commit/galaxy-central: 6 new changesets

7 May 2014

6 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/fef831b5e2bd/
Changeset:   fef831b5e2bd
User:        nsoranzo
Date:        2014-05-05 19:07:07
Summary:     Update code checks and documentation after commit 17a2dc7.
Affected #:  1 file

diff -r fe6c48de949dd4e640d3632ab23cfe6ab5fa0494 -r fef831b5e2bd3feaaef58212eb695943d8969212 lib/galaxy/webapps/galaxy/api/workflows.py

--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1,9 +1,9 @@
-from __future__ import absolute_import
-
 """
 API operations for Workflows
 """
 
+from __future__ import absolute_import
+
 import logging
 from sqlalchemy import desc, or_
 from galaxy import exceptions
@@ -12,7 +12,6 @@
 from galaxy.web import _future_expose_api as expose_api
 from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
 from galaxy.web.base.controller import UsesHistoryMixin
-from galaxy.workflow.modules import module_factory
 from galaxy.workflow.run import invoke
 from galaxy.workflow.run import WorkflowRunConfig
 from galaxy.workflow.extract import extract_workflow
@@ -120,76 +119,79 @@
         workflow will be created for this user. Otherwise, workflow_id must be
         specified and this API method will cause a workflow to execute.
 
-        :param  installed_repository_file    The path of a workflow to import. Either workflow_id or installed_repository_file must be specified
+        :param  installed_repository_file    The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   installed_repository_file    str
 
-        :param  workflow_id:                 an existing workflow id. Either workflow_id or installed_repository_file must be specified
+        :param  workflow_id:                 An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   workflow_id:                 str
 
-        :param  parameters:                  See _update_step_parameters()
+        :param  parameters:                  If workflow_id is set - see _update_step_parameters()
         :type   parameters:                  dict
 
-        :param  ds_map:                      A dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
+        :param  ds_map:                      If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
         :type   ds_map:                      dict
 
-        :param  no_add_to_history:           if present in the payload with any value, the input datasets will not be added to the selected history
+        :param  no_add_to_history:           If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
         :type   no_add_to_history:           str
 
-        :param  history:                     Either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history
+        :param  history:                     If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
         :type   history:                     str
 
-        :param  replacement_params:          A dictionary used when renaming datasets
+        :param  replacement_params:          If workflow_id is set - an optional dictionary used when renaming datasets
         :type   replacement_params:          dict
 
-        :param  from_history_id:             Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file.
+        :param  from_history_id:             Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   from_history_id:             str
 
-        :param  job_ids:                     If from_history_id is set - this should be a list of jobs to include when extracting workflow from history.
+        :param  job_ids:                     If from_history_id is set - optional list of jobs to include when extracting workflow from history.
         :type   job_ids:                     str
 
-        :param  dataset_ids:                 If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history.
+        :param  dataset_ids:                 If from_history_id is set - optional list of HDA ids corresponding to workflow inputs when extracting workflow from history.
         :type   dataset_ids:                 str
+
+        :param  workflow_name:               If from_history_id is set - name of the workflow to create
+        :type   workflow_name:               str
         """
 
-        # Pull parameters out of payload.
-        workflow_id = payload.get('workflow_id', None)
-        param_map = payload.get('parameters', {})
-        ds_map = payload.get('ds_map', {})
+        if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1:
+            trans.response.status = 403
+            return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified"
+
+        if 'installed_repository_file' in payload:
+            workflow_controller = trans.webapp.controllers[ 'workflow' ]
+            result = workflow_controller.import_workflow( trans=trans,
+                                                          cntrller='api',
+                                                          **payload)
+            return result
+
+        if 'from_history_id' in payload:
+            from_history_id = payload.get( 'from_history_id' )
+            history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
+            job_ids = map( trans.security.decode_id, payload.get( 'job_ids', [] ) )
+            dataset_ids = map( trans.security.decode_id, payload.get( 'dataset_ids', [] ) )
+            workflow_name = payload[ 'workflow_name' ]
+            stored_workflow = extract_workflow(
+                trans=trans,
+                user=trans.get_user(),
+                history=history,
+                job_ids=job_ids,
+                dataset_ids=dataset_ids,
+                workflow_name=workflow_name,
+            )
+            item = stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
+            item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] )
+            return item
+
+        workflow_id = payload.get( 'workflow_id', None )
+        if not workflow_id:
+            trans.response.status = 403
+            return "Either workflow_id, installed_repository_file or from_history_id must be specified"
+
+        # Pull other parameters out of payload.
+        param_map = payload.get( 'parameters', {} )
+        ds_map = payload.get( 'ds_map', {} )
         add_to_history = 'no_add_to_history' not in payload
-        history_param = payload.get('history', '')
-
-        # Get/create workflow.
-        if not workflow_id:
-            # create new
-            if 'installed_repository_file' in payload:
-                workflow_controller = trans.webapp.controllers[ 'workflow' ]
-                result = workflow_controller.import_workflow( trans=trans,
-                                                              cntrller='api',
-                                                              **payload)
-                return result
-            if 'from_history_id' in payload:
-                from_history_id = payload.get( 'from_history_id' )
-                history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
-                job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) )
-                dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) )
-                workflow_name = payload[ "workflow_name" ]
-                stored_workflow = extract_workflow(
-                    trans=trans,
-                    user=trans.get_user(),
-                    history=history,
-                    job_ids=job_ids,
-                    dataset_ids=dataset_ids,
-                    workflow_name=workflow_name,
-                )
-                item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } )
-                item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] )
-                return item
-
-            trans.response.status = 403
-            return "Either workflow_id or installed_repository_file must be specified"
-        if 'installed_repository_file' in payload:
-            trans.response.status = 403
-            return "installed_repository_file may not be specified with workflow_id"
+        history_param = payload.get( 'history', '' )
 
         # Get workflow + accessibility check.
         stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(


https://bitbucket.org/galaxy/galaxy-central/commits/ef7bd8c935bc/
Changeset:   ef7bd8c935bc
User:        nsoranzo
Date:        2014-05-06 19:15:26
Summary:     Merged galaxy/galaxy-central into default
Affected #:  117 files

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 config/plugins/visualizations/charts/static/charts/heatmap/config.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js
@@ -1,10 +1,12 @@
 define([], function() {
 
 return {
-    title   : 'Heatmap',
-    library : '',
-    tag     : 'div',
+    title       : 'Heatmap',
+    library     : '',
+    tag         : 'div',
     use_panels  : true,
+    
+    // columns
     columns : {
         col_label : {
             title       : 'Columns',
@@ -19,6 +21,7 @@
         },
     },
     
+    // settings
     settings: {
         color_set : {
             title       : 'Color scheme',
@@ -107,6 +110,38 @@
                     value   : 'wysiwyg'
                 }
             ]
+        },
+       
+        sorting : {
+            title       : 'Sorting',
+            info        : 'How should the columns be clustered?',
+            type        : 'select',
+            init        : 'hclust',
+            data        : [
+                {
+                    label   : 'Read from dataset',
+                    value   : 'hclust'
+                },
+                {
+                    label   : 'Sort column and row labels',
+                    value   : 'byboth'
+                },
+                {
+                    label   : 'Sort column labels',
+                    value   : 'bycolumns'
+                },
+                {
+                    label   : 'Sort by rows',
+                    value   : 'byrow'
+                }
+            ]
+        }
+    },
+    
+    // menu definition
+    menu : function() {
+        return {
+            color_set : this.settings.color_set
         }
     }
 };

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
@@ -180,26 +180,22 @@
         //
         // add ui elements
         //
-        // create ui elements
+        // create tooltip
         this.$tooltip = $(this._templateTooltip());
-        this.$select  = $(this._templateSelect());
-        
-        // append
         this.$el.append(this.$tooltip);
-        this.$el.append(this.$select);
-        
-        // add event to select field
-        this.$select.on('change', function(){
-            self._sortByOrder(this.value);
-        });
         
         //
         // finally draw the heatmap
         //
-        this._draw();
+        this._build();
+        
+        // catch window resize event
+        $(window).resize(function () {
+            self._build();
+        });
     },
     
-    _draw: function() {
+    _build: function() {
         // link this
         var self = this;
         
@@ -212,7 +208,7 @@
         this.height = this.heightContainer;
         
         // calculate cell size
-        this.cellSize = Math.min(((this.height - 50) / (this.rowNumber + this.margin.top + this.margin.bottom)),
+        this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)),
                                  (this.width / (this.colNumber + this.margin.left + this.margin.right)));
         
         // set font size
@@ -227,22 +223,27 @@
         var width               = this.width;
         var height              = this.height;
         
+        // reset svg
+        if (this.svg !== undefined) {
+            this.$el.find('svg').remove();
+        }
+        
         // add main group and translate
         this.svg = d3.select(this.$el[0]).append('svg')
             .append('g')
             .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' +
-                                              (this.heightContainer - height) / 2 + ')')
-      
+                                              (this.heightContainer - height) / 2 + ')');
+                            
         // reset sorting
         this.rowSortOrder   = false;
         this.colSortOrder   = false;
         
         // build
-        this._buildRowLabels();
-        this._buildColLabels();
-        this._buildHeatMap();
-        this._buildLegend();
-        this._buildTitle();
+        this.d3RowLabels = this._buildRowLabels();
+        this.d3ColLabels = this._buildColLabels();
+        this.d3HeatMap = this._buildHeatMap();
+        this.d3Legend = this._buildLegend();
+        this.d3Title = this._buildTitle();
     },
         
     // build title
@@ -258,7 +259,7 @@
         var title       = this.options.title;
         
         // add title
-        this.svg.append('g')
+        return this.svg.append('g')
             .append('text')
             .attr('x', width / 2)
             .attr('y', height + 3 * cellSize + fontSize + 3)
@@ -323,6 +324,9 @@
             })
             .attr('y', height + cellSize - 3)
             .style('font-size', fontSize + 'px');
+            
+        // return
+        return legend;
     },
     
     // build column labels
@@ -366,6 +370,9 @@
                 self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder);
                 d3.select('#order').property('selectedIndex', 4).node().focus();
             });
+            
+        // return
+        return colLabels;
     },
     
     // build row labels
@@ -409,6 +416,9 @@
                 self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder);
                 d3.select('#order').property('selectedIndex', 4).node().focus();
             });
+            
+        // return
+        return rowLabels;
     },
     
     // build heat map
@@ -424,7 +434,7 @@
         var colLabel = this.colLabel;
         
         // heat map
-        var heatMap = this.svg.append('g').attr('class','g3')
+        var heatmap = this.svg.append('g').attr('class','g3')
             .selectAll('.cellg')
             .data(self.data, function(d) {
                 return d.row + ':' + d.col;
@@ -466,6 +476,9 @@
                 d3.selectAll('.colLabel').classed('text-highlight',false);
                 d3.select('#heatmap-tooltip').classed('hidden', true);
             });
+            
+        // return
+        return heatmap;
     },
     
     // change ordering of cells

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -6,7 +6,8 @@
 return Backbone.View.extend({
 
     // list of canvas elements
-    canvas: [],
+    container_list: [],
+    canvas_list: [],
     
     // initialize
     initialize: function(app, options) {
@@ -26,7 +27,7 @@
         this._fullscreen(this.$el, 80);
         
         // create canvas element
-        this._createCanvas('div');
+        this._createContainer('div');
         
         // events
         var self = this;
@@ -38,6 +39,7 @@
         this.chart.on('set:state', function() {
             // get info element
             var $info = self.$el.find('#info');
+            var $container = self.$el.find('container');
             
             // get icon
             var $icon = $info.find('#icon');
@@ -49,11 +51,15 @@
             $info.show();
             $info.find('#text').html(self.chart.get('state_info'));
 
+            // hide containers
+            $container.hide();
+
             // check status
             var state = self.chart.get('state');
             switch (state) {
                 case 'ok':
                     $info.hide();
+                    $container.show()
                     break;
                 case 'failed':
                     $icon.addClass('fa fa-warning');
@@ -86,29 +92,35 @@
     },
     
     // creates n canvas elements
-    _createCanvas: function(tag, n) {
+    _createContainer: function(tag, n) {
         // check size of requested canvas elements
         n = n || 1;
     
         // clear previous canvas elements
-        for (var i in this.canvas) {
-            this.canvas[i].remove();
-            this.canvas.slice(i, 0);
+        for (var i in this.container_list) {
+            this.container_list[i].remove();
         }
         
+        // reset lists
+        this.container_list = [];
+        this.canvas_list = [];
+        
         // create requested canvas elements
         for (var i = 0; i < n; i++) {
             // create element
-            var canvas_el = $(this._templateCanvas(tag, parseInt(100 / n)));
+            var canvas_el = $(this._templateContainer(tag, parseInt(100 / n)));
             
             // add to view
             this.$el.append(canvas_el);
             
