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         try:
 138             with Perf(metrics, "create %s" % self.name):
 139                 response = self.arvrunner.api.jobs().create(
 140                     body={
 141                         "owner_uuid": self.arvrunner.project_uuid,
 142                         "script": "crunchrunner",
 143                         "repository": "arvados",
 144                         "script_version": "master",
 145                         "minimum_script_version": crunchrunner_git_commit,
 146                         "script_parameters": {"tasks": [script_parameters]},
 147                         "runtime_constraints": runtime_constraints
 148                     },
 149                     filters=filters,
 150                     find_or_create=enable_reuse
 151                 ).execute(num_retries=self.arvrunner.num_retries)
 152
 153             self.uuid = response["uuid"]
 154             self.arvrunner.process_submitted(self)
 155
 156             self.update_pipeline_component(response)
 157
 158             if response["state"] == "Complete":
 159                 logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
 160                 # Give read permission to the desired project on reused jobs
 161                 if response["owner_uuid"] != self.arvrunner.project_uuid:
 162                     try:
 163                         self.arvrunner.api.links().create(body={
 164                             'link_class': 'permission',
 165                             'name': 'can_read',
 166                             'tail_uuid': self.arvrunner.project_uuid,
 167                             'head_uuid': response["uuid"],
 168                             }).execute(num_retries=self.arvrunner.num_retries)
 169                     except ApiError as e:
 170                         # The user might not have "manage" access on the job: log
 171                         # a message and continue.
 172                         logger.info("Creating read permission on job %s: %s",
 173                                     response["uuid"],
 174                                     e)
 175
 176                 with Perf(metrics, "done %s" % self.name):
 177                     self.done(response)
 178             else:
 179                 logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 180         except Exception as e:
 181             logger.exception("%s error" % (self.arvrunner.label(self)))
 182             self.output_callback({}, "permanentFail")
 183
 184     def update_pipeline_component(self, record):
 185         if self.arvrunner.pipeline:
 186             self.arvrunner.pipeline["components"][self.name] = {"job": record}
 187             with Perf(metrics, "update_pipeline_component %s" % self.name):
 188                 self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
 189                     uuid=self.arvrunner.pipeline["uuid"],
 190                     body={
 191                         "components": self.arvrunner.pipeline["components"]
 192                     }).execute(num_retries=self.arvrunner.num_retries)
 193         if self.arvrunner.uuid:
 194             try:
 195                 job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
 196                 if job:
 197                     components = job["components"]
 198                     components[self.name] = record["uuid"]
 199                     self.arvrunner.api.jobs().update(
 200                         uuid=self.arvrunner.uuid,
 201                         body={
 202                             "components": components
 203                         }).execute(num_retries=self.arvrunner.num_retries)
 204             except Exception as e:
 205                 logger.info("Error adding to components: %s", e)
 206
 207     def done(self, record):
 208         try:
 209             self.update_pipeline_component(record)
 210         except:
 211             pass
 212
 213         try:
 214             if record["state"] == "Complete":
 215                 processStatus = "success"
 216             else:
 217                 processStatus = "permanentFail"
 218
 219             outputs = {}
 220             try:
 221                 if record["output"]:
 222                     with Perf(metrics, "inspect log %s" % self.name):
 223                         logc = arvados.collection.CollectionReader(record["log"],
 224                                                                    api_client=self.arvrunner.api,
 225                                                                    keep_client=self.arvrunner.keep_client,
 226                                                                    num_retries=self.arvrunner.num_retries)
 227                         log = logc.open(logc.keys()[0])
 228                         dirs = {
 229                             "tmpdir": "/tmpdir",
 230                             "outdir": "/outdir",
 231                             "keep": "/keep"
 232                         }
 233                         for l in log:
 234                             # Determine the tmpdir, outdir and keep paths from
 235                             # the job run.  Unfortunately, we can't take the first
 236                             # values we find (which are expected to be near the
 237                             # top) and stop scanning because if the node fails and
 238                             # the job restarts on a different node these values
 239                             # will different runs, and we need to know about the
 240                             # final run that actually produced output.
