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## $Id$
## BibIndxes bibliographic data, reference and fulltext indexing utility.
## This file is part of the CERN Document Server Software (CDSware).
## Copyright (C) 2002 CERN.
##
## The CDSware 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.
##
## The CDSware 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 CDSware; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
## read config variables:
#include "config.wml"
#include "configbis.wml"
## start Python:
<protect>#!</protect><PYTHON>
<protect># -*- coding: utf-8 -*-</protect>
<protect>## $Id$</protect>
<protect>## DO NOT EDIT THIS FILE! IT WAS AUTOMATICALLY GENERATED FROM CDSware WML SOURCES.</protect>
"""
BibIndex bibliographic data, reference and fulltext indexing utility.
Usage: bibindex %s [options]
Examples:
bibindex -a -i 234-250,293,300-500 -u admin@cdsware
bibindex -a -w author,fulltext -M 8192 -v3
bibindex -d -m +4d -A on --flush=10000
Indexing options:
-a, --add add or update words for selected records
-d, --del delete words for selected records
-i, --id=low[-high] select according to record recID.
-m, --modified=from[,to] select according to modification date
-c, --collection=c1[,c2] select according to collection
Repairing options:
-k, --check check consistency for all records in the table(s)
-r, --repair try to repair all records in the table(s)
Specific options:
-w, --windex=w1[,w2] word/phrase indexes to consider (all)
-M, --maxmem=XXX maximum memory usage in kB (no limit)
-f, --flush=NNN full consistent table flush after NNN records (10000)
Scheduling options:
-u, --user=USER user name to store task, password needed
-s, --sleeptime=SLEEP time after which to repeat task (no)
e.g.: 1s, 30m, 24h, 7d
-t, --time=TIME moment for the task to be active (now)
e.g.: +15s, 5m, 3h, 2002-10-27 13:57:26
General options:
-h, --help print this help and exit
-V, --version print version and exit
-v, --verbose=LEVEL verbose level (from 0 to 9, default 1)
"""
## fill config variables:
pylibdir = "<LIBDIR>/python"
## programs used to convert fulltext files to text:
conv_programs = {#"ps": ["<PSTOTEXT>","<PSTOASCII>"], # switched off at the moment, since PDF is faster
#"ps.gz": ["<PSTOTEXT>","<PSTOASCII>"],
"pdf": ["<PDFTOTEXT>","<PSTOTEXT>","<PSTOASCII>"],
"doc": ["<ANTIWORD>","<CATDOC>","<WVTEXT>"],
"ppt": ["<PPTHTML>"],
"xls": ["<XLHTML>"]
}
## helper programs used if the above programs convert only to html or other intermediate file formats:
conv_programs_helpers = {"html": "<HTMLTOTEXT>",
"gz": "<GZIP>" }
## okay, rest of the Python code goes below
#######
## version number:
__version__ = "$Id$"
## import interesting modules:
try:
from marshal import loads,dumps
from zlib import compress,decompress
from string import split,translate,lower,upper
import getopt
import getpass
import string
import os
import sre
import sys
import time
import MySQLdb
import Numeric
import urllib
import signal
import tempfile
import unicodedata
import traceback
import cStringIO
except ImportError, e:
print "Error: %s" % e
import sys
sys.exit(1)
try:
sys.path.append('%s' % pylibdir)
from cdsware.config import *
from cdsware.search_engine_config import cfg_max_recID
from cdsware.search_engine import perform_request_search, strip_accents
from cdsware.dbquery import run_sql
from cdsware.access_control_engine import acc_authorize_action
except ImportError, e:
print "Error: %s" % e
import sys
sys.exit(1)
## import optional modules:
try:
import psyco
psyco.bind(get_words_from_phrase)
psyco.bind(merge_with_old_recIDs)
psyco.bind(serialize_via_numeric_array)
psyco.bind(serialize_via_marshal)
psyco.bind(deserialize_via_numeric_array)
psyco.bind(deserialize_via_marshal)
except:
pass
## safety parameters concerning MySQL thread-multiplication problem:
cfg_check_mysql_threads = 0 # to check or not to check the problem?
cfg_max_mysql_threads = 50 # how many threads (connections) we consider as still safe
cfg_mysql_thread_timeout = 20 # we'll kill threads that were sleeping for more than X seconds
## override urllib's default password-asking behaviour:
class MyFancyURLopener(urllib.FancyURLopener):
def prompt_user_passwd(self, host, realm):
# supply some dummy credentials by default
return ("mysuperuser", "mysuperpass")
def http_error_401(self, url, fp, errcode, errmsg, headers):
# do not bother with protected pages
raise IOError, (999, 'unauthorized access')
return None
#urllib._urlopener = MyFancyURLopener()
def write_message(msg, stream=sys.stdout):
"""Write message and flush output stream (may be sys.stdout or sys.stderr). Useful for debugging stuff."""
if stream == sys.stdout or stream == sys.stderr:
stream.write(time.strftime("%Y-%m-%d %H:%M:%S --> ", time.localtime()))
stream.write("%s\n" % msg)
stream.flush()
else:
sys.stderr.write("Unknown stream %s. [must be sys.stdout or sys.stderr]\n" % stream)
return
## precompile some often-used regexp for speed reasons:
re_subfields = sre.compile('\$\$\w');
nb_char_in_line = 50 # for verbose pretty printing
chunksize = 1000 # default size of chunks that the records will be treated by
wordTables = []
task_id = -1
base_process_size = 4500 # process base size
opts_dict = {} # will hold task options
## Dictionary merging functions
def intersection(dict, dict2):
"Returns intersection of the two dictionaries."
int_dict = {}
if len(dict1) > len(dict2):
for e in dict2:
if dict1.has_key(e):
int_dict[e] = 1
else:
for e in dict1:
if dict2.has_key(e):
int_dict[e] = 1
return int_dict
def union(dict1, dict2):
"Returns union of the two dictionaries."
union_dict = {}
for e in dict1.keys():
union_dict[e] = 1
for e in dict2.keys():
union_dict[e] = 1
return union_dict
def diff(dict1, dict2):
"Returns dict1 - dict2."
diff_dict = {}
for e in dict1.keys():
if not dict2.has_key(e):
diff_dict[e] = 1
return diff_dict
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()
## safety function for killing slow MySQL threads:
def kill_sleepy_mysql_threads(max_threads=cfg_max_mysql_threads, thread_timeout=cfg_mysql_thread_timeout):
"""Check the number of MySQL threads and if there are more than
MAX_THREADS of them, lill all threads that are in a sleeping
state for more than THREAD_TIMEOUT seconds. (This is useful
for working around the the max_connection problem that appears
during indexation in some not-yet-understood cases.) If some
threads are to be killed, write info into the log file.
