Add missing functional tests for history features.

lib/galaxy/web/controllers/root.py

@@ -59,7 +59,7 @@ class RootController( BaseController ):
             return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' )
         if as_xml:
             trans.response.set_content_type('text/xml')
-            return trans.fill_template_mako( "root/history_as_xml.mako", history=history )
+            return trans.fill_template_mako( "root/history_as_xml.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) )
         else:
             template = "root/history.mako"
             return trans.fill_template( "root/history.mako", history = history, show_deleted = util.string_as_bool( show_deleted ) )

templates/root/history_as_xml.mako

@@ -1,8 +1,16 @@
 <?xml version="1.0"?>
 <history>
-  %for data in history.active_datasets:
-    <data id="${data.id}" hid="${data.hid}" name="${data.name}" state="${data.state}" dbkey="${data.dbkey}">
-      ${_(data.blurb)}
-    </data>
-  %endfor
+    %if show_deleted:
+        %for data in history.activatable_datasets:
+            <data id="${data.id}" hid="${data.hid}" name="${data.name}" state="${data.state}" dbkey="${data.dbkey}">
+                ${_(data.blurb)}
+            </data>
+        %endfor
+    %else:
+        %for data in history.active_datasets:
+            <data id="${data.id}" hid="${data.hid}" name="${data.name}" state="${data.state}" dbkey="${data.dbkey}">
+                ${_(data.blurb)}
+            </data>
+        %endfor
+    %endif
 </history>

test/base/twilltestcase.py

@@ -98,6 +98,7 @@ class TwillTestCase( unittest.TestCase ):
     # Functions associated with histories
     def check_history_for_errors( self ):
         """Raises an exception if there are errors in a history"""
+        self.home()
         self.visit_page( "history" )
         page = self.last_page()
         if page.find( 'error' ) > -1:
@@ -105,6 +106,7 @@ class TwillTestCase( unittest.TestCase ):
 
     def check_history_for_string( self, patt ):
         """Looks for 'string' in history page"""
+        self.home()
         self.visit_page( "history" )
         for subpatt in patt.split():
             tc.find(subpatt)
@@ -130,16 +132,16 @@ class TwillTestCase( unittest.TestCase ):
         data_list = [ elem for elem in tree.findall("data") ]
         return data_list
 
-    def get_history( self ):
+    def get_history( self, show_deleted=False ):
         """Returns a history"""
-        tree = self.history_as_xml_tree()
+        tree = self.history_as_xml_tree( show_deleted=show_deleted )
         data_list = [ elem for elem in tree.findall("data") ]
         return data_list
 
-    def history_as_xml_tree( self ):
+    def history_as_xml_tree( self, show_deleted=False ):
         """Returns a parsed xml object of a history"""
         self.home()
-        self.visit_page( 'history?as_xml=True' )
+        self.visit_page( 'history?as_xml=True&show_deleted=%s' % show_deleted )
         xml = self.last_page()
         tree = ElementTree.fromstring(xml)
         return tree
@@ -201,6 +203,7 @@ class TwillTestCase( unittest.TestCase ):
         name = elem.get( 'name' )
         self.assertTrue( name )
         self.visit_url( "%s/history/share?id=%s&email=%s&history_share_btn=Submit" % ( self.url, id, email ) )
+        self.check_page_for_string( 'History (%s) has been shared with: %s' % ( name, email ) )
         return id, name, email
     def share_history_containing_private_datasets( self, history_id, email='test@bx.psu.edu' ):
         """Attempt to share a history containing private datasets with a different user"""
@@ -237,8 +240,10 @@ class TwillTestCase( unittest.TestCase ):
         self.assertEqual(len(elems), 1)
         self.visit_page( "history/list?operation=switch&id=%s" % elems[0].get('id') )
 
-    def view_stored_histories( self ):
+    def view_stored_histories( self, check_str='' ):
         self.visit_page( "history/list" )
+        if check_str:
+            self.check_page_for_string( check_str )
 
