[arvados] updated: 2.7.0-6829-g6fa7f9fbcf
git repository hosting
git at public.arvados.org
Mon Jun 3 14:35:54 UTC 2024
Summary of changes:
build/run-build-packages-python-and-ruby.sh | 15 +-
cmd/arvados-server/arvados-controller.service | 2 -
cmd/arvados-server/arvados-dispatch-cloud.service | 2 -
cmd/arvados-server/arvados-dispatch-lsf.service | 2 -
cmd/arvados-server/arvados-health.service | 2 -
cmd/arvados-server/arvados-ws.service | 2 -
cmd/arvados-server/crunch-dispatch-slurm.service | 2 -
cmd/arvados-server/keep-balance.service | 2 -
cmd/arvados-server/keep-web.service | 2 -
cmd/arvados-server/keepproxy.service | 2 -
cmd/arvados-server/keepstore.service | 2 -
doc/admin/upgrading.html.textile.liquid | 4 +
doc/api/methods/groups.html.textile.liquid | 5 +-
...configure-s3-object-storage.html.textile.liquid | 13 +-
.../install-dispatch-cloud.html.textile.liquid | 6 +-
doc/sdk/cli/subcommands.html.textile.liquid | 65 +-
doc/sdk/fuse/options.html.textile.liquid | 29 +-
doc/sdk/python/api-client.html.textile.liquid | 9 +-
doc/user/reference/api-tokens.html.textile.liquid | 15 +-
doc/user/topics/arv-copy.html.textile.liquid | 54 +-
go.mod | 50 +-
go.sum | 128 +-
lib/cloud/ec2/ec2.go | 267 +-
lib/cloud/ec2/ec2_test.go | 179 +-
lib/config/config.default.yml | 1 -
lib/controller/router/request.go | 12 +-
lib/controller/router/request_test.go | 97 +-
lib/crunchrun/crunchrun.go | 22 +-
lib/crunchrun/crunchrun_test.go | 4 +-
lib/install/arvados.service | 1 -
lib/install/deps.go | 2 +-
lib/pam/docker_test.go | 2 +-
sdk/cwl/arvados_cwl/arvdocker.py | 9 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 2 +-
sdk/cwl/arvados_cwl/runner.py | 7 +-
sdk/cwl/setup.py | 4 +-
sdk/go/arvados/api.go | 4 +-
sdk/go/arvados/client.go | 10 -
sdk/go/arvados/config.go | 1 -
sdk/python/arvados-v1-discovery.json | 4 +-
sdk/python/arvados/api.py | 21 +-
sdk/python/arvados/arvfile.py | 62 +-
sdk/python/arvados/collection.py | 3 +-
sdk/python/arvados/commands/_util.py | 22 -
sdk/python/arvados/commands/arv_copy.py | 40 +-
sdk/python/arvados/commands/keepdocker.py | 14 +-
sdk/python/arvados/commands/put.py | 34 +-
sdk/python/arvados/config.py | 29 +-
sdk/python/arvados/keep.py | 3 +-
sdk/python/arvados/util.py | 171 +
sdk/python/tests/arvados_testutil.py | 8 -
sdk/python/tests/test_arv_copy.py | 70 +
sdk/python/tests/test_arv_keepdocker.py | 10 +
sdk/python/tests/test_arv_put.py | 73 +
sdk/python/tests/test_cache.py | 33 +-
sdk/python/tests/test_collections.py | 32 +-
sdk/python/tests/test_config.py | 58 +
sdk/python/tests/test_keep_client.py | 40 +-
sdk/python/tests/test_util.py | 182 +-
.../controllers/arvados/v1/groups_controller.rb | 47 +-
.../arvados/v1/groups_controller_test.rb | 37 +
services/api/test/integration/groups_test.rb | 17 +
.../crunch-dispatch-local.service | 3 -
services/fuse/arvados_fuse/__init__.py | 29 +-
services/fuse/arvados_fuse/command.py | 2 +-
services/fuse/arvados_fuse/fusefile.py | 2 +-
services/fuse/fpm-info.sh | 8 +-
services/fuse/tests/mount_test_base.py | 25 +-
services/keep-web/s3aws_test.go | 60 +-
services/keepstore/s3_volume.go | 227 +-
services/keepstore/s3_volume_test.go | 184 +-
services/keepstore/volume_generic_test.go | 2 +-
services/workbench2/config/env.js | 108 +
services/workbench2/config/getHttpsConfig.js | 70 +
services/workbench2/config/jest/babelTransform.js | 33 +
services/workbench2/config/jest/cssTransform.js | 18 +
services/workbench2/config/jest/fileTransform.js | 44 +
services/workbench2/config/modules.js | 138 +
services/workbench2/config/paths.js | 81 +
services/workbench2/config/webpack.config.js | 758 ++
.../persistentCache/createEnvironmentHash.js | 13 +
.../workbench2/config/webpackDevServer.config.js | 131 +
.../workbench2/cypress/e2e/banner-tooltip.cy.js | 27 +-
services/workbench2/cypress/e2e/details-card.cy.js | 271 +
.../cypress/e2e/multiselect-toolbar.cy.js | 9 +-
