require 'test_helper'
class DisabledApiTest < ActiveSupport::TestCase
- test 'Job.creatable? reflects whether jobs.create API is enabled' do
- use_token(:active) do
- assert(Job.creatable?)
- end
- dd = ArvadosApiClient.new_or_current.discovery.deep_dup
- dd[:resources][:jobs][:methods].delete(:create)
- ArvadosApiClient.any_instance.stubs(:discovery).returns(dd)
+ test 'Job.creatable? is false' do
use_token(:active) do
refute(Job.creatable?)
end
AssignNodeHostname: "compute%<slot_number>d"
JobsAPI:
- # Enable the legacy Jobs API. This value must be a string.
+ # Enable the legacy 'jobs' API (crunch v1). This value must be a string.
+ #
+ # Note: this only enables read-only access, creating new
+ # legacy jobs and pipelines is not supported.
+ #
# 'auto' -- (default) enable the Jobs API only if it has been used before
# (i.e., there are job records in the database)
# 'true' -- enable the Jobs API despite lack of existing records.
# {git_repositories_dir}/arvados/.git
GitInternalDir: /var/lib/arvados/internal.git
- # Docker image to be used when none found in runtime_constraints of a job
- DefaultDockerImage: ""
-
- # none or slurm_immediate
- CrunchJobWrapper: none
-
- # username, or false = do not set uid when running jobs.
- CrunchJobUser: crunch
-
- # The web service must be able to create/write this file, and
- # crunch-job must be able to stat() it.
- CrunchRefreshTrigger: /tmp/crunch_refresh_trigger
-
- # Control job reuse behavior when two completed jobs match the
- # search criteria and have different outputs.
- #
- # If true, in case of a conflict, reuse the earliest job (this is
- # similar to container reuse behavior).
- #
- # If false, in case of a conflict, do not reuse any completed job,
- # but do reuse an already-running job if available (this is the
- # original job reuse behavior, and is still the default).
- ReuseJobIfOutputsDiffer: false
-
CloudVMs:
# Enable the cloud scheduler (experimental).
Enable: false
"net/http"
"os"
"testing"
- "time"
"git.curoverse.com/arvados.git/sdk/go/arvadostest"
. "gopkg.in/check.v1"
c.Assert(len(getback), Equals, 0)
}
-func (s *ServerRequiredSuite) TestCreatePipelineTemplate(c *C) {
- arv, err := MakeArvadosClient()
-
- for _, idleConnections := range []bool{
- false,
- true,
- } {
- if idleConnections {
- arv.lastClosedIdlesAt = time.Now().Add(-time.Minute)
- } else {
- arv.lastClosedIdlesAt = time.Now()
- }
-
- getback := make(Dict)
- err = arv.Create("pipeline_templates",
- Dict{"pipeline_template": Dict{
- "name": "tmp",
- "components": Dict{
- "c1": map[string]string{"script": "script1"},
- "c2": map[string]string{"script": "script2"}}}},
- &getback)
- c.Assert(err, Equals, nil)
- c.Assert(getback["name"], Equals, "tmp")
- c.Assert(getback["components"].(map[string]interface{})["c2"].(map[string]interface{})["script"], Equals, "script2")
-
- uuid := getback["uuid"].(string)
-
- getback = make(Dict)
- err = arv.Get("pipeline_templates", uuid, nil, &getback)
- c.Assert(err, Equals, nil)
- c.Assert(getback["name"], Equals, "tmp")
- c.Assert(getback["components"].(map[string]interface{})["c1"].(map[string]interface{})["script"], Equals, "script1")
-
- getback = make(Dict)
- err = arv.Update("pipeline_templates", uuid,
- Dict{
- "pipeline_template": Dict{"name": "tmp2"}},
- &getback)
- c.Assert(err, Equals, nil)
- c.Assert(getback["name"], Equals, "tmp2")
-
- c.Assert(getback["uuid"].(string), Equals, uuid)
- getback = make(Dict)
- err = arv.Delete("pipeline_templates", uuid, nil, &getback)
- c.Assert(err, Equals, nil)
- c.Assert(getback["name"], Equals, "tmp2")
- }
-}
-
func (s *ServerRequiredSuite) TestErrorResponse(c *C) {
arv, _ := MakeArvadosClient()
from arvados._version import __version__
-logger = logging.getLogger('arvados.arv-run')
-logger.setLevel(logging.INFO)
-
-arvrun_parser = argparse.ArgumentParser(parents=[arv_cmd.retry_opt])
-arvrun_parser.add_argument('--dry-run', action="store_true",
- help="Print out the pipeline that would be submitted and exit")
-arvrun_parser.add_argument('--local', action="store_true",
- help="Run locally using arv-run-pipeline-instance")
-arvrun_parser.add_argument('--docker-image', type=str,
- help="Docker image to use, otherwise use instance default.")
