def packed_workflow(arvrunner, tool, merged_map): """Create a packed workflow. A "packed" workflow is one where all the components have been combined into a single document.""" rewrites = {} packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"], tool.metadata, rewrite_out=rewrites) rewrite_to_orig = {} for k,v in rewrites.items(): rewrite_to_orig[v] = k def visit(v, cur_id): if isinstance(v, dict): if v.get("class") in ("CommandLineTool", "Workflow"): cur_id = rewrite_to_orig.get(v["id"], v["id"]) if "location" in v and not v["location"].startswith("keep:"): v["location"] = merged_map[cur_id][v["location"]] for l in v: visit(v[l], cur_id) if isinstance(v, list): for l in v: visit(l, cur_id) visit(packed, None) return packed
def packed_workflow(arvrunner, tool, merged_map): """Create a packed workflow. A "packed" workflow is one where all the components have been combined into a single document.""" rewrites = {} packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"], tool.metadata, rewrite_out=rewrites) rewrite_to_orig = {v: k for k,v in rewrites.items()} def visit(v, cur_id): if isinstance(v, dict): if v.get("class") in ("CommandLineTool", "Workflow"): if "id" not in v: raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field") cur_id = rewrite_to_orig.get(v["id"], v["id"]) if "location" in v and not v["location"].startswith("keep:"): v["location"] = merged_map[cur_id].resolved[v["location"]] if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles: v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]] for l in v: visit(v[l], cur_id) if isinstance(v, list): for l in v: visit(l, cur_id) visit(packed, None) return packed
def packed_workflow(arvrunner, tool): """Create a packed workflow. A "packed" workflow is one where all the components have been combined into a single document.""" return pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"], tool.metadata)
def packed_workflow(arvrunner, tool, merged_map): """Create a packed workflow. A "packed" workflow is one where all the components have been combined into a single document.""" rewrites = {} packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"], tool.metadata, rewrite_out=rewrites) rewrite_to_orig = {v: k for k,v in rewrites.items()} def visit(v, cur_id): if isinstance(v, dict): if v.get("class") in ("CommandLineTool", "Workflow"): if "id" not in v: raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field") cur_id = rewrite_to_orig.get(v["id"], v["id"]) if "location" in v and not v["location"].startswith("keep:"): v["location"] = merged_map[cur_id].resolved[v["location"]] if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles: v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]] if v.get("class") == "DockerRequirement": v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True, arvrunner.project_uuid) for l in v: visit(v[l], cur_id) if isinstance(v, list): for l in v: visit(l, cur_id) visit(packed, None) return packed
def packed_workflow(arvrunner, tool, merged_map): """Create a packed workflow. A "packed" workflow is one where all the components have been combined into a single document.""" rewrites = {} packed = pack(arvrunner.loadingContext, tool.tool["id"], rewrite_out=rewrites, loader=tool.doc_loader) rewrite_to_orig = {v: k for k, v in viewitems(rewrites)} def visit(v, cur_id): if isinstance(v, dict): if v.get("class") in ("CommandLineTool", "Workflow", "ExpressionTool"): if tool.metadata["cwlVersion"] == "v1.0" and "id" not in v: raise SourceLine(v, None, Exception).makeError( "Embedded process object is missing required 'id' field, add an 'id' or use to cwlVersion: v1.1" ) if "id" in v: cur_id = rewrite_to_orig.get(v["id"], v["id"]) if "path" in v and "location" not in v: v["location"] = v["path"] del v["path"] if "location" in v and cur_id in merged_map: if v["location"] in merged_map[cur_id].resolved: v["location"] = merged_map[cur_id].resolved[v["location"]] if v["location"] in merged_map[cur_id].secondaryFiles: v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[ v["location"]] if v.get("class") == "DockerRequirement": v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image( arvrunner.api, v, True, arvrunner.project_uuid, arvrunner.runtimeContext.force_docker_pull, arvrunner.runtimeContext.tmp_outdir_prefix, arvrunner.runtimeContext.match_local_docker) for l in v: visit(v[l], cur_id) if isinstance(v, list): for l in v: visit(l, cur_id) visit(packed, None) return packed
