opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Upgrade to SQLAlchemy 0.4.7 and correct conflicts in ~/model/__init__.py.

Browse Source
This commit is contained in:
Greg Von Kuster
2008-09-18 15:18:12 -04:00
parent e53c5a15a3
commit 8e17384a79
17 changed files with 144 additions and 99 deletions
Download Patch File Download Diff File Expand all files Collapse all files
eggs.ini
+2 -2
View File
@@ -39,7 +39,7 @@ PasteDeploy = 1.3.1
PasteScript = 1.3.6
Routes = 1.6.3
simplejson = 1.5
SQLAlchemy = 0.3.11
SQLAlchemy = 0.4.7p1
Tempita = 0.1
twill = 0.9
WebError = 0.8a
@@ -84,7 +84,7 @@ PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDe
PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.6.tar.gz
Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz
simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.tar.gz
SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz
SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.gz
Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz
twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz
WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz
lib/galaxy/app.py
+1 -1
View File
@@ -21,7 +21,7 @@ class UniverseApplication( object ):
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Setup the database engine and ORM
self.model = galaxy.model.mapping.init( self.config.file_path,
db_url,
lib/galaxy/model/__init__.py
+9 -39
View File
@@ -103,28 +103,9 @@ class JobToOutputDatasetAssociation( object ):
self.name = name
self.dataset = dataset
<<<<<<< local
class HistoryDatasetAssociation( object ):
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, copied_from_history_dataset_association = None, validation_errors=None, visible=True, create_dataset = False ):
self.name = name or "Unnamed dataset"
self.id = id
self.hid = hid
self.info = info
self.blurb = blurb
self.peek = peek
self.extension = extension
self.designation = designation
self.metadata = metadata or dict()
self.dbkey = dbkey
self.deleted = deleted
self.visible = visible
# Relationships
=======
class GroupDatasetAssociation( object ):
def __init__( self, group, dataset, permitted_actions=[] ):
if isinstance( group, GroupDatasetAssociation ) or \
if isinstance( group, GroupDatasetAssociation ) or \
isinstance( group, DefaultUserGroupAssociation ) or \
isinstance( group, DefaultHistoryGroupAssociation ):
group = group.group
@@ -182,16 +163,9 @@ class DefaultHistoryGroupAssociation( object ):
isinstance( group, DefaultUserGroupAssociation ) or \
isinstance( group, DefaultHistoryGroupAssociation ):
group = group.group
>>>>>>> other
self.history = history
<<<<<<< local
if not dataset and create_dataset:
dataset = Dataset()
dataset.flush()
self.dataset = dataset
self.parent_id = parent_id
self.validation_errors = validation_errors
self.copied_from_history_dataset_association = copied_from_history_dataset_association
self.group = group
self.permitted_actions = permitted_actions
@property
def ext( self ):
@@ -342,8 +316,6 @@ class DefaultHistoryGroupAssociation( object ):
for child in self.children:
child.mark_deleted()
class History( object ):
def __init__( self, id=None, name=None, user=None ):
self.id = id
@@ -415,10 +387,6 @@ class History( object ):
# # Relationships
# self.history = history
# self.datasets = []
=======
self.group = group
self.permitted_actions = permitted_actions
>>>>>>> other
class Dataset( object ):
states = Bunch( NEW = 'new',
@@ -528,7 +496,7 @@ class DatasetInstance( object ):
self.extension = extension
self.dbkey = dbkey
self.designation = designation
self._metadata = metadata or dict()
self.metadata = metadata or dict()
self.deleted = deleted
self.visible = visible
# Relationships
@@ -559,9 +527,9 @@ class DatasetInstance( object ):
def datatype( self ):
return datatypes_registry.get_datatype_by_extension( self.extension )
def get_metadata( self ):
if not self._metadata:
self._metadata = dict()
return MetadataCollection( self, self.datatype.metadata_spec )
if not hasattr( self, '_metadata_collection' ):
self._metadata_collection = MetadataCollection( self, self.datatype.metadata_spec )
return self._metadata_collection
def set_metadata( self, bunch ):
# Needs to accept a MetadataCollection, a bunch, or a dict
self._metadata = dict( bunch.items() )
@@ -587,6 +555,8 @@ class DatasetInstance( object ):
dbkey = property( get_dbkey, set_dbkey )
def change_datatype( self, new_ext ):
self.clear_associated_files()
if hasattr( self, '_metadata_collection' ):
del self._metadata_collection
datatypes_registry.change_datatype( self, new_ext )
def get_size( self ):
"""Returns the size of the data on disk"""
lib/galaxy/model/custom_types.py
+8 -9
View File
@@ -16,16 +16,15 @@ class JSONType( TypeDecorator ):
self.mutable = mutable
super( JSONType, self).__init__()
def convert_result_value( self, value, dialect ):
def process_bind_param( self, value, dialect ):
if value is None:
return None
buf = self.impl.convert_result_value( value, dialect )
return self.jsonifyer.loads( str(buf) )
def convert_bind_param( self, value, dialect ):
return self.jsonifyer.dumps( value )
def process_result_value( self, value, dialect ):
if value is None:
return None
return self.impl.convert_bind_param( self.jsonifyer.dumps(value), dialect )
return self.jsonifyer.loads( str( value ) )
def copy_value( self, value ):
if self.mutable:
@@ -58,10 +57,10 @@ class MetadataType( JSONType ):
self.mutable = mutable
super( MetadataType, self).__init__()
def convert_result_value( self, value, dialect ):
def process_result_value( self, value, dialect ):
if value is None:
return None
buf = self.impl.convert_result_value( value, dialect )
buf = value
ret = None
try:
ret = self.pickler.loads( str(buf) )
@@ -75,7 +74,7 @@ class MetadataType( JSONType ):
class TrimmedString( TypeDecorator ):
impl = String
def convert_bind_param( self, value, dialect ):
def process_bind_param( self, value, dialect ):
"""Automatically truncate string values"""
if self.impl.length and value is not None:
value = value[0:self.impl.length]
lib/galaxy/model/mapping.py
+34 -34
View File
@@ -5,24 +5,21 @@ are encapsulated here.
