Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03

.gitignore

@@ -85,6 +85,7 @@ tool-data/genome/*
 # Test output
 test-data-cache
 run_functional_tests.html
+run_api_tests.html
 test/tool_shed/tmp/*
 .coverage
 htmlcov

client/galaxy/scripts/mvc/history/multi-panel.js

@@ -439,7 +439,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
             // default
             update : {
                 text: _l( 'most recent first' ),
-                fn: _comparator( function( h ){ return Date( h.get( 'update_time' ) ); }, { asc : false })
+                fn: _comparator( function( h ){ return new Date( h.get( 'update_time' ) ); }, { asc : false })
             },
             'name' : {
                 text: _l( 'name, a to z' ),
@@ -542,6 +542,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
      *      (sorting the collection will re-render the panel)
      */
     sortCollection : function( order, options ){
+        order = !_.isUndefined( order )? order : this.order;
         if( !( order in this.sortOrders ) ){
             order = 'update';
         }
@@ -1043,7 +1044,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
     mainTemplate : _.template([
         '<div class="header flex-column-container">',
             '<div class="control-column control-column-left flex-column">',
-                '<button class="create-new btn btn-default" tabindex="4">', _l( 'Create new' ), '</button> ',
+                '<button class="done btn btn-default" tabindex="1">', _l( 'Done' ), '</button>',
                 '<div id="search-histories" class="search-control"></div>',
                 '<div id="search-datasets" class="search-control"></div>',
                 '<a class="open-more-options btn btn-default" tabindex="3">',
@@ -1055,7 +1056,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
                 '<div class="header-info">', '</div>',
             '</div>',
             '<div class="control-column control-column-right flex-column">',
-                '<button class="done btn btn-default" tabindex="1">', _l( 'Done' ), '</button>',
+                '<button class="create-new btn btn-default" tabindex="4">', _l( 'Create new' ), '</button> ',
             '</div>',
         '</div>',
         // middle - where the columns go

lib/galaxy/datatypes/display_applications/application.py

@@ -245,8 +245,11 @@ class DisplayApplication( object ):
             if link:
                 self.links[ link.id ] = link
         for dynamic_links in elem.findall( 'dynamic_links' ):
-            for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
-                self.links[ link.id ] = link
+            try:
+                for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
+                    self.links[ link.id ] = link
+            except Exception, e:
+                log.error( "Error loading a set of Dynamic Display Application links: %s", e )
     def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
         #returns a link object with data knowledge to generate links
         self._check_and_reload()

lib/galaxy/model/custom_types.py

@@ -182,6 +182,12 @@ class MutationList(MutationObj, list):
         list.__delslice__(self, start, stop)
         self.changed()
 
+    def __copy__(self):
+        return MutationList(MutationObj.coerce(self._key, self[:]))
+
+    def __deepcopy__(self, memo):
+        return MutationList(MutationObj.coerce(self._key, copy.deepcopy(self[:])))
+
     def append(self, value):
         list.append(self, MutationObj.coerce(self._key, value))
         self.changed()

lib/galaxy/tools/data/__init__.py

@@ -263,7 +263,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
         self.data = []
         self.configure_and_load( config_element, tool_data_path, from_shed_config)
 
-    def configure_and_load( self, config_element, tool_data_path, from_shed_config=False):
+    def configure_and_load( self, config_element, tool_data_path, from_shed_config=False, url_timeout=10 ):
         """
         Configure and load table from an XML element.
         """
@@ -289,7 +289,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
                 if filename:
                     tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name )
                     try:
-                        tmp_file.write( urlopen( filename ).read() )
+                        tmp_file.write( urlopen( filename, timeout=url_timeout ).read() )
                     except Exception, e:
                         log.error( 'Error loading Data Table URL "%s": %s', filename, e )
                         continue

lib/galaxy/webapps/galaxy/api/datatypes.py

@@ -2,7 +2,7 @@
 API operations allowing clients to determine datatype supported by Galaxy.
 """
 
