[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025) [![GeneNetwork2 CI badge](https://ci.genenetwork.org/badge/genenetwork2.svg)](https://ci.genenetwork.org/jobs/genenetwork2) # GeneNetwork This repository contains the current source code for GeneNetwork (GN) (https://www.genenetwork.org/ (version 2). GN2 is a Web 2.0-style framework that includes data and computational tools for online genetics and genomic analysis of many different populations and many types of molecular, cellular, and physiological data. The system is used by scientists and clinicians in the field of precision health care and systems genetics. GN and its predecessors have been in operation since Jan 1994, making it one of the longest-lived web services in biomedical research (https://en.wikipedia.org/wiki/GeneNetwork, and see a partial list of publications using GN and its predecessor, WebQTL (https://genenetwork.org/references/). ## Install The recommended installation is with GNU Guix which allows you to deploy GN2 and dependencies as a self contained unit on any machine. The database can be run separately as well as the source tree (for developers). See the [installation docs](doc/README.org). ## Configuration 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, ```sh .../genenetwork2$ cp etc/default_settings.py "${HOME}/configurations/gn2.py" ``` then change the appropriate values in the new file. You can then pass in the new file as the configuration file when launching the application, ```sh .../genenetwork2$ bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run> ``` The other option is to override the configurations in `etc/default_settings.py` by setting the configuration you want to override as an environment variable e.g. to override the `SQL_URI` value, you could do something like: ```sh .../genenetwork2$ 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) ## Run Once having installed GN2 it can be run through a browser interface ```sh genenetwork2 ``` A quick example is ```sh env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \ GENENETWORK_FILES=~/data/gn2_data/ \ GN_PROXY_URL="http://localhost:8080"\ GN3_LOCAL_URL="http://localhost:8081"\ ./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). ## Development 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://gn2dev.genenetwork.org/](https://gn2dev.genenetwork.org/). This instance is redeployed on every commit provided that the [continuous integration tests](https://ci.genenetwork.org/jobs/genenetwork2) pass. ## Testing 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: ```sh env GN_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \ SQL_URI=<uri-to-override-the-default> \ ./bin/genenetwork2 ./etc/default_settings.py \ -c -m unittest -v ``` 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: ```sh 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: ```sh # 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: ```sh 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. ### Troubleshooting 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. ## Documentation User documentation can be found [here](http://gn2.genenetwork.org/help). The architecture of the software stack is described [here](./doc/Architecture.org). The database schema is (still) shared with GN1 and currently described [here](http://www.genenetwork.org/webqtl/main.py?FormID=schemaShowPage). Software documentation is being expanded in the [source code repository](https://github.com/genenetwork/genenetwork2/tree/master/doc). ## Contributing Issues can be raised through [github](https://github.com/genenetwork/genenetwork2/issues). Contribute to GN2 source code by forking the [github repository](https://github.com/genenetwork/genenetwork2/) with git and sending us pull requests. For development GN2 has a [mailing list](http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev) and an active IRC channel #genenetwork on freenode.net with a [web interface](http://webchat.freenode.net/). ## License The GeneNetwork2 source code is released under the Affero General Public License 3 (AGPLv3). See [LICENSE.txt](LICENSE.txt). ## More information For more information visit http://www.genenetwork.org/ ## Cite [![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025) GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins You may also cite the software using [![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2). ## Contact IRC on #genenetwork on irc.freenode.net. Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, Memphis TN, USA.