def merge(inputs, dbout, acceptLanguage='any'):
logging.info('merging %i databases, accepting "%s" language' %
(len(inputs), acceptLanguage))
db_merged = ArticleDB.ArticleDB(common.dbFile(dbout, acceptLanguage),
mode='override')
lang_failed = 0
for dbId, dbBaseDir in inputs.iteritems():
db_part = ArticleDB.ArticleDB(common.dbFile('gensim', dbId),
mode='open')
logging.info("processing %i articles from %s" %
(len(db_part.db), dbId))
inserted = 0
for rec in db_part.db:
if acceptLanguage == 'any' or rec['language'] == acceptLanguage:
db_merged.insertArticle(Article.Article(rec))
inserted += 1
else:
lang_failed += 1
logging.info("accepted %i articles of %s language from %s" %
(inserted, acceptLanguage, dbId))
db_merged.commit()
logging.info(
'%i total articles in the merged database; %i rejected due to different language'
% (len(db_merged), lang_failed))
def create_merged(baseDir):
"""merge main and reference databases, store them into merged_baseDir.pdl file"""
db_main = ArticleDB.ArticleDB(common.dbFile('main', baseDir), mode = 'open')
db_refs = ArticleDB.ArticleDB(common.dbFile('refs', baseDir), mode = 'open')
db_merged = ArticleDB.ArticleDB(common.dbFile('merged', baseDir), mode = 'override')
db_merged.mergeWith(db_main) # db_main comes first, so that potentially overlapping attributes stay from db_main, not db_refs (such as id_int and body)
db_merged.mergeWith(db_refs)
db_merged.commit()
logging.info('%i total articles in the database (originally %i in reference database + %i in main database = %i)' % (len(db_merged), len(db_refs), len(db_main), len(db_refs) + len(db_main)))
def create_maindb(dbId, dbBaseDir):
"""Look for any subdirs (arbitrary level under dbBaseDir) that start with '#'.
From these subdirs, try to load ./fulltext.txt and ./meta.xml files, create an article and insert it into database.
Store the database persistently as PyDbLite (pickle) file 'gensim_dbId.pdl'.
"""
dbFname = common.dbFile('gensim', dbId)
logging.info("opening database %s" % dbFname)
db = ArticleDB.ArticleDB(dbFname, mode = 'override', autocommit = False)
proc_total = 0
logging.info("processing database %s, directory %s" % (dbId, dbBaseDir))
for root, dirs, files in os.walk(dbBaseDir):
root = os.path.normpath(root)
if os.path.basename(root).startswith('#'):
proc_total += 1
try:
meta = utils_iddb.parseMeta(os.path.join(root, 'meta.xml'))
#meta = {'msc' : []}
#meta['id_int'] = Article.idFromDir(root)
meta['id_int'] = os.path.join(dbId, root[len(dbBaseDir) + 1: ])
meta['body'] = unicode(open(os.path.join(root, 'fulltext.txt'), 'r').read(), 'utf8', 'ignore').encode('utf8')
meta['references'] = None # TODO add
art = Article.Article(record = meta)
db.insertArticle(art)
except Exception, e:
logging.warning('invalid entries in %s; ignoring article (%s)' % (root, e))
continue
def create_refsdb(baseDir, downloadMSC = False):
"""read references from baseDir files and merge them together into an ArticleDB database.
also check for consistency and print some stats
store the resulting database on disk as 'refs_baseDir.pdl'.
