[ARVADOS] updated: 2.1.0-1554-g4816e450e
Git user
git at public.arvados.org
Thu Oct 28 18:20:07 UTC 2021
Summary of changes:
doc/_config.yml | 13 +-
.../_container_scheduling_parameters.liquid | 2 +-
doc/_includes/_install_custom_certificates.liquid | 26 +++
.../_singularity_mksquashfs_configuration.liquid | 15 ++
doc/admin/upgrading.html.textile.liquid | 35 ++--
doc/api/execution.html.textile.liquid | 2 +-
.../methods/container_requests.html.textile.liquid | 2 +-
doc/architecture/singularity.html.textile.liquid | 35 ++++
.../arvados-on-kubernetes-GKE.html.textile.liquid | 2 +-
.../install-compute-node.html.textile.liquid | 17 +-
.../install-dispatch-cloud.html.textile.liquid | 2 +-
.../install-dispatch.html.textile.liquid | 13 +-
.../configure-slurm.html.textile.liquid | 8 +-
.../install-dispatch.html.textile.liquid | 8 +-
.../crunch2-slurm/install-test.html.textile.liquid | 4 +-
...nstall-compute-node-docker.html.textile.liquid} | 13 +-
...ll-compute-node-singularity.html.textile.liquid | 56 ++++++
doc/install/index.html.textile.liquid | 2 +-
doc/install/salt-multi-host.html.textile.liquid | 4 +-
doc/install/salt-single-host.html.textile.liquid | 6 +
doc/install/singularity.html.textile.liquid | 49 -----
doc/sdk/index.html.textile.liquid | 2 +-
doc/user/topics/arv-docker.html.textile.liquid | 2 +-
lib/config/config.default.yml | 65 +++++-
lib/config/export.go | 2 +
lib/config/generated_config.go | 65 +++++-
lib/config/load.go | 10 +
lib/crunchrun/background.go | 54 +++--
lib/crunchrun/bufthenwrite.go | 34 ++++
lib/crunchrun/crunchrun.go | 221 ++++++++++++++++++---
lib/crunchrun/crunchrun_test.go | 14 +-
lib/crunchrun/integration_test.go | 82 +++++++-
lib/crunchrun/logging.go | 51 +++++
lib/crunchrun/logging_test.go | 34 ++++
lib/dispatchcloud/node_size.go | 1 +
lib/dispatchcloud/test/stub_driver.go | 11 +-
lib/dispatchcloud/worker/pool.go | 2 +
lib/dispatchcloud/worker/pool_test.go | 70 ++++---
lib/dispatchcloud/worker/runner.go | 20 +-
lib/dispatchcloud/worker/worker_test.go | 21 +-
lib/lsf/dispatch.go | 41 ++--
lib/lsf/dispatch_test.go | 9 +-
sdk/cwl/arvados_cwl/executor.py | 2 +-
sdk/cwl/setup.py | 4 +-
sdk/go/arvados/config.go | 2 +
services/api/app/models/user.rb | 6 +
...7154300_delete_disabled_user_tokens_and_keys.rb | 15 ++
.../api/lib/tasks/manage_long_lived_tokens.rake | 4 +-
services/api/script/get_anonymous_user_token.rb | 3 +
services/api/test/integration/users_test.rb | 8 +
services/keep-web/handler_test.go | 32 +--
services/keepstore/azure_blob_volume.go | 3 +
services/keepstore/handler_test.go | 31 +--
services/keepstore/handlers.go | 31 +--
services/login-sync/bin/arvados-login-sync | 37 +++-
tools/compute-images/arvados-images-aws.json | 3 +-
tools/compute-images/arvados-images-azure.json | 3 +-
tools/compute-images/build.sh | 12 +-
tools/compute-images/scripts/base.sh | 5 +
tools/salt-install/Vagrantfile | 8 +-
.../letsencrypt_controller_configuration.sls | 10 +-
.../letsencrypt_keepproxy_configuration.sls | 10 +-
.../pillars/letsencrypt_keepweb_configuration.sls | 11 -
.../pillars/letsencrypt_webshell_configuration.sls | 8 -
.../letsencrypt_websocket_configuration.sls | 10 +-
.../letsencrypt_workbench2_configuration.sls | 8 -
.../letsencrypt_workbench_configuration.sls | 8 -
.../aws/pillars/nginx_api_configuration.sls | 2 +-
