diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index 085e2cb60ce..6376531d9da 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -4,6 +4,7 @@ from galaxy.util import string_as_bool, relpath, stringify_dictionary_keys, list
from galaxy.util.odict import odict
from galaxy.web import form_builder
import galaxy.model
+from sqlalchemy.orm import object_session
import pkg_resources
pkg_resources.require("simplejson")
@@ -298,7 +299,6 @@ class SelectParameter( MetadataParameter ):
if not isinstance( value, list ): return [value]
return value
-
class DBKeyParameter( SelectParameter ):
def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd):
try:
@@ -387,26 +387,28 @@ class FileParameter( MetadataParameter ):
return "No display available for Metadata Files
"
def wrap( self, value ):
+ if value is None:
+ return None
if isinstance( value, galaxy.model.MetadataFile ) or isinstance( value, MetadataTempFile ):
return value
if DATABASE_CONNECTION_AVAILABLE:
try:
- # FIXME: GVK ( 11/11/09 ) had to add the monkey patch back into assignmapper for the get
- # method for this since Metadata has no hook into mapping.context ( the salalchemy session ).
+ # FIXME: this query requires a monkey patch in assignmapper.py since
+ # MetadataParameters do not have a handle to the sqlalchemy session
return galaxy.model.MetadataFile.get( value )
except:
#value was not a valid id
return None
- elif value is not None:
+ else:
mf = galaxy.model.MetadataFile()
mf.id = value #we assume this is a valid id, since we cannot check it
return mf
- return None
- def make_copy( self, value, target_context = None, source_context = None ):
+ def make_copy( self, value, target_context, source_context ):
value = self.wrap( value )
if value:
new_value = galaxy.model.MetadataFile( dataset = target_context.parent, name = self.spec.name )
- new_value.flush()
+ object_session( target_context.parent ).add( new_value )
+ object_session( target_context.parent ).flush()
shutil.copy( value.file_name, new_value.file_name )
return self.unwrap( new_value )
return None
@@ -441,7 +443,8 @@ class FileParameter( MetadataParameter ):
def new_file( self, dataset = None, **kwds ):
if DATABASE_CONNECTION_AVAILABLE:
mf = galaxy.model.MetadataFile( name = self.spec.name, dataset = dataset, **kwds )
- mf.flush() #flush to assign id
+ object_session( dataset ).add( mf )
+ object_session( dataset ).flush() #flush to assign id
return mf
else:
#we need to make a tmp file that is accessable to the head node,
@@ -557,7 +560,8 @@ class JobExternalOutputMetadataWrapper( object ):
#file to store kwds passed to set_meta()
metadata_files.filename_kwds = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name )
simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
- metadata_files.flush()
+ sa_session.add( metadata_files )
+ sa_session.flush()
metadata_files_list.append( metadata_files )
#return command required to build
return "%s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, datatypes_config, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
@@ -586,4 +590,5 @@ class JobExternalOutputMetadataWrapper( object ):
def set_job_runner_external_pid( self, pid, sa_session ):
for metadata_files in sa_session.query( galaxy.model.Job ).get( self.job_id ).external_output_metadata:
metadata_files.job_runner_external_pid = pid
- metadata_files.flush()
+ sa_session.add( metadata_files )
+ sa_session.flush()
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 73963f47708..b1afd755eef 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -17,6 +17,7 @@ from galaxy.util.hash_util import *
from galaxy.web.form_builder import *
import logging
log = logging.getLogger( __name__ )
+from sqlalchemy.orm import object_session
datatypes_registry = galaxy.datatypes.registry.Registry() #Default Value Required for unit tests
@@ -205,7 +206,8 @@ class History( object ):
def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid = True ):