"""
res = run_sql("SHOW FULL PROCESSLIST")
if len(res) > max_threads:
for row in res:
r_id,r_user,r_host,r_db,r_command,r_time,r_state,r_info = row
if r_command == "Sleep" and int(r_time) > thread_timeout:
run_sql("KILL %s", (r_id,))
if opts_dict["verbose"] >= 1:
write_message("WARNING: too many MySQL threads, killing thread %s" % r_id)
return
## MARC-21 tag/field access functions
def get_fieldvalues(recID, tag):
"""Returns list of values of the MARC-21 'tag' fields for the record
'recID'."""
out = []
bibXXx = "bib" + tag[0] + tag[1] + "x"
bibrec_bibXXx = "bibrec_" + bibXXx
query = "SELECT value FROM %s AS b, %s AS bb WHERE bb.id_bibrec=%s AND bb.id_bibxxx=b.id AND tag LIKE '%s'" \
% (bibXXx, bibrec_bibXXx, recID, tag)
res = run_sql(query)
for row in res:
out.append(row[0])
return out
def get_field_tags(field):
"""Returns a list of MARC tags for the field code 'field'.
Returns empty list in case of error.
Example: field='author', output=['100__%','700__%']."""
out = []
query = """SELECT t.value 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""" % field
res = run_sql(query)
for row in res:
out.append(row[0])
return out
## Fulltext word extraction functions
def get_fulltext_urls_from_html_page(htmlpagebody):
"""Parses htmlpagebody data looking for url_directs referring to
probable fulltexts.
Returns an array of (ext,url_direct) to fulltexts.
Note: it looks for file format extensions as defined by global
'conv_programs'structure.
"""
out = []
for ext in conv_programs.keys():
expr = sre.compile( r"(\"http://[\w]+\.+[\w]+[^\"'><]*\.)(" + \
ext + r")\"")
match = expr.search(htmlpagebody)
if match:
out.append([ext,match.group()])
return out
def get_words_from_fulltext(url_indirect,separators="[^\w]",split=string.split):
"""Returns all the words contained in the fulltext whose url
is contained in the document pointed to in phrase.
Please note the double indirection. url_indirect
returns a document that has to be parsed to get the actual
urls."""
if opts_dict["verbose"] >= 2:
write_message("... reading fulltext files from %s started" % url_indirect)
url_direct = None
fulltext_urls = None
# check for direct link in url
url_indirect_ext = lower(split(url_indirect,".")[-1])
if url_indirect_ext in conv_programs.keys():
fulltext_urls = [(url_indirect_ext,url_indirect)]
# Indirect url. Try to fetch the real fulltext(s)
if not fulltext_urls:
# read "setlink" data
try:
htmlpagebody = urllib.urlopen(url_indirect).read()
except:
sys.stderr.write("Error: Cannot read %s.\n" % url_indirect)
return []
fulltext_urls = get_fulltext_urls_from_html_page(htmlpagebody)
words = {}
# process as many urls as they were found:
for (ext,url_direct) in fulltext_urls:
if opts_dict["verbose"] >= 2:
write_message(".... processing %s from %s started" % (ext,url_direct))
# sanity check:
if not url_direct:
break;
# read fulltext file:
try:
url = urllib.urlopen(url_direct[1:-1])
except:
sys.stderr.write("Error: Cannot read %s.\n" % url_direct[1:-1])
break # try other fulltext files...
tmp_name = tempfile.mktemp('cdsware.tmp')
tmp_fd = open(tmp_name, "w")
data_chunk = url.read(8*1024)
while data_chunk:
tmp_fd.write(data_chunk)
data_chunk = url.read(8*1024)
tmp_fd.close()
# try all available conversion programs according to their order:
bingo = 0
for conv_program in conv_programs[ext]:
if os.path.exists(conv_program):
# intelligence on how to run various conversion programs:
cmd = "" # wil keep command to run
bingo = 0 # had we success?
if os.path.basename(conv_program) == "pdftotext":
cmd = "%s %s %s.txt" % (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "pstotext":
if ext == "ps.gz":
# is there gzip available?
if os.path.exists(conv_programs_helpers["gz"]):
cmd = "%s -cd %s | %s > %s.txt" \
% (conv_programs_helpers["gz"], tmp_name, conv_program, tmp_name)
else:
cmd = "%s %s > %s.txt" \
% (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "ps2ascii":
if ext == "ps.gz":
# is there gzip available?
if os.path.exists(conv_programs_helpers["gz"]):
cmd = "%s -cd %s | %s > %s.txt"\
% (conv_programs_helpers["gz"], tmp_name,
conv_program, tmp_name)
else:
cmd = "%s %s %s.txt" \
% (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "antiword":
cmd = "%s %s > %s.txt" % (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "catdoc":
cmd = "%s %s > %s.txt" % (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "wvText":
cmd = "%s %s %s.txt" % (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "ppthtml":
# is there html2text available?
if os.path.exists(conv_programs_helpers["html"]):
cmd = "%s %s | %s > %s.txt"\
% (conv_program, tmp_name,
conv_programs_helpers["html"], tmp_name)
else:
cmd = "%s %s > %s.txt" \
% (conv_program, tmp_name, tmp_name)
elif os.path.basename(conv_program) == "xlhtml":
# is there html2text available?
if os.path.exists(conv_programs_helpers["html"]):
cmd = "%s %s | %s > %s.txt" % \
(conv_program, tmp_name,
conv_programs_helpers["html"], tmp_name)
else:
cmd = "%s %s > %s.txt" % \
(conv_program, tmp_name, tmp_name)
else:
sys.stderr.write("Error: Do not know how to handle %s conversion program.\n" % conv_program)
# try to run it:
try:
if opts_dict["verbose"] >= 9:
write_message("..... launching %s" % cmd)
errcode = os.system(cmd)
if errcode == 0 and os.path.exists("%s.txt" % tmp_name):
bingo = 1
break # bingo!
else:
write_message("Error while running %s for %s.\n" % (cmd, url_direct), sys.stderr)
except:
write_message("Error running %s for %s.\n" % (cmd, url_direct), sys.stderr)
# were we successful?
if bingo:
tmp_name_txt_file = open("%s.txt" % tmp_name)
for phrase in tmp_name_txt_file.xreadlines():
for word in get_words_from_phrase(phrase):
if not words.has_key(word):
words[word] = 1;
tmp_name_txt_file.close()
else:
if opts_dict["verbose"]:
write_message("No conversion success for %s.\n" % (url_direct), sys.stderr)
# delete temp files (they might not exist):
try:
os.unlink(tmp_name)
os.unlink(tmp_name + ".txt")
except StandardError:
write_message("Error: Could not delete file. It didn't exist", sys.stderr)
if opts_dict["verbose"] >= 2:
write_message(".... processing %s from %s ended" % (ext,url_direct))
if opts_dict["verbose"] >= 2:
write_message("... reading fulltext files from %s ended" % url_indirect)
return words.keys()
# tagToFunctions mapping. It offers an indirection level necesary for
# indexing fulltext. The default is get_words_from_phrase
tagToWordsFunctions = {'8564_u':get_words_from_fulltext}
def get_words_from_phrase(phrase,
chars_punctuation=r"[\.\,\:\;\?\!\"]",
chars_alphanumericseparators=r"[\!\"\#\$\%\&\'\(\)\*\+\,\-\.\/\:\;\<\=\>\?\@\[\\\]\^\_\`\{\|\}\~]",
split=string.split):
"Returns list of words from phrase 'phrase'."
words = {}
# 1st split phrase into blocks according to whitespace
for block in split(strip_accents(phrase)):
# 2nd remove leading/trailing punctuation and add block:
block = sre.sub(r"^"+chars_punctuation+"+", "", block)
block = sre.sub(chars_punctuation+"+$", "", block)
if block:
words[block] = 1
# 3rd break each block into subblocks according to punctuation and add subblocks:
for subblock in sre.split(chars_punctuation, block):
if subblock:
words[subblock] = 1
# 4th break each subblock into alphanumeric groups and add groups:
for alphanumeric_group in sre.split(chars_alphanumericseparators, subblock):
if alphanumeric_group:
words[alphanumeric_group] = 1
return words.keys()
def remove_subfields(s):
"Removes subfields from string, e.g. 'foo $$c bar' becomes 'foo bar'."
return re_subfields.sub(' ', s)
def get_field_tags(field):
"""Returns a list of MARC tags for the field code 'field'.
