def update(self, indexer, iterable):
"""Update an index from a queryset."""
self._open_index()
for o in ifilter(indexer.should_index, iterable):
# Clear a potential old object out of the index
self.remove(o)
# Create a new document to index.
doc = PyLucene.Document()
# Index the model identifier so we can easily deal with only models of a certain type
doc.add(
PyLucene.Field(MODEL_FIELD, str(o._meta), STORE_YES,
UN_TOKENIZED))
# Index the "identifier" (app_label.module_name.pk) for this object
doc.add(
PyLucene.Field(IDENTIFIER_FIELD, self.get_identifier(o),
STORE_YES, INDEX_NO))
# Index the default content for the object
# Don't actually store the complete contents; just index them.
doc.add(
PyLucene.Field(CONTENTS_FIELD, indexer.flatten(o), STORE_NO,
TOKENIZED))
# Index each field that needs to be individually searchable.
for (name, value) in indexer.get_field_values(o).items():
doc.add(PyLucene.Field(name, value, STORE_NO, TOKENIZED))
self._index.addDocument(doc)
self._close_index()
def indexDocs(self, root, writer):
for root, dirnames, filenames in os.walk(root):
for filename in filenames:
#if not filename.endswith('.txt'):
# continue
print "adding", filename
try:
path = os.path.join(root, filename)
file = open(path)
contents = unicode(file.read(), 'iso-8859-1')
file.close()
doc = PyLucene.Document()
doc.add(
PyLucene.Field("name", filename,
PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field("path", path, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
if len(contents) > 0:
doc.add(
PyLucene.Field("contents", contents,
PyLucene.Field.Store.YES,
PyLucene.Field.Index.TOKENIZED))
else:
print "warning: no content in %s" % filename
writer.addDocument(doc)
except Exception, e:
print "Failed in indexDocs:", e
def _create_empty_document(self):
"""create an empty document to be filled and added to the index later
:return: the new document object
:rtype: PyLucene.Document
"""
return PyLucene.Document()
def create_index(self, arg):
""" Post download setup callback for creating a lucene index """
moreinfo("Creating lucene index")
storeDir = "index"
if not os.path.exists(storeDir):
os.mkdir(storeDir)
store = PyLucene.FSDirectory.getDirectory(storeDir, True)
self.lucene_writer = PyLucene.IndexWriter(store,
PyLucene.StandardAnalyzer(),
True)
# Uncomment this line to enable a PorterStemmer analyzer
# self.lucene_writer = PyLucene.IndexWriter(store, PorterStemmerAnalyzer(), True)
self.lucene_writer.setMaxFieldLength(1048576)
count = 0
urllist = []
for urlobj in self._urldict.values():
filename = urlobj.get_full_filename()
url = urlobj.get_full_url()
try:
urllist.index(url)
continue
except ValueError:
urllist.append(url)
if not filename in self._downloaddict['_savedfiles']: continue
data = ''
moreinfo('Adding index for URL', url)
if os.path.isfile(filename):
try:
data = unicode(open(filename).read(), 'iso-8859-1')
except UnicodeDecodeError, e:
data = ''
doc = PyLucene.Document()
doc.add(
PyLucene.Field("name", filename, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field("path", url, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
if data and len(data) > 0:
doc.add(
PyLucene.Field("contents", data, PyLucene.Field.Store.YES,
PyLucene.Field.Index.TOKENIZED))
else:
extrainfo("warning: no content in %s" % filename)
self.lucene_writer.addDocument(doc)
count += 1
def index_files(board, time_delta):
store = PyLucene.FSDirectory.getDirectory(
BOARDSPATH + board + '/' + RECENT_INDEX, True)
writer = PyLucene.IndexWriter(store, PyLucene.StandardAnalyzer(), True)
writer.setMaxFieldLength(1048576) # 1MB
flist = get_all_files(board, time_delta)
for filename, owner, title in flist:
path = BOARDSPATH + board + '/' + filename
if not os.path.exists(path):
continue
f = open(path, 'r')
contents = filter_file(f)
debug(contents)
try:
title = title.decode('gbk')
owner = owner.decode('gbk')
contents = unicode(contents, 'gbk')
