sdk/cwl/arvados_cwl/arvjob.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import logging
   6 import re
   7 import copy
   8 import json
   9 import time
  10
  11 from cwltool.process import get_feature, shortname, UnsupportedRequirement
  12 from cwltool.errors import WorkflowException
  13 from cwltool.command_line_tool import revmap_file, CommandLineTool
  14 from cwltool.load_tool import fetch_document
  15 from cwltool.builder import Builder
  16 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
  17
  18 from schema_salad.sourceline import SourceLine
  19
  20 import ruamel.yaml as yaml
  21
  22 import arvados.collection
  23 from arvados.errors import ApiError
  24
  25 from .arvdocker import arv_docker_get_image
  26 from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
  27 from .pathmapper import VwdPathMapper, trim_listing
  28 from .perf import Perf
  29 from . import done
  30 from ._version import __version__
  31
  32 logger = logging.getLogger('arvados.cwl-runner')
  33 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  34
  35 crunchrunner_re = re.compile(r"^.*crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)$")
  36
  37 crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d'
  38
  39 class ArvadosJob(object):
  40     """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
  41
  42     def __init__(self, runner):
  43         self.arvrunner = runner
  44         self.running = False
  45         self.uuid = None
  46
  47     def run(self, dry_run=False, pull_image=True, **kwargs):
  48         script_parameters = {
  49             "command": self.command_line
  50         }
  51         runtime_constraints = {}
  52
  53         with Perf(metrics, "generatefiles %s" % self.name):
  54             if self.generatefiles["listing"]:
  55                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
  56                                                     keep_client=self.arvrunner.keep_client,
  57                                                     num_retries=self.arvrunner.num_retries)
  58                 script_parameters["task.vwd"] = {}
  59                 generatemapper = VwdPathMapper([self.generatefiles], "", "",
  60                                                separateDirs=False)
  61
  62                 with Perf(metrics, "createfiles %s" % self.name):
  63                     for f, p in generatemapper.items():
  64                         if p.type == "CreateFile":
  65                             with vwd.open(p.target, "w") as n:
  66                                 n.write(p.resolved.encode("utf-8"))
  67
  68                 if vwd:
  69                     with Perf(metrics, "generatefiles.save_new %s" % self.name):
  70                         vwd.save_new()
  71
  72                 for f, p in generatemapper.items():
  73                     if p.type == "File":
  74                         script_parameters["task.vwd"][p.target] = p.resolved
  75                     if p.type == "CreateFile":
  76                         script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
  77
  78         script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
  79         if self.environment:
  80             script_parameters["task.env"].update(self.environment)
  81
  82         if self.stdin:
  83             script_parameters["task.stdin"] = self.stdin
  84
  85         if self.stdout:
  86             script_parameters["task.stdout"] = self.stdout
  87
  88         if self.stderr:
  89             script_parameters["task.stderr"] = self.stderr
  90
  91         if self.successCodes:
  92             script_parameters["task.successCodes"] = self.successCodes
  93         if self.temporaryFailCodes:
  94             script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes
  95         if self.permanentFailCodes:
  96             script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
  97
  98         with Perf(metrics, "arv_docker_get_image %s" % self.name):
  99             (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
 100             if docker_req and kwargs.get("use_container") is not False:
 101                 if docker_req.get("dockerOutputDirectory"):
 102                     raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
 103                         "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
 104                 runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
 105             else:
 106                 runtime_constraints["docker_image"] = "arvados/jobs"
 107
 108         resources = self.builder.resources
 109         if resources is not None:
 110             runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
 111             runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
 112             runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
 113
 114         runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
 115         if runtime_req:
 116             if "keep_cache" in runtime_req:
 117                 runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"]
 118                 runtime_constraints["min_ram_mb_per_node"] += runtime_req["keep_cache"]
 119             if "outputDirType" in runtime_req:
 120                 if runtime_req["outputDirType"] == "local_output_dir":
 121                     script_parameters["task.keepTmpOutput"] = False
 122                 elif runtime_req["outputDirType"] == "keep_output_dir":
 123                     script_parameters["task.keepTmpOutput"] = True
 124
 125         filters = [["repository", "=", "arvados"],
 126                    ["script", "=", "crunchrunner"],
 127                    ["script_version", "in git", crunchrunner_git_commit]]
 128         if not self.arvrunner.ignore_docker_for_reuse:
 129             filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
 130
 131         enable_reuse = kwargs.get("enable_reuse", True)