"""
import cPickle
reffiles = utils_iddb.getRefFiles(common.inputPath(baseDir))
cPickle.dump(reffiles, open(common.dataFile('reffiles.pkl'), 'w'), protocol = -1) # store filesystem paths to references.xml files
refdb = {}
for reffile, refid in reffiles.iteritems():
refs = utils_iddb.parseReferences(reffile, downloadMSC = downloadMSC)
refdb[refid] = refs
logging.info('id=%s: retrieved %i references' % (refid, len(refs)))
if downloadMSC:
cPickle.dump(refdb, open(common.dataFile('refs_partial.pkl'), 'w'), protocol = -1) # dump database immediately after each iteration
f = open(common.dataFile('refs.pkl'), 'w')
cPickle.dump(refdb, f, protocol = -1) # dump database immediately after each iteration
f.close()
#print some statistics
logging.info("%i MSC download attemps (%i ok, %i failed)" % (utils_iddb.attempts_all, utils_iddb.attempts_success, utils_iddb.attempts_failed))
logging.info('reference database size: %i references in %i articles' % (sum([len(refs) for refs in refdb.itervalues()]), len(refdb)))
db = ArticleDB.ArticleDB(common.dbFile('refs', baseDir), mode = 'override')
insert_errors = 0
for id, reflist in refdb.iteritems():
for num, ref in enumerate(reflist):
ref.id_int = id + ':' + str(num + 1) # references.xml reference counting starts with '1'
if not db.insertArticle(ref):
insert_errors += 1
#print '.',
db.commit()
logging.info('resulting database has %i records (originally %i)' % (len(db), sum([len(refs) for refs in refdb.itervalues()])))
logging.info('detected %i inconsistency collisions' % insert_errors)
def create_merged(baseDir):
"""merge main and reference databases, store them into merged_baseDir.pdl file"""
db_main = ArticleDB.ArticleDB(common.dbFile('main', baseDir), mode='open')
db_refs = ArticleDB.ArticleDB(common.dbFile('refs', baseDir), mode='open')
db_merged = ArticleDB.ArticleDB(common.dbFile('merged', baseDir),
mode='override')
db_merged.mergeWith(
db_main
) # db_main comes first, so that potentially overlapping attributes stay from db_main, not db_refs (such as id_int and body)
db_merged.mergeWith(db_refs)
db_merged.commit()
logging.info(
'%i total articles in the database (originally %i in reference database + %i in main database = %i)'
% (len(db_merged), len(db_refs), len(db_main),
len(db_refs) + len(db_main)))
def create_maindb(dbId, dbBaseDir):
"""Look for any subdirs (arbitrary level under dbBaseDir) that start with '#'.
From these subdirs, try to load ./fulltext.txt and ./meta.xml files, create an article and insert it into database.
Store the database persistently as PyDbLite (pickle) file 'gensim_dbId.pdl'.
"""
dbFname = common.dbFile('gensim', dbId)
logging.info("opening database %s" % dbFname)
db = ArticleDB.ArticleDB(dbFname, mode='override', autocommit=False)
proc_total = 0
logging.info("processing database %s, directory %s" % (dbId, dbBaseDir))
for root, dirs, files in os.walk(dbBaseDir):
root = os.path.normpath(root)
if os.path.basename(root).startswith('#'):
proc_total += 1
try:
meta = utils_iddb.parseMeta(os.path.join(root, 'meta.xml'))
#meta = {'msc' : []}
#meta['id_int'] = Article.idFromDir(root)
meta['id_int'] = os.path.join(dbId, root[len(dbBaseDir) + 1:])
meta['body'] = unicode(
open(os.path.join(root, 'fulltext.txt'), 'r').read(),
'utf8', 'ignore').encode('utf8')
meta['references'] = None # TODO add
art = Article.Article(record=meta)
db.insertArticle(art)
except Exception, e:
logging.warning(
'invalid entries in %s; ignoring article (%s)' % (root, e))
continue
def merge(inputs, dbout, acceptLanguage = 'any'):
logging.info('merging %i databases, accepting "%s" language' % (len(inputs), acceptLanguage))
db_merged = ArticleDB.ArticleDB(common.dbFile(dbout, acceptLanguage), mode = 'override')
lang_failed = 0
for dbId, dbBaseDir in inputs.iteritems():
db_part = ArticleDB.ArticleDB(common.dbFile('gensim', dbId), mode = 'open')
logging.info("processing %i articles from %s" % (len(db_part.db), dbId))
inserted = 0
for rec in db_part.db:
if acceptLanguage == 'any' or rec['language'] == acceptLanguage:
db_merged.insertArticle(Article.Article(rec))
inserted += 1
else:
lang_failed += 1
logging.info("accepted %i articles of %s language from %s" % (inserted, acceptLanguage, dbId))
db_merged.commit()
logging.info('%i total articles in the merged database; %i rejected due to different language' % (len(db_merged), lang_failed))
def create_refsdb(baseDir, downloadMSC=False):
"""read references from baseDir files and merge them together into an ArticleDB database.
also check for consistency and print some stats
store the resulting database on disk as 'refs_baseDir.pdl'.
