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Source code for tool_shed.webapp.search.repo_search
"""Module for searching the toolshed repositories"""
import logging
import whoosh.index
from whoosh import scoring
from whoosh.fields import (
KEYWORD,
NUMERIC,
Schema,
STORED,
TEXT,
)
from whoosh.qparser import MultifieldParser
from whoosh.query import (
And,
Every,
Term,
)
from galaxy import exceptions
from galaxy.exceptions import ObjectNotFound
from galaxy.util.search import parse_filters
log = logging.getLogger(__name__)
schema = Schema(
id=NUMERIC(stored=True),
name=TEXT(field_boost=1.7, stored=True),
description=TEXT(field_boost=1.5, stored=True),
long_description=TEXT(stored=True),
homepage_url=TEXT(stored=True),
remote_repository_url=TEXT(stored=True),
repo_owner_username=TEXT(stored=True),
categories=KEYWORD(stored=True, commas=True, scorable=True),
times_downloaded=STORED,
approved=STORED,
last_updated=STORED,
repo_lineage=STORED,
full_last_updated=STORED,
)
[docs]class RepoWeighting(scoring.BM25F):
"""
Affect the BM25G scoring model through the final method.
source: https://groups.google.com/forum/#!msg/whoosh/1AKNbW8R_l8/XySW0OecH6gJ
"""
use_final = True
[docs] def final(self, searcher, docnum, score):
# Arbitrary for now
reasonable_hits = 100.0
stored_times_downloaded = searcher.stored_fields(docnum)["times_downloaded"]
if not isinstance(stored_times_downloaded, int):
times_downloaded = int(stored_times_downloaded)
else:
times_downloaded = stored_times_downloaded
# Add 1 to prevent 0 being divided
if times_downloaded == 0:
times_downloaded = 1
popularity_modifier = times_downloaded / reasonable_hits
cert_modifier = 2 if searcher.stored_fields(docnum)["approved"] == "yes" else 1
# Adjust the computed score for this document by the popularity
# and by the certification level.
final_score = score * popularity_modifier * cert_modifier
return final_score
[docs]class RepoSearch:
[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)
:param boosts: namedtuple containing custom boosts for searchfields, see api/repositories.py
:param page_size: integer defining a length of one page
:param page: integer with the number of page requested
:returns results: dictionary containing hits themselves and the hits summary
"""
log.debug(f"raw search query: #{str(search_term)}")
lower_search_term = search_term.lower()
allow_query, search_term_without_filters = self._parse_reserved_filters(lower_search_term)
log.debug(f"term without filters: #{str(search_term_without_filters)}")
whoosh_index_dir = trans.app.config.whoosh_index_dir
index_exists = whoosh.index.exists_in(whoosh_index_dir)
if index_exists:
index = whoosh.index.open_dir(whoosh_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.
repo_weighting = RepoWeighting(
field_B={
"name_B": boosts.repo_name_boost,
"description_B": boosts.repo_description_boost,
"long_description_B": boosts.repo_long_description_boost,
"homepage_url_B": boosts.repo_homepage_url_boost,
"remote_repository_url_B": boosts.repo_remote_repository_url_boost,
"repo_owner_username_B": boosts.repo_owner_username_boost,
"categories_B": boosts.categories_boost,
}
)
searcher = index.searcher(weighting=repo_weighting)
parser = MultifieldParser(
[
"name",
"description",
"long_description",
"homepage_url",
"remote_repository_url",
"repo_owner_username",
"categories",
],
schema=schema,
)
# If user query has just filters prevent wildcard search.
if len(search_term_without_filters) < 1:
user_query = Every("name")
sortedby = "name"
else:
user_query = parser.parse(f"*{search_term_without_filters}*")
sortedby = ""
try:
hits = searcher.search_page(
user_query, page, pagelen=page_size, filter=allow_query, terms=True, sortedby=sortedby
)
log.debug(f"total hits: {str(len(hits))}")
log.debug(f"scored hits: {str(hits.scored_length())}")
except ValueError:
raise ObjectNotFound("The requested page does not exist.")