 132         if enable_reuse:
 133             reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement")
 134             if reuse_req:
 135                 enable_reuse = reuse_req["enableReuse"]
 136
 137         self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 138
 139         try:
 140             with Perf(metrics, "create %s" % self.name):
 141                 response = self.arvrunner.api.jobs().create(
 142                     body={
 143                         "owner_uuid": self.arvrunner.project_uuid,
 144                         "script": "crunchrunner",
 145                         "repository": "arvados",
 146                         "script_version": "master",
 147                         "minimum_script_version": crunchrunner_git_commit,
 148                         "script_parameters": {"tasks": [script_parameters]},
 149                         "runtime_constraints": runtime_constraints
 150                     },
 151                     filters=filters,
 152                     find_or_create=enable_reuse
 153                 ).execute(num_retries=self.arvrunner.num_retries)
 154
 155             self.uuid = response["uuid"]
 156             self.arvrunner.process_submitted(self)
 157
 158             self.update_pipeline_component(response)
 159
 160             if response["state"] == "Complete":
 161                 logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
 162                 # Give read permission to the desired project on reused jobs
 163                 if response["owner_uuid"] != self.arvrunner.project_uuid:
 164                     try:
 165                         self.arvrunner.api.links().create(body={
 166                             'link_class': 'permission',
 167                             'name': 'can_read',
 168                             'tail_uuid': self.arvrunner.project_uuid,
 169                             'head_uuid': response["uuid"],
 170                             }).execute(num_retries=self.arvrunner.num_retries)
 171                     except ApiError as e:
 172                         # The user might not have "manage" access on the job: log
 173                         # a message and continue.
 174                         logger.info("Creating read permission on job %s: %s",
 175                                     response["uuid"],
 176                                     e)
 177
 178                 with Perf(metrics, "done %s" % self.name):
 179                     self.done(response)
 180             else:
 181                 logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 182         except Exception as e:
 183             logger.exception("%s error" % (self.arvrunner.label(self)))
 184             self.output_callback({}, "permanentFail")
 185
 186     def update_pipeline_component(self, record):
 187         if self.arvrunner.pipeline:
 188             self.arvrunner.pipeline["components"][self.name] = {"job": record}
 189             with Perf(metrics, "update_pipeline_component %s" % self.name):
 190                 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
 191                     uuid=self.arvrunner.pipeline["uuid"],
 192                     body={
 193                         "components": self.arvrunner.pipeline["components"]
 194                     }).execute(num_retries=self.arvrunner.num_retries)
 195         if self.arvrunner.uuid:
 196             try:
 197                 job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
 198                 if job:
 199                     components = job["components"]
 200                     components[self.name] = record["uuid"]
 201                     self.arvrunner.api.jobs().update(
 202                         uuid=self.arvrunner.uuid,
 203                         body={
 204                             "components": components
 205                         }).execute(num_retries=self.arvrunner.num_retries)
 206             except Exception as e:
 207                 logger.info("Error adding to components: %s", e)
 208
 209     def done(self, record):
 210         try:
 211             self.update_pipeline_component(record)
 212         except:
 213             pass
 214
 215         try:
 216             if record["state"] == "Complete":
 217                 processStatus = "success"
 218             else:
 219                 processStatus = "permanentFail"
 220
 221             outputs = {}
 222             try:
 223                 if record["output"]:
 224                     with Perf(metrics, "inspect log %s" % self.name):
 225                         logc = arvados.collection.CollectionReader(record["log"],
 226                                                                    api_client=self.arvrunner.api,
 227                                                                    keep_client=self.arvrunner.keep_client,
 228                                                                    num_retries=self.arvrunner.num_retries)
 229                         log = logc.open(logc.keys()[0])
 230                         dirs = {
 231                             "tmpdir": "/tmpdir",
 232                             "outdir": "/outdir",
 233                             "keep": "/keep"
 234                         }
 235                         for l in log:
 236                             # Determine the tmpdir, outdir and keep paths from
 237                             # the job run.  Unfortunately, we can't take the first
 238                             # values we find (which are expected to be near the
 239                             # top) and stop scanning because if the node fails and
 240                             # the job restarts on a different node these values
 241                             # will different runs, and we need to know about the
 242                             # final run that actually produced output.