-            // find canvas element
+            // add to list
+            this.container_list[i] = canvas_el;
+            
+            // add a separate list for canvas elements
             if (tag == 'svg') {
-                this.canvas[i] = d3.select(canvas_el[0]);
+                this.canvas_list[i] = d3.select(canvas_el.find('#canvas')[0]);
             } else {
-                this.canvas[i] = canvas_el;
+                this.canvas_list[i] = canvas_el.find('#canvas');
             }
         }
     },
@@ -137,7 +149,7 @@
         }
         
         // create canvas element and add to canvas list
-        this._createCanvas(this.chart_settings.tag, n_panels);
+        this._createContainer(this.chart_settings.tag, n_panels);
             
         // set chart state
         chart.state('wait', 'Please wait...');
@@ -145,6 +157,7 @@
         // clean up data if there is any from previous jobs
         if (!this.chart_settings.execute ||
             (this.chart_settings.execute && chart.get('modified'))) {
+            
             // reset jobs
             this.app.jobs.cleanup(chart);
             
@@ -156,7 +169,7 @@
         var self = this;
         require(['plugin/charts/' + chart_type + '/' + chart_type], function(ChartView) {
             // create chart
-            var view = new ChartView(self.app, {canvas : self.canvas});
+            var view = new ChartView(self.app, {canvas : self.canvas_list});
             
             // request data
             if (self.chart_settings.execute) {
@@ -269,8 +282,11 @@
     },
     
     // template svg/div element
-    _templateCanvas: function(tag, width) {
-        return '<' + tag + ' class="canvas" style="float: left; display: block; width:' + width + '%; height: 100%;"/>';
+    _templateContainer: function(tag, width) {
+        return  '<div class="container" style="float: left; display: block; width:' + width + '%; height: 100%;">' +
+                    '<div id="menu"/>' +
+                    '<' + tag + ' id="canvas" class="canvas" style="display: block; width:100%; height: inherit;">' +
+                '</div>';
     }
     
 });

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -5,6 +5,7 @@
 from galaxy import config, jobs
 import galaxy.model
 import galaxy.security
+from galaxy import dataset_collections
 import galaxy.quota
 from galaxy.tags.tag_handler import GalaxyTagHandler
 from galaxy.visualization.genomes import Genomes
@@ -54,6 +55,8 @@
         self._configure_security()
         # Tag handler
         self.tag_handler = GalaxyTagHandler()
+        # Dataset Collection Plugins
+        self.dataset_collections_service = dataset_collections.DatasetCollectionsService(self)
         # Genomes
         self.genomes = Genomes( self )
         # Data providers registry.

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/__init__.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/__init__.py
@@ -0,0 +1,274 @@
+from .registry import DatasetCollectionTypesRegistry
+from .matching import MatchingCollections
+from .type_description import CollectionTypeDescriptionFactory
+
+from galaxy import model
+from galaxy.exceptions import MessageException
+from galaxy.exceptions import ItemAccessibilityException
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.web.base.controller import (
+    UsesHistoryDatasetAssociationMixin,
+    UsesLibraryMixinItems,
+    UsesTagsMixin,
+)
+from galaxy.managers import hdas  # TODO: Refactor all mixin use into managers.
+
+from galaxy.util import validation
+from galaxy.util import odict
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers."
+ERROR_NO_COLLECTION_TYPE = "Create called without specifing a collection type."
+
+
+class DatasetCollectionsService(
+    UsesHistoryDatasetAssociationMixin,
+    UsesLibraryMixinItems,
+    UsesTagsMixin,
+):
+    """
+    Abstraction for interfacing with dataset collections instance - ideally abstarcts
+    out model and plugin details.
+    """
+
+    def __init__( self, app ):
+        self.type_registry = DatasetCollectionTypesRegistry( app )
+        self.collection_type_descriptions = CollectionTypeDescriptionFactory( self.type_registry )
+        self.model = app.model
+        self.security = app.security
+        self.hda_manager = hdas.HDAManager()
+
+    def create(
+        self,
+        trans,
+        parent,  # PRECONDITION: security checks on ability to add to parent occurred during load.
+        name,
+        collection_type,
+        element_identifiers=None,
+        elements=None,
+        implicit_collection_info=None,
+    ):
+        """
+        """
+        dataset_collection = self.__create_dataset_collection(
+            trans=trans,
+            collection_type=collection_type,
+            element_identifiers=element_identifiers,
+            elements=elements,
+        )
+        if isinstance( parent, model.History ):
+            dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
+                collection=dataset_collection,
+                name=name,
+            )
+            if implicit_collection_info:
+                for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]:
+                    dataset_collection_instance.add_implicit_input_collection( input_name, input_collection )
+                for output_dataset in implicit_collection_info.get( "outputs_datasets" ):
+                    output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
+                    trans.sa_session.add( output_dataset )
+
+                dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ]
+            # Handle setting hid
+            parent.add_dataset_collection( dataset_collection_instance )
+        elif isinstance( parent, model.LibraryFolder ):
+            dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
+                collection=dataset_collection,
+                folder=parent,
+                name=name,
+            )
+        else:
+            message = "Internal logic error - create called with unknown parent type %s" % type( parent )
+            log.exception( message )
+            raise MessageException( message )
+
+        return self.__persist( dataset_collection_instance )
+
+    def __create_dataset_collection(
+        self,
+        trans,
+        collection_type,
+        element_identifiers=None,
+        elements=None,
+    ):
+        if element_identifiers is None and elements is None:
+            raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION )
+        if not collection_type:
+            raise RequestParameterInvalidException( ERROR_NO_COLLECTION_TYPE )
+        collection_type_description = self.collection_type_descriptions.for_collection_type( collection_type )
+        if elements is None:
+            if collection_type_description.has_subcollections( ):
+                # Nested collection - recursively create collections and update identifiers.
+                self.__recursively_create_collections( trans, element_identifiers )
+            elements = self.__load_elements( trans, element_identifiers )
+        # else if elements is set, it better be an ordered dict!
+
+        type_plugin = collection_type_description.rank_type_plugin()
+        dataset_collection = type_plugin.build_collection( elements )
+        dataset_collection.collection_type = collection_type
+        return dataset_collection
+
+    def delete( self, trans, instance_type, id ):
+        dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True )
+        dataset_collection_instance.deleted = True
+        trans.sa_session.add( dataset_collection_instance )
+        trans.sa_session.flush( )
+
+    def update( self, trans, instance_type, id, payload ):
+        dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True )
+        if trans.user is None:
+            anon_allowed_payload = {}
+            if 'deleted' in payload:
+                anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ]
+            if 'visible' in payload:
+                anon_allowed_payload[ 'visible' ] = payload[ 'visible' ]
+            payload = self._validate_and_parse_update_payload( anon_allowed_payload )
+        else:
+            payload = self._validate_and_parse_update_payload( payload )
+        changed = self._set_from_dict( trans, dataset_collection_instance, payload )
+        return changed
+
+    def _set_from_dict( self, trans, dataset_collection_instance, new_data ):
+        # Blatantly stolen from UsesHistoryDatasetAssociationMixin.set_hda_from_dict.
+
+        # send what we can down into the model
+        changed = dataset_collection_instance.set_from_dict( new_data )
+        # the rest (often involving the trans) - do here
+        if 'annotation' in new_data.keys() and trans.get_user():
+            dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance.collection, new_data[ 'annotation' ] )
+            changed[ 'annotation' ] = new_data[ 'annotation' ]
+        if 'tags' in new_data.keys() and trans.get_user():
+            self.set_tags_from_list( trans, dataset_collection_instance.collection, new_data[ 'tags' ], user=trans.user )
+
+        if changed.keys():
+            trans.sa_session.flush()
+
+        return changed
+
+    def _validate_and_parse_update_payload( self, payload ):
+        validated_payload = {}
+        for key, val in payload.items():
+            if val is None:
+                continue
+            if key in ( 'name' ):
+                val = validation.validate_and_sanitize_basestring( key, val )
+                validated_payload[ key ] = val
+            if key in ( 'deleted', 'visible' ):
+                validated_payload[ key ] = validation.validate_boolean( key, val )
+            elif key == 'tags':
+                validated_payload[ key ] = validation.validate_and_sanitize_basestring_list( key, val )
+        return validated_payload
+
+    def history_dataset_collections(self, history, query):
+        collections = history.dataset_collections
+        collections = filter( query.direct_match, collections )
+        return collections
+
+    def __persist( self, dataset_collection_instance ):
+        context = self.model.context
+        context.add( dataset_collection_instance )
+        context.flush()
+        return dataset_collection_instance
+
+    def __recursively_create_collections( self, trans, element_identifiers ):
+        # TODO: Optimize - don't recheck parent, reload created model, just use as is.
+        for index, element_identifier in enumerate( element_identifiers ):
+            try:
+                if not element_identifier[ "src" ] == "new_collection":
+                    # not a new collection, keep moving...
+                    continue
+            except KeyError:
+                # Not a dictionary, just an id of an HDA - move along.
+                continue
+
+            # element identifier is a dict with src new_collection...
+            collection_type = element_identifier.get( "collection_type", None )
+            if not collection_type:
+                raise RequestParameterInvalidException( "No collection_type define for nested collection." )
+            collection = self.__create_dataset_collection(
+                trans=trans,
+                collection_type=collection_type,
+                element_identifiers=element_identifier[ "element_identifiers" ],
+            )
+            self.__persist( collection )
+            element_identifier[ "src" ] = "dc"
+            element_identifier[ "id" ] = trans.security.encode_id( collection.id )
+
+        return element_identifiers
+
+    def __load_elements( self, trans, element_identifiers ):
+        elements = odict.odict()
+        for element_identifier in element_identifiers:
+            elements[ element_identifier[ "name" ] ] = self.__load_element( trans, element_identifier )
+        return elements
+
+    def __load_element( self, trans, element_identifier ):
+        #if not isinstance( element_identifier, dict ):
+        #    # Is allowing this to just be the id of an hda too clever? Somewhat
+        #    # consistent with other API methods though.
+        #    element_identifier = dict( src='hda', id=str( element_identifier ) )
+
+        # dateset_identifier is dict {src=hda|ldda, id=<encoded_id>}
+        try:
+            src_type = element_identifier.get( 'src', 'hda' )
+        except AttributeError:
+            raise MessageException( "Dataset collection element definition (%s) not dictionary-like." % element_identifier )
+        encoded_id = element_identifier.get( 'id', None )
+        if not src_type or not encoded_id:
+            raise RequestParameterInvalidException( "Problem decoding element identifier %s" % element_identifier )
+
+        if src_type == 'hda':
+            decoded_id = int( trans.app.security.decode_id( encoded_id ) )
+            element = self.hda_manager.get( trans, decoded_id, check_ownership=False )
+        elif src_type == 'ldda':
+            element = self.get_library_dataset_dataset_association( trans, encoded_id )
+        elif src_type == 'hdca':
+            # TODO: Option to copy? Force copy? Copy or allow if not owned?
+            element = self.__get_history_collection_instance( trans, encoded_id ).collection
+        # TODO: ldca.
+        elif src_type == "dc":
+            # TODO: Force only used internally during nested creation so no
+            # need to recheck security.
+            element = self.get_dataset_collection( trans, encoded_id )
+        else:
+            raise RequestParameterInvalidException( "Unknown src_type parameter supplied '%s'." % src_type )
+        return element
+
+    def match_collections( self, collections_to_match ):
+        """
+        May seem odd to place it here, but planning to grow sophistication and
+        get plugin types involved so it will likely make sense in the future.
+        """
+        return MatchingCollections.for_collections( collections_to_match, self.collection_type_descriptions )
+
+    def get_dataset_collection_instance( self, trans, instance_type, id, **kwds ):
+        """
+        """
+        if instance_type == "history":
+            return self.__get_history_collection_instance( trans, id, **kwds )
+        elif instance_type == "library":
+            return self.__get_library_collection_instance( trans, id, **kwds )
+
+    def get_dataset_collection( self, trans, encoded_id ):
+        collection_id = int( trans.app.security.decode_id( encoded_id ) )
+        collection = trans.sa_session.query( trans.app.model.DatasetCollection ).get( collection_id )
+        return collection
+
+    def __get_history_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
+        instance_id = int( trans.app.security.decode_id( id ) )
+        collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id )
+        self.security_check( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible )
+        return collection_instance
+
+    def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
+        if check_ownership:
+            raise NotImplemented( "Functionality (getting library dataset collection with ownership check) unimplemented." )
+        instance_id = int( trans.security.decode_id( id ) )
+        collection_instance = trans.sa_session.query( trans.app.model.LibraryDatasetCollectionAssociation ).get( instance_id )
+        if check_accessible:
+            if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), collection_instance, trans.user ):
+                raise ItemAccessibilityException( "LibraryDatasetCollectionAssociation is not accessible to the current user", type='error' )
+        return collection_instance

