sdk/cwl/arvados_cwl/arvcontainer.py

   1 import logging
   2 import json
   3 import os
   4
   5 from cwltool.errors import WorkflowException
   6 from cwltool.process import get_feature, UnsupportedRequirement, shortname
   7 from cwltool.pathmapper import adjustFiles
   8 from cwltool.utils import aslist
   9
  10 import arvados.collection
  11
  12 from .arvdocker import arv_docker_get_image
  13 from . import done
  14 from .runner import Runner, arvados_jobs_image
  15
  16 logger = logging.getLogger('arvados.cwl-runner')
  17
  18 class ArvadosContainer(object):
  19     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
  20
  21     def __init__(self, runner):
  22         self.arvrunner = runner
  23         self.running = False
  24         self.uuid = None
  25
  26     def update_pipeline_component(self, r):
  27         pass
  28
  29     def run(self, dry_run=False, pull_image=True, **kwargs):
  30         container_request = {
  31             "command": self.command_line,
  32             "owner_uuid": self.arvrunner.project_uuid,
  33             "name": self.name,
  34             "output_path": self.outdir,
  35             "cwd": self.outdir,
  36             "priority": 1,
  37             "state": "Committed"
  38         }
  39         runtime_constraints = {}
  40         mounts = {
  41             self.outdir: {
  42                 "kind": "tmp"
  43             }
  44         }
  45         scheduling_parameters = {}
  46
  47         dirs = set()
  48         for f in self.pathmapper.files():
  49             _, p, tp = self.pathmapper.mapper(f)
  50             if tp == "Directory" and '/' not in p[6:]:
  51                 mounts[p] = {
  52                     "kind": "collection",
  53                     "portable_data_hash": p[6:]
  54                 }
  55                 dirs.add(p[6:])
  56         for f in self.pathmapper.files():
  57             _, p, tp = self.pathmapper.mapper(f)
  58             if p[6:].split("/")[0] not in dirs:
  59                 mounts[p] = {
  60                     "kind": "collection",
  61                     "portable_data_hash": p[6:]
  62                 }
  63
  64         if self.generatefiles["listing"]:
  65             raise UnsupportedRequirement("Generate files not supported")
  66
  67         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
  68         if self.environment:
  69             container_request["environment"].update(self.environment)
  70
  71         if self.stdin:
  72             raise UnsupportedRequirement("Stdin redirection currently not suppported")
  73
  74         if self.stderr:
  75             raise UnsupportedRequirement("Stderr redirection currently not suppported")
  76
  77         if self.stdout:
  78             mounts["stdout"] = {"kind": "file",
  79                                 "path": "%s/%s" % (self.outdir, self.stdout)}
  80
  81         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
  82         if not docker_req:
  83             docker_req = {"dockerImageId": arvados_jobs_image(self.arvrunner)}
  84
  85         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
  86                                                                      docker_req,
  87                                                                      pull_image,
  88                                                                      self.arvrunner.project_uuid)
  89
  90         resources = self.builder.resources
  91         if resources is not None:
  92             runtime_constraints["vcpus"] = resources.get("cores", 1)
  93             runtime_constraints["ram"] = resources.get("ram") * 2**20
  94
  95         api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
  96         if api_req:
  97             runtime_constraints["API"] = True
  98
  99         runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
 100         if runtime_req:
 101             if "keep_cache" in runtime_req:
 102                 runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
 103
 104         partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
 105         if partition_req:
 106             scheduling_parameters["partitions"] = aslist(partition_req["partition"])
 107
 108         container_request["mounts"] = mounts
 109         container_request["runtime_constraints"] = runtime_constraints
 110         container_request["use_existing"] = kwargs.get("enable_reuse", True)
 111         container_request["scheduling_parameters"] = scheduling_parameters
 112
 113         try:
 114             response = self.arvrunner.api.container_requests().create(
 115                 body=container_request
 116             ).execute(num_retries=self.arvrunner.num_retries)
 117
 118             self.arvrunner.processes[response["container_uuid"]] = self
 119
 120             container = self.arvrunner.api.containers().get(
 121                 uuid=response["container_uuid"]
 122             ).execute(num_retries=self.arvrunner.num_retries)
 123
 124             logger.info("Container request %s (%s) state is %s with container %s %s", self.name, response["uuid"], response["state"], container["uuid"], container["state"])
 125
 126             if container["state"] in ("Complete", "Cancelled"):
 127                 self.done(container)
 128         except Exception as e:
 129             logger.error("Got error %s" % str(e))
 130             self.output_callback({}, "permanentFail")
 131
 132     def done(self, record):
 133         try:
 134             if record["state"] == "Complete":
 135                 rcode = record["exit_code"]
 136                 if self.successCodes and rcode in self.successCodes:
 137                     processStatus = "success"
 138                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 139                     processStatus = "temporaryFail"
 140                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 141                     processStatus = "permanentFail"
 142                 elif rcode == 0:
 143                     processStatus = "success"
 144                 else:
 145                     processStatus = "permanentFail"
 146             else:
 147                 processStatus = "permanentFail"
 148
 149             try:
 150                 outputs = {}
 151                 if record["output"]:
 152                     outputs = done.done(self, record, "/tmp", self.outdir, "/keep")
 153             except WorkflowException as e:
 154                 logger.error("Error while collecting container outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
 155                 processStatus = "permanentFail"
 156             except Exception as e:
 157                 logger.exception("Got unknown exception while collecting job outputs:")
 158                 processStatus = "permanentFail"
 159
 160             self.output_callback(outputs, processStatus)
 161         finally:
 162             del self.arvrunner.processes[record["uuid"]]
 163
 164
 165 class RunnerContainer(Runner):
 166     """Submit and manage a container that runs arvados-cwl-runner."""