except UnicodeDecodeError:
f.close()
debug(filename)
continue
f.close()
if len(contents) > 0:
doc = PyLucene.Document()
doc.add(
PyLucene.Field("name", filename, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field("owner", owner, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field("title", title, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field("contents", contents, PyLucene.Field.Store.YES,
PyLucene.Field.Index.TOKENIZED))
writer.addDocument(doc)
debug('adding ' + filename)
writer.optimize()
writer.close()
def add(self, message):
doc = PyLucene.Document()
for part in message.textParts():
doc.add(
PyLucene.Field(
'text',
part.translate({
ord(u'@'): u' ',
ord(u'-'): u' ',
ord(u'.'): u' '
}).encode('utf-8'), PyLucene.Field.Store.NO,
PyLucene.Field.Index.TOKENIZED))
for (k, v) in message.keywordParts().iteritems():
doc.add(
PyLucene.Field(
k,
v.translate({
ord(u'@'): u' ',
ord(u'-'): u' ',
ord(u'.'): u' '
}).encode('utf-8'), PyLucene.Field.Store.YES,
PyLucene.Field.Index.TOKENIZED))
doc.add(
PyLucene.Field('documentType', message.documentType(),
PyLucene.Field.Store.YES,
PyLucene.Field.Index.TOKENIZED))
doc.add(
PyLucene.Field('storeID', message.uniqueIdentifier(),
PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field('sortKey', message.sortKey(),
PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
# Deprecated. use Field(name, value, Field.Store.YES, Field.Index.UN_TOKENIZED) instead
self.writer.addDocument(doc)
def index_feed(self, feed, feed_data=None):
""" Indexes the given feed """
#remove any existing entries for this feed
self.delete_existing_feed_docs(feed)
writer = self.feed_modifier.get_writer()
doc = lucene.Document()
doc.add(
lucene.Field('id', str(feed.id), lucene.Field.Store.YES,
lucene.Field.Index.UN_TOKENIZED))
doc.add(
lucene.Field('url', feed.xml_url, lucene.Field.Store.YES,
lucene.Field.Index.UN_TOKENIZED))
if feed.channel_link:
doc.add(
lucene.Field('link', feed.channel_link, lucene.Field.Store.YES,
lucene.Field.Index.UN_TOKENIZED))
if feed.title:
doc.add(
lucene.Field('title', feed.title, lucene.Field.Store.YES,
lucene.Field.Index.TOKENIZED))
if feed.subtitle:
doc.add(
lucene.Field('subtitle', feed.subtitle, lucene.Field.Store.YES,
lucene.Field.Index.TOKENIZED))
writer.addDocument(doc)
writer.close()
logging.info('Indexed Feed: %s' % feed.xml_url)
writer = self.entry_modifier.get_writer()
for entry in feed.get_entries():
try:
doc = lucene.Document()
id = '%s:%s' % (feed.xml_url, entry.get('id', None))
doc.add(
lucene.Field('id', id, lucene.Field.Store.YES,
lucene.Field.Index.UN_TOKENIZED))
doc.add(
lucene.Field('feed_url', feed.xml_url,
lucene.Field.Store.YES,
lucene.Field.Index.UN_TOKENIZED))
if entry.get('title', None):
doc.add(
lucene.Field('title', entry['title'],
lucene.Field.Store.YES,
lucene.Field.Index.TOKENIZED))
if entry.get('summary', None):
doc.add(
lucene.Field('summary', entry['summary'],
lucene.Field.Store.YES,
lucene.Field.Index.TOKENIZED))
if entry.get('link', None):
doc.add(
lucene.Field('link', entry['link'],
lucene.Field.Store.YES,
lucene.Field.Index.UN_TOKENIZED))
updated = parse_date(entry.get('updated', None))
if updated:
doc.add(
lucene.Field('updated', updated.isoformat(' '),
lucene.Field.Store.YES,
lucene.Field.Index.NO))
doc.add(
lucene.Field('pickle', pickle.dumps(entry),
lucene.Field.Store.YES,
lucene.Field.Index.NO))
writer.addDocument(doc)
logging.info(
'Indexed Feed Entry: %s' % entry.get('title', None) or id)
except:
{}
writer.close()
def create_index(self):
""" Post download setup callback for creating a lucene index """
info("Creating lucene index")
count = 0
urllist = []
urldb = objects.datamgr.get_urldb()
storeDir = "index"
if not os.path.exists(storeDir):
os.mkdir(storeDir)
store = PyLucene.FSDirectory.getDirectory(storeDir, True)
lucene_writer = PyLucene.IndexWriter(store,
PyLucene.StandardAnalyzer(), True)
lucene_writer.setMaxFieldLength(1048576)