import logging
log = logging.getLogger( __name__ )
import pkg_resources
pkg_resources.require( "sqlalchemy>=0.3" )
import sys
import datetime
from sqlalchemy.ext.sessioncontext import SessionContext
from sqlalchemy.ext.assignmapper import assign_mapper
from sqlalchemy.ext.orderinglist import ordering_list
from sqlalchemy import *
from galaxy.model import *
from galaxy.model.orm import *
from galaxy.model.orm.ext.assignmapper import *
from galaxy.model.custom_types import *
from galaxy.util.bunch import Bunch
from galaxy.security import GalaxyRBACAgent
metadata = DynamicMetaData( threadlocal=False )
context = SessionContext( create_session )
metadata = MetaData()
context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) )
# For backward compatibility with "context.current"
context.current = Session
dialect_to_egg = {
"sqlite" : "pysqlite>=2",
@@ -224,15 +221,15 @@ Job.table = Table( "job", metadata,
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
Column( "tool_id", String( 255 ) ),
Column( "tool_version", String, default="1.0.0" ),
Column( "tool_version", TEXT, default="1.0.0" ),
Column( "state", String( 64 ) ),
Column( "info", TrimmedString( 255 ) ),
Column( "command_line", String() ),
Column( "command_line", TEXT ),
Column( "param_filename", String( 1024 ) ),
Column( "runner_name", String( 255 ) ),
Column( "stdout", String() ),
Column( "stderr", String() ),
Column( "traceback", String() ),
Column( "stdout", TEXT ),
Column( "stderr", TEXT ),
Column( "traceback", TEXT ),
Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ),
Column( "job_runner_name", String( 255 ) ),
Column( "job_runner_external_id", String( 255 ) ) )
@@ -292,7 +289,7 @@ StoredWorkflow.table = Table( "stored_workflow", metadata,
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ),
Column( "latest_workflow_id", Integer,
ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ),
Column( "name", String ),
Column( "name", TEXT ),
Column( "deleted", Boolean, default=False ),
)
@@ -301,7 +298,7 @@ Workflow.table = Table( "workflow", metadata,
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ),
Column( "name", String ),
Column( "name", TEXT ),
Column( "has_cycles", Boolean ),
Column( "has_errors", Boolean )
)
@@ -312,8 +309,8 @@ WorkflowStep.table = Table( "workflow_step", metadata,
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
Column( "type", String(64) ),
Column( "tool_id", String ),
Column( "tool_version", String ), # Reserved for future
Column( "tool_id", TEXT ),
Column( "tool_version", TEXT ), # Reserved for future
Column( "tool_inputs", JSONType ),
Column( "tool_errors", JSONType ),
Column( "position", JSONType ),
@@ -326,8 +323,8 @@ WorkflowStepConnection.table = Table( "workflow_step_connection", metadata,
Column( "id", Integer, primary_key=True ),
Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
Column( "output_name", String ),
Column( "input_name", String)
Column( "output_name", TEXT ),
Column( "input_name", TEXT)
)
StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata,
@@ -352,9 +349,7 @@ assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.tab
dataset=relation(
Dataset,
primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ),
history=relation(
History,
primaryjoin=( History.table.c.id == HistoryDatasetAssociation.table.c.history_id ) ),
# .history defined in History mapper
copied_to_history_dataset_associations=relation(
HistoryDatasetAssociation,
primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ),
@@ -415,11 +410,11 @@ assign_mapper( context, Group, Group.table,
assign_mapper( context, UserGroupAssociation, UserGroupAssociation.table,
properties=dict( user=relation( User, backref = "groups" ),
group=relation( Group, backref = "users" ) ) )
group=relation( Group, backref = "members" ) ) )
assign_mapper( context, GroupDatasetAssociation, GroupDatasetAssociation.table,
properties=dict( dataset=relation( Dataset, backref = "groups" ),
group=relation( Group, backref = "datasets" ) ) )
group=relation( Group, backref = "group_datasets" ) ) )
assign_mapper( context, DefaultUserGroupAssociation, DefaultUserGroupAssociation.table,
properties=dict( user=relation( User, backref = "default_groups" ),
@@ -555,11 +550,12 @@ def db_next_hid( self ):
Override __next_hid to generate from the database in a concurrency
safe way.
