From e73e6b3587a98e1537b82283f8935f770648b2e3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 10 Jun 2016 00:18:11 -0400
Subject: [PATCH 1/5] Allow disabling separating tools commands into their own
 script.

Forcing them there broke Pulsar-on-Windows functionality - this fix is courtesy of @jj-umn.
---
 config/job_conf.xml.sample_advanced | 2 +-
 lib/galaxy/jobs/command_factory.py  | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 92dbe4e3410..197ca089cce 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -87,7 +87,7 @@
                higher value (in seconds) (or `None` to use blocking connections). -->
           <!-- <param id="amqp_consumer_timeout">None</param> -->
         </plugin>
-        <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner">
+        <plugin id="pulsar_legacy" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner" shell="none">
           <!-- Pulsar job runner with default parameters matching those
                of old LWR job runner. If your Pulsar server is running on a
                Windows machine for instance this runner should still be used.
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index 62b5384088f..cef3f4b7151 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -103,6 +103,11 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
     tool_commands = commands_builder.build()
     config = job_wrapper.app.config
     integrity_injection = ""
+    # Setting shell to none in job_conf.xml disables creating a tool command script,
+    # set -e doesn't work for composite commands but this is nessecary for Windows jobs
+    # for instance.
+    if shell and shell.lower() == 'none':
+        return tool_commands
     if check_script_integrity(config):
         integrity_injection = INTEGRITY_INJECTION
     set_e = ""

From 54bffd93ac2a78f248e0d937ae0ea8e1aaafb131 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 13 Jun 2016 10:51:41 -0400
Subject: [PATCH 2/5] Spelling fix thanks to @nsoranzo.

---
 lib/galaxy/jobs/command_factory.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index cef3f4b7151..1783411905e 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -104,7 +104,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_
     config = job_wrapper.app.config
     integrity_injection = ""
     # Setting shell to none in job_conf.xml disables creating a tool command script,
-    # set -e doesn't work for composite commands but this is nessecary for Windows jobs
+    # set -e doesn't work for composite commands but this is necessary for Windows jobs
     # for instance.
     if shell and shell.lower() == 'none':
         return tool_commands

From 4bf9955d0333af12d5b6dbdfe4336fda64f5a55e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 May 2016 10:09:10 -0400
Subject: [PATCH 3/5] Backport fac2efc4bd6b2214fa6d17e27b43d26fe4de7d37 to
 16.04 to enable functional stats on main.

---
 lib/galaxy/webapps/galaxy/buildapp.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index fdf96e2a70d..5ea3422fc7b 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -713,6 +713,15 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
     # other middleware):
     app = httpexceptions.make_middleware( app, conf )
     log.debug( "Enabling 'httpexceptions' middleware" )
+    # Statsd request timing and profiling
+    statsd_host = conf.get('statsd_host', None)
+    if statsd_host:
+        from galaxy.web.framework.middleware.statsd import StatsdMiddleware
+        app = StatsdMiddleware( app,
+                                statsd_host,
+                                conf.get('statsd_port', 8125),
+                                conf.get('statsd_prefix', 'galaxy') )
+        log.debug( "Enabling 'statsd' middleware" )
     # If we're using remote_user authentication, add middleware that
     # protects Galaxy from improperly configured authentication in the
     # upstream server
@@ -771,13 +780,6 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
         from galaxy.web.framework.middleware.translogger import TransLogger
         app = TransLogger( app )
         log.debug( "Enabling 'trans logger' middleware" )
-    # Statsd request timing and profiling
-    statsd_host = conf.get('statsd_host', None)
-    if statsd_host:
-        from galaxy.web.framework.middleware.statsd import StatsdMiddleware
-        app = StatsdMiddleware( app, statsd_host, conf.get('statsd_port'))
-        log.debug( "Enabling 'statsd' middleware" )
-
     # X-Forwarded-Host handling
     from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
     app = XForwardedHostMiddleware( app )

From e1cafd6ab45d385cfa46b16a2c4ab120fc3fde6f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 14 Apr 2016 15:49:37 -0400
Subject: [PATCH 4/5] Add conditional statsd requirement.  Wheel is live on
 wheels.galaxyproject.org.

---
 lib/galaxy/dependencies/__init__.py                  | 3 +++
 lib/galaxy/dependencies/conditional-requirements.txt | 1 +
 2 files changed, 4 insertions(+)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index d2079f15905..73b16326801 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -66,6 +66,9 @@ class ConditionalDependencies( object ):
     def check_raven( self ):
         return self.config.get("sentry_dsn", None) is not None
 
+    def check_statsd( self ):
+        return self.config.get("statsd_host", None) is not None
+
     def check_weberror( self ):
         return ( asbool( self.config["debug"] ) and
                  asbool( self.config["use_interactive"] ) )
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 5302ad69528..1b414c45a49 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -10,4 +10,5 @@ fluent-logger
 raven
 pbs_python
 drmaa
+statsd
 # PyRods not in PyPI

From 2aab4ee72198651a5017d37676853e74edec3b46 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 14 Apr 2016 15:51:41 -0400
Subject: [PATCH 5/5] More backporting of stats to make it functional on main.

---
 config/galaxy.ini.sample                      | 5 ++++-
 lib/galaxy/config.py                          | 1 +
 lib/galaxy/web/framework/middleware/statsd.py | 5 +++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index d3dad195807..504efe76631 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -768,9 +768,12 @@ use_interactive = True
 # Log to statsd
 # Statsd is an external statistics aggregator (https://github.com/etsy/statsd)
 # Enabling the following options will cause galaxy to log request timing and
-# other statistics to the configured statsd instance.
+# other statistics to the configured statsd instance.  The statsd_prefix is
+# useful if you are running multiple Galaxy instances and want to segment
+# statistics between them within the same aggregator.
 #statsd_host=
 #statsd_port=8125
+#statsd_prefix=galaxy
 
 # -- Data Libraries
 
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index bfae71b72db..deaa516716f 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -446,6 +446,7 @@ class Configuration( object ):
         # Statistics and profiling with statsd
         self.statsd_host = kwargs.get( 'statsd_host', '')
         self.statsd_port = int( kwargs.get( 'statsd_port', 8125 ) )
+        self.statsd_prefix = kwargs.get( 'statsd_prefix', 'galaxy' )
         # Logging with fluentd
         self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) )
         self.fluent_host = kwargs.get( 'fluent_host', 'localhost' )
diff --git a/lib/galaxy/web/framework/middleware/statsd.py b/lib/galaxy/web/framework/middleware/statsd.py
index 2e0ccd7603d..e831e31639f 100644
--- a/lib/galaxy/web/framework/middleware/statsd.py
+++ b/lib/galaxy/web/framework/middleware/statsd.py
@@ -21,12 +21,13 @@ class StatsdMiddleware(object):
     def __init__(self,
                  application,
                  statsd_host,
-                 statsd_port):
+                 statsd_port,
+                 statsd_prefix):
         if not statsd:
             raise ImportError( "Statsd middleware configured, but no statsd python module found. "
                            "Please install the python statsd module to use this functionality." )
         self.application = application
-        self.statsd_client = statsd.StatsClient(statsd_host, statsd_port, prefix='galaxy')
+        self.statsd_client = statsd.StatsClient(statsd_host, statsd_port, prefix=statsd_prefix)
 
     def __call__(self, environ, start_response):
         start_time = time.time()