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/matching.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/matching.py
@@ -0,0 +1,68 @@
+from galaxy.util import bunch
+from galaxy import exceptions
+from .structure import get_structure
+
+CANNOT_MATCH_ERROR_MESSAGE = "Cannot match collection types."
+
+
+class CollectionsToMatch( object ):
+    """ Structure representing a set of collections that need to be matched up
+    when running tools (possibly workflows in the future as well).
+    """
+
+    def __init__( self ):
+        self.collections = {}
+
+    def add( self, input_name, hdca, subcollection_type=None ):
+        self.collections[ input_name ] = bunch.Bunch(
+            hdca=hdca,
+            subcollection_type=subcollection_type,
+        )
+
+    def has_collections( self ):
+        return len( self.collections ) > 0
+
+    def iteritems( self ):
+        return self.collections.iteritems()
+
+
+class MatchingCollections( object ):
+    """ Structure holding the result of matching a list of collections
+    together. This class being different than the class above and being
+    created in the dataset_collections_service layer may seem like
+    overkill but I suspect in the future plugins will be subtypable for
+    instance so matching collections will need to make heavy use of the
+    dataset collection type registry managed by the dataset collections
+    sevice - hence the complexity now.
+    """
+
+    def __init__( self ):
+        self.structure = None
+        self.collections = {}
+
+    def __attempt_add_to_match( self, input_name, hdca, collection_type_description, subcollection_type ):
+        structure = get_structure( hdca, collection_type_description, leaf_subcollection_type=subcollection_type )
+        if not self.structure:
+            self.structure = structure
+            self.collections[ input_name ] = hdca
+        else:
+            if not self.structure.can_match( structure ):
+                raise exceptions.MessageException( CANNOT_MATCH_ERROR_MESSAGE )
+            self.collections[ input_name ] = hdca
+
+    def slice_collections( self ):
+        return self.structure.walk_collections( self.collections )
+
+    @staticmethod
+    def for_collections( collections_to_match, collection_type_descriptions ):
+        if not collections_to_match.has_collections():
+            return None
+
+        matching_collections = MatchingCollections()
+        for input_key, to_match in collections_to_match.iteritems():
+            hdca = to_match.hdca
+            subcollection_type = to_match = to_match.subcollection_type
+            collection_type_description = collection_type_descriptions.for_collection_type( hdca.collection.collection_type )
+            matching_collections.__attempt_add_to_match( input_key, hdca, collection_type_description, subcollection_type )
+
+        return matching_collections

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/registry.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/registry.py
@@ -0,0 +1,14 @@
+from .types import list
+from .types import paired
+
+
+PLUGIN_CLASSES = [list.ListDatasetCollectionType, paired.PairedDatasetCollectionType]
+
+
+class DatasetCollectionTypesRegistry(object):
+
+    def __init__( self, app ):
+        self.__plugins = dict( [ ( p.collection_type, p() ) for p in PLUGIN_CLASSES ] )
+
+    def get( self, plugin_type ):
+        return self.__plugins[ plugin_type ]

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/structure.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/structure.py
@@ -0,0 +1,105 @@
+""" Module for reasoning about structure of and matching hierarchical collections of data.
+"""
+import logging
+log = logging.getLogger( __name__ )
+
+
+class Leaf( object ):
+
+    def __len__( self ):
+        return 1
+
+    @property
+    def is_leaf( self ):
+        return True
+
+leaf = Leaf()
+
+
+class Tree( object ):
+
+    def __init__( self, dataset_collection, collection_type_description, leaf_subcollection_type ):
+        self.collection_type_description = collection_type_description
+        self.leaf_subcollection_type = leaf_subcollection_type  # collection_type to trim tree at...
+        children = []
+        for element in dataset_collection.elements:
+            child_collection = element.child_collection
+            if child_collection:
+                subcollection_type_description = collection_type_description.subcollection_type_description()  # Type description of children
+                if subcollection_type_description.can_match_type( leaf_subcollection_type ):
+                    children.append( ( element.element_identifier, leaf  ) )
+                else:
+                    children.append( ( element.element_identifier, Tree( child_collection, collection_type_description=subcollection_type_description, leaf_subcollection_type=leaf_subcollection_type )  ) )
+            elif element.hda:
+                children.append( ( element.element_identifier, leaf ) )
+
+        self.children = children
+
+    def walk_collections( self, hdca_dict ):
+        return self._walk_collections( dict_map( lambda hdca: hdca.collection, hdca_dict ) )
+
+    def _walk_collections( self, collection_dict ):
+        for ( identifier, substructure ) in self.children:
+            def element( collection ):
+                return collection[ identifier ]
+
+            if substructure.is_leaf:
+                yield dict_map( element, collection_dict )
+            else:
+                sub_collections = dict_map( lambda collection: element( collection ).child_collection )
+                for element in substructure._walk_collections( sub_collections ):
+                    yield element
+
+    @property
+    def is_leaf( self ):
+        return False
+
+    def can_match( self, other_structure ):
+        if not self.collection_type_description.can_match_type( other_structure.collection_type_description ):
+            # TODO: generalize
+            return False
+
+        if len( self.children ) != len( other_structure.children ):
+            return False
+
+        for my_child, other_child in zip( self.children, other_structure.children ):
+            if my_child[ 0 ] != other_child[ 0 ]:  # Different identifiers, TODO: generalize
+                return False
+
+            # At least one is nested collection...
+            if my_child[ 1 ].is_leaf != other_child[ 1 ].is_leaf:
+                return False
+
+            if not my_child[ 1 ].is_leaf and not my_child[ 1 ].can_match( other_child[ 1 ]):
+                return False
+
+        return True
+
+    def __len__( self ):
+        return sum( [ len( c[ 1 ] ) for c in self.children ] )
+
+    def element_identifiers_for_datasets( self, trans, datasets ):
+        element_identifiers = []
+        for identifier, child in self.children:
+            if isinstance( child, Tree ):
+                child_identifiers = child.element_identifiers_for_datasets( trans, datasets[ 0:len( child ) ] )
+                child_identifiers[ "name" ] = identifier
+                element_identifiers.append( child_identifiers )
+            else:
+                element_identifiers.append( dict( name=identifier, src="hda", id=trans.security.encode_id( datasets[ 0 ].id ) ) )
+
+            datasets = datasets[ len( child ): ]
+
+        return dict(
+            src="new_collection",
+            collection_type=self.collection_type_description.collection_type,
+            element_identifiers=element_identifiers,
+        )
+
+
+def dict_map( func, input_dict ):
+    return dict( [ ( k, func(v) ) for k, v in input_dict.iteritems() ] )
+
+
+def get_structure( dataset_collection_instance, collection_type_description, leaf_subcollection_type=None ):
+    return Tree( dataset_collection_instance.collection, collection_type_description, leaf_subcollection_type=leaf_subcollection_type )

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/subcollections.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/subcollections.py
@@ -0,0 +1,25 @@
+from galaxy import exceptions
+
+
+def split_dataset_collection_instance( dataset_collection_instance, collection_type ):
+    """ Split up collection into collection.
+    """
+    return _split_dataset_collection( dataset_collection_instance.collection, collection_type )
+
+
+def _split_dataset_collection( dataset_collection, collection_type ):
+    this_collection_type = dataset_collection.collection_type
+    if not this_collection_type.endswith( collection_type ) or this_collection_type == collection_type:
+        raise exceptions.MessageException( "Cannot split collection in desired fashion." )
+        
+    split_elements = []
+    for element in dataset_collection.elements:
+        child_collection = element.child_collection
+        if child_collection is None:
+            raise exceptions.MessageException( "Cannot split collection in desired fashion." )
+        if child_collection.collection_type == collection_type:
+            split_elements.append( element )
+        else:
+            split_elements.extend( _split_dataset_collection( element.child_collection ) )
+
+    return split_elements

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/type_description.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/type_description.py
@@ -0,0 +1,89 @@
+
+
+class CollectionTypeDescriptionFactory( object ):
+
+    def __init__( self, type_registry ):
+        # taking in type_registry though not using it, because we will someday
+        # I think.
+        self.type_registry = type_registry
+
+    def for_collection_type( self, collection_type ):
+        return CollectionTypeDescription( collection_type, self )
+
+
+class CollectionTypeDescription( object ):
+    """ Abstraction over dataset collection type that ties together string
+    reprentation in database/model with type registry.
+
+
+    >>> nested_type_description = CollectionTypeDescription( "list:paired", None )
+    >>> paired_type_description = CollectionTypeDescription( "paired", None )
+    >>> nested_type_description.has_subcollections_of_type( "list" )
+    False
+    >>> nested_type_description.has_subcollections_of_type( "list:paired" )
+    False
+    >>> nested_type_description.has_subcollections_of_type( "paired" )
+    True
+    >>> nested_type_description.has_subcollections_of_type( paired_type_description )
+    True
+    >>> nested_type_description.has_subcollections( )
+    True
+    >>> paired_type_description.has_subcollections( )
+    False
+    >>> paired_type_description.rank_collection_type()
+    'paired'
+    >>> nested_type_description.rank_collection_type()
+    'list'
+    """
+
+    def __init__( self, collection_type, collection_type_description_factory ):
+        self.collection_type = collection_type
+        self.collection_type_description_factory = collection_type_description_factory
+        self.__has_subcollections = self.collection_type.find( ":" ) > 0
+
+    def has_subcollections_of_type( self, other_collection_type ):
+        """ Take in another type (either flat string or another
+        CollectionTypeDescription) and determine if this collection contains
+        subcollections matching that type.
+
+        The way this is used in map/reduce it seems to make the most sense
+        for this to return True if these subtypes are proper (i.e. a type
+        is not considered to have subcollections of its own type).
+        """
+        if hasattr( other_collection_type, 'collection_type' ):
+            other_collection_type = other_collection_type.collection_type
+        collection_type = self.collection_type
+        return collection_type.endswith( other_collection_type ) and collection_type != other_collection_type
+
+    def is_subcollection_of_type( self, other_collection_type ):
+        if not hasattr( other_collection_type, 'collection_type' ):
+            other_collection_type = self.collection_type_description_factory.for_collection_type( other_collection_type )
+        return other_collection_type.has_subcollections_of_type( self )
+
+    def can_match_type( self, other_collection_type ):
+        if hasattr( other_collection_type, 'collection_type' ):
+            other_collection_type = other_collection_type.collection_type
+        collection_type = self.collection_type
+        return other_collection_type == collection_type
+
+    def subcollection_type_description( self ):
+        if not self.__has_subcollections:
+            raise ValueError( "Cannot generate subcollection type description for flat type %s" % self.collection_type )
+        subcollection_type = self.collection_type.split( ":", 1 )[ 1 ]
+        return self.collection_type_description_factory.for_collection_type( subcollection_type )
+
+    def has_subcollections( self ):
+        return self.__has_subcollections
+
+    def rank_collection_type( self ):
+        """ Return the top-level collection type corresponding to this
+        collection type. For instance the "rank" type of a list of paired
+        data ("list:paired") is "list".
+        """
+        return self.collection_type.split( ":" )[ 0 ]
+
+    def rank_type_plugin( self ):
+        return self.collection_type_description_factory.type_registry.get( self.rank_collection_type() )
+
+    def __str__( self ):
+        return "CollectionTypeDescription[%s]" % self.collection_type

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/types/__init__.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/types/__init__.py
@@ -0,0 +1,34 @@
+from galaxy import exceptions
+from abc import ABCMeta
+from abc import abstractmethod
+
+from galaxy import model
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+class DatasetCollectionType(object):
+    __metaclass__ = ABCMeta
+
+    @abstractmethod
+    def build_collection( self, dataset_instances ):
+        """
+        Build DatasetCollection with populated DatasetcollectionElement objects
+        corresponding to the supplied dataset instances or throw exception if
+        this is not a valid collection of the specified type.
+        """
+
+
+class BaseDatasetCollectionType( DatasetCollectionType ):
+
+    def _validation_failed( self, message ):
+        raise exceptions.ObjectAttributeInvalidException( message )
+
+    def _new_collection_for_elements( self, elements ):
+        dataset_collection = model.DatasetCollection( )
+        for index, element in enumerate( elements ):
+            element.element_index = index
+            element.collection = dataset_collection
+        dataset_collection.elements = elements
+        return dataset_collection

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/types/list.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/types/list.py
@@ -0,0 +1,23 @@
+from ..types import BaseDatasetCollectionType
+
+from galaxy.model import DatasetCollectionElement
+
+
+class ListDatasetCollectionType( BaseDatasetCollectionType ):
+    """ A flat list of named elements.
+    """
+    collection_type = "list"
+
+    def __init__( self ):
+        pass
+
+    def build_collection( self, elements ):
+        associations = []
+        for identifier, element in elements.iteritems():
+            association = DatasetCollectionElement(
+                element=element,
+                element_identifier=identifier,
+            )
+            associations.append( association )
+
+        return self._new_collection_for_elements( associations )

