📚 [Documentation]: Doc related to configuration

[huard]

Description

This is the configuration doc found on pavics-sdi. I fear it is outdated and suggest to merge it (if useful) into the doc here.

.. _config:

===============================
Birdhouse service configuration
===============================

All birdhouse components are deployed and configured using the following methods:

* Run ``docker-compose`` on a :file:`docker-compose.yml` config file to launch a group of containers using their images and some options.
* When a container is starting a make call with the target update-config and start is done (specified by the dockerfile CMD statement)

  * The update-config target update the container application config using buildout and the custom.cfg config file
  * The start target launch the application using supervisor

To customize the container application config we must also update the custom.cfg file used by the buildout recipe of each container.

  * Since custom.cfg is built into the docker image and thus reset each time we run an image the only way to alter it is to mount a host file inside the container using the volume option. Therefore a :file:`custom.cfg` is configured on host for each birdhouse component and mounted inside the container using the volume option of the :file:`docker-compose.yml` file. This way each time a container is started, it is configured by the host :file:`custom.cfg` file which indeed persist the lifecycle of a container

  * The :file:`custom.cfg` is a buildout configuration file which extends :file:`buildout.cfg` providing default parameters. Each birdhouse component has it's own buildout recipe looking for particular parameters to configure their application.

.. note::
	An exemple recipe for ncWMS configuration can be found here: https://github.com/bird-house/birdhousebuilder.recipe.ncwms. Look on github for other components recipe : https://github.com/bird-house.

Hummingbird
-----------

For more information on Hummingbird, see the `Hummingbird-Birdhouse documentation <https://birdhouse-hummingbird.readthedocs.io/en/latest/>`_.

.. warning::
	First try at running CDO operation using the Hummingbird WPS (with url for input NetCDF file, only seems to work with the fileserver, not OPeNDAP), e.g. : http://132.217.140.31:8092/wps?service=WPS&version=1.0.0&request=Execute&identifier=cdo_operation&DataInputs=dataset=http://192.168.101.175:8083/thredds/fileServer/birdhouse/nrcan/nrcan_canada_daily/nrcan_canada_daily_pr_1960.nc;operator=monmax returns "PyWPS Process cdo_operation successfully calculated". However the output points to a NetCDF file on localhost (http://localhost:38092/wpsoutputs/hummingbird/output-4f80cb02-58db-11e6-8a37-533b457038a6.nc). Need to substitute localhost for the ip (132.217.140.31) and keep the same port : http://132.217.140.31:38092/wpsoutputs/hummingbird/output-4f80cb02-58db-11e6-8a37-533b457038a6.nc Previous note: the same operation with the command-line, and using the OPeNDAP link (i.e. >> cdo monmax http://132.217.140.31:8083/thredds/dodsC/birdhouse/nrcan/nrcan_canada_daily/nrcan_canada_daily_pr_1960.nc output.nc) succeeds, in ~3 minutes. It is much faster if the file is local. This brings up the question of whether we should pass the catalogue url when we know the file is actually on a local machine... Trying to execute the same process via our Phoenix installation is not possible. The execute button remains greyed out after entering an url and selecting an operator.


Phoenix
-------

.. note::
	The Phoenix service requires a valid ssl certificate and key prior to running ``docker-compose`` in order to make use of HTTPS. In the :file:`docker-compose.yml` file, within the `phoenix/volumes` configuration, set the environment variable SSL_CERTIFICATE  to a valid certificate. This certificate file should contain both the CERTIFICATE and PRIVATE KEY parts as required by the nginx "ssl_certificate_key" and "ssl_certificate" parameters.

For more information on Phoenix, see the `Pyramid-Phoenix documentation <https://pyramid-phoenix.readthedocs.io/en/latest/>`_.

.. code-block:: bash
   :caption: :file:`/config/phoenix/custom.cfg`

   [settings]
   # User: admin, Password: querty
   phoenix-password = sha256:...