Returns empty list in case of error.
Example: field='author', output=['100__%','700__%']."""
out = []
query = """SELECT t.value 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""" % field
res = run_sql(query)
for row in res:
out.append(row[0])
return out
def get_index_id(indexname):
"""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""" % indexname
res = run_sql(query, None, 1)
if res:
out = res[0][0]
return out
def get_index_tags(indexname):
"""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__%']."""
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""" % indexname
res = run_sql(query)
for row in res:
out.extend(get_field_tags(row[0]))
return out
def get_all_indexes():
"""Returns the list of the names of all defined words indexes.
Returns empty list in case there are no tags indexed in this index.
Example: output=['global', 'author']."""
out = []
query = """SELECT name FROM idxINDEX"""
res = run_sql(query)
for row in res:
out.append(row[0])
return out
def usage(code, msg=''):
"Prints usage for this module."
if msg:
sys.stderr.write("Error: %s.\n" % msg)
<protect>
print >> sys.stderr, \
""" Usage: %s [options]
Examples:
%s -a -i 234-250,293,300-500 -u admin@cdsware
%s -a -w author,fulltext -M 8192 -v3
%s -d -m +4d -A on --flush=10000
Indexing options:
-a, --add add or update words for selected records
-d, --del delete words for selected records
-i, --id=low[-high] select according to doc recID
-m, --modified=from[,to] select according to modification date
-c, --collection=c1[,c2] select according to collection
Repairing options:
-k, --check check consistency for all records in the table(s)
-r, --repair try to repair all records in the table(s)
Specific options:
-w, --windex=w1[,w2] word/phrase indexes to consider (all)
-M, --maxmem=XXX maximum memory usage in kB (no limit)
-f, --flush=NNN full consistent table flush after NNN records (10000)
Scheduling options:
-u, --user=USER user name to store task, password needed
-s, --sleeptime=SLEEP time after which to repeat tasks (no)
e.g.: 1s, 30m, 24h, 7d
-t, --time=TIME moment for the task to be active (now)
e.g.: +15s, 5m, 3h , 2002-10-27 13:57:26
General options:
-h, --help print this help and exit
-V, --version print version and exit
-v, --verbose=LEVEL verbose level (from 0 to 9, default 1)
""" % ((sys.argv[0],) * 4)
</protect>
sys.exit(code)
def authenticate(user, header="BibIndex Task Submission", action="runbibindex"):
"""Authenticate the user against the user database.
Check for its password, if it exists.
Check for action access rights.
Return user name upon authorization success,
do system exit upon authorization failure.
"""
print header
print "=" * len(header)
if user == "":
print >> sys.stdout, "\rUsername: ",
user = string.strip(string.lower(sys.stdin.readline()))
else:
print >> sys.stdout, "\rUsername: ", user
## first check user pw:
res = run_sql("select id,password from user where email=%s", (user,), 1)
if not res:
print "Sorry, %s does not exist." % user
sys.exit(1)
else:
(uid_db, password_db) = res[0]
if password_db:
password_entered = getpass.getpass()
if password_db == password_entered:
pass
else:
print "Sorry, wrong credentials for %s." % user
sys.exit(1)
## secondly check authorization for the action:
if not acc_authorize_action(uid_db, action):
print "Sorry, %s has no right to %s." % (user, action)
sys.exit(1)
return user
def split_ranges(parse_string):
recIDs = []
ranges = string.split(parse_string, ",")
for range in ranges:
tmp_recIDs = string.split(range, "-")
if len(tmp_recIDs)==1:
recIDs.append([int(tmp_recIDs[0]), int(tmp_recIDs[0])])
else:
if int(tmp_recIDs[0]) > int(tmp_recIDs[1]): # sanity check
tmp = tmp_recIDs[0]
tmp_recIDs[0] = tmp_recIDs[1]
tmp_recIDs[1] = tmp
recIDs.append([int(tmp_recIDs[0]), int(tmp_recIDs[1])])
return recIDs
def get_word_tables(tables):
wordTables = []
if tables:
indexes = string.split(tables, ",")
for index in indexes:
index_id = get_index_id(index)
if index_id:
wordTables.append({"idxWORD%02dF" % index_id: \
get_index_tags(index)})
else:
write_message("Error: There is no %s words table." % index, sys.stderr)
else:
for index in get_all_indexes():
index_id = get_index_id(index)
wordTables.append({"idxWORD%02dF" % index_id: \
get_index_tags(index)})
return wordTables
def get_date_range(var):
"Returns the two dates contained as a low,high tuple"
limits = string.split(var, ",")
if len(limits)==1:
low = get_date(limits[0])
return low,None
if len(limits)==2:
low = get_date(limits[0])
high = get_date(limits[1])
return low,high
def get_datetime(var, format_string="%Y-%m-%d %H:%M:%S"):
"""Returns a date string according to the format string.
It can handle normal date strings and shifts with respect
to now."""
date = time.time()
shift_re=sre.compile("([-\+]{0,1})([\d]+)([dhms])")
factors = {"d":24*3600, "h":3600, "m":60, "s":1}
m = shift_re.match(var)
if m:
sign = m.groups()[0] == "-" and -1 or 1
factor = factors[m.groups()[2]]
value = float(m.groups()[1])
date = time.localtime(date + sign * factor * value)
date = time.strftime(format_string, date)
else:
date = time.strptime(var, format_string)
date = time.strftime(format_string, date)
return date
def create_range_list(res):
"""Creates a range list from a recID select query result contained
in res. The result is expected to have ascending numerical order."""
if not res:
return []
row = res[0]
if not row:
return []
else:
range_list = [[row[0],row[0]]]
for row in res[1:]:
id = row[0]
if id == range_list[-1][1] + 1:
range_list[-1][1] = id
else:
range_list.append([id,id])
return range_list
def beautify_range_list(range_list):
"""Returns a non overlapping, maximal range list"""
ret_list = []
for new in range_list:
found = 0
for old in ret_list:
if new[0] <= old[0] <= new[1] + 1 or new[0] - 1 <= old[1] <= new[1]:
old[0] = min(old[0], new[0])
old[1] = max(old[1], new[1])
found = 1
break
if not found:
ret_list.append(new)
return ret_list
def serialize_via_numeric_array_dumps(arr):
return Numeric.dumps(arr)
def serialize_via_numeric_array_compr(str):
return compress(str)
def serialize_via_numeric_array_escape(str):
return MySQLdb.escape_string(str)
def serialize_via_numeric_array(arr):
"""Serialize Numeric array into a compressed string."""