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/types/paired.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/types/paired.py
@@ -0,0 +1,31 @@
+from ..types import BaseDatasetCollectionType
+
+from galaxy.model import DatasetCollectionElement
+
+LEFT_IDENTIFIER = "left"
+RIGHT_IDENTIFIER = "right"
+
+
+class PairedDatasetCollectionType( BaseDatasetCollectionType ):
+    """
+    Paired (left/right) datasets.
+    """
+    collection_type = "paired"
+
+    def __init__( self ):
+        pass
+
+    def build_collection( self, elements ):
+        left_dataset = elements.get("left", None)
+        right_dataset = elements.get("right", None)
+        if not left_dataset or not right_dataset:
+            self._validation_failed("Paired instance must define 'left' and 'right' datasets .")
+        left_association = DatasetCollectionElement(
+            element=left_dataset,
+            element_identifier=LEFT_IDENTIFIER,
+        )
+        right_association = DatasetCollectionElement(
+            element=right_dataset,
+            element_identifier=RIGHT_IDENTIFIER,
+        )
+        return self._new_collection_for_elements([left_association, right_association])

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/dataset_collections/util.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/util.py
@@ -0,0 +1,52 @@
+from galaxy import exceptions
+from galaxy import web
+from galaxy import model
+
+
+def api_payload_to_create_params( payload ):
+    """
+    Cleanup API payload to pass into dataset_collections.
+    """
+    required_parameters = [ "collection_type", "element_identifiers" ]
+    missing_parameters = [ p for p in required_parameters if p not in payload ]
+    if missing_parameters:
+        message = "Missing required parameters %s" % missing_parameters
+        raise exceptions.ObjectAttributeMissingException( message )
+
+    params = dict(
+        collection_type=payload.get( "collection_type" ),
+        element_identifiers=payload.get( "element_identifiers" ),
+        name=payload.get( "name", None ),
+    )
+
+    return params
+
+
+def dictify_dataset_collection_instance( dataset_colleciton_instance, parent, security, view="element" ):
+    dict_value = dataset_colleciton_instance.to_dict( view=view )
+    encoded_id = security.encode_id( dataset_colleciton_instance.id )
+    if isinstance( parent, model.History ):
+        encoded_history_id = security.encode_id( parent.id )
+        dict_value[ 'url' ] = web.url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" )
+    elif isinstance( parent, model.LibraryFolder ):
+        encoded_library_id = security.encode_id( parent.library.id )
+        encoded_folder_id = security.encode_id( parent.id )
+        # TODO: Work in progress - this end-point is not right yet...
+        dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id )
+    if view == "element":
+        dict_value[ 'elements' ] = map( dictify_element, dataset_colleciton_instance.collection.elements )
+    security.encode_all_ids( dict_value, recursive=True )  # TODO: Use Kyle's recusrive formulation of this.
+    return dict_value
+
+
+def dictify_element( element ):
+    dictified = element.to_dict( view="element" )
+    object_detials = element.element_object.to_dict()
+    if element.child_collection:
+        # Recursively yield elements for each nested collection...
+        object_detials[ "elements" ] = map( dictify_element, element.child_collection.elements )
+
+    dictified[ "object" ] = object_detials
+    return dictified
+
+__all__ = [ api_payload_to_create_params, dictify_dataset_collection_instance ]

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/exceptions/__init__.py
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -68,6 +68,10 @@
     status_code = 400
     err_code = error_codes.USER_REQUEST_MISSING_PARAMETER
 
+class ToolMetaParameterException( MessageException ):
+    status_code = 400
+    err_code = error_codes.USER_TOOL_META_PARAMETER_PROBLEM
+
 class RequestParameterInvalidException( MessageException ):
     status_code = 400
     err_code = error_codes.USER_REQUEST_INVALID_PARAMETER

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/exceptions/error_codes.json
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -55,6 +55,11 @@
     "message": "The request contains unknown type of contents."
     },
    {
+    "name": "USER_TOOL_META_PARAMETER_PROBLEM",
+    "code": 400011,
+    "message": "Supplied incorrect or incompatible tool meta parameters."
+   },
+   {
     "name": "USER_NO_API_KEY",
     "code": 403001,
     "message": "API authentication required for this request"

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -964,6 +964,8 @@
                         trynum += 1
                         log.warning( 'Error accessing %s, will retry: %s', dataset.dataset.file_name, e )
                         time.sleep( 2 )
+                if getattr( dataset, "hidden_beneath_collection_instance", None ):
+                    dataset.visible = False
                 dataset.blurb = 'done'
                 dataset.peek = 'no peek'
                 dataset.info = (dataset.info or '')

diff -r fef831b5e2bd3feaaef58212eb695943d8969212 -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -315,6 +315,8 @@
         self.parameters = []
         self.input_datasets = []
         self.output_datasets = []
+        self.input_dataset_collections = []
+        self.output_dataset_collections = []
         self.input_library_datasets = []
         self.output_library_datasets = []
         self.state = Job.states.NEW
@@ -454,6 +456,10 @@
         self.input_datasets.append( JobToInputDatasetAssociation( name, dataset ) )
     def add_output_dataset( self, name, dataset ):
         self.output_datasets.append( JobToOutputDatasetAssociation( name, dataset ) )
+    def add_input_dataset_collection( self, name, dataset ):
+        self.input_dataset_collections.append( JobToInputDatasetCollectionAssociation( name, dataset ) )
+    def add_output_dataset_collection( self, name, dataset ):
+        self.output_dataset_collections.append( JobToOutputDatasetCollectionAssociation( name, dataset ) )
     def add_input_library_dataset( self, name, dataset ):
         self.input_library_datasets.append( JobToInputLibraryDatasetAssociation( name, dataset ) )
     def add_output_library_dataset( self, name, dataset ):
@@ -696,6 +702,19 @@
         self.name = name
         self.dataset = dataset
 
+
+class JobToInputDatasetCollectionAssociation( object ):
+    def __init__( self, name, dataset ):
+        self.name = name
+        self.dataset = dataset
+
+
+class JobToOutputDatasetCollectionAssociation( object ):
+    def __init__( self, name, dataset_collection ):
+        self.name = name
+        self.dataset_collection = dataset_collection
+
+
 class JobToInputLibraryDatasetAssociation( object ):
     def __init__( self, name, dataset ):
         self.name = name
@@ -706,6 +725,13 @@
         self.name = name
         self.dataset = dataset
 
+
+class ImplicitlyCreatedDatasetCollectionInput( object ):
+    def __init__( self, name, input_dataset_collection ):
+        self.name = name
+        self.input_dataset_collection = input_dataset_collection
+
+
 class PostJobAction( object ):
     def __init__( self, action_type, workflow_step, output_name = None, action_arguments = None):
         self.action_type = action_type
@@ -907,6 +933,14 @@
         self.datasets.append( dataset )
         return dataset
 
+    def add_dataset_collection( self, history_dataset_collection, set_hid=True ):
+        if set_hid:
+            history_dataset_collection.hid = self._next_hid()
+        history_dataset_collection.history = self
+        # TODO: quota?
+        self.dataset_collections.append( history_dataset_collection )
+        return history_dataset_collection
+
     def copy( self, name=None, target_user=None, activatable=False, all_datasets=False ):
         """
         Return a copy of this history using the given `name` and `target_user`.
@@ -947,6 +981,19 @@
             db_session.flush()
             # Copy annotation.
             self.copy_item_annotation( db_session, self.user, hda, target_user, new_hda )
+        # Copy history dataset collections
+        if all_datasets:
+            hdcas = self.dataset_collections
+        else:
+            hdcas = self.active_dataset_collections
+        for hdca in hdcas:
+            new_hdca = hdca.copy( )
+            new_history.add_dataset_collection( new_hdca, set_hid=False )
+            db_session.add( new_hdca )
+            db_session.flush()
+            # Copy annotation.
+            self.copy_item_annotation( db_session, self.user, hdca, target_user, new_hdca )
+
         new_history.hid_counter = self.hid_counter
         db_session.add( new_history )
         db_session.flush()
@@ -1045,6 +1092,12 @@
             self._active_datasets_children_and_roles = query.all()
         return self._active_datasets_children_and_roles
 
+    @property
+    def active_contents( self ):
+        """ Return all active contents ordered by hid.
+        """
+        return self.contents_iter( types=[ "dataset", "dataset_collection" ], deleted=False, visible=True )
+
     def contents_iter( self, **kwds ):
         """
         Fetch filtered list of contents of history.
@@ -1056,6 +1109,8 @@
         iters = []
         if 'dataset' in types:
             iters.append( self.__dataset_contents_iter( **kwds ) )
+        if 'dataset_collection' in types:
+            iters.append( self.__collection_contents_iter( **kwds ) )
         return galaxy.util.merge_sorted_iterables( operator.attrgetter( "hid" ), *iters )
 
     def __dataset_contents_iter(self, **kwds):
@@ -1085,6 +1140,9 @@
         else:
             return query
 
+    def __collection_contents_iter( self, **kwds ):
+        return self.__filter_contents( HistoryDatasetCollectionAssociation, **kwds )
+
     def copy_tags_from(self,target_user,source_history):
         for src_shta in source_history.tags:
             new_shta = src_shta.copy()
@@ -1932,6 +1990,7 @@
                      purged = hda.purged,
                      visible = hda.visible,
                      state = hda.state,
+                     history_content_type=hda.history_content_type,
                      file_size = int( hda.get_size() ),
                      update_time = hda.update_time.isoformat(),
                      data_type = hda.ext,
@@ -2001,6 +2060,10 @@
 
         return changed
 
+    @property
+    def history_content_type( self ):
+        return "dataset"
+
 
 class HistoryDatasetAssociationDisplayAtAuthorization( object ):
     def __init__( self, hda=None, user=None, site=None ):
@@ -2516,6 +2579,313 @@
             try: os.unlink( self.file_name )
             except Exception, e: print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e )
 
