self.loadingContext = loadingContext
def job(self, joborder, output_callback, runtimeContext):
+
+ cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
+ if runtimeContext.cluster_target is None or runtimeContext.cluster_target.instance != id(cluster_target_req):
+ runtimeContext.cluster_target = ClusterTarget(id(cluster_target_req),
+ builder.do_eval(cluster_target_req.get("clusterID")),
+ builder.do_eval(cluster_target_req.get("ownerUUID")))
+
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"])
+ if not req:
+ return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
- discover_secondary_files(self.tool["inputs"], joborder)
+ # RunInSingleContainer is true
- with Perf(metrics, "subworkflow upload_deps"):
- upload_dependencies(self.arvrunner,
- os.path.basename(joborder.get("id", "#")),
- document_loader,
- joborder,
- joborder.get("id", "#"),
- False)
+ 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)
- 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)
-
- builder = Builder(joborder,
- requirements=workflowobj["requirements"],
- hints=workflowobj["hints"],
- resources={})
-
- def visit(item):
- 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,
- document_loader,
- packed,
- uri,
- 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:
builder = Builder(joborder,
- requirements=self.requirements,
- hints=self.hints,
+ requirements=workflowobj["requirements"],
+ hints=workflowobj["hints"],
resources={})
- # 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)
-
- 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": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
- "id": "#"
- })
- return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
+ def visit(item):
+ 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,
+ document_loader,
+ packed,
+ uri,
+ 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:
+ builder = Builder(joborder,
+ requirements=self.requirements,
+ hints=self.hints,
+ resources={})
+
+ # 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:
- return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
+ 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)
+
+ 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": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
+ "id": "#"
+ })
+ return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
projects / arvados.git / commitdiff