-arvrun_parser.add_argument('--ignore-rcode', action="store_true",
- help="Commands that return non-zero return codes should not be considered failed.")
-arvrun_parser.add_argument('--no-reuse', action="store_true",
- help="Do not reuse past jobs.")
-arvrun_parser.add_argument('--no-wait', action="store_true",
- help="Do not wait and display logs after submitting command, just exit.")
-arvrun_parser.add_argument('--project-uuid', type=str,
- help="Parent project of the pipeline")
-arvrun_parser.add_argument('--git-dir', type=str, default="",
- help="Git repository passed to arv-crunch-job when using --local")
-arvrun_parser.add_argument('--repository', type=str, default="arvados",
- help="repository field of component, default 'arvados'")
-arvrun_parser.add_argument('--script-version', type=str, default="master",
- help="script_version field of component, default 'master'")
-arvrun_parser.add_argument('--version', action='version',
- version="%s %s" % (sys.argv[0], __version__),
- help='Print version and exit.')
-arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
class ArvFile(object):
def __init__(self, prefix, fn):
def main(arguments=None):
- args = arvrun_parser.parse_args(arguments)
-
- if len(args.args) == 0:
- arvrun_parser.print_help()
- return
-
- starting_args = args.args
-
- reading_into = 2
-
- # Parse the command arguments into 'slots'.
- # All words following '>' are output arguments and are collected into slots[0].
- # All words following '<' are input arguments and are collected into slots[1].
- # slots[2..] store the parameters of each command in the pipeline.
- #
- # e.g. arv-run foo arg1 arg2 '|' bar arg3 arg4 '<' input1 input2 input3 '>' output.txt
- # will be parsed into:
- # [['output.txt'],
- # ['input1', 'input2', 'input3'],
- # ['foo', 'arg1', 'arg2'],
- # ['bar', 'arg3', 'arg4']]
- slots = [[], [], []]
- for c in args.args:
- if c.startswith('>'):
- reading_into = 0
- if len(c) > 1:
- slots[reading_into].append(c[1:])
- elif c.startswith('<'):
- reading_into = 1
- if len(c) > 1:
- slots[reading_into].append(c[1:])
- elif c == '|':
- reading_into = len(slots)
- slots.append([])
- else:
- slots[reading_into].append(c)
-
- if slots[0] and len(slots[0]) > 1:
- logger.error("Can only specify a single stdout file (run-command substitutions are permitted)")
- return
-
- if not args.dry_run:
- api = arvados.api('v1')
- if args.project_uuid:
- project = args.project_uuid
- else:
- project = determine_project(os.getcwd(), api.users().current().execute()["uuid"])
-
- # Identify input files. Look at each parameter and test to see if there is
- # a file by that name. This uses 'patterns' to look for within
- # command line arguments, such as --foo=file.txt or -lfile.txt
- patterns = [re.compile("([^=]+=)(.*)"),
- re.compile("(-[A-Za-z])(.+)")]
- for j, command in enumerate(slots[1:]):
- for i, a in enumerate(command):
- if j > 0 and i == 0:
- # j == 0 is stdin, j > 0 is commands
- # always skip program executable (i == 0) in commands
- pass
- elif a.startswith('\\'):
- # if it starts with a \ then don't do any interpretation
- command[i] = a[1:]
- else:
- # See if it looks like a file
- command[i] = statfile('', a)
-
- # If a file named command[i] was found, it would now be an
- # ArvFile or UploadFile. If command[i] is a basestring, that
- # means it doesn't correspond exactly to a file, so do some
- # pattern matching.