services/workbench2/cypress/e2e/workflow.cy.js | 25 +
services/workbench2/package.json | 122 +-
services/workbench2/scripts/build.js | 221 +
services/workbench2/scripts/start.js | 158 +
services/workbench2/scripts/test.js | 56 +
services/workbench2/src/common/redirect-to.test.ts | 22 +-
.../src/components/data-explorer/data-explorer.tsx | 38 +-
.../data-table-multiselect-popover.tsx | 4 +-
.../src/components/data-table/data-table.tsx | 34 +-
.../expand-chevron-right/expand-chevron-right.tsx | 48 +
services/workbench2/src/components/icon/icon.tsx | 7 +
.../multiselect-toolbar/MultiselectToolbar.tsx | 63 +-
.../ms-kind-action-differentiator.ts | 4 +-
.../multiselect-toolbar/ms-menu-actions.ts | 28 +
.../ms-toolbar-action-filters.ts | 7 +
.../ms-toolbar-overflow-menu.tsx | 4 +-
.../ms-toolbar-overflow-wrapper.tsx | 3 +-
.../components/search-input/search-input.test.tsx | 24 +-
services/workbench2/src/index.tsx | 2 +
services/workbench2/src/models/details.ts | 3 +-
services/workbench2/src/models/user.test.ts | 28 +-
services/workbench2/src/react-app-env.d.ts | 72 +-
.../api-client-authorization-service.test.ts | 10 +-
.../collection-service/collection-service.test.ts | 26 +-
.../common-service/common-resource-service.test.ts | 6 +-
.../project-service/project-service.test.ts | 6 +-
.../workbench2/src/store/auth/auth-reducer.test.ts | 16 +-
.../store/details-panel/details-panel-action.ts | 33 +-
.../groups-panel-middleware-service.test.ts | 4 +-
.../src/store/multiselect/multiselect-reducer.tsx | 8 +-
.../project-panel-middleware-service.ts | 2 +-
.../src/store/projects/project-lock-actions.ts | 18 +-
.../selected-resource/selected-resource-actions.ts | 17 +
.../selected-resource/selected-resource-reducer.ts | 14 +
.../side-panel-tree/side-panel-tree-actions.ts | 8 +-
services/workbench2/src/store/store.ts | 2 +
.../workbench2/src/store/users/users-actions.ts | 11 +-
.../store/workflow-panel/workflow-panel-actions.ts | 67 +-
.../auto-logout/auto-logout.test.tsx | 12 +-
.../src/views-components/baner/banner.tsx | 4 +-
.../action-sets/user-details-action-set.ts | 37 +
.../action-sets/workflow-action-set.ts | 10 +-
.../context-menu/context-menu-action-set.ts | 1 +
.../context-menu/menu-item-sort.ts | 11 +
.../data-explorer/data-explorer.tsx | 14 +-
.../views-components/data-explorer/renderers.tsx | 15 +-
.../details-card/details-card-root.tsx | 39 +
.../details-card/project-details-card.tsx | 303 +
.../details-card/user-details-card.tsx | 128 +
.../details-panel/details-panel.tsx | 33 +-
.../details-panel/project-details.tsx | 6 +-
.../details-panel/root-project-details.tsx | 74 +
.../main-content-bar/main-content-bar.tsx | 20 +-
.../multiselect-toolbar/ms-menu-actions.ts | 4 +-
.../multiselect-toolbar/ms-process-action-set.ts | 6 +-
.../multiselect-toolbar/ms-project-action-set.ts | 2 +-
.../ms-user-details-action-set.ts | 42 +
.../multiselect-toolbar/ms-workflow-action-set.ts | 12 +-
.../resource-properties-form/property-chip.tsx | 10 +-
.../resource-properties-form.tsx | 6 +-
.../search-bar/search-bar-view.test.tsx | 16 +-
.../side-panel-tree/side-panel-tree.tsx | 3 +
.../workflow-remove-dialog.tsx} | 8 +-
.../views/collection-panel/collection-panel.tsx | 2 +-
.../src/views/main-panel/main-panel-root.tsx | 21 +-
.../workbench2/src/views/main-panel/main-panel.tsx | 8 +-
.../src/views/project-panel/project-panel.tsx | 4 +
.../workbench2/src/views/workbench/workbench.tsx | 2 +
services/workbench2/yarn.lock | 10382 ++++++++-----------
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 4 +-
.../arvbox/docker/service/workbench2/run-service | 2 +-
tools/salt-install/provision.sh | 3 +-
tools/salt-install/tests/run-test.sh | 7 +
158 files changed, 9602 insertions(+), 7160 deletions(-)
create mode 100644 sdk/python/tests/test_config.py
create mode 100644 services/workbench2/config/env.js
create mode 100644 services/workbench2/config/getHttpsConfig.js
create mode 100644 services/workbench2/config/jest/babelTransform.js
create mode 100644 services/workbench2/config/jest/cssTransform.js
create mode 100644 services/workbench2/config/jest/fileTransform.js
create mode 100644 services/workbench2/config/modules.js
create mode 100644 services/workbench2/config/paths.js
create mode 100644 services/workbench2/config/webpack.config.js
create mode 100644 services/workbench2/config/webpack/persistentCache/createEnvironmentHash.js
create mode 100644 services/workbench2/config/webpackDevServer.config.js
create mode 100644 services/workbench2/cypress/e2e/details-card.cy.js
create mode 100644 services/workbench2/scripts/build.js
create mode 100644 services/workbench2/scripts/start.js
create mode 100644 services/workbench2/scripts/test.js
create mode 100644 services/workbench2/src/components/expand-chevron-right/expand-chevron-right.tsx
create mode 100644 services/workbench2/src/components/multiselect-toolbar/ms-menu-actions.ts
create mode 100644 services/workbench2/src/store/selected-resource/selected-resource-actions.ts
create mode 100644 services/workbench2/src/store/selected-resource/selected-resource-reducer.ts
create mode 100644 services/workbench2/src/views-components/context-menu/action-sets/user-details-action-set.ts
create mode 100644 services/workbench2/src/views-components/details-card/details-card-root.tsx
create mode 100644 services/workbench2/src/views-components/details-card/project-details-card.tsx
create mode 100644 services/workbench2/src/views-components/details-card/user-details-card.tsx
create mode 100644 services/workbench2/src/views-components/details-panel/root-project-details.tsx
create mode 100644 services/workbench2/src/views-components/multiselect-toolbar/ms-user-details-action-set.ts
copy services/workbench2/src/views-components/{process-remove-dialog/process-remove-dialog.tsx => workflow-remove-dialog/workflow-remove-dialog.tsx} (67%)
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 6fa7f9fbcf20aa866eed0618bd09e1ce2e109baa
Merge: e98e166cea 0c731f4151
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Mon Jun 3 10:16:17 2024 -0400
Merge branch 'main' into 15397-remove-obsolete-apis
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --cc doc/admin/upgrading.html.textile.liquid
index 3d2aa16f8e,4d4081e355..e5e930d539
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@@ -32,18 -32,10 +32,22 @@@ h2(#main). development mai
"previous: Upgrading to 2.7.1":#v2_7_1
+h3. Configuration entries have been removed or renamed
+
+The following configuration keys have been renamed or removed. Renamed keys will still be loaded if they appear with their old names, but you should update your @/etc/arvados/config.yml@ file to avoid warnings when services start up.
+* @Containers.JobsAPI.Enable@ has been removed
+* @Mail.EmailFrom@ has been removed
+* @Mail.IssueReporterEmailFrom@ has been removed
+* @Mail.IssueReporterEmailTo@ has been removed
+* @Mail.MailchimpAPIKey@ has been removed
+* @Mail.MailchimpListID@ has been removed
+* @Mail.SendUserSetupNotificationEmail@ has moved to @Users.SendUserSetupNotificationEmail@
+* @Mail.SupportEmailAddress@ has moved to @Users.SupportEmailAddress@
+
+ h3. S3 volume IAMRole configuration entry has been removed
+
+ The @Volumes.*.DriverParameters.IAMRole@ configuration entry for S3 volumes has been removed. You should remove it from your @/etc/arvados/config.yml@ file to avoid warnings when services start up. As before, if @AccessKeyID@ and @SecretAccessKey@ are blank, keepstore will retrieve IAM role credentials from instance metadata. Previously, documentation indicated that keepstore would refuse to use the IAM credentials if @IAMRole@ was specified and did not match the instance metadata, but that check has not been working for some time.
