
self.visit(l, uploadfiles)
def addentry(self, obj, c, path, subdirs):
if obj["location"] in self._pathmap:
src, srcpath = self.arvrunner.fs_access.get_collection(
self._pathmap[obj["location"]].resolved)
c.copy(srcpath,
path + "/" + obj["basename"],
source_collection=src,
overwrite=True)
for l in obj.get("secondaryFiles", []):
self.addentry(l, c, path, subdirs)
elif obj["class"] == "Directory":
for l in obj["listing"]:
self.addentry(l, c, path + "/" + obj["basename"], subdirs)
subdirs.append((obj["location"], path + "/" + obj["basename"]))
elif obj["location"].startswith("_:") and "contents" in obj:
with c.open(path + "/" + obj["basename"], "w") as f:
f.write(obj["contents"].encode("utf-8"))
else:
raise WorkflowException("Don't know what to do with '%s'" %
obj["location"])
def job(self, joborder, output_callback, runtimeContext):
builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
if not req:
return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
# RunInSingleContainer is true
with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "id" not in self.tool:
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
discover_secondary_files(self.arvrunner.fs_access, builder,
self.tool["inputs"], joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
self.doc_loader,
joborder,
joborder.get("id", "#"),
False)
if self.wf_pdh is None:
packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader)
for p in packed["$graph"]:
if p["id"] == "#main":
p["requirements"] = dedup_reqs(self.requirements)
p["hints"] = dedup_reqs(self.hints)
def visit(item):
if "requirements" in item:
item["requirements"] = [i for i in item["requirements"] if i["class"] != "DockerRequirement"]
for t in ("hints", "requirements"):
if t not in item:
continue
for req in item[t]:
if req["class"] == "ResourceRequirement":
dyn = False
for k in max_res_pars + sum_res_pars:
if k in req:
if isinstance(req[k], basestring):
if item["id"] == "#main":
# only the top-level requirements/hints may contain expressions
self.dynamic_resource_req.append(req)
dyn = True
break
else:
with SourceLine(req, k, WorkflowException):
raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions")
if not dyn:
self.static_resource_req.append(req)
visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit)
if self.static_resource_req:
self.static_resource_req = [get_overall_res_req(self.static_resource_req)]
upload_dependencies(self.arvrunner,
runtimeContext.name,
self.doc_loader,
packed,
self.tool["id"],
False)
# Discover files/directories referenced by the
# workflow (mainly "default" values)
visit_class(packed, ("File", "Directory"), self.wf_reffiles.append)
if self.dynamic_resource_req:
# Evaluate dynamic resource requirements using current builder
rs = copy.copy(self.static_resource_req)
for dyn_rs in self.dynamic_resource_req:
eval_req = {"class": "ResourceRequirement"}
for a in max_res_pars + sum_res_pars:
if a in dyn_rs:
eval_req[a] = builder.do_eval(dyn_rs[a])
rs.append(eval_req)
job_res_reqs = [get_overall_res_req(rs)]
else:
job_res_reqs = self.static_resource_req
with Perf(metrics, "subworkflow adjust"):
joborder_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
reffiles = []
visit_class(joborder_keepmount, ("File", "Directory"), reffiles.append)
mapper = ArvPathMapper(self.arvrunner, reffiles+self.wf_reffiles, runtimeContext.basedir,
"/keep/%s",
"/keep/%s/%s")
# For containers API, we need to make sure any extra
# referenced files (ie referenced by the workflow but
# not in the inputs) are included in the mounts.
if self.wf_reffiles:
runtimeContext = runtimeContext.copy()
runtimeContext.extra_reffiles = copy.deepcopy(self.wf_reffiles)
def keepmount(obj):
remove_redundant_fields(obj)
with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
del obj["location"]
else:
raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
def resolved(obj):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).resolved
visit_class(joborder_resolved, ("File", "Directory"), resolved)
if self.wf_pdh is None:
adjustFileObjs(packed, keepmount)
adjustDirObjs(packed, keepmount)
self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed)
self.loadingContext = self.loadingContext.copy()
self.loadingContext.metadata = self.loadingContext.metadata.copy()
self.loadingContext.metadata["http://commonwl.org/cwltool#original_cwlVersion"] = "v1.0"
if len(job_res_reqs) == 1:
# RAM request needs to be at least 128 MiB or the workflow
# runner itself won't run reliably.
if job_res_reqs[0].get("ramMin", 1024) < 128:
job_res_reqs[0]["ramMin"] = 128
arguments = ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl", "cwl.input.yml"]
if runtimeContext.debug:
arguments.insert(0, '--debug')
wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
"requirements": self.requirements+job_res_reqs+[
{"class": "InlineJavascriptRequirement"},
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entryname": "workflow.cwl",
"entry": '$({"class": "File", "location": "keep:%s/workflow.cwl"})' % self.wf_pdh
}, {
"entryname": "cwl.input.yml",
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
"hints": self.hints,
"arguments": arguments,
"id": "#"
})
return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
def job(self, joborder, output_callback, **kwargs):
kwargs["work_api"] = self.work_api
req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
if req:
with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "id" not in self.tool:
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
discover_secondary_files(self.tool["inputs"], joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
document_loader,
joborder,
joborder.get("id", "#"),
False)
if self.wf_pdh is None:
workflowobj["requirements"] = dedup_reqs(self.requirements)
workflowobj["hints"] = dedup_reqs(self.hints)
packed = pack(document_loader, workflowobj, uri, self.metadata)
upload_dependencies(self.arvrunner,
kwargs.get("name", ""),
document_loader,
packed,
uri,
False)
with Perf(metrics, "subworkflow adjust"):
joborder_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
reffiles = []
visit_class(joborder_keepmount, ("File", "Directory"), lambda x: reffiles.append(x))
mapper = ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
"/keep/%s",
"/keep/%s/%s",
**kwargs)
def keepmount(obj):
remove_redundant_fields(obj)
with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
del obj["location"]
else:
raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
def resolved(obj):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).resolved
visit_class(joborder_resolved, ("File", "Directory"), resolved)
if self.wf_pdh is None:
adjustFileObjs(packed, keepmount)
adjustDirObjs(packed, keepmount)
self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed)
wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
"requirements": self.requirements+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entryname": "workflow.cwl",
"entry": {
"class": "File",
"location": "keep:%s/workflow.cwl" % self.wf_pdh
}
}, {
"entryname": "cwl.input.yml",
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
"hints": self.hints,
"arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
"id": "#"
})
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema
return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs)
else:
return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)
