[arvados] created: 2.6.0-558-g25bd0899e1

git repository hosting git at public.arvados.org
Sun Sep 3 17:38:14 UTC 2023 

        at  25bd0899e19240eb1468f94c7b174959ff547761 (commit)


commit 25bd0899e19240eb1468f94c7b174959ff547761
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Sun Sep 3 13:36:49 2023 -0400

    20840: Add deprecations to upgrade notes
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 1534d1eb6e..a8482b48d0 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -29,7 +29,7 @@ TODO: extract this information based on git commit messages and generate changel
 </notextile>
 
 
-h2(#main). development main (as of 2023-08-15)
+h2(#main). development main (as of 2023-09-03)
 
 "previous: Upgrading to 2.6.3":#v2_6_3
 
@@ -52,6 +52,14 @@ h3. UseAWSS3v2Driver option removed
 
 The old "v1" S3 driver for keepstore has been removed. The new "v2" implementation, which has been the default since Arvados 2.5.0, is always used. The @Volumes.*.DriverParameters.UseAWSS3v2Driver@ configuration key is no longer recognized. If your config file uses it, remove it to avoid warning messages at startup.
 
+h3. Deprecated/legacy APIs slated for removal
+
+The legacy APIs "humans":../api/methods/humans.html, "specimens":../api/methods/specimens.html, "traits":../api/methods/traits.html, "jobs":../api/methods/jobs.html, "job_tasks":../api/methods/job_tasks.html, "pipeline_instances":../api/methods/pipeline_instances.html, "pipeline_templates":../api/methods/pipeline_templates.html, "nodes":../api/methods/nodes.html, "repositories":../api/methods/repositories.html, and "keep_disks":../api/methods/keep_disks.html are deprecated and will be removed in a future major version of Arvados.
+
+h3. Workbench 1 deprecated
+
+The original Arvados Workbench application (referred to as "Workbench 1") is deprecated and will be removed in a future major version of Arvados.  Users are advised to migrate to "Workbench 2".  Starting with this release, new installations of Arvados will only set up Workbench 2 and no longer include Workbench 1 by default.
+
 h2(#v2_6_3). v2.6.3 (2023-06-06)
 
 h3. Python SDK automatically retries failed requests much more

commit 13d9ed51e225684409712d6da4715c0f6037e930
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Sun Sep 3 13:27:03 2023 -0400

    20840: Add warning boxes to legacy APIs and rearrange API listing
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/doc/_config.yml b/doc/_config.yml
index b42a3c8b95..cbb082aefb 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -109,19 +109,14 @@ navbar:
       - api/methods.html.textile.liquid
       - api/resources.html.textile.liquid
     - Permission and authentication:
+      - api/methods/users.html.textile.liquid
+      - api/methods/groups.html.textile.liquid
       - api/methods/api_client_authorizations.html.textile.liquid
-      - api/methods/api_clients.html.textile.liquid
+      - api/methods/links.html.textile.liquid
       - api/methods/authorized_keys.html.textile.liquid
-      - api/methods/groups.html.textile.liquid
-      - api/methods/users.html.textile.liquid
+      - api/methods/api_clients.html.textile.liquid
       - api/methods/user_agreements.html.textile.liquid
-    - System resources:
-      - api/methods/keep_services.html.textile.liquid
-      - api/methods/links.html.textile.liquid
-      - api/methods/logs.html.textile.liquid
-      - api/methods/nodes.html.textile.liquid
       - api/methods/virtual_machines.html.textile.liquid
-      - api/methods/keep_disks.html.textile.liquid
     - Data management:
       - api/keep-webdav.html.textile.liquid
       - api/keep-s3.html.textile.liquid
@@ -129,12 +124,12 @@ navbar:
       - api/projects.html.textile.liquid
       - api/properties.html.textile.liquid
       - api/methods/collections.html.textile.liquid
-      - api/methods/repositories.html.textile.liquid
+      - api/methods/logs.html.textile.liquid
+      - api/methods/keep_services.html.textile.liquid
     - Container engine:
       - api/methods/container_requests.html.textile.liquid
       - api/methods/containers.html.textile.liquid
       - api/methods/workflows.html.textile.liquid
-    - Management (admin/system):
       - api/dispatch.html.textile.liquid
     - Jobs engine (legacy):
       - api/crunch-scripts.html.textile.liquid
@@ -142,7 +137,10 @@ navbar:
       - api/methods/job_tasks.html.textile.liquid
       - api/methods/pipeline_instances.html.textile.liquid
       - api/methods/pipeline_templates.html.textile.liquid
-    - Metadata for bioinformatics (deprecated):
+      - api/methods/nodes.html.textile.liquid
+      - api/methods/repositories.html.textile.liquid
+      - api/methods/keep_disks.html.textile.liquid
+    - Metadata for bioinformatics (legacy):
       - api/methods/humans.html.textile.liquid
       - api/methods/specimens.html.textile.liquid
       - api/methods/traits.html.textile.liquid
diff --git a/doc/api/crunch-scripts.html.textile.liquid b/doc/api/crunch-scripts.html.textile.liquid
index 3d6ccbdd5b..5d7fe5d98f 100644
--- a/doc/api/crunch-scripts.html.textile.liquid
+++ b/doc/api/crunch-scripts.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Legacy.  The job APIs are read-only and disabled by default in new installations.  Use "container requests":methods/container_requests.html .*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "container requests.":methods/container_requests.html
+{% include 'notebox_end' %}
 