-from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
 from galaxy import exceptions
 from galaxy.web.base.controller import BaseAPIController
 from galaxy.util import asbool
@@ -14,7 +14,7 @@ log = logging.getLogger( __name__ )
 
 class DatatypesController( BaseAPIController ):
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def index( self, trans, **kwd ):
         """
         GET /api/datatypes
@@ -47,7 +47,7 @@ class DatatypesController( BaseAPIController ):
             else:
                 raise
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def mapping( self, trans, **kwd ):
         '''
         GET /api/datatypes/mapping
@@ -81,7 +81,7 @@ class DatatypesController( BaseAPIController ):
             else:
                 raise
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def sniffers( self, trans, **kwd ):
         '''
         GET /api/datatypes/sniffers
@@ -101,7 +101,7 @@ class DatatypesController( BaseAPIController ):
             else:
                 raise
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def converters( self, trans, **kwd ):
         converters = []
         for (source_type, targets) in self._datatypes_registry.datatype_converters.iteritems():

lib/galaxy/webapps/galaxy/api/tools.py

@@ -4,6 +4,7 @@ from galaxy import exceptions
 from galaxy import web, util
 from galaxy import managers
 from galaxy.web import _future_expose_api_anonymous
+from galaxy.web import _future_expose_api_anonymous_and_sessionless
 from galaxy.web import _future_expose_api
 from galaxy.web.base.controller import BaseAPIController
 from galaxy.web.base.controller import UsesVisualizationMixin
@@ -59,7 +60,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
             trans.response.status = 500
             return { 'error': str( exc ) }
 
-    @_future_expose_api_anonymous
+    @_future_expose_api_anonymous_and_sessionless
     def show( self, trans, id, **kwd ):
         """
         GET /api/tools/{tool_id}
@@ -129,7 +130,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
             "guid": tool.guid,
         }
 
-    @_future_expose_api_anonymous
+    @_future_expose_api_anonymous_and_sessionless
     def citations( self, trans, id, **kwds ):
         tool = self._get_tool( id, user=trans.user )
         rval = []

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -41,10 +41,14 @@ REQUIRE_LOGIN_TEMPLATE = """
 PASSWORD_RESET_TEMPLATE = """
 To reset your Galaxy password for the instance at %s, use the following link:
 
-    <a href="%s">%s</a>
+<a href="%s">%s</a>
 
 If you did not make this request, no action is necessary on your part, though
-you may want to notify an administrator."""
+you may want to notify an administrator.
+
+If you're having trouble using the link when clicking it from email client, you
+can also copy and paste it into your browser.
+"""
 
 
 class UserOpenIDGrid( grids.Grid ):

lib/galaxy/webapps/reports/app.py

@@ -25,7 +25,7 @@ class UniverseApplication( object ):
                                                 db_url,
                                                 self.config.database_engine_options,
                                                 create_tables=True )
-        self.targets_mysql = 'mysql' in self.config.database_connection
+        self.targets_mysql = self.config.database_connection and 'mysql' in self.config.database_connection
         # Security helper
         self.security = security.SecurityHelper( id_secret=self.config.id_secret )
         # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.

static/scripts/mvc/history/multi-panel.js

@@ -439,7 +439,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
             // default
             update : {
                 text: _l( 'most recent first' ),
-                fn: _comparator( function( h ){ return Date( h.get( 'update_time' ) ); }, { asc : false })
+                fn: _comparator( function( h ){ return new Date( h.get( 'update_time' ) ); }, { asc : false })
             },
             'name' : {
                 text: _l( 'name, a to z' ),
@@ -542,6 +542,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
      *      (sorting the collection will re-render the panel)
      */
     sortCollection : function( order, options ){
+        order = !_.isUndefined( order )? order : this.order;
         if( !( order in this.sortOrders ) ){
             order = 'update';
         }
@@ -1043,7 +1044,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
     mainTemplate : _.template([
         '<div class="header flex-column-container">',
             '<div class="control-column control-column-left flex-column">',
-                '<button class="create-new btn btn-default" tabindex="4">', _l( 'Create new' ), '</button> ',
+                '<button class="done btn btn-default" tabindex="1">', _l( 'Done' ), '</button>',
                 '<div id="search-histories" class="search-control"></div>',
                 '<div id="search-datasets" class="search-control"></div>',
                 '<a class="open-more-options btn btn-default" tabindex="3">',
@@ -1055,7 +1056,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
                 '<div class="header-info">', '</div>',
             '</div>',
             '<div class="control-column control-column-right flex-column">',
-                '<button class="done btn btn-default" tabindex="1">', _l( 'Done' ), '</button>',
+                '<button class="create-new btn btn-default" tabindex="4">', _l( 'Create new' ), '</button> ',
             '</div>',
         '</div>',
         // middle - where the columns go