.../pillars/nginx_collections_configuration.sls} | 27 +--
.../aws/pillars/nginx_controller_configuration.sls | 11 +-
.../aws/pillars/nginx_download_configuration.sls} | 31 +--
.../aws/pillars/nginx_keepproxy_configuration.sls | 11 +-
.../aws/pillars/nginx_keepweb_configuration.sls | 75 +------
.../aws/pillars/nginx_webshell_configuration.sls | 11 +-
.../aws/pillars/nginx_websocket_configuration.sls | 9 +-
.../aws/pillars/nginx_workbench2_configuration.sls | 9 +-
.../aws/pillars/nginx_workbench_configuration.sls | 9 +-
.../multiple_hostnames/pillars/arvados.sls | 4 +-
.../pillars/nginx_controller_configuration.sls | 9 +-
.../pillars/nginx_keepproxy_configuration.sls | 5 +-
.../pillars/nginx_keepweb_configuration.sls | 19 +-
.../multiple_hostnames/pillars/nginx_passenger.sls | 4 -
.../pillars/nginx_webshell_configuration.sls | 5 +-
.../pillars/nginx_websocket_configuration.sls | 5 +-
.../pillars/nginx_workbench2_configuration.sls | 5 +-
.../pillars/nginx_workbench_configuration.sls | 5 +-
.../multiple_hostnames/states/custom_certs.sls | 31 +++
.../multiple_hostnames/states/snakeoil_certs.sls | 116 ++++++-----
.../single_hostname/pillars/arvados.sls | 2 +-
.../local.params.example.multiple_hosts | 22 +-
...l.params.example.single_host_multiple_hostnames | 21 +-
tools/salt-install/provision.sh | 153 ++++++++++++--
92 files changed, 1387 insertions(+), 613 deletions(-)
create mode 100644 doc/_includes/_install_custom_certificates.liquid
create mode 100644 doc/_includes/_singularity_mksquashfs_configuration.liquid
create mode 100644 doc/architecture/singularity.html.textile.liquid
rename doc/install/{crunch2-slurm/install-compute-node.html.textile.liquid => crunch2/install-compute-node-docker.html.textile.liquid} (56%)
create mode 100644 doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
delete mode 100644 doc/install/singularity.html.textile.liquid
create mode 100644 lib/crunchrun/bufthenwrite.go
create mode 100644 services/api/db/migrate/20211027154300_delete_disabled_user_tokens_and_keys.rb
copy tools/salt-install/config_examples/{single_host/multiple_hostnames/pillars/nginx_keepweb_configuration.sls => multi_host/aws/pillars/nginx_collections_configuration.sls} (65%)
copy tools/salt-install/config_examples/{single_host/multiple_hostnames/pillars/nginx_keepweb_configuration.sls => multi_host/aws/pillars/nginx_download_configuration.sls} (57%)
create mode 100644 tools/salt-install/config_examples/single_host/multiple_hostnames/states/custom_certs.sls
discards ef950edc12c3ec560427b92537c54fb010edf970 (commit)
via 4816e450e1d71ba23c1b4c53053c0341120c2415 (commit)
via b9dfa440d0ca7547f8e403cb513e300c4d405cba (commit)
via f2788dd5fc3ef725969d6c0fcc4ddee3754829fc (commit)
via 54836b787450bf23abcf7be291831799093a17b0 (commit)
via e1e1a215d954c3337a969019da7f7becc8d14012 (commit)
via deb104b3706fab06bf21a70fb9d85d2717f4f0c1 (commit)
via 808a32f8d2b174b293154257a72c687cbb8bb280 (commit)
via bad2728b2ed147badcd67ff0d21be20d17f0c9ea (commit)
via b7ec820ac297bc316ef9ffa36242e7928acbc0b4 (commit)
via 39a723673e92b842233b1da5fde27aa595fcc59f (commit)
via 83c996d75698093446fbfff89ea4abeb36cbc8c4 (commit)
via 623ffe7320d0a159ba9a5912fc1948cac12ad505 (commit)
via aaabfc20e05a635a36be0049b38b2034f041398d (commit)
