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R3600/invenio/modules/upgrader/upgrades/invenio_2012_11_15_bibdocfile_model.py
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invenio_2012_11_15_bibdocfile_model.py
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# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2012, 2013 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later version.
#
# Invenio is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Invenio; if not, write to the Free Software Foundation, Inc.,
# 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
from invenio.legacy.dbquery import run_sql, OperationalError
from six.moves import cPickle
import logging
depends_on = ['invenio_release_1_1_0']
update_needed = True
def info():
return "Change of the underlying data model allowing extended BibDocs and MoreInfo"
def do_upgrade():
""" Implement your upgrades here """
logger = logging.getLogger('invenio_upgrader')
if update_needed:
_backup_tables(logger)
_update_database_structure_pre(logger)
recids = _retrieve_fulltext_recids()
for recid in recids:
if not _fix_recid(recid, logger):
logger.info("ERROR: Failed fixing the record %s" % (str(recid)))
_update_database_structure_post(logger)
else:
logger.info("Update executed but not needed. skipping")
def estimate():
""" Estimate running time of upgrade in seconds (optional). """
res = run_sql("select count(*) from bibdoc")
if res:
return int(float(res[0][0]) / 40)
return 0
def pre_upgrade():
""" Run pre-upgrade checks (optional). """
# Example of raising errors:
res = run_sql("show create table bibdoc")[0][1]
global update_needed
if not "more_info" in res:
update_needed = False
def post_upgrade():
""" Run post-upgrade checks (optional). """
# Example of issuing warnings:
# warnings.warn("A continuable error occurred")
pass
# private methods
def _update_database_structure_pre(logger):
"""This function alters the already existing database by adding additional columns ... the step from before modification"""
logger.info("Adding missing columns to tables")
try:
run_sql("ALTER TABLE bibdoc ADD COLUMN doctype varchar(255) AFTER more_info")
except Exception as e:
logger.info("WARNING: Problem when altering table. Is the database really in the state from before the upgrade ? " + str(e))
try:
run_sql("ALTER TABLE bibdoc CHANGE COLUMN docname docname varchar(250) COLLATE utf8_bin default NULL")
except Exception as e:
logger.info("WARNING: Problem when altering table. Is the database really in the state from before the upgrade ? " + str(e))
try:
run_sql("ALTER TABLE bibrec_bibdoc ADD COLUMN docname varchar(250) COLLATE utf8_bin NOT NULL default 'file' AFTER id_bibdoc, ADD KEY docname(docname)")
except Exception as e:
logger.info("WARNING: Problem when altering table. Is the database really in the state from before the upgrade ? " + str(e))
try:
run_sql("ALTER TABLE bibdoc_bibdoc CHANGE COLUMN id_bibdoc1 id_bibdoc1 mediumint(9) unsigned DEFAULT NULL")
run_sql("ALTER TABLE bibdoc_bibdoc CHANGE COLUMN id_bibdoc2 id_bibdoc2 mediumint(9) unsigned DEFAULT NULL")
run_sql("ALTER TABLE bibdoc_bibdoc ADD COLUMN id mediumint(9) unsigned NOT NULL auto_increment FIRST, ADD COLUMN version1 tinyint(4) unsigned AFTER id_bibdoc1, ADD COLUMN format1 varchar(50) AFTER version1, ADD COLUMN version2 tinyint(4) unsigned AFTER id_bibdoc2, ADD COLUMN format2 varchar(50) AFTER version2, CHANGE COLUMN type rel_type varchar(255) AFTER format2, ADD KEY (id)")
except Exception as e:
logger.info("WARNING: Problem when altering table. Is the database really in the state from before the upgrade ? " + str(e))
run_sql("""CREATE TABLE IF NOT EXISTS bibdocmoreinfo (
id_bibdoc mediumint(9) unsigned DEFAULT NULL,
version tinyint(4) unsigned DEFAULT NULL,
format VARCHAR(50) DEFAULT NULL,
id_rel mediumint(9) unsigned DEFAULT NULL,
namespace VARCHAR(25) DEFAULT NULL,
data_key VARCHAR(25),
data_value MEDIUMBLOB,
KEY (id_bibdoc, version, format, id_rel, namespace, data_key)
) ENGINE=MyISAM;""")
def _update_database_structure_post(logger):
"""This function alters the already existing database by removing columns ... the step after the modification"""
logger.info("Removing unnecessary columns from tables")
run_sql("ALTER TABLE bibdoc DROP COLUMN more_info")
def _backup_tables(logger):
"""This function create a backup of bibrec_bibdoc, bibdoc and bibdoc_bibdoc tables. Returns False in case dropping of previous table is needed."""
logger.info("droping old backup tables")
run_sql('DROP TABLE IF EXISTS bibrec_bibdoc_backup_newdatamodel')
run_sql('DROP TABLE IF EXISTS bibdoc_backup_newdatamodel')
run_sql('DROP TABLE IF EXISTS bibdoc_bibdoc_backup_newdatamodel')
try:
run_sql("""CREATE TABLE bibrec_bibdoc_backup_newdatamodel SELECT * FROM bibrec_bibdoc""")
run_sql("""CREATE TABLE bibdoc_backup_newdatamodel SELECT * FROM bibdoc""")
run_sql("""CREATE TABLE bibdoc_bibdoc_backup_newdatamodel SELECT * FROM bibdoc_bibdoc""")
except OperationalError as e:
logger.info("Problem when backing up tables")
raise
return True
def _retrieve_fulltext_recids():
"""Returns the list of all the recid number linked with at least a fulltext
file."""
res = run_sql('SELECT DISTINCT id_bibrec FROM bibrec_bibdoc')
return [int(x[0]) for x in res]
def _fix_recid(recid, logger):
"""Fix a given recid."""
