Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.webapps.reports.controllers.system

import logging
import os
import subprocess
from datetime import datetime, timedelta
from decimal import Decimal

from sqlalchemy import and_, desc, false, null, true
from sqlalchemy.orm import eagerload

from galaxy.web.base.controller import BaseUIController, web
from galaxy import model, util

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.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
[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): is_sym_link = os.path.islink(file_path) file_system = disk_size = disk_used = disk_avail = disk_cap_pct = mount = None df_output = subprocess.check_output(['df', '-h', file_path]) for df_line in df_output: 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 return (file_system, disk_size, disk_used, disk_avail, disk_cap_pct, mount)
[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 = "%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