sdk/cwl/arvados_cwl/__init__.py

   1 #!/usr/bin/env python
   2 # Copyright (C) The Arvados Authors. All rights reserved.
   3 #
   4 # SPDX-License-Identifier: Apache-2.0
   5
   6 # Implement cwl-runner interface for submitting and running work on Arvados, using
   7 # either the Crunch jobs API or Crunch containers API.
   8
   9 import argparse
  10 import logging
  11 import os
  12 import sys
  13 import re
  14 import pkg_resources  # part of setuptools
  15
  16 import cwltool.main
  17 import cwltool.workflow
  18 import cwltool.process
  19 from schema_salad.sourceline import SourceLine
  20 import schema_salad.validate as validate
  21 import cwltool.argparser
  22
  23 import arvados
  24 import arvados.config
  25 from arvados.keep import KeepClient
  26 from arvados.errors import ApiError
  27 import arvados.commands._util as arv_cmd
  28
  29 from .perf import Perf
  30 from ._version import __version__
  31 from .executor import ArvCwlExecutor
  32
  33 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
  34 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
  35
  36 from arvados.api import OrderedJsonModel
  37
  38 logger = logging.getLogger('arvados.cwl-runner')
  39 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  40 logger.setLevel(logging.INFO)
  41
  42 arvados.log_handler.setFormatter(logging.Formatter(
  43         '%(asctime)s %(name)s %(levelname)s: %(message)s',
  44         '%Y-%m-%d %H:%M:%S'))
  45
  46 DEFAULT_PRIORITY = 500
  47
  48 def versionstring():
  49     """Print version string of key packages for provenance and debugging."""
  50
  51     arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
  52     arvpkg = pkg_resources.require("arvados-python-client")
  53     cwlpkg = pkg_resources.require("cwltool")
  54
  55     return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
  56                                     "arvados-python-client", arvpkg[0].version,
  57                                     "cwltool", cwlpkg[0].version)
  58
  59
  60 def arg_parser():  # type: () -> argparse.ArgumentParser
  61     parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
  62
  63     parser.add_argument("--basedir", type=str,
  64                         help="Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).")
  65     parser.add_argument("--outdir", type=str, default=os.path.abspath('.'),
  66                         help="Output directory, default current directory")
  67
  68     parser.add_argument("--eval-timeout",
  69                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
  70                         type=float,
  71                         default=20)
  72
  73     exgroup = parser.add_mutually_exclusive_group()
  74     exgroup.add_argument("--print-dot", action="store_true",
  75                          help="Print workflow visualization in graphviz format and exit")
  76     exgroup.add_argument("--version", action="version", help="Print version and exit", version=versionstring())
  77     exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
  78
  79     exgroup = parser.add_mutually_exclusive_group()
  80     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
  81     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
  82     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
  83
  84     parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
  85
  86     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
  87
  88     exgroup = parser.add_mutually_exclusive_group()
  89     exgroup.add_argument("--enable-reuse", action="store_true",
  90                         default=True, dest="enable_reuse",
  91                         help="Enable job or container reuse (default)")
  92     exgroup.add_argument("--disable-reuse", action="store_false",
  93                         default=True, dest="enable_reuse",
  94                         help="Disable job or container reuse")
  95
  96     parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
  97     parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
  98     parser.add_argument("--output-tags", type=str, help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
  99     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
 100                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
 101                         default=False)
 102
 103     exgroup = parser.add_mutually_exclusive_group()
 104     exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
 105                         default=True, dest="submit")
 106     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
 107                         default=True, dest="submit")
 108     exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
 109                          dest="create_workflow")
 110     exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.")
 111     exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.")
 112
 113     exgroup = parser.add_mutually_exclusive_group()
 114     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
 115                         default=True, dest="wait")
 116     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
 117                         default=True, dest="wait")
 118
 119     exgroup = parser.add_mutually_exclusive_group()
 120     exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
 121                         default=True, dest="log_timestamps")
 122     exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
 123                         default=True, dest="log_timestamps")
 124
 125     parser.add_argument("--api", type=str,
 126                         default=None, dest="work_api",
 127                         choices=("jobs", "containers"),
 128                         help="Select work submission API.  Default is 'jobs' if that API is available, otherwise 'containers'.")
 129
 130     parser.add_argument("--compute-checksum", action="store_true", default=False,
 131                         help="Compute checksum of contents while collecting outputs",
 132                         dest="compute_checksum")
 133
 134     parser.add_argument("--submit-runner-ram", type=int,
 135                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
 136                         default=None)
 137
 138     parser.add_argument("--submit-runner-image", type=str,
 139                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
 140                         default=None)
 141
 142     exgroup = parser.add_mutually_exclusive_group()
 143     exgroup.add_argument("--submit-request-uuid", type=str,
 144                         default=None,
 145                         help="Update and commit to supplied container request instead of creating a new one (containers API only).")