def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None, submit_runner_ram=0, name=None): upload_docker(arvRunner, tool) document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"]) packed = pack(document_loader, workflowobj, uri, tool.metadata) adjustDirObjs(job_order, trim_listing) main = [p for p in packed["$graph"] if p["id"] == "#main"][0] for inp in main["inputs"]: sn = shortname(inp["id"]) if sn in job_order: inp["default"] = job_order[sn] if not name: name = tool.tool.get("label", os.path.basename(tool.tool["id"])) upload_dependencies(arvRunner, name, document_loader, packed, uri, False) # TODO nowhere for submit_runner_ram to go. body = { "workflow": { "name": name, "description": tool.tool.get("doc", ""), "definition":yaml.safe_dump(packed) }} if project_uuid: body["workflow"]["owner_uuid"] = project_uuid if uuid: call = arvRunner.api.workflows().update(uuid=uuid, body=body) else: call = arvRunner.api.workflows().create(body=body) return call.execute(num_retries=arvRunner.num_retries)["uuid"]
def job(self, joborder, output_callback, runtimeContext): builder = make_builder(joborder, self.hints, self.requirements, runtimeContext) runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext) req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") if not req: return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext) # RunInSingleContainer is true with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)): if "id" not in self.tool: raise WorkflowException("%s object must have 'id'" % (self.tool["class"])) discover_secondary_files(self.arvrunner.fs_access, builder, self.tool["inputs"], joborder) with Perf(metrics, "subworkflow upload_deps"): upload_dependencies(self.arvrunner, os.path.basename(joborder.get("id", "#")), self.doc_loader, joborder, joborder.get("id", "#"), False) if self.wf_pdh is None: packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader) for p in packed["$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)
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): 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"]) 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_keepmount = copy.deepcopy(joborder) def keepmount(obj): with SourceLine(obj, None, WorkflowException): if "location" not in obj: raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj)) with SourceLine(obj, "location", WorkflowException): 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"]) adjustFileObjs(joborder_keepmount, keepmount) adjustDirObjs(joborder_keepmount, keepmount) 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": workflowobj["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": workflowobj["hints"], "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"] }) kwargs["loader"] = self.doc_loader kwargs["avsc_names"] = self.doc_schema return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs) else: return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)
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"])) 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) 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) if req["class"] == "DockerRequirement": if "http://arvados.org/cwl#dockerCollectionPDH" in req: del req["http://arvados.org/cwl#dockerCollectionPDH"] 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: # 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 job(self, joborder, output_callback, **kwargs): kwargs["work_api"] = self.work_api req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") if req: document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"]) with Perf(metrics, "subworkflow upload_deps"): workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", []) workflowobj["hints"] = self.hints + workflowobj.get("hints", []) packed = pack(document_loader, workflowobj, uri, self.metadata) upload_dependencies(self.arvrunner, kwargs.get("name", ""), document_loader, packed, uri, False) upload_dependencies(self.arvrunner, os.path.basename(joborder.get("id", "#")), document_loader, joborder, joborder.get("id", "#"), False) with Perf(metrics, "subworkflow adjust"): joborder_keepmount = copy.deepcopy(joborder) 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"]) adjustFileObjs(joborder_keepmount, keepmount) adjustDirObjs(joborder_keepmount, keepmount) adjustFileObjs(packed, keepmount) adjustDirObjs(packed, keepmount) wf_runner = { "class": "CommandLineTool", "baseCommand": "cwltool", "inputs": self.tool["inputs"], "outputs": self.tool["outputs"], "stdout": "cwl.output.json", "requirements": workflowobj["requirements"]+[ { "class": "InitialWorkDirRequirement", "listing": [{ "entryname": "workflow.cwl", "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${') }, { "entryname": "cwl.input.yml", "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${') }] }], "hints": workflowobj["hints"], "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"] } kwargs["loader"] = self.doc_loader kwargs["avsc_names"] = self.doc_schema return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs) else: return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)