[ARVADOS] updated: 2.3.0-8-g4c53d93b1
Git user
git at public.arvados.org
Thu Nov 4 20:07:44 UTC 2021
Summary of changes:
doc/Rakefile | 3 ++-
doc/_includes/_tutorial_expectations.liquid | 2 +-
doc/admin/upgrading.html.textile.liquid | 2 +-
doc/admin/user-activity.html.textile.liquid | 4 ++--
doc/api/permission-model.html.textile.liquid | 4 ++--
doc/api/projects.html.textile.liquid | 2 +-
doc/architecture/keep-components-overview.html.textile.liquid | 10 +++++-----
doc/install/arvados-on-kubernetes-GKE.html.textile.liquid | 2 +-
.../arvados-on-kubernetes-minikube.html.textile.liquid | 2 +-
doc/install/arvados-on-kubernetes.html.textile.liquid | 2 +-
.../crunch2/install-compute-node-docker.html.textile.liquid | 2 +-
.../install-compute-node-singularity.html.textile.liquid | 2 +-
doc/install/salt-multi-host.html.textile.liquid | 11 +----------
doc/user/topics/arvados-sync-groups.html.textile.liquid | 2 +-
14 files changed, 21 insertions(+), 29 deletions(-)
via 4c53d93b1c9356aea2c509fcfc79cc48aa0e2fa1 (commit)
via 17bf8752a8b110a95cde3683bc0a6c586fae3ac9 (commit)
via c0ba291cfb28192b1a3255008aefaf13583fea97 (commit)
from 7d39fd29dbf5b6b9bad90cee69dce24498f3e5ed (commit)
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 4c53d93b1c9356aea2c509fcfc79cc48aa0e2fa1
Author: Ward Vandewege <ward at curii.com>
Date: Thu Nov 4 16:06:03 2021 -0400
Remve last reference to terraform for now.
refs #17450
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
diff --git a/doc/install/salt-multi-host.html.textile.liquid b/doc/install/salt-multi-host.html.textile.liquid
index a0a38c3b9..fdfd05ead 100644
--- a/doc/install/salt-multi-host.html.textile.liquid
+++ b/doc/install/salt-multi-host.html.textile.liquid
@@ -101,7 +101,7 @@ The <i>multi_host</i> include LetsEncrypt salt code to automatically request and
h3(#further_customization). Further customization of the installation (modifying the salt pillars and states)
-You will need further customization to suit your environment, which can be done editing the Saltstack pillars and states files. Pay particular attention to the <i>pillars/arvados.sls</i> file, where you will need to provide some information that can be retrieved as output of the terraform run.
+You will need further customization to suit your environment, which can be done editing the Saltstack pillars and states files. Pay particular attention to the <i>pillars/arvados.sls</i> file, where you will need to provide some information that describes your environment.
Any extra <i>state</i> file you add under <i>local_config_dir/states</i> will be added to the salt run and applied to the hosts.
commit 17bf8752a8b110a95cde3683bc0a6c586fae3ac9
Author: Ward Vandewege <ward at curii.com>
Date: Thu Nov 4 15:59:26 2021 -0400
Remove reference to terraform code that was never checked in.
refs #17450
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
diff --git a/doc/install/salt-multi-host.html.textile.liquid b/doc/install/salt-multi-host.html.textile.liquid
index 0d7fb916e..a0a38c3b9 100644
--- a/doc/install/salt-multi-host.html.textile.liquid
+++ b/doc/install/salt-multi-host.html.textile.liquid
@@ -11,7 +11,6 @@ SPDX-License-Identifier: CC-BY-SA-3.0
# "Introduction":#introduction
# "Hosts preparation":#hosts_preparation
-## "Hosts setup using terraform (experimental)":#hosts_setup_using_terraform
## "Create a compute image":#create_a_compute_image
# "Multi host install using the provision.sh script":#multi_host
# "Choose the desired configuration":#choose_configuration
@@ -65,14 +64,6 @@ Note that these hosts can be virtual machines in your infrastructure and they do
Again, if your infrastructure differs from the setup proposed above (ie, using RDS or an existing DB server), remember that you will need to edit the configuration files for the scripts so they work with your infrastructure.