for node in urldb.preorder():
urlobj = node.get()
# Only index if web-page or document
if not urlobj.is_webpage() and not urlobj.is_document(): continue
filename = urlobj.get_full_filename()
url = urlobj.get_full_url()
try:
urllist.index(urlobj.index)
continue
except ValueError:
urllist.append(urlobj.index)
if not os.path.isfile(filename): continue
data = ''
extrainfo('Adding index for URL', url)
try:
data = unicode(open(filename).read(), 'iso-8859-1')
except UnicodeDecodeError, e:
data = ''
try:
doc = PyLucene.Document()
doc.add(
PyLucene.Field("name", 'file://' + filename,
PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
doc.add(
PyLucene.Field("path", url, PyLucene.Field.Store.YES,
PyLucene.Field.Index.UN_TOKENIZED))
if data and len(data) > 0:
doc.add(
PyLucene.Field("contents", data,
PyLucene.Field.Store.YES,
PyLucene.Field.Index.TOKENIZED))
else:
warning("warning: no content in %s" % filename)
lucene_writer.addDocument(doc)
except PyLucene.JavaError, e:
print e
continue
def _document_node(self, iba_node):
d = PyLucene.Document()
# Index the NID
d.add(
Field(COLUMN_NID, iba_node.nid, Field.Store.YES,
Field.Index.UN_TOKENIZED))
# Index the Names
for name in iba_node.names:
d.add(
Field(COLUMN_NAME, name[0], Field.Store.NO,
Field.Index.TOKENIZED))
# Index the Attributes
for att in iba_node.attributes:
# allowing search for nodes having a particular attribute type
d.add(
Field(COLUMN_ATTRIBUTE_TYPE_NID, att.type, Field.Store.NO,
Field.Index.TOKENIZED))
# allowing the search of nodes with any attribute having a particular value
d.add(
Field(COLUMN_ATTRIBUTE_VALUE, att.value, Field.Store.NO,
Field.Index.TOKENIZED))
# allowing the search of nodes having aparticular attribute with a particular value
d.add(
Field(COLUMN_ATTRIBUTE_TYPE_NID, att.value, Field.Store.NO,
Field.Index.TOKENIZED))
# Index the Statements
for stat in iba_node.statements:
for att in stat.attributes:
# allowing the search of nodes have any predicate with the specified attribute type
d.add(
Field(COLUMN_PREDICATE_NID + COLUMN_ATTRIBUTE_TYPE_NID,
att.type, Field.Store.NO, Field.Index.TOKENIZED))
# allowing the search of nodes having the specified predicate with the specified attribute type of any value
d.add(
Field(stat.predicate + COLUMN_ATTRIBUTE_TYPE_NID, att.type,
Field.Store.NO, Field.Index.TOKENIZED))
# allowing the search of nodes having the specified predicate with any attribute type and any value
d.add(
Field(COLUMN_PREDICATE_NID, stat.predicate, Field.Store.NO,
Field.Index.TOKENIZED))
# allowing the search of nodes have any predicate with any attribute type of the specified value
d.add(
Field(COLUMN_PREDICATE_NID + COLUMN_ATTRIBUTE_TYPE_NID,
att.value, Field.Store.NO, Field.Index.TOKENIZED))
# allowing the search of node having any predicate with the specified attribute type and value
d.add(
Field(COLUMN_PREDICATE_NID + att.type, att.value,
Field.Store.NO, Field.Index.TOKENIZED))
# allowing the search of nodes having the specified predicate with any attribute type and the specified value
d.add(
Field(stat.predicate + COLUMN_ATTRIBUTE_TYPE_NID,
att.value, Field.Store.NO, Field.Index.TOKENIZED))
# allowign the search of nodes having a specified predicate and attribute type and value
d.add(
Field(stat.predicate + att.type, att.value, Field.Store.NO,
Field.Index.TOKENIZED))
return d
def index_record(self, record, writer=None):
# field, value, store?, index?, token?
try:
if not writer:
had_writer = False
writer = self.context.get_search_index_writer(False)
else:
had_writer = True
study = Study(self.context, record.study_id)
self.logger.debug('starting document')
doc = PyLucene.Document()
# First, we need to create a unique key so we can later delete
# if necessary. Will try simply uid for now.
doc.add(PyLucene.Field('uid', str(record.uid), True, True, False))
doc.add(PyLucene.Field('all', str(record.uid), True, True, False))
