From 0c7106202cd0cb549e731a43a64a95116756daf6 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 22 May 2023 08:32:12 +0300
Subject: Enable running application under pdb.

Add an option to help with running the application under pdb, and add
some documentation to help other developers figure it out.
---
 README.md        | 22 ++++++++++++++++++++++
 bin/genenetwork2 | 12 ++++++++++++
 2 files changed, 34 insertions(+)

diff --git a/README.md b/README.md
index 37a2bed3..7572cd5f 100644
--- a/README.md
+++ b/README.md
@@ -78,6 +78,28 @@ startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/
 Also mariadb and redis need to be running, see
 [INSTALL](./doc/README.org).
 
+## Debugging
+
+To run the application under the pdb debugger, you can add the `--with-pdb`
+option when launching the application, for example:
+
+```sh
+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"\
+	SPARQL_ENDPOINT=http://localhost:8892/sparql\
+    ./bin/genenetwork2 ./etc/default_settings.py --with-pdb
+```
+
+**NOTE**: This should only ever be run in development.
+**NOTE 2**: You will probably need to tell pdb to continue at least once before
+the system begins serving the pages.
+
+Now, you can add the `breakpoint()` call wherever you need to debug and the
+terminal where you started the application with `--with-pdb` will allow you to
+issue commands to pdb to debug your application.
+
 ## Development
 
 It may be useful to pull in the GN3 python modules locally. For this
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 57fd8588..d0aa5d71 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -221,6 +221,18 @@ fi
 # Overrides for packages that are not yet public (currently r-auwerx)
 # export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
 
+
+
+if [ "$1" = "--with-pdb" ] ; then
+    cd "${GN2_BASE_DIR}/wqflask"
+    cmd=$2
+    echo PYTHONPATH="${PYTHONPATH}"
+    shift ; shift
+    echo "RUNNING COMMAND python3 -m runserver.py"
+    python3 -m pdb runserver.py
+    exit $?
+fi
+
 # Start the flask server running GN2
 cd "${GN2_BASE_DIR}/wqflask"
 echo "Starting with $settings"
-- 
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