Merge pull request #41 from FAIRDataTeam/release/1.14.0

Release 1.14.0
FAIRDataTeam · Jun 27, 2022 · 57f5f78 · 57f5f78
2 parents 2324300 + 706a2cb
commit 57f5f78
Show file tree

Hide file tree

Showing 7 changed files with 112 additions and 48 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -22,15 +22,24 @@
 author = 'Dutch Techcentre for Life Sciences'
 
 # The full version, including alpha/beta/rc tags
-release = '1.13.0'
+release = '1.14'
+
+
+rst_prolog = f"""
+
+.. |compose_ver| replace:: {release}
+
+"""
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = []
+extensions = [
+    'sphinx_substitution_extensions',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = []

diff --git a/docs/deployment/advanced-configuration.rst b/docs/deployment/advanced-configuration.rst
@@ -24,7 +24,7 @@ FDP uses InMemory triple store by default. In previous examples, there is Blazeg
 
 There is no need to configure additional properties to run FDP with In-Memory Store because it's the default option. If you want to explicitly type in configuration provided in ``application.yml``, add following lines there:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -36,7 +36,7 @@ There is no need to configure additional properties to run FDP with In-Memory St
 
 With this option, FDP will simply save the data to the file system. If you want to use the Native Store, make sure that you have these lines in your ``application.yml`` file:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -52,7 +52,7 @@ where ``/tmp/fdp-store`` is a path to a location where you want to keep your dat
 
 For running `Allegro Graph <https://franz.com/agraph/allegrograph/>`_, you need to first set up your Allegro Graph instance. For configuring the connection from FDP, add these lines to your ``application.yml`` file:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -71,7 +71,7 @@ For running `Allegro Graph <https://franz.com/agraph/allegrograph/>`_, you need
 
 For running `GraphDB <http://graphdb.ontotext.com>`_, you need to first set up your GraphDB instance and **create the repository**. For configuring the connection from FDP, add these lines to your ``application.yml`` file:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -90,7 +90,7 @@ For running `GraphDB <http://graphdb.ontotext.com>`_, you need to first set up y
 
 For running `Blazegraph <https://blazegraph.com/>`_, you need to first set up your Blazegraph instance. For configuring the connection from FDP, add these lines to your ``application.yml`` file:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -108,7 +108,7 @@ Mongo DB
 ========
 We store users, permissions, etc. in the `MongoDB database <https://www.mongodb.com/>`_. The default connection string is ``mongodb://mongo:27017/fdp``. If you want to modify it, add these lines to your ``application.yml`` file:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -124,7 +124,7 @@ Default attached metadata
 
 There are several default values that are attached to each created metadata. If you want to modify it, add the lines below to your ``application.yml`` file. The default values are listed below, too:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -147,7 +147,7 @@ Hosting FDP Index
 
 To enable FDP Index mode on your FDP server, just simply adjust your ``application.yml`` file:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -157,7 +157,8 @@ To enable FDP Index mode on your FDP server, just simply adjust your ``applicati
 
 Then for the FDP client, you need to use ``fairdata/fairdatapoint-index-client`` Docker image for browsing indexed FDPs and searching harvested metadata. In case you want to use your deployment both as FDP and FDP Index, you can deploy both FDP and FDP Index client applications. The configuration of both clients are identical.
 
-.. code:: yaml
+.. code-block:: yaml
+   :substitutions:
 
     # docker-compose.yml
 
@@ -167,7 +168,7 @@ Then for the FDP client, you need to use ``fairdata/fairdatapoint-index-client``
     # ...
 
     index_client:
-      image: fairdata/fairdatapoint-index-client:1.13
+      image: fairdata/fairdatapoint-index-client:|compose_ver|
       restart: always
       # ...
 
@@ -177,7 +178,7 @@ Connecting to FDP Index
 
 By default, FDPs use https://home.fairdatapoint.org as their primary FDP Index that they ping every 7 days. You can adjust that in  your ``application.yml`` file if needed:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -187,7 +188,7 @@ By default, FDPs use https://home.fairdatapoint.org as their primary FDP Index t
 
 You can also set multiple endpoints if needed:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -203,7 +204,7 @@ FDP Index behind proxy
 
 FDP Index uses IP-based rate limits to avoid excessive communication caused by bots or misconfigured FDPs. If the FDP Index is deployed behind a proxy, it must correctly set header, e.g., ``X-Forwarded-For``. Furthermore, you need to add this to ``application.yml``:
 
-.. code:: yaml
+.. code-block:: yaml
     
     # application.yml
 
@@ -235,7 +236,7 @@ you define the values that you want to change.
 
 Here is an example of changing the primary color.
 
-.. code:: scss
+.. code-block:: scss
 
     // _variables.scss
 
@@ -265,15 +266,15 @@ To change the logo, you need to do three steps:
 2. Mount the new logo to the assets folder
 3. Mount ``_variables.scss`` to SCSS custom folder
 
-.. code:: scss
+.. code-block:: scss
 
     // _variables.scss
 
     $header-logo-url: '/assets/my-logo.png';  // new logo file
     $header-logo-width: 80px;  // width of the new logo 
     $header-logo-height: 40px;  // height of the new logo
 
-.. code:: yaml
+.. code-block:: yaml
 
     # docker-compose.yml
 
@@ -301,34 +302,35 @@ same domain. Here is an example of running FDP on
 have to set ``PUBLIC\_PATH`` ENV variable, in this example to
 ``/fairdatapoint``. Also, don't forget to set correct client URL in the application config.
 
