[ARVADOS] created: 6bf3b279cd2d5ea5c1d6b849265b7206461467b8
Git user
git at public.curoverse.com
Wed Oct 19 11:44:49 EDT 2016
at 6bf3b279cd2d5ea5c1d6b849265b7206461467b8 (commit)
commit 6bf3b279cd2d5ea5c1d6b849265b7206461467b8
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Oct 19 11:44:12 2016 -0400
10291: Check discovery document before trying to choose/use a work API.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7ebb13f..f5f326b 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -58,7 +58,6 @@ class ArvCwlRunner(object):
self.uploaded = {}
self.num_retries = 4
self.uuid = None
- self.work_api = work_api
self.stop_polling = threading.Event()
self.poll_api = None
self.pipeline = None
@@ -71,12 +70,20 @@ class ArvCwlRunner(object):
else:
self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
- if self.work_api is None:
- # todo: autodetect API to use.
- self.work_api = "jobs"
-
- if self.work_api not in ("containers", "jobs"):
- raise Exception("Unsupported API '%s'" % self.work_api)
+ for api in ["jobs", "containers"]:
+ try:
+ methods = self.api._rootDesc.get('resources')[api]['methods']
+ if ('httpMethod' in methods['create'] and
+ (work_api == api or work_api is None)):
+ self.work_api = api
+ break
+ except KeyError:
+ pass
+ if not self.work_api:
+ if work_api is None:
+ raise Exception("No supported APIs")
+ else:
+ raise Exception("Unsupported API '%s'" % work_api)
def arv_make_tool(self, toolpath_object, **kwargs):
kwargs["work_api"] = self.work_api
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index db1c494..7abc567 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,10 +1,11 @@
+import functools
+import json
import logging
import mock
-import unittest
import os
-import functools
-import json
+import unittest
+import arvados
import arvados_cwl
import cwltool.process
from schema_salad.ref_resolver import Loader
@@ -215,7 +216,10 @@ class TestWorkflow(unittest.TestCase):
def test_run(self, mockcollection):
arvados_cwl.add_arv_hints()
- runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ api = mock.MagicMock()
+ api._rootDesc = arvados.api('v1')._rootDesc
+ runner = arvados_cwl.ArvCwlRunner(api)
+ self.assertEqual(runner.work_api, 'jobs')
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
@@ -270,3 +274,12 @@ class TestWorkflow(unittest.TestCase):
['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
+
+ def test_default_work_api(self):
+ arvados_cwl.add_arv_hints()
+
+ api = mock.MagicMock()
+ api._rootDesc = arvados.api('v1')._rootDesc
+ del api._rootDesc.get('resources')['jobs']['methods']['create']
+ runner = arvados_cwl.ArvCwlRunner(api)
+ self.assertEqual(runner.work_api, 'containers')
diff --git a/sdk/cwl/tests/test_make_output.py b/sdk/cwl/tests/test_make_output.py
index 2671297..cd66eb1 100644
--- a/sdk/cwl/tests/test_make_output.py
+++ b/sdk/cwl/tests/test_make_output.py
@@ -1,20 +1,24 @@
+import functools
+import json
import logging
import mock
-import unittest
import os
-import functools
-import json
import StringIO
+import unittest
+import arvados
import arvados_cwl
class TestMakeOutput(unittest.TestCase):
+ def setUp(self):
+ self.api = mock.MagicMock()
+ self.api._rootDesc = arvados.api('v1')._rootDesc
+
@mock.patch("arvados.collection.Collection")
@mock.patch("arvados.collection.CollectionReader")
def test_make_output_collection(self, reader, col):
- api = mock.MagicMock()
keep_client = mock.MagicMock()
- runner = arvados_cwl.ArvCwlRunner(api, keep_client=keep_client)
+ runner = arvados_cwl.ArvCwlRunner(self.api, keep_client=keep_client)
runner.project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
final = mock.MagicMock()
diff --git a/sdk/cwl/tests/test_pathmapper.py b/sdk/cwl/tests/test_pathmapper.py
index 7e13066..57958f7 100644
--- a/sdk/cwl/tests/test_pathmapper.py
+++ b/sdk/cwl/tests/test_pathmapper.py
@@ -21,10 +21,14 @@ def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPatter
c.fn = fnPattern % (pdh, os.path.basename(c.fn))
class TestPathmap(unittest.TestCase):
+ def setUp(self):
+ self.api = mock.MagicMock()
+ self.api._rootDesc = arvados.api('v1')._rootDesc
+
def test_keepref(self):
"""Test direct keep references."""
- arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ arvrunner = arvados_cwl.ArvCwlRunner(self.api)
p = ArvPathMapper(arvrunner, [{
"class": "File",
@@ -38,7 +42,7 @@ class TestPathmap(unittest.TestCase):
def test_upload(self, upl):
"""Test pathmapper uploading files."""
- arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ arvrunner = arvados_cwl.ArvCwlRunner(self.api)
upl.side_effect = upload_mock
@@ -54,7 +58,7 @@ class TestPathmap(unittest.TestCase):
def test_prev_uploaded(self, upl):
"""Test pathmapper handling previously uploaded files."""
- arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ arvrunner = arvados_cwl.ArvCwlRunner(self.api)
arvrunner.add_uploaded('tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='', type='File'))
upl.side_effect = upload_mock
@@ -71,7 +75,7 @@ class TestPathmap(unittest.TestCase):
@mock.patch("arvados.commands.run.statfile")
def test_statfile(self, statfile, upl):
"""Test pathmapper handling ArvFile references."""
- arvrunner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+ arvrunner = arvados_cwl.ArvCwlRunner(self.api)
# An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
# keep mount, so we can construct a direct reference directly without upload.
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index d3bdf8f..0ff9da9 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1,16 +1,17 @@
-import arvados
-import arvados.keep
-import arvados.collection
-import arvados_cwl
import copy
import cStringIO
import functools
import hashlib
+import json
+import logging
import mock
import sys
import unittest
-import json
-import logging
+
+import arvados
+import arvados.collection
+import arvados_cwl
+import arvados.keep
from .matcher import JsonDiffMatcher
@@ -38,6 +39,7 @@ def stubs(func):
stubs.api = mock.MagicMock()
+ stubs.api._rootDesc = arvados.api('v1')._rootDesc
stubs.api.users().current().execute.return_value = {
"uuid": stubs.fake_user_uuid,
}
commit 3ec9630b7d8b4be9d9ca149e45fa5d9cc4ea0f42
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Oct 19 11:30:31 2016 -0400
10291: Fix catching all exceptions in test case.
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 8d12aab..db1c494 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -213,62 +213,60 @@ class TestWorkflow(unittest.TestCase):
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.collection.Collection")
def test_run(self, mockcollection):
- try:
- arvados_cwl.add_arv_hints()
+ arvados_cwl.add_arv_hints()
- runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
- runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
- runner.ignore_docker_for_reuse = False
- runner.num_retries = 0
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+ runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
- tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
- metadata["cwlVersion"] = tool["cwlVersion"]
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ runner.num_retries = 0
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
- mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+ tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
+ metadata["cwlVersion"] = tool["cwlVersion"]
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
- arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
- basedir="", make_fs_access=make_fs_access, loader=document_loader,
- makeTool=runner.arv_make_tool, metadata=metadata)
- arvtool.formatgraph = None
- it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
- it.next().run()
- it.next().run()
+ mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
- with open("tests/wf/scatter2_subwf.cwl") as f:
- subwf = f.read()
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
+ basedir="", make_fs_access=make_fs_access, loader=document_loader,
+ makeTool=runner.arv_make_tool, metadata=metadata)
+ arvtool.formatgraph = None
+ it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
+ it.next().run()
+ it.next().run()
- mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
- mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+ with open("tests/wf/scatter2_subwf.cwl") as f:
+ subwf = f.read()
- runner.api.jobs().create.assert_called_with(
- body={
- 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
- 'repository': 'arvados',
- 'script_version': 'master',
- 'script': 'crunchrunner',
- 'script_parameters': {