 243                             g = crunchrunner_re.match(l)
 244                             if g:
 245                                 dirs[g.group(1)] = g.group(2)
 246
 247                     if processStatus == "permanentFail":
 248                         done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
 249
 250                     with Perf(metrics, "output collection %s" % self.name):
 251                         outputs = done.done(self, record, dirs["tmpdir"],
 252                                             dirs["outdir"], dirs["keep"])
 253             except WorkflowException as e:
 254                 logger.error("%s unable to collect output from %s:\n%s",
 255                              self.arvrunner.label(self), record["output"], e, exc_info=(e if self.arvrunner.debug else False))
 256                 processStatus = "permanentFail"
 257             except Exception as e:
 258                 logger.exception("Got unknown exception while collecting output for job %s:", self.name)
 259                 processStatus = "permanentFail"
 260
 261             # Note: Currently, on error output_callback is expecting an empty dict,
 262             # anything else will fail.
 263             if not isinstance(outputs, dict):
 264                 logger.error("Unexpected output type %s '%s'", type(outputs), outputs)
 265                 outputs = {}
 266                 processStatus = "permanentFail"
 267         finally:
 268             self.output_callback(outputs, processStatus)
 269             self.arvrunner.process_done(record["uuid"])
 270
 271
 272 class RunnerJob(Runner):
 273     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
 274
 275     def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
 276         """Create an Arvados job specification for this workflow.
 277
 278         The returned dict can be used to create a job (i.e., passed as
 279         the +body+ argument to jobs().create()), or as a component in
 280         a pipeline template or pipeline instance.
 281         """
 282
 283         if self.tool.tool["id"].startswith("keep:"):
 284             self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
 285         else:
 286             packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
 287             wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
 288             self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
 289
 290         adjustDirObjs(self.job_order, trim_listing)
 291         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 292         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 293
 294         if self.output_name:
 295             self.job_order["arv:output_name"] = self.output_name
 296
 297         if self.output_tags:
 298             self.job_order["arv:output_tags"] = self.output_tags
 299
 300         self.job_order["arv:enable_reuse"] = self.enable_reuse
 301
 302         if self.on_error:
 303             self.job_order["arv:on_error"] = self.on_error
 304
 305         if kwargs.get("debug"):
 306             self.job_order["arv:debug"] = True
 307
 308         return {
 309             "script": "cwl-runner",
 310             "script_version": "master",
 311             "minimum_script_version": "570509ab4d2ef93d870fd2b1f2eab178afb1bad9",
 312             "repository": "arvados",
 313             "script_parameters": self.job_order,
 314             "runtime_constraints": {
 315                 "docker_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
 316                 "min_ram_mb_per_node": self.submit_runner_ram
 317             }
 318         }
 319
 320     def run(self, **kwargs):
 321         job_spec = self.arvados_job_spec(**kwargs)
 322
 323         job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
 324
 325         job = self.arvrunner.api.jobs().create(
 326             body=job_spec,
 327             find_or_create=self.enable_reuse
 328         ).execute(num_retries=self.arvrunner.num_retries)
 329
 330         for k,v in job_spec["script_parameters"].items():
 331             if v is False or v is None or isinstance(v, dict):
 332                 job_spec["script_parameters"][k] = {"value": v}
 333
 334         del job_spec["owner_uuid"]
 335         job_spec["job"] = job
 336
 337         instance_spec = {
 338             "owner_uuid": self.arvrunner.project_uuid,
 339             "name": self.name,
 340             "components": {
 341                 "cwl-runner": job_spec,
 342             },
 343             "state": "RunningOnServer",
 344         }
 345         if not self.enable_reuse:
 346             instance_spec["properties"] = {"run_options": {"enable_job_reuse": False}}
 347
 348         self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
 349             body=instance_spec).execute(num_retries=self.arvrunner.num_retries)
 350         logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"])
 351
 352         if kwargs.get("wait") is False:
 353             self.uuid = self.arvrunner.pipeline["uuid"]
 354             return
 355
 356         self.uuid = job["uuid"]
 357         self.arvrunner.process_submitted(self)
 358
 359         if job["state"] in ("Complete", "Failed", "Cancelled"):
 360             self.done(job)
 361
 362
 363 class RunnerTemplate(object):
 364     """An Arvados pipeline template that invokes a CWL workflow."""