-
-h3(#hosts_setup_using_terraform). Hosts setup using terraform (AWS, experimental)
-
-We added a few "terraform":https://terraform.io/ scripts (https://github.com/arvados/arvados/tree/main/tools/terraform) to let you create these instances easier in an AWS account. Check "the Arvados terraform documentation":/doc/install/terraform.html for more details.
-
-
-
-
h2(#multi_host). Multi host install using the provision.sh script
{% include 'branchname' %}
commit c0ba291cfb28192b1a3255008aefaf13583fea97
Author: Ward Vandewege <ward at curii.com>
Date: Thu Nov 4 15:55:17 2021 -0400
Make the linkchecker more strict so it objects to relative links within
our doc tree that do not have the {{ site.baseurl }} prefix.
Fix all the links that were incorrect that way.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at curii.com>
diff --git a/doc/Rakefile b/doc/Rakefile
index 2b4b6af2e..4427f7822 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -160,7 +160,8 @@ task :linkchecker => [ :generate ] do
Dir.chdir(".site") do
`which linkchecker`
if $? == 0
- system "linkchecker index.html --ignore-url='!file://'" or exit $?.exitstatus
+ # we need --check-extern to check relative links, weird but true
+ system "linkchecker index.html --check-extern --ignore-url='!file://'" or exit $?.exitstatus
else
puts "Warning: linkchecker not found, skipping run".colorize(:light_red)
end
diff --git a/doc/_includes/_tutorial_expectations.liquid b/doc/_includes/_tutorial_expectations.liquid
index 09b18f0d4..d4d05078f 100644
--- a/doc/_includes/_tutorial_expectations.liquid
+++ b/doc/_includes/_tutorial_expectations.liquid
@@ -5,5 +5,5 @@ SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
{% include 'notebox_begin' %}
-This tutorial assumes that you have access to the "Arvados command line tools":/user/getting_started/setup-cli.html and have set the "API token":{{site.baseurl}}/user/reference/api-tokens.html and confirmed a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html .
+This tutorial assumes that you have access to the "Arvados command line tools":{{ site.baseurl }}/user/getting_started/setup-cli.html and have set the "API token":{{site.baseurl}}/user/reference/api-tokens.html and confirmed a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html .
{% include 'notebox_end' %}
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 304eedb1d..5a5154ce5 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -396,7 +396,7 @@ h3. Python packaging change
As part of story "#9945":https://dev.arvados.org/issues/9945, the distribution packaging (deb/rpm) of our Python packages has changed. These packages now include a built-in virtualenv to reduce dependencies on system packages. We have also stopped packaging and publishing backports for all the Python dependencies of our packages, as they are no longer needed.
-One practical consequence of this change is that the use of the Arvados Python SDK (aka "import arvados") will require a tweak if the SDK was installed from a distribution package. It now requires the loading of the virtualenv environment from our packages. The "Install documentation for the Arvados Python SDK":/sdk/python/sdk-python.html reflects this change. This does not affect the use of the command line tools (e.g. arv-get, etc.).
+One practical consequence of this change is that the use of the Arvados Python SDK (aka "import arvados") will require a tweak if the SDK was installed from a distribution package. It now requires the loading of the virtualenv environment from our packages. The "Install documentation for the Arvados Python SDK":{{ site.baseurl }}/sdk/python/sdk-python.html reflects this change. This does not affect the use of the command line tools (e.g. arv-get, etc.).
Python scripts that rely on the distribution Arvados Python SDK packages to import the Arvados SDK will need to be tweaked to load the correct Python environment.
diff --git a/doc/admin/user-activity.html.textile.liquid b/doc/admin/user-activity.html.textile.liquid
index 21bfb7655..01715ff6e 100644
--- a/doc/admin/user-activity.html.textile.liquid
+++ b/doc/admin/user-activity.html.textile.liquid
@@ -17,7 +17,7 @@ h2. Option 1: Install from a distribution package
This installation method is recommended to make the CLI tools available system-wide. It can coexist with the installation method described in option 2, below.
-First, configure the "Arvados package repositories":../../install/packages.html
+First, configure the "Arvados package repositories":{{ site.baseurl }}/install/packages.html
{% assign arvados_component = 'python3-arvados-user-activity' %}
@@ -31,7 +31,7 @@ Step 2: Change directory to @arvados/tools/user-activity@
Step 3: Run @pip install .@ in an appropriate installation environment, such as a @virtualenv at .