     # Functions associated with datasets (history items) and meta data
     def get_job_stderr( self, id ):
@@ -264,16 +269,36 @@ class TwillTestCase( unittest.TestCase ):
         self.visit_page( "edit?hid=%d" % hid )
         for subpatt in patt.split():
             tc.find(subpatt)
-
-    def delete_history_item( self, hid ):
+    def delete_history_item( self, hid, check_str='' ):
         """Deletes an item from a history"""
+        try:
+            hid = int( hid )
+        except:
+            raise AssertionError, "Invalid hid '%s' - must be int" % hid
         hid = str(hid)
         data_list = self.get_history()
         self.assertTrue( data_list )
-        elems = [ elem for elem in data_list if elem.get('hid') == hid ]
-        self.assertEqual(len(elems), 1)
-        self.visit_page( "delete?id=%s" % elems[0].get('id') )
-
+        elems = [ elem for elem in data_list if elem.get( 'hid' ) == hid ]
+        self.assertEqual( len( elems ), 1 )
+        self.home()
+        self.visit_page( "delete?id=%s" % elems[0].get( 'id' ) )
+        if check_str:
+            self.check_page_for_string( check_str )
+    def undelete_history_item( self, hid, show_deleted=False, check_str='' ):
+        """Un-deletes a deleted item in a history"""
+        try:
+            hid = int( hid )
+        except:
+            raise AssertionError, "Invalid hid '%s' - must be int" % hid
+        hid = str( hid )
+        data_list = self.get_history( show_deleted=show_deleted )
+        self.assertTrue( data_list )
+        elems = [ elem for elem in data_list if elem.get( 'hid' ) == hid ]
+        self.assertEqual( len( elems ), 1 )
+        self.home()
+        self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, elems[0].get( 'id' ) ) )
+        if check_str:
+            self.check_page_for_string( check_str )
     def edit_metadata( self, hid=None, form_no=0, **kwd ):
         """
         Edits the metadata associated with a history item."""

test/functional/test_history_functions.py

@@ -1,4 +1,6 @@
-from base.twilltestcase import TwillTestCase
+import galaxy.model
+from galaxy.model.orm import *
+from base.twilltestcase import *
 
 class TestHistory( TwillTestCase ):
 
