def createMscsDb():
"""Create MSC database of all languages."""
db = ArticleDB.ArticleDB(ARTS_FILE, mode='override', autocommit=False)
baseDir = ''
proc_total = 0
logging.info("processing directory %s" % common.inputPath(baseDir))
for root, dirs, files in os.walk(common.inputPath(baseDir)):
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'))
try:
meta['body'] = open(os.path.join(root,
'fulltext.txt')).read()
except Exception, e:
meta['body'] = None
meta['id_int'] = root[len(common.INPUT_PATH) + 1:]
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 processDir(baseDir):
proc_total = proc_ok = 0
logging.info("processing directory %s" % common.inputPath(baseDir))
for root, dirs, files in os.walk(baseDir):
root = os.path.normpath(root)
for f in filter(lambda f: f.endswith('.xhtml'), files):
proc_total += 1
fname = os.path.join(root, f)
if processArxivXhtml(fname):
proc_ok += 1
logging.info('%i xhtml files processed; %i articles output' % (proc_total, proc_ok))
def createMscsDb():
"""Create MSC database of all languages."""
db = ArticleDB.ArticleDB(ARTS_FILE, mode="override", autocommit=False)
baseDir = ""
proc_total = 0
logging.info("processing directory %s" % common.inputPath(baseDir))
for root, dirs, files in os.walk(common.inputPath(baseDir)):
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"))
try:
meta["body"] = open(os.path.join(root, "fulltext.txt")).read()
except Exception, e:
meta["body"] = None
meta["id_int"] = root[len(common.INPUT_PATH) + 1 :]
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)
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 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))
if __name__ == '__main__':
logging.basicConfig(level = logging.DEBUG)
baseDir = common.inputPath('numdam')
# create_refsdb(baseDir, downloadMSC = False)
create_maindb(baseDir)
# create_merged(baseDir)
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))
if __name__ == '__main__':
logging.basicConfig(level=logging.DEBUG)
baseDir = common.inputPath('numdam')
# create_refsdb(baseDir, downloadMSC = False)
create_maindb(baseDir)
# create_merged(baseDir)