"""
conn = self.table.engine.contextual_connect()
conn = object_session( self ).connection()
table = self.table
trans = conn.begin()
try:
next_hid = select( [self.c.hid_counter], self.c.id == self.id, for_update=True ).scalar()
self.table.update( self.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) )
next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar()
table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) )
trans.commit()
return next_hid
except:
@@ -588,17 +584,21 @@ def init( file_path, url, engine_options={}, create_tables=False ):
# Create the database engine
engine = create_engine( url, **engine_options )
# Connect the metadata to the database.
metadata.connect( engine )
## metadata.engine.echo = True
metadata.bind = engine
# Clear any existing contextual sessions and reconfigure
Session.remove()
Session.configure( bind=engine )
# Create tables if needed
if create_tables:
metadata.create_all()
# metadata.engine.commit()
# Pack everything into a bunch
result = Bunch( **globals() )
result.engine = metadata.engine
result.flush = lambda *args, **kwargs: context.current.flush( *args, **kwargs )
result.context = context
result.engine = engine
result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs )
result.session = Session
# For backward compatibility with "model.context.current"
result.context = Session
result.create_tables = create_tables
#load local galaxy security policy
result.security_agent = GalaxyRBACAgent( result )
lib/galaxy/model/orm/__init__.py
+7
View File
@@ -0,0 +1,7 @@
import pkg_resources
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.ext.orderinglist import ordering_list
lib/galaxy/model/orm/ext/__init__.py
+3
View File
@@ -0,0 +1,3 @@
"""
Galaxy specific SQLAlchemy extensions.
"""
lib/galaxy/model/orm/ext/assignmapper.py
+62
View File
@@ -0,0 +1,62 @@
"""
This is similar to the assignmapper extensions in SQLAclhemy 0.3 and 0.4 but
with some compatibility fixes. It assumes that the session is a ScopedSession,
and thus has the "mapper" method to attach contextual mappers to a class. It
adds additional query and session methods to the class to support the
SQLAlchemy 0.3 style of access. The following methods which would normally be
accessed through "Object.query().method()" are available directly through the
object:
'get', 'filter', 'filter_by', 'select', 'select_by',
'selectfirst', 'selectfirst_by', 'selectone', 'selectone_by',
'get_by', 'join_to', 'join_via', 'count', 'count_by',
'options', 'instances'
Additionally, the following Session methods, which normally accept an instance
or list of instances, are available directly through the objects, e.g.
"Session.flush( [instance] )" can be performed as "instance.flush()":
'refresh', 'expire', 'delete', 'expunge', 'update'
"""
__all__ = [ 'assign_mapper' ]
from sqlalchemy import util, exceptions
import types
from sqlalchemy.orm import mapper, Query
def _monkeypatch_query_method( name, session, class_ ):
def do(self, *args, **kwargs):
## util.warn_deprecated('Query methods on the class are deprecated; use %s.query.%s instead' % (class_.__name__, name))
return getattr( class_.query, name)(*args, **kwargs)
try:
do.__name__ = name
except:
pass
if not hasattr(class_, name):
setattr(class_, name, classmethod(do))
def _monkeypatch_session_method(name, session, class_, make_list=False):
def do(self, *args, **kwargs):
if make_list:
self = [ self ]
return getattr(session, name)( self, *args, **kwargs )
try:
do.__name__ = name
except:
pass
if not hasattr(class_, name):
setattr(class_, name, do)
def assign_mapper( session, class_, *args, **kwargs ):
m = class_.mapper = session.mapper( class_, *args, **kwargs )
for name in ('get', 'filter', 'filter_by', 'select', 'select_by',
'selectfirst', 'selectfirst_by', 'selectone', 'selectone_by',
'get_by', 'join_to', 'join_via', 'count', 'count_by',
'options', 'instances'):
_monkeypatch_query_method(name, session, class_)
for name in ('refresh', 'expire', 'delete', 'expunge', 'update'):
_monkeypatch_session_method(name, session, class_)
for name in ( 'flush', ):
_monkeypatch_session_method( name, session, class_, make_list=True )
return m
lib/galaxy/web/controllers/admin.py
+4 -4
View File
@@ -6,7 +6,7 @@ from galaxy.security import RBACAgent
import galaxy.model
from xml.sax.saxutils import escape, unescape
import pkg_resources
pkg_resources.require( "sqlalchemy>=0.3" )
pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
import logging
@@ -251,7 +251,7 @@ class Admin( BaseController ):