To change password get into the phoenix running container and use ``make passwd``. This will update the persistant host :file:`custom.cfg` with the new password hash.
If an error about missing ``IPython.lib`` occurs install `ipython`_ like this::

   source $ANACONDA_HOME/bin/activate birdhouse
   pip install ipython

Phoenix still requires manual configuration in order for Solr to correctly index the THREDDS catalog:

#. Go to https://<platform_url>:8443/
#. Click on the login button |login|
#. Use the admin phoenix access with 'querty' password:

   .. image:: images/phoenix_username.*

#. Go to the settings page |settings|
#. Click on the |service| button:

   .. image:: images/phoenix_services.*

#. Register a new service:

   .. image:: images/phoenix_register.*

#. Fill the form using the thredds catalog url (use the OpenStack internal IP), a service name of your choice and be sure to check the Thredds Catalog service type :

   .. image:: images/phoenix_register_thredds.*

#. Click on the register button
#. Go to the Solr settings page by repeating the steps 4 and 5 but this time using the Solr button.

   .. image:: images/phoenix_solr.*

#. Use the Parameters tab and increase the crawling depth to match the deepest catalog depth :
#. Activate the crawling in the Thredds Services tab by clicking on the toggle button near the + symbol.

   .. image:: images/phoenix_thredds_activate.png

#. The status should turn to green when you click on the refresh button.


ncWMS
-----

.. code-block:: bash
   :caption: :file:`/config/ncwms2/custom.mfg`

   [settings]
   tomcat-ncwms-password = <enter ncwms password>

   [ncwms]
   data_dir = /pavics-data

Manual setup of the running docker
----------------------------------
To access the ncWMS admin page (changes be overriden each time the container is restarted), edit the file: :file:`/opt/conda/envs/birdhouse/opt/apache-tomcat/conf/tomcat-users.xml` and remove the comment block around the manager-gui and ncWMS-admin role.
The administration page allow administrators to add new datasets but again it will not persist upon container restarting.


Default Tomcat credentials::

   username="birdhouse"
   password="4FO72WcTt7K9gYiNKApf"

Default ncWMS credentials::

   username="admin"
   password="ju68hfld"

Dynamic services
----------------

.. warning::
	The dynamic services section allow with only one command to enable access to all the database available at :file:`M:\data16\projets\multi\PAVICS\data` by configuring a file system entrypoint. The only thing to do is to use the following url: http://<domain>:8080/ncWMS2/wms?SERVICE=WMS&REQUEST=GetCapabilities&VERSION=1.3.0&DATASET=outputs/<path> and replace ``<path>`` by the relative path to :file:`M:\data16\projets\multi\PAVICS\data` to the required dataset. So thanks to this config and to the catalog service we should be able to get the entire database list from the catalog and access their WMS by using the relative path in the wms url.

THREDDS
-------

.. code-block:: bash

   [thredds]
   data_root = /pavics-data
   allow_wcs = true
   allow_wms = true


PAVICS-DataCatalog
------------------

In the catalog.cfg file:
* Provide the solr and THREDDS host.
* Set the wps host to the server that will be exposing the catalog (this is the server where wps temporary output files will be saved).
* Set the WMS alternate server if desired.


.. |login| image:: images/phoenix_login.*
.. |settings| image:: images/phoenix_setting.*
.. |refresh| image:: images/phoenix_refresh.*
.. |service| image:: images/phoenix_services.*

.. _pavics-sdi: https://github.com/Ouranosinc/pavics-sdi.git
.. _Docker: http://docker.com
.. _DockerHub: https://hub.docker.com/
.. _ipython:  https://ipython.org


Magpie
------

Emu
---

Other Birds?
------------


.. todo::
   Examine the Birdhouse/Birdhouse-Docs to see if this section can be merged back to it and joined as a submodule here. Birds of interest are listed there.

References

Information	Value
Server/Platform URL
Related issues/PR
Related documentation

[tlvu]

The entire birdhouse-deploy config is in the env.local config file, with each config item fully documented in the example file, see https://github.com/bird-house/birdhouse-deploy/blob/93ed91b9223e2eb89c8b83109282d2f79e8218e7/birdhouse/env.local.example

Let me know if this can be closed.

[huard]

The question is, is any of the information copied here still relevant and missing from the birdhouse-deploy docs. If not, we simply close this issue and the material disapears.