Documentation: Add section on configurations.

2 files changed, 127 insertions, 4 deletions

diff --git a/README.org b/README.org
index d7a0dcb..9e0324a 100644
--- a/README.org
+++ b/README.org
@@ -1,5 +1,6 @@
 #+STARTUP: inlineimages
 #+TITLE: GeneNetwork Quality Control Application
+#+OPTIONS: ^:{}
 
 ** Project Goals
 
@@ -40,6 +41,130 @@ This repository can be used as a guix channel.
         "F370 F409 854B 90E3 52F3  AB01 362B 0BB8 B81D 5A42"))))
 #+END_SRC
 
+** Configuration
+
+This system requires that some configurations be in place to operate correctly.
+The following sections detail the configuration variables.
+
+*** System Configurations
+
+**** *Config*: =LOG_LEVEL=
+*Default*: WARNING
+
+We use logging to track the operation of the system, noting major events, and
+conditions in the system as it runs. The =LOG_LEVEL= variable controls how much
+of that information we want to track, and the severity of said information.
+
+**** *Config*: =SECRET_KEY=
+
+*Mandatory*
+
+This is a key used for signing cookies for more secure tamper-proof sessions.
+Without it, Flask will generate a random key for each running thread/process of
+the system, leading to some really difficult to debug consequences.
+
+/Avoid the aggravation! Just set a secret key and be done with it/.
+
+For some more information on Flask's =SECRET_KEY= have a look at the following
+resources:
+
+- https://flask.palletsprojects.com/en/3.0.x/config/#SECRET_KEY
+- https://flask.palletsprojects.com/en/3.0.x/quickstart/#sessions
+- https://stackoverflow.com/a/48596852
+
+**** *Config*: `UPLOAD_FOLDER`
+
+*Default*: /tmp/qc_app_files
+
+This is the directory where all uploaded files are stored.
+
+Files are to be stored here temporary, while they are still being processed.
+Down the line, we will probably have a different location for files that have
+passed QC and whose data has been accepted into the system.
+
+*Development Note*: Other files we store here that we will need to extract to a
+separate configuration are:
+
+- Files with outputs from background processes triggered by this system
+- /list others here…/
+
+**** *Config*: =SQL_URI=
+*Mandatory*
+
+This defines the connection URI to the database.
+
+This is a *MANDATORY* configuration variable: without it, the uploader will not
+work as expected, if at all.
+
+Presently, we use the MariaDB database, and thus, the URI to the database will
+take the form
+
+#+BEGIN_EXAMPLE
+mysql://<username>:<password>@<hostname-or-ip>:<port>/<database-name>
+#+END_EXAMPLE
+
+The parts of the URI of note are:
+
+- =<username>=: This is the username to use to connect to the MariaDB server
+- =<password>=: A password to authenticate the user with the MariaDB server
+- =<hostname-or-ip>=: The domain name or IP address of the computer hosting the
+  MariaDB server
+- =<port>=: The port to connect to for the MariaDB server, on the computer
+  hosting MariaDB
+- =<database-name>=: The database to connect to
+
+*** Redis Configurations
+
+**** *Config*: =REDIS_URL=
+
+*Default*: redis://
+
+This is the connection URI to the Redis server. The default connection parameter
+above tries to connect to a redis server on the same host that the uploader is
+running on.
+
+*Note to Fred*: We should probably rename this =REDIS_URI= for consistency.
+
+The Redis connection URI has the general form:
+
+#+BEGIN_EXAMPLE
+redis://<username>:<password>@<hostname-or-ip>:<port>/<dbnum>
+#+END_EXAMPLE
+
+and the parts of the URI of note are:
+
+- =<username>=: This is the username to use to connect to the Redis server
+- =<password>=: A password to authenticate the user with the Redis server
+- =<hostname-or-ip>=: The domain name or IP address of the computer hosting the
+  Redis server
+- =<port>=: The port to connect to for the Redis server, on the computer
+  hosting Redis
+- =<dbnum>=: A number identifying the database to connect to
+
+  Here is [a resource](https://github.com/lettuce-io/lettuce-core/wiki/Redis-URI-and-connection-details)
+  on other ways to construct Redis connection URIs.
+
+**** *Config*: =JOBS_TTL_SECONDS=
+
+*Default*: 1209600 seconds (14 days)
+
+This is the "Time-To-Live" for the keys in redis. Most of the keys we store in
+Redis from this system do not need to be retained forever. The TTL determines
+how long (in seconds) to keep the keys around for.
+
+**** *Config*: =GNQC_REDIS_PREFIX=
+
+*Default*: GNQC
+
+This system could find itself sharing a Redis server with other (related)
+applications such as [GN2](https://github.com/genenetwork/genenetwork2) and
+[GN3](https://github.com/genenetwork/genenetwork3).
+
+The =GNQC_REDIS_PREFIX= configuration is prepended to the keys being saved by
+this system to redis. For example, if ~GNQC_REDIS_PREFIX=GNQC~ and you want to
+set up a hash with the key =users=, the effective key in redis will be
+~GNQC:users~.
+
 ** Development
 
 For reproducibility, this project is developed using guix.
@@ -136,7 +261,7 @@ guix package [-p /path/to/qc/profile] -f guix.scm
 :CUSTOM_ID: run-cli-version
 :END:
 
-Install the application as shown in the [[Installing QC]] section above.
+Install the application as shown in the /Installing QC/ section above.
 
 To run qc against a file, the syntax is:
 #+BEGIN_SRC shell
diff --git a/etc/default_config.py b/etc/default_config.py
index 45272de..7a9da0f 100644
--- a/etc/default_config.py
+++ b/etc/default_config.py
@@ -11,6 +11,4 @@ UPLOAD_FOLDER = "/tmp/qc_app_files"
 REDIS_URL = "redis://"
 JOBS_TTL_SECONDS = 1209600 # 14 days
 GNQC_REDIS_PREFIX="GNQC"
-GN3_URL="http://localhost:8080"
-SQL_URI = os.getenv(
-    "SQL_URI", "mysql://gn2:mysql_password@localhost/db_webqtl_s")
+SQL_URI = ""