-Note: depends on the "Arvados Python SDK":../sdk/python/sdk-python.html and its associated build prerequisites (e.g. @pycurl@).
+Note: depends on the "Arvados Python SDK":{{ site.baseurl }}/sdk/python/sdk-python.html and its associated build prerequisites (e.g. @pycurl@).
h2. Usage
diff --git a/doc/api/permission-model.html.textile.liquid b/doc/api/permission-model.html.textile.liquid
index 82e8128c6..a44d2eefa 100644
--- a/doc/api/permission-model.html.textile.liquid
+++ b/doc/api/permission-model.html.textile.liquid
@@ -46,7 +46,7 @@ This grants the permission in @name@ for @tail_uuid@ accessing @head_uuid at .
If a User has *can_manage* permission on some object, the user has the ability to read, create, update and delete permission links with @head_uuid@ of the managed object. In other words, the user has the ability to modify the permission grants on the object.
-The *can_login* @name@ is only meaningful on a permission link with with @tail_uuid@ a user UUID and @head_uuid@ a Virtual Machine UUID. A permission link of this type gives the user UUID permission to log into the Virtual Machine UUID. The username for the VM is specified in the @properties@ field. Group membership can be specified that way as well, optionally. See the "VM login section on the CLI cheat sheet":/install/cheat_sheet.html#vm-login for an example.
+The *can_login* @name@ is only meaningful on a permission link with with @tail_uuid@ a user UUID and @head_uuid@ a Virtual Machine UUID. A permission link of this type gives the user UUID permission to log into the Virtual Machine UUID. The username for the VM is specified in the @properties@ field. Group membership can be specified that way as well, optionally. See the "VM login section on the 'User management at the CLI' page":{{ site.baseurl }}/admin/user-management-cli.html#vm-login for an example.
h3. Transitive permissions
@@ -66,7 +66,7 @@ A "project" is a subtype of Group that is displayed as a "Project" in Workbench,
* The name of a project is unique only among projects and filters with the same owner_uuid.
* Projects can be targets (@head_uuid@) of permission links, but not origins (@tail_uuid@). Putting a project in a @tail_uuid@ field is an error.
-A "filter" is a subtype of Group that is displayed as a "Project" in Workbench, and as a directory by @arv-mount at . See "the groups API documentation":/api/methods/groups.html for more information.
+A "filter" is a subtype of Group that is displayed as a "Project" in Workbench, and as a directory by @arv-mount at . See "the groups API documentation":{{ site.baseurl }}/api/methods/groups.html for more information.
* A filter group cannot own things (cannot appear in @owner_uuid@). Putting a filter group in an @owner_uuid@ field is an error.
* A filter group can be owned by a user or a project.
* The name of a filter is unique only among projects and filters with the same owner_uuid.
diff --git a/doc/api/projects.html.textile.liquid b/doc/api/projects.html.textile.liquid
index b1c74fe0d..9aa3d85d4 100644
--- a/doc/api/projects.html.textile.liquid
+++ b/doc/api/projects.html.textile.liquid
@@ -11,7 +11,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
Arvados @projects@ are used to organize objects. Projects can contain @collections@, @container requests@, @workflows@, etc. Projects can also contain other projects. An object is part of a project if the @owner_uuid@ of the object is set to the uuid of the project.
-Projects are implemented as a subtype of the Arvados @group@ object type, with @group_class@ set to the value "project". More information is available in the "groups API reference":/api/methods/groups.html.
+Projects are implemented as a subtype of the Arvados @group@ object type, with @group_class@ set to the value "project". More information is available in the "groups API reference":{{ site.baseurl }}/api/methods/groups.html.
