diff options
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 47 |
1 files changed, 39 insertions, 8 deletions
@@ -19,7 +19,8 @@ developers). See the [installation docs](doc/README.org). ## 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 genenetwork2 @@ -35,14 +36,18 @@ 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 Mysql and Elasticsearch need to be running, see +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/master/test/lib) -which can be run with something like +[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 @@ -54,6 +59,32 @@ 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 @@ -73,10 +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 |