diff options
| -rw-r--r-- | README.md | 17 | ||||
| -rwxr-xr-x | bin/genenetwork2 | 83 |
2 files changed, 63 insertions, 37 deletions
@@ -30,7 +30,7 @@ genenetwork2 A quick example is ```sh -env SERVER_PORT=5300 \ +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"\ @@ -69,16 +69,19 @@ We are building 'Mechanical Rob' automated testing using Python which can be run with: ```sh -env ./bin/genenetwork2 \ +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 ./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. +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 @@ -99,9 +102,9 @@ runcmd coverage html The `runcmd` and `runpython` are shell aliases defined in the following way: ```sh -alias runpython="env 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 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 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" +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. diff --git a/bin/genenetwork2 b/bin/genenetwork2 index f1e04eef..ea5a4f50 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -5,45 +5,55 @@ # # Typical usage # -# ./bin/genenetwork2 ~/my_settings.py +# env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py +# +# Where GN2_PROFILE points to the GNU Guix profile used for deployment. # # This will run the GN2 server (with default settings if none -# supplied). +# supplied). Typically you need a GNU Guix profile which is set with +# an environment variable (this profile is dictated by the +# installation path of genenetwork). Say your profile is in +# ~/opt/gn-latest-guix +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 +# +# You can pass in your own settings file, e.g. +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py # # To run a maintenance python script with settings (instead of the # webserver) run from the base-dir with settings file and add that # script with a -c switch, e.g. # -# env TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py +# env GN2_PROFILE=/usr/local/guix-profiles/gn-latest-20190905 TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py # # To run any script in the environment # -# ./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(!) # -# ./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 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! # -# env SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod +# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod # # For development use # -# env SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev +# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev # # For extra flexibility you can also provide gunicorn parameters yourself with something like # -# ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi" +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi" SCRIPT=$(realpath "$0") echo SCRIPT=$SCRIPT -export GN2_PROFILE=$GUIX_ENVIRONMENT echo GN2_PROFILE=$GN2_PROFILE GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) @@ -91,27 +101,40 @@ fi export GN2_SETTINGS=$settings # Python echo GN2_SETTINGS=$settings -export PATH=$GN2_PROFILE/bin:$PATH -export PYTHONPATH="$GN2_PROFILE/lib/python3.8/site-packages" # never inject another PYTHONPATH!! -export R_LIBS_SITE=$GN2_PROFILE/site-library -export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript -export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" -export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" -export XDG_DATA_DIRS="$GN2_PROFILE/share" -export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules" -export LC_ALL=C # FIXME -export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2" -export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" -export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" -if [ -z $GEMMA_WRAPPER_COMMAND ]; then - export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" +if [ -z $GN2_PROFILE ] ; then + echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" + export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) + if [ -d $GN2_PROFILE ]; then + echo "Best guess is $GN2_PROFILE" + fi + echo "ERROR: always set GN2_PROFILE" + exit 1 +fi +if [ -z $GN2_PROFILE ]; then + read -p "PRESS [ENTER] TO CONTINUE..." +else + export PATH=$GN2_PROFILE/bin:$PATH + export PYTHONPATH="$GN2_PROFILE/lib/python3.8/site-packages" # never inject another PYTHONPATH!! + export R_LIBS_SITE=$GN2_PROFILE/site-library + export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript + export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" + export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" + export XDG_DATA_DIRS="$GN2_PROFILE/share" + export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules" + export LC_ALL=C # FIXME + export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2" + export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" + export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" + if [ -z $GEMMA_WRAPPER_COMMAND ]; then + export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + fi + while IFS=":" read -ra PPATH; do + for PPART in "${PPATH[@]}"; do + if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi + done + done <<< "$PYTHONPATH" + if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi fi -while IFS=":" read -ra PPATH; do - for PPART in "${PPATH[@]}"; do - if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi - done -done <<< "$PYTHONPATH" -if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi if [ -z $PYTHONPATH ] ; then echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!" exit 1 |