 h2. Crunch scripts
 
diff --git a/doc/api/methods/api_client_authorizations.html.textile.liquid b/doc/api/methods/api_client_authorizations.html.textile.liquid
index bcf77564c5..597760bb90 100644
--- a/doc/api/methods/api_client_authorizations.html.textile.liquid
+++ b/doc/api/methods/api_client_authorizations.html.textile.liquid
@@ -27,8 +27,6 @@ table(table table-bordered table-condensed).
 |_. Attribute|_. Type|_. Description|_. Example|
 |uuid|string|An identifier used to refer to the token without exposing the actual token.||
 |api_token|string|The actual token string that is expected in the Authorization header.||
-|api_client_id|integer|-||
-|user_id|integer|-||
 |created_by_ip_address|string|-||
 |last_used_by_ip_address|string|The network address of the most recent client using this token.||
 |last_used_at|datetime|Timestamp of the most recent request using this token.||
diff --git a/doc/api/methods/collections.html.textile.liquid b/doc/api/methods/collections.html.textile.liquid
index 5871337b0a..29d28d42a2 100644
--- a/doc/api/methods/collections.html.textile.liquid
+++ b/doc/api/methods/collections.html.textile.liquid
@@ -19,7 +19,7 @@ Example UUID: @zzzzz-4zz18-0123456789abcde@
 
 h2. Resource
 
-Collections describe sets of files in terms of data blocks stored in Keep.  See "Keep - Content-Addressable Storage":{{site.baseurl}}/architecture/storage.html for details.
+Collections describe sets of files in terms of data blocks stored in Keep.  See "Keep - Content-Addressable Storage":{{site.baseurl}}/architecture/storage.html and "using collection versioning":../../user/topics/collection-versioning.html for details.
 
 Each collection has, in addition to the "Common resource fields":{{site.baseurl}}/api/resources.html:
 
diff --git a/doc/api/methods/humans.html.textile.liquid b/doc/api/methods/humans.html.textile.liquid
index e08e941cf6..1c338217eb 100644
--- a/doc/api/methods/humans.html.textile.liquid
+++ b/doc/api/methods/humans.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Deprecated, likely to be removed in a future version.  The recommended way to store metadata is "collection properties":collections.html*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  The recommended way to store metadata is with "'properties' field on collections and projects.":../properties.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/humans@
 
diff --git a/doc/api/methods/job_tasks.html.textile.liquid b/doc/api/methods/job_tasks.html.textile.liquid
index 69c3f07e30..2700708d6e 100644
--- a/doc/api/methods/job_tasks.html.textile.liquid
+++ b/doc/api/methods/job_tasks.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Legacy.  This endpoint is read-only and disabled by default in new installations.*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "container requests.":container_requests.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_tasks@
 