#return MySQLdb.escape_string(compress(Numeric.dumps(arr)))
return serialize_via_numeric_array_escape(serialize_via_numeric_array_compr(serialize_via_numeric_array_dumps(arr)))
def deserialize_via_numeric_array(string):
"""Decompress and deserialize string into a Numeric array."""
return Numeric.loads(decompress(string))
def serialize_via_marshal(obj):
"""Serialize Python object via marshal into a compressed string."""
return MySQLdb.escape_string(compress(dumps(obj)))
def deserialize_via_marshal(string):
"""Decompress and deserialize string into a Python object via marshal."""
return loads(decompress(string))
class WordTable:
"A class to hold the words table."
def __init__(self, tablename, fields_to_index, separators="[^\s]"):
"Creates words table instance."
self.tablename = tablename
self.recIDs_in_mem = []
self.fields_to_index = fields_to_index
self.separators = separators
self.value = {}
def get_field(self, recID, tag):
"""Returns list of values of the MARC-21 'tag' fields for the
record 'recID'."""
out = []
bibXXx = "bib" + tag[0] + tag[1] + "x"
bibrec_bibXXx = "bibrec_" + bibXXx
query = """SELECT value FROM %s AS b, %s AS bb
WHERE bb.id_bibrec=%s AND bb.id_bibxxx=b.id
AND tag LIKE '%s'""" % (bibXXx, bibrec_bibXXx, recID, tag);
res = run_sql(query)
for row in res:
out.append(row[0])
return out
def clean(self):
"Cleans the words table."
self.value={}
def put_into_db(self, mode="normal", split=string.split):
"""Updates the current words table in the corresponding MySQL's
idxFOO table. Mode 'normal' means normal execution,
mode 'emergency' means words index reverting to old state.
"""
if opts_dict["verbose"]:
write_message("%s %s wordtable flush started" % (self.tablename,mode))
write_message('...updating %d words into %s started' % \
(len(self.value), self.tablename))
task_update_progress("%s flushed %d/%d words" % (self.tablename, 0, len(self.value)))
self.recIDs_in_mem = beautify_range_list(self.recIDs_in_mem)
if mode == "normal":
for group in self.recIDs_in_mem:
query = """UPDATE %sR SET type='TEMPORARY' WHERE id_bibrec
BETWEEN '%d' AND '%d' AND type='CURRENT'""" % \
(self.tablename[:-1], group[0], group[1])
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
nb_words_total = len(self.value)
nb_words_report = int(nb_words_total/10)
nb_words_done = 0
for word in self.value.keys():
self.put_word_into_db(word)
nb_words_done += 1
if nb_words_report!=0 and ((nb_words_done % nb_words_report) == 0):
if opts_dict["verbose"]:
write_message('......processed %d/%d words' % (nb_words_done, nb_words_total))
task_update_progress("%s flushed %d/%d words" % (self.tablename, nb_words_done, nb_words_total))
if opts_dict["verbose"] >= 9:
write_message('...updating %d words into %s ended' % \
(nb_words_total, self.tablename))
if opts_dict["verbose"]:
write_message('...updating reverse table %sR started' % self.tablename[:-1])
if mode == "normal":
for group in self.recIDs_in_mem:
query = """UPDATE %sR SET type='CURRENT' WHERE id_bibrec
BETWEEN '%d' AND '%d' AND type='FUTURE'""" % \
(self.tablename[:-1], group[0], group[1])
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
query = """DELETE FROM %sR WHERE id_bibrec
BETWEEN '%d' AND '%d' AND type='TEMPORARY'""" % \
(self.tablename[:-1], group[0], group[1])
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
if opts_dict["verbose"] >= 9:
write_message('End of updating wordTable into %s' % self.tablename)
elif mode == "emergency":
for group in self.recIDs_in_mem:
query = """UPDATE %sR SET type='CURRENT' WHERE id_bibrec
BETWEEN '%d' AND '%d' AND type='TEMPORARY'""" % \
(self.tablename[:-1], group[0], group[1])
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
query = """DELETE FROM %sR WHERE id_bibrec
BETWEEN '%d' AND '%d' AND type='FUTURE'""" % \
(self.tablename[:-1], group[0], group[1])
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
if opts_dict["verbose"] >= 9:
write_message('End of emergency flushing wordTable into %s' % self.tablename)
if opts_dict["verbose"]:
write_message('...updating reverse table %sR ended' % self.tablename[:-1])
self.clean()
self.recIDs_in_mem = []
if opts_dict["verbose"]:
write_message("%s %s wordtable flush ended" % (self.tablename, mode))
task_update_progress("%s flush ended" % (self.tablename))
def load_old_recIDs(self,word):
"""Load existing hitlist for the word from the database index files."""
query = "SELECT hitlist FROM %s WHERE term=%%s" % self.tablename
res = run_sql(query, (word,))
if res:
return deserialize_via_numeric_array(res[0][0])
else:
return None
def merge_with_old_recIDs(self,word,set):
"""Merge the system numbers stored in memory (hash of recIDs with value +1 or -1
according to whether to add/delete them) with those stored in the database index
and received in set universe of recIDs for the given word.
Return 0 in case no change was done to SET, return 1 in case SET was changed.
"""
set_changed_p = 0
for recID,sign in self.value[word].items():
if sign == -1 and set[recID]==1:
# delete recID if existent in set and if marked as to be deleted
set[recID] = 0
set_changed_p = 1
elif set[recID] == 0:
# add recID if not existent in set and if marked as to be added
set[recID] = 1
set_changed_p = 1
return set_changed_p
def put_word_into_db(self, word, split=string.split):
"""Flush a single word to the database and delete it from memory"""
set = self.load_old_recIDs(word)
if set: # merge the word recIDs found in memory:
if self.merge_with_old_recIDs(word,set) == 0:
# nothing to update:
if opts_dict["verbose"] >= 9:
write_message("......... unchanged hitlist for ``%s''" % word)
pass
else:
# yes there were some new words:
if opts_dict["verbose"] >= 9:
write_message("......... updating hitlist for ``%s''" % word)
query = "UPDATE %s SET hitlist='%s' WHERE term='%s'" % \
(self.tablename, serialize_via_numeric_array(set),
MySQLdb.escape_string(word))
run_sql(query)
else: # the word is new, will create new set:
set = Numeric.zeros(cfg_max_recID+1, Numeric.Int0)
Numeric.put(set, self.value[word].keys(), 1)
if opts_dict["verbose"] >= 9:
write_message("......... inserting hitlist for ``%s''" % word)
query = "INSERT INTO %s (term, hitlist) VALUES ('%s', '%s')" %\
(self.tablename, MySQLdb.escape_string(word),
serialize_via_numeric_array(set))
run_sql(query)
if not set: # never store empty words
query = "DELETE from %s WHERE term='%s'" % \
(self.tablename, MySQLdb.escape_string(word))
run_sql(query)
del self.value[word]
def display(self):
"Displays the word table."
