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Source code for galaxy.webapps.reports.controllers.system
import logging
import shutil
from datetime import datetime, timedelta
from decimal import Decimal
from sqlalchemy import and_, desc, false, null, true
from sqlalchemy.orm import eagerload
from galaxy import model, util
from galaxy.webapps.base.controller import BaseUIController, web
log = logging.getLogger(__name__)
[docs]class System(BaseUIController):
[docs] @web.expose
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 == null(),
model.History.table.c.deleted == true(),
model.History.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.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 Exception:
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 Exception:
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
[docs] @web.expose
def dataset_info(self, trans, **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):
disk_usage = shutil.disk_usage(file_path)
pct_used = round(disk_usage.used / disk_usage.total * 100, 2)
return (nice_size(disk_usage.total), nice_size(disk_usage.used), nice_size(disk_usage.free), pct_used)
[docs] @web.expose
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 = f"{nsize:3.1f} {x}"
niced = True
break
nsize /= Decimal("1024.0")
if not niced:
nice_string = "{:3.1f} {}".format(nsize, 'TB')
niced = True
if include_bytes and x != 'bytes':
nice_string = f"{nice_string} ({size} bytes)"
except Exception:
pass
return nice_string