Project Goals
The project seeks to handle the checking of data files for correct syntax and other errors before allowing the code to be uploaded.
The files are "tab-separated" values (TSV) files, and must conform to the following criteria:
Line-Level Checks
- Must be tab-separated
Cell-Level Checks
- No empty data cells
- no data cells with spurious characters like `eeeee`, `5.555iloveguix`, etc.
- decimal numbers must conform to the following criteria:
- - when checking an average file decimal numbers must contain exactly three places to the right side of the dot.
- - when checking a standard error file decimal numbers must contain six or greater places to the right side of the dot.
- - there must be a number to the left side of the dot (e.g. 0.55555 is allowed but .55555 is not).
- check line endings to make sure they are Unix and not DOS
- check strain headers against a source of truth (see strains.csv)
Guix Channel
This repository can be used as a guix channel.
(channel (name 'gn-uploader) (url "https://git.genenetwork.org/gn-uploader") (branch "main") (introduction (make-channel-introduction "93c77842315d304abbfc27d78d98b7d42da32a61" (openpgp-fingerprint "F370 F409 854B 90E3 52F3 AB01 362B 0BB8 B81D 5A42"))))
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:
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 hereā¦
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
mysql://<username>:<password>@<hostname-or-ip>:<port>/<database-name>
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:
redis://<username>:<password>@<hostname-or-ip>:<port>/<dbnum>
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 toHere 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.
To launch a guix shell for development, do
guix shell --container --network --share=/some/host/directory=/the/upload/directory --development --file=guix.scm
which environment that is isolated from the rest of your system.
We share a host directory with the container (that is writeable by the user that started the web application) to serve as the upload directory for the application.
Run the CLI version
Run the CLI version of the application, with
python3 -m scripts.qc --help
Run the web version
You need to have a running Redis instance, and configure the application to connect to it.
To run the web-version of the qc app in development mode, you need to set up a few environment variables
export FLASK_APP=wsgi.py export FLASK_ENV=development export UPLOADER_CONF=/path/to/directory/with/uploader/configuration.py
then you can run the application with
flask run
Checks
To run the linter over the code base, run:
pylint setup.py tests quality_control uploader r_qtl scripts
To check for correct type usage in the application, run:
mypy --show-error-codes .
Run unit tests with:
$ export UPLOADER_CONF=</path/to/configuration/file.py> $ pytest -m unit_test
To run ALL tests (not just unit tests):
$ export UPLOADER_CONF=</path/to/configuration/file.py> $ pytest
Deploying/Installing QC
NOTE: All tests should pass before you deploy the uploader!
CLI: Docker
Generate the docker image file with
guix pack -f docker -S /bin=bin genenetwork-qc
That creates the image file with a path such as:
/gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz
You can now load this file into docker withe
docker load < /gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz
and from there, you can run the application as detailed in the Running QC: CLI-Version section below
CLI: Guix
The application can be installed using guix by pointing to the guix.scm file as follows:
guix package [-p /path/to/qc/profile] -f guix.scm
Web-Version
TODO Document deployment details for the web version of GeneNetwork QC better
Running QC
Command-Line Version
Install the application as shown in the Installing QC section above.
To run qc against a file, the syntax is:
qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>
where
<filetype>
is one of "average" or "standard-error"<filepath>
is either an absolute path to the file, or a path relative to the current working directory- if the
--strainsfile
option is not provided, it will default to the one in the root directory of this repository - the
--verbose
option is a flag, defaulting toFalse
that controls the display of optional progress messages
To view the usage information for the application, run
qc --help
Web Version
TODO Document usage of the web-UI version of the application
Docker
Download the docker image file from the releases page of the application and load it to docker with something like:
docker load < genenetwork-qc-0.0.1-1-oxu472i-docker.tar.gz
replacing genenetwork-qc-0.0.1-1-oxu472i.tar.gz
with the actual name of the
release you downloaded
Run the application with something like:
docker run -v /path/to/qnqc_py/tests/test_data:/data -ti \ genenetwork-qc:latest /bin/qc average /data/average_error_at_end_200MB.tsv
replacing /path/to/qnqc_py/tests/test_data
with the path to the folder where
the file you want to check is in, and average_error_at_end_200MB.tsv
with the
name of the file you want to check for errors.