via 1f23032c8a10c03e9f4ff00b45576ad5c5e5afd9 (commit)
via e31979e7ef752c9adef3d3fa6096a47d720d524e (commit)
via 22516d3663a3c11384824dad0e052dc0630f08f0 (commit)
via 39464fc833e3ee2fb771f83dce9f94e3856c1075 (commit)
via 125dd3b1e5f34156b002951f504f5346cc5d7e8d (commit)
via 2582dc22a24ee7cdaf1a68c6b4b1c639f88c2efe (commit)
via c5e4fb5838d2f447ae126159a71340b90cfea33c (commit)
via 3dcd4659f10710621f429066f11ab7b67cd6e878 (commit)
via 01698bea4703ce073425e2080c7cad83e2f873cc (commit)
via 9f6f07fe6790e7c3a8f1b57990c16447c9d2713f (commit)
via 58df9c45cc6288b4424c6571b35373de8837a85f (commit)
via b03d26d7607c11e45f49a960ce147bbb2ebfb53c (commit)
via 169a7755916e1f3227ab9c3959447149ecb99503 (commit)
via 3c3cae35fe5b3cf0371e1cbb1ff295baf555f77a (commit)
via 9539317a22d8ea16f94b0e086507ab595d758216 (commit)
via 67d842388bc0542a7c3d8843635c3ccf5add20c7 (commit)
via dd5a2a0c2da55c95cb94cb67538c6693cf989bf9 (commit)
via 242e740db430759c3a09de3bf9ece89987c6b9b0 (commit)
via 332c20ac4de0d2706a7e6c9e3a96f1d4287eb4c5 (commit)
via 0bfda57681195c431e3b6063577fdab23ff40cd5 (commit)
via e1c4967befc7b4dd273b3d9d047a4e4262f5ba2f (commit)
via 0d9bc75b61d5227917ef43e4c716ae284d548644 (commit)
via ccb603fe5a8ca989d6db97cc723ccfcaba2781f5 (commit)
via 64194cf50545e1b6894b45cc18edbefbc3ac8707 (commit)
via 93131b473366ae5442103511d455d1ed5b73bcab (commit)
via b98969108fbda1754a03665a5be58bb9e0d16c01 (commit)
via 8fde01ca2dae5169917de4e8b25eada543a8223f (commit)
via f9582f44d4f31e941902f84fce760a8b770bc969 (commit)
via 68259bcde57277cb709296fc24e86826d9c131d5 (commit)
via b7aa839c669f1c2055ade415b99378e5c9ba0baa (commit)
via a0080bdf353bcc107eb80a5755958c6c276d49eb (commit)
via d68c3776fee61329f665ede740cca51946395d1c (commit)
via 089aaca1ed6fe672f01c5049f1bf3956bdd35065 (commit)
via 53b2e5895715c73febffb563ebc89153339e02ab (commit)
via c8d252f51c23484484e4aa023fcd1f86ee961eab (commit)
via d8d9b01ba4a5f9cbc216c43f8af88af1413673d4 (commit)
via f54cc984969657be50c093b917feb49a19d78c22 (commit)
via 3b0f80205c1942cc954eb891691c7c382aa9c87c (commit)
via 2eeaf4eacf23e166b60cf95562ea2727a68e1e08 (commit)
via bda9093be4d24d45a6fff29148fbb5438e283897 (commit)
via 6b39f96311c832de21bcacc3f17a611682d522a9 (commit)
via 5f95bfc2c5c7706c7961aeca3aabd90ea5661f0a (commit)
via e04586707b923f857c61a17ad38a9ce795e9af14 (commit)
via f968e4a8eeb562964f265d7555eaf295f8bac7f6 (commit)
via 146c1e2c5d12f478e4dbf35c5a675f05a793f5b7 (commit)
via c6e6a2531ef791e7fdae10b440c778244dd62019 (commit)
via 9a615740476541185073f98d8bc6e69e06ecf340 (commit)
via 6b3a880d607ee3e3dd273f019981fd6cae62373c (commit)
via 6f84dbb74b46470e937a52cbbb5de4c5b825e122 (commit)
via 03338fd9d7416560331bb96fd356f3d35de6760f (commit)
via b4bb4815b9e23c54d6bbf7ec166acdf7ddfcb10b (commit)
This update added new revisions after undoing existing revisions. That is
to say, the old revision is not a strict subset of the new revision. This
situation occurs when you --force push a change and generate a repository
containing something like this:
* -- * -- B -- O -- O -- O (ef950edc12c3ec560427b92537c54fb010edf970)
\
N -- N -- N (4816e450e1d71ba23c1b4c53053c0341120c2415)
When this happens we assume that you've already had alert emails for all
of the O revisions, and so we here report only the revisions in the N
branch from the common base, B.