"""
import cPickle
reffiles = utils_iddb.getRefFiles(common.inputPath(baseDir))
cPickle.dump(reffiles,
open(common.dataFile('reffiles.pkl'), 'w'),
protocol=-1) # store filesystem paths to references.xml files
refdb = {}
for reffile, refid in reffiles.iteritems():
refs = utils_iddb.parseReferences(reffile, downloadMSC=downloadMSC)
refdb[refid] = refs
logging.info('id=%s: retrieved %i references' % (refid, len(refs)))
if downloadMSC:
cPickle.dump(
refdb,
open(common.dataFile('refs_partial.pkl'), 'w'),
protocol=-1) # dump database immediately after each iteration
f = open(common.dataFile('refs.pkl'), 'w')
cPickle.dump(refdb, f,
protocol=-1) # dump database immediately after each iteration
f.close()
#print some statistics
logging.info("%i MSC download attemps (%i ok, %i failed)" %
(utils_iddb.attempts_all, utils_iddb.attempts_success,
utils_iddb.attempts_failed))
logging.info('reference database size: %i references in %i articles' %
(sum([len(refs) for refs in refdb.itervalues()]), len(refdb)))
db = ArticleDB.ArticleDB(common.dbFile('refs', baseDir), mode='override')
insert_errors = 0
for id, reflist in refdb.iteritems():
for num, ref in enumerate(reflist):
ref.id_int = id + ':' + str(
num + 1) # references.xml reference counting starts with '1'
if not db.insertArticle(ref):
insert_errors += 1
#print '.',
db.commit()
logging.info('resulting database has %i records (originally %i)' %
(len(db), sum([len(refs) for refs in refdb.itervalues()])))
logging.info('detected %i inconsistency collisions' % insert_errors)
import os.path
import gc
import common
import iddb
import docsim
if __name__ == '__main__':
logging.basicConfig(level = common.PRINT_LEVEL)
logging.root.level = common.PRINT_LEVEL
logging.info("running %s" % ' '.join(sys.argv))
program = os.path.basename(sys.argv[0])
# check and process input arguments
if len(sys.argv) < 2:
print globals()['__doc__'] % (program)
sys.exit(1)
language = sys.argv[1]
inputs = common.INPUT_PATHS
prefix = common.PREFIX
# merge databases into one, keeping only articles in the specified language (or 'any' to keep all languages)
iddb.merge(inputs, prefix, language)
# build and store tfidf matrix
docsim.buildTFIDFMatrices(dbFile = common.dbFile(prefix, language), prefix = prefix + '_' + language, contentType = 'alphanum_nohtml', saveMatrices = False)
logging.info("finished running %s" % program)
import common
import iddb
import docsim
if __name__ == '__main__':
logging.basicConfig(level=common.PRINT_LEVEL)
logging.root.level = common.PRINT_LEVEL
logging.info("running %s" % ' '.join(sys.argv))
program = os.path.basename(sys.argv[0])
# check and process input arguments
if len(sys.argv) < 2:
print globals()['__doc__'] % (program)
sys.exit(1)
language = sys.argv[1]
inputs = common.INPUT_PATHS
prefix = common.PREFIX
# merge databases into one, keeping only articles in the specified language (or 'any' to keep all languages)
iddb.merge(inputs, prefix, language)
# build and store tfidf matrix
docsim.buildTFIDFMatrices(dbFile=common.dbFile(prefix, language),
prefix=prefix + '_' + language,
contentType='alphanum_nohtml',
saveMatrices=False)
logging.info("finished running %s" % program)
import os.path
import numpy
import docsim
import matutils
import common
import DocumentCollection
import mscs
import ipyutils
import utils_dml
import ArticleDB
import Article
import utils_iddb
ARTS_FILE = common.dbFile(
'mscs', 'serial') # persistent db (file) where all mscs info is stored
def rmseFile(matfile1, matfile2):
data1 = matutils.loadMatrix(common.matrixFile(matfile1))
data2 = matutils.loadMatrix(common.matrixFile(matfile2))
return matutils.rmse(data1, data2)
def loadMsc2Id(lang):
cats = [
item.strip().split('\t')
for item in open(common.dataFile('serial_mscids_%s.txt' %
lang)).readlines()
]
cats = dict([(int(id), val) for id, val in cats]) # map int -> id
import numpy
import docsim
import matutils
import common
import DocumentCollection
import mscs
import ipyutils
import utils_dml
import ArticleDB
import Article
import utils_iddb
ARTS_FILE = common.dbFile("mscs", "serial") # persistent db (file) where all mscs info is stored
def rmseFile(matfile1, matfile2):
data1 = matutils.loadMatrix(common.matrixFile(matfile1))
data2 = matutils.loadMatrix(common.matrixFile(matfile2))
return matutils.rmse(data1, data2)
def loadMsc2Id(lang):
cats = [item.strip().split("\t") for item in open(common.dataFile("serial_mscids_%s.txt" % lang)).readlines()]
cats = dict([(int(id), val) for id, val in cats]) # map int -> id
rcats = dict([(v, k) for k, v in cats.iteritems()]) # map id -> int
return cats, rcats