- if isinstance(command[i], basestring):
- for p in patterns:
- m = p.match(a)
- if m:
- command[i] = statfile(m.group(1), m.group(2))
- break
-
- files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)]
- if files:
- uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.retries, project=project)
-
- for i in range(1, len(slots)):
- slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]]
-
- component = {
- "script": "run-command",
- "script_version": args.script_version,
- "repository": args.repository,
- "script_parameters": {
- },
- "runtime_constraints": {}
- }
-
- if args.docker_image:
- component["runtime_constraints"]["docker_image"] = args.docker_image
-
- task_foreach = []
- group_parser = argparse.ArgumentParser()
- group_parser.add_argument('-b', '--batch-size', type=int)
- group_parser.add_argument('args', nargs=argparse.REMAINDER)
-
- for s in range(2, len(slots)):
- for i in range(0, len(slots[s])):
- if slots[s][i] == '--':
- inp = "input%i" % (s-2)
- groupargs = group_parser.parse_args(slots[2][i+1:])
- if groupargs.batch_size:
- component["script_parameters"][inp] = {"value": {"batch":groupargs.args, "size":groupargs.batch_size}}
- slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%s)" % inp}]
- else:
- component["script_parameters"][inp] = groupargs.args
- slots[s] = slots[s][0:i] + ["$(%s)" % inp]
- task_foreach.append(inp)
- break
- if slots[s][i] == '\--':
- slots[s][i] = '--'
-
- if slots[0]:
- component["script_parameters"]["task.stdout"] = slots[0][0]
- if slots[1]:
- task_foreach.append("stdin")
- component["script_parameters"]["stdin"] = slots[1]
- component["script_parameters"]["task.stdin"] = "$(stdin)"
-
- if task_foreach:
- component["script_parameters"]["task.foreach"] = task_foreach
-
- component["script_parameters"]["command"] = slots[2:]
- if args.ignore_rcode:
- component["script_parameters"]["task.ignore_rcode"] = args.ignore_rcode
-
- pipeline = {
- "name": "arv-run " + " | ".join([s[0] for s in slots[2:]]),
- "description": "@" + " ".join(starting_args) + "@",
- "components": {
- "command": component
- },
- "state": "RunningOnClient" if args.local else "RunningOnServer"
- }
-
- if args.dry_run:
- print(json.dumps(pipeline, indent=4))
- else:
- pipeline["owner_uuid"] = project
- pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute()
- logger.info("Running pipeline %s", pi["uuid"])
-
- if args.local:
- subprocess.call(["arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here"] + (["--no-reuse"] if args.no_reuse else []))
- elif not args.no_wait:
- ws.main(["--pipeline", pi["uuid"]])
-
- pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute()
- logger.info("Pipeline is %s", pi["state"])
- if "output_uuid" in pi["components"]["command"]:
- logger.info("Output is %s", pi["components"]["command"]["output_uuid"])
- else:
- logger.info("No output")
+ raise Exception("Legacy arv-run removed.")