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 4816e450e1d71ba23c1b4c53053c0341120c2415
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Thu Oct 14 15:09:00 2021 -0400
18273: Increase default java sdk timeouts & make them configuable
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/java-v2/src/main/java/org/arvados/client/api/client/BaseApiClient.java b/sdk/java-v2/src/main/java/org/arvados/client/api/client/BaseApiClient.java
index a8d1a08cb..51f2f4a81 100644
--- a/sdk/java-v2/src/main/java/org/arvados/client/api/client/BaseApiClient.java
+++ b/sdk/java-v2/src/main/java/org/arvados/client/api/client/BaseApiClient.java
@@ -23,6 +23,7 @@ import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.nio.charset.StandardCharsets;
import java.util.Objects;
+import java.util.concurrent.TimeUnit;
abstract class BaseApiClient {
@@ -34,7 +35,12 @@ abstract class BaseApiClient {
BaseApiClient(ConfigProvider config) {
this.config = config;
- this.client = OkHttpClientFactory.INSTANCE.create(config.isApiHostInsecure());
+ this.client = OkHttpClientFactory.INSTANCE.create(config.isApiHostInsecure())
+ .newBuilder()
+ .connectTimeout(config.getConnectTimeout(), TimeUnit.MILLISECONDS)
+ .readTimeout(config.getReadTimeout(), TimeUnit.MILLISECONDS)
+ .writeTimeout(config.getWriteTimeout(), TimeUnit.MILLISECONDS)
+ .build();
}
Request.Builder getRequestBuilder() {
diff --git a/sdk/java-v2/src/main/java/org/arvados/client/config/ConfigProvider.java b/sdk/java-v2/src/main/java/org/arvados/client/config/ConfigProvider.java
index c9a410931..116a46b3e 100644
--- a/sdk/java-v2/src/main/java/org/arvados/client/config/ConfigProvider.java
+++ b/sdk/java-v2/src/main/java/org/arvados/client/config/ConfigProvider.java
@@ -26,6 +26,11 @@ public interface ConfigProvider {
String getApiProtocol();
+ int getConnectTimeout();
+
+ int getReadTimeout();
+
+ int getWriteTimeout();
//FILE UPLOAD
int getFileSplitSize();
diff --git a/sdk/java-v2/src/main/java/org/arvados/client/config/ExternalConfigProvider.java b/sdk/java-v2/src/main/java/org/arvados/client/config/ExternalConfigProvider.java
index 17e06966f..d592b23ac 100644
--- a/sdk/java-v2/src/main/java/org/arvados/client/config/ExternalConfigProvider.java
+++ b/sdk/java-v2/src/main/java/org/arvados/client/config/ExternalConfigProvider.java
@@ -22,8 +22,35 @@ public class ExternalConfigProvider implements ConfigProvider {
private File fileSplitDirectory;
private int numberOfCopies;
private int numberOfRetries;
+ private int connectTimeout;
+ private int readTimeout;
+ private int writeTimeout;
+
+ ExternalConfigProvider(boolean apiHostInsecure, String keepWebHost, int keepWebPort, String apiHost, int apiPort,
+ String apiToken, String apiProtocol, int fileSplitSize, File fileSplitDirectory,
+ int numberOfCopies, int numberOfRetries)
+ {
+ this.apiHostInsecure = apiHostInsecure;
+ this.keepWebHost = keepWebHost;
+ this.keepWebPort = keepWebPort;
+ this.apiHost = apiHost;
+ this.apiPort = apiPort;
+ this.apiToken = apiToken;
+ this.apiProtocol = apiProtocol;
+ this.fileSplitSize = fileSplitSize;