 167
 168     def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
 169         """Create an Arvados container request for this workflow.
 170
 171         The returned dict can be used to create a container passed as
 172         the +body+ argument to container_requests().create().
 173         """
 174
 175         workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
 176
 177         with arvados.collection.Collection(api_client=self.arvrunner.api,
 178                                            keep_client=self.arvrunner.keep_client,
 179                                            num_retries=self.arvrunner.num_retries) as jobobj:
 180             with jobobj.open("cwl.input.json", "w") as f:
 181                 json.dump(self.job_order, f, sort_keys=True, indent=4)
 182             jobobj.save_new(owner_uuid=self.arvrunner.project_uuid)
 183
 184         workflowname = os.path.basename(self.tool.tool["id"])
 185         workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 186         workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
 187         workflowcollection = workflowcollection[5:workflowcollection.index('/')]
 188         jobpath = "/var/lib/cwl/job/cwl.input.json"
 189
 190         command = ["arvados-cwl-runner", "--local", "--api=containers"]
 191         if self.output_name:
 192             command.append("--output-name=" + self.output_name)
 193
 194         if self.output_tags:
 195             command.append("--output-tags=" + self.output_tags)
 196
 197         if self.enable_reuse:
 198             command.append("--enable-reuse")
 199         else:
 200             command.append("--disable-reuse")
 201
 202         command.extend([workflowpath, jobpath])
 203
 204         return {
 205             "command": command,
 206             "owner_uuid": self.arvrunner.project_uuid,
 207             "name": self.name,
 208             "output_path": "/var/spool/cwl",
 209             "cwd": "/var/spool/cwl",
 210             "priority": 1,
 211             "state": "Committed",
 212             "container_image": arvados_jobs_image(self.arvrunner),
 213             "mounts": {
 214                 "/var/lib/cwl/workflow": {
 215                     "kind": "collection",
 216                     "portable_data_hash": "%s" % workflowcollection
 217                 },
 218                 jobpath: {
 219                     "kind": "collection",
 220                     "portable_data_hash": "%s/cwl.input.json" % jobobj.portable_data_hash()
 221                 },
 222                 "stdout": {
 223                     "kind": "file",
 224                     "path": "/var/spool/cwl/cwl.output.json"
 225                 },
 226                 "/var/spool/cwl": {
 227                     "kind": "collection",
 228                     "writable": True
 229                 }
 230             },
 231             "runtime_constraints": {
 232                 "vcpus": 1,
 233                 "ram": 1024*1024*256,
 234                 "API": True
 235             }
 236         }
 237
 238     def run(self, *args, **kwargs):
 239         kwargs["keepprefix"] = "keep:"
 240         job_spec = self.arvados_job_spec(*args, **kwargs)
 241         job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
 242
 243         response = self.arvrunner.api.container_requests().create(
 244             body=job_spec
 245         ).execute(num_retries=self.arvrunner.num_retries)
 246
 247         self.uuid = response["uuid"]
 248         self.arvrunner.processes[response["container_uuid"]] = self
 249
 250         logger.info("Submitted container %s", response["uuid"])
 251
 252         if response["state"] in ("Complete", "Failed", "Cancelled"):
 253             self.done(response)