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engine_utils.py
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# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015 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.
"""bibindex.engine_utils: here are some useful regular experssions for tokenizers
and several helper functions.
"""
import re
import sys
from invenio.base.helpers import utf8ifier
from invenio.legacy.dbquery import run_sql, \
DatabaseError
from invenio.legacy.bibsched.bibtask import write_message
from invenio.legacy.bibrecord import get_fieldvalues
from invenio.config import \
CFG_BIBINDEX_CHARS_PUNCTUATION, \
CFG_BIBINDEX_CHARS_ALPHANUMERIC_SEPARATORS
from invenio.legacy.bibindex.engine_config import CFG_BIBINDEX_COLUMN_VALUE_SEPARATOR
latex_formula_re = re.compile(r'\$.*?\$|\\\[.*?\\\]')
phrase_delimiter_re = re.compile(r'[\.:;\?\!]')
space_cleaner_re = re.compile(r'\s+')
re_block_punctuation_begin = re.compile(r"^" + CFG_BIBINDEX_CHARS_PUNCTUATION + "+")
re_block_punctuation_end = re.compile(CFG_BIBINDEX_CHARS_PUNCTUATION + "+$")
re_punctuation = re.compile(CFG_BIBINDEX_CHARS_PUNCTUATION)
re_separators = re.compile(CFG_BIBINDEX_CHARS_ALPHANUMERIC_SEPARATORS)
re_arxiv = re.compile(r'^arxiv:\d\d\d\d\.\d\d\d\d')
re_pattern_fuzzy_author_trigger = re.compile(r'[\s\,\.]')
# FIXME: re_pattern_fuzzy_author_trigger could be removed and an
# BibAuthorID API function could be called instead after we
# double-check that there are no circular imports.
def load_tokenizers():
"""
Load all the bibindex tokenizers and returns it.
"""
import warnings
warnings.warn("The function is deprecated. Please use the "
"`load_tokenizers()` from `invenio.modules.indexer.utils`",
DeprecationWarning)
from invenio.modules.indexer.registry import tokenizers
return dict((module.__name__.split('.')[-1],
getattr(module, module.__name__.split('.')[-1], ''))
for module in tokenizers)
def get_all_index_names_and_column_values(column_name):
"""Returns a list of tuples of name and another column of all defined words indexes.
Returns empty list in case there are no tags indexed in this index or in case
the column name does not exist.
Example: output=[('global', something), ('title', something)]."""
out = []
query = """SELECT name, %s FROM idxINDEX""" % column_name
try:
res = run_sql(query)
for row in res:
out.append((row[0], row[1]))
except DatabaseError:
write_message("Exception caught for SQL statement: %s; column %s might not exist" % (query, column_name), sys.stderr)
return out
def get_all_synonym_knowledge_bases():
"""Returns a dictionary of name key and knowledge base name and match type tuple value
information of all defined words indexes that have knowledge base information.
Returns empty dictionary in case there are no tags indexed.
Example: output['global'] = ('INDEX-SYNONYM-TITLE', 'exact'), output['title'] = ('INDEX-SYNONYM-TITLE', 'exact')."""
res = get_all_index_names_and_column_values("synonym_kbrs")
out = {}
for row in res:
kb_data = row[1]
# ignore empty strings
if len(kb_data):
out[row[0]] = tuple(kb_data.split(CFG_BIBINDEX_COLUMN_VALUE_SEPARATOR))
return out
def get_index_remove_stopwords(index_id):
"""Returns value of a remove_stopword field from idxINDEX database table
if it's not 'No'. If it's 'No' returns False.
Just for consistency with WordTable.
@param index_id: id of the index
"""
try:
result = run_sql("SELECT remove_stopwords FROM idxINDEX WHERE ID=%s", (index_id, ))[0][0]
except:
return False
if result == 'No' or result == '':
return False
return result
def get_index_remove_html_markup(index_id):
""" Gets remove_html_markup parameter from database ('Yes' or 'No') and
changes it to True, False.
Just for consistency with WordTable."""
try:
result = run_sql("SELECT remove_html_markup FROM idxINDEX WHERE ID=%s", (index_id, ))[0][0]
except:
return False
if result == 'Yes':
return True
return False
def get_index_remove_latex_markup(index_id):
""" Gets remove_latex_markup parameter from database ('Yes' or 'No') and
changes it to True, False.
