Fixes for transferring sample datasets and viewing . managing transferred sample datasets.

lib/galaxy/web/controllers/requests_admin.py

@@ -493,6 +493,7 @@ class RequestsAdmin( BaseUIController, UsesFormDefinitions ):
         return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                           action='select_datasets_to_transfer',
                                                           request_id=trans.security.encode_id( request.id ),
+                                                          external_service_id=trans.security.encode_id( external_service.id ),
                                                           status=status,
                                                           message=message ) )
     def __create_sample_datasets( self, trans, sample, selected_datasets_to_transfer, external_service ):

lib/galaxy/web/controllers/requests_common.py

@@ -1011,6 +1011,8 @@ class RequestsCommon( BaseUIController, UsesFormDefinitions ):
             sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
         except:
             return invalid_id_redirect( trans, cntrller, sample_id, 'sample' )
+        external_service_id = params.get( 'external_service_id', None )
+        external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
         # See if a library and folder have been set for this sample.
         if is_admin and not sample.library or not sample.folder:
             status = 'error'
@@ -1043,6 +1045,7 @@ class RequestsCommon( BaseUIController, UsesFormDefinitions ):
         return trans.fill_template( '/requests/common/view_sample_datasets.mako', 
                                     cntrller=cntrller,
                                     title=title,
+                                    external_service=external_service,
                                     sample=sample,
                                     sample_datasets=sample_datasets,
                                     transfer_status=transfer_status,

templates/requests/common/common.mako

@@ -298,9 +298,14 @@
                 ## This link will direct the admin to a page allowing them to manage datasets.
                 <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
             %elif sample.datasets:
+                <%
+                    # Get an external_service from one of the sample datasets.  This assumes all sample datasets are associated with
+                    # the same external service - hopefully this is a good assumption.
+                    external_service = sample.datasets[0].external_service
+                %>
                 ## Since this is a regular user, only display a link if there is at least 1
                 ## selected dataset for the sample.
-                <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
+                <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
             %else:
                 ## Since this is a regular user, do not display a link if there are no datasets.
                 <a id="sampleDatasets-${sample.id}">${len( sample.datasets )}</a>
@@ -424,8 +429,13 @@
                                     %endif
                                     %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ) and sample.library and sample.folder:
                                         <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li>
-                                    %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ):
-                                        <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li>
+                                    %elif sample.datasets and len( sample.datasets ) == len( transferred_dataset_files ):
+                                        <%
+                                            # Get an external_service from one of the sample datasets.  This assumes all sample datasets are associated with
+                                            # the same external service - hopefully this is a good assumption.
+                                            external_service = sample.datasets[0].external_service
+                                        %>
+                                        <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li>
                                     %endif
                                 </div>
                             %else:
@@ -483,6 +493,11 @@
                                     ## This link will direct the admin to a page allowing them to manage datasets.
                                     <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
                                 %elif sample.library and sample.datasets:
+                                    <%
+                                        # Get an external_service from one of the sample datasets.  This assumes all sample datasets are associated with
+                                        # the same external service - hopefully this is a good assumption.
+                                        external_service = sample.datasets[0].external_service
+                                    %>
                                     ## Since this is a regular user, only display a link if there is at least 1
                                     ## selected dataset for the sample.
                                     <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>

templates/requests/common/find_samples.mako

@@ -78,7 +78,12 @@
                             %else:
                                 State: ${sample.state.name}<br/>
                             %endif
-                            Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/>
+                            <%
+                                # Get an external_service from one of the sample datasets.  This assumes all sample datasets are associated with
+                                # the same external service - hopefully this is a good assumption.
+                                external_service = sample.datasets[0].external_service
+                            %>
+                            Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/>
                             %if is_admin:
                                <i>User: ${sample.request.user.email}</i>
                             %endif

templates/requests/common/view_sample_datasets.mako

@@ -25,7 +25,7 @@
     <li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li>
     <div popupmenu="sample-${sample.id}-popup">
         %if can_select_datasets:
-            <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( sample.request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select more datasets</a></li>
+            <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), request_id=trans.security.encode_id( sample.request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select more datasets</a></li>
         %endif
         <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">View target Data Library</a></li>
         <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li>

test/base/twilltestcase.py

@@ -13,6 +13,7 @@ from markupsafe import escape
 from elementtree import ElementTree
 from galaxy.web import security
 from galaxy.web.framework.helpers import iff
+from galaxy.util.json import from_json_string
 from base.asserts import verify_assertions
 
 buffer = StringIO.StringIO()
@@ -34,7 +35,14 @@ class TwillTestCase( unittest.TestCase ):
         self.host = os.environ.get( 'GALAXY_TEST_HOST' )
         self.port = os.environ.get( 'GALAXY_TEST_PORT' )
         self.url = "http://%s:%s" % ( self.host, self.port )
-        self.file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR' )
+        self.file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', None )
+        self.migrated_tools_file = os.environ.get( 'GALAXY_MIGRATED_TOOLS_FILE', None )
+        if self.migrated_tools_file:
+            f = open( self.migrated_tools_file, 'r' )
+            self.migrated_tools_dict = from_json_string( f.readlines() )
+            f.close()
+        else:
+            self.migrated_tools_dict = {}
         self.keepOutdir = os.environ.get( 'GALAXY_TEST_SAVE', '' )
         if self.keepOutdir > '':
            try:
@@ -1792,9 +1800,10 @@ class TwillTestCase( unittest.TestCase ):
         tc.submit( "save_samples_button" )
         for check_str in strings_displayed_after_submit:
             self.check_page_for_string( check_str )
-    def add_datasets_to_sample( self, request_id, sample_id, sample_datasets, strings_displayed=[], strings_displayed_after_submit=[] ):
+    def add_datasets_to_sample( self, request_id, sample_id, external_service_id, sample_datasets, strings_displayed=[], strings_displayed_after_submit=[] ):
         # visit the dataset selection page
-        url = "%s/requests_admin/select_datasets_to_transfer?cntrller=requests_admin&sample_id=%s&request_id=%s" % ( self.url, sample_id, request_id )
+        url = "%s/requests_admin/select_datasets_to_transfer?cntrller=requests_admin&sample_id=%s&request_id=%s&external_service_id=%s" % \
+            ( self.url, sample_id, request_id, external_service_id )
         self.visit_url( url )
         for check_str in strings_displayed:
             self.check_page_for_string( check_str )

test/functional/test_sample_tracking.py

@@ -800,11 +800,13 @@ class TestFormsAndSampleTracking( TwillTestCase ):
         sample_dataset_file_names = [ dataset.split( '/' )[-1] for dataset in sample_datasets ]
         global request1_sample1
         request1_sample1 = request1.get_sample( 'Sample1_renamed' )
+        external_service = request1_sample1.external_service
         strings_displayed_after_submit = [ 'Datasets (%s) have been selected for sample (%s)' % \
                                            ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), request1_sample1.name ) ]
         strings_displayed = [ 'Select datasets to transfer from data directory configured for the sequencer' ]
         self.add_datasets_to_sample( request_id=self.security.encode_id( request2.id ),
                                      sample_id= self.security.encode_id( request1_sample1.id ),
+                                     external_service_id=self.security.encode_id( external_serviceexternal_service.id ),
                                      sample_datasets=sample_datasets,
                                      strings_displayed=strings_displayed,
                                      strings_displayed_after_submit=strings_displayed_after_submit )