X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/07a2b2c0e743f36be03e746a7e265986db555d3e..eb58fd945645f5a670c761f7046b10885941167e:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index 316af0e528..f514476b90 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -12,23 +12,28 @@ from schema_salad.sourceline import SourceLine, cmap from cwltool.pack import pack from cwltool.load_tool import fetch_document from cwltool.process import shortname -from cwltool.workflow import Workflow, WorkflowException +from cwltool.workflow import Workflow, WorkflowException, WorkflowStep from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class +from cwltool.context import LoadingContext import ruamel.yaml as yaml -from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields +from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection, + trim_anonymous_location, remove_redundant_fields, discover_secondary_files) from .pathmapper import ArvPathMapper, trim_listing -from .arvtool import ArvadosCommandTool +from .arvtool import ArvadosCommandTool, set_cluster_target, make_builder from .perf import Perf logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') +max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax") +sum_res_pars = ("outdirMin", "outdirMax") + def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None, - submit_runner_ram=0, name=None): + submit_runner_ram=0, name=None, merged_map=None): - packed = packed_workflow(arvRunner, tool) + packed = packed_workflow(arvRunner, tool, merged_map) adjustDirObjs(job_order, trim_listing) adjustFileObjs(job_order, trim_anonymous_location) @@ -46,13 +51,24 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None, upload_dependencies(arvRunner, name, tool.doc_loader, packed, tool.tool["id"], False) - # TODO nowhere for submit_runner_ram to go. + if submit_runner_ram: + hints = main.get("hints", []) + found = False + for h in hints: + if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources": + h["ramMin"] = submit_runner_ram + found = True + break + if not found: + hints.append({"class": "http://arvados.org/cwl#WorkflowRunnerResources", + "ramMin": submit_runner_ram}) + main["hints"] = hints body = { "workflow": { "name": name, "description": tool.tool.get("doc", ""), - "definition":yaml.round_trip_dump(packed) + "definition":json.dumps(packed, sort_keys=True, indent=4, separators=(',',': ')) }} if project_uuid: body["workflow"]["owner_uuid"] = project_uuid @@ -70,110 +86,232 @@ def dedup_reqs(reqs): dedup[r["class"]] = r return [dedup[r] for r in sorted(dedup.keys())] +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) + +class ArvadosWorkflowStep(WorkflowStep): + def __init__(self, + toolpath_object, # type: Dict[Text, Any] + pos, # type: int + loadingContext, # type: LoadingContext + arvrunner, + *argc, + **argv + ): # type: (...) -> None + + super(ArvadosWorkflowStep, self).__init__(toolpath_object, pos, loadingContext, *argc, **argv) + self.tool["class"] = "WorkflowStep" + self.arvrunner = arvrunner + + def job(self, joborder, output_callback, runtimeContext): + runtimeContext = runtimeContext.copy() + runtimeContext.toplevel = True # Preserve behavior for #13365 + + builder = make_builder({shortname(k): v for k,v in joborder.items()}, self.hints, self.requirements, runtimeContext) + runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext) + return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext) + + class ArvadosWorkflow(Workflow): """Wrap cwltool Workflow to override selected methods.""" - def __init__(self, arvrunner, toolpath_object, **kwargs): - super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs) + def __init__(self, arvrunner, toolpath_object, loadingContext): self.arvrunner = arvrunner - self.work_api = kwargs["work_api"] self.wf_pdh = None + self.dynamic_resource_req = [] + self.static_resource_req = [] + self.wf_reffiles = [] + self.loadingContext = loadingContext + super(ArvadosWorkflow, self).__init__(toolpath_object, loadingContext) + self.cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget") + + def job(self, joborder, output_callback, runtimeContext): + + builder = self._init_job(joborder, runtimeContext) + runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, 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"]) + 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) + + visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit) + + if self.static_resource_req: + self.static_resource_req = [get_overall_res_req(self.static_resource_req)] - with Perf(metrics, "subworkflow upload_deps"): upload_dependencies(self.arvrunner, - os.path.basename(joborder.get("id", "#")), + runtimeContext.name, document_loader, - joborder, - joborder.get("id", "#"), + packed, + uri, 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": 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_resolved, output_callback, **kwargs) + # 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: - return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs) + 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 make_workflow_step(self, + toolpath_object, # type: Dict[Text, Any] + pos, # type: int + loadingContext, # type: LoadingContext + *argc, + **argv + ): + # (...) -> WorkflowStep + return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, self.arvrunner, *argc, **argv)