diff options
Diffstat (limited to 'gn3/api/search.py')
| -rw-r--r-- | gn3/api/search.py | 22 |
1 files changed, 18 insertions, 4 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py index e497743..328baf5 100644 --- a/gn3/api/search.py +++ b/gn3/api/search.py @@ -148,6 +148,15 @@ def parse_position(spec: str) -> tuple[Maybe[int], Maybe[int]]: return Just(max(0, point - width)), Just(point + width) +def parse_position_field(location_slot: int, query: bytes) -> xapian.Query: + """Parse position and return a xapian query.""" + start, end = parse_position(query.decode("utf-8")) + # TODO: Convert the xapian index to use bases instead of megabases. + to_megabases = lambda x: str(Decimal(x)/10**6) + return (xapian.NumberRangeProcessor(location_slot) + (start.maybe("", to_megabases), end.maybe("", to_megabases))) # type: ignore + + def parse_location_field(species_query: xapian.Query, chromosome_prefix: str, location_slot: int, liftover_function: IntervalLiftoverFunction, @@ -183,6 +192,7 @@ def parse_location_field(species_query: xapian.Query, .maybe(xapian.Query.MatchNothing, make_query)) +# pylint: disable=too-many-locals def parse_query(synteny_files_directory: Path, query: str): """Parse search query using GeneNetwork specific field processors.""" queryparser = xapian.QueryParser() @@ -201,10 +211,14 @@ def parse_query(synteny_files_directory: Path, query: str): queryparser.add_prefix("description", "XD") range_prefixes = ["mean", "peak", "position", "peakmb", "additive", "year"] for i, prefix in enumerate(range_prefixes): - queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":")) - # Alias the position prefix with pos. - queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(range_prefixes.index("position"), - "pos:")) + # Treat position specially since it needs its own field processor. + if prefix == "position": + position_field_processor = FieldProcessor(partial(parse_position_field, i)) + queryparser.add_boolean_prefix(prefix, position_field_processor) + # Alias the position prefix with pos. + queryparser.add_boolean_prefix("pos", position_field_processor) + else: + queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":")) # Add field processors for synteny triplets. species_shorthands = {"Hs": "human", |