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Migrate central repo to alchemy 4.

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This commit is contained in:
Greg Von Kuster
2008-10-30 16:17:46 -04:00
parent aafccaa367
commit 5be8fefaf5
18 changed files with 147 additions and 78 deletions
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eggs.ini
+2 -2
View File
@@ -40,7 +40,7 @@ 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
@@ -85,7 +85,7 @@ 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
@@ -20,7 +20,7 @@ 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/jobs/__init__.py
+3 -4
View File
@@ -97,11 +97,10 @@ class JobQueue( object ):
model = self.app.model
# Jobs in the NEW state won't be requeued unless we're tracking in the database
if not self.track_jobs_in_database:
for job in model.Job.select( model.Job.c.state == model.Job.states.NEW ):
for job in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all():
log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id )
self.queue.put( ( job.id, job.tool_id ) )
for job in model.Job.select( (model.Job.c.state == model.Job.states.RUNNING)
| (model.Job.c.state == model.Job.states.QUEUED) ):
for job in model.Job.filter( (model.Job.c.state == model.Job.states.RUNNING) | (model.Job.c.state == model.Job.states.QUEUED) ).all():
if job.job_runner_name is not None:
# why are we passing the queue to the wrapper?
job_wrapper = JobWrapper( job.id, self.app.toolbox.tools_by_id[ job.tool_id ], self )
@@ -136,7 +135,7 @@ class JobQueue( object ):
new_jobs = []
if self.track_jobs_in_database:
model = self.app.model
for j in model.Job.select( model.Job.c.state == model.Job.states.NEW ):
for j in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all():
job = JobWrapper( j.id, self.app.toolbox.tools_by_id[ j.tool_id ], self )
new_jobs.append( job )
else:
lib/galaxy/model/custom_types.py
+8 -9
View File
@@ -18,16 +18,15 @@ 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:
@@ -60,10 +59,10 @@ 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) )
@@ -77,7 +76,7 @@ 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
+33 -33
View File
@@ -5,23 +5,20 @@ 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
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",
@@ -120,15 +117,15 @@ 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 ) ) )
@@ -188,7 +185,7 @@ 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 ),
)
@@ -197,7 +194,7 @@ 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 )
)
@@ -208,8 +205,8 @@ 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 ),
@@ -222,8 +219,8 @@ 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,
@@ -240,7 +237,7 @@ StoredWorkflowMenuEntry.table = Table( "stored_workflow_menu_entry", metadata,
MetadataFile.table = Table( "metadata_file", metadata,
Column( "id", Integer, primary_key=True ),
Column( "name", String ),
Column( "name", TEXT ),
Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
@@ -257,9 +254,7 @@ 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 ),
@@ -380,11 +375,12 @@ 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:
@@ -413,17 +409,21 @@ 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
return result
lib/galaxy/model/mapping_tests.py
+3 -3
View File
@@ -22,13 +22,13 @@ class MappingTests( unittest.TestCase ):
model.context.current.flush()
model.context.current.clear()
# Check
users = model.User.select()
users = model.User.query().all()
assert len( users ) == 1
assert users[0].email == "james@foo.bar.baz"
assert users[0].password == "password"
assert len( users[0].histories ) == 1
assert users[0].histories[0].name == "History 1"
hists = model.History.select()
hists = model.History.query().all()
assert hists[0].name == "History 1"
assert hists[1].name == ( "H" * 255 )
assert hists[0].user == users[0]
@@ -40,7 +40,7 @@ class MappingTests( unittest.TestCase ):
hists[1].name = "History 2b"
model.context.current.flush()
model.context.current.clear()
hists = model.History.select()
hists = model.History.query().all()
assert hists[0].name == "History 1"
assert hists[1].name == "History 2b"
# gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like.
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/root.py
+4 -4
View File
@@ -429,7 +429,7 @@ class RootController( BaseController ):
if not email:
return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err)
user = trans.get_user()
send_to_user = trans.app.model.User.get_by( email = email )
send_to_user = trans.app.model.User.filter_by( email=email ).first()
if not send_to_user:
send_to_err = "No such user"
elif user.email == email:
@@ -488,7 +488,7 @@ class RootController( BaseController ):
new_history.user_id = user.id
galaxy_session = trans.get_galaxy_session()
try:
association = trans.app.model.GalaxySessionToHistoryAssociation.selectone_by( session_id=galaxy_session.id, history_id=new_history.id )
association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first()
except:
association = None
new_history.add_galaxy_session( galaxy_session, association=association )
@@ -505,7 +505,7 @@ class RootController( BaseController ):
new_history.user_id = None
galaxy_session = trans.get_galaxy_session()
try:
association = trans.app.model.GalaxySessionToHistoryAssociation.selectone_by( session_id=galaxy_session.id, history_id=new_history.id )
association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first()
except:
association = None
new_history.add_galaxy_session( galaxy_session, association=association )
@@ -530,7 +530,7 @@ class RootController( BaseController ):
if new_history:
galaxy_session = trans.get_galaxy_session()
try:
association = trans.app.model.GalaxySessionToHistoryAssociation.selectone_by( session_id=galaxy_session.id, history_id=new_history.id )
association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first()
except:
association = None
new_history.add_galaxy_session( galaxy_session, association=association )
lib/galaxy/web/controllers/user.py
+4 -4
View File
@@ -53,7 +53,7 @@ class User( BaseController ):
email_err = "Please enter a real email address"
elif len( email) > 255:
email_err = "Email address exceeds maximum allowable length"
elif len( trans.app.model.User.select_by( email=email ) ) > 0:
elif trans.app.model.User.filter_by( email=email ).first():
email_err = "User with that email already exists"
elif email != conf_email:
conf_email_err = "Email addresses do not match."
