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bibmatch_engine.py
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bibmatch_engine.py
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## $Id$
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS 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.
##
## CDS 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 CDS Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
"""BibMatch tool to match records with database content."""
__revision__ = "$Id$"
import fileinput
import string
import os
import sys
import getopt
from invenio.config import \
CFG_BINDIR, \
CFG_VERSION
from invenio.search_engine import perform_request_search
from invenio.bibrecord import *
from invenio import bibconvert
from invenio.dbquery import run_sql
def usage():
"""Print help"""
print >> sys.stderr, \
""" Usage: %s [options]
Examples:
$ bibmatch [--print-new] --field=\"title\" < input.xml > output.xml
$ bibmatch --print-match --field=\"245__a\" --mode=\"a\" < input.xml > output.xml
$ bibmatch --print-ambiguous --query-string=\"245__a||100__a\" < input.xml > output.xml
$bibmatch [options] < input.xml > output.xml
Options:
Output:
-0 --print-new (default)
-1 --print-match
-2 --print-ambiguous
-b --batch-output=(filename)
Simple query:
-f --field=(field)
Advanced query:
-c --config=(config-filename)
-q --query-string=(uploader_querystring)
-m --mode=(a|e|o|p|r)[3]
-o --operator=(a|o)[2]
General options:
-h, --help print this help and exit
-V, --version print version information and exit
-v, --verbose=LEVEL verbose level (from 0 to 9, default 1)
""" % sys.argv[0]
sys.exit(1)
return
class Querystring:
"Holds the information about querystring (p1,f1,m1,op1,p2,f2,m2,op2,p3,f3,m3,as)."
def __init__(self, mode="1"):
"""Creates querystring instance"""
self.pattern = []
self.field = []
self.mode = []
self.operator = []
self.format = []
self.pattern.append("")
self.pattern.append("")
self.pattern.append("")
self.field.append("")
self.field.append("")
self.field.append("")
self.mode.append("")
self.mode.append("")
self.mode.append("")
self.operator.append("")
self.operator.append("")
self.format.append([])
self.format.append([])
self.format.append([])
self.advanced = 0
return
def from_qrystr(self, qrystr="", search_mode="eee", operator="aa"):
"""Converts qrystr into querystring (uploader format)"""
self.default()
self.field = []
self.format = []
self.mode = ["e","e","e"]
fields = string.split(qrystr,"||")
for field in fields:
tags = string.split(field, "::")
i = 0
format = []
for tag in tags:
if(i==0):
self.field.append(tag)
else:
format.append(tag)
i +=1
self.format.append(format)
while(len(self.format) < 3):
self.format.append("")
while(len(self.field) < 3):
self.field.append("")
i = 0
for lett in search_mode:
self.mode[i] = lett
i += 1
i = 0
for lett in operator:
self.operator[i] = lett
i += 1
return
def default(self):
self.pattern = []
self.field = []
self.mode = []
self.operator = []
self.format = []
self.pattern.append("")
self.pattern.append("")
self.pattern.append("")
self.field.append("245__a")
self.field.append("")
self.field.append("")
self.mode.append("a")
self.mode.append("")
self.mode.append("")
self.operator.append("")
self.operator.append("")
self.format.append([])
self.format.append([])
self.format.append([])
self.advanced = 1
return
def change_search_mode(self, mode="a"):
self.mode = [mode,mode,mode]
return
def search_engine_encode(self):
field_ = []
for field in self.field:
i = 0
field__ = ""
for letter in field:
if(letter == "%"):
if(i==5):
letter = "a"
else:
letter = "_"
i+=1
field__ += str(letter)
field_.append(field__)
self.field = field_
return
def get_field_tags(field):
"Gets list of field 'field' for the record with 'sysno' system number from the database."
query = "select tag.value from tag left join field_tag on tag.id=field_tag.id_tag left join field on field_tag.id_field=field.id where field.code='%s'" % field;
out = []
res = run_sql(query)
for row in res:
out.append(row[0])
return out
def get_subfield(field, subfield):
"Return subfield of a field."
for sbf in field:
if(sbf[0][0][0] == subfield):
return sbf[0][0][1]
return ""
def matched_records(recID_lists):
"Analyze list of matches. Ambiguous record result is always preferred."