-.. code :: yaml
+.. code-block:: yaml
+   :substitutions:
 
     # docker-compose.yml
 
     version: '3'
     services:
         fdp:
-            image: fairdata/fairdatapoint:1.13
+            image: fairdata/fairdatapoint:|compose_ver|
             volumes:
                 - ./application.yml:/fdp/application.yml:ro
                 # ... other volumes
 
         fdp-client:
-            image: fairdata/fairdatapoint-client:1.13
+            image: fairdata/fairdatapoint-client:|compose_ver|
             ports:
                 - 80:80
             environment:
             	- FDP_HOST=fdp
                 - PUBLIC_PATH=/fairdatapoint
 
-.. code :: yaml
+.. code-block:: yaml
 
     # application.yml
 
     instance:
         clientUrl: https://example.com/fairdatapoint
 
-.. code :: nginx
+.. code-block:: nginx
 
     # Snippet for nginx configuration
 
@@ -343,7 +345,8 @@ have to set ``PUBLIC\_PATH`` ENV variable, in this example to
         }
     }
 
-.. Attention::
 
-When running on nested route, don't forget to change paths to all
-custom assets referenced in SCSS files.
+.. HINT::
+
+   When running on nested route, don't forget to change paths to all
+   custom assets referenced in SCSS files.
diff --git a/docs/deployment/local-deployment.rst b/docs/deployment/local-deployment.rst
@@ -6,18 +6,26 @@ FAIR Data Point is distributed in Docker images. For a simple local deployment,
 
 Here is an example of the simplest `Docker Compose <https://docs.docker.com/compose/>`__ configuration to run FDP.
 
-.. code :: yaml
+.. code-block:: yaml
+   :substitutions:
 
     # docker-compose.yml
 
     version: '3'
     services:
 
         fdp:
+<<<<<<< HEAD
             image: fairdata/fairdatapoint:1.13
 
         fdp-client:
             image: fairdata/fairdatapoint-client:1.13
+=======
+            image: fairdata/fairdatapoint:|compose_ver|
+
+        fdp-client:
+            image: fairdata/fairdatapoint-client:|compose_ver|
+>>>>>>> 9847a0d (Release 1.14.0)
             ports:
                 - 80:80
             environment:
@@ -50,7 +58,7 @@ Running locally on a different port
 
 If you want to run the FAIR Data Point locally on a different port than the default ``80``, additional configuration is necessary. First, we need to create a new file ``application.yml`` and set the client URL to the actual URL we want to use.
 
-.. code :: yaml
+.. code-block:: yaml
 
     # application.yml
 
@@ -59,20 +67,29 @@ If you want to run the FAIR Data Point locally on a different port than the defa
 
 Then, we need to mount the application config into the FDP container and update the port which the FDP client runs on.
 
-.. code :: yaml
+.. code-block:: yaml
+   :substitutions:
 
     # docker-compose.yml
 
     version: '3'
     services:
 
         fdp:
+<<<<<<< HEAD
             image: fairdata/fairdatapoint:1.13
+=======
+            image: fairdata/fairdatapoint:|compose_ver|
+>>>>>>> 9847a0d (Release 1.14.0)
             volumes:
                 - ./application.yml:/fdp/application.yml:ro
 
         fdp-client:
+<<<<<<< HEAD
             image: fairdata/fairdatapoint-client:1.13
+=======
+            image: fairdata/fairdatapoint-client:|compose_ver|
+>>>>>>> 9847a0d (Release 1.14.0)
             ports:
                 - 8080:80
             environment:
@@ -97,18 +114,19 @@ We can also expose port ``27017`` so we can access MongoDB from our local comput
 
 Here is the updated docker-compose file:
 
-.. code :: yaml
+.. code-block:: yaml
+   :substitutions:
 
     # docker-compose.yml
 
     version: '3'
     services:
 
         fdp:
-            image: fairdata/fairdatapoint:1.13
+            image: fairdata/fairdatapoint:|compose_ver|
 
         fdp-client:
-            image: fairdata/fairdatapoint-client:1.13
+            image: fairdata/fairdatapoint-client:|compose_ver|
             ports:
                 - 80:80
             environment:
@@ -132,7 +150,7 @@ In this example, we will configure Blazegraph as a triple store. See :ref:`Tripl
 If we don't have it already, we need to create a new file ``application.yml``. We will use this file to configure the repository and mount it as a read-only volume to the ``fdp`` container. This file can be used for other configuration, see :ref:`Advanced Configuration <advanced-configuration>` for more details.
 
 
-.. code :: yaml
+.. code-block:: yaml
 
     # application.yml
 
@@ -145,20 +163,21 @@ If we don't have it already, we need to create a new file ``application.yml``. W
 
 We now need to update our ``docker-compose.yml`` file, we add a new volume for the ``fdp`` and add ``blazegraph`` service. We can also expose port ``8080`` for Blazegraph so we can access its user interface.
 
-.. code :: yaml
+.. code-block:: yaml
+   :substitutions:
 
     # docker-compose.yml
 
     version: '3'
     services:
 
         fdp:
-            image: fairdata/fairdatapoint:1.13
+            image: fairdata/fairdatapoint:|compose_ver|
             volumes:
                 - ./application.yml:/fdp/application.yml:ro
 
         fdp-client:
-            image: fairdata/fairdatapoint-client:1.13
+            image: fairdata/fairdatapoint-client:|compose_ver|
             ports:
                 - 80:80
             environment: