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__)

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=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.')