Just for consistency with WordTable."""
try:
result = run_sql("SELECT remove_latex_markup FROM idxINDEX WHERE ID=%s", (index_id, ))[0][0]
except:
return False
if result == 'Yes':
return True
return False
def author_name_requires_phrase_search(p):
"""
Detect whether author query pattern p requires phrase search.
Notably, look for presence of spaces and commas.
"""
if re_pattern_fuzzy_author_trigger.search(p):
return True
return False
def get_field_count(recID, tags):
"""
Return number of field instances having TAGS in record RECID.
@param recID: record ID
@type recID: int
@param tags: list of tags to count, e.g. ['100__a', '700__a']
@type tags: list
@return: number of tags present in record
@rtype: int
@note: Works internally via getting field values, which may not be
very efficient. Could use counts only, or else retrieve stored
recstruct format of the record and walk through it.
"""
out = 0
for tag in tags:
out += len(get_fieldvalues(recID, tag))
return out
def run_sql_drop_silently(query):
"""
SQL DROP statement with IF EXISTS part generates
warning if table does not exist. To mute the warning
we can remove IF EXISTS and catch SQL exception telling
us that table does not exist.
"""
try:
query = query.replace(" IF EXISTS", "")
run_sql(query)
except Exception as e:
if str(e).find("Unknown table") > -1:
pass
else:
raise e
from invenio.modules.indexer.utils import get_idx_indexer
def get_all_indexes(virtual=True, with_ids=False):
"""Returns the list of the names of all defined words indexes.
Returns empty list in case there are no tags indexed in this index.
@param virtual: if True function will return also virtual indexes
@param with_ids: if True function will return also IDs of found indexes
Example: output=['global', 'author']."""
out = []
if virtual:
query = """SELECT %s name FROM idxINDEX"""
query = query % (with_ids and "id," or "")
else:
query = """SELECT %s w.name FROM idxINDEX AS w
WHERE w.id NOT IN (SELECT DISTINCT id_virtual FROM idxINDEX_idxINDEX)"""
query = query % (with_ids and "w.id," or "")
res = run_sql(query)
if with_ids:
out = [row for row in res]
else:
out = [row[0] for row in res]
return out
def get_all_virtual_indexes():
""" Returns all defined 'virtual' indexes. """
query = """SELECT DISTINCT v.id_virtual, w.name FROM idxINDEX_idxINDEX AS v,
idxINDEX AS w
WHERE v.id_virtual=w.id"""
res = run_sql(query)
return res
def get_index_virtual_indexes(index_id):
"""Returns 'virtual' indexes that should be indexed together with
given index."""
query = """SELECT v.id_virtual, w.name FROM idxINDEX_idxINDEX AS v,
idxINDEX AS w
WHERE v.id_virtual=w.id AND
v.id_normal=%s"""
res = run_sql(query, (index_id,))
return res
def is_index_virtual(index_id):
"""Checks if index is virtual"""
query = """SELECT id_virtual FROM idxINDEX_idxINDEX
WHERE id_virtual=%s"""
res = run_sql(query, (index_id,))
if res:
return True
return False
def filter_for_virtual_indexes(index_list):
"""
Function removes all non-virtual indexes
from given list of indexes.
@param index_list: list of index names
"""
try:
virtual = zip(*get_all_virtual_indexes())[1]
selected = set(virtual) & set(index_list)
return list(selected)
except IndexError:
return []
return []
def get_virtual_index_building_blocks(index_id):
"""Returns indexes that made up virtual index of given index_id.
If index_id is an id of normal index (not virtual) returns
empty tuple.
"""
query = """SELECT v.id_normal, w.name FROM idxINDEX_idxINDEX AS v,
idxINDEX AS w
WHERE v.id_normal=w.id AND
v.id_virtual=%s"""
res = run_sql(query, (index_id,))
return res
def get_index_id_from_index_name(index_name):
"""Returns the words/phrase index id for INDEXNAME.
Returns empty string in case there is no words table for this index.
Example: field='author', output=4."""
out = 0
query = """SELECT w.id FROM idxINDEX AS w
WHERE w.name=%s LIMIT 1"""
res = run_sql(query, (index_name,), 1)
if res:
out = res[0][0]
return out
def get_index_name_from_index_id(index_id):
"""Returns the words/phrase index name for INDEXID.
