Merge pull request #13 from neicnordic/update/dependencies-info

Update/dependencies info

docs/connection.rst

@@ -27,7 +27,7 @@ Configuration
 
 The following environment variables can be used to configure the broker:
 
-.. note:: We use `RabbitMQ 3.7.8`_ including the management plugins.
+.. note:: We use `RabbitMQ 3.8.16`_ including the management plugins.
 
 +----------------------+----------------------------------------------+
 | Variable             | Description                                  |
@@ -248,7 +248,7 @@ which will respond with the same content, but adding the `Accession ID`.
       ]
    }
 
-``Finalize`` service should receive the message below and assign the `Accession ID` to the
+``Finalize`` service should receive the message below and assign the ``Accession ID`` to the
 corresponding file and send a message to ``backup`` queue for the backup services or in case there 
 is no backup service to the ``completed`` queue.
 
@@ -279,4 +279,4 @@ containing accession IDs mapping between files and datasets
 
 .. |connect| unicode:: U+21cc .. <->
 .. _RabbitMQ: http://www.rabbitmq.com
-.. _RabbitMQ 3.7.8: https://hub.docker.com/_/rabbitmq
+.. _RabbitMQ 3.8.16: https://hub.docker.com/_/rabbitmq

docs/dataout.rst

@@ -3,7 +3,12 @@
 Data Retrieval API
 ==================
 
-.. note:: Source code repository for Data Out API is available at: https://github.com/neicnordic/sda-doa
+.. note:: We maintain two Data Out API solutions, for which REST APIs are the same.
+
+SDA-DOA
+-------
+
+.. note:: Source code repository is available at: https://github.com/neicnordic/sda-doa
 
 Configuration
 -------------
@@ -82,18 +87,8 @@ Configuration
 | ``LOGSTASH_PORT``                      |                                                                      | Port of the Logstash instance (if any)             |
 +----------------------------------------+----------------------------------------------------------------------+----------------------------------------------------+
 
-REST API Endpoints
-------------------
-
-.. note:: REST API can be disabled using ``REST_ENABLED`` environment variable.
-
-API endpoints listed as OpenAPI specification is available:
-
-.. literalinclude::  ./static/doa-api.yml
-    :language: yaml
-
 Outbox functionality
---------------------
+~~~~~~~~~~~~~~~~~~~~
 
 .. note:: Outbox can be disabled using ``OUTBOX_ENABLED`` environment variable.
 
@@ -172,3 +167,32 @@ Dataset permissions are read from GA4GH RI claims of the type "ControlledAccessG
         }
     }
 
+
+SDA-download
+------------
+
+.. note:: Source code repository is available at: https://github.com/neicnordic/sda-download
+
+
+Recommended provisioning method for production is:
+
+* on a ``kubernetes cluster`` using the `helm chart <https://github.com/neicnordic/sda-helm/>`_.
+
+
+``sda-download`` focuses on enabling deployment of a stand-alone version of SDA, with features such as:
+* trusted ``JKU`` and ``ISS`` pairs;
+* custom dataset names including DOI URLs;
+* etc.
+
+
+REST API Endpoints
+------------------
+
+.. note:: REST API can be disabled using ``REST_ENABLED`` environment variable.
+
+API endpoints listed as OpenAPI specification is available:
+
+.. literalinclude::  ./static/doa-api.yml
+    :language: yaml
+
+

docs/db.rst

@@ -3,7 +3,7 @@
 Database Setup
 ==============
 
-We use a Postgres database (version 11.6+ ) to store intermediate data,
+We use a Postgres database (version 13+ ) to store intermediate data,
 in order to track progress in file ingestion. The ``lega`` database
 schema is documented below.
 
@@ -82,7 +82,7 @@ releases of the secure data archive and database schema versions. A
 new secure data archive release may increase several schema
 versions/migrations or none.
 
-.. IMPORTANT::
+.. important::
    Any changes done to database schema initialization should be
    reflected in a schema migration script.
 
@@ -91,10 +91,10 @@ changing both the database initialization scripts (and bumping the
 bootstrapped schema version) as well as creating the corresponding
 migration script to perform the changes on a database in use.
 
