sdk/python/tests/fed-migrate/*.cwl
sdk/python/tests/fed-migrate/*.cwlex
doc/install/*.xlsx
+sdk/cwl/tests/wf/hello.txt
+sdk/cwl/tests/wf/indir1/hello2.txt
\ No newline at end of file
Now that Python 3 is part of the base repository in CentOS 7, the Python 3 dependency for Centos7 Arvados packages was changed from SCL rh-python36 to python3.
+h3. ForceLegacyAPI14 option removed
+
+The ForceLegacyAPI14 configuration option has been removed. In the unlikely event it is mentioned in your config file, remove it to avoid "deprecated/unknown config" warning logs.
+
h2(#v2_1_0). v2.1.0 (2020-10-13)
"Upgrading from 2.0.0":#v2_0_0
# ID > Web application) and add your controller's /login URL
# (e.g., "https://zzzzz.example.com/login") as an authorized
# redirect URL.
- #
- # Incompatible with ForceLegacyAPI14. ProviderAppID must be
- # blank.
ClientID: ""
ClientSecret: ""
# this blank.
SSHHelpHostSuffix: ""
- # Bypass new (Arvados 1.5) API implementations, and hand off
- # requests directly to Rails instead. This can provide a temporary
- # workaround for clients that are incompatible with the new API
- # implementation. Note that it also disables some new federation
- # features and will be removed in a future release.
- ForceLegacyAPI14: false
-
# (Experimental) Restart services automatically when config file
# changes are detected. Only supported by `arvados-server boot` in
# dev/test mode.
"Containers.SupportedDockerImageFormats": true,
"Containers.SupportedDockerImageFormats.*": true,
"Containers.UsePreemptibleInstances": true,
- "ForceLegacyAPI14": false,
"Git": false,
"InstanceTypes": true,
"InstanceTypes.*": true,
# ID > Web application) and add your controller's /login URL
# (e.g., "https://zzzzz.example.com/login") as an authorized
# redirect URL.
- #
- # Incompatible with ForceLegacyAPI14. ProviderAppID must be
- # blank.
ClientID: ""
ClientSecret: ""
# this blank.
SSHHelpHostSuffix: ""
- # Bypass new (Arvados 1.5) API implementations, and hand off
- # requests directly to Rails instead. This can provide a temporary
- # workaround for clients that are incompatible with the new API
- # implementation. Note that it also disables some new federation
- # features and will be removed in a future release.
- ForceLegacyAPI14: false
-
# (Experimental) Restart services automatically when config file
# changes are detected. Only supported by ` + "`" + `arvados-server boot` + "`" + ` in
# dev/test mode.
s.fakeProvider.ValidClientSecret = "test#client/secret"
cluster := &arvados.Cluster{
- ClusterID: "zhome",
- PostgreSQL: integrationTestCluster().PostgreSQL,
- ForceLegacyAPI14: forceLegacyAPI14,
- SystemRootToken: arvadostest.SystemRootToken,
+ ClusterID: "zhome",
+ PostgreSQL: integrationTestCluster().PostgreSQL,
+ SystemRootToken: arvadostest.SystemRootToken,
}
cluster.TLS.Insecure = true
cluster.API.MaxItemsPerResponse = 1000
c.Assert(s.remoteMock.Start(), check.IsNil)
cluster := &arvados.Cluster{
- ClusterID: "zhome",
- PostgreSQL: integrationTestCluster().PostgreSQL,
- ForceLegacyAPI14: forceLegacyAPI14,
+ ClusterID: "zhome",
+ PostgreSQL: integrationTestCluster().PostgreSQL,
}
cluster.TLS.Insecure = true
cluster.API.MaxItemsPerResponse = 1000
oidcAuthorizer := localdb.OIDCAccessTokenAuthorizer(h.Cluster, h.db)
rtr := router.New(federation.New(h.Cluster), api.ComposeWrappers(ctrlctx.WrapCallsInTransactions(h.db), oidcAuthorizer.WrapCalls))
mux.Handle("/arvados/v1/config", rtr)
- mux.Handle("/"+arvados.EndpointUserAuthenticate.Path, rtr)
-
- if !h.Cluster.ForceLegacyAPI14 {
- mux.Handle("/arvados/v1/collections", rtr)
- mux.Handle("/arvados/v1/collections/", rtr)
- mux.Handle("/arvados/v1/users", rtr)
- mux.Handle("/arvados/v1/users/", rtr)
- mux.Handle("/arvados/v1/connect/", rtr)
- mux.Handle("/arvados/v1/container_requests", rtr)
- mux.Handle("/arvados/v1/container_requests/", rtr)
- mux.Handle("/arvados/v1/groups", rtr)
- mux.Handle("/arvados/v1/groups/", rtr)
- mux.Handle("/login", rtr)
- mux.Handle("/logout", rtr)
- }
+ mux.Handle("/"+arvados.EndpointUserAuthenticate.Path, rtr) // must come before .../users/
+ mux.Handle("/arvados/v1/collections", rtr)
+ mux.Handle("/arvados/v1/collections/", rtr)
+ mux.Handle("/arvados/v1/users", rtr)
+ mux.Handle("/arvados/v1/users/", rtr)
+ mux.Handle("/arvados/v1/connect/", rtr)
+ mux.Handle("/arvados/v1/container_requests", rtr)
+ mux.Handle("/arvados/v1/container_requests/", rtr)
+ mux.Handle("/arvados/v1/groups", rtr)
+ mux.Handle("/arvados/v1/groups/", rtr)
+ mux.Handle("/login", rtr)
+ mux.Handle("/logout", rtr)
hs := http.NotFoundHandler()
hs = prepend(hs, h.proxyRailsAPI)