+
+DEFAULT_COLLECTION_NAME = "Unnamed Collection"
+
+
+class DatasetCollection( object, Dictifiable, UsesAnnotations ):
+    """
+    """
+    dict_collection_visible_keys = ( 'id', 'name', 'collection_type' )
+    dict_element_visible_keys = ( 'id', 'name', 'collection_type' )
+
+    def __init__(
+        self,
+        id=None,
+        collection_type=None,
+    ):
+        self.id = id
+        self.collection_type = collection_type
+
+    @property
+    def dataset_instances( self ):
+        instances = []
+        for element in self.elements:
+            if element.is_collection:
+                instances.extend( element.child_collection.dataset_instances )
+            else:
+                instance = element.dataset_instance
+                instances.append( instance )
+        return instances
+
+    @property
+    def state( self ):
+        # TODO: DatasetCollection state handling...
+        return 'ok'
+
+    def validate( self ):
+        if self.collection_type is None:
+            raise Exception("Each dataset collection must define a collection type.")
+
+    def __getitem__( self, key ):
+        get_by_attribute = "element_index" if isinstance( key, int ) else "element_identifier"
+        for element in self.elements:
+            if getattr( element, get_by_attribute ) == key:
+                return element
+        error_message = "Dataset collection has no %s with key %s." % ( get_by_attribute, key )
+        raise KeyError( error_message )
+
+    def copy( self ):
+        new_collection = DatasetCollection(
+            collection_type=self.collection_type,
+        )
+        for element in self.elements:
+            element.copy_to_collection( new_collection )
+        object_session( self ).add( new_collection )
+        object_session( self ).flush()
+        return new_collection
+
+    def set_from_dict( self, new_data ):
+        editable_keys = ( 'name' )
+        changed = {}
+
+        # unknown keys are ignored here
+        for key in [ k for k in new_data.keys() if k in editable_keys ]:
+            new_val = new_data[ key ]
+            old_val = self.__getattribute__( key )
+            if new_val == old_val:
+                continue
+
+            self.__setattr__( key, new_val )
+            changed[ key ] = new_val
+
+        return changed
+
+
+class DatasetCollectionInstance( object, HasName ):
+    """
+    """
+    def __init__(
+        self,
+        collection=None,
+        deleted=False,
+    ):
+        # Relationships
+        self.collection = collection
+        # Since deleted property is shared between history and dataset collections,
+        # it could be on either table - some places in the code however it is convient
+        # it is on instance instead of collection.
+        self.deleted = deleted
+
+    @property
+    def state( self ):
+        return self.collection.state
+
+    def display_name( self ):
+        return self.get_display_name()
+
+    def _base_to_dict( self, view ):
+        return dict(
+            id=self.id,
+            name=self.name,
+            collection_type=self.collection.collection_type,
+            type="collection",  # contents type (distinguished from file or folder (in case of library))
+        )
+
+    def set_from_dict( self, new_data ):
+        """
+        Set object attributes to the values in dictionary new_data limiting
+        to only those keys in dict_element_visible_keys.
+
+        Returns a dictionary of the keys, values that have been changed.
+        """
+        # precondition: keys are proper, values are parsed and validated
+        changed = self.collection.set_from_dict( new_data )
+
+        # unknown keys are ignored here
+        for key in [ k for k in new_data.keys() if k in self.editable_keys ]:
+            new_val = new_data[ key ]
+            old_val = self.__getattribute__( key )
+            if new_val == old_val:
+                continue
+
+            self.__setattr__( key, new_val )
+            changed[ key ] = new_val
+
+        return changed
+
+
+class HistoryDatasetCollectionAssociation( DatasetCollectionInstance, Dictifiable ):
+    """ Associates a DatasetCollection with a History. """
+    editable_keys = ( 'name', 'deleted', 'visible' )
+
+    def __init__(
+        self,
+        id=None,
+        hid=None,
+        collection=None,
+        history=None,
+        name=None,
+        deleted=False,
+        visible=True,
+        copied_from_history_dataset_collection_association=None,
+        implicit_output_name=None,
+        implicit_input_collections=[],
+    ):
+        super( HistoryDatasetCollectionAssociation, self ).__init__(
+            collection=collection,
+            deleted=deleted,
+        )
+        self.id = id
+        self.hid = hid
+        self.history = history
+        self.name = name
+        self.visible = visible
+        self.copied_from_history_dataset_collection_association = copied_from_history_dataset_collection_association
+        self.implicit_output_name = implicit_output_name
+        self.implicit_input_collections = implicit_input_collections
+
+    @property
+    def history_content_type( self ):
+        return "dataset_collection"
+
+    def to_dict( self, view='collection' ):
+        dict_value = dict(
+            hid=self.hid,
+            history_id=self.history.id,
+            history_content_type=self.history_content_type,
+            visible=self.visible,
+            deleted=self.deleted,
+            **self._base_to_dict(view=view)
+        )
+        return dict_value
+
+    def add_implicit_input_collection( self, name, history_dataset_collection ):
+        self.implicit_input_collections.append( ImplicitlyCreatedDatasetCollectionInput( name, history_dataset_collection)  )
+
+    def find_implicit_input_collection( self, name ):
+        matching_collection = None
+        for implicit_input_collection in self.implicit_input_collections:
+            if implicit_input_collection.name == name:
+                matching_collection = implicit_input_collection.input_dataset_collection
+                break
+        return matching_collection
+
+    def copy( self ):
+        """
+        Create a copy of this history dataset collection association. Copy
+        underlying collection.
+        """
+        hdca = HistoryDatasetCollectionAssociation(
+            hid=self.hid,
+            collection=self.collection.copy(),
+            visible=self.visible,
+            deleted=self.deleted,
+            name=self.name,
+            copied_from_history_dataset_collection_association=self,
+        )
+
+        object_session( self ).add( hdca )
+        object_session( self ).flush()
+        return hdca
+
+
+class LibraryDatasetCollectionAssociation( DatasetCollectionInstance, Dictifiable ):
+    """ Associates a DatasetCollection with a library folder. """
+    editable_keys = ( 'name', 'deleted' )
+
+    def __init__(
+        self,
+        id=None,
+        collection=None,
+        name=None,
+        deleted=False,
+        folder=None,
+    ):
+        super(LibraryDatasetCollectionAssociation, self).__init__(
+            collection=collection,
+            deleted=deleted,
+        )
+        self.id = id
+        self.folder = folder
+        self.name = name
+
+    def to_dict( self, view='collection' ):
+        dict_value = dict(
+            folder_id=self.folder.id,
+            **self._base_to_dict(view=view)
+        )
+        return dict_value
+
+
+class DatasetCollectionElement( object, Dictifiable ):
+    """ Associates a DatasetInstance (hda or ldda) with a DatasetCollection. """
+    # actionable dataset id needs to be available via API...
+    dict_collection_visible_keys = ( 'id', 'element_type', 'element_index', 'element_identifier' )
+    dict_element_visible_keys = ( 'id', 'element_type', 'element_index', 'element_identifier' )
+
+    def __init__(
+        self,
+        id=None,
+        collection=None,
+        element=None,
+        element_index=None,
+        element_identifier=None,
+    ):
+        if isinstance(element, HistoryDatasetAssociation):
+            self.hda = element
+            #self.instance_type = 'hda'
+        elif isinstance(element, LibraryDatasetDatasetAssociation):
+            self.ldda = element
+            #self.instance_type = 'ldda'
+        elif isinstance( element, DatasetCollection ):
+            self.child_collection = element
+        else:
+            raise AttributeError( 'Unknown element type provided: %s' % type( element ) )
+
+        self.id = id
+        self.collection = collection
+        self.element_index = element_index
+        self.element_identifier = element_identifier or str(element_index)
+
+    @property
+    def element_type( self ):
+        if self.hda:
+            return "hda"
+        elif self.ldda:
+            return "ldda"
+        elif self.child_collection:
+            #TOOD: Rename element_type to element_type.
+            return "dataset_collection"
+        else:
+            raise Exception( "Unknown element instance type" )
+
+    @property
+    def is_collection( self ):
+        return self.element_type == "dataset_collection"
+
+    @property
+    def element_object( self ):
+        if self.hda:
+            return self.hda
+        elif self.ldda:
+            return self.ldda
+        elif self.child_collection:
+            return self.child_collection
+        else:
+            raise Exception( "Unknown element instance type" )
+
+    @property
+    def dataset_instance( self ):
+        element_object = self.element_object
+        if isinstance( element_object, DatasetCollection ):
+            raise AttributeError( "Nested collection has no associated dataset_instance." )
+        return element_object
+
+    @property
+    def dataset( self ):
+        return self.dataset_instance.dataset
+
+    def copy_to_collection( self, collection ):
+        new_element = DatasetCollectionElement(
+            element=self.element_object,
+            collection=collection,
+            element_index=self.element_index,
+            element_identifier=self.element_identifier,
+        )
+        return new_element
+
+
 class Event( object ):
     def __init__( self, message=None, history=None, user=None, galaxy_session=None ):
         self.history = history
@@ -3520,6 +3890,15 @@
 class VisualizationTagAssociation ( ItemTagAssociation ):
     pass
 
+
+class HistoryDatasetCollectionTagAssociation( ItemTagAssociation ):
+    pass
+
+
+class LibraryDatasetCollectionTagAssociation( ItemTagAssociation ):
+    pass
+
+
 class ToolTagAssociation( ItemTagAssociation ):
     def __init__( self, id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None ):
         self.id = id
@@ -3550,6 +3929,15 @@
 class VisualizationAnnotationAssociation( object ):
     pass
 
+
+class HistoryDatasetCollectionAnnotationAssociation( object ):
+    pass
+
+
+class LibraryDatasetCollectionAnnotationAssociation( object ):
+    pass
+
+
 # Item rating classes.
 
 class ItemRatingAssociation( object ):
@@ -3583,6 +3971,17 @@
     def set_item( self, visualization ):
         self.visualization = visualization
 
+
+class HistoryDatasetCollectionRatingAssociation( ItemRatingAssociation ):
+    def set_item( self, dataset_collection ):
+        self.dataset_collection = dataset_collection
+
+
+class LibraryDatasetCollectionRatingAssociation( ItemRatingAssociation ):
+    def set_item( self, dataset_collection ):
+        self.dataset_collection = dataset_collection
+
+
 #Data Manager Classes
 class DataManagerHistoryAssociation( object ):
     def __init__( self, id=None, history=None, user=None ):

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/45fd6f57a7a6/
Changeset:   45fd6f57a7a6
User:        nsoranzo
Date:        2014-05-07 11:32:54
Summary:     Merged galaxy/galaxy-central into default
Affected #:  10 files

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f lib/galaxy/webapps/galaxy/api/configuration.py
--- a/lib/galaxy/webapps/galaxy/api/configuration.py
+++ b/lib/galaxy/webapps/galaxy/api/configuration.py
@@ -9,6 +9,7 @@
 import logging
 log = logging.getLogger( __name__ )
 
+
 class ConfigurationController( BaseAPIController ):
     # config attributes viewable by non-admin users
     EXPOSED_USER_OPTIONS = [
@@ -20,6 +21,7 @@
         'logo_url',
         'terms_url',
         'allow_user_dataset_purge',
+        'use_remote_user'
     ]
     # config attributes viewable by admin users
     EXPOSED_ADMIN_OPTIONS = [

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -168,8 +168,8 @@
             from_history_id = payload.get( 'from_history_id' )
             history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
             job_ids = map( trans.security.decode_id, payload.get( 'job_ids', [] ) )
-            dataset_ids = map( trans.security.decode_id, payload.get( 'dataset_ids', [] ) )
-            dataset_collection_ids = map( trans.security.decode_id, payload.get( 'dataset_collection_ids', [] ) )
+            dataset_ids = payload.get( 'dataset_ids', [] )
+            dataset_collection_ids = payload.get( 'dataset_collection_ids', [] )
             workflow_name = payload[ 'workflow_name' ]
             stored_workflow = extract_workflow(
                 trans=trans,

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -87,7 +87,8 @@
     for hid in dataset_collection_ids:
         step = model.WorkflowStep()
         step.type = 'data_collection_input'
-        step.tool_inputs = dict( name="Input Dataset Collection" )
+        collection_type = summary.collection_types[ hid ]
+        step.tool_inputs = dict( name="Input Dataset Collection", collection_type=collection_type )
         hid_to_output_pair[ hid ] = ( step, 'output' )
         steps.append( step )
     # Tool steps
@@ -167,6 +168,8 @@
         self.warnings = set()
         self.jobs = odict()
         self.implicit_map_jobs = []
+        self.collection_types = {}
+
         self.__summarize()
 
     def __summarize( self ):
@@ -177,7 +180,9 @@
         implicit_outputs = []
         for content in self.history.active_contents:
             if content.history_content_type == "dataset_collection":
+                hid = content.hid
                 content = self.__original_hdca( content )
+                self.collection_types[ hid ] = content.collection.collection_type
                 if not content.implicit_output_name:
                     job = DatasetCollectionCreationJob( content )
                     self.jobs[ job ] = [ ( None, content ) ]

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/api/helpers.py
--- a/test/api/helpers.py
+++ b/test/api/helpers.py
@@ -1,3 +1,5 @@
+from operator import itemgetter
+
 import time
 import json
 import StringIO
@@ -12,6 +14,35 @@
 DEFAULT_HISTORY_TIMEOUT = 5  # Secs to wait on history to turn ok
 
 
+def skip_without_tool( tool_id ):
+    """ Decorate an API test method as requiring a specific tool,
+    have nose skip the test case is the tool is unavailable.
+    """
+
+    def method_wrapper( method ):
+
+        def get_tool_ids( api_test_case ):
+            index = api_test_case.galaxy_interactor.get( "tools", data=dict(in_panel=False) )
+            tools = index.json()
+            # In panels by default, so flatten out sections...
+            tool_ids = map( itemgetter( "id" ), tools )
+            return tool_ids
+
+        def wrapped_method( api_test_case, *args, **kwargs ):
+            if tool_id not in get_tool_ids( api_test_case ):
+                from nose.plugins.skip import SkipTest
+                raise SkipTest( )
+
+            return method( api_test_case, *args, **kwargs )
+
+        # Must preserve method name so nose can detect and report tests by
+        # name.
+        wrapped_method.__name__ = method.__name__
+        return wrapped_method
+
+    return method_wrapper
+
+
 # Deprecated mixin, use dataset populator instead.
 # TODO: Rework existing tests to target DatasetPopulator in a setup method instead.
 class TestsDatasets:
@@ -84,8 +115,8 @@
 class WorkflowPopulator( object ):
     # Impulse is to make this a Mixin, but probably better as an object.
 
