#+STARTUP: inlineimages
#+TITLE: 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 --manifest=manifest.scm
#+END_SRC

to get an environment that is isolated from the rest of your system.

*** 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

*** Command-Line Version

Clone this repository
#+BEGIN_SRC shell
  git clone http://git.genenetwork.org/fredmanglis/gnqc_py.git
#+END_SRC
then install the application
#+BEGIN_SRC shell
  $ python3 -m venv .venv
  $ source .venv/bin/activate
  (.venv) $ pip install .
#+END_SRC


To run qc against a file, the syntax is:
#+BEGIN_SRC shell
  python3 -m 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
  python3 -m qc --help
#+END_SRC

**** TODO Figure out how to put qc.py in a /bin or /scripts directory and still be able to import the modules in the repo
**** TODO Reduce the command to simply ~qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>~

*** Web Version

Coming soon...