[ARVADOS] updated: 1.3.0-1992-g6da6b8460

Git user git at public.arvados.org
Fri Dec 13 16:44:30 UTC 2019


Summary of changes:
 doc/Rakefile                                                 | 4 ++++
 doc/admin/upgrading.html.textile.liquid                      | 4 ++--
 doc/api/crunch-scripts.html.textile.liquid                   | 2 +-
 doc/architecture/federation.html.textile.liquid              | 4 ++--
 doc/install/index.html.textile.liquid                        | 2 +-
 doc/install/install-manual-prerequisites.html.textile.liquid | 3 +--
 doc/install/install-shell-server.html.textile.liquid         | 4 ++--
 doc/sdk/python/sdk-python.html.textile.liquid                | 2 +-
 doc/user/cwl/cwl-runner.html.textile.liquid                  | 2 +-
 9 files changed, 15 insertions(+), 12 deletions(-)

       via  6da6b846097364da3abed2abad272e9607b15ca8 (commit)
      from  195843671127671da9e3ddbc5d3a9fe44d15daba (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 6da6b846097364da3abed2abad272e9607b15ca8
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri Dec 13 11:43:57 2019 -0500

    15572: Passes link checking
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/doc/Rakefile b/doc/Rakefile
index 63dc16d25..71d86c32d 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -43,6 +43,8 @@ file "sdk/R/arvados/index.html" do |t|
     tgt = Dir.pwd
     Dir.mkdir("sdk/R")
     Dir.mkdir("sdk/R/arvados")
+    puts("tgt", tgt)
+    cp('css/R.css', 'sdk/R/arvados')
     docfiles = []
     Dir.chdir("../sdk/R/") do
       STDERR.puts `Rscript createDoc.R README.Rmd #{tgt}/sdk/R/README.md 2>&1`
@@ -114,6 +116,8 @@ file "sdk/java-v2/javadoc/index.html" do |t|
       Dir.chdir("../sdk/java-v2") do
         STDERR.puts `gradle javadoc 2>&1`
         raise if $? != 0
+        puts `sed -i "s/@import.*dejavu.css.*//g" build/docs/javadoc/stylesheet.css`
+        raise if $? != 0
       end
       cp_r("../sdk/java-v2/build/docs/javadoc", "sdk/java-v2")
       raise if $? != 0
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 52a41c267..e93b58723 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -235,7 +235,7 @@ h3(#v1_3_0). v1.3.0 (2018-12-05)
 
 This release includes several database migrations, which will be executed automatically as part of the API server upgrade. On large Arvados installations, these migrations will take a while. We've seen the upgrade take 30 minutes or more on installations with a lot of collections.
 
-The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present. See <a href="{{ site.baseurl }}/install/install-controller.html#configuration">the @arvados-controller@ installation instructions</a>.
+The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present.
 
 Support for the deprecated "jobs" API is broken in this release.  Users who rely on it should not upgrade.  This will be fixed in an upcoming 1.3.1 patch release, however users are "encouraged to migrate":upgrade-crunch2.html as support for the "jobs" API will be dropped in an upcoming release.  Users who are already using the "containers" API are not affected.
 
@@ -269,7 +269,7 @@ h4. New component: arvados-controller
 
 Commit "db5107dca":https://dev.arvados.org/projects/arvados/repository/revisions/db5107dca adds a new system service, arvados-controller. More detail is available in story "#13496":https://dev.arvados.org/issues/13497.
 
-To add the Arvados Controller to your system please refer to the "installation instructions":../install/install-controller.html after upgrading your system to 1.2.0.
+To add the Arvados Controller to your system please refer to the "installation instructions":../install/install-api-server.html after upgrading your system to 1.2.0.
 
 Verify your setup by confirming that API calls appear in the controller's logs (_e.g._, @journalctl -fu arvados-controller@) while loading a workbench page.
 
diff --git a/doc/api/crunch-scripts.html.textile.liquid b/doc/api/crunch-scripts.html.textile.liquid
index 86a22ed6c..3d6ccbdd5 100644
--- a/doc/api/crunch-scripts.html.textile.liquid
+++ b/doc/api/crunch-scripts.html.textile.liquid
@@ -11,7 +11,7 @@ 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":container_requests.html.textile.liquid .*
+p=. *Legacy.  The job APIs are read-only and disabled by default in new installations.  Use "container requests":methods/container_requests.html .*
 
 h2. Crunch scripts
 
diff --git a/doc/architecture/federation.html.textile.liquid b/doc/architecture/federation.html.textile.liquid
index 82f7a33be..e2b80de70 100644
--- a/doc/architecture/federation.html.textile.liquid
+++ b/doc/architecture/federation.html.textile.liquid
@@ -22,11 +22,11 @@ Clusters are identified by a five-digit alphanumeric id (numbers and lowercase l
 
 * For automated tests purposes, use "z****"
 * For experimental/local-only/private clusters that won't ever be visible on the public Internet, use "x****"
-* For long-lived clusters, we recommend reserving a cluster id.  Contact "mailto:support at curoverse.com":support at curoverse.com
+* For long-lived clusters, we recommend reserving a cluster id.  Contact "info at curii.com":mailto:info at curii.com
 
 Cluster identifiers are mapped API server hosts one of two ways:
 
-* Through DNS resolution, under the @arvadosapi.com@ domain.  For example, the API server for the cluster @qr1hi@ can be found at @qr1hi.arvadosapi.com at .  To register a cluster id for free under @arvadosapi.com@, contact "mailto:support at curoverse.com":support at curoverse.com
+* Through DNS resolution, under the @arvadosapi.com@ domain.  For example, the API server for the cluster @qr1hi@ can be found at @qr1hi.arvadosapi.com at .  To register a cluster id for free under @arvadosapi.com@, contact "info at curii.com":mailto:info at curii.com
 * Through explicit configuration:
 