+
h3. Legacy container logging system has been removed
The following configuration keys are no longer supported. Remove them from your @/etc/arvados/config.yml@ file to avoid warnings when services start up.
diff --cc sdk/python/arvados-v1-discovery.json
index 27474d87c1,0dcec6bb20..6ee3741705
--- a/sdk/python/arvados-v1-discovery.json
+++ b/sdk/python/arvados-v1-discovery.json
@@@ -1923,32 -2757,11 +1923,32 @@@
"description": "Include items whose is_trashed attribute is true.",
"location": "query"
},
- "include": {
+ "uuid": {
"type": "string",
"required": false,
+ "default": "",
"description": "",
"location": "query"
+ },
+ "recursive": {
+ "type": "boolean",
+ "required": false,
+ "default": "false",
+ "description": "Include contents from child groups recursively.",
+ "location": "query"
+ },
+ "include": {
- "type": "string",
++ "type": "array",
+ "required": false,
- "description": "Include objects referred to by listed field in \"included\" (only owner_uuid).",
++ "description": "Include objects referred to by listed fields in \"included\" response field. Subsets of [\"owner_uuid\", \"container_uuid\"] are supported.",
+ "location": "query"
+ },
+ "include_old_versions": {
+ "type": "boolean",
+ "required": false,
+ "default": "false",
+ "description": "Include past collection versions.",
+ "location": "query"
}
},
"response": {
diff --cc sdk/python/arvados/util.py
index 63fee7093b,4f0c165e18..bc87bb8357
--- a/sdk/python/arvados/util.py
+++ b/sdk/python/arvados/util.py
@@@ -66,7 -75,16 +75,9 @@@ link_uuid_pattern = re.compile(r'[a-z0-
"""Regular expression to match any Arvados link UUID"""
user_uuid_pattern = re.compile(r'[a-z0-9]{5}-tpzed-[a-z0-9]{15}')
"""Regular expression to match any Arvados user UUID"""
-job_uuid_pattern = re.compile(r'[a-z0-9]{5}-8i9sb-[a-z0-9]{15}')
-"""Regular expression to match any Arvados job UUID
-
-.. WARNING:: Deprecated
- Arvados job resources are deprecated and will be removed in a future
- release. Prefer the containers API instead.
-"""
+ logger = logging.getLogger('arvados')
+
def _deprecated(version=None, preferred=None):
"""Mark a callable as deprecated in the SDK
diff --cc sdk/python/tests/test_collections.py
index 6671aa10b5,45e6056d19..ba59043536
--- a/sdk/python/tests/test_collections.py
+++ b/sdk/python/tests/test_collections.py
@@@ -7,21 -8,30 +8,27 @@@ import datetim
import os
import random
import re
+ import shutil
import sys
- import datetime
- import ciso8601
+ import tempfile
import time
import unittest
- import parameterized
+ import parameterized
from unittest import mock
+from . import run_test_server
+from arvados._ranges import Range, LocatorAndRange, locators_and_ranges
++
+ import arvados
+ import arvados.keep
++
from arvados.collection import Collection, CollectionReader
+ from arvados._ranges import Range, LocatorAndRange
+
from . import arvados_testutil as tutil
- from .arvados_testutil import make_block_cache
+ from . import run_test_server
-class TestResumableWriter(arvados.ResumableCollectionWriter):
- KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K.
-
- def current_state(self):
- return self.dump_state(copy.deepcopy)
-
-
@parameterized.parameterized_class([{"disk_cache": True}, {"disk_cache": False}])
class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
tutil.ArvadosBaseTestCase):
@@@ -36,18 -54,30 +51,23 @@@
cls.api_client = arvados.api('v1')
cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
local_store=cls.local_store,
- block_cache=make_block_cache(cls.disk_cache))
+ block_cache=block_cache)
+
+ @classmethod
+ def tearDownClass(cls):
+ if cls._disk_cache_dir:
+ shutil.rmtree(cls._disk_cache_dir)
def write_foo_bar_baz(self):
- cw = arvados.CollectionWriter(self.api_client)
- self.assertEqual(cw.current_stream_name(), '.',
- 'current_stream_name() should be "." now')
- cw.set_current_file_name('foo.txt')
- cw.write(b'foo')
- self.assertEqual(cw.current_file_name(), 'foo.txt',
- 'current_file_name() should be foo.txt now')
- cw.start_new_file('bar.txt')
- cw.write(b'bar')
- cw.start_new_stream('baz')
- cw.write(b'baz')
- cw.set_current_file_name('baz.txt')
- self.assertEqual(cw.manifest_text(),
- ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
- "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
- "wrong manifest: got {}".format(cw.manifest_text()))
+ with arvados.collection.Collection(api_client=self.api_client).open('zzz', 'wb') as f:
+ f.write(b'foobar')
+ f.flush()
+ f.write(b'baz')
+ cw = arvados.collection.Collection(
+ api_client=self.api_client,
+ manifest_locator_or_text=
+ ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
+ "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n")
cw.save_new()
return cw.portable_data_hash()
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