# simpler approach of deleting all existing members and creating
# new records for user_ids in the received members param.
# First remove existing members that are not in the received members param
for user_group_assoc in group.users:
for user_group_assoc in group.members:
if user_group_assoc.user_id not in members:
user = galaxy.model.User.get( user_group_assoc.user_id )
# Delete DefaultUserGroupAssociations
@@ -272,7 +272,7 @@ class Admin( BaseController ):
# Then add all new members to the group
for user_id in members:
user = galaxy.model.User.get( user_id )
if user not in group.users:
if user not in group.members:
user_group_association = galaxy.model.UserGroupAssociation( user, group )
user_group_association.flush()
msg = "Group membership has been updated with a total of %s members" % len( members )
@@ -405,7 +405,7 @@ class Admin( BaseController ):
group_id = params.group_id
group = galaxy.model.Group.get( group_id )
# Remove members and all associations
for user_group_assoc in group.users:
for user_group_assoc in group.members:
user = galaxy.model.User.get( user_group_assoc.user_id )
# Delete DefaultUserGroupAssociations
for default_user_group_association in user.default_groups:
lib/galaxy/web/framework/__init__.py
+1 -1
View File
@@ -24,7 +24,7 @@ import mako.lookup
pkg_resources.require( "simplejson" )
import simplejson
pkg_resources.require( "sqlalchemy>=0.3" )
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy import desc
import logging
lib/galaxy/webapps/reports/controllers/jobs.py
+1 -1
View File
@@ -5,7 +5,7 @@ import calendar
from galaxy.webapps.reports.base.controller import *
import galaxy.model
import pkg_resources
pkg_resources.require( "sqlalchemy>=0.3" )
pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
import logging
log = logging.getLogger( __name__ )
lib/galaxy/webapps/reports/controllers/system.py
+3 -2
View File
@@ -2,8 +2,9 @@ import operator, os
from datetime import datetime, timedelta
from galaxy.webapps.reports.base.controller import *
import pkg_resources
pkg_resources.require( "sqlalchemy>=0.3" )
from sqlalchemy import eagerload, desc
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy.orm import eagerload
from sqlalchemy import desc
import logging
log = logging.getLogger( __name__ )
lib/galaxy/webapps/reports/controllers/users.py
+1 -1
View File
@@ -3,7 +3,7 @@ import calendar
from galaxy.webapps.reports.base.controller import *
import galaxy.model
import pkg_resources
pkg_resources.require( "sqlalchemy>=0.3" )
pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
import logging
log = logging.getLogger( __name__ )
scripts/cleanup_datasets/cleanup_datasets.py
+2 -2
View File
@@ -13,8 +13,8 @@ from galaxy import eggs
import galaxy.model.mapping
import pkg_resources
pkg_resources.require( "sqlalchemy>=0.3" )
from sqlalchemy import eagerload
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy.orm import eagerload
assert sys.version_info[:2] >= ( 2, 4 )
test/functional/test_history_functions.py
+4 -1
View File
@@ -48,7 +48,10 @@ class TestHistory( TwillTestCase ):
"""Testing sharing a history with another user"""
self.upload_file('1.bed', dbkey='hg18')
id, name, email = self.share_history()
self.check_page_for_string( 'History (%s) has been shared with: %s' %(name, email) )
try:
self.check_page_for_string( 'History (%s) has been shared with: %s' %(name, email) )
except TwillAssertionError:
self.check_page_for_string( "The history or histories you've chosen to share contain datasets that the user you're sharing with does not have permission to access." )
self.logout()
self.login( email='test2@bx.psu.edu' )
self.view_stored_histories()
test/functional/test_security_and_libraries.py
+1 -1
View File
@@ -85,7 +85,7 @@ class TestHistory( TwillTestCase ):
def test_20_create_library( self ):
"""Testing creating new library"""
self.create_library( name='New Test Library', description='New test Library Description' )
self.create_library( name='New Test Library', description='New Test Library Description' )
self.visit_page( 'admin/libraries' )
self.check_page_for_string( "New Test Library" )
tools/stats/grouping.py
+1 -1
View File
@@ -90,7 +90,7 @@ def main():
for ii, line in enumerate( file( tmpfile.name )):
if line and not line.startswith( '#' ):
line = line.strip()
line = line.rstrip( '\r\n' )
try:
fields = line.split("\t")
item = fields[group_col]