From 31b908226a7cbab946787271ff35ffae1a43516c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 28 Oct 2020 14:08:25 -0400
Subject: [PATCH] Set uwsgi's honor-stdin when in debug mode

---
 doc/source/admin/galaxy_options.rst         | 5 +++++
 lib/galaxy/config/sample/galaxy.yml.sample  | 5 +++++
 lib/galaxy/webapps/galaxy/config_schema.yml | 6 ++++++
 scripts/get_uwsgi_args.py                   | 5 +++++
 4 files changed, 21 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 95436b2103d..405907fbf89 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -2388,6 +2388,11 @@
     use_printdebug.  It also causes the files used by PBS/SGE
     (submission script, output, and error) to remain on disk after the
     job is complete.
+    In addition, this will set uWSGI's `honour-stdin` option to
+    `true`; thus, preventing uWSGI from remapping stdin to `/dev/null`
+    and enabling debugging with tools like pdb. To keep uWSGI's
+    default setting, set `honor-stdin` to `false` in the `uwsgi`
+    section of this configuration file.
 :Default: ``false``
 :Type: bool
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index bd2d9c22ce1..ac582b5ffea 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1217,6 +1217,11 @@ galaxy:
   # use_printdebug.  It also causes the files used by PBS/SGE
   # (submission script, output, and error) to remain on disk after the
   # job is complete.
+  # In addition, this will set uWSGI's `honour-stdin` option to `true`;
+  # thus, preventing uWSGI from remapping stdin to `/dev/null` and
+  # enabling debugging with tools like pdb. To keep uWSGI's default
+  # setting, set `honor-stdin` to `false` in the `uwsgi` section of this
+  # configuration file.
   #debug: false
 
   # Check for WSGI compliance.
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 543c904c964..e97db7fc045 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1731,6 +1731,12 @@ mapping:
           causes the files used by PBS/SGE (submission script, output, and error)
           to remain on disk after the job is complete.
 
+          In addition, this will set uWSGI's `honour-stdin` option to `true`;
+          thus, preventing uWSGI from remapping stdin to `/dev/null` and
+          enabling debugging with tools like pdb. To keep uWSGI's default
+          setting, set `honor-stdin` to `false` in the `uwsgi` section of this
+          configuration file.
+
       use_lint:
         type: bool
         default: false
diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index dd7f3f8aa2f..2ca9cf60934 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -118,6 +118,11 @@ def _get_uwsgi_args(cliargs, kwargs):
     # We always want to append client/src/assets as static-safe.
     __add_arg(args, 'static-safe', f'{os.getcwd()}/client/src/assets')
 
+    # Do not let uwsgi remap stdin to /dev/null if galaxy is in debug mode
+    galaxy_kwargs = load_app_properties(config_file=config_file, config_section='galaxy')
+    if __arg_set('debug', galaxy_kwargs) and not __arg_set('honour-stdin', uwsgi_kwargs):
+        __add_arg(args, 'honour-stdin', True)
+
     for arg in DEFAULT_ARGS['_all_'] + DEFAULT_ARGS[cliargs.app]:
         if not __arg_set(arg, uwsgi_kwargs):
             __add_arg(args, arg, defaults[arg])