 The @RemoteClusters@ section of @/etc/arvados/config.yml@ (for arvados-controller)
diff --git a/doc/install/index.html.textile.liquid b/doc/install/index.html.textile.liquid
index 506ff4d4b..327ac0c45 100644
--- a/doc/install/index.html.textile.liquid
+++ b/doc/install/index.html.textile.liquid
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-Arvados components run on GNU/Linux systems, and supports AWS, GCP and Azure cloud platforms as well as on-premises installs.  Arvados supports Debian and derivatives such as Ubuntu, as well as Red Hat and derivatives such as CentOS.  "Arvados is Free Software":{{site.baseurl}}/copying/copying.html and self-install installations are not limited in any way.  Commercial support and development are also available from "Curii Corporation.":mailto:info at curii.com
+Arvados components run on GNU/Linux systems, and supports AWS, GCP and Azure cloud platforms as well as on-premises installs.  Arvados supports Debian and derivatives such as Ubuntu, as well as Red Hat and derivatives such as CentOS.  "Arvados is Free Software":{{site.baseurl}}/user/copying/copying.html and self-install installations are not limited in any way.  Commercial support and development are also available from "Curii Corporation.":mailto:info at curii.com
 
 Arvados components can be installed and configured in a number of different ways.
 
diff --git a/doc/install/install-manual-prerequisites.html.textile.liquid b/doc/install/install-manual-prerequisites.html.textile.liquid
index 36298b832..dd8dd7b0a 100644
--- a/doc/install/install-manual-prerequisites.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites.html.textile.liquid
@@ -101,11 +101,10 @@ For a production installation, this is a reasonable configuration:
 <div class="offset1">
 table(table table-bordered table-condensed).
 |_. Function|_. Number of nodes|_. Recommended specs|
-|Postgres database, Arvados API server, Arvados controller, Git, Websockets|1|16+ GiB RAM, 4+ cores, fast disk for database|
+|Postgres database, Arvados API server, Arvados controller, Git, Websockets, Container dispatcher|1|16+ GiB RAM, 4+ cores, fast disk for database|
 |Single Sign-On (SSO) server ^1^|1|2 GiB RAM|
 |Workbench, Keepproxy, Keep-web, Keep-balance|1|8 GiB RAM, 2+ cores|
 |Keepstore servers ^2^|2+|4 GiB RAM|
-|Compute scheduler|1|2 GiB RAM|
 |Compute worker nodes ^2^|2+ |Depends on workload|
 |User shell nodes ^3^|0+|Depends on workload|
 </div>
diff --git a/doc/install/install-shell-server.html.textile.liquid b/doc/install/install-shell-server.html.textile.liquid
index 99d618b37..00aae6c3c 100644
--- a/doc/install/install-shell-server.html.textile.liquid
+++ b/doc/install/install-shell-server.html.textile.liquid
@@ -31,7 +31,7 @@ h2(#dependencies). Install Dependecies and SDKs
 # "Install Ruby and Bundler":ruby.html
 # "Install the Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html
 # "Install the CLI":{{site.baseurl}}/sdk/cli/install.html
-# "Install the R SDK":{{site.baseurl}}/sdk/R/install.html (optional)
+# "Install the R SDK":{{site.baseurl}}/sdk/R/index.html (optional)
 # "Install Docker":install-docker.html (optional)
 
 {% assign arvados_component = 'git curl' %}
@@ -110,4 +110,4 @@ A user should be able to log in to the shell server when the following condition
 # As an admin user, you have given the user permission to log in using the Workbench → Admin menu → "Users" item → "Show" button → "Admin" tab → "Setup account" button.
 # The cron job has run.
 
-See also "how to add a VM login permission link at the command line":admin/user-management-cli.html
+See also "how to add a VM login permission link at the command line":../admin/user-management-cli.html
diff --git a/doc/sdk/python/sdk-python.html.textile.liquid b/doc/sdk/python/sdk-python.html.textile.liquid
index 381c01d53..b1aca316a 100644
--- a/doc/sdk/python/sdk-python.html.textile.liquid
+++ b/doc/sdk/python/sdk-python.html.textile.liquid
@@ -10,7 +10,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-The Python SDK provides access from Python to the Arvados API and Keep.  It also includes a number of command line tools for using and administering Arvados and Keep, and some conveniences for use in Crunch scripts; see "Crunch utility libraries":crunch-utility-libraries.html for details.
+The Python SDK provides access from Python to the Arvados API and Keep, along with a number of command line tools for using and administering Arvados and Keep.
 
 h2. Installation
 
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index f38cbf1de..2be803b52 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -84,7 +84,7 @@ When running a workflow on an Arvados cluster, the input files must be stored in
 
 A URI reference to Keep uses the @keep:@ scheme followed by either the portable data hash or UUID of the collection and then the location of the file inside the collection.  For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@ or @keep:zzzzz-4zz18-zzzzzzzzzzzzzzz/19.fasta.bwt at .
 
-If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount.html, such as @/home/example/keep/by_id/2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@, then @arvados-cwl-runner@ will automatically determine the appropriate Keep URI reference.
+If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html, such as @/home/example/keep/by_id/2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@, then @arvados-cwl-runner@ will automatically determine the appropriate Keep URI reference.
 
 If you reference a local file which is not in @arv-mount@, then @arvados-cwl-runner@ will upload the file to Keep and use the Keep URI reference from the upload.
 

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