From a737ddd9e5b73a1a602c48ed6f1546581479faca Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 14 Aug 2014 13:19:43 -0700
Subject: [PATCH 1/2] Adding method for workflows to use input with 'src' set
 as 'uuid', it will then scan datasets for a matching uuid.

---
 lib/galaxy/workflow/run_request.py |  9 +++++++++
 templates/show_params.mako         | 14 ++++++++------
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 804df21f0e8..67001ad83cc 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -188,6 +188,15 @@ def build_workflow_run_config( trans, workflow, payload ):
                 content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get(
                     trans.security.decode_id(input_id))
                 assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset )
+            elif input_source == 'uuid':
+                dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid==input_id).first()
+                if dataset is None:
+                    #this will need to be changed later. If federation code is avalible, then a missing UUID
+                    #could be found amoung fereration partners
+                    message = "Input cannot find UUID: %s." % input_id
+                    raise exceptions.RequestParameterInvalidException( message )
+                content = history.add_dataset(dataset)
+                assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset )
             elif input_source == 'hdca':
                 content = app.dataset_collections_service.get_dataset_collection_instance(
                     trans,
diff --git a/templates/show_params.mako b/templates/show_params.mako
index b4952f64360..acdaedad9c0 100644
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -23,7 +23,7 @@
                     ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) }
                 %endfor
             %elif input.type == "conditional":
-                <% 
+                <%
                 try:
                     current_case = param_values[input.name]['__current_case__']
                     is_valid = True
@@ -53,7 +53,7 @@
                         <td></td>
                     </tr>
             %elif input.visible:
-                <% 
+                <%
                 if  hasattr( input, "label" ) and input.label:
                     label = input.label
                 else:
@@ -70,7 +70,7 @@
             ## Parameter does not have a stored value.
             <tr>
                 <%
-                    # Get parameter label.  
+                    # Get parameter label.
                     if input.type == "conditional":
                         label = input.test_param.label
                     elif input.type == "repeat":
@@ -83,7 +83,7 @@
                 <td></td>
             </tr>
         %endif
-        
+
     %endfor
 </%def>
 
@@ -91,7 +91,7 @@
 <%def name="inputs_recursive_indent( text, depth )">
     <td style="padding-left: ${ ( depth - 1 ) * 10 }px">
         ${text | h}
-    </td> 
+    </td>
 </%def>
 
 <table class="tabletip">
@@ -120,6 +120,9 @@
         <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr>
         <tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr>
         <tr><td>API ID:</td><td>${encoded_hda_id}</td></tr>
+        %if hda.dataset.uuid:
+        <tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr>
+        %endif
         %if trans.user_is_admin() or trans.app.config.expose_dataset_path:
             <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr>
         %endif
@@ -168,4 +171,3 @@
             '${dep[0].name | h}' in ${dep[1]}<br/>
         </div>
     % endfor
-

From d1986d4db238e1750888e01c4e7bbe8d45266461 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 14 Aug 2014 13:38:55 -0700
Subject: [PATCH 2/2] Checking security before creating the HDA

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

diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 67001ad83cc..3a9a475eba2 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -195,8 +195,8 @@ def build_workflow_run_config( trans, workflow, payload ):
                     #could be found amoung fereration partners
                     message = "Input cannot find UUID: %s." % input_id
                     raise exceptions.RequestParameterInvalidException( message )
+                assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset )
                 content = history.add_dataset(dataset)
-                assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset )
             elif input_source == 'hdca':
                 content = app.dataset_collections_service.get_dataset_collection_instance(
                     trans,