keys = self.value.keys()
keys.sort()
for k in keys:
if opts_dict["verbose"]:
write_message("%s: %s" % (k, self.value[k]))
def count(self):
"Returns the number of words in the table."
return len(self.value)
def info(self):
"Prints some information on the words table."
if opts_dict["verbose"]:
write_message("The words table contains %d words." % self.count())
def lookup_words(self, word=""):
"Lookup word from the words table."
if not word:
done = 0
while not done:
try:
word = raw_input("Enter word: ")
done = 1
except (EOFError, KeyboardInterrupt):
return
if self.value.has_key(word):
if opts_dict["verbose"]:
write_message("The word '%s' is found %d times." \
% (word, len(self.value[word])))
else:
if opts_dict["verbose"]:
write_message("The word '%s' does not exist in the word file."\
% word)
def update_last_updated(self, starting_time=None):
"""Update last_updated column of the index table in the database.
Puts starting time there so that if the task was interrupted for record download,
the records will be reindexed next time."""
if starting_time is None:
return None
if opts_dict["verbose"] >= 9:
write_message("updating last_updated to %s...", starting_time)
return run_sql("UPDATE idxINDEX SET last_updated=%s WHERE id=%s",
(starting_time, self.tablename[len("idxWORD"):-1],))
def add_recIDs(self, recIDs):
"""Fetches records which id in the recIDs range list and adds
them to the wordTable. The recIDs range list is of the form:
[[i1_low,i1_high],[i2_low,i2_high], ..., [iN_low,iN_high]].
"""
global chunksize
flush_count = 0
records_done = 0
records_to_go = 0
for range in recIDs:
records_to_go = records_to_go + range[1] - range[0] + 1
time_started = time.time() # will measure profile time
for range in recIDs:
i_low = range[0]
chunksize_count = 0
while i_low <= range[1]:
# calculate chunk group of recIDs and treat it:
i_high = min(i_low+opts_dict["flush"]-flush_count-1,range[1])
i_high = min(i_low+chunksize-chunksize_count-1, i_high)
try:
self.chk_recID_range(i_low, i_high)
except StandardError, e:
write_message("Exception caught: %s" % e, sys.stderr)
if opts_dict["verbose"] >= 9:
traceback.print_tb(sys.exc_info()[2])
task_update_status("ERROR")
task_sig_stop_commands()
sys.exit(1)
if opts_dict["verbose"]:
write_message("%s adding records #%d-#%d started" % \
(self.tablename, i_low, i_high))
if cfg_check_mysql_threads:
kill_sleepy_mysql_threads()
task_update_progress("%s adding recs %d-%d" % (self.tablename, i_low, i_high))
self.del_recID_range(i_low, i_high)
just_processed = self.add_recID_range(i_low, i_high)
flush_count = flush_count + i_high - i_low + 1
chunksize_count = chunksize_count + i_high - i_low + 1
records_done = records_done + just_processed
if opts_dict["verbose"]:
write_message("%s adding records #%d-#%d ended " % \
(self.tablename, i_low, i_high))
if chunksize_count >= chunksize:
chunksize_count = 0
# flush if necessary:
if flush_count >= opts_dict["flush"]:
self.put_into_db()
self.clean()
if opts_dict["verbose"]:
write_message("%s backing up" % (self.tablename))
flush_count = 0
self.log_progress(time_started,records_done,records_to_go)
# iterate:
i_low = i_high + 1
if flush_count > 0:
self.put_into_db()
self.log_progress(time_started,records_done,records_to_go)
def add_date(self, date):
# If date is not set, then retrieve it from the database.
# Reindex all formats newer than the modification date
if not date:
id = self.tablename[len("bibindex"):]
query = """SELECT last_updated FROM idxINDEX WHERE id='%s'
""" % id
res = run_sql(query)
if not res:
return
if not res[0][0]:
date = "0000-00-00"
else:
date = res[0][0]
query = """SELECT b.id FROM bibrec AS b WHERE b.modification_date >=
'%s' ORDER BY b.id ASC""" % date
res = run_sql(query)
list = create_range_list(res)
if not list:
if opts_dict["verbose"]:
write_message( "No new records added. %s is up to date" % self.tablename)
else:
self.add_recIDs(list)
def add_recID_range(self, recID1, recID2):
empty_list_string = serialize_via_marshal([])
wlist = {}
self.recIDs_in_mem.append([recID1,recID2])
# secondly fetch all needed tags:
for tag in self.fields_to_index:
if tag in tagToWordsFunctions.keys():
get_words_function = tagToWordsFunctions[ tag ]
else: get_words_function = get_words_from_phrase
bibXXx = "bib" + tag[0] + tag[1] + "x"
bibrec_bibXXx = "bibrec_" + bibXXx
query = """SELECT bb.id_bibrec,b.value FROM %s AS b, %s AS bb
WHERE bb.id_bibrec BETWEEN %d AND %d
AND bb.id_bibxxx=b.id AND tag LIKE '%s'""" % (bibXXx, bibrec_bibXXx, recID1, recID2, tag)
res = run_sql(query)
nb_total_to_read = len(res)
verbose_idx = 0 # for verbose pretty printing
for row in res:
recID,phrase = row
if not wlist.has_key(recID): wlist[recID] = []
new_words = get_words_function(phrase) # ,self.separators
wlist[recID] = list_union(new_words,wlist[recID])
# were there some words for these recIDs found?
if len(wlist) == 0: return 0
recIDs = wlist.keys()
for recID in recIDs:
# was this record marked as deleted?
if "DELETED" in self.get_field(recID, "980__c"):
wlist[recID] = []
if opts_dict["verbose"] >= 9:
write_message("... record %d was declared deleted, removing its word list" % recID)
if opts_dict["verbose"] >= 9:
write_message("... record %d, termlist: %s" % (recID, wlist[recID]))
# Using cStringIO for speed.
query_factory = cStringIO.StringIO()
qwrite = query_factory.write
qwrite( "INSERT INTO %sR (id_bibrec,termlist,type) VALUES" % self.tablename[:-1])
qwrite( "('" )
qwrite( str(recIDs[0]) )
qwrite( "','" )
qwrite( serialize_via_marshal(wlist[recIDs[0]]) )
qwrite( "','FUTURE')" )
for recID in recIDs[1:]:
qwrite(",('")
qwrite(str(recID))
qwrite("','")
qwrite(serialize_via_marshal(wlist[recID]))
qwrite("','FUTURE')")
query = query_factory.getvalue()
query_factory.close()
run_sql(query)
query_factory = cStringIO.StringIO()
qwrite = query_factory.write
qwrite("INSERT INTO %sR (id_bibrec,termlist,type) VALUES" % self.tablename[:-1])
qwrite("('")
qwrite(str(recIDs[0]))
qwrite("','")
qwrite(serialize_via_marshal(wlist[recIDs[0]]))
qwrite("','CURRENT')")
for recID in recIDs[1:]:
qwrite( ",('" )
qwrite( str(recID) )
qwrite( "','" )
qwrite( empty_list_string )
qwrite( "','CURRENT')" )
query = query_factory.getvalue()
query_factory.close()
try:
run_sql(query)
except MySQLdb.DatabaseError:
# ok, we tried to add an existent record. No problem
pass
put = self.put
for recID in recIDs:
for w in wlist[recID]:
put(recID, w, 1)
return len(recIDs)
def log_progress(self, start, done, todo):
"""Calculate progress and store it.
