diff options
| -rw-r--r-- | README.md | 13 | ||||
| -rwxr-xr-x | bin/genenetwork2 | 15 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 3 |
3 files changed, 16 insertions, 15 deletions
@@ -25,7 +25,11 @@ Once installed GN2 can be run online through a browser interface ./bin/genenetwork2 ``` -(default is http://localhost:5003/). We are building up automated +(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL +see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2). + + +We are building up automated testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with ```sh @@ -70,16 +74,15 @@ 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. diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 18e02388..b3a8d8c2 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -15,28 +15,29 @@ # installation path of genenetwork). Say your profile is in # ~/opt/gn-latest-guix # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 # # You can pass in your own settings file, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py # # To run a maintenance python script with settings (instead of the -# webserver) add that with a -c switch, e.g. +# webserver) run from the base-dir with settings file and add that +# script with a -c switch, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 -c ./wqflask/maintenance/gen_select_dataset.py +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py # # To run any script in the environment # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" # # To get a python REPL(!) # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli python +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python # # For development you may want to run # -# env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 # # For staging and production we use gunicorn. Run with something like # (note you have to provide the server port). Provide a settings file! diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index f62d0cc1..79242661 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -63,9 +63,6 @@ from pprint import pformat as pf #conn = Engine.connect() -print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') - - def parse_db_uri(db_uri): """Converts a database URI to the db name, host name, user name, and password""" |