Returns '' in case there is no words table for this indexid.
Example: field=9, output='fulltext'."""
res = run_sql("SELECT name FROM idxINDEX WHERE id=%s", (index_id,))
if res:
return res[0][0]
return ''
def get_field_tags(field, tagtype="marc"):
"""Returns a list of tags for the field code 'field'. Works
for both MARC and nonMARC tags.
Returns empty list in case of error.
Example: field='author', output=['100__%','700__%'].
@param tagtype: can be: "marc" or "nonmarc", default value
is "marc" for backward compatibility
"""
out = []
query = """SELECT t.%s FROM tag AS t,
field_tag AS ft,
field AS f
WHERE f.code=%%s AND
ft.id_field=f.id AND
t.id=ft.id_tag
ORDER BY ft.score DESC"""
if tagtype == "marc":
query = query % "value"
res = run_sql(query, (field,))
return [row[0] for row in res]
else:
query = query % "recjson_value"
res = run_sql(query, (field,))
values = []
for row in res:
if row[0] is not None:
values.extend(row[0].split(","))
return values
def get_marc_tag_indexes(tag, virtual=True):
"""Returns indexes names and ids corresponding to the given tag
@param tag: MARC tag in one of the forms:
'xx%', 'xxx', 'xxx__a', 'xxx__%'
@param virtual: if True function will also return virtual indexes"""
tag2 = tag[0:2] + "%" #for tags in the form: 10%
tag3 = tag[:-1] + "%" #for tags in the form: 100__%
query = """SELECT DISTINCT w.id,w.name FROM idxINDEX AS w,
idxINDEX_field AS wf,
field_tag AS ft,
tag as t
WHERE (t.value=%%s OR
t.value=%%s OR
%s) AND
t.id=ft.id_tag AND
ft.id_field=wf.id_field AND
wf.id_idxINDEX=w.id"""
if tag[-1] == "%":
missing_piece = "t.value LIKE %s"
elif tag[-1] != "%" and len(tag) == 3:
missing_piece = "t.value LIKE %s"
tag3 = tag + "%" #for all tags which start from 'tag'
else:
missing_piece = "t.value=%s"
query = query % missing_piece
res = run_sql(query, (tag, tag2, tag3))
if res:
if virtual:
response = list(res)
index_ids = map(str, zip(*res)[0])
query = """SELECT DISTINCT v.id_virtual,w.name FROM idxINDEX_idxINDEX AS v,
idxINDEX as w
WHERE v.id_virtual=w.id AND
v.id_normal IN ("""
query = query + ", ".join(index_ids) + ")"
response.extend(run_sql(query))
return tuple(response)
return res
return ()
def get_nonmarc_tag_indexes(nonmarc_tag, virtual=True):
"""Returns index names and ids corresponding to the given nonmarc tag
(nonmarc tag can be also called 'bibfield field').
If param 'virtual' is set to True function will also return
virtual indexes"""
query = """SELECT DISTINCT w.id, w.name FROM idxINDEX AS w,
idxINDEX_field AS wf,
field_tag AS ft,
tag as t
WHERE (t.recjson_value LIKE %s OR
t.recjson_value LIKE %s OR
t.recjson_value LIKE %s OR
t.recjson_value=%s) AND
t.id=ft.id_tag AND
ft.id_field=wf.id_field AND
wf.id_idxINDEX=w.id"""
at_the_begining = nonmarc_tag + ',%%'
in_the_middle = '%%,' + nonmarc_tag + ',%%'
at_the_end = '%%,' + nonmarc_tag
res = run_sql(query, (at_the_begining, in_the_middle, at_the_end, nonmarc_tag))
if res:
if virtual:
response = list(res)
index_ids = map(str, zip(*res)[0])
query = """SELECT DISTINCT v.id_virtual,w.name FROM idxINDEX_idxINDEX AS v,
idxINDEX as w
WHERE v.id_virtual=w.id AND
v.id_normal IN ("""
query = query + ", ".join(index_ids) + ")"
response.extend(run_sql(query))
return tuple(response)
return res
return ()
def get_index_tags(indexname, virtual=True, tagtype="marc"):
"""Returns the list of tags that are indexed inside INDEXNAME.