start: start time,
done: records processed,
todo: total number of records"""
time_elapsed = time.time() - start
# consistency check
if time_elapsed == 0 or done > todo:
return
time_recs_per_min = done/(time_elapsed/60.0)
if opts_dict["verbose"]:
write_message("%d records took %.1f seconds to complete.(%1.f recs/min)"\
% (done, time_elapsed, time_recs_per_min))
if time_recs_per_min:
if opts_dict["verbose"]:
write_message("Estimated runtime: %.1f minutes" % \
((todo-done)/time_recs_per_min))
def put(self, recID, word, sign):
"Adds/deletes a word to the word list."
try:
word = lower(word[:50])
if self.value.has_key(word):
# the word 'word' exist already: update sign
self.value[word][recID] = sign
else:
self.value[word] = {recID: sign}
except:
write_message("Error: Cannot put word %s with sign %d for recID %s." % (word, sign, recID))
def del_recIDs(self, recIDs):
"""Fetches records which id in the recIDs range list and adds
them to the wordTable. The recIDs range list is of the form:
[[i1_low,i1_high],[i2_low,i2_high], ..., [iN_low,iN_high]].
"""
count = 0
for range in recIDs:
self.del_recID_range(range[0],range[1])
count = count + range[1] - range[0]
self.put_into_db()
def del_recID_range(self, low, high):
"""Deletes records with 'recID' system number between low
and high from memory words index table."""
if opts_dict["verbose"] > 2:
write_message("%s fetching existing words for records #%d-#%d started" % \
(self.tablename, low, high))
self.recIDs_in_mem.append([low,high])
query = """SELECT id_bibrec,termlist FROM %sR as bb WHERE bb.id_bibrec
BETWEEN '%d' AND '%d'""" % (self.tablename[:-1], low, high)
recID_rows = run_sql(query)
for recID_row in recID_rows:
recID = recID_row[0]
wlist = deserialize_via_marshal(recID_row[1])
for word in wlist:
self.put(recID, word, -1)
if opts_dict["verbose"] > 2:
write_message("%s fetching existing words for records #%d-#%d ended" % \
(self.tablename, low, high))
def report_on_table_consistency(self):
"""Check reverse words index tables (e.g. idxWORD01R) for
interesting states such as 'TEMPORARY' state.
Prints small report (no of words, no of bad words).
"""
# find number of words:
query = """SELECT COUNT(*) FROM %s""" % (self.tablename)
res = run_sql(query, None, 1)
if res:
nb_words = res[0][0]
else:
nb_words = 0
# find number of records:
query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR""" % (self.tablename[:-1])
res = run_sql(query, None, 1)
if res:
nb_records = res[0][0]
else:
nb_records = 0
# report stats:
if opts_dict["verbose"]:
write_message("%s contains %d words from %d records" % (self.tablename, nb_words, nb_records))
# find possible bad states in reverse tables:
query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR WHERE type <> 'CURRENT'""" % (self.tablename[:-1])
res = run_sql(query)
if res:
nb_bad_records = res[0][0]
else:
nb_bad_records = 999999999
if nb_bad_records:
write_message("EMERGENCY: %s needs to repair %d of %d records" % \
(self.tablename, nb_bad_records, nb_records))
else:
if opts_dict["verbose"]:
write_message("%s is in consistent state" % (self.tablename))
return nb_bad_records
def repair(self):
"""Repair the whole table"""
# find possible bad states in reverse tables:
query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR WHERE type <> 'CURRENT'""" % (self.tablename[:-1])
res = run_sql(query, None, 1)
if res:
nb_bad_records = res[0][0]
else:
nb_bad_records = 0
# find number of records:
query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR""" % (self.tablename[:-1])
res = run_sql(query)
if res:
nb_records = res[0][0]
else:
nb_records = 0
if nb_bad_records == 0:
return
query = """SELECT id_bibrec FROM %sR WHERE type <> 'CURRENT' ORDER BY id_bibrec""" \
% (self.tablename[:-1])
res = run_sql(query)
recIDs = create_range_list(res)
flush_count = 0
records_done = 0
records_to_go = 0
for range in recIDs:
records_to_go = records_to_go + range[1] - range[0] + 1
time_started = time.time() # will measure profile time
for range in recIDs:
i_low = range[0]
chunksize_count = 0
while i_low <= range[1]:
# calculate chunk group of recIDs and treat it:
i_high = min(i_low+opts_dict["flush"]-flush_count-1,range[1])
i_high = min(i_low+chunksize-chunksize_count-1, i_high)
try:
self.fix_recID_range(i_low, i_high)
except StandardError, e:
write_message("Exception caught: %s" % e, sys.stderr)
if opts_dict["verbose"] >= 9:
traceback.print_tb(sys.exc_info()[2])
task_update_status("ERROR")
task_sig_stop_commands()
sys.exit(1)
flush_count = flush_count + i_high - i_low + 1
chunksize_count = chunksize_count + i_high - i_low + 1
records_done = records_done + i_high - i_low + 1
if chunksize_count >= chunksize:
chunksize_count = 0
# flush if necessary:
if flush_count >= opts_dict["flush"]:
self.put_into_db("emergency")
self.clean()
flush_count = 0
self.log_progress(time_started,records_done,records_to_go)
# iterate:
i_low = i_high + 1
if flush_count > 0:
self.put_into_db("emergency")
self.log_progress(time_started,records_done,records_to_go)
write_message("%s inconsistencies repaired." % self.tablename)
def chk_recID_range(self, low, high):
"""Check if the reverse index table is in proper state"""
## check db
query = """SELECT COUNT(*) FROM %sR WHERE type <> 'CURRENT'
AND id_bibrec BETWEEN '%d' AND '%d'""" % (self.tablename[:-1], low, high)
res = run_sql(query, None, 1)
if res[0][0]==0:
if opts_dict["verbose"]:
write_message("%s for %d-%d is in consistent state"%(self.tablename,low,high))
return # okay, words table is consistent
## inconsistency detected!
write_message("EMERGENCY: %s inconsistencies detected..." % self.tablename)
write_message("""EMERGENCY: Errors found. You should check consistency of the %s - %sR tables.\nRunning 'bibindex --repair' is recommended.""" \
% (self.tablename, self.tablename[:-1]))
raise StandardError
def fix_recID_range(self, low, high):
"""Try to fix reverse index database consistency (e.g. table idxWORD01R) in the low,high doc-id range.
Possible states for a recID follow:
CUR TMP FUT: very bad things have happened: warn!
CUR TMP : very bad things have happened: warn!