-    def __init__( self, api_test_case ):
-        self.api_test_case = api_test_case
+    def __init__( self, galaxy_interactor ):
+        self.galaxy_interactor = galaxy_interactor
 
     def load_workflow( self, name, content=workflow_str, add_pja=False ):
         workflow = json.loads( content )
@@ -111,7 +142,7 @@
             workflow=json.dumps( workflow ),
             **create_kwds
         )
-        upload_response = self.api_test_case._post( "workflows/upload", data=data )
+        upload_response = self.galaxy_interactor.post( "workflows/upload", data=data )
         uploaded_workflow_id = upload_response.json()[ "id" ]
         return uploaded_workflow_id
 
@@ -189,6 +220,99 @@
         return show().json()
 
 
+class DatasetCollectionPopulator( object ):
+
+    def __init__( self, galaxy_interactor ):
+        self.galaxy_interactor = galaxy_interactor
+        self.dataset_populator = DatasetPopulator( galaxy_interactor )
+
+    def create_list_from_pairs( self, history_id, pairs ):
+        element_identifiers = []
+        for i, pair in enumerate( pairs ):
+            element_identifiers.append( dict(
+                name="test%d" % i,
+                src="hdca",
+                id=pair
+            ) )
+
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=json.dumps(element_identifiers),
+            collection_type="list:paired",
+        )
+        return self.__create( payload )
+
+    def create_pair_in_history( self, history_id, **kwds ):
+        payload = self.create_pair_payload(
+            history_id,
+            instance_type="history",
+            **kwds
+        )
+        return self.__create( payload )
+
+    def create_list_in_history( self, history_id, **kwds ):
+        payload = self.create_list_payload(
+            history_id,
+            instance_type="history",
+            **kwds
+        )
+        return self.__create( payload )
+
+    def create_list_payload( self, history_id, **kwds ):
+        return self.__create_payload( history_id, identifiers_func=self.list_identifiers, collection_type="list", **kwds )
+
+    def create_pair_payload( self, history_id, **kwds ):
+        return self.__create_payload( history_id, identifiers_func=self.pair_identifiers, collection_type="paired", **kwds )
+
+    def __create_payload( self, history_id, identifiers_func, collection_type, **kwds ):
+        contents = None
+        if "contents" in kwds:
+            contents = kwds[ "contents" ]
+            del kwds[ "contents" ]
+
+        if "element_identifiers" not in kwds:
+            kwds[ "element_identifiers" ] = json.dumps( identifiers_func( history_id, contents=contents ) )
+
+        payload = dict(
+            history_id=history_id,
+            collection_type=collection_type,
+            **kwds
+        )
+        return payload
+
+    def pair_identifiers( self, history_id, contents=None ):
+        hda1, hda2 = self.__datasets( history_id, count=2, contents=contents )
+
+        element_identifiers = [
+            dict( name="left", src="hda", id=hda1[ "id" ] ),
+            dict( name="right", src="hda", id=hda2[ "id" ] ),
+        ]
+        return element_identifiers
+
+    def list_identifiers( self, history_id, contents=None ):
+        hda1, hda2, hda3 = self.__datasets( history_id, count=3, contents=contents )
+        element_identifiers = [
+            dict( name="data1", src="hda", id=hda1[ "id" ] ),
+            dict( name="data2", src="hda", id=hda2[ "id" ] ),
+            dict( name="data3", src="hda", id=hda3[ "id" ] ),
+        ]
+        return element_identifiers
+
+    def __create( self, payload ):
+        create_response = self.galaxy_interactor.post( "dataset_collections", data=payload )
+        return create_response
+
+    def __datasets( self, history_id, count, contents=None ):
+        datasets = []
+        for i in xrange( count ):
+            new_kwds = {}
+            if contents:
+                new_kwds[ "content" ] = contents[ i ]
+            datasets.append( self.dataset_populator.new_dataset( history_id, **new_kwds ) )
+        return datasets
+
+
 def wait_on_state( state_func, assert_ok=False, timeout=5 ):
     delta = .1
     iteration = 0

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/api/test_dataset_collections.py
--- /dev/null
+++ b/test/api/test_dataset_collections.py
@@ -0,0 +1,113 @@
+from base import api
+import json
+from .helpers import DatasetPopulator
+from .helpers import DatasetCollectionPopulator
+
+
+class DatasetCollectionApiTestCase( api.ApiTestCase ):
+
+    def setUp( self ):
+        super( DatasetCollectionApiTestCase, self ).setUp()
+        self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
+        self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
+        self.history_id = self.dataset_populator.new_history()
+
+    def test_create_pair_from_history( self ):
+        payload = self.dataset_collection_populator.create_pair_payload(
+            self.history_id,
+            instance_type="history",
+        )
+        create_response = self._post( "dataset_collections", payload )
+        dataset_collection = self._check_create_response( create_response )
+        returned_datasets = dataset_collection[ "elements" ]
+        assert len( returned_datasets ) == 2, dataset_collection
+
+    def test_create_list_from_history( self ):
+        element_identifiers = self.dataset_collection_populator.list_identifiers( self.history_id )
+
+        payload = dict(
+            instance_type="history",
+            history_id=self.history_id,
+            element_identifiers=json.dumps(element_identifiers),
+            collection_type="list",
+        )
+
+        create_response = self._post( "dataset_collections", payload )
+        dataset_collection = self._check_create_response( create_response )
+        returned_datasets = dataset_collection[ "elements" ]
+        assert len( returned_datasets ) == 3, dataset_collection
+
+    def test_create_list_of_existing_pairs( self ):
+        pair_payload = self.dataset_collection_populator.create_pair_payload(
+            self.history_id,
+            instance_type="history",
+        )
+        pair_create_response = self._post( "dataset_collections", pair_payload )
+        dataset_collection = self._check_create_response( pair_create_response )
+        hdca_id = dataset_collection[ "id" ]
+
+        element_identifiers = [
+            dict( name="test1", src="hdca", id=hdca_id )
+        ]
+
+        payload = dict(
+            instance_type="history",
+            history_id=self.history_id,
+            element_identifiers=json.dumps(element_identifiers),
+            collection_type="list",
+        )
+        create_response = self._post( "dataset_collections", payload )
+        dataset_collection = self._check_create_response( create_response )
+        returned_collections = dataset_collection[ "elements" ]
+        assert len( returned_collections ) == 1, dataset_collection
+
+    def test_create_list_of_new_pairs( self ):
+        pair_identifiers = self.dataset_collection_populator.pair_identifiers( self.history_id )
+        element_identifiers = [ dict(
+            src="new_collection",
+            name="test_pair",
+            collection_type="paired",
+            element_identifiers=pair_identifiers,
+        ) ]
+        payload = dict(
+            collection_type="list:paired",
+            instance_type="history",
+            history_id=self.history_id,
+            name="nested_collecion",
+            element_identifiers=json.dumps( element_identifiers ),
+        )
+        create_response = self._post( "dataset_collections", payload )
+        dataset_collection = self._check_create_response( create_response )
+        assert dataset_collection[ "collection_type" ] == "list:paired"
+        returned_collections = dataset_collection[ "elements" ]
+        assert len( returned_collections ) == 1, dataset_collection
+        pair_1_element = returned_collections[ 0 ]
+        self._assert_has_keys( pair_1_element, "element_index" )
+        pair_1_object = pair_1_element[ "object" ]
+        self._assert_has_keys( pair_1_object, "collection_type", "elements" )
+        self.assertEquals( pair_1_object[ "collection_type" ], "paired" )
+        pair_elements = pair_1_object[ "elements" ]
+        assert len( pair_elements ) == 2
+        pair_1_element_1 = pair_elements[ 0 ]
+        assert pair_1_element_1[ "element_index" ] == 0
+
+    def test_hda_security( self ):
+        element_identifiers = self.dataset_collection_populator.pair_identifiers( self.history_id )
+
+        with self._different_user( ):
+            history_id = self.dataset_populator.new_history()
+            payload = dict(
+                instance_type="history",
+                history_id=history_id,
+                element_identifiers=json.dumps(element_identifiers),
+                collection_type="paired",
+            )
+
+            create_response = self._post( "dataset_collections", payload )
+            self._assert_status_code_is( create_response, 403 )
+
+    def _check_create_response( self, create_response ):
+        self._assert_status_code_is( create_response, 200 )
+        dataset_collection = create_response.json()
+        self._assert_has_keys( dataset_collection, "elements", "url", "name", "collection_type" )
+        return dataset_collection

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/api/test_history_contents.py
--- a/test/api/test_history_contents.py
+++ b/test/api/test_history_contents.py
@@ -3,7 +3,7 @@
 
 from .helpers import TestsDatasets
 from .helpers import LibraryPopulator
-from .test_dataset_collections import DatasetCollectionPopulator
+from .helpers import DatasetCollectionPopulator
 from base.interactor import (
     put_request,
     delete_request,

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/api/test_search.py
--- a/test/api/test_search.py
+++ b/test/api/test_search.py
@@ -7,7 +7,7 @@
 class SearchApiTestCase( api.ApiTestCase ):
 
     def test_search_workflows( self ):
-        workflow_populator = WorkflowPopulator( self )
+        workflow_populator = WorkflowPopulator( self.galaxy_interactor )
         workflow_id = workflow_populator.simple_workflow( "test_for_search" )
         search_response = self.__search( "select * from workflow" )
         assert self.__has_result_with_name( search_response, "test_for_search (imported from API)" ), search_response.json()

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/api/test_tools.py
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -2,7 +2,8 @@
 from base import api
 from operator import itemgetter
 from .helpers import DatasetPopulator
-from .test_dataset_collections import DatasetCollectionPopulator
+from .helpers import DatasetCollectionPopulator
+from .helpers import skip_without_tool
 
 
 class ToolsTestCase( api.ApiTestCase ):
@@ -51,8 +52,8 @@
         result_content = self._upload_and_get_content( table )
         self.assertEquals( result_content, table )
 
+    @skip_without_tool( "cat1" )
     def test_run_cat1( self ):
-        self.__skip_without_tool( "cat1" )
         # Run simple non-upload tool with an input data parameter.
         history_id = self.dataset_populator.new_history()
         new_dataset = self.dataset_populator.new_dataset( history_id, content='Cat1Test' )
@@ -66,8 +67,8 @@
         output1_content = self._get_content( history_id, dataset=output1 )
         self.assertEqual( output1_content.strip(), "Cat1Test" )
 
+    @skip_without_tool( "cat1" )
     def test_run_cat1_with_two_inputs( self ):
-        self.__skip_without_tool( "cat1" )
         # Run tool with an multiple data parameter and grouping (repeat)
         history_id = self.dataset_populator.new_history()
         new_dataset1 = self.dataset_populator.new_dataset( history_id, content='Cat1Test' )
@@ -83,8 +84,8 @@
         output1_content = self._get_content( history_id, dataset=output1 )
         self.assertEqual( output1_content.strip(), "Cat1Test\nCat2Test" )
 
+    @skip_without_tool( "cat1" )
     def test_multirun_cat1( self ):
-        self.__skip_without_tool( "cat1" )
         history_id = self.dataset_populator.new_history()
         new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' )
         new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' )
@@ -104,8 +105,8 @@
         self.assertEquals( output1_content.strip(), "123" )
         self.assertEquals( output2_content.strip(), "456" )
 
+    @skip_without_tool( "cat1" )
     def test_multirun_in_repeat( self ):
-        self.__skip_without_tool( "cat1" )
         history_id = self.dataset_populator.new_history()
         new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' )
         new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' )
@@ -127,8 +128,8 @@
         self.assertEquals( output1_content.strip(), "Common\n123" )
         self.assertEquals( output2_content.strip(), "Common\n456" )
 
+    @skip_without_tool( "cat1" )
     def test_multirun_on_multiple_inputs( self ):
-        self.__skip_without_tool( "cat1" )
         history_id = self.dataset_populator.new_history()
         new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' )
         new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' )
@@ -153,8 +154,8 @@
         assert "123\n0ab" in outputs_contents
         assert "456\n0ab" in outputs_contents
 
+    @skip_without_tool( "cat1" )
     def test_map_over_collection( self ):
-        self.__skip_without_tool( "cat1" )
         history_id = self.dataset_populator.new_history()
         hdca_id = self.__build_pair( history_id, [ "123", "456" ] )
         inputs = {
@@ -167,7 +168,6 @@
         self.assertEquals( len( jobs ), 2 )
         self.assertEquals( len( outputs ), 2 )
         self.assertEquals( len( implicit_collections ), 1 )
-        
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         output1 = outputs[ 0 ]
         output2 = outputs[ 1 ]
@@ -176,8 +176,8 @@
         self.assertEquals( output1_content.strip(), "123" )
         self.assertEquals( output2_content.strip(), "456" )
 
+    @skip_without_tool( "cat1" )
     def test_map_over_nested_collections( self ):
-        self.__skip_without_tool( "cat1" )
         history_id = self.dataset_populator.new_history()
         hdca_id = self.__build_nested_list( history_id )
         inputs = {
@@ -204,6 +204,7 @@
         first_object_left_element = first_object[ "elements" ][ 0 ]
         self.assertEquals( outputs[ 0 ][ "id" ], first_object_left_element[ "object" ][ "id" ] )
 
+    @skip_without_tool( "cat1" )
     def test_map_over_two_collections( self ):
         history_id = self.dataset_populator.new_history()
         hdca1_id = self.__build_pair( history_id, [ "123", "456" ] )
@@ -222,8 +223,8 @@
         self.assertEquals( output1_content.strip(), "123\n789" )
         self.assertEquals( output2_content.strip(), "456\n0ab" )
 
+    @skip_without_tool( "cat1" )
     def test_cannot_map_over_incompatible_collections( self ):
-        self.__skip_without_tool( "cat1" )
         history_id = self.dataset_populator.new_history()
         hdca1_id = self.__build_pair( history_id, [ "123", "456" ] )
         hdca2_id = self.dataset_collection_populator.create_list_in_history( history_id  ).json()[ "id" ]
@@ -236,8 +237,8 @@
         # on server.
         assert run_response.status_code >= 400
 
+    @skip_without_tool( "multi_data_param" )
     def test_reduce_collections( self ):
-        self.__skip_without_tool( "multi_data_param" )
         history_id = self.dataset_populator.new_history()
         hdca1_id = self.__build_pair( history_id, [ "123", "456" ] )
         hdca2_id = self.dataset_collection_populator.create_list_in_history( history_id  ).json()[ "id" ]
@@ -258,8 +259,8 @@
         assert output1_content.strip() == "123\n456"
         assert len( output2_content.strip().split("\n") ) == 3, output2_content
 