 146     exgroup.add_argument("--submit-runner-cluster", type=str,
 147                         help="Submit toplevel runner to a remote cluster (containers API only)",
 148                         default=None)
 149
 150     parser.add_argument("--name", type=str,
 151                         help="Name to use for workflow execution instance.",
 152                         default=None)
 153
 154     parser.add_argument("--on-error", type=str,
 155                         help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
 156                         "Default is 'continue'.", default="continue", choices=("stop", "continue"))
 157
 158     parser.add_argument("--enable-dev", action="store_true",
 159                         help="Enable loading and running development versions "
 160                              "of CWL spec.", default=False)
 161     parser.add_argument('--storage-classes', default="default", type=str,
 162                         help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
 163
 164     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
 165                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
 166                         default=0)
 167
 168     parser.add_argument("--priority", type=int,
 169                         help="Workflow priority (range 1..1000, higher has precedence over lower, containers api only)",
 170                         default=DEFAULT_PRIORITY)
 171
 172     parser.add_argument("--disable-validate", dest="do_validate",
 173                         action="store_false", default=True,
 174                         help=argparse.SUPPRESS)
 175
 176     parser.add_argument("--disable-js-validation",
 177                         action="store_true", default=False,
 178                         help=argparse.SUPPRESS)
 179
 180     parser.add_argument("--thread-count", type=int,
 181                         default=4, help="Number of threads to use for job submit and output collection.")
 182
 183     parser.add_argument("--http-timeout", type=int,
 184                         default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
 185
 186     exgroup = parser.add_mutually_exclusive_group()
 187     exgroup.add_argument("--trash-intermediate", action="store_true",
 188                         default=False, dest="trash_intermediate",
 189                          help="Immediately trash intermediate outputs on workflow success.")
 190     exgroup.add_argument("--no-trash-intermediate", action="store_false",
 191                         default=False, dest="trash_intermediate",
 192                         help="Do not trash intermediate outputs (default).")
 193
 194     parser.add_argument("workflow", type=str, default=None, help="The workflow to execute")
 195     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 196
 197     return parser
 198
 199 def add_arv_hints():
 200     cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
 201     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
 202     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
 203     use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
 204     res.close()
 205     cwltool.process.supportedProcessRequirements.extend([
 206         "http://arvados.org/cwl#RunInSingleContainer",
 207         "http://arvados.org/cwl#OutputDirType",
 208         "http://arvados.org/cwl#RuntimeConstraints",
 209         "http://arvados.org/cwl#PartitionRequirement",
 210         "http://arvados.org/cwl#APIRequirement",
 211         "http://commonwl.org/cwltool#LoadListingRequirement",
 212         "http://arvados.org/cwl#IntermediateOutput",
 213         "http://arvados.org/cwl#ReuseRequirement",
 214         "http://arvados.org/cwl#ClusterTarget"
 215     ])
 216
 217 def exit_signal_handler(sigcode, frame):
 218     logger.error("Caught signal {}, exiting.".format(sigcode))
 219     sys.exit(-sigcode)
 220
 221 def main(args, stdout, stderr, api_client=None, keep_client=None,
 222          install_sig_handlers=True):
 223     parser = arg_parser()
 224
 225     job_order_object = None
 226     arvargs = parser.parse_args(args)
 227
 228     if len(arvargs.storage_classes.strip().split(',')) > 1:
 229         logger.error("Multiple storage classes are not supported currently.")
 230         return 1
 231
 232     arvargs.use_container = True
 233     arvargs.relax_path_checks = True
 234     arvargs.print_supported_versions = False
 235
 236     if install_sig_handlers:
 237         arv_cmd.install_signal_handlers()
 238
 239     if arvargs.update_workflow:
 240         if arvargs.update_workflow.find('-7fd4e-') == 5:
 241             want_api = 'containers'
 242         elif arvargs.update_workflow.find('-p5p6p-') == 5:
 243             want_api = 'jobs'
 244         else:
 245             want_api = None
 246         if want_api and arvargs.work_api and want_api != arvargs.work_api:
 247             logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format(
 248                 arvargs.update_workflow, want_api, arvargs.work_api))
 249             return 1
 250         arvargs.work_api = want_api
 251
 252     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
 253         job_order_object = ({}, "")
 254
 255     add_arv_hints()
 256
 257     for key, val in cwltool.argparser.get_default_args().items():
 258         if not hasattr(arvargs, key):
 259             setattr(arvargs, key, val)
 260
 261     try:
 262         if api_client is None:
 263             api_client = arvados.safeapi.ThreadSafeApiCache(
 264                 api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
 265                 keep_params={"num_retries": 4})
 266             keep_client = api_client.keep
 267             # Make an API object now so errors are reported early.
 268             api_client.users().current().execute()
 269         if keep_client is None:
 270             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
 271         executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
 272     except Exception as e:
 273         logger.error(e)
 274         return 1
 275
 276     if arvargs.debug:
 277         logger.setLevel(logging.DEBUG)
 278         logging.getLogger('arvados').setLevel(logging.DEBUG)
 279
 280     if arvargs.quiet:
 281         logger.setLevel(logging.WARN)
 282         logging.getLogger('arvados').setLevel(logging.WARN)
 283         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 284
 285     if arvargs.metrics:
 286         metrics.setLevel(logging.DEBUG)
 287         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 288
 289     if arvargs.log_timestamps:
 290         arvados.log_handler.setFormatter(logging.Formatter(
 291             '%(asctime)s %(name)s %(levelname)s: %(message)s',
 292             '%Y-%m-%d %H:%M:%S'))
 293     else:
 294         arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
 295
 296     return cwltool.main.main(args=arvargs,
 297                              stdout=stdout,
 298                              stderr=stderr,
 299                              executor=executor.arv_executor,
 300                              versionfunc=versionstring,
 301                              job_order_object=job_order_object,
 302                              logger_handler=arvados.log_handler,
 303                              custom_schema_callback=add_arv_hints,
 304                              loadingContext=executor.loadingContext,
 305                              runtimeContext=executor.runtimeContext)