def _build_filter(self, only_in=[], filter_by=None):
'''Return list of hits based on given value on a specific field.
@param filter_by: A dictionary of {<field>: <value>} or
a list of (<field>, <value>) tuple, e.g.,
{'tag': 'chart', 'species': 'human'}
[('tag', 'chart'), ('species', ['human', 'mouse'])]
Note that <value> can be a list for multiple values.
@param kwargs: refer to self.query method.
'''
if only_in == ['gene']:
filter = BoolQuery()
else:
filter = self._get_user_filter()
if filter_by:
if isinstance(filter_by, dict):
_filter_by = filter_by.items()
else:
_filter_by = filter_by
for (field, value) in _filter_by:
if type(value) is types.ListType:
sub_filter = BoolQuery()
for v in value:
sub_filter.add_should(TermQuery(field, v))
filter.add_must(sub_filter)
else:
filter.add_must(TermQuery(field, value))
return None if filter.is_empty() else filter
def search_type(text):
q = BoolQuery(minimum_number_should_match=0)
#TODO add synonyms instead of relying on 'french'
q.add_must(MatchQuery('french', normalize_query_string(text)))
types = conn.search(query=q, indices="types")
if len(types) < 1:
log("KO", text)
return [t.get_id() for t in types[:1]]
def search_city(text):
q = BoolQuery(minimum_number_should_match=0)
q.add_must(MatchQuery('name', normalize_query_string(text)))
q.add_should(MatchQuery('zipcode', normalize_query_string(text)))
cities = conn.search(query=q, indices="cities")
if len(cities) < 1:
log("KO", text)
return [city.get_id() for city in cities[:1]]
return result
def search_city(text):
q = BoolQuery(minimum_number_should_match=0)
q.add_must(MatchQuery('name', normalize_query_string(text)))
q.add_should(MatchQuery('zipcode', normalize_query_string(text)))
cities = conn.search(query=q, indices="cities")
if len(cities) < 1:
log("KO", text)
return [city.get_id() for city in cities[:1]]
return result
def query_gene_by_interval(self, chr, gstart, gend,
taxid=None, species=None, assembly=None,
**kwargs):
'''query genes by genome interval.'''
if (taxid, species, assembly) == (None, None, None):
raise ValueError('At least one of "taxid", "species", "assembly" need to be specified.')
qrange = ESRange(field='pos',
from_value=safe_genome_pos(gstart),
to_value=safe_genome_pos(gend),
include_lower=True,
include_upper=True)
q = RangeQuery(qrange)
filter = BoolQuery()
filter.add_must(TermQuery('chr', chr))
if taxid:
filter.add_must(TermQuery('taxid', taxid))
if species:
filter.add_must(TermQuery('species', species))
if assembly:
filter.add_must(TermQuery('assembly', assembly))
q = FilteredQuery(q, filter)
return self.query(q, only_in=['gene'], **kwargs)
def _create_term_query(self, must_list):
# TODO: add remaining conditional list functionality.
query = BoolQuery()
for term in must_list:
query.add_must(term)