CUR FUT: delete FUT (crash before flushing)
CUR : database is ok
TMP FUT: add TMP to memory and del FUT from memory
flush (revert to old state)
TMP : very bad things have happened: warn!
FUT: very bad things have happended: warn!
"""
state = {}
query = "SELECT id_bibrec,type FROM %sR WHERE id_bibrec BETWEEN '%d' AND '%d'"\
% (self.tablename[:-1], low, high)
res = run_sql(query)
for row in res:
if not state.has_key(row[0]):
state[row[0]]=[]
state[row[0]].append(row[1])
ok = 1 # will hold info on whether we will be able to repair
for recID in state.keys():
if not 'TEMPORARY' in state[recID]:
if 'FUTURE' in state[recID]:
if 'CURRENT' not in state[recID]:
write_message("EMERGENCY: Record %d is in inconsistent state. Can't repair it" % recID)
ok = 0
else:
write_message("EMERGENCY: Inconsistency in record %d detected" % recID)
query = """DELETE FROM %sR
WHERE id_bibrec='%d'""" % (self.tablename[:-1], recID)
run_sql(query)
write_message("EMERGENCY: Inconsistency in record %d repaired." % recID)
else:
if 'FUTURE' in state[recID] and not 'CURRENT' in state[recID]:
self.recIDs_in_mem.append([recID,recID])
# Get the words file
query = """SELECT type,termlist FROM %sR
WHERE id_bibrec='%d'""" % (self.tablename[:-1], recID)
if opts_dict["verbose"] >= 9:
write_message(query)
res = run_sql(query)
for row in res:
wlist = deserialize_via_marshal(row[1])
if opts_dict["verbose"] >= 9:
write_message("Words are %s " % wlist)
if row[0] == 'TEMPORARY':
sign = 1
else:
sign = -1
for word in wlist:
self.put(recID, word, sign)
else:
write_message("EMERGENCY: %s for %d is in inconsistent state. Couldn't repair it." % (self.tablename, recID))
ok = 0
if not ok:
write_message("""EMERGENCY: Unrepairable errors found. You should check consistency
of the %s - %sR tables. Deleting affected records is
recommended.""" % (self.tablename, self.tablename[:-1]))
raise StandardError
def task_run(row):
"""Run the indexing task. The row argument is the BibSched task
queue row, containing if, arguments, etc.
Return 1 in case of success and 0 in case of failure.
"""
global opts_dict, task_id, wordTables
# read from SQL row:
task_id = row[0]
task_proc = row[1]
opts_dict = loads(row[6])
task_status = row[7]
# sanity check:
if task_proc != "bibindex":
write_message("The task #%d does not seem to be a BibIndex task." % task_id, sys.stderr)
return 0
if task_status != "WAITING":
write_message("The task #%d is %s. I expected WAITING." % (task_id, task_status), sys.stderr)
return 0
# we can run the task now:
if opts_dict["verbose"]:
write_message("Task #%d started." % task_id)
task_starting_time = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
task_update_status("RUNNING")
# install signal handlers
signal.signal(signal.SIGUSR1, task_sig_sleep)
signal.signal(signal.SIGTERM, task_sig_stop)
signal.signal(signal.SIGABRT, task_sig_suicide)
signal.signal(signal.SIGCONT, task_sig_wakeup)
signal.signal(signal.SIGINT, task_sig_unknown)
## go ahead and treat each table :
for table in opts_dict["windex"]:
wordTable = WordTable(table.keys()[0], table.values()[0])
wordTable.report_on_table_consistency()
try:
if opts_dict["cmd"] == "del":
if opts_dict["id"]:
wordTable.del_recIDs(opts_dict["id"])
elif opts_dict["collection"]:
l_of_colls = string.split(opts_dict["collection"], ",")
recIDs = perform_request_search(c=l_of_colls)
recIDs_range = []
for recID in recIDs:
recIDs_range.append([recID,recID])
wordTable.del_recIDs(recIDs_range)
else:
write_message("Missing IDs of records to delete from index %s.", wordTable.tablename,
sys.stderr)
raise StandardError
elif opts_dict["cmd"] == "add":
if opts_dict["id"]:
wordTable.add_recIDs(opts_dict["id"])
elif opts_dict["collection"]:
l_of_colls = string.split(opts_dict["collection"], ",")
recIDs = perform_request_search(c=l_of_colls)
recIDs_range = []
for recID in recIDs:
recIDs_range.append([recID,recID])
wordTable.add_recIDs(recIDs_range)
else:
wordTable.add_date(opts_dict["modified"])
# only update last_updated if run via automatic mode:
wordTable.update_last_updated(task_starting_time)
elif opts_dict["cmd"] == "repair":
wordTable.repair()
else:
write_message("Invalid command found processing %s" % \
wordTable.tablename, sys.stderr)
raise StandardError
except StandardError, e:
write_message("Exception caught: %s" % e, sys.stderr)
if opts_dict["verbose"] >= 9:
traceback.print_tb(sys.exc_info()[2])
task_update_status("ERROR")
task_sig_stop_commands()
sys.exit(1)
wordTable.report_on_table_consistency()
# We are done. State it in the database, close and quit
task_update_status("DONE")
if opts_dict["verbose"]:
write_message("Task #%d finished." % task_id)
return 1
def command_line():
global opts_dict
long_flags =["add","del","id=","modified=","collection=", "windex=",
"check","repair","maxmem=", "flush=","user=","sleeptime=",
"time=","help", "version", "verbose="]
short_flags ="adi:m:c:w:krM:f:u:s:t:hVv:"
format_string = "%Y-%m-%d %H:%M:%S"
tables = None
sleeptime = ""
try:
opts, args = getopt.getopt(sys.argv[1:], short_flags, long_flags)
except getopt.GetoptError, err:
write_message(err, sys.stderr)
usage(1)
if args:
usage(1)
opts_dict={"cmd":"add", "id":[], "modified":[], "collection":[], "maxmem":0,
"flush":10000, "sleeptime":0, "verbose":1 }
sched_time = time.strftime(format_string)
user = ""
# Check for key options
try:
for opt in opts:
if opt == ("-h","") or opt == ("--help",""):
usage(1)
elif opt == ("-V","") or opt == ("--version",""):
print __version__
sys.exit(1)
elif opt[0] in ["--verbose", "-v"]:
opts_dict["verbose"] = int(opt[1])
elif opt == ("-a","") or opt == ("--add",""):
opts_dict["cmd"] = "add"
if ("-x","") in opts or ("--del","") in opts:
usage(1)
elif opt == ("-k","") or opt == ("--check",""):
opts_dict["cmd"] = "check"
elif opt == ("-r","") or opt == ("--repair",""):
opts_dict["cmd"] = "repair"
elif opt == ("-d","") or opt == ("--del",""):
opts_dict["cmd"]="del"
elif opt[0] in [ "-i", "--id" ]:
opts_dict["id"] = opts_dict["id"] + split_ranges(opt[1])
elif opt[0] in [ "-m", "--modified" ]:
opts_dict["modified"] = get_date_range(opt[1])
elif opt[0] in [ "-c", "--collection" ]:
opts_dict["collection"] = opt[1]
elif opt[0] in [ "-w", "--windex" ]:
tables = opt[1]
elif opt[0] in [ "-M", "--maxmem"]:
opts_dict["maxmem"]=int(opt[1])
if opts_dict["maxmem"] < base_process_size + 1000:
raise StandardError, "Memory usage should be higher than %d kB" % (base_process_size + 1000)
elif opt[0] in [ "-f", "--flush"]:
opts_dict["flush"]=int(opt[1])
elif opt[0] in [ "-u", "--user"]:
user = opt[1]
elif opt[0] in [ "-s", "--sleeptime" ]:
get_datetime(opt[1]) # see if it is a valid shift
sleeptime= opt[1]
elif opt[0] in [ "-t", "--time" ]:
sched_time= get_datetime(opt[1])
else: usage(1)
except StandardError, e:
write_message(e, sys.stderr)
sys.exit(1)
opts_dict["windex"]=get_word_tables(tables)
if opts_dict["cmd"] == "check":
for table in opts_dict["windex"]:
wordTable = WordTable(table.keys()[0], table.values()[0])
wordTable.report_on_table_consistency()
return
user = authenticate(user)
if opts_dict["verbose"] >= 9:
print ""
write_message("storing task options %s\n" % opts_dict)
query = """INSERT INTO schTASK (proc,user,runtime,sleeptime,arguments,status)
VALUES ('bibindex','%s',CAST('%s' AS DATE),'%s','%s','WAITING')""" % \
(MySQLdb.escape_string(user),MySQLdb.escape_string(sched_time), sleeptime, \
MySQLdb.escape_string(dumps(opts_dict)))
new_task_id = run_sql(query)
print "Task #%d was successfully scheduled for execution." % new_task_id
return
def write_message(msg, stream=sys.stdout):
"""Prints message and flush output stream (may be sys.stdout or sys.stderr)."""