results = {}
results["total_results"] = str(len(hits))
results["page"] = str(page)
results["page_size"] = str(page_size)
results["hits"] = []
for hit in hits:
log.debug(f"matched terms: {str(hit.matched_terms())}")
hit_dict = {}
hit_dict["id"] = trans.security.encode_id(hit.get("id"))
hit_dict["repo_owner_username"] = hit.get("repo_owner_username")
hit_dict["name"] = hit.get("name")
hit_dict["long_description"] = hit.get("long_description")
hit_dict["remote_repository_url"] = hit.get("remote_repository_url")
hit_dict["homepage_url"] = hit.get("homepage_url")
hit_dict["description"] = hit.get("description")
hit_dict["last_updated"] = hit.get("last_updated")
hit_dict["full_last_updated"] = hit.get("full_last_updated")
hit_dict["repo_lineage"] = hit.get("repo_lineage")
hit_dict["categories"] = hit.get("categories")
hit_dict["approved"] = hit.get("approved")
hit_dict["times_downloaded"] = hit.get("times_downloaded")
results["hits"].append({"repository": hit_dict, "score": hit.score})
return results
finally:
searcher.close()
else:
raise exceptions.InternalServerError("The search index file is missing.")
def _parse_reserved_filters(self, search_term):
"""
Support github-like filters for narrowing the results.
Order of chunks does not matter, only recognized
filter names are allowed.
:param search_term: the original search str from user input
:returns allow_query: whoosh Query object used for filtering
results of searching in index
:returns search_term_without_filters: str that represents user's
search phrase without the filters
>>> rs = RepoSearch()
>>> rs._parse_reserved_filters("category:assembly")
(And([Term('categories', 'assembly')]), '')
>>> rs._parse_reserved_filters("category:assembly abyss")
(And([Term('categories', 'assembly')]), 'abyss')
>>> rs._parse_reserved_filters("category:'Climate Analysis' psy_maps")
(And([Term('categories', 'Climate Analysis')]), 'psy_maps')
>>> rs._parse_reserved_filters("climate category:'Climate Analysis' owner:'bjoern gruening' psy_maps")
(And([Term('categories', 'Climate Analysis'), Term('repo_owner_username', 'bjoern gruening')]), 'climate psy_maps')
>>> rs._parse_reserved_filters("climate category:'John Says This Fails' owner:'bjoern gruening' psy_maps")
(And([Term('categories', 'John Says This Fails'), Term('repo_owner_username', 'bjoern gruening')]), 'climate psy_maps')
>>> rs._parse_reserved_filters("climate o:'bjoern gruening' middle strings c:'John Says This Fails' psy_maps")
(And([Term('repo_owner_username', 'bjoern gruening'), Term('categories', 'John Says This Fails')]), 'climate middle strings psy_maps')
>>> rs._parse_reserved_filters("abyss category:assembly")
(And([Term('categories', 'assembly')]), 'abyss')
>>> rs._parse_reserved_filters("abyss category:assembly greg")
(And([Term('categories', 'assembly')]), 'abyss greg')
>>> rs._parse_reserved_filters("owner:greg")
(And([Term('repo_owner_username', 'greg')]), '')
>>> rs._parse_reserved_filters("owner:greg category:assembly abyss")
(And([Term('repo_owner_username', 'greg'), Term('categories', 'assembly')]), 'abyss')
>>> rs._parse_reserved_filters("meaningoflife:42")
(None, 'meaningoflife:42')
"""
filters = {
"category": "categories",
"c": "categories",
"owner": "repo_owner_username",
"o": "repo_owner_username",
}
allow_query, search_term_without_filters = parse_filters(search_term, filters)
allow_query = (
And([Term(t, v) for (t, v, _) in allow_query] if len(allow_query) > 0 else None) if allow_query else None
)
return allow_query, search_term_without_filters