committing backout from 5765 which included reversions from a broken galaxy-central repository

lib/galaxy/security/__init__.py

@@ -1005,8 +1005,7 @@ class HostAgent( RBACAgent ):
         ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu',
                       'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ),
         ucsc_test = ( 'hgwdev.cse.ucsc.edu', ),
-        ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ),
-        ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'),
+        ucsc_archaea = ( 'lowepub.cse.ucsc.edu', )
     )
     def __init__( self, model, permitted_actions=None ):
         self.model = model
@@ -1037,7 +1036,7 @@ class HostAgent( RBACAgent ):
                 # We're going to search in order, but if the remote site is load
                 # balancing their connections (as UCSC does), this is okay.
                 try:
-                    if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38':
+                    if socket.gethostbyname( server ) == addr:
                         break # remote host is in the server list
                 except ( socket.error, socket.gaierror ):
                     pass # can't resolve, try next

lib/galaxy/tools/__init__.py

@@ -922,8 +922,6 @@ class Tool:
         if not self.check_values:
             return
         for input in self.inputs.itervalues():
-            if input.name not in value:
-                value[input.name] = input.get_initial_value( None, value )
             if isinstance( input, ToolParameter ):
                 callback( "", input, value[input.name] )
             else:

lib/galaxy/tools/parameters/basic.py

@@ -748,6 +748,9 @@ class SelectToolParameter( ToolParameter ):
             # Dependency on a value that does not yet exist
             if isinstance( dep_value, RuntimeValue ):
                 return True
+            #dataset not ready yet
+            if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ):
+                return True
         # Dynamic, but all dependenceis are known and have values
         return False 
     def get_initial_value( self, trans, context ):
@@ -878,6 +881,7 @@ class ColumnListParameter( SelectToolParameter ):
         self.force_select = string_as_bool( elem.get( "force_select", True ))
         self.accept_default = string_as_bool( elem.get( "accept_default", False ))
         self.data_ref = elem.get( "data_ref", None )
+        self.ref_input = None
         self.default_value = elem.get( "default_value", None )
         self.is_dynamic = True
     def from_html( self, value, trans=None, context={} ):
@@ -973,7 +977,7 @@ class ColumnListParameter( SelectToolParameter ):
             if not dataset.metadata.columns:
                 # Only allow late validation if the dataset is not yet ready
                 # (since we have reason to expect the metadata to be ready eventually)
-                if dataset.is_pending:
+                if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ):
                     return True
         # No late validation
         return False
@@ -1353,7 +1357,7 @@ class DataToolParameter( ToolParameter ):
                         selected = ( value and ( hda in value ) )
                         field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected )
                     else:
-                        target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) )
+                        target_ext, converted_dataset = hda.find_conversion_destination( self.formats )
                         if target_ext:
                             if converted_dataset:
                                 hda = converted_dataset
@@ -1402,13 +1406,22 @@ class DataToolParameter( ToolParameter ):
                 pass #no valid options
         def dataset_collector( datasets ):
             def is_convertable( dataset ):
-                target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) )
+                target_ext, converted_dataset = dataset.find_conversion_destination( self.formats )
                 if target_ext is not None:
                     return True
                 return False
             for i, data in enumerate( datasets ):
-                if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ):
-                    if self.options and self._options_filter_attribute( data ) != filter_value:
+                if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]:
+                    is_valid = False
+                    if isinstance( data.datatype, self.formats ):
+                        is_valid = True
+                    else:
+                        target_ext, converted_dataset = data.find_conversion_destination( self.formats )
+                        if target_ext:
+                            is_valid = True
+                        if converted_dataset:
+                            data = converted_dataset
+                    if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ):
                         continue
                     most_recent_dataset[0] = data
                 # Also collect children via association object

lib/galaxy/web/framework/middleware/remoteuser.py

@@ -36,7 +36,6 @@ errorpage = """
 """
 
 UCSC_MAIN_SERVERS = (
-    'omics.bhri.internal',
     'hgw1.cse.ucsc.edu',
     'hgw2.cse.ucsc.edu',
     'hgw3.cse.ucsc.edu',
@@ -50,7 +49,6 @@ UCSC_ARCHAEA_SERVERS = (
     'lowepub.cse.ucsc.edu',
 )
 
-
 class RemoteUser( object ):
     def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ):
         self.app = app
@@ -58,7 +56,7 @@ class RemoteUser( object ):
         self.allow_ucsc_main = False
         self.allow_ucsc_archaea = False
         self.admin_users = admin_users
-        if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites:
+        if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites:
             self.allow_ucsc_main = True
         if 'archaea' in ucsc_display_sites:
             self.allow_ucsc_archaea = True

scripts/cleanup_datasets/purge_libraries.sh

@@ -1,5 +1,4 @@
 #!/bin/sh
 
 cd `dirname $0`/../..
-#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log
-python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log
+python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log