import os
import logging
from datetime import datetime, timedelta
from galaxy.web.base.controller import BaseUIController, web
from decimal import Decimal
from galaxy import model, util
from galaxy.model.orm import and_, desc, eagerload
log = logging.getLogger( __name__ )
[docs]class System( BaseUIController ):
@web.expose
[docs] def index( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
if params.userless_histories_days:
userless_histories_days = params.userless_histories_days
else:
userless_histories_days = '60'
if params.deleted_histories_days:
deleted_histories_days = params.deleted_histories_days
else:
deleted_histories_days = '60'
if params.deleted_datasets_days:
deleted_datasets_days = params.deleted_datasets_days
else:
deleted_datasets_days = '60'
file_path, disk_usage, datasets, file_size_str = self.disk_usage( trans, **kwd )
if 'action' in kwd:
if kwd['action'] == "userless_histories":
userless_histories_days, message = self.userless_histories( trans, **kwd )
elif kwd['action'] == "deleted_histories":
deleted_histories_days, message = self.deleted_histories( trans, **kwd )
elif kwd['action'] == "deleted_datasets":
deleted_datasets_days, message = self.deleted_datasets( trans, **kwd )
return trans.fill_template( '/webapps/reports/system.mako',
file_path=file_path,
disk_usage=disk_usage,
datasets=datasets,
file_size_str=file_size_str,
userless_histories_days=userless_histories_days,
deleted_histories_days=deleted_histories_days,
deleted_datasets_days=deleted_datasets_days,
message=message,
nice_size=nice_size )
[docs] def userless_histories( self, trans, **kwd ):
"""The number of userless histories and associated datasets that have not been updated for the specified number of days."""
params = util.Params( kwd )
message = ''
if params.userless_histories_days:
userless_histories_days = int( params.userless_histories_days )
cutoff_time = datetime.utcnow() - timedelta( days=userless_histories_days )
history_count = 0
dataset_count = 0
for history in trans.sa_session.query( model.History ) \
.filter( and_( model.History.table.c.user_id == None,
model.History.table.c.deleted == True,
model.History.table.c.update_time < cutoff_time ) ):
for dataset in history.datasets:
if not dataset.deleted:
dataset_count += 1
history_count += 1
message = "%d userless histories ( including a total of %d datasets ) have not been updated for at least %d days." %( history_count, dataset_count, userless_histories_days )
else:
message = "Enter the number of days."
return str( userless_histories_days ), message
[docs] def deleted_histories( self, trans, **kwd ):
"""
The number of histories that were deleted more than the specified number of days ago, but have not yet been purged.
Also included is the number of datasets associated with the histories.
"""
params = util.Params( kwd )
message = ''
if params.deleted_histories_days:
deleted_histories_days = int( params.deleted_histories_days )
cutoff_time = datetime.utcnow() - timedelta( days=deleted_histories_days )
history_count = 0
dataset_count = 0
disk_space = 0
histories = trans.sa_session.query( model.History ) \
.filter( and_( model.History.table.c.deleted == True,
model.History.table.c.purged == False,
model.History.table.c.update_time < cutoff_time ) ) \
.options( eagerload( 'datasets' ) )
for history in histories:
for hda in history.datasets:
if not hda.dataset.purged:
dataset_count += 1
try:
disk_space += hda.dataset.file_size
except:
pass
history_count += 1
message = "%d histories ( including a total of %d datasets ) were deleted more than %d days ago, but have not yet been purged, " \
"disk space: %s." % ( history_count, dataset_count, deleted_histories_days, nice_size( disk_space, True ) )
else:
message = "Enter the number of days."
return str( deleted_histories_days ), message
[docs] def deleted_datasets( self, trans, **kwd ):
"""The number of datasets that were deleted more than the specified number of days ago, but have not yet been purged."""
params = util.Params( kwd )
message = ''
if params.deleted_datasets_days:
deleted_datasets_days = int( params.deleted_datasets_days )
cutoff_time = datetime.utcnow() - timedelta( days=deleted_datasets_days )
dataset_count = 0
disk_space = 0
for dataset in trans.sa_session.query( model.Dataset ) \
.filter( and_( model.Dataset.table.c.deleted == True,
model.Dataset.table.c.purged == False,
model.Dataset.table.c.update_time < cutoff_time ) ):
dataset_count += 1
try:
disk_space += dataset.file_size
except:
pass
message = "%d datasets were deleted more than %d days ago, but have not yet been purged," \
" disk space: %s." % ( dataset_count, deleted_datasets_days, nice_size( disk_space, True ))
else:
message = "Enter the number of days."
return str( deleted_datasets_days ), message
@web.expose
[docs] def dataset_info( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
dataset = trans.sa_session.query( model.Dataset ).get( trans.security.decode_id( kwd.get( 'id', '' ) ) )
# Get all associated hdas and lddas that use the same disk file.
associated_hdas = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \
.filter( and_( trans.model.HistoryDatasetAssociation.deleted == False,
trans.model.HistoryDatasetAssociation.dataset_id == dataset.id ) ) \
.all()
associated_lddas = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ) \
.filter( and_( trans.model.LibraryDatasetDatasetAssociation.deleted == False,
trans.model.LibraryDatasetDatasetAssociation.dataset_id == dataset.id ) ) \
.all()
return trans.fill_template( '/webapps/reports/dataset_info.mako',
dataset=dataset,
associated_hdas=associated_hdas,
associated_lddas=associated_lddas,
message=message )
[docs] def get_disk_usage( self, file_path ):
df_cmd = 'df -h ' + file_path
is_sym_link = os.path.islink( file_path )
file_system = disk_size = disk_used = disk_avail = disk_cap_pct = mount = None
df_file = os.popen( df_cmd )
while True:
df_line = df_file.readline()
df_line = df_line.strip()
if df_line:
df_line = df_line.lower()
if 'filesystem' in df_line or 'proc' in df_line:
continue
elif is_sym_link:
if ':' in df_line and '/' in df_line:
mount = df_line
else:
try:
disk_size, disk_used, disk_avail, disk_cap_pct, file_system = df_line.split()
break
except:
pass
else:
try:
file_system, disk_size, disk_used, disk_avail, disk_cap_pct, mount = df_line.split()
break
except:
pass
else:
break # EOF
df_file.close()
return ( file_system, disk_size, disk_used, disk_avail, disk_cap_pct, mount )
@web.expose
[docs] def disk_usage( self, trans, **kwd ):
file_path = trans.app.config.file_path
disk_usage = self.get_disk_usage( file_path )
min_file_size = 2**32 # 4 Gb
file_size_str = nice_size( min_file_size )
datasets = trans.sa_session.query( model.Dataset ) \
.filter( and_( model.Dataset.table.c.purged == False,
model.Dataset.table.c.file_size > min_file_size ) ) \
.order_by( desc( model.Dataset.table.c.file_size ) )
return file_path, disk_usage, datasets, file_size_str
[docs]def nice_size(size, include_bytes=False):
"""Returns a readably formatted string with the size"""
niced = False
nice_string = "%s bytes" % size
try:
nsize = Decimal(size)
for x in ['bytes','KB','MB','GB']:
if nsize.compare(Decimal("1024.0")) == Decimal("-1"):
nice_string = "%3.1f %s" % (nsize, x)
niced = True
break
nsize /= Decimal("1024.0")
if not niced:
nice_string = "%3.1f %s" % (nsize, 'TB')
niced = True
if include_bytes and x != 'bytes':
nice_string = "%s (%s bytes)" % (nice_string, size)
except:
pass
return nice_string