+ this.fileSplitDirectory = fileSplitDirectory;
+ this.numberOfCopies = numberOfCopies;
+ this.numberOfRetries = numberOfRetries;
+ this.connectTimeout = 60000;
+ this.readTimeout = 60000;
+ this.writeTimeout = 60000;
+ }
- ExternalConfigProvider(boolean apiHostInsecure, String keepWebHost, int keepWebPort, String apiHost, int apiPort, String apiToken, String apiProtocol, int fileSplitSize, File fileSplitDirectory, int numberOfCopies, int numberOfRetries) {
+ ExternalConfigProvider(boolean apiHostInsecure, String keepWebHost, int keepWebPort, String apiHost, int apiPort,
+ String apiToken, String apiProtocol, int fileSplitSize, File fileSplitDirectory,
+ int numberOfCopies, int numberOfRetries,
+ int connectTimeout, int readTimeout, int writeTimeout)
+ {
this.apiHostInsecure = apiHostInsecure;
this.keepWebHost = keepWebHost;
this.keepWebPort = keepWebPort;
@@ -35,6 +62,9 @@ public class ExternalConfigProvider implements ConfigProvider {
this.fileSplitDirectory = fileSplitDirectory;
this.numberOfCopies = numberOfCopies;
this.numberOfRetries = numberOfRetries;
+ this.connectTimeout = connectTimeout;
+ this.readTimeout = readTimeout;
+ this.writeTimeout = writeTimeout;
}
public static ExternalConfigProviderBuilder builder() {
@@ -102,6 +132,18 @@ public class ExternalConfigProvider implements ConfigProvider {
return this.numberOfRetries;
}
+ public int getConnectTimeout() {
+ return this.connectTimeout;
+ }
+
+ public int getReadTimeout() {
+ return this.readTimeout;
+ }
+
+ public int getWriteTimeout() {
+ return this.writeTimeout;
+ }
+
public static class ExternalConfigProviderBuilder {
private boolean apiHostInsecure;
private String keepWebHost;
diff --git a/sdk/java-v2/src/main/java/org/arvados/client/config/FileConfigProvider.java b/sdk/java-v2/src/main/java/org/arvados/client/config/FileConfigProvider.java
index 589c3346b..99c1af810 100644
--- a/sdk/java-v2/src/main/java/org/arvados/client/config/FileConfigProvider.java
+++ b/sdk/java-v2/src/main/java/org/arvados/client/config/FileConfigProvider.java
@@ -104,4 +104,19 @@ public class FileConfigProvider implements ConfigProvider {
public String getIntegrationTestProjectUuid() {
return this.getString("integration-tests.project-uuid");
}
+
+ @Override
+ public int getConnectTimeout() {
+ return this.getInt("connectTimeout");
+ }
+
+ @Override
+ public int getReadTimeout() {
+ return this.getInt("readTimeout");
+ }
+
+ @Override
+ public int getWriteTimeout() {
+ return this.getInt("writeTimeout");
+ }
}
diff --git a/sdk/java-v2/src/main/resources/reference.conf b/sdk/java-v2/src/main/resources/reference.conf
index 3ff2bb0a9..8933e2bc6 100644
--- a/sdk/java-v2/src/main/resources/reference.conf
+++ b/sdk/java-v2/src/main/resources/reference.conf
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+#
# Arvados client default configuration
#
# Remarks:
@@ -20,4 +24,7 @@ arvados {
temp-dir = /tmp/file-split
copies = 2
retries = 0
+ connectTimeout = 60000
+ readTimeout = 60000
+ writeTimeout = 60000
}
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list