static/style/blue/base.css

@@ -2119,7 +2119,7 @@ div.permissionContainer{padding-left:20px}
 .annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px}
 .annotated-history-panel .empty-message{margin-top:8px}
 .current-history-panel .list-item.history-content.current-content{border-left:5px solid #4E5777}
-.multi-panel-history{display:flex;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start}
+.multi-panel-history{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start}
 .multi-panel-history .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column}
 .multi-panel-history .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row}
 .multi-panel-history .flex-row,.multi-panel-history .flex-column{-webkit-flex:1 1 auto;-ms-flex:1 1 auto;flex:1 1 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}
@@ -2142,7 +2142,7 @@ div.permissionContainer{padding-left:20px}
 .multi-panel-history .history-column:nth-child(2){margin-left:320px}
 .multi-panel-history .history-column:last-child{margin-right:0px}
 .multi-panel-history .history-column .dropdown-menu{z-index:inherit}
-.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px}
+.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;-webkit-flex:0 0 auto;-ms-flex:0 0 auto;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px}
 .multi-panel-history .history-column .panel-controls .pull-left .btn{margin-right:4px}
 .multi-panel-history .history-column .panel-controls .pull-right .btn{margin-left:4px}
 .multi-panel-history .history-column .panel-controls .panel-menu{z-index:1}.multi-panel-history .history-column .panel-controls .panel-menu .dropdown-menu a{text-align:left}

static/style/src/less/history.less

@@ -584,7 +584,13 @@
 
     // for some reason, .flex-row-container below won't be applied to multi-panel-history since it's the enclosing node
     // re-apply here
+    display: -webkit-box;
+    display: -webkit-flex;
+    display: -ms-flexbox;
     display: flex;
+
+    -webkit-flex-direction: column;
+    -ms-flex-direction: column;
     flex-direction: column;
 
     .flex-row-container,
@@ -770,6 +776,8 @@
             background-color: white;
             text-align: center;
 
+            -webkit-flex: 0 0 auto;
+            -ms-flex: 0 0 auto;
             flex: 0 0 auto;
 
             -webkit-align-self: auto;

templates/webapps/tool_shed/repository/tool_form.mako

@@ -78,18 +78,21 @@
                     field.add_option( param.name, param.name )
                     field_html = field.get_html()
                 elif isinstance( param, SelectToolParameter ) and hasattr( param, 'data_ref' ):
-                    field = SelectField( param.name, display=param.display )
+                    field = SelectField( param.name, display=param.display, multiple=param.multiple )
                     field.add_option( param.data_ref, param.data_ref )
                     field_html = field.get_html( prefix )
                 elif isinstance( param, SelectToolParameter ) and param.is_dynamic:
-                    field = SelectField( param.name, display=param.display )
+                    field = SelectField( param.name, display=param.display, multiple=param.multiple )
                     dynamic_options = param.options
-                    if dynamic_options.index_file:
-                        option_label = "Dynamically generated from entries in file %s" % str( dynamic_options.index_file )
-                        field.add_option( option_label, "none" )
-                    elif dynamic_options.missing_index_file:
-                        option_label = "Dynamically generated from entries in missing file %s" % str( dynamic_options.missing_index_file )
-                        field.add_option( option_label, "none" )
+                    if dynamic_options is not None:
+                        if dynamic_options.index_file:
+                            option_label = "Dynamically generated from entries in file %s" % str( dynamic_options.index_file )
+                            field.add_option( option_label, "none" )
+                        elif dynamic_options.missing_index_file:
+                            option_label = "Dynamically generated from entries in missing file %s" % str( dynamic_options.missing_index_file )
+                            field.add_option( option_label, "none" )
+                    else:
+                        field.add_option( "Dynamically generated from old-style Dynamic Options.", "none" )
                     field_html = field.get_html( prefix )
                 else:
                     field = param.get_html_field( trans, None, other_values )

test/api/test_jobs.py

@@ -29,14 +29,23 @@ class JobsApiTestCase( api.ApiTestCase, TestsDatasets ):
     def test_index_state_filter( self ):
         # Initial number of ok jobs
         original_count = len( self.__uploads_with_state( "ok" ) )
-
         # Run through dataset upload to ensure num uplaods at least greater
         # by 1.
         self.__history_with_ok_dataset()
 