recID_tmp = []
for recID_list in recID_lists:
if(len(recID_list) > 1):
return 2
if(len(recID_list) == 1):
if(len(recID_tmp) == 0):
recID_tmp.append(recID_list[0])
else:
if(recID_list[0] in recID_tmp):
pass
else:
return 2
if(len(recID_tmp) == 1):
return 1
return 0
def matched_records_min(recID_lists):
"Analyze lists of matches. New record result is preferred if result is unmatched."
min = 2
for recID_list in recID_lists:
if(len(recID_list) < min):
min = len(recID_list)
if(min==1):
return min
return min
def matched_records_max(recID_lists):
"Analyze lists of matches. Ambiguous result is preferred if result is unmatched."
max = 0
for recID_list in recID_lists:
if(len(recID_list) == 1):
return 1
if(len(recID_list) > max):
max = len(recID_list)
if (max > 1):
return 2
elif (max == 1):
return 1
else:
return 0
return 2
def main():
# Record matches database content when defined search gives exactly one record in the result set.
# By default the match is done on the title field.
# Using advanced search only 3 fields can be queried concurrently
# qrystr - querystring in the UpLoader format
try:
opts, args = getopt.getopt(sys.argv[1:],"012hVm:f:q:c:nv:o:b:",
[
"print-new",
"print-match",
"print-ambiguous",
"help",
"version",
"mode=",
"field=",
"query-string=",
"config=",
"no-process",
"verbose=",
"operator=",
"batch-output="
])
except getopt.GetoptError, e:
usage()
recs_out = []
recID_list = []
recID_lists = []
qrystrs = []
match_mode = 0 # default match mode to print new records
rec_new = 0 # indicator that record is new
rec_match = 0 # indicator that record is matched
matched = 0 # number of records matched
record_counter = 0 # number of records processed
noprocess = 0
result = [0,0,0]
perform_request_search_mode = "eee"
operator = "aa"
verbose = 1 # 0..be quiet
level = 1 # 1..exact match
file_read = ""
records = []
batch_output = ""
predefined_fields = ["title", "author"]
for opt, opt_value in opts:
if opt in ["-0", "--print-new"]:
match_mode = 0
if opt in ["-1", "--print-match"]:
match_mode = 1
if opt in ["-2", "--print-ambiguous"]:
match_mode = 2
if opt in ["-n", "--no-process"]:
noprocess = 1
if opt in ["-h", "--help"]:
usage()
sys.exit(0)
if opt in ["-V", "--version"]:
print __revision__
sys.exit(0)
if opt in ["-v", "--verbose"]:
verbose = int(opt_value)
if opt in ["-q", "--query-string"]:
qrystrs.append(opt_value)
if opt in ["-m", "--mode"]:
perform_request_search_mode = opt_value
if opt in ["-o", "--operator"]:
operator = opt_value
if opt in ["-b", "--batch-output"]:
batch_output = opt_value
if opt in ["-f", "--field"]:
alternate_querystring = []
if opt_value in predefined_fields:
alternate_querystring = get_field_tags(opt_value)
for item in alternate_querystring:
qrystrs.append(item)
else:
qrystrs.append(opt_value)
if opt in ["-c", "--config"]:
config_file = opt_value
config_file_read = bibconvert.read_file(config_file, 0)
for line in config_file_read:
tmp = string.split(line, "---")
if(tmp[0] == "QRYSTR"):
qrystrs.append(tmp[1])
if verbose:
sys.stderr.write("\nBibMatch: Parsing input file ... ")
for line_in in sys.stdin:
file_read += line_in
records = create_records(file_read)
if len(records) == 0:
if verbose:
sys.stderr.write("\nBibMatch: Input file contains no records.\n")
sys.exit()
else:
if verbose:
sys.stderr.write("read %d records" % len(records))
sys.stderr.write("\nBibMatch: Matching ...")