if isinstance( dataset, Dataset ):
dataset = HistoryDatasetAssociation( dataset = dataset, copied_from = dataset )
- dataset.flush()
+ object_session( self ).add( dataset )
+ object_session( self ).flush()
elif not isinstance( dataset, HistoryDatasetAssociation ):
raise TypeError, "You can only add Dataset and HistoryDatasetAssociation instances to a history ( you tried to add %s )." % str( dataset )
if parent_id:
@@ -229,7 +231,8 @@ class History( object ):
if not target_user:
target_user = self.user
new_history = History( name=name, user=target_user )
- new_history.flush()
+ object_session( self ).add( new_history )
+ object_session( self ).flush()
if activatable:
hdas = self.activatable_datasets
else:
@@ -237,9 +240,11 @@ class History( object ):
for hda in hdas:
new_hda = hda.copy( copy_children=True, target_history=new_history )
new_history.add_dataset( new_hda, set_hid = False )
- new_hda.flush()
+ object_session( self ).add( new_hda )
+ object_session( self ).flush()
new_history.hid_counter = self.hid_counter
- new_history.flush()
+ object_session( self ).add( new_history )
+ object_session( self ).flush()
return new_history
@property
def activatable_datasets( self ):
@@ -439,7 +444,7 @@ class DatasetInstance( object ):
permitted_actions = Dataset.permitted_actions
def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None,
dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None,
- parent_id=None, validation_errors=None, visible=True, create_dataset=False ):
+ parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None ):
self.name = name or "Unnamed dataset"
self.id = id
self.info = info
@@ -454,8 +459,10 @@ class DatasetInstance( object ):
self.visible = visible
# Relationships
if not dataset and create_dataset:
+ # Had to pass the sqlalchemy session in order to create a new dataset
dataset = Dataset( state=Dataset.states.NEW )
- dataset.flush()
+ sa_session.add( dataset )
+ sa_session.flush()
self.dataset = dataset
self.parent_id = parent_id
self.validation_errors = validation_errors
@@ -466,7 +473,8 @@ class DatasetInstance( object ):
return self.dataset.state
def set_dataset_state ( self, state ):
self.dataset.state = state
- self.dataset.flush() #flush here, because hda.flush() won't flush the Dataset object
+ object_session( self ).add( self.dataset )
+ object_session( self ).flush() #flush here, because hda.flush() won't flush the Dataset object
state = property( get_dataset_state, set_dataset_state )
def get_file_name( self ):
return self.dataset.get_file_name()
@@ -616,8 +624,11 @@ class HistoryDatasetAssociation( DatasetInstance ):
history = None,
copied_from_history_dataset_association = None,
copied_from_library_dataset_dataset_association = None,
+ sa_session = None,
**kwd ):
- DatasetInstance.__init__( self, **kwd )
+ # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
+ # parameter is True so that the new object can be flushed. Is there a better way?
+ DatasetInstance.__init__( self, sa_session=sa_session, **kwd )
self.hid = hid
# Relationships
self.history = history
@@ -637,7 +648,8 @@ class HistoryDatasetAssociation( DatasetInstance ):
parent_id=parent_id,
copied_from_history_dataset_association=self,
history = target_history )
- hda.flush()
+ object_session( self ).add( hda )
+ object_session( self ).flush()
hda.set_size()
# Need to set after flushed, as MetadataFiles require dataset.id
hda.metadata = self.metadata
@@ -647,7 +659,7 @@ class HistoryDatasetAssociation( DatasetInstance ):
if not self.datatype.copy_safe_peek:
# In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
hda.set_peek()
- hda.flush()
+ object_session( self ).flush()
return hda
def to_library_dataset_dataset_association( self, target_folder, replace_dataset=None, parent_id=None, user=None ):
if replace_dataset:
@@ -657,7 +669,8 @@ class HistoryDatasetAssociation( DatasetInstance ):