 365
 366     type_to_dataclass = {
 367         'boolean': 'boolean',
 368         'File': 'File',
 369         'Directory': 'Collection',
 370         'float': 'number',
 371         'int': 'number',
 372         'string': 'text',
 373     }
 374
 375     def __init__(self, runner, tool, job_order, enable_reuse, uuid,
 376                  submit_runner_ram=0, name=None, merged_map=None):
 377         self.runner = runner
 378         self.tool = tool
 379         self.job = RunnerJob(
 380             runner=runner,
 381             tool=tool,
 382             job_order=job_order,
 383             enable_reuse=enable_reuse,
 384             output_name=None,
 385             output_tags=None,
 386             submit_runner_ram=submit_runner_ram,
 387             name=name,
 388             merged_map=merged_map)
 389         self.uuid = uuid
 390
 391     def pipeline_component_spec(self):
 392         """Return a component that Workbench and a-r-p-i will understand.
 393
 394         Specifically, translate CWL input specs to Arvados pipeline
 395         format, like {"dataclass":"File","value":"xyz"}.
 396         """
 397
 398         spec = self.job.arvados_job_spec()
 399
 400         # Most of the component spec is exactly the same as the job
 401         # spec (script, script_version, etc.).
 402         # spec['script_parameters'] isn't right, though. A component
 403         # spec's script_parameters hash is a translation of
 404         # self.tool.tool['inputs'] with defaults/overrides taken from
 405         # the job order. So we move the job parameters out of the way
 406         # and build a new spec['script_parameters'].
 407         job_params = spec['script_parameters']
 408         spec['script_parameters'] = {}
 409
 410         for param in self.tool.tool['inputs']:
 411             param = copy.deepcopy(param)
 412
 413             # Data type and "required" flag...
 414             types = param['type']
 415             if not isinstance(types, list):
 416                 types = [types]
 417             param['required'] = 'null' not in types
 418             non_null_types = [t for t in types if t != "null"]
 419             if len(non_null_types) == 1:
 420                 the_type = [c for c in non_null_types][0]
 421                 dataclass = None
 422                 if isinstance(the_type, basestring):
 423                     dataclass = self.type_to_dataclass.get(the_type)
 424                 if dataclass:
 425                     param['dataclass'] = dataclass
 426             # Note: If we didn't figure out a single appropriate
 427             # dataclass, we just left that attribute out.  We leave
 428             # the "type" attribute there in any case, which might help
 429             # downstream.
 430
 431             # Title and description...
 432             title = param.pop('label', '')
 433             descr = param.pop('doc', '').rstrip('\n')
 434             if title:
 435                 param['title'] = title
 436             if descr:
 437                 param['description'] = descr
 438
 439             # Fill in the value from the current job order, if any.
 440             param_id = shortname(param.pop('id'))
 441             value = job_params.get(param_id)
 442             if value is None:
 443                 pass
 444             elif not isinstance(value, dict):
 445                 param['value'] = value
 446             elif param.get('dataclass') in ('File', 'Collection') and value.get('location'):
 447                 param['value'] = value['location'][5:]
 448
 449             spec['script_parameters'][param_id] = param
 450         spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
 451         return spec
 452
 453     def save(self):
 454         body = {
 455             "components": {
 456                 self.job.name: self.pipeline_component_spec(),
 457             },
 458             "name": self.job.name,
 459         }
 460         if self.runner.project_uuid:
 461             body["owner_uuid"] = self.runner.project_uuid
 462         if self.uuid:
 463             self.runner.api.pipeline_templates().update(
 464                 uuid=self.uuid, body=body).execute(
 465                     num_retries=self.runner.num_retries)
 466             logger.info("Updated template %s", self.uuid)
 467         else:
 468             self.uuid = self.runner.api.pipeline_templates().create(
 469                 body=body, ensure_unique_name=True).execute(
 470                     num_retries=self.runner.num_retries)['uuid']
 471             logger.info("Created template %s", self.uuid)