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@@ -17,21 +17,74 @@ 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). -## Test +## Run -Once installed GN2 can be run online through a browser interface +Once having installed GN2 it can be run through a browser +interface ```sh -./bin/genenetwork2 +genenetwork2 ``` -(default is http://localhost:5003/). We are building up automated -testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with +(default is http://localhost:5003/). A quick example is ```sh -./bin/test-website +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). + +## Testing + +To have tests pass, the redis and mariadb instance should be running, because of +asserts sprinkled in the code base(these will be removed in due time). + +#### 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 ./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/ ./bin/genenetwork2 + +alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -cli" +``` + +Replace some of the env variables as per your use case. + ## Documentation User documentation can be found @@ -51,10 +104,10 @@ 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/). +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 @@ -70,16 +123,15 @@ For more information visit http://www.genenetwork.org/ [](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 +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 -[](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2). +[](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. - +University of Tennessee Health Science Center, Memphis TN, USA. |