check "gopkg.in/check.v1"
)
-var forceLegacyAPI14 bool
-
// Gocheck boilerplate
func Test(t *testing.T) {
- for _, forceLegacyAPI14 = range []bool{false, true} {
- check.TestingT(t)
- }
+ check.TestingT(t)
}
var _ = check.Suite(&HandlerSuite{})
s.ctx, s.cancel = context.WithCancel(context.Background())
s.ctx = ctxlog.Context(s.ctx, ctxlog.New(os.Stderr, "json", "debug"))
s.cluster = &arvados.Cluster{
- ClusterID: "zzzzz",
- PostgreSQL: integrationTestCluster().PostgreSQL,
- ForceLegacyAPI14: forceLegacyAPI14,
+ ClusterID: "zzzzz",
+ PostgreSQL: integrationTestCluster().PostgreSQL,
}
s.cluster.API.RequestTimeout = arvados.Duration(5 * time.Minute)
s.cluster.TLS.Insecure = true
}
func (s *HandlerSuite) TestLogoutGoogle(c *check.C) {
- if s.cluster.ForceLegacyAPI14 {
- // Google login N/A
- return
- }
s.cluster.Login.Google.Enable = true
s.cluster.Login.Google.ClientID = "test"
req := httptest.NewRequest("GET", "https://0.0.0.0:1/logout?return_to=https://example.com/foo", nil)
}
func (s *IntegrationSuite) SetUpSuite(c *check.C) {
- if forceLegacyAPI14 {
- c.Skip("heavy integration tests don't run with forceLegacyAPI14")
- return
- }
-
cwd, _ := os.Getwd()
s.oidcprovider = arvadostest.NewOIDCProvider(c)
log := ctxlog.TestLogger(c)
handler := &Handler{Cluster: &arvados.Cluster{
- ClusterID: "zzzzz",
- PostgreSQL: integrationTestCluster().PostgreSQL,
- ForceLegacyAPI14: forceLegacyAPI14,
+ ClusterID: "zzzzz",
+ PostgreSQL: integrationTestCluster().PostgreSQL,
}}
handler.Cluster.TLS.Insecure = true
arvadostest.SetServiceURL(&handler.Cluster.Services.RailsAPI, "https://"+os.Getenv("ARVADOS_TEST_API_HOST"))
from cwltool.load_tool import fetch_document, resolve_and_validate_document
from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException, WorkflowStep
-from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class
+from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class, normalizeFilesDirs
from cwltool.context import LoadingContext
import ruamel.yaml as yaml
discover_secondary_files(self.arvrunner.fs_access, builder,
self.tool["inputs"], joborder)
+ normalizeFilesDirs(joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
"size": 4
tool: 17267-broken-schemas.cwl
doc: "Test issue 17267 - inaccessible $schemas URL is not a fatal error"
+
+- job: null
+ output: {}
+ tool: wf/trick_defaults2.cwl
+ doc: "Test issue 17462 - secondary file objects on file defaults are not resolved"
--- /dev/null
+#!/usr/bin/env cwl-runner
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+ inp1:
+ type: File
+ default:
+ class: File
+ location: hello.txt
+ secondaryFiles:
+ - class: Directory
+ location: indir1
+outputs: []
+baseCommand: 'true'
SSHHelpHostSuffix string
IdleTimeout Duration
}
-
- ForceLegacyAPI14 bool
}
type Volume struct {
return cache.SafeHTTPCache(path, max_age=60*60*24*2)
def api(version=None, cache=True, host=None, token=None, insecure=False,
- request_id=None, timeout=5*60, **kwargs):
+ request_id=None, timeout=10, **kwargs):
"""Return an apiclient Resources object for an Arvados instance.
:version:
_group.add_argument('--stream', action='store_true',
help="""
Store the file content and display the resulting manifest on
-stdout. Do not write the manifest to Keep or save a Collection object
-in Arvados.
+stdout. Do not save a Collection object in Arvados.
""")
_group.add_argument('--as-manifest', action='store_true', dest='manifest',
def _write_stdin(self, filename):
output = self._local_collection.open(filename, 'wb')
- self._write(sys.stdin, output)
+ self._write(sys.stdin.buffer, output)
output.close()
def _check_file(self, source, filename):
text = "X" * maxsize
arvados.api('v1').collections().create(body={"manifest_text": text}).execute()
+ # Checks for bug #17171
+ def test_default_request_timeout(self):
+ api = arvados.api('v1')
+ self.assertEqual(api._http.timeout, 10,
+ "Default timeout value should be 10")
+
def test_ordered_json_model(self):
mock_responses = {
'arvados.humans.get': (
[sys.executable, arv_put.__file__, '--stream'],
stdin=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, env=self.ENVIRON)
- pipe.stdin.write(b'stdin test\n')
+ pipe.stdin.write(b'stdin test\xa6\n')
pipe.stdin.close()
deadline = time.time() + 5
while (pipe.poll() is None) and (time.time() < deadline):
elif returncode != 0:
sys.stdout.write(pipe.stdout.read())
self.fail("arv-put returned exit code {}".format(returncode))
- self.assertIn('4a9c8b735dce4b5fa3acf221a0b13628+11',
+ self.assertIn('1cb671b355a0c23d5d1c61d59cdb1b2b+12',
pipe.stdout.read().decode())
def test_sigint_logs_request_id(self):
projects / arvados.git / commitdiff