# If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new
# LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset.
library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info )
- library_dataset.flush()
+ object_session( self ).add( library_dataset )
+ object_session( self ).flush()
if not user:
user = self.history.user
ldda = LibraryDatasetDatasetAssociation( name=self.name,
@@ -673,15 +686,18 @@ class HistoryDatasetAssociation( DatasetInstance ):
parent_id=parent_id,
copied_from_history_dataset_association=self,
user=user )
- ldda.flush()
+ object_session( self ).add( ldda )
+ object_session( self ).flush()
# Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
# Must set metadata after ldda flushed, as MetadataFiles require ldda.id
ldda.metadata = self.metadata
if not replace_dataset:
target_folder.add_library_dataset( library_dataset, genome_build=ldda.dbkey )
- target_folder.flush()
+ object_session( self ).add( target_folder )
+ object_session( self ).flush()
library_dataset.library_dataset_dataset_association_id = ldda.id
- library_dataset.flush()
+ object_session( self ).add( library_dataset )
+ object_session( self ).flush()
for child in self.children:
child_copy = child.to_library_dataset_dataset_association( target_folder=target_folder,
replace_dataset=replace_dataset,
@@ -690,7 +706,7 @@ class HistoryDatasetAssociation( DatasetInstance ):
if not self.datatype.copy_safe_peek:
# In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
ldda.set_peek()
- ldda.flush()
+ object_session( self ).flush()
return ldda
def clear_associated_files( self, metadata_safe = False, purge = False ):
# metadata_safe = True means to only clear when assoc.metadata_safe == False
@@ -814,8 +830,8 @@ class LibraryDataset( object ):
def set_library_dataset_dataset_association( self, ldda ):
self.library_dataset_dataset_association = ldda
ldda.library_dataset = self
- ldda.flush()
- self.flush()
+ object_session( self ).add_all( ( ldda, self ) )
+ object_session( self ).flush()
def get_info( self ):
if self.library_dataset_dataset_association:
return self.library_dataset_dataset_association.info
@@ -853,8 +869,11 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
copied_from_library_dataset_dataset_association=None,
library_dataset=None,
user=None,
+ sa_session=None,
**kwd ):
- DatasetInstance.__init__( self, **kwd )
+ # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
+ # parameter in kwd is True so that the new object can be flushed. Is there a better way?
+ DatasetInstance.__init__( self, sa_session=sa_session, **kwd )
self.copied_from_history_dataset_association = copied_from_history_dataset_association
self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association
self.library_dataset = library_dataset
@@ -872,7 +891,8 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
parent_id=parent_id,
copied_from_library_dataset_dataset_association=self,
history=target_history )
- hda.flush()
+ object_session( self ).add( hda )
+ object_session( self ).flush()
hda.metadata = self.metadata #need to set after flushed, as MetadataFiles require dataset.id
if add_to_history and target_history:
target_history.add_dataset( hda )
@@ -880,7 +900,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
child_copy = child.to_history_dataset_association( target_history = target_history, parent_id = hda.id, add_to_history = False )
if not self.datatype.copy_safe_peek:
hda.set_peek() #in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
- hda.flush()
+ object_session( self ).flush()
return hda
def copy( self, copy_children = False, parent_id = None, target_folder = None ):
ldda = LibraryDatasetDatasetAssociation( name=self.name,
@@ -895,7 +915,8 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
parent_id=parent_id,
copied_from_library_dataset_dataset_association=self,
folder=target_folder )
- ldda.flush()
+ object_session( self ).add( ldda )
+ object_session( self ).flush()
# Need to set after flushed, as MetadataFiles require dataset.id
ldda.metadata = self.metadata
if copy_children:
@@ -904,7 +925,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
if not self.datatype.copy_safe_peek:
# In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
ldda.set_peek()
- ldda.flush()
+ object_session( self ).flush()
return ldda
def clear_associated_files( self, metadata_safe = False, purge = False ):
return
diff --git a/lib/galaxy/model/mapping_tests.py b/lib/galaxy/model/mapping_tests.py
index c06f3815acc..ef41b1d3b11 100644
--- a/lib/galaxy/model/mapping_tests.py
+++ b/lib/galaxy/model/mapping_tests.py
@@ -15,11 +15,12 @@ class MappingTests( unittest.TestCase ):
#h1.queries.append( model.Query( "h1->q1" ) )
#h1.queries.append( model.Query( "h1->q2" ) )
h2 = model.History( name=( "H" * 1024 ) )
+ model.session.add_all( ( u, h1, h2 ) )
#q1 = model.Query( "h2->q1" )
- d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True )
+ d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True, sa_session=model.session )
#h2.queries.append( q1 )
#h2.queries.append( model.Query( "h2->q2" ) )
- model.session.add_all( ( u, h1, h2, d1 ) )
+ model.session.add( ( d1 ) )
model.session.flush()
model.session.expunge_all()
# Check
diff --git a/lib/galaxy/model/orm/ext/assignmapper.py b/lib/galaxy/model/orm/ext/assignmapper.py
index d418281e0bb..caace811c3b 100644
--- a/lib/galaxy/model/orm/ext/assignmapper.py
+++ b/lib/galaxy/model/orm/ext/assignmapper.py
@@ -19,7 +19,6 @@ from sqlalchemy.orm import Query
from sqlalchemy.orm import mapper as sqla_mapper
def _monkeypatch_query_method( name, session, class_ ):
- # TODO: eliminate this method by fixing the single query in ~/datatypes/metadata.py ( line 396 )
def do(self, *args, **kwargs):
return getattr( class_.query, name)(*args, **kwargs)
try:
@@ -28,20 +27,6 @@ def _monkeypatch_query_method( name, session, class_ ):
pass
if not hasattr(class_, name):
setattr(class_, name, classmethod(do))
-def _monkeypatch_session_method( name, session, class_ ):
- # TODO: eliminate this method by fixing the session flushes in ~/model/__init__.py ( 20 of them )
- # and ~/datatypes/metadata.py ( 4 of them ). The affected objects have no known hook into mapping.context
- # ( i.e., sqlalchemy session ).