+    @skip_without_tool( "collection_paired_test" )
     def test_subcollection_mapping( self ):
-        self.__skip_without_tool( "collection_paired_test" )
         history_id = self.dataset_populator.new_history()
         hdca_list_id = self.__build_nested_list( history_id )
         inputs = {
@@ -285,7 +286,8 @@
         return self._run_outputs( self._run( tool_id, history_id, inputs ) )
 
     def _run_outputs( self, create_response ):
-        self._assert_status_code_is( create_response, 200, assert_ok=True )[ 'outputs' ]
+        self._assert_status_code_is( create_response, 200 )
+        return create_response.json()[ 'outputs' ]
 
     def _run_cat1( self, history_id, inputs, assert_ok=False ):
         return self._run( 'cat1', history_id, inputs, assert_ok=assert_ok )
@@ -334,11 +336,6 @@
         tool_ids = map( itemgetter( "id" ), tools )
         return tool_ids
 
-    def __skip_without_tool( self, tool_id ):
-        from nose.plugins.skip import SkipTest
-        if tool_id not in self.__tool_ids( ):
-            raise SkipTest( )
-
     def __build_nested_list( self, history_id ):
         hdca1_id = self.__build_pair( history_id, [ "123", "456" ] )
         hdca2_id = self.__build_pair( history_id, [ "789", "0ab" ] )

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1,8 +1,11 @@
 from base import api
 from json import dumps
+from json import loads
 import time
-from .helpers import TestsDatasets
 from .helpers import WorkflowPopulator
+from .helpers import DatasetPopulator
+from .helpers import DatasetCollectionPopulator
+from .helpers import skip_without_tool
 
 from base.interactor import delete_request  # requests like delete
 
@@ -12,11 +15,13 @@
 # - Allow post to workflows/<workflow_id>/run in addition to posting to
 #    /workflows with id in payload.
 # - Much more testing obviously, always more testing.
-class WorkflowsApiTestCase( api.ApiTestCase, TestsDatasets ):
+class WorkflowsApiTestCase( api.ApiTestCase ):
 
     def setUp( self ):
         super( WorkflowsApiTestCase, self ).setUp()
-        self.workflow_populator = WorkflowPopulator( self )
+        self.workflow_populator = WorkflowPopulator( self.galaxy_interactor )
+        self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
+        self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
 
     def test_delete( self ):
         workflow_id = self.workflow_populator.simple_workflow( "test_delete" )
@@ -58,6 +63,7 @@
         first_input = downloaded_workflow[ "steps" ][ "0" ][ "inputs" ][ 0 ]
         assert first_input[ "name" ] == "WorkflowInput1"
 
+    @skip_without_tool( "cat1" )
     def test_run_workflow( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_run" )
         workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -65,19 +71,20 @@
         # something like that.
         run_workflow_response = self._post( "workflows", data=workflow_request )
         self._assert_status_code_is( run_workflow_response, 200 )
-        self._wait_for_history( history_id, assert_ok=True )
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
 
+    @skip_without_tool( "cat1" )
     def test_extract_from_history( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_extract" )
         workflow_request, history_id = self._setup_workflow_run( workflow )
         contents_response = self._get( "histories/%s/contents" % history_id )
         self._assert_status_code_is( contents_response, 200 )
-        hda_ids = map( lambda c: c[ "id" ], contents_response.json() )
+        hda_ids = map( lambda c: c[ "hid" ], contents_response.json() )
 
         run_workflow_response = self._post( "workflows", data=workflow_request )
         self._assert_status_code_is( run_workflow_response, 200 )
 
-        self._wait_for_history( history_id, assert_ok=True )
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         data = dict( history_id=history_id, tool_id="cat1" )
         jobs_response = self._get( "jobs", data=data )
         self._assert_status_code_is( jobs_response, 200 )
@@ -90,26 +97,66 @@
             job_ids=dumps( [ cat1_job_id ] ),
             workflow_name="test import from history",
         )
-        run_workflow_response = self._post( "workflows", data=create_from_data )
-        self._assert_status_code_is( run_workflow_response, 200 )
+        create_workflow_response = self._post( "workflows", data=create_from_data )
+        self._assert_status_code_is( create_workflow_response, 200 )
 
-        new_workflow_id = run_workflow_response.json()[ "id" ]
+        new_workflow_id = create_workflow_response.json()[ "id" ]
         download_response = self._get( "workflows/%s/download" % new_workflow_id )
         self._assert_status_code_is( download_response, 200 )
         downloaded_workflow = download_response.json()
         self.assertEquals( downloaded_workflow[ "name" ], "test import from history" )
         assert len( downloaded_workflow[ "steps" ] ) == 3
 
+    @skip_without_tool( "collection_paired_test" )
+    def test_extract_workflows_with_dataset_collections( self ):
+        history_id = self.dataset_populator.new_history()
+        hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json()
+        hdca_id = hdca[ "id" ]
+        inputs = {
+            "f1": dict( src="hdca", id=hdca_id )
+        }
+        payload = self.dataset_populator.run_tool_payload(
+            tool_id="collection_paired_test",
+            inputs=inputs,
+            history_id=history_id,
+        )
+        tool_response = self._post( "tools", data=payload )
+        self._assert_status_code_is( tool_response, 200 )
+        job_id = tool_response.json()[ "jobs" ][ 0 ][ "id" ]
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        create_from_data = dict(
+            from_history_id=history_id,
+            dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
+            job_ids=dumps( [ job_id ] ),
+            workflow_name="test import from history",
+        )
+        create_workflow_response = self._post( "workflows", data=create_from_data )
+        self._assert_status_code_is( create_workflow_response, 200 )
+        create_workflow_response.json()[ "id" ]
+
+        new_workflow_id = create_workflow_response.json()[ "id" ]
+        download_response = self._get( "workflows/%s/download" % new_workflow_id )
+        self._assert_status_code_is( download_response, 200 )
+        downloaded_workflow = download_response.json()
+        assert len( downloaded_workflow[ "steps" ] ) == 2
+        collection_steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == "data_collection_input" ]
+        assert len( collection_steps ) == 1
+        collection_step = collection_steps[ 0 ]
+        collection_step_state = loads( collection_step[ "tool_state" ] )
+        self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+
+    @skip_without_tool( "random_lines1" )
     def test_run_replace_params_by_tool( self ):
         workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" )
         workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) )
         run_workflow_response = self._post( "workflows", data=workflow_request )
         self._assert_status_code_is( run_workflow_response, 200 )
-        self._wait_for_history( history_id, assert_ok=True )
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         # Would be 8 and 6 without modification
         self.__assert_lines_hid_line_count_is( history_id, 2, 5 )
         self.__assert_lines_hid_line_count_is( history_id, 3, 5 )
 
+    @skip_without_tool( "random_lines1" )
     def test_run_replace_params_by_steps( self ):
         workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" )
         workflow_summary_response = self._get( "workflows/%s" % workflow_request[ "workflow_id" ] )
@@ -120,7 +167,7 @@
         workflow_request[ "parameters" ] = params
         run_workflow_response = self._post( "workflows", data=workflow_request )
         self._assert_status_code_is( run_workflow_response, 200 )
-        self._wait_for_history( history_id, assert_ok=True )
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         # Would be 8 and 6 without modification
         self.__assert_lines_hid_line_count_is( history_id, 2, 8 )
         self.__assert_lines_hid_line_count_is( history_id, 3, 5 )
@@ -136,6 +183,7 @@
         pja = pjas[ 0 ]
         self._assert_has_keys( pja, "action_type", "output_name", "action_arguments" )
 
+    @skip_without_tool( "cat1" )
     def test_invocation_usage( self ):
         workflow = self.workflow_populator.load_workflow( name="test_usage" )
         workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -159,6 +207,7 @@
         for step in usage_details[ "steps" ].values():
             self._assert_has_keys( step, "workflow_step_id", "order_index" )
 
+    @skip_without_tool( "cat1" )
     def test_post_job_action( self ):
         """ Tests both import and execution of post job actions.
         """
@@ -166,7 +215,7 @@
         workflow_request, history_id = self._setup_workflow_run( workflow )
         run_workflow_response = self._post( "workflows", data=workflow_request )
         self._assert_status_code_is( run_workflow_response, 200 )
-        self._wait_for_history( history_id, assert_ok=True )
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         time.sleep(.1)  # Give another little bit of time for rename (needed?)
         contents = self._get( "histories/%s/contents" % history_id ).json()
         # loading workflow with add_pja=True causes workflow output to be
@@ -183,9 +232,9 @@
                 step_1 = key
             if label == "WorkflowInput2":
                 step_2 = key
-        history_id = self._new_history()
-        hda1 = self._new_dataset( history_id, content="1 2 3" )
-        hda2 = self._new_dataset( history_id, content="4 5 6" )
+        history_id = self.dataset_populator.new_history()
+        hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
+        hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" )
         workflow_request = dict(
             history="hist_id=%s" % history_id,
             workflow_id=uploaded_workflow_id,
@@ -201,9 +250,9 @@
         uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
         workflow_inputs = self._workflow_inputs( uploaded_workflow_id )
         key = workflow_inputs.keys()[ 0 ]
-        history_id = self._new_history()
+        history_id = self.dataset_populator.new_history()
         ten_lines = "\n".join( map( str, range( 10 ) ) )
-        hda1 = self._new_dataset( history_id, content=ten_lines )
+        hda1 = self.dataset_populator.new_dataset( history_id, content=ten_lines )
         workflow_request = dict(
             history="hist_id=%s" % history_id,
             workflow_id=uploaded_workflow_id,