# Second, save internal-use metadata. These should probably
# be x'd out at Query-time.
doc.add(
PyLucene.Field('record-status', str(record.status), False,
True, False))
doc.add(
PyLucene.Field('article-type', str(study.article_type), False,
True, False))
source_catalog = self.context.get_source_catalog()
complete_term_map = source_catalog.get_complete_mapping()
mapped_metadata = record.get_mapped_metadata(complete_term_map)
# First index all the non-multiple metadata fields
for field in ('abstract', 'affiliation', 'issn', 'journal',
'pubdate', 'issue', 'pages', 'title', 'volume'):
val = mapped_metadata.get(field, None)
if val:
doc.add(PyLucene.Field(field, val, False, True, True))
doc.add(PyLucene.Field('all', val, False, True, True))
# Be sure to index all of (abbrev, full title, issn) as "journal"
issn = mapped_metadata.get('issn')
if issn:
j = Journal()
j.load_from_issn(self.context, issn)
no_dash = j.no_dash()
self.logger.debug('indexing journal: %s, abbv:%s, issn:%s' % \
(j.journal_title, j.abbreviation, issn))
doc.add(PyLucene.Field('journal', issn, False, True, True))
doc.add(PyLucene.Field('journal', no_dash, False, True, True))
doc.add(PyLucene.Field('all', issn, False, True, True))
doc.add(PyLucene.Field('all', no_dash, False, True, True))
if j.abbreviation:
doc.add(
PyLucene.Field('journal', j.abbreviation, False, True,
True))
doc.add(
PyLucene.Field('all', j.abbreviation, False, True,
True))
if j.journal_title:
doc.add(
PyLucene.Field('journal', j.journal_title, False, True,
True))
doc.add(
PyLucene.Field('all', j.journal_title, False, True,
True))
# If a page range is given, index the first page, assuming
# the delimiter is '-'
pages = mapped_metadata.get('pages', None)
if pages \
and '-' in pages:
first_page = pages[0:pages.index('-')]
doc.add(PyLucene.Field('pages', first_page, False, True, True))
doc.add(PyLucene.Field('all', first_page, False, True, True))
# 'unique_identifier' must be specially treated because
# of the '_'
val = mapped_metadata.get('unique_identifier', None)
if val:
doc.add(
PyLucene.Field('unique-identifier', val, False, True,
True))
doc.add(PyLucene.Field('all', val, False, True, True))
# Next, index all the possibly-multiple metadata fields
# Give these (especially for author and subject) a little
# boost, less than for canary UMLS concepts
for field in ('author', 'grantnum', 'keyword', 'registrynum',
'subject'):
vals = mapped_metadata.get(field, None)
for val in vals:
doc.add(PyLucene.Field(field, val, False, True, True))
f = PyLucene.Field('all', val, False, True, True)
f.setBoost(1.3)
doc.add(f)
# If at least one author name is available, index the first
# author to support first-author searching. Also, boost it
# slightly higher than the other authors.
authors = mapped_metadata.get('author', None)
if authors:
doc.add(
PyLucene.Field('first-author', authors[0], False, True,
True))
f = PyLucene.Field('all', authors[0], False, True, True)
f.setBoost(1.5)
doc.add(f)
# All the booleans
for bool in ('has_outcomes', 'has_exposures', 'has_relationships',
'has_interspecies', 'has_exposure_linkage',
'has_outcome_linkage', 'has_genomic'):
val = getattr(study, bool)
# NOTE: I think lucene dislikes '_' in field names ??
boolstr = bool.replace('_', '-')
doc.add(
PyLucene.Field(boolstr, str(int(val)), False, True, False))
# NOTE: no need to add this to 'all'. I think.
# Now, all the UMLS concepts. Simpler approach to
# lucene "synonym injection", but it works! Give it
# slightly bigger boost than keywords/subjects
for ctype in ('exposures', 'outcomes', 'risk_factors', 'species'):
# NOTE: I think lucene dislikes '_' in field names ??
ctype_search = ctype.replace('_', '-')
for val in getattr(study, ctype):
concept = Concept(self.context, val.concept_id)
for syn in concept.synonyms:
doc.add(
PyLucene.Field(ctype_search,
unicode(syn, 'latin-1'), False,
True, True))
f = PyLucene.Field('all', unicode(syn, 'latin-1'),
False, True, True)
f.setBoost(2.0)
doc.add(f)
# And, the locations
gazeteer = self.context.get_gazeteer()
locs = []
for location in study.locations:
feature = Feature(self.context, uid=location.feature_id)
feature.load(self.context)
if gazeteer.fips_codes.has_key(
(feature.country_code, feature.adm1)):
region_name = gazeteer.fips_codes[(feature.country_code,
feature.adm1)]
else:
region_name = ''
full_name = '%s (%s, %s, %s)' % (
feature.name, gazeteer.feature_codes[feature.feature_type],
render_capitalized(region_name),
render_capitalized(
gazeteer.country_codes[feature.country_code]))
doc.add(
PyLucene.Field('location', unicode(full_name, 'latin-1'),
False, True, True))
doc.add(
PyLucene.Field('all', unicode(full_name, 'latin-1'), False,
True, True))
# Finally, the methodologies
for meth in study.methodologies:
doc.add(
PyLucene.Field('methodology',
meth.get_study_type(text=True), False, True,
True))
doc.add(
PyLucene.Field('all', meth.get_study_type(text=True),
False, True, True))
# And each exposure route term
for route in meth.get_routes(True):
doc.add(
PyLucene.Field('exposure_route', route, False, True,
True))
doc.add(PyLucene.Field('all', route, False, True, True))
writer.addDocument(doc)
if not had_writer:
writer.close()
except Exception, e:
self.logger.error('Failed to index record: %s', e)
self.logger.error(traceback.print_exc())