-Migration scripts should be placed in `/migratedb.d/` in the
+Migration scripts should be placed in ``/migratedb.d/`` in the
 sda-db repo (https://github.com/neicnordic/sda-db). We
 recommend naming them corresponding to the schema version they provide
-migration to. There is an "eqmpty" migration script (`01.sql`) that can
+migration to. There is an "eqmpty" migration script (``01.sql``) that can
 be used as a template.
 
 local_ega tables

docs/deploy.rst

@@ -14,8 +14,8 @@ The production deployment repositories are:
 The following container images are used in the deployments:
 
 * ``neicnordic/sda-pipeline``, provides the LocalEGA services (minimal container with static binary and support files).
-* ``neicnordic/sda-mq``, provides the broker (mq) service (based on `rabbitmq:3.7.8-management-alpine`);
-* ``neicnordic/sda-db``, provides the database service (based on `postgres:11.2-alpine`);
+* ``neicnordic/sda-mq``, provides the broker (mq) service (based on `rabbitmq:3.8.16-management-alpine`);
+* ``neicnordic/sda-db``, provides the database service (based on `postgres:13-alpine3.14`);
 * ``neicnordic/sda-inbox-sftp``, provides the inbox service via sftp (based on Apache Mina, container base `openjdk:13-alpine`);
 * ``neicnordic/sda-doa``, provides the data out service (Data Out API);
 * ``neicnordic/sda-s3-proxy``, provides the inbox service via a s3 proxy (S3 proxy inbox, minimal container with static binary and support files).

docs/index.rst

@@ -60,8 +60,8 @@ whether the ingestion was successful, or whether there was an error.
 More details about the :ref:`ingestion process`.
 
 Once a file has been successfully submitted and the ingestion process has been finalised,
-including receiving an `Accession ID` from Central EGA. The Data Out API can be
-utilised to retrieve set file by utilising the `Accession ID`. More details in :ref:`data out`.
+including receiving an ``Accession ID`` from Central EGA. The Data Out API can be
+utilised to retrieve set file by utilising the ``Accession ID``. More details in :ref:`data out`.
 
 ----
 
@@ -70,7 +70,6 @@ Getting started
 
 .. toctree::
    :maxdepth: 2
-   :name: setup
 
    Getting started                   <setup>
    Database Setup                    <db>
@@ -81,7 +80,6 @@ Information about the Architecture
 
 .. toctree::
    :maxdepth: 2
-   :name: architecture
 
    Encryption                <encryption>
    Data Submission           <submission>
@@ -93,7 +91,6 @@ Miscellaneous
 
 .. toctree::
    :maxdepth: 1
-   :name: extra
 
    SDA-Pipeline              <https://neicnordic.github.io/sda-pipeline/pkg/sda-pipeline/>
    Tests                     <tests>

docs/submission.rst

@@ -20,7 +20,7 @@ Ingestion Workflow
 .. image:: /static/ingestion-sequence.svg
    :alt: Ingestion sequence diagram
 
-.. admonition:: Ingestion Workflow Legend
+.. note:: Ingestion Workflow Legend
 
    The sequence diagram describes the different phases during the ingestion process. 
    The elements at the top represent each of the services or actuators involved in the workflow. 
@@ -39,7 +39,7 @@ The ``Ingest`` service (can be replicated) reads file from the ``Submission Inbo
 and splits Crypt4GH header from the beginning of the file, puts it in
 a database and sends the remainder to the ``Archive``, leveraging the Crypt4GH format.
 
-.. hint:: There is no decryption key retrieved during that step. The ``Archive`` can be
+.. note:: There is no decryption key retrieved during that step. The ``Archive`` can be
           either a regular file system on disk, or an S3 object storage.
           ``Submission Inbox`` can also have as a backend a regular file system
           or S3 object storage.
@@ -96,8 +96,8 @@ checksum. This information is provided to CentralEGA via a
 :doc:`shovel mechanism on the local message broker <connection>`.
 We can configure default cache TTL via ``CACHE_TTL`` environment variable.
 
-Configuration
-"""""""""""""
+Apache Mina Configuration
+"""""""""""""""""""""""""
 
 Environment variables used:
 
@@ -112,9 +112,9 @@ Environment variables used:
 +-------------------------+--------------------+------------------------------------------------------------+
 | ``BROKER_PORT``         | 5672               | RabbitMQ broker port                                       |
 +-------------------------+--------------------+------------------------------------------------------------+
-| ``BROKER_VHOST``        | /                  | RabbitMQ broker vhost                                      |
+| ``BROKER_VHOST``        | ``/``              | RabbitMQ broker vhost                                      |
 +-------------------------+--------------------+------------------------------------------------------------+
-| ``INBOX_PORT``          | 2222               | Inbox port                                                 |
+| ``INBOX_PORT``          | ``2222``           | Inbox port                                                 |
 +-------------------------+--------------------+------------------------------------------------------------+
 | ``INBOX_LOCATION``      | /ega/inbox/        | Path to POSIX Inbox backend                                |
 +-------------------------+--------------------+------------------------------------------------------------+
@@ -169,8 +169,8 @@ CEGA REST endpoint authentication to a JWT that can be used when uploading to th
 The proxy requires the user to set the bucket name the same as the username when uploading data,
 ``s3cmd put FILE s3://USER_NAME/path/to/file``
 
-Configuration
-"""""""""""""
+S3 proxy Configuration
+""""""""""""""""""""""
 
 The S3 proxy server can be configured via a yaml formatted file with the
 top level blocks, ``aws:``, ``broker:`` and ``server:``.