- def do( self, *args, **kwargs ):
- if self not in session.deleted:
- session.add( self )
- return session.flush()
- try:
- do.__name__ = name
- except:
- pass
- if not hasattr( class_, name ):
- setattr( class_, name, do )
def session_mapper( scoped_session, class_, *args, **kwargs ):
def mapper( cls, *arg, **kw ):
validate = kw.pop( 'validate', False )
@@ -54,8 +39,9 @@ def session_mapper( scoped_session, class_, *args, **kwargs ):
setattr( self, key, value )
cls.__init__ = __init__
cls.query = scoped_session.query_property()
+ # FIXME: eliminate the need for the following monkey patch by fixing the single
+ # query in ~/datatypes/metadata.py in the FileParameter.wrap() method
_monkeypatch_query_method( 'get', scoped_session, cls )
- _monkeypatch_session_method( 'flush', scoped_session, cls )
return sqla_mapper( cls, *arg, **kw )
return mapper( class_, *args, **kwargs )
def assign_mapper( session, class_, *args, **kwargs ):
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index fff66f9d627..4d2b15e63b0 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1495,7 +1495,13 @@ class Tool:
if visible == "visible": visible = True
else: visible = False
ext = fields.pop(0).lower()
- child_dataset = self.app.model.HistoryDatasetAssociation( extension=ext, parent_id=outdata.id, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True )
+ child_dataset = self.app.model.HistoryDatasetAssociation( extension=ext,
+ parent_id=outdata.id,
+ designation=designation,
+ visible=visible,
+ dbkey=outdata.dbkey,
+ create_dataset=True,
+ sa_session=self.sa_session )
self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset )
# Move data from temp location to dataset location
shutil.move( filename, child_dataset.file_name )
@@ -1548,7 +1554,12 @@ class Tool:
if fields:
dbkey = fields[ 0 ]
# Create new primary dataset
- primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=dbkey, create_dataset=True )
+ primary_data = self.app.model.HistoryDatasetAssociation( extension=ext,
+ designation=designation,
+ visible=visible,
+ dbkey=dbkey,
+ create_dataset=True,
+ sa_session=self.sa_session )
self.app.security_agent.copy_dataset_permissions( outdata.dataset, primary_data.dataset )
self.sa_session.add( primary_data )
self.sa_session.flush()
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 730b73e0fc0..6796905710e 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -198,7 +198,7 @@ class DefaultToolAction( object ):
if check is not None:
if str( getattr( check, when_elem.get( 'attribute' ) ) ) == when_elem.get( 'value', None ):
ext = when_elem.get( 'format', ext )
- data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True )
+ data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True, sa_session=trans.sa_session )
# Commit the dataset immediately so it gets database assigned unique id
trans.sa_session.add( data )
trans.sa_session.flush()
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index f4e49c93d75..b4aa9007fe4 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -112,7 +112,8 @@ def new_history_upload( trans, uploaded_dataset, state=None ):
extension = uploaded_dataset.file_type,
dbkey = uploaded_dataset.dbkey,
history = trans.history,
- create_dataset = True )
+ create_dataset = True,
+ sa_session = trans.sa_session )
if state:
hda.state = state
else:
@@ -159,13 +160,14 @@ def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ):
dbkey = uploaded_dataset.dbkey,
library_dataset = ld,
user = trans.user,
- create_dataset = True )
+ create_dataset = True,
+ sa_session = trans.sa_session )
+ trans.sa_session.add( ldda )
if state:
ldda.state = state
else:
ldda.state = ldda.states.QUEUED
ldda.message = library_bunch.message
- trans.sa_session.add( ldda )
trans.sa_session.flush()
# Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
trans.app.security_agent.copy_library_permissions( ld, ldda )
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 44b53207735..395af0df158 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -730,7 +730,7 @@ class ColumnListParameter( SelectToolParameter ):
>>> hist = History()
>>> sa_session.add( hist )
>>> sa_session.flush()
- >>> hist.add_dataset( HistoryDatasetAssociation( id=1, extension='interval', create_dataset=True ) )
+ >>> hist.add_dataset( HistoryDatasetAssociation( id=1, extension='interval', create_dataset=True, sa_session=sa_session ) )
>>> dtp = DataToolParameter( None, XML( '' ) )
>>> print dtp.name
blah
diff --git a/lib/galaxy/web/controllers/async.py b/lib/galaxy/web/controllers/async.py
index adda6654751..d6a51dff469 100644
--- a/lib/galaxy/web/controllers/async.py
+++ b/lib/galaxy/web/controllers/async.py
@@ -103,7 +103,7 @@ class ASync( BaseController ):
#data.state = jobs.JOB_OK
#history.datasets.add_dataset( data )
- data = trans.app.model.HistoryDatasetAssociation( create_dataset = True, extension = GALAXY_TYPE )
+ data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE )
trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history ) )
data.name = GALAXY_NAME
data.dbkey = GALAXY_BUILD
diff --git a/lib/galaxy/web/controllers/requests.py b/lib/galaxy/web/controllers/requests.py
index 328428cab24..2b938a6a362 100644
--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -667,7 +667,8 @@ class Requests( BaseController ):
request.library = library
request.folder = folder
request.state = trans.app.model.Request.states.UNSUBMITTED
- request.flush()
+ trans.sa_session.add( request )
+ trans.sa_session.flush()
return request
@web.expose
@web.require_login( "create/submit sequencing requests" )
diff --git a/lib/galaxy/web/controllers/root.py b/lib/galaxy/web/controllers/root.py
index fad523f953d..8d06ae3d0d7 100644
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -501,7 +501,12 @@ class RootController( BaseController ):
"""Adds a POSTed file to a History"""
try:
history = trans.sa_session.query( trans.app.model.History ).get( history_id )
- data = trans.app.model.HistoryDatasetAssociation( name = name, info = info, extension = ext, dbkey = dbkey, create_dataset = True )
+ data = trans.app.model.HistoryDatasetAssociation( name = name,
+ info = info,
+ extension = ext,
+ dbkey = dbkey,
+ create_dataset = True,
+ sa_session = trans.sa_session )
if copy_access_from:
copy_access_from = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( copy_access_from )
trans.app.security_agent.copy_dataset_permissions( copy_access_from.dataset, data.dataset )
diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py
index 49365291477..4efa96a13a7 100644
--- a/tools/data_source/microbial_import_code.py
+++ b/tools/data_source/microbial_import_code.py
@@ -131,7 +131,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
dbkey = fields[3]
filepath = fields[4]
file_type = fields[5]
- newdata = app.model.HistoryDatasetAssociation( create_dataset = True ) #This import should become a library
+ newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library
newdata.set_size()
newdata.extension = file_type
newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
diff --git a/tools/maf/maf_to_bed_code.py b/tools/maf/maf_to_bed_code.py
index 1fb40b32d15..cedb144ff66 100644
--- a/tools/maf/maf_to_bed_code.py
+++ b/tools/maf/maf_to_bed_code.py
@@ -27,7 +27,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
fields = line.split("\t")
dbkey = fields[1]
filepath = fields[2]
- newdata = app.model.HistoryDatasetAssociation( create_dataset = True )
+ newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context )
newdata.set_size()
newdata.extension = "bed"
newdata.name = basic_name + " (" + dbkey + ")"