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Source code for galaxy.webapps.tool_shed.search.tool_search
"""Module for searching the toolshed tools within all repositories"""
import logging
import os
import whoosh.index
from whoosh import scoring
from whoosh.fields import (
Schema,
STORED,
TEXT
)
from whoosh.qparser import MultifieldParser
from galaxy import exceptions
from galaxy.exceptions import ObjectNotFound
log = logging.getLogger(__name__)
tool_schema = Schema(
name=TEXT(stored=True),
description=TEXT(stored=True),
owner=TEXT(stored=True),
id=TEXT(stored=True),
help=TEXT(stored=True),
version=TEXT(stored=True),
repo_name=TEXT(stored=True),
repo_owner_username=TEXT(stored=True),
repo_id=STORED)
[docs]class ToolSearch(object):
[docs] def search(self, trans, search_term, page, page_size, boosts):
"""
Perform the search on the given search_term
:param search_term: unicode encoded string with the search term(s)
:returns results: dictionary containing number of hits, hits themselves and matched terms for each
"""
tool_index_dir = os.path.join(trans.app.config.whoosh_index_dir, 'tools')
index_exists = whoosh.index.exists_in(tool_index_dir)
if index_exists:
index = whoosh.index.open_dir(tool_index_dir)
try:
# Some literature about BM25F:
# http://trec.nist.gov/pubs/trec13/papers/microsoft-cambridge.web.hard.pdf
# http://en.wikipedia.org/wiki/Okapi_BM25
# __Basically__ the higher number the bigger weight.
tool_weighting = scoring.BM25F(field_B={
'name_B' : boosts.tool_name_boost,
'description_B' : boosts.tool_description_boost,
'help_B' : boosts.tool_help_boost,
'repo_owner_username_B' : boosts.tool_repo_owner_username_boost})
searcher = index.searcher(weighting=tool_weighting)
parser = MultifieldParser([
'name',
'description',
'help',
'repo_owner_username'], schema=tool_schema)
user_query = parser.parse('*' + search_term + '*')
try:
hits = searcher.search_page(user_query, page, pagelen=page_size, terms=True)
except ValueError:
raise ObjectNotFound('The requested page does not exist.')
log.debug('searching tools for: #' + str(search_term))
log.debug('total hits: ' + str(len(hits)))
log.debug('scored hits: ' + str(hits.scored_length()))
results = {}
results['total_results'] = str(len(hits))
results['page'] = str(page)
results['page_size'] = str(page_size)
results['hits'] = []
for hit in hits:
hit_dict = {}
hit_dict['id'] = hit.get('id')
hit_dict['repo_owner_username'] = hit.get('repo_owner_username')
hit_dict['repo_name'] = hit.get('repo_name')
hit_dict['name'] = hit.get('name')
hit_dict['description'] = hit.get('description')
results['hits'].append({'tool': hit_dict, 'matched_terms': hit.matched_terms(), 'score': hit.score})
return results
finally:
searcher.close()
else:
raise exceptions.InternalServerError('The search index file is missing.')