From 9973943adc7cb8f7866f8e18289ae841775dad6f Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Mon, 3 Jan 2022 17:45:14 +0530
Subject: bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.

`guix shell' sets the profile path in an environment
variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as
an input in GN2_PROFILE.

* README.md: Remove all references to GN2_PROFILE.
* bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not
check the value of GN2_PROFILE now that it is set
automatically. Remove all references to GN2_PROFILE in example
invocations.
---
 README.md        | 17 +++++-------
 bin/genenetwork2 | 83 ++++++++++++++++++++------------------------------------
 2 files changed, 37 insertions(+), 63 deletions(-)

diff --git a/README.md b/README.md
index 972d5c50..d5539a9f 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ genenetwork2
 A quick example is
 
 ```sh
-env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \
+env SERVER_PORT=5300 \
     GENENETWORK_FILES=~/data/gn2_data/ \
     GN_PROXY_URL="http://localhost:8080"\
     GN3_LOCAL_URL="http://localhost:8081"\
@@ -69,19 +69,16 @@ We are building 'Mechanical Rob' automated testing using Python
 which can be run with:
 
 ```sh
-env GN2_PROFILE=~/opt/gn-latest \
-    ./bin/genenetwork2 \
+env ./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.
+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
 
@@ -102,9 +99,9 @@ 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 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 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"
+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"
 ```
 
 Replace some of the env variables as per your use case.
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index b5c940a8..93ab02f8 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -5,55 +5,45 @@
 #
 # Typical usage
 #
-#   env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py
-#
-# Where GN2_PROFILE points to the GNU Guix profile used for deployment.
+#   ./bin/genenetwork2 ~/my_settings.py
 #
 # This will run the GN2 server (with default settings if none
-# 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
+# supplied).
 #
 # 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 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
+#   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
 #
 # To run any script in the environment
 #
-#   env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD"
+#   ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD"
 #
 # To get a python REPL(!)
 #
-#   env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python
+#   ./bin/genenetwork2 ./etc/default_settings.py -cli python
 #
 # For development you may want to run
 #
-#   env GN2_PROFILE=~/opt/gn-latest WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2
+#   env 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 GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod
+#   env SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod
 #
 # For development use
 #
-#   env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev
+#   env SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev
 #
 # For extra flexibility you can also provide gunicorn parameters yourself with something like
 #
-#   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi"
+#   ./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 $GN2_BASE_DIR)
@@ -101,40 +91,27 @@ fi
 export GN2_SETTINGS=$settings     # Python
 echo GN2_SETTINGS=$settings
 
-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
+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
 if [ -z $PYTHONPATH ] ; then
     echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
     exit 1
-- 
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