#logger.info("Upgrading record %s:" % recid)
# 1) moving docname and type to the relation with bibrec
bibrec_docs = run_sql("select id_bibdoc, type from bibrec_bibdoc where id_bibrec=%s", (recid, ))
are_equal = True
for docid_str in bibrec_docs:
docid = str(docid_str[0])
doctype = str(docid_str[1])
#logger.info("Upgrading document %s:" % (docid, ))
res2 = run_sql("select docname, more_info from bibdoc where id=%s", (docid,))
if not res2:
logger.error("Error when migrating document %s attached to the record %s: can not retrieve from the bibdoc table " % (docid, recid))
else:
docname = str(res2[0][0])
run_sql("update bibrec_bibdoc set docname=%%s where id_bibrec=%s and id_bibdoc=%s" % (str(recid), docid), (docname, ))
run_sql("update bibdoc set doctype=%%s where id=%s" % (docid,), (doctype, ))
# 2) moving moreinfo to the new moreinfo structures (default namespace)
if res2[0][1]:
minfo = cPickle.loads(res2[0][1])
# 2a migrating descriptions->version->format
new_value = cPickle.dumps(minfo.get('descriptions', {}))
run_sql("INSERT INTO bibdocmoreinfo (id_bibdoc, namespace, data_key, data_value) VALUES (%s, %s, %s, %s)", (str(docid), "", "descriptions", new_value))
# 2b migrating comments->version->format
new_value = cPickle.dumps(minfo.get('comments', {}))
run_sql("INSERT INTO bibdocmoreinfo (id_bibdoc, namespace, data_key, data_value) VALUES (%s, %s, %s, %s)", (str(docid), "", "comments", new_value))
# 2c migrating flags->flagname->version->format
new_value = cPickle.dumps(minfo.get('flags', {}))
run_sql("INSERT INTO bibdocmoreinfo (id_bibdoc, namespace, data_key, data_value) VALUES (%s, %s, %s, %s)", (str(docid), "", "flags", new_value))
# 3) Verify the correctness of moreinfo transformations
try:
descriptions = cPickle.loads(run_sql("SELECT data_value FROM bibdocmoreinfo WHERE id_bibdoc=%s AND namespace=%s AND data_key=%s", (str(docid), '', 'descriptions'))[0][0])
for version in minfo.get('descriptions', {}):
for docformat in minfo['descriptions'][version]:
v1 = descriptions[version][docformat]
v2 = minfo['descriptions'][version][docformat]
if v1 != v2:
are_equal = False
logger.info("ERROR: Document %s: Expected description %s and got %s" % (str(docid), str(v2), str(v1)))
except Exception as e:
logger.info("ERROR: Document %s: Problem with retrieving descriptions: %s MoreInfo: %s Descriptions: %s" % (str(docid), str(e), str(minfo), str(descriptions)))
try:
comments = cPickle.loads(run_sql("SELECT data_value FROM bibdocmoreinfo WHERE id_bibdoc=%s AND namespace=%s AND data_key=%s", (str(docid), '', 'comments'))[0][0])
for version in minfo.get('comments', {}):
for docformat in minfo['comments'][version]:
v1 = comments[version][docformat]
v2 = minfo['comments'][version][docformat]
if v1 != v2:
are_equal = False
logger.info("ERROR: Document %s: Expected comment %s and got %s" % (str(docid), str(v2), str(v1)))
except Exception as e:
logger.info("ERROR: Document %s: Problem with retrieving comments: %s MoreInfo: %s Comments: %s" % (str(docid), str(e), str(minfo), str(comments)))
try:
flags = cPickle.loads(run_sql("SELECT data_value FROM bibdocmoreinfo WHERE id_bibdoc=%s AND namespace=%s AND data_key=%s", (str(docid), '', 'flags'))[0][0])
for flagname in minfo.get('flags', {}):
for version in minfo['flags'][flagname]:
for docformat in minfo['flags'][flagname][version]:
if minfo['flags'][flagname][version][docformat]:
are_equal = are_equal and (docformat in flags[flagname][version])
if not (docformat in flags[flagname][version]):
logger.info("ERROR: Document %s: Expected %s" % (str(docid), str(minfo) ))
except Exception as e:
logger.info("ERROR: Document %s: Problem with retrieving flags. %s MoreInfo: %s flags: %s" % (str(docid), str(e), str(minfo), str(flags)))
if not are_equal:
logger.info("Failed to move MoreInfo structures from old database to the new one docid: %s" % (str(docid),))
return are_equal
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