From 633f958e1b6f2179264cdad06d9cda8cc13d0e93 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 25 Aug 2016 16:49:37 -0400
Subject: [PATCH 1/3] Open tool executions in a different tab from
 admin/tool_lineage, instead of loading galaxy(whole) within the tab

---
 lib/galaxy/webapps/galaxy/controllers/admin.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 7757e5aada0..19152591905 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -445,7 +445,7 @@ class ToolVersionListGrid( grids.Grid ):
             toolbox = trans.app.toolbox
             if toolbox.has_tool( tool_version.tool_id, exact=True ):
                 link = url_for( controller='tool_runner', tool_id=tool_version.tool_id )
-                link_str = '<a href="%s">' % link
+                link_str = '<a target="_blank" href="%s">' % link
                 return '<div class="count-box state-color-ok">%s%s</a></div>' % ( link_str, tool_version.tool_id )
             return tool_version.tool_id
 
@@ -456,7 +456,7 @@ class ToolVersionListGrid( grids.Grid ):
             for tool_id in tool_version.get_version_ids( trans.app ):
                 if toolbox.has_tool( tool_id, exact=True ):
                     link = url_for( controller='tool_runner', tool_id=tool_version.tool_id )
-                    link_str = '<a href="%s">' % link
+                    link_str = '<a target="_blank" href="%s">' % link
                     tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % ( link_str, tool_id )
                 else:
                     tool_ids_str += '%s<br/>' % tool_id

From ed76484af2ba5d86a9cfee82118f74dde70f21ae Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 26 Aug 2016 11:42:45 -0400
Subject: [PATCH 2/3] Fix toolbox's get_tool 'exact' matching.  Previously it'd
 return a tool even when exact was specified, though no exact match was made
 (so, exact=False behavior, always)

---
 lib/galaxy/tools/toolbox/base.py               | 2 ++
 lib/galaxy/webapps/galaxy/controllers/admin.py | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index e23d91b8732..a0a3602ce4c 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -399,6 +399,8 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
                     return self._tool_versions_by_id[ tool_id ][ tool_version ]
                 # tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
                 return self._tools_by_id[ tool_id ]
+            elif exact:
+                return None
             # exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions
             rval = []
             tool_lineage = self._lineage_map.get( tool_id )
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 19152591905..d061506bc2a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -455,7 +455,7 @@ class ToolVersionListGrid( grids.Grid ):
             toolbox = trans.app.toolbox
             for tool_id in tool_version.get_version_ids( trans.app ):
                 if toolbox.has_tool( tool_id, exact=True ):
-                    link = url_for( controller='tool_runner', tool_id=tool_version.tool_id )
+                    link = url_for( controller='tool_runner', tool_id=tool_id )
                     link_str = '<a target="_blank" href="%s">' % link
                     tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % ( link_str, tool_id )
                 else:

From d14b43abf2694ce3ef6933a9bede181ff1d7f79d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 26 Aug 2016 11:45:58 -0400
Subject: [PATCH 3/3] Probably still want to match identical tool guids against
 multiple sheds?

---
 lib/galaxy/tools/toolbox/base.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index a0a3602ce4c..5f160d08f6c 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -400,7 +400,10 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
                 # tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
                 return self._tools_by_id[ tool_id ]
             elif exact:
-                return None
+                # We're looking for an exact match, so we skip lineage and
+                # versionless mapping, though we may want to check duplicate
+                # toolsheds
+                continue
             # exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions
             rval = []
             tool_lineage = self._lineage_map.get( tool_id )