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#+STARTUP: inlineimages
#+TITLE: GeneNetwork Quality Control Application
** 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)
** Development
For reproducibility, this project is developed using guix.
To launch a guix shell for development, do
#+BEGIN_SRC shell
guix shell --container --network --pure --manifest=manifest.scm --share=/some/host/directory=/the/upload/directory
#+END_SRC
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
To run the CLI version of the application, we need to set up the correct ~PYTHONPATH~
#+BEGIN_SRC shell
export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}$(pwd)"
#+END_SRC
which enables us to run the script with
#+BEGIN_SRC shell
python3 scripts/qc.py --help
#+END_SRC
Without setting up the ~PYTHONPATH~ environment variable, you might get an error
like the following
#+BEGIN_EXAMPLE shell
$ python3 scripts/qc.py --help
Traceback (most recent call last):
File "/home/frederick/genenetwork/gnqc_py/scripts/qc.py", line 8, in <module>
from quality_control.errors import ParseError
ModuleNotFoundError: No module named 'quality_control'
#+END_EXAMPLE
*NOTE*: Setting up the ~PYTHONPATH~ environment variable is only necessary for
the development environment. It *MUST NOT* require that the end-user set this up
at all!
*** Run the web version
To run the web-version of the qc app in development mode, you need to set up a
few environment variables
#+BEGIN_SRC shell
export FLASK_APP=wsgi.py
export FLASK_ENV=development
export QCAPP_INSTANCE_PATH=/path/to/directory/with/config.py
#+END_SRC
then you can run the application with
#+BEGIN_SRC shell
flask run
#+END_SRC
You then need to manually start the *rq* worker(s)
#+BEGIN_SRC shell
rq worker qcapp_queue
#+END_SRC
*** Checks
Run tests with:
#+BEGIN_SRC shell
pytest
#+END_SRC
To run the linter over the code base, run:
#+BEGIN_SRC shell
pylint tests quality_control qc_app
#+END_SRC
To check for correct type usage in the application, run:
#+BEGIN_SRC shell
mypy --show-error-codes .
#+END_SRC
** Running QC
*** Installing QC
The application can be installed using guix by pointing to the [[./guix.scm][guix.scm]] file as
follows:
#+BEGIN_SRC shell
guix package [-p /path/to/qc/profile] -f guix.scm
#+END_SRC
Once installed, the sections that follow show how to use the *qc* application
*** Command-Line Version
Install the application as shown in the [[Installing QC]] section above.
To run qc against a file, the syntax is:
#+BEGIN_SRC shell
qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>
#+END_SRC
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 to ~False~ that controls the
display of optional progress messages
To view the usage information for the application, run
#+BEGIN_SRC shell
qc --help
#+END_SRC
*** Web Version
Coming soon...
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