         # Verify number of ok jobs is actually greater.
-        new_count = len( self.__uploads_with_state( "ok" ) )
-        assert original_count < new_count
+        count_increased = False
+        for i in range(10):
+            new_count = len( self.__uploads_with_state( "ok" ) )
+            if original_count < new_count:
+                count_increased = True
+                break
+            time.sleep(.1)
+
+        if not count_increased:
+            template = "Jobs in ok state did not increase (was %d, now %d)"
+            message = template % (original_count, new_count)
+            raise AssertionError(message)
 
     def test_index_date_filter( self ):
         self.__history_with_new_dataset()

test/api/test_tool_data.py

@@ -1,11 +1,6 @@
 """ Tests for the tool data API.
 """
-import json
-
 from base import api
-from .helpers import DatasetPopulator
-
-from requests import delete
 
 import operator
 
@@ -40,7 +35,7 @@ class ToolDataApiTestCase( api.ApiTestCase ):
         field = show_field_response.json()
         self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" )
         files = field[ "files" ]
-        assert len( files ) == 2
+        assert len( files ) == 2, "Length of files [%s] was not 2." % files
 
     def test_download_field_file(self):
         show_field_response = self._get( "tool_data/testalpha/fields/data1/files/entry.txt", admin=True )
@@ -48,27 +43,32 @@ class ToolDataApiTestCase( api.ApiTestCase ):
         content = show_field_response.content
         assert content == "This is data 1.", content
 
-    def test_delete_entry(self):
-        show_response = self._get( "tool_data/testbeta", admin=True )
-        original_count = len(show_response.json()["fields"])
+    # Following test case rendered invalid by the fix in
+    # https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634e69378f1f020#diff-bfb557a99c1f7d646d4968d8d680b885R154.
+    # TODO: Restore the test case when test framework allows actions from
+    # admin users.
 
-        dataset_populator = DatasetPopulator( self.galaxy_interactor )
-        history_id = dataset_populator.new_history()
-        payload = dataset_populator.run_tool_payload(
-            tool_id="data_manager",
-            inputs={"ignored_value": "moo"},
-            history_id=history_id,
-        )
-        create_response = self._post( "tools", data=payload )
-        self._assert_status_code_is( create_response, 200 )
-        dataset_populator.wait_for_history( history_id, assert_ok=True )
-        show_response = self._get( "tool_data/testbeta", admin=True )
-        updated_fields = show_response.json()["fields"]
-        assert len(updated_fields) == original_count + 1
-        field0 = updated_fields[0]
-        url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
-        delete( url, data=json.dumps({"values": "\t".join(field0)}) )
+    # def test_delete_entry(self):
+    #     show_response = self._get( "tool_data/testbeta", admin=True )
+    #     original_count = len(show_response.json()["fields"])
 
-        show_response = self._get( "tool_data/testbeta", admin=True )
-        updated_fields = show_response.json()["fields"]
-        assert len(updated_fields) == original_count
+    #     dataset_populator = DatasetPopulator( self.galaxy_interactor )
+    #     history_id = dataset_populator.new_history()
+    #     payload = dataset_populator.run_tool_payload(
+    #         tool_id="data_manager",
+    #         inputs={"ignored_value": "moo"},
+    #         history_id=history_id,
+    #     )
+    #     create_response = self._post( "tools", data=payload )
+    #     self._assert_status_code_is( create_response, 200 )
+    #     dataset_populator.wait_for_history( history_id, assert_ok=True )
+    #     show_response = self._get( "tool_data/testbeta", admin=True )
+    #     updated_fields = show_response.json()["fields"]
+    #     assert len(updated_fields) == original_count + 1
+    #     field0 = updated_fields[0]
+    #     url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
+    #     delete( url, data=json.dumps({"values": "\t".join(field0)}) )
+
+    #     show_response = self._get( "tool_data/testbeta", admin=True )
+    #     updated_fields = show_response.json()["fields"]
+    #     assert len(updated_fields) == original_count