if stream == sys.stdout or stream == sys.stderr:
stream.write(time.strftime("%Y-%m-%d %H:%M:%S --> ", time.localtime()))
stream.write("%s\n" % msg)
stream.flush()
else:
sys.stderr.write("Unknown stream %s. [must be sys.stdout or sys.stderr]\n" % stream)
def task_sig_sleep(sig, frame):
"""Signal handler for the 'sleep' signal sent by BibSched."""
if opts_dict["verbose"] >= 9:
write_message("got signal %d" % sig)
write_message("sleeping...")
task_update_status("SLEEPING")
signal.pause() # wait for wake-up signal
def task_sig_wakeup(sig, frame):
"""Signal handler for the 'wakeup' signal sent by BibSched."""
if opts_dict["verbose"] >= 9:
write_message("got signal %d" % sig)
write_message("continuing...")
task_update_status("CONTINUING")
def task_sig_stop(sig, frame):
"""Signal handler for the 'stop' signal sent by BibSched."""
if opts_dict["verbose"] >= 9:
write_message("got signal %d" % sig)
write_message("stopping...")
task_update_status("STOPPING")
errcode = 0
try:
task_sig_stop_commands()
write_message("stopped")
task_update_status("STOPPED")
except StandardError, err:
write_message("Error during stopping! %e" % err)
task_update_status("STOPPINGFAILED")
errcode = 1
sys.exit(errcode)
def task_sig_stop_commands():
"""Do all the commands necessary to stop the task before quitting.
Useful for task_sig_stop() handler.
"""
write_message("stopping commands started")
for table in wordTables:
table.put_into_db()
write_message("stopping commands ended")
def task_sig_suicide(sig, frame):
"""Signal handler for the 'suicide' signal sent by BibSched."""
if opts_dict["verbose"] >= 9:
write_message("got signal %d" % sig)
write_message("suiciding myself now...")
task_update_status("SUICIDING")
write_message("suicided")
task_update_status("SUICIDED")
sys.exit(0)
def task_sig_unknown(sig, frame):
"""Signal handler for the other unknown signals sent by shell or user."""
if opts_dict["verbose"] >= 9:
write_message("got signal %d" % sig)
write_message("unknown signal %d ignored" % sig) # do nothing for other signals
def task_update_progress(msg):
"""Updates progress information in the BibSched task table."""
query = "UPDATE schTASK SET progress='%s' where id=%d" % (MySQLdb.escape_string(msg), task_id)
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
return
def task_update_status(val):
"""Updates state information in the BibSched task table."""
query = "UPDATE schTASK SET status='%s' where id=%d" % (MySQLdb.escape_string(val), task_id)
if opts_dict["verbose"] >= 9:
write_message(query)
run_sql(query)
return
def test_fulltext_indexing():
"""Tests fulltext indexing programs on PDF, PS, DOC, PPT,
XLS. Prints list of words and word table on the screen. Does not
integrate anything into the database. Useful when debugging
problems with fulltext indexing: call this function instead of main().
"""
opts_dict = {}
opts_dict["verbose"] = 9
print get_words_from_fulltext("http://doc.cern.ch/cgi-bin/setlink?base=atlnot&categ=Communication&id=com-indet-2002-012") # protected URL
print get_words_from_fulltext("http://doc.cern.ch/cgi-bin/setlink?base=agenda&categ=a00388&id=a00388s2t7") # XLS
print get_words_from_fulltext("http://doc.cern.ch/cgi-bin/setlink?base=agenda&categ=a02883&id=a02883s1t6/transparencies") # PPT
print get_words_from_fulltext("http://doc.cern.ch/cgi-bin/setlink?base=agenda&categ=a99149&id=a99149s1t10/transparencies") # DOC
print get_words_from_fulltext("http://doc.cern.ch/cgi-bin/setlink?base=preprint&categ=cern&id=lhc-project-report-601") # PDF
sys.exit(0)
def test_word_separators(phrase="hep-th/0101001"):
"""Tests word separating policy on various input."""
print "%s:" % phrase
for word in get_words_from_phrase(phrase):
print "\t-> %s" % word
def main():
"""Reads arguments and either runs the task, or starts user-interface (command line)."""
if len(sys.argv) == 2:
try:
id = int(sys.argv[1])
except StandardError, err:
command_line()
sys.exit()
res = run_sql("SELECT * FROM schTASK WHERE id='%d'" % (id), None, 1)
if not res:
write_message("Selected task not found.", sys.stderr)
sys.exit(1)
try:
if not task_run(res[0]):
write_message("Error occurred. Exiting.", sys.stderr)
except StandardError, e:
write_message("Unexpected error occurred: %s." % e, sys.stderr)
if opts_dict["verbose"] >= 9:
traceback.print_tb(sys.exc_info()[2])
write_message("Exiting.")
task_update_status("ERROR")
else:
command_line()
if __name__ == "__main__":
#print get_fieldvalues(600336,"700__a")
#print get_all_indexes()
#test_fulltext_indexing()
#test_word_separators()
#test_word_separators("?C++.NET")
#test_word_separators("\x4C\x6F\xC3\xAF\x65\x7A")
#test_word_separators("O'Neil and pi- in real.business")
#test_word_separators("CERN-TH-1995-001 CERN-TH-95-01 CERN-TH/95-1")
main()
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