From b75f793ea4c58786747da3a9571ba3bd938cd181 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 29 Aug 2017 14:11:26 -0400
Subject: [PATCH] Load tools with collection type source attributes into the
 workflow editor.

Should allow using filter failed and merge collection tools within workflows.
---
 .../mvc/workflow/workflow-terminals.js        | 24 ++++++++++++++++---
 .../mvc/workflow/workflow-view-terminals.js   |  3 ++-
 lib/galaxy/tools/__init__.py                  | 16 -------------
 lib/galaxy/workflow/modules.py                |  1 +
 4 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
index 45c2cf8f629..0aa05c2f699 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js
@@ -476,11 +476,29 @@ define(['mvc/workflow/workflow-globals'], function( Globals ) {
         initialize: function( attr ) {
             Terminal.prototype.initialize.call( this, attr );
             this.datatypes = attr.datatypes;
-            this.collectionType = new CollectionTypeDescription( attr.collection_type );
-            this.isCollection = true;
+            if( attr.collection_type ) {
+                this.collectionType = new CollectionTypeDescription( attr.collection_type );
+            } else {
+                var collectionTypeSource = attr.collection_type_source;
+                if(! collectionTypeSource) {
+                    console.log("Warning: No collection type or collection type source defined.");
+                }
+                this.collectionType = ANY_COLLECTION_TYPE_DESCRIPTION;
+            }
+            this.isCollection =  true;
         },
         update: function( output ) {
-            var newCollectionType = new CollectionTypeDescription( output.collection_type );
+            var newCollectionType;
+            if( output.collection_type ) {
+                newCollectionType = new CollectionTypeDescription( output.collection_type );
+            } else {
+                var collectionTypeSource = output.collection_type_source;
+                if(! collectionTypeSource) {
+                    console.log("Warning: No collection type or collection type source defined.");
+                }
+                newCollectionType = ANY_COLLECTION_TYPE_DESCRIPTION;
+            }
+
             if( newCollectionType.collectionType != this.collectionType.collectionType ) {
                 _.each( this.connectors, function( connector ) {
                     // TODO: consider checking if connection valid before removing...
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 0e0f1398d79..67351bf117e 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -224,7 +224,8 @@ define(['mvc/workflow/workflow-globals', 'mvc/workflow/workflow-terminals',
         terminalMappingViewClass: TerminalMappingView,
         terminalForOutput: function( output ) {
             var collection_type = output.collection_type;
-            var terminal = new Terminals.OutputCollectionTerminal( { element: this.el, collection_type: collection_type, datatypes: output.extensions } );
+            var collection_type_source = output.collection_type_source;
+            var terminal = new Terminals.OutputCollectionTerminal( { element: this.el, collection_type: collection_type, collection_type_source: collection_type_source, datatypes: output.extensions } );
             return terminal;
         }
     });
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6241409850a..0e0be12652f 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -472,18 +472,6 @@ class Tool(object, Dictifiable):
                                                             installed_changeset_revision=self.installed_changeset_revision)
         return None
 
-    @property
-    def produces_collections_of_unknown_type(self):
-
-        def output_is_dynamic_collection(output):
-            if not output.collection:
-                return False
-            if output.structure.collection_type:
-                return False
-            return True
-
-        return any(map(output_is_dynamic_collection, self.outputs.values()))
-
     @property
     def produces_collections_with_unknown_structure(self):
 
@@ -1192,10 +1180,6 @@ class Tool(object, Dictifiable):
         if self.tool_type.startswith('data_source'):
             return False
 
-        if self.produces_collections_of_unknown_type:
-            # Getting there...
-            return False
-
         if hasattr(tool_source, "root"):
             root = tool_source.root
             if not string_as_bool(root.get("workflow_compatible", "True")):
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index aa0ff7e741a..ca41e7b133f 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -686,6 +686,7 @@ class ToolModule(WorkflowModule):
                 if tool_output.collection:
                     extra_kwds["collection"] = True
                     extra_kwds["collection_type"] = tool_output.structure.collection_type
+                    extra_kwds["collection_type_source"] = tool_output.structure.collection_type_source
                     formats = ['input']  # TODO: fix
                 elif tool_output.format_source is not None:
                     formats = ['input']  # default to special name "input" which remove restrictions on connections