- 'tasks': [{'task.env': {
- 'HOME': '$(task.outdir)',
- 'TMPDIR': '$(task.tmpdir)'},
- 'task.vwd': {
- 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
- 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
- },
- 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
- 'task.stdout': 'cwl.output.json'}]},
- 'runtime_constraints': {
- 'min_scratch_mb_per_node': 2048,
- 'min_cores_per_node': 1,
- 'docker_image': 'arvados/jobs',
- 'min_ram_mb_per_node': 1024
- },
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
- filters=[['repository', '=', 'arvados'],
- ['script', '=', 'crunchrunner'],
- ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
- ['docker_image_locator', 'in docker', 'arvados/jobs']],
- find_or_create=True)
- except:
- logging.exception("")
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
+ mockcollection().open().__enter__().write.assert_has_calls([mock.call('{sleeptime: 5}')])
+
+ runner.api.jobs().create.assert_called_with(
+ body={
+ 'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
+ 'repository': 'arvados',
+ 'script_version': 'master',
+ 'script': 'crunchrunner',
+ 'script_parameters': {
+ 'tasks': [{'task.env': {
+ 'HOME': '$(task.outdir)',
+ 'TMPDIR': '$(task.tmpdir)'},
+ 'task.vwd': {
+ 'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
+ 'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+ },
+ 'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
+ 'task.stdout': 'cwl.output.json'}]},
+ 'runtime_constraints': {
+ 'min_scratch_mb_per_node': 2048,
+ 'min_cores_per_node': 1,
+ 'docker_image': 'arvados/jobs',
+ 'min_ram_mb_per_node': 1024
+ },
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'},
+ filters=[['repository', '=', 'arvados'],
+ ['script', '=', 'crunchrunner'],
+ ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
+ ['docker_image_locator', 'in docker', 'arvados/jobs']],
+ find_or_create=True)
commit 787856704fb3e4421f0367eaca17c7743e844962
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Oct 19 11:32:44 2016 -0400
10291: Add config to disable API methods.
diff --git a/services/api/app/controllers/arvados/v1/schema_controller.rb b/services/api/app/controllers/arvados/v1/schema_controller.rb
index ba0f90f..2c55b15 100644
--- a/services/api/app/controllers/arvados/v1/schema_controller.rb
+++ b/services/api/app/controllers/arvados/v1/schema_controller.rb
@@ -399,6 +399,10 @@ class Arvados::V1::SchemaController < ApplicationController
end
end
end
+ Rails.configuration.disable_api_methods.each do |method|
+ ctrl, action = method.split('.', 2)
+ discovery[:resources][ctrl][:methods].delete(action.to_sym)
+ end
discovery
end
send_json discovery
diff --git a/services/api/config/application.default.yml b/services/api/config/application.default.yml
index bc752ed..b4b396a 100644
--- a/services/api/config/application.default.yml
+++ b/services/api/config/application.default.yml
@@ -264,6 +264,12 @@ common:
# Use at your own risk.
unlogged_attributes: []
+ # API methods to disable. Disabled methods are not listed in the
+ # discovery document. Note: currently, disabled methods are still
+ # accessible to clients that don't pay attention to the discovery
+ # document. Example: ["jobs.create"]
+ disable_api_methods: []
+
###
### Crunch, DNS & compute node management
###
diff --git a/services/api/test/functional/arvados/v1/schema_controller_test.rb b/services/api/test/functional/arvados/v1/schema_controller_test.rb
index f651d81..ee132f0 100644
--- a/services/api/test/functional/arvados/v1/schema_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/schema_controller_test.rb
@@ -42,4 +42,21 @@ class Arvados::V1::SchemaControllerTest < ActionController::TestCase
discovery_doc = JSON.parse(@response.body)
assert_equal 'aaa888fff', discovery_doc['source_version']
end
+
+ test "empty disable_api_methods" do
+ get :index
+ assert_response :success
+ discovery_doc = JSON.parse(@response.body)
+ assert_equal('POST',
+ discovery_doc['resources']['jobs']['methods']['create']['httpMethod'])
+ end
+
+ test "non-empty disable_api_methods" do
+ Rails.configuration.disable_api_methods = ['jobs.create']
+ get :index
+ assert_response :success
+ discovery_doc = JSON.parse(@response.body)
+ refute_includes(discovery_doc['resources']['jobs']['methods'].keys(),
+ 'create')
+ end
end
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