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Developing against GeneNetwork


GeneNetwork2 comes with a [default configuration file](./etc/default_settings.py) which can be used as a starting point.

The recommended way to deal with the configurations is to **copy** this default configuration file to a location outside of the repository, say,

.../genenetwork2$ cp etc/default_settings.py "${HOME}/configurations/gn2.py"

then change the appropriate values in the new file. You can then pass in the new file as the configuration file when launching the application,

.../genenetwork2$ bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run>

The other option is to override the configurations in `etc/default_settings.py` by setting the configuration you want to override as an environment variable e.g. to override the `SQL_URI` value, you could do something like:

.../genenetwork2$ env SQL_URI="mysql://<user>:<passwd>@<host>:<port>/<db_name>" \
	bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run>

replacing the placeholders in the angle brackets with appropriate values.

For a detailed breakdown of the configuration variables and their use, see the [configuration documentation](doc/configurations.org)


Once having installed GN2 it can be run through a browser interface


A quick example is

env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
    GENENETWORK_FILES=~/data/gn2_data/ \
    ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev

For full examples (you may need to set a number of environment variables), including running scripts and a Python REPL, also see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).

Also mariadb and redis need to be running, see [INSTALL](./doc/README.org).


To run the application under the pdb debugger, you can add the `--with-pdb` option when launching the application, for example:

env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
    GENENETWORK_FILES=~/data/gn2_data/ \
    ./bin/genenetwork2 ./etc/default_settings.py --with-pdb

**NOTE**: This should only ever be run in development. **NOTE 2**: You will probably need to tell pdb to continue at least once before the system begins serving the pages.

Now, you can add the `breakpoint()` call wherever you need to debug and the terminal where you started the application with `--with-pdb` will allow you to issue commands to pdb to debug your application.


It may be useful to pull in the GN3 python modules locally. For this use `GN3_PYTHONPATH` environment that gets injected in the ./bin/genenetwork2 startup.

A continuously deployed instance of genenetwork2 is available at [https://cd.genenetwork.org/](https://cd.genenetwork.org/). This instance is redeployed on every commit provided that the [continuous integration tests](https://ci.genenetwork.org/jobs/genenetwork2) pass.


To have tests pass, the redis and mariadb instance should be running, because of asserts sprinkled in the code base.

Right now, the only tests running in CI are unittests. Please make sure the existing unittests are green when submitting a PR.

From the root directory of the repository, you can run the tests with something like:

env GN_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
	SQL_URI=<uri-to-override-the-default> \
	./bin/genenetwork2 ./etc/default_settings.py \
	-c -m pytest -vv

In the case where you use the default `etc/default_settings.py` configuration file, you can override any setting as demonstrated with the `SQL_URI` setting in the command above.

In order to avoid having to set up a whole host of settings every time with the `env` command, you could copy the `etc/default_settings.py` file to a new location (outside the repository is best), and pass that to `bin/genenetwork2` instead.

See [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org) for more details.

#### Mechanical Rob

We are building 'Mechanical Rob' automated testing using Python [requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests) which can be run with:

env GN2_PROFILE=~/opt/gn-latest \
    ./bin/genenetwork2 \
    GN_PROXY_URL="http://localhost:8080" \
    GN3_LOCAL_URL="http://localhost:8081 "\
    ./etc/default_settings.py -c \
    ../test/requests/test-website.py -a http://localhost:5003

The GN2_PROFILE is the Guix profile that contains all dependencies. The ./bin/genenetwork2 script sets up the environment and executes test-website.py in a Python interpreter. The -a switch says to run all tests and the URL points to the running GN2 http server.

#### Unit tests

To run unittests, first `cd` into the genenetwork2 directory:

# You can use the coverage tool to run the tests
# You could omit the -v which makes the output verbose
runcmd coverage run -m unittest discover -v

# Alternatively, you could run the unittests using:
runpython -m unittest discover -v

# To generate a report in wqflask/coverage_html_report/:
runcmd coverage html

The `runcmd` and `runpython` are shell aliases defined in the following way:

alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2

alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2 ./etc/default_settings.py -cli"

Replace some of the env variables as per your use case.


If the menu does not pop up check your `GN2_BASE_URL`. E.g.

curl http://gn2-pjotr.genenetwork.org/api/v_pre1/gen_dropdown

check the logs. If there is ERROR 1054 (42S22): Unknown column 'InbredSet.Family' in 'field list' it may be you are trying the small database.

Run Scripts

As part of the profiling effort, some scripts are added to run specific parts of the system under a profiler without running the entire web-server - as such, to run the script, you could do something like:

env HOME=/home/frederick \
    GN2_PROFILE=~/opt/gn2-latest \
    GN3_DEV_REPO_PATH=~/genenetwork/genenetwork3 \
    SQL_URI="mysql://username:password@host-ip:host-port/db_webqtl" \
    SERVER_PORT=5001 \
    bin/genenetwork2 ../gn2_settings.py \
    -cli python3 -m scripts.profile_corrs \
	../performance_$(date +"%Y%m%dT%H:%M:%S").profile

and you can find the performance metrics at the file specified, in this case, a file starting with `performance_` with the date and time of the run, and ending with `.profile`.

Please replace the environment variables in the sample command above with the appropriate values for your environment.

(made with skribilo)