Projects can be manipulated via Workbench, the cli tools, the SDKs, and the Arvados APIs.
diff --git a/doc/architecture/keep-components-overview.html.textile.liquid b/doc/architecture/keep-components-overview.html.textile.liquid
index b07716aac..4b1ca9b84 100644
--- a/doc/architecture/keep-components-overview.html.textile.liquid
+++ b/doc/architecture/keep-components-overview.html.textile.liquid
@@ -14,13 +14,13 @@ Keep has a number of components. This page describes each component and the role
h3. Keep clients for data access
In order to access data in Keep, a client is needed to store data in and retrieve data from Keep. Different types of Keep clients exist:
-* a command line client like "@arv-get@":/user/tutorials/tutorial-keep-get.html#download-using-arv or "@arv-put@":/user/tutorials/tutorial-keep.html#upload-using-command
-* a FUSE mount provided by "@arv-mount@":/user/tutorials/tutorial-keep-mount-gnu-linux.html
+* a command line client like "@arv-get@":{{ site.baseurl }}/user/tutorials/tutorial-keep-get.html#download-using-arv or "@arv-put@":{{ site.baseurl }}/user/tutorials/tutorial-keep.html#upload-using-command
+* a FUSE mount provided by "@arv-mount@":{{ site.baseurl }}/user/tutorials/tutorial-keep-mount-gnu-linux.html
* a WebDAV mount provided by @keep-web@
* an S3-compatible endpoint provided by @keep-web@
-* programmatic access via the "Arvados SDKs":/sdk/index.html
+* programmatic access via the "Arvados SDKs":{{ site.baseurl }}/sdk/index.html
-In essense, these clients all do the same thing: they translate file and directory references into requests for Keep blocks and collection manifests. How Keep clients work, and how they use rendezvous hashing, is described in greater detail in "the next section":/architecture/keep-clients.html.
+In essense, these clients all do the same thing: they translate file and directory references into requests for Keep blocks and collection manifests. How Keep clients work, and how they use rendezvous hashing, is described in greater detail in "the next section":{{ site.baseurl }}/architecture/keep-clients.html.
For example, when a request comes in to read a file from Keep, the client will
* request the collection object (including its manifest) from the API server
@@ -32,7 +32,7 @@ All of those steps are subject to access control, which applies at the level of
h3. API server
-The API server stores collection objects and all associated metadata. That includes data about where the blocks for a collection are to be stored, e.g. when "storage classes":/admin/storage-classes.html are configured, as well as the desired and confirmed replication count for each block. It also stores the ACLs that control access to the collections. Finally, the API server provides Keep clients with time-based block signatures for access.
+The API server stores collection objects and all associated metadata. That includes data about where the blocks for a collection are to be stored, e.g. when "storage classes":{{ site.baseurl }}/admin/storage-classes.html are configured, as well as the desired and confirmed replication count for each block. It also stores the ACLs that control access to the collections. Finally, the API server provides Keep clients with time-based block signatures for access.
h3. Keepstore
diff --git a/doc/install/arvados-on-kubernetes-GKE.html.textile.liquid b/doc/install/arvados-on-kubernetes-GKE.html.textile.liquid
index f7b7a1641..5a5d59bc8 100644
--- a/doc/install/arvados-on-kubernetes-GKE.html.textile.liquid
+++ b/doc/install/arvados-on-kubernetes-GKE.html.textile.liquid
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-This page documents setting up and running the "Arvados on Kubernetes":/install/arvados-on-kubernetes.html @Helm@ chart on @Google Kubernetes Engine@ (GKE).
+This page documents setting up and running the "Arvados on Kubernetes":{{ site.baseurl }}/install/arvados-on-kubernetes.html @Helm@ chart on @Google Kubernetes Engine@ (GKE).
h2. Prerequisites
diff --git a/doc/install/arvados-on-kubernetes-minikube.html.textile.liquid b/doc/install/arvados-on-kubernetes-minikube.html.textile.liquid
index 9ecb2c895..6b292caf3 100644
--- a/doc/install/arvados-on-kubernetes-minikube.html.textile.liquid
+++ b/doc/install/arvados-on-kubernetes-minikube.html.textile.liquid
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-This page documents setting up and running the "Arvados on Kubernetes":/install/arvados-on-kubernetes.html @Helm@ chart on @Minikube at .