 241                             g = crunchrunner_re.match(l)
 242                             if g:
 243                                 dirs[g.group(1)] = g.group(2)
 244
 245                     if processStatus == "permanentFail":
 246                         done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
 247
 248                     with Perf(metrics, "output collection %s" % self.name):
 249                         outputs = done.done(self, record, dirs["tmpdir"],
 250                                             dirs["outdir"], dirs["keep"])
 251             except WorkflowException as e:
 252                 logger.error("%s unable to collect output from %s:\n%s",
 253                              self.arvrunner.label(self), record["output"], e, exc_info=(e if self.arvrunner.debug else False))
 254                 processStatus = "permanentFail"
 255             except Exception as e:
 256                 logger.exception("Got unknown exception while collecting output for job %s:", self.name)
 257                 processStatus = "permanentFail"
 258
 259             # Note: Currently, on error output_callback is expecting an empty dict,
 260             # anything else will fail.
 261             if not isinstance(outputs, dict):
 262                 logger.error("Unexpected output type %s '%s'", type(outputs), outputs)
 263                 outputs = {}
 264                 processStatus = "permanentFail"
 265         finally:
 266             self.output_callback(outputs, processStatus)
 267             self.arvrunner.process_done(record["uuid"])
 268
 269
 270 class RunnerJob(Runner):
 271     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
 272
 273     def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
 274         """Create an Arvados job specification for this workflow.
 275
 276         The returned dict can be used to create a job (i.e., passed as
 277         the +body+ argument to jobs().create()), or as a component in
 278         a pipeline template or pipeline instance.
 279         """
 280
 281         if self.tool.tool["id"].startswith("keep:"):
 282             self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
 283         else:
 284             packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
 285             wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
 286             self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
 287
 288         adjustDirObjs(self.job_order, trim_listing)
 289         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 290         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 291
 292         if self.output_name:
 293             self.job_order["arv:output_name"] = self.output_name
 294
 295         if self.output_tags:
 296             self.job_order["arv:output_tags"] = self.output_tags
 297
 298         self.job_order["arv:enable_reuse"] = self.enable_reuse
 299
 300         if self.on_error:
 301             self.job_order["arv:on_error"] = self.on_error
 302
 303         if kwargs.get("debug"):
 304             self.job_order["arv:debug"] = True
 305
 306         return {
 307             "script": "cwl-runner",
 308             "script_version": "master",
 309             "minimum_script_version": "570509ab4d2ef93d870fd2b1f2eab178afb1bad9",
 310             "repository": "arvados",
 311             "script_parameters": self.job_order,
 312             "runtime_constraints": {
 313                 "docker_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
 314                 "min_ram_mb_per_node": self.submit_runner_ram
 315             }
 316         }
 317
 318     def run(self, *args, **kwargs):
 319         job_spec = self.arvados_job_spec(*args, **kwargs)
 320
 321         job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
 322
 323         job = self.arvrunner.api.jobs().create(
 324             body=job_spec,
 325             find_or_create=self.enable_reuse
 326         ).execute(num_retries=self.arvrunner.num_retries)
 327
 328         for k,v in job_spec["script_parameters"].items():
 329             if v is False or v is None or isinstance(v, dict):
 330                 job_spec["script_parameters"][k] = {"value": v}
 331
 332         del job_spec["owner_uuid"]
 333         job_spec["job"] = job
 334
 335         instance_spec = {
 336             "owner_uuid": self.arvrunner.project_uuid,
 337             "name": self.name,
 338             "components": {
 339                 "cwl-runner": job_spec,
 340             },
 341             "state": "RunningOnServer",
 342         }
 343         if not self.enable_reuse:
 344             instance_spec["properties"] = {"run_options": {"enable_job_reuse": False}}
 345
 346         self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
 347             body=instance_spec).execute(num_retries=self.arvrunner.num_retries)
 348         logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"])
 349
 350         if kwargs.get("wait") is False:
 351             self.uuid = self.arvrunner.pipeline["uuid"]
 352             return
 353
 354         self.uuid = job["uuid"]
 355         self.arvrunner.process_submitted(self)
 356
 357         if job["state"] in ("Complete", "Failed", "Cancelled"):
 358             self.done(job)
 359
 360
 361 class RunnerTemplate(object):
 362     """An Arvados pipeline template that invokes a CWL workflow."""