if __name__ == '__main__':
main()
+++ /dev/null
-#!/usr/bin/env python
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-from arvados.commands.run import main
-main()
'bin/arv-federation-migrate',
'bin/arv-normalize',
'bin/arv-put',
- 'bin/arv-run',
'bin/arv-ws'
],
data_files=[
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-from __future__ import absolute_import
-import os
-import sys
-import tempfile
-import unittest
-
-import arvados.commands.run as arv_run
-from . import arvados_testutil as tutil
-
-class ArvRunTestCase(unittest.TestCase, tutil.VersionChecker):
- def run_arv_run(self, args):
- sys.argv = ['arv-run'] + args
- return arv_run.main()
-
- def test_unsupported_arg(self):
- with self.assertRaises(SystemExit):
- self.run_arv_run(['-x=unknown'])
-
- def test_version_argument(self):
- with tutil.redirected_streams(
- stdout=tutil.StringIO, stderr=tutil.StringIO) as (out, err):
- with self.assertRaises(SystemExit):
- self.run_arv_run(['--version'])
- self.assertVersionOutput(out, err)
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-from __future__ import absolute_import
-# usage example:
-#
-# ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover
-
-import unittest
-import arvados
-import apiclient
-from . import run_test_server
-
-class PipelineTemplateTest(run_test_server.TestCaseWithServers):
- MAIN_SERVER = {}
- KEEP_SERVER = {}
-
- def runTest(self):
- run_test_server.authorize_with("admin")
- pt_uuid = arvados.api('v1').pipeline_templates().create(
- body={'name':__file__}
- ).execute()['uuid']
- self.assertEqual(len(pt_uuid), 27,
- 'Unexpected format of pipeline template UUID ("%s")'
- % pt_uuid)
- components = {
- 'x': 'x',
- '-x-': [1,2,{'foo':'bar'}],
- 'Boggis': {'Bunce': '[\'Bean\']'},
- 'SpassBox': True,
- 'spass_box': False,
- 'spass-box': [True, 'Maybe', False]
- }
- update_response = arvados.api('v1').pipeline_templates().update(
- uuid=pt_uuid,
- body={'components':components}
- ).execute()
- self.assertEqual('uuid' in update_response, True,
- 'update() response did not include a uuid')
- self.assertEqual(update_response['uuid'], pt_uuid,
- 'update() response has a different uuid (%s, not %s)'
- % (update_response['uuid'], pt_uuid))
- self.assertEqual(update_response['name'], __file__,
- 'update() response has a different name (%s, not %s)'
- % (update_response['name'], __file__))
- get_response = arvados.api('v1').pipeline_templates().get(
- uuid=pt_uuid
- ).execute()
- self.assertEqual(get_response['components'], components,
- 'components got munged by server (%s -> %s)'
- % (components, update_response['components']))
- delete_response = arvados.api('v1').pipeline_templates().delete(
- uuid=pt_uuid
- ).execute()
- self.assertEqual(delete_response['uuid'], pt_uuid,
- 'delete() response has wrong uuid (%s, not %s)'
- % (delete_response['uuid'], pt_uuid))
- with self.assertRaises(apiclient.errors.HttpError):
- geterror_response = arvados.api('v1').pipeline_templates().get(
- uuid=pt_uuid
- ).execute()
def run_method(self):
arvados.current_job()
-
-
-class CurrentTaskTestCase(ApiClientRetryTestMixin, unittest.TestCase):
-
- DEFAULT_EXCEPTION = arvados.errors.ApiError
-
- def setUp(self):
- super(CurrentTaskTestCase, self).setUp()
- os.environ['TASK_UUID'] = 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
- os.environ['TASK_WORK'] = '.'
-
- def tearDown(self):
- del os.environ['TASK_UUID']
- del os.environ['TASK_WORK']
- arvados._current_task = None
- super(CurrentTaskTestCase, self).tearDown()
-
- def run_method(self):
- arvados.current_task()
-
-
-class TaskSetOutputTestCase(CurrentTaskTestCase, unittest.TestCase):
-
- DEFAULT_EXCEPTION = arvados.errors.ApiError
-
- def tearDown(self):
- super(TaskSetOutputTestCase, self).tearDown()
- run_test_server.reset()
-
- def run_method(self, locator=ApiClientRetryTestMixin.TEST_LOCATOR):
- arvados.task_set_output({'uuid':self.TEST_UUID},s=locator)
test 'enable legacy api configuration option = true' do
Rails.configuration.Containers.JobsAPI.Enable = "true"
check_enable_legacy_jobs_api
- assert_equal({}, Rails.configuration.API.DisabledAPIs)
+ assert_equal(Disable_update_jobs_api_method_list, Rails.configuration.API.DisabledAPIs)
end
test 'enable legacy api configuration option = false' do
Rails.configuration.Containers.JobsAPI.Enable = "auto"
assert Job.count > 0
check_enable_legacy_jobs_api
- assert_equal({}, Rails.configuration.API.DisabledAPIs)
+ assert_equal(Disable_update_jobs_api_method_list, Rails.configuration.API.DisabledAPIs)
end
test 'enable legacy api configuration option = auto, no jobs' do
projects / arvados.git / commitdiff