diff -r ef7bd8c935bc2a01cf51dff8daa36e8ed7ac8ae6 -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f test/functional/api/test_dataset_collections.py
--- a/test/functional/api/test_dataset_collections.py
+++ /dev/null
@@ -1,206 +0,0 @@
-from base import api
-import json
-from .helpers import DatasetPopulator
-
-
-# TODO: Move into helpers with rest of populators
-class DatasetCollectionPopulator( object ):
-
-    def __init__( self, galaxy_interactor ):
-        self.galaxy_interactor = galaxy_interactor
-        self.dataset_populator = DatasetPopulator( galaxy_interactor )
-
-    def create_list_from_pairs( self, history_id, pairs ):
-        element_identifiers = []
-        for i, pair in enumerate( pairs ):
-            element_identifiers.append( dict(
-                name="test%d" % i,
-                src="hdca",
-                id=pair
-            ) )
-
-        payload = dict(
-            instance_type="history",
-            history_id=history_id,
-            element_identifiers=json.dumps(element_identifiers),
-            collection_type="list:paired",
-        )
-        return self.__create( payload )
-
-    def create_pair_in_history( self, history_id, **kwds ):
-        payload = self.create_pair_payload(
-            history_id,
-            instance_type="history",
-            **kwds
-        )
-        return self.__create( payload )
-
-    def create_list_in_history( self, history_id, **kwds ):
-        payload = self.create_list_payload(
-            history_id,
-            instance_type="history",
-            **kwds
-        )
-        return self.__create( payload )
-
-    def create_list_payload( self, history_id, **kwds ):
-        return self.__create_payload( history_id, identifiers_func=self.list_identifiers, collection_type="list", **kwds )
-
-    def create_pair_payload( self, history_id, **kwds ):
-        return self.__create_payload( history_id, identifiers_func=self.pair_identifiers, collection_type="paired", **kwds )
-
-    def __create_payload( self, history_id, identifiers_func, collection_type, **kwds ):
-        contents = None
-        if "contents" in kwds:
-            contents = kwds[ "contents" ]
-            del kwds[ "contents" ]
-
-        if "element_identifiers" not in kwds:
-            kwds[ "element_identifiers" ] = json.dumps( identifiers_func( history_id, contents=contents ) )
-
-        payload = dict(
-            history_id=history_id,
-            collection_type=collection_type,
-            **kwds
-        )
-        return payload
-
-    def pair_identifiers( self, history_id, contents=None ):
-        hda1, hda2 = self.__datasets( history_id, count=2, contents=contents )
-
-        element_identifiers = [
-            dict( name="left", src="hda", id=hda1[ "id" ] ),
-            dict( name="right", src="hda", id=hda2[ "id" ] ),
-        ]
-        return element_identifiers
-
-    def list_identifiers( self, history_id, contents=None ):
-        hda1, hda2, hda3 = self.__datasets( history_id, count=3, contents=contents )
-        element_identifiers = [
-            dict( name="data1", src="hda", id=hda1[ "id" ] ),
-            dict( name="data2", src="hda", id=hda2[ "id" ] ),
-            dict( name="data3", src="hda", id=hda3[ "id" ] ),
-        ]
-        return element_identifiers
-
-    def __create( self, payload ):
-        create_response = self.galaxy_interactor.post( "dataset_collections", data=payload )
-        return create_response
-
-    def __datasets( self, history_id, count, contents=None ):
-        datasets = []
-        for i in xrange( count ):
-            new_kwds = {}
-            if contents:
-                new_kwds[ "content" ] = contents[ i ]
-            datasets.append( self.dataset_populator.new_dataset( history_id, **new_kwds ) )
-        return datasets
-
-
-class DatasetCollectionApiTestCase( api.ApiTestCase ):
-
-    def setUp( self ):
-        super( DatasetCollectionApiTestCase, self ).setUp()
-        self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
-        self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
-        self.history_id = self.dataset_populator.new_history()
-
-    def test_create_pair_from_history( self ):
-        payload = self.dataset_collection_populator.create_pair_payload(
-            self.history_id,
-            instance_type="history",
-        )
-        create_response = self._post( "dataset_collections", payload )
-        dataset_collection = self._check_create_response( create_response )
-        returned_datasets = dataset_collection[ "elements" ]
-        assert len( returned_datasets ) == 2, dataset_collection
-
-    def test_create_list_from_history( self ):
-        element_identifiers = self.dataset_collection_populator.list_identifiers( self.history_id )
-
-        payload = dict(
-            instance_type="history",
-            history_id=self.history_id,
-            element_identifiers=json.dumps(element_identifiers),
-            collection_type="list",
-        )
-
-        create_response = self._post( "dataset_collections", payload )
-        dataset_collection = self._check_create_response( create_response )
-        returned_datasets = dataset_collection[ "elements" ]
-        assert len( returned_datasets ) == 3, dataset_collection
-
-    def test_create_list_of_existing_pairs( self ):
-        pair_payload = self.dataset_collection_populator.create_pair_payload(
-            self.history_id,
-            instance_type="history",
-        )
-        pair_create_response = self._post( "dataset_collections", pair_payload )
-        dataset_collection = self._check_create_response( pair_create_response )
-        hdca_id = dataset_collection[ "id" ]
-
-        element_identifiers = [
-            dict( name="test1", src="hdca", id=hdca_id )
-        ]
-
-        payload = dict(
-            instance_type="history",
-            history_id=self.history_id,
-            element_identifiers=json.dumps(element_identifiers),
-            collection_type="list",
-        )
-        create_response = self._post( "dataset_collections", payload )
-        dataset_collection = self._check_create_response( create_response )
-        returned_collections = dataset_collection[ "elements" ]
-        assert len( returned_collections ) == 1, dataset_collection
-
-    def test_create_list_of_new_pairs( self ):
-        pair_identifiers = self.dataset_collection_populator.pair_identifiers( self.history_id )
-        element_identifiers = [ dict(
-            src="new_collection",
-            name="test_pair",
-            collection_type="paired",
-            element_identifiers=pair_identifiers,
-        ) ]
-        payload = dict(
-            collection_type="list:paired",
-            instance_type="history",
-            history_id=self.history_id,
-            name="nested_collecion",
-            element_identifiers=json.dumps( element_identifiers ),
-        )
-        create_response = self._post( "dataset_collections", payload )
-        dataset_collection = self._check_create_response( create_response )
-        assert dataset_collection[ "collection_type" ] == "list:paired"
-        returned_collections = dataset_collection[ "elements" ]
-        assert len( returned_collections ) == 1, dataset_collection
-        pair_1_element = returned_collections[ 0 ]
-        self._assert_has_keys( pair_1_element, "element_index" )
-        pair_1_object = pair_1_element[ "object" ]
-        self._assert_has_keys( pair_1_object, "collection_type", "elements" )
-        self.assertEquals( pair_1_object[ "collection_type" ], "paired" )
-        pair_elements = pair_1_object[ "elements" ]
-        assert len( pair_elements ) == 2
-        pair_1_element_1 = pair_elements[ 0 ]
-        assert pair_1_element_1[ "element_index" ] == 0
-
-    def test_hda_security( self ):
-        element_identifiers = self.dataset_collection_populator.pair_identifiers( self.history_id )
-
-        with self._different_user( ):
-            history_id = self.dataset_populator.new_history()
-            payload = dict(
-                instance_type="history",
-                history_id=history_id,
-                element_identifiers=json.dumps(element_identifiers),
-                collection_type="paired",
-            )
-
-            create_response = self._post( "dataset_collections", payload )
-            self._assert_status_code_is( create_response, 403 )
-
-    def _check_create_response( self, create_response ):
-        self._assert_status_code_is( create_response, 200 )
-        dataset_collection = create_response.json()
-        self._assert_has_keys( dataset_collection, "elements", "url", "name", "collection_type" )
-        return dataset_collection


https://bitbucket.org/galaxy/galaxy-central/commits/f58a4a9185e1/
Changeset:   f58a4a9185e1
User:        nsoranzo
Date:        2014-05-07 11:39:06
Summary:     Workflow API: Add documentation for dataset_collection_ids param.
Affected #:  1 file

diff -r 45fd6f57a7a66298e4c9b5dd468f73c71225209f -r f58a4a9185e133a987d032e4563c043477790a71 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -143,13 +143,16 @@
         :param  from_history_id:             Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   from_history_id:             str
 
-        :param  job_ids:                     If from_history_id is set - optional list of jobs to include when extracting workflow from history.
+        :param  job_ids:                     If from_history_id is set - optional list of jobs to include when extracting a workflow from history
         :type   job_ids:                     str
 
-        :param  dataset_ids:                 If from_history_id is set - optional list of HDA ids corresponding to workflow inputs when extracting workflow from history.
+        :param  dataset_ids:                 If from_history_id is set - optional list of HDA ids corresponding to workflow inputs when extracting a workflow from history
         :type   dataset_ids:                 str
 
-        :param  workflow_name:               If from_history_id is set - name of the workflow to create
+        :param  dataset_collection_ids:      If from_history_id is set - optional list of HDCA ids corresponding to workflow inputs when extracting a workflow from history
+        :type   dataset_collection_ids:      str
+
+        :param  workflow_name:               If from_history_id is set - name of the workflow to create when extracting a workflow from history
         :type   workflow_name:               str
         """
 


https://bitbucket.org/galaxy/galaxy-central/commits/83531e44b244/
Changeset:   83531e44b244
User:        jmchilton
Date:        2014-05-07 18:43:03
Summary:     Merge pull request #383.
Affected #:  1 file

diff -r 9e502242af28473660ee70ee0f98345f3604e137 -r 83531e44b2445dad9a4cf2c262e210c12498d9bd lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1,9 +1,9 @@
-from __future__ import absolute_import
-
 """
 API operations for Workflows
 """
 
+from __future__ import absolute_import
+
 import logging
 from sqlalchemy import desc, or_
 from galaxy import exceptions
@@ -12,7 +12,6 @@
 from galaxy.web import _future_expose_api as expose_api
 from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
 from galaxy.web.base.controller import UsesHistoryMixin
-from galaxy.workflow.modules import module_factory
 from galaxy.workflow.run import invoke
 from galaxy.workflow.run import WorkflowRunConfig
 from galaxy.workflow.extract import extract_workflow
@@ -120,79 +119,85 @@
         workflow will be created for this user. Otherwise, workflow_id must be
         specified and this API method will cause a workflow to execute.
 
-        :param  installed_repository_file    The path of a workflow to import. Either workflow_id or installed_repository_file must be specified
+        :param  installed_repository_file    The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   installed_repository_file    str
 
-        :param  workflow_id:                 an existing workflow id. Either workflow_id or installed_repository_file must be specified
+        :param  workflow_id:                 An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   workflow_id:                 str
 
-        :param  parameters:                  See _update_step_parameters()
+        :param  parameters:                  If workflow_id is set - see _update_step_parameters()
         :type   parameters:                  dict
 
-        :param  ds_map:                      A dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
+        :param  ds_map:                      If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
         :type   ds_map:                      dict
 
-        :param  no_add_to_history:           if present in the payload with any value, the input datasets will not be added to the selected history
+        :param  no_add_to_history:           If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
         :type   no_add_to_history:           str
 
-        :param  history:                     Either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history
+        :param  history:                     If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
         :type   history:                     str
 
-        :param  replacement_params:          A dictionary used when renaming datasets
+        :param  replacement_params:          If workflow_id is set - an optional dictionary used when renaming datasets
         :type   replacement_params:          dict
 
-        :param  from_history_id:             Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file.
+        :param  from_history_id:             Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
         :type   from_history_id:             str
 
-        :param  job_ids:                     If from_history_id is set - this should be a list of jobs to include when extracting workflow from history.
+        :param  job_ids:                     If from_history_id is set - optional list of jobs to include when extracting a workflow from history
         :type   job_ids:                     str
 
-        :param  dataset_ids:                 If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history.
+        :param  dataset_ids:                 If from_history_id is set - optional list of HDA ids corresponding to workflow inputs when extracting a workflow from history
         :type   dataset_ids:                 str
+
+        :param  dataset_collection_ids:      If from_history_id is set - optional list of HDCA ids corresponding to workflow inputs when extracting a workflow from history
+        :type   dataset_collection_ids:      str
+
+        :param  workflow_name:               If from_history_id is set - name of the workflow to create when extracting a workflow from history
+        :type   workflow_name:               str
         """
 
-        # Pull parameters out of payload.
-        workflow_id = payload.get('workflow_id', None)
-        param_map = payload.get('parameters', {})
-        ds_map = payload.get('ds_map', {})
+        if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1:
+            trans.response.status = 403
+            return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified"
+
+        if 'installed_repository_file' in payload:
+            workflow_controller = trans.webapp.controllers[ 'workflow' ]
+            result = workflow_controller.import_workflow( trans=trans,
+                                                          cntrller='api',
+                                                          **payload)
+            return result
+
+        if 'from_history_id' in payload:
+            from_history_id = payload.get( 'from_history_id' )
+            history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
+            job_ids = map( trans.security.decode_id, payload.get( 'job_ids', [] ) )
+            dataset_ids = payload.get( 'dataset_ids', [] )
+            dataset_collection_ids = payload.get( 'dataset_collection_ids', [] )
+            workflow_name = payload[ 'workflow_name' ]
+            stored_workflow = extract_workflow(
+                trans=trans,
+                user=trans.get_user(),
+                history=history,
+                job_ids=job_ids,
+                dataset_ids=dataset_ids,
+                dataset_collection_ids=dataset_collection_ids,
+                workflow_name=workflow_name,
+            )
+            item = stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
+            item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] )
+            return item
+
+        workflow_id = payload.get( 'workflow_id', None )
+        if not workflow_id:
+            trans.response.status = 403
+            return "Either workflow_id, installed_repository_file or from_history_id must be specified"
+
+        # Pull other parameters out of payload.
+        param_map = payload.get( 'parameters', {} )
+        ds_map = payload.get( 'ds_map', {} )
         add_to_history = 'no_add_to_history' not in payload
         history_param = payload.get('history', '')
 
-        # Get/create workflow.
-        if not workflow_id:
-            # create new
-            if 'installed_repository_file' in payload:
-                workflow_controller = trans.webapp.controllers[ 'workflow' ]
-                result = workflow_controller.import_workflow( trans=trans,
-                                                              cntrller='api',
-                                                              **payload)
-                return result
-            if 'from_history_id' in payload:
-                from_history_id = payload.get( 'from_history_id' )
-                history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
-                job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) )
-                dataset_ids = payload.get( "dataset_ids", [] )
-                dataset_collection_ids = payload.get( "dataset_collection_ids", [] )
-                workflow_name = payload[ "workflow_name" ]
-                stored_workflow = extract_workflow(
-                    trans=trans,
-                    user=trans.get_user(),
-                    history=history,
-                    job_ids=job_ids,
-                    dataset_ids=dataset_ids,
-                    dataset_collection_ids=dataset_collection_ids,
-                    workflow_name=workflow_name,
-                )
-                item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } )
-                item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] )
-                return item
-
-            trans.response.status = 403
-            return "Either workflow_id or installed_repository_file must be specified"
-        if 'installed_repository_file' in payload:
-            trans.response.status = 403
-            return "installed_repository_file may not be specified with workflow_id"
-
         # Get workflow + accessibility check.
         stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(
                         trans.security.decode_id(workflow_id))


https://bitbucket.org/galaxy/galaxy-central/commits/a014c2d841a8/
Changeset:   a014c2d841a8
User:        jmchilton
Date:        2014-05-07 18:49:59
Summary:     Re-update documentation for fixes in a44bea8.
Affected #:  1 file

diff -r 83531e44b2445dad9a4cf2c262e210c12498d9bd -r a014c2d841a8490f017086c687997a191f3a602f lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -146,10 +146,10 @@
         :param  job_ids:                     If from_history_id is set - optional list of jobs to include when extracting a workflow from history
         :type   job_ids:                     str
 
-        :param  dataset_ids:                 If from_history_id is set - optional list of HDA ids corresponding to workflow inputs when extracting a workflow from history
+        :param  dataset_ids:                 If from_history_id is set - optional list of HDA `hid`s corresponding to workflow inputs when extracting a workflow from history
         :type   dataset_ids:                 str
 
-        :param  dataset_collection_ids:      If from_history_id is set - optional list of HDCA ids corresponding to workflow inputs when extracting a workflow from history
+        :param  dataset_collection_ids:      If from_history_id is set - optional list of HDCA `hid`s corresponding to workflow inputs when extracting a workflow from history
         :type   dataset_collection_ids:      str
 
         :param  workflow_name:               If from_history_id is set - name of the workflow to create when extracting a workflow from history

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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