+This page documents setting up and running the "Arvados on Kubernetes":{{ site.baseurl }}/install/arvados-on-kubernetes.html @Helm@ chart on @Minikube at .
h2. Prerequisites
diff --git a/doc/install/arvados-on-kubernetes.html.textile.liquid b/doc/install/arvados-on-kubernetes.html.textile.liquid
index 9169b7810..5ef757d10 100644
--- a/doc/install/arvados-on-kubernetes.html.textile.liquid
+++ b/doc/install/arvados-on-kubernetes.html.textile.liquid
@@ -28,5 +28,5 @@ h2. Requirements
* Minikube or Google Kubernetes Engine (Kubernetes 1.10+ with at least 3 nodes, 2+ cores per node)
* @kubectl@ and @Helm 3@ installed locally, and able to connect to your Kubernetes cluster
-Please refer to "Arvados on Minikube":/install/arvados-on-kubernetes-minikube.html or "Arvados on GKE":/install/arvados-on-kubernetes-GKE.html for detailed installation instructions.
+Please refer to "Arvados on Minikube":{{ site.baseurl }}/install/arvados-on-kubernetes-minikube.html or "Arvados on GKE":{{ site.baseurl }}/install/arvados-on-kubernetes-GKE.html for detailed installation instructions.
diff --git a/doc/install/crunch2/install-compute-node-docker.html.textile.liquid b/doc/install/crunch2/install-compute-node-docker.html.textile.liquid
index 876bb6ae5..66bd85b7c 100644
--- a/doc/install/crunch2/install-compute-node-docker.html.textile.liquid
+++ b/doc/install/crunch2/install-compute-node-docker.html.textile.liquid
@@ -10,7 +10,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
{% include 'notebox_begin_warning' %}
-This page describes the requirements for a compute node in a Slurm or LSF cluster that will run containers dispatched by @crunch-dispatch-slurm@ or @arvados-dispatch-lsf at . If you are installing a cloud cluster, refer to "Build a cloud compute node image":/install/crunch2-cloud/install-compute-node.html.
+This page describes the requirements for a compute node in a Slurm or LSF cluster that will run containers dispatched by @crunch-dispatch-slurm@ or @arvados-dispatch-lsf at . If you are installing a cloud cluster, refer to "Build a cloud compute node image":{{ site.baseurl }}/install/crunch2-cloud/install-compute-node.html.
{% include 'notebox_end' %}
{% include 'notebox_begin_warning' %}
diff --git a/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid b/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
index 09a3b4e3a..8e9db0c4e 100644
--- a/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
+++ b/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
@@ -10,7 +10,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
{% include 'notebox_begin_warning' %}
-This page describes the requirements for a compute node in a Slurm or LSF cluster that will run containers dispatched by @crunch-dispatch-slurm@ or @arvados-dispatch-lsf at . If you are installing a cloud cluster, refer to "Build a cloud compute node image":/install/crunch2-cloud/install-compute-node.html.
+This page describes the requirements for a compute node in a Slurm or LSF cluster that will run containers dispatched by @crunch-dispatch-slurm@ or @arvados-dispatch-lsf at . If you are installing a cloud cluster, refer to "Build a cloud compute node image":{{ site.baseurl }}/install/crunch2-cloud/install-compute-node.html.
{% include 'notebox_end' %}
{% include 'notebox_begin_warning' %}
diff --git a/doc/user/topics/arvados-sync-groups.html.textile.liquid b/doc/user/topics/arvados-sync-groups.html.textile.liquid
index 26be56782..1f7eede4b 100644
--- a/doc/user/topics/arvados-sync-groups.html.textile.liquid
+++ b/doc/user/topics/arvados-sync-groups.html.textile.liquid
@@ -19,7 +19,7 @@ Every line on the file should have 3 values: a group name, a local user identifi
Users can be identified by their email address or username: the tool will check if every user exist on the system, and report back when not found. Groups on the other hand, are identified by their name.
-Permission level can be one of the following: @can_read@, @can_write@ or @can_manage@, giving the group member read, read/write or managing privileges on the group. For backwards compatibility purposes, if any record omits the third (permission) field, it will default to @can_write@ permission. You can read more about permissions on the "group management admin guide":/admin/group-management.html.
+Permission level can be one of the following: @can_read@, @can_write@ or @can_manage@, giving the group member read, read/write or managing privileges on the group. For backwards compatibility purposes, if any record omits the third (permission) field, it will default to @can_write@ permission. You can read more about permissions on the "group management admin guide":{{ site.baseurl }}/admin/group-management.html.
This tool is designed to be run periodically reading a file created by a remote auth system (ie: LDAP) dump script, applying what's included on the file as the source of truth.
-----------------------------------------------------------------------
hooks/post-receive
--
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