diff --git a/doc/api/methods/jobs.html.textile.liquid b/doc/api/methods/jobs.html.textile.liquid
index aa7a58898a..3b806200c9 100644
--- a/doc/api/methods/jobs.html.textile.liquid
+++ b/doc/api/methods/jobs.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Legacy.  This endpoint is read-only and disabled by default in new installations.*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "container requests.":container_requests.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/jobs@
 
diff --git a/doc/api/methods/keep_disks.html.textile.liquid b/doc/api/methods/keep_disks.html.textile.liquid
index 7624b6699f..f35ff80ad3 100644
--- a/doc/api/methods/keep_disks.html.textile.liquid
+++ b/doc/api/methods/keep_disks.html.textile.liquid
@@ -2,7 +2,7 @@
 layout: default
 navsection: api
 navmenu: API Methods
-title: "keep_disks (deprecated)"
+title: "keep_disks"
 
 ...
 {% comment %}
@@ -11,6 +11,10 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "keep services.":keep_services.html
+{% include 'notebox_end' %}
+
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disks@
 
 Object type: @penuu@
diff --git a/doc/api/methods/nodes.html.textile.liquid b/doc/api/methods/nodes.html.textile.liquid
index 7ddc62519c..40c9d0dfe0 100644
--- a/doc/api/methods/nodes.html.textile.liquid
+++ b/doc/api/methods/nodes.html.textile.liquid
@@ -11,6 +11,10 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "cloud dispatcher API.":dispatch.html
+{% include 'notebox_end' %}
+
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/nodes@
 
 Object type: @7ekkf@
diff --git a/doc/api/methods/pipeline_instances.html.textile.liquid b/doc/api/methods/pipeline_instances.html.textile.liquid
index 55baee9b5a..889056c146 100644
--- a/doc/api/methods/pipeline_instances.html.textile.liquid
+++ b/doc/api/methods/pipeline_instances.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Legacy.  This endpoint is read-only and disabled by default in new installations.*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "container requests.":container_requests.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instances@
 
diff --git a/doc/api/methods/pipeline_templates.html.textile.liquid b/doc/api/methods/pipeline_templates.html.textile.liquid
index 141072c51c..8d2d0cd7b1 100644
--- a/doc/api/methods/pipeline_templates.html.textile.liquid
+++ b/doc/api/methods/pipeline_templates.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Legacy.  This endpoint is read-only and disabled by default in new installations.*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "registered workflows.":workflows.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_templates@
 
diff --git a/doc/api/methods/repositories.html.textile.liquid b/doc/api/methods/repositories.html.textile.liquid
index 7a47da6a3b..3bef8bd489 100644
--- a/doc/api/methods/repositories.html.textile.liquid
+++ b/doc/api/methods/repositories.html.textile.liquid
@@ -11,6 +11,10 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  Is is replaced by "collection versioning.":collections.html
+{% include 'notebox_end' %}
+
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repositories@
 
 Object type: @s0uqq@
diff --git a/doc/api/methods/specimens.html.textile.liquid b/doc/api/methods/specimens.html.textile.liquid
index be3712a206..3820eeb242 100644
--- a/doc/api/methods/specimens.html.textile.liquid
+++ b/doc/api/methods/specimens.html.textile.liquid
@@ -10,7 +10,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Deprecated, likely to be removed in a future version.  The recommended way to store metadata is "collection properties":collections.html*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  The recommended way to store metadata is with "'properties' field on collections and projects.":../properties.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimens@
 
diff --git a/doc/api/methods/traits.html.textile.liquid b/doc/api/methods/traits.html.textile.liquid
index e48804702e..4e356b9523 100644
--- a/doc/api/methods/traits.html.textile.liquid
+++ b/doc/api/methods/traits.html.textile.liquid
@@ -11,7 +11,9 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-p=. *Deprecated, likely to be removed in a future version.  The recommended way to store metadata is "collection properties":collections.html*
+{% include 'notebox_begin_warning' %}
+This is a legacy API.  This endpoint is deprecated, disabled by default in new installations, and is slated to be removed entirely in a future major release of Arvados.  The recommended way to store metadata is with "'properties' field on collections and projects.":../properties.html
+{% include 'notebox_end' %}
 
 API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/traits@
 

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