From 670cd9558ada4a4ac4d45dc2e61472b2adf67157 Mon Sep 17 00:00:00 2001 From: Martijn Vermaat <martijn@vermaat.name> Date: Tue, 11 Aug 2015 14:55:25 +0200 Subject: [PATCH] Document configuration settings --- doc/config.rst | 170 +++++++++++++++++++++++++++++++++++++++++++++++-- doc/deploy.rst | 12 ++-- 2 files changed, 168 insertions(+), 14 deletions(-) diff --git a/doc/config.rst b/doc/config.rst index 4d43c420..43535b13 100644 --- a/doc/config.rst +++ b/doc/config.rst @@ -47,8 +47,6 @@ The next section describes all available configuration settings. Configuration settings ---------------------- -.. note:: Todo: This section is incomplete. - Note that the configuration file is interpreted as a Python module, so you can use arbitrary Python expressions as configuration values, or even import other modules in it. @@ -57,6 +55,50 @@ Unsetting a configuration setting is done by using the value `None`. If no default value is mentioned for any configuration setting below it means it is not set by default. +.. _config-email: + +EMAIL + The email address used in contact information on the website, as sender in + batch job notifications, and in communication with the NCBI webservices + using Entrez. + + `Default value:` ``mutalyzer@humgen.nl`` + +.. _config-debug: + +DEBUG + If set to `True`, Mutalyzer runs in debug mode and will show more + information with errors. + + `Default value:` `False` + +.. _config-cache-dir: + +CACHE_DIR + The cache directory which is used to store uploaded and downloaded files + such as reference files from the NCBI and batch job results. + + `Default value:` ``/tmp`` + + +User input settings +^^^^^^^^^^^^^^^^^^^ + +MAX_FILE_SIZE + Maximum size for uploaded and downloaded files (in bytes). + + `Default value:` `10 * 1048576` (10 MB) + +EXTRACTOR_MAX_INPUT_LENGTH + Maximum sequence length for description extractor (in bases). + + `Default value:` `50 * 1000` (50 Kbp) + +BATCH_JOBS_ERROR_THRESHOLD + Allow for this fraction of errors in batch jobs. + + `Default value:` `0.05` + Database settings ^^^^^^^^^^^^^^^^^ @@ -80,13 +122,127 @@ DATABASE_URI `Default value:` ``sqlite://`` (in-memory SQLite database) +REDIS_URI + Redis connection URI (can be any `redis-py + <https://github.com/andymccurdy/redis-py>`_ connection URI). Set to `None` + to silently use a mock Redis. Redis is only used for non-essential + features. + + `Default value:` `None` + + +Settings for output and logging +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +All Mutalyzer messages come with a level which can be one of: + +====== ======== ====================================================== +Level Alias Meaning +====== ======== ====================================================== +-1 Log Specifically log a message. +0 Debug Debug information. +1 Info Info. +2 Warning Regular warnings. +3 Error Serious errors that can be compensated for. +4 Fatal Errors that are not recoverable. +5 Off Can be used as a log/output level to turn off output. +====== ======== ====================================================== + +LOG_FILE + Name and location of the log file. + + `Default value:` ``/tmp/mutalyzer.log`` + +LOG_LEVEL + Level of logged messages. + + `Default value:` `3` + +OUTPUT_LEVEL + Level of output messages. + + `Default value:` `1` + +LOG_TIME_FORMAT + Format of time prefix for log messages. Can be anything that is accepted as + the format argument of `time.strftime + <http://docs.python.org/2/library/time.html#time.strftime>`_. + + `Default value:` ``%Y-%m-%d %H:%M:%S`` + + +Website settings +^^^^^^^^^^^^^^^^ + +REVERSE_PROXIED + If set to `True`, the WSGI application runs behind a reverse proxy (e.g., + nginx using ``proxy_pass``). This needs to be set if the application is + mapped to a URL other than / or a different HTTP scheme is used by the + reverse proxy. + + `Default value:` `False` + +.. _config-soap-wsdl-url: + +SOAP_WSDL_URL + URL to the SOAP webservice WSDL document. Used for linking to it from the + documentation page on the website. + + `Default value:` ``https://mutalyzer.nl/services/?wsdl`` + +.. _config-json-root-url: + +JSON_ROOT_URL + URL to the HTTP/RPC+JSON webservice root (without trailing slash). Used for + linking to it from the documentation page on the website. + + `Default value:` ``https://mutalyzer.nl/json`` + + +Piwik settings +^^^^^^^^^^^^^^ + +`Piwik <http://piwik.org/>`_ is an Open Source analytics platform. Mutalyzer +has built-in support for visitor tracking with Piwik. + +PIWIK + If set to `True`, Piwik is enabled and some Javascript tracking code is + included in every Mutalyzer website page. + + `Default value:` `False` + +PIWIK_BASE_URL + Base URL for the Piwik server. + + `Default value:` ``https://piwik.example.com`` + +PIWIK_SITE_ID + Piwik site ID for Mutalyzer. + + `Default value:` `1` + Miscellaneous settings ^^^^^^^^^^^^^^^^^^^^^^ -TESTING - If set to `True`, Mutalyzer assumes to be running its unit tests. This is - done automatically in the provided test suite, so you should never have to - change this setting. +LRG_PREFIX_URL + Prefix URL from where LRG files are fetched. - `Default value:` `False` + `Default value:` ``ftp://ftp.ebi.ac.uk/pub/databases/lrgex/SCHEMA_1_7_ARCHIVE/`` + +DEFAULT_ASSEMBLY + Default genome assembly (by name or alias). + + `Default value:` ``hg19`` + +PROTEIN_LINK_EXPIRATION + Expiration time for cached transcript->protein links from the NCBI (in + seconds). + + `Default value:` `60 * 60 * 24 * 30` (30 days) + +NEGATIVE_PROTEIN_LINK_EXPIRATION + Expiration time for cached negative transcript->protein links from the NCBI + (in seconds). + + `Default value:` `60 * 60 * 24 * 5` (5 days) diff --git a/doc/deploy.rst b/doc/deploy.rst index e0dccc88..ca0d90b2 100644 --- a/doc/deploy.rst +++ b/doc/deploy.rst @@ -22,15 +22,13 @@ using Gunicorn, nginx and Supervisor. Configuration settings ---------------------- -Todo: Link to the description of these configuration settings. - It is recommended to at least set the following configuration settings: -- DEBUG -- EMAIL -- CACHE_DIR -- SOAP_WSDL_URL -- JSON_ROOT_URL +- :ref:`EMAIL <config-email>` +- :ref:`DEBUG <config-debug>` +- :ref:`CACHE_DIR <config-cache-dir>` +- :ref:`SOAP_WSDL_URL <config-soap-wsdl-url>` +- :ref:`JSON_ROOT_URL <config-json-root-url>` WSGI application server: Gunicorn -- GitLab