### Prepare batch output
if (batch_output != ""):
out_0 = []
out_1 = []
out_2 = []
for rec in records:
### for each query-string
record_counter += 1
if (verbose > 1):
sys.stderr.write("\n Processing record: #%d .." % record_counter)
recID_lists = []
if(len(qrystrs)==0):
qrystrs.append("")
more_detailed_info = ""
for qrystr in qrystrs:
querystring = Querystring()
querystring.default()
if(qrystr != ""):
querystring.from_qrystr(qrystr, perform_request_search_mode, operator)
else:
querystring.default()
### search engine qrystr encode
querystring.search_engine_encode()
### get field values
inst = []
### get appropriate corresponding fields from database
i = 0
for field in querystring.field:
### use expanded tags
tag = field[0:3]
ind1 = field[3:4]
ind2 = field[4:5]
code = field[5:6]
if((ind1 == "_")or(ind1 == "%")):
ind1 = ""
if((ind2 == "_")or(ind2 == "%")):
ind2 = ""
if((code == "_")or(code == "%")):
code = "a"
if(field != "001"):
sbf = get_subfield(record_get_field_instances(rec[0], tag, ind1, ind2), code)
inst.append(sbf)
elif(field in ["001"]):
sbf = record_get_field_values(rec[0], field, ind1="", ind2="", code="")
inst.append(sbf)
else:
inst.append("")
i += 1
### format acquired field values
i = 0
for instance in inst:
for format in querystring.format[i]:
inst[i] = bibconvert.FormatField(inst[i],format)
i += 1
### perform sensible request search only
if(inst[0]!=""):
recID_list = perform_request_search(
p1=inst[0], f1=querystring.field[0], m1=querystring.mode[0], op1=querystring.operator[0],
p2=inst[1], f2=querystring.field[1], m2=querystring.mode[1], op2=querystring.operator[1],
p3=inst[2], f3=querystring.field[2], m3=querystring.mode[2], as=querystring.advanced)
else:
recID_list = []
recID_lists.append(recID_list)
### more detailed info ...
if(verbose > 8):
more_detailed_info = "%s\n Matched recIDs: %s" % (more_detailed_info, recID_lists)
if(verbose > 2):
more_detailed_info = "%s\n On query: %s, %s, %s, %s\n %s, %s, %s, %s\n %s, %s, %s\n" % (more_detailed_info, inst[0], querystring.field[0], querystring.mode[0], querystring.operator[0], inst[1], querystring.field[1], querystring.mode[1], querystring.operator[1], inst[2], querystring.field[2], querystring.mode[2])
### for multitagged fields (e.g. title), unmatched result corresponds to the item in extreme
rec_match = matched_records_max(recID_lists)
### print-new
if (rec_match==0):
result[0] += 1
if(match_mode==0):
recs_out.append(rec)
if (batch_output != ""):
out_0.append(rec)
if verbose:
sys.stderr.write(".")
if (verbose > 1):
sys.stderr.write("NEW")
### print-match
elif (rec_match <= level):
result[1] += 1
if(match_mode==1):
recs_out.append(rec)
if (batch_output != ""):
out_1.append(rec)
if verbose:
sys.stderr.write(".")
if (verbose > 1):
sys.stderr.write("MATCH")
### print-ambiguous
elif(rec_match > level):
result[2] += 1
if(match_mode==2):
recs_out.append(rec)
if (batch_output != ""):
out_2.append(rec)
if verbose:
sys.stderr.write(".")
if (verbose > 1):
sys.stderr.write("AMBIGUOUS")
else:
pass
sys.stderr.write(more_detailed_info)
if verbose:
sys.stderr.write("\n\n Bibmatch report\n")
sys.stderr.write("=" * 35)
sys.stderr.write("\n New records : %d" % result[0])
sys.stderr.write("\n Matched records : %d" % result[1])
sys.stderr.write("\n Ambiguous records : %d\n" % result[2])
sys.stderr.write("=" * 35)
sys.stderr.write("\n Total records : %d\n" % record_counter)
if noprocess:
pass
else:
for record in recs_out:
print print_rec(record[0])
if (batch_output != ""):
filename = "%s.0" % batch_output
file_0 = open(filename,"w")
filename = "%s.1" % batch_output
file_1 = open(filename,"w")
filename = "%s.2" % batch_output
file_2 = open(filename,"w")
for record in out_0:
file_0.write(print_rec(record[0]))
for record in out_1:
file_1.write(print_rec(record[0]))
for record in out_2:
file_2.write(print_rec(record[0]))
file_0.close()
file_1.close()
file_2.close()

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