@@ -73,7 +73,7 @@ class User( BaseController ):
email_error = password_error = None
# Attempt login
if email or password:
user = trans.app.model.User.get_by( email = email )
user = trans.app.model.User.filter_by( email=email ).first()
if not user:
email_error = "No such user"
elif user.external:
@@ -108,7 +108,7 @@ class User( BaseController ):
email_error = "Please enter a real email address"
elif len( email) > 255:
email_error = "Email address exceeds maximum allowable length"
elif len( trans.app.model.User.select_by( email=email ) ) > 0:
elif trans.app.model.User.filter_by( email=email ).first():
email_error = "User with that email already exists"
elif len( password ) < 6:
password_error = "Please use a password of at least 6 characters"
@@ -143,7 +143,7 @@ class User( BaseController ):
@web.expose
def reset_password(self, trans, email=None, **kwd):
error = ''
reset_user = trans.app.model.User.get_by( email = email )
reset_user = trans.app.model.User.filter_by( email=email ).first()
user = trans.get_user()
if reset_user:
if user and user.id != reset_user.id:
lib/galaxy/web/controllers/workflow.py
+1 -1
View File
@@ -44,7 +44,7 @@ class WorkflowController( BaseController ):
# Load workflow from database
stored = get_stored_workflow( trans, id )
if email:
other = model.User.get_by( email=email )
other = model.User.filter_by( email=email ).first()
if not other:
mtype = "error"
msg = ( "User '%s' does not exist" % email )
lib/galaxy/web/framework/__init__.py
+7 -7
View File
@@ -24,7 +24,7 @@ pkg_resources.require( "Mako" )
import mako.template
import mako.lookup
pkg_resources.require( "sqlalchemy>=0.3" )
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy import desc
import logging
@@ -172,7 +172,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
if secure_id:
session_key = self.security.decode_session_key( secure_id )
try:
galaxy_session = self.app.model.GalaxySession.selectone_by( session_key=session_key )
galaxy_session = self.app.model.GalaxySession.filter_by( session_key=session_key ).first()
if galaxy_session and galaxy_session.is_valid and galaxy_session.current_history_id:
history = self.app.model.History.get( galaxy_session.current_history_id )
if history and not history.deleted:
@@ -216,7 +216,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
galaxy_session.user_id = self.user.id
try:
# See if we have already associated the history with the session
association = self.app.model.GalaxySessionToHistoryAssociation.select_by( session_id=galaxy_session.id, history_id=history.id )[0]
association = self.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=history.id ).first()
except:
association = None
history.add_galaxy_session( galaxy_session, association=association )
@@ -265,7 +265,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
"""Return the user in $HTTP_REMOTE_USER and create if necessary"""
# remote_user middleware ensures HTTP_REMOTE_USER exists
try:
user = self.app.model.User.selectone_by( email=self.environ[ 'HTTP_REMOTE_USER' ] )
user = self.app.model.User.filter_by( email=self.environ[ 'HTTP_REMOTE_USER' ] ).first()
except:
user = self.app.model.User( email=self.environ[ 'HTTP_REMOTE_USER' ] )
user.set_password_cleartext( 'external' )
@@ -281,7 +281,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
if secure_id:
session_key = self.security.decode_session_key( secure_id )
try:
galaxy_session = self.app.model.GalaxySession.selectone_by( session_key=session_key )
galaxy_session = self.app.model.GalaxySession.filter_by( session_key=session_key ).first()
if galaxy_session and galaxy_session.is_valid and galaxy_session.user_id:
user = self.app.model.User.get( galaxy_session.user_id )
if user:
@@ -321,7 +321,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
session_key = self.security.decode_session_key( secure_id )
try:
# Retrive the galaxy_session id via the unique session_key
galaxy_session = self.app.model.GalaxySession.selectone_by( session_key=session_key )
galaxy_session = self.app.model.GalaxySession.filter_by( session_key=session_key ).first()
if galaxy_session and galaxy_session.is_valid:
self.__galaxy_session = galaxy_session
except:
@@ -382,7 +382,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
if self.history is not None:
# See if we have already associated the session with the history
try:
association = self.app.model.GalaxySessionToHistoryAssociation.select_by( session_id=galaxy_session.id, history_id=self.history.id )[0]
association = self.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=self.history.id ).first()
except:
association = None
galaxy_session.add_history( self.history, association=association )
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
+3 -5
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 )
@@ -191,8 +191,6 @@ def purge_histories( h, d, m, cutoff_time, remove_from_disk ):
if errmsg:
errors = True
print errmsg
else:
print "%s" % dataset.file_name
else:
dataset.purged = True
dataset.flush()
@@ -258,7 +256,6 @@ def purge_datasets( d, m, cutoff_time, remove_from_disk ):
print errmsg
else:
dataset_count += 1
print "%s" % dataset.file_name
else:
dataset.purged = True
dataset.file_size = 0
@@ -302,6 +299,7 @@ def purge_dataset( dataset, m ):
else:
# Remove dataset file from disk
os.unlink( dataset.file_name )
print "%s" % dataset.file_name
# Mark all associated MetadataFiles as deleted and purged and remove them from disk
print "The following metadata files associated with dataset '%s' have been purged" % dataset.file_name
for hda in dataset.history_associations:
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]