@@ -20,15 +22,28 @@ class TestHistory( TwillTestCase ):
     def test_10_history_options_when_logged_in( self ):
         """Testing history options when logged in"""
         self.history_options()
-        self.check_page_for_string( 'Rename</a> current history')
-        self.check_page_for_string( 'List</a> previously stored histories')
-        self.check_page_for_string( 'Share</a> current history')
-        self.check_page_for_string( 'Delete</a> current history')
-    def test_10_history_rename( self ):
+        self.check_page_for_string( 'Rename</a> current history' )
+        self.check_page_for_string( 'List</a> previously stored histories' )
+        self.check_page_for_string( 'Construct workflow</a> from the current history' )
+        self.check_page_for_string( 'Share</a> current history' )
+        # Tests for changing default history permissions are done in test_security_and_libraries.py
+        self.check_page_for_string( 'Change default permissions</a> for the current history' )
+        self.check_page_for_string( 'Show deleted</a> datasets in history' )
+        self.check_page_for_string( 'Delete</a> current history' )
+        # Need to add a history item in order to create a new empty history
+        try:
+            self.check_page_for_string( 'Create</a> a new empty history' )
+            raise AssertionError, "Incorrectly able to create a new empty history when the current history is empty."
+        except:
+            pass
+        self.upload_file( '1.bed', dbkey='hg18' )
+        self.history_options()
+        self.check_page_for_string( 'Create</a> a new empty history' )
+    def test_15_history_rename( self ):
         """Testing renaming a history"""
         id, old_name, new_name = self.rename_history()
         self.check_page_for_string( 'History: %s renamed to: %s' %(old_name, new_name) )
-    def test_15_history_view( self ):
+    def test_20_history_list( self ):
         """Testing viewing previously stored histories"""
         self.view_stored_histories()
         self.check_page_for_string( 'Stored histories' )
@@ -36,24 +51,15 @@ class TestHistory( TwillTestCase ):
         self.check_page_for_string( 'operation=Rename&id' )
         self.check_page_for_string( 'operation=Switch&id' )
         self.check_page_for_string( 'operation=Delete&id' )
-    def test_20_delete_history_item( self ):
-        """Testing deleting history item"""
-        self.upload_file('1.bed', dbkey='hg15')
-        self.check_history_for_string('hg15 bed')
-        self.assertEqual ( len(self.get_history()), 1)
-        self.delete_history_item(1)
-        self.check_history_for_string("Your history is empty")
-        self.assertEqual ( len(self.get_history()), 0)
-    def test_25_share_history( self ):
+    def test_25_history_share( self ):
         """Testing sharing a history with another user"""
         self.upload_file('1.bed', dbkey='hg18')
         id, name, email = self.share_history()
-        self.last_page()
-        self.check_page_for_string( 'History (%s) has been shared with: %s' %(name, email) )
         self.logout()
-        self.login( email='test2@bx.psu.edu' )
-        self.view_stored_histories()
-        self.check_page_for_string( 'Unnamed history from test@bx.psu.edu' )
+        self.login( email=email )
+        self.home()
+        check_str = 'Unnamed history from test@bx.psu.edu'
+        self.view_stored_histories( check_str=check_str )
         histories = self.get_histories()
         for history in histories:
             if history.get( 'name' ) == 'Unnamed history from test@bx.psu.edu':
@@ -63,6 +69,47 @@ class TestHistory( TwillTestCase ):
         self.delete_history( id )
         self.logout()
         self.login( email='test@bx.psu.edu' )
+    def test_30_history_show_and_hide_deleted_datasets( self ):
+        """Testing displaying deleted history items"""
+        self.new_history()
+        self.upload_file('1.bed', dbkey='hg18')
+        latest_hda = galaxy.model.HistoryDatasetAssociation.query() \
+            .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
+        self.home()
+        self.visit_url( "%s/root/delete?show_deleted_on_refresh=False&id=%s" % ( self.url, str( latest_hda.id ) ) )
+        self.check_history_for_string( 'Your history is empty' )
+        self.home()
+        self.visit_url( "%s/history/?show_deleted=True" % self.url )
+        self.check_page_for_string( 'This dataset has been deleted.' )
+        self.check_page_for_string( '1.bed' )
+        self.home()
+        self.visit_url( "%s/history/?show_deleted=False" % self.url )
+        self.check_page_for_string( 'Your history is empty' )
+    def test_35_deleting_and_undeleting_history_items( self ):
+        """Testing deleting and un-deleting history items"""
+        self.new_history()
+        # Add a new history item
+        self.upload_file( '1.bed', dbkey='hg15' )
+        self.home()
+        self.visit_url( "%s/history/?show_deleted=False" % self.url )
+        self.check_page_for_string( '1.bed' )
+        self.check_page_for_string( 'hg15' )
+        self.assertEqual ( len( self.get_history() ), 1 )
+        # Delete the history item
+        self.delete_history_item( 1, check_str="Your history is empty" )
+        self.assertEqual ( len( self.get_history() ), 0 )
+        # Try deleting an invalid hid
+        try:
+            self.delete_history_item( 'XXX' )
+            raise AssertionError, "Inproperly able to delete hid 'XXX' which is not an integer"
+        except:
+            pass
+        # Undelete the history item
+        self.undelete_history_item( 1, show_deleted=True )
+        self.home()
+        self.visit_url( "%s/history/?show_deleted=False" % self.url )
+        self.check_page_for_string( '1.bed' )
+        self.check_page_for_string( 'hg15' )
     def test_9999_clean_up( self ):
         self.delete_history()
         self.logout()