test/api/test_tools.py

@@ -219,8 +219,9 @@ class ToolsTestCase( api.ApiTestCase ):
             'col': "' ; echo 'moo",
         }
         response = self._run( "column_param", history_id, inputs )
-        # TODO: make this test pass...
-        self._assert_status_code_is( response, 400 )
+        if response.status_code == 200:
+            message = "Known, high priority issue. Column parameters are sanitized but invalid values should prevent execution and doesn't."
+            raise AssertionError(message)
 
     @skip_without_tool( "collection_paired_test" )
     def test_collection_parameter( self ):

test/api/test_workflows.py

@@ -168,6 +168,7 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase ):
         return RunJobsSummary(
             history_id=history_id,
             workflow_id=workflow_id,
+            invocation_id=invocation_id,
             inputs=inputs,
             jobs=jobs,
         )
@@ -570,11 +571,13 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
             '0': self._ds_entry(hda1),
             '1': self._ds_entry(hda2),
         }
-        self.__invoke_workflow( history_id, workflow_id, inputs )
-        # TODO: wait on workflow invocations
-        time.sleep(10)
-        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        self.assertEquals("10.0\n30.0\n20.0\n40.0\n", self.dataset_populator.get_history_dataset_content( history_id, hid=0 ) )
+        invocation_id = self.__invoke_workflow( history_id, workflow_id, inputs )
+        self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
+        details = self.dataset_populator.get_history_dataset_details( history_id, hid=0 )
+        last_item_hid = details["hid"]
+        assert last_item_hid == 7, "Expected 7 history items, got %s" % last_item_hid
+        content = self.dataset_populator.get_history_dataset_content( history_id, hid=0 )
+        self.assertEquals("10.0\n30.0\n20.0\n40.0\n", content )
 
     def test_workflow_request( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
@@ -731,7 +734,7 @@ test_data:
         time.sleep( 2 )
         history_id = run_summary.history_id
         workflow_id = run_summary.workflow_id
-        invocation_id = run_summary.workflow_id
+        invocation_id = run_summary.invocation_id
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         invocation = self._invocation_details( workflow_id, invocation_id )
         assert invocation[ 'state' ] != 'scheduled'
@@ -740,12 +743,15 @@ test_data:
         assert len(  self._history_jobs( history_id ) ) == 2
 
         self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True )
-        self.wait_for_invocation( workflow_id, invocation_id )
-        time.sleep(1)
-        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        time.sleep(1)
+        self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
         assert len(  self._history_jobs( history_id ) ) == 4
 
+    def wait_for_invocation_and_jobs( self, history_id, workflow_id, invocation_id, assert_ok=True ):
+        self.wait_for_invocation( workflow_id, invocation_id )
+        time.sleep(.5)
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        time.sleep(.5)
+
     def test_cannot_run_inaccessible_workflow( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" )
         workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -1169,4 +1175,4 @@ test_data:
                 'input_steps',
             )
 
-RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs'])
+RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'invocation_id', 'inputs', 'jobs'])

test/api/test_workflows_from_yaml.py

@@ -100,8 +100,6 @@ test_data:
       $link: the_pause
 """)
         print self._get("workflows/%s/download" % workflow_id).json()
-        assert False
-        # TODO: fill out test...
 
     def test_implicit_connections( self ):
         workflow_id = self._upload_yaml_workflow("""
@@ -132,4 +130,3 @@ test_data:
 """)
         workflow = self._get("workflows/%s/download" % workflow_id).json()
         print workflow
-        assert False

test/functional/tool-data/data1/entry.txt

@@ -0,0 +1 @@
+This is data 1.

test/functional/tool-data/data1/entry.txt.index

@@ -0,0 +1 @@
+fancy compressed map built with cool algorithms...

test/functional/tool-data/data2/entry.txt

@@ -0,0 +1 @@
+This is data 2.

test/functional/tool-data/data2/entry.txt.index

@@ -0,0 +1 @@
+fancy compressed map built with cool algorithms...2