def _extra_query_options(self, search, options):
search = AsyncSearch().query(
"function_score",
query=search.query,
functions=[
{"filter": {"term": {"name": "pseudogene"}}, "weight": "0.5"}, # downgrade
{"filter": {"term": {"taxid": 9606}}, "weight": "1.55"},
{"filter": {"term": {"taxid": 10090}}, "weight": "1.3"},
{"filter": {"term": {"taxid": 10116}}, "weight": "1.1"},
], score_mode="first")
if options.entrezonly:
search = search.filter('exists', field="entrezgene")
if options.ensemblonly:
search = search.filter('exists', field="ensembl.gene")
if options.missing:
for field in options.missing:
search = search.exclude('exists', field=field)
if options.exists:
for field in options.exists:
search = search.filter('exists', field=field)
if options.species:
if 'all' in options.species:
pass # do not apply any filters
elif not all(isinstance(string, str) for string in options.species):
raise BadRequest(reason="species must be strings or integer strings.")
elif not all(string.isnumeric() for string in options.species):
raise BadRequest(reason="cannot map some species to taxids.")
else: # filter by taxid numeric strings
search = search.filter('terms', taxid=options.species)
if options.aggs and options.species_facet_filter:
search = search.post_filter('terms', taxid=options.species_facet_filter)
return search
def _extra_query_options(self, search, options):
search = AsyncSearch().query(
"function_score",
query=search.query,
functions=[
{
"filter": {
"term": {
"name": "pseudogene"
}
},
"weight": "0.5"
}, # downgrade
{
"filter": {
"term": {
"taxid": 9606
}
},
"weight": "1.55"
},
{
"filter": {
"term": {
"taxid": 10090
}
},
"weight": "1.3"
},
{
"filter": {
"term": {
"taxid": 10116
}
},
"weight": "1.1"
},
],
score_mode="first")
if options.entrezonly:
search = search.filter('exists', field="entrezgene")
if options.ensemblonly:
search = search.filter('exists', field="ensembl.gene")
if options.missing:
for field in options.missing:
search = search.exclude('exists', field=field)
if options.exists:
for field in options.exists:
search = search.filter('exists', field=field)
if options.species:
if 'all' not in options.species: # TODO
search = search.filter('terms', taxid=options.species)
if options.aggs and options.species_facet_filter:
search = search.post_filter('terms',
taxid=options.species_facet_filter)
return search