Merge branch 'release_16.01' into dev

config/galaxy.ini.sample

@@ -656,6 +656,13 @@ nglims_config_file = tool-data/nglims.yaml
 # log_events and log_actions functionality will eventually be merged.
 #log_actions = True
 
+
+# Fluentd configuration.  Various events can be logged to the fluentd instance
+# configured below by enabling fluent_log.
+#fluent_log = False
+#fluent_host = localhost
+#fluent_port = 24224
+
 # Sanitize all HTML tool output.  By default, all tool output served as
 # 'text/html' will be sanitized thoroughly.  This can be disabled if you have
 # special tools that require unaltered output.  WARNING: disabling this does

lib/galaxy/util/log/fluent_log.py

@@ -3,6 +3,7 @@ Provides a `TraceLogger` implementation that logs to a fluentd collector
 """
 
 import threading
+import time
 
 try:
     from fluent.sender import FluentSender
@@ -34,11 +35,10 @@ class FluentTraceLogger( object ):
         del self.thread_local.context[key]
         self.lock.release()
 
-    def log( self, label, time=None, **kwargs ):
+    def log( self, label, event_time=None, **kwargs ):
         self.lock.acquire()
         if hasattr( self.thread_local, 'context' ):
             kwargs.update( self.thread_local.context )
         self.lock.release()
-        if time is None:
-            time = int( time.time() )
-        self.sender.emit_with_time( label, time, kwargs )
+        event_time = event_time or time.time()
+        self.sender.emit_with_time( label, int(event_time), kwargs )

lib/galaxy/webapps/galaxy/api/metrics.py

@@ -87,7 +87,7 @@ class MetricsController( BaseAPIController ):
         """
         if trans.app.trace_logger:
             for label, time, kwargs in metrics:
-                trans.app.trace_logger.log( label, time=int( time ), **kwargs )
+                trans.app.trace_logger.log( label, event_time=int( time ), **kwargs )
         elif self.debugging:
             for label, time, kwargs in metrics:
                 log.debug( '%s %s %s', label, time, kwargs )

run_reports.sh

@@ -13,6 +13,13 @@ cd `dirname $0`
 
 ./scripts/common_startup.sh --skip-samples
 
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
+if [ -d "$GALAXY_VIRTUAL_ENV" ];
+then
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
+fi
+
 if [ -z "$GALAXY_REPORTS_CONFIG" ]; then
     if [ -f reports_wsgi.ini ]; then
         GALAXY_REPORTS_CONFIG=reports_wsgi.ini

run_tool_shed.sh

@@ -4,6 +4,14 @@ cd `dirname $0`
 
 ./scripts/common_startup.sh
 
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
+if [ -d "$GALAXY_VIRTUAL_ENV" ];
+then
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
+fi
+
+
 tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@`
 args=$@