 363
 364     type_to_dataclass = {
 365         'boolean': 'boolean',
 366         'File': 'File',
 367         'Directory': 'Collection',
 368         'float': 'number',
 369         'int': 'number',
 370         'string': 'text',
 371     }
 372
 373     def __init__(self, runner, tool, job_order, enable_reuse, uuid,
 374                  submit_runner_ram=0, name=None, merged_map=None):
 375         self.runner = runner
 376         self.tool = tool
 377         self.job = RunnerJob(
 378             runner=runner,
 379             tool=tool,
 380             job_order=job_order,
 381             enable_reuse=enable_reuse,
 382             output_name=None,
 383             output_tags=None,
 384             submit_runner_ram=submit_runner_ram,
 385             name=name,
 386             merged_map=merged_map)
 387         self.uuid = uuid
 388
 389     def pipeline_component_spec(self):
 390         """Return a component that Workbench and a-r-p-i will understand.
 391
 392         Specifically, translate CWL input specs to Arvados pipeline
 393         format, like {"dataclass":"File","value":"xyz"}.
 394         """
 395
 396         spec = self.job.arvados_job_spec()
 397
 398         # Most of the component spec is exactly the same as the job
 399         # spec (script, script_version, etc.).
 400         # spec['script_parameters'] isn't right, though. A component
 401         # spec's script_parameters hash is a translation of
 402         # self.tool.tool['inputs'] with defaults/overrides taken from
 403         # the job order. So we move the job parameters out of the way
 404         # and build a new spec['script_parameters'].
 405         job_params = spec['script_parameters']
 406         spec['script_parameters'] = {}
 407
 408         for param in self.tool.tool['inputs']:
 409             param = copy.deepcopy(param)
 410
 411             # Data type and "required" flag...
 412             types = param['type']
 413             if not isinstance(types, list):
 414                 types = [types]
 415             param['required'] = 'null' not in types
 416             non_null_types = [t for t in types if t != "null"]
 417             if len(non_null_types) == 1:
 418                 the_type = [c for c in non_null_types][0]
 419                 dataclass = None
 420                 if isinstance(the_type, basestring):
 421                     dataclass = self.type_to_dataclass.get(the_type)
 422                 if dataclass:
 423                     param['dataclass'] = dataclass
 424             # Note: If we didn't figure out a single appropriate
 425             # dataclass, we just left that attribute out.  We leave
 426             # the "type" attribute there in any case, which might help
 427             # downstream.
 428
 429             # Title and description...
 430             title = param.pop('label', '')
 431             descr = param.pop('doc', '').rstrip('\n')
 432             if title:
 433                 param['title'] = title
 434             if descr:
 435                 param['description'] = descr
 436
 437             # Fill in the value from the current job order, if any.
 438             param_id = shortname(param.pop('id'))
 439             value = job_params.get(param_id)
 440             if value is None:
 441                 pass
 442             elif not isinstance(value, dict):
 443                 param['value'] = value
 444             elif param.get('dataclass') in ('File', 'Collection') and value.get('location'):
 445                 param['value'] = value['location'][5:]
 446
 447             spec['script_parameters'][param_id] = param
 448         spec['script_parameters']['cwl:tool'] = job_params['cwl:tool']
 449         return spec
 450
 451     def save(self):
 452         body = {
 453             "components": {
 454                 self.job.name: self.pipeline_component_spec(),
 455             },
 456             "name": self.job.name,
 457         }
 458         if self.runner.project_uuid:
 459             body["owner_uuid"] = self.runner.project_uuid
 460         if self.uuid:
 461             self.runner.api.pipeline_templates().update(
 462                 uuid=self.uuid, body=body).execute(
 463                     num_retries=self.runner.num_retries)
 464             logger.info("Updated template %s", self.uuid)
 465         else:
 466             self.uuid = self.runner.api.pipeline_templates().create(
 467                 body=body, ensure_unique_name=True).execute(
 468                     num_retries=self.runner.num_retries)['uuid']
 469             logger.info("Created template %s", self.uuid)