Returns empty list in case there are no tags indexed in this index.
Note: uses get_field_tags() defined before.
Example: field='author', output=['100__%', '700__%'].
@param tagtype: can be: "marc" or "nonmarc", default value
is "marc" for backward compatibility
"""
out = []
query = """SELECT f.code FROM idxINDEX AS w,
idxINDEX_field AS wf,
field AS f
WHERE w.name=%s AND
w.id=wf.id_idxINDEX AND
f.id=wf.id_field"""
res = run_sql(query, (indexname,))
for row in res:
out.extend(get_field_tags(row[0], tagtype))
if not out and virtual:
index_id = get_index_id_from_index_name(indexname)
try:
dependent_indexes = map(str, zip(*get_virtual_index_building_blocks(index_id))[0])
except IndexError:
return out
tags = set()
query = """SELECT DISTINCT f.code FROM idxINDEX AS w, idxINDEX_field AS wf, field AS f
WHERE w.id=wf.id_idxINDEX AND
f.id=wf.id_field AND
w.id IN ("""
query = query + ", ".join(dependent_indexes) + ")"
res = run_sql(query)
for row in res:
tags |= set(get_field_tags(row[0], tagtype))
out = list(tags)
out = [tag for tag in out if tag]
return out
def get_min_last_updated(indexes):
"""Returns min modification date for 'indexes':
min(last_updated)
@param indexes: list of indexes
"""
query= """SELECT min(last_updated) FROM idxINDEX WHERE name IN ("""
for index in indexes:
query += "%s,"
query = query[:-1] + ")"
res = run_sql(query, tuple(indexes))
return res
def remove_inexistent_indexes(indexes, leave_virtual=False):
"""Removes indexes that don't exist from the given list of indexes.
@param indexes: list of indexes
@param leave_virtual: should we leave virtual indexes in the list?
"""
correct_indexes = get_all_indexes(leave_virtual)
cleaned = []
for index in indexes:
if index in correct_indexes:
cleaned.append(index)
return cleaned
def get_records_range_for_index(index_id):
"""
Get records range for given index.
"""
try:
query = """SELECT min(id_bibrec), max(id_bibrec) FROM idxWORD%02dR""" % index_id
resp = run_sql(query)
if resp:
return resp[0]
return None
except Exception:
return None
def make_prefix(index_name):
"""
Creates a prefix for specific index which is added
to every word from this index stored in reversed table
of corresponding virtual index.
@param index_name: name of the dependent index we want to create prefix for
"""
return "__" + index_name + "__"
class UnknownTokenizer(Exception):
pass
def list_union(list1, list2):
"Returns union of the two lists."
union_dict = {}
for e in list1:
union_dict[e] = 1
for e in list2:
union_dict[e] = 1
return union_dict.keys()
def get_index_fields(index_id):
"""Returns fields that are connected to index specified by
index_id.
"""
query = """SELECT f.id, f.name FROM field as f,
idxINDEX as w,
idxINDEX_field as wf
WHERE f.id=wf.id_field AND
wf.id_idxINDEX=w.id AND
w.id=%s
"""
index_fields = run_sql(query, (index_id, ) )
return index_fields
def recognize_marc_tag(tag):
"""Checks if tag is a MARC tag or not"""
tag_len = len(tag)
if 3 <= tag_len <= 6 and tag[0:3].isdigit():
return True
if tag_len == 3 and tag[0:2].isdigit() and tag[2] == '%':
return True
return False
def _is_collection(subfield):
"""Checks if a type is a collection;
get_values_recursively internal function."""
return hasattr(subfield, '__iter__')
def _get_values(subfield):
"""Returns values of a subfield suitable for later tokenizing;
get_values_recursively internal function."""
if type(subfield) == dict:
return subfield.values()
else:
return subfield
def get_values_recursively(subfield, phrases):
"""Finds all values suitable for later tokenizing in
field/subfield of bibfield record.
@param subfield: name of the field/subfield
@param phrases: container for phrases (for example empty list)
FIXME: move this function to bibfield!
As soon as possible. Note that journal tokenizer
also needs to be changed.
"""
if _is_collection(subfield):
for s in _get_values(subfield):
get_values_recursively(s, phrases)
elif subfield is not None:
phrases.append(utf8ifier(subfield))

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