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-rw-r--r--gn3/api/search.py171
1 files changed, 47 insertions, 124 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py
index 8ce51e3..d25f362 100644
--- a/gn3/api/search.py
+++ b/gn3/api/search.py
@@ -40,28 +40,6 @@ def combine_queries(operator: int, *queries: xapian.Query) -> xapian.Query:
return reduce(partial(xapian.Query, operator), queries)
-def query_subqueries(query: xapian.Query) -> list[xapian.Query]:
- """Return list of child queries in query."""
- return [query.get_subquery(i) for i in range(query.get_num_subqueries())]
-
-
-def query_terms(query: xapian.Query) -> list[str]:
- """Return list of terms in query."""
- # Unfortunately, the TermIterator from python xapian bindings seems
- # buggy. So, we resort to traversing the query tree.
- # python xapian bindings do not expose xapian.Query.LEAF_TERM. This is
- # most likely a bug.
- leaf_type = 100
- if query.get_type() == leaf_type:
- # We have no choice but to access the protected _get_terms_begin method.
- # pylint: disable=protected-access
- return [query._get_terms_begin().get_term().decode("utf-8")]
- else:
- return reduce(lambda result, subquery: result + query_terms(subquery),
- query_subqueries(query),
- [])
-
-
class FieldProcessor(xapian.FieldProcessor):
"""
Field processor for use in a xapian query parser.
@@ -200,110 +178,55 @@ def parse_location_field(species_query: xapian.Query,
.maybe(xapian.Query.MatchNothing, make_query))
-def parse_synteny_field(synteny_prefix: str, query: bytes) -> xapian.Query:
- """Parse synteny field and return a xapian query."""
- if query.decode("utf-8") in ["on", "off"]:
- return xapian.Query(synteny_prefix + query.decode("utf-8"))
- else:
- return xapian.Query(xapian.Query.OP_INVALID)
-
-
-def is_synteny_on(synteny_prefix: str, query: xapian.Query) -> bool:
- """Check if synteny search is requested in query."""
- return synteny_prefix + "on" in query_terms(query)
-
-
-def remove_synteny_field(synteny_prefix: str, query: xapian.Query,
- parent_operator: int = xapian.Query.OP_AND) -> xapian.Query:
- """Return a new query with the synteny field removed."""
- # Note that this function only supports queries that exclusively use the
- # AND, OR, FILTER, WEIGHT, RANGE and INVALID operators.
- # python xapian bindings do not expose xapian.Query.LEAF_TERM. This is
- # most likely a bug.
- leaf_type = 100
- # Handle leaf node.
- if query.get_type() == leaf_type:
- if not any(term.startswith(synteny_prefix) for term in query_terms(query)):
- return query
- elif parent_operator in [xapian.Query.OP_AND, xapian.Query.OP_FILTER]:
- return xapian.Query.MatchAll
- elif parent_operator == xapian.Query.OP_OR:
- return xapian.Query.MatchNothing
- else:
- raise ValueError("Unexpected operator in query", query.get_type())
- # Recurse on non-leaf nodes with the AND, OR or FILTER operators as root.
- elif query.get_type() in (xapian.Query.OP_AND, xapian.Query.OP_OR,
- xapian.Query.OP_FILTER, xapian.Query.OP_SCALE_WEIGHT):
- return combine_queries(query.get_type(),
- *[remove_synteny_field(synteny_prefix, subquery, query.get_type())
- for subquery in query_subqueries(query)])
- # Return other supported non-leaf nodes verbatim.
- elif query.get_type() in [xapian.Query.OP_VALUE_RANGE, xapian.Query.OP_INVALID]:
- return query
- # Raise an exception on unsupported non-leaf nodes.
- else:
- raise ValueError("Unexpected operator in query", query.get_type())
-
-
def parse_query(synteny_files_directory: Path, query: str):
"""Parse search query using GeneNetwork specific field processors."""
- synteny_prefix = "XSYN"
-
- def make_query_parser(synteny: bool) -> xapian.QueryParser:
- queryparser = xapian.QueryParser()
- queryparser.set_stemmer(xapian.Stem("en"))
- queryparser.set_stemming_strategy(queryparser.STEM_SOME)
- species_prefix = "XS"
- chromosome_prefix = "XC"
- queryparser.add_boolean_prefix("author", "A")
- queryparser.add_boolean_prefix("species", species_prefix)
- queryparser.add_boolean_prefix("group", "XG")
- queryparser.add_boolean_prefix("tissue", "XI")
- queryparser.add_boolean_prefix("dataset", "XDS")
- queryparser.add_boolean_prefix("symbol", "XY")
- queryparser.add_boolean_prefix("chr", chromosome_prefix)
- queryparser.add_boolean_prefix("peakchr", "XPC")
- queryparser.add_prefix("description", "XD")
- queryparser.add_prefix("synteny", FieldProcessor(partial(parse_synteny_field,
- synteny_prefix)))
- range_prefixes = ["mean", "peak", "mb", "peakmb", "additive", "year"]
- for i, prefix in enumerate(range_prefixes):
- queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":"))
-
- # Add field processors for location shorthands.
- species_shorthands = {"Hs": "human",
- "Mm": "mouse"}
- for shorthand, species in species_shorthands.items():
- field_processors = [partial(parse_location_field,
- xapian.Query(species_prefix + species),
- chromosome_prefix,
- range_prefixes.index("mb"),
- Just)]
- # If human and synteny is requested, add liftover.
- # With synteny search, we search for the same gene sequences
- # across different species. But, the same gene sequences may be
- # present in very different chromosomal positions in different
- # species. So, we first liftover.
- if shorthand == "Hs" and synteny:
- chain_files = {"mouse": "hg19ToMm10-chains.over.chain.gz"}
- for lifted_species, chain_file in chain_files.items():
- field_processors.append(
- partial(parse_location_field,
- xapian.Query(species_prefix + lifted_species),
- chromosome_prefix,
- range_prefixes.index("mb"),
- partial(liftover_interval,
- synteny_files_directory / chain_file)))
- queryparser.add_boolean_prefix(
- shorthand,
- FieldProcessor(field_processor_or(*field_processors)))
- return queryparser
-
- return remove_synteny_field(
- synteny_prefix,
- make_query_parser(is_synteny_on(synteny_prefix,
- make_query_parser(False).parse_query(query)))
- .parse_query(query))
+ queryparser = xapian.QueryParser()
+ queryparser.set_stemmer(xapian.Stem("en"))
+ queryparser.set_stemming_strategy(queryparser.STEM_SOME)
+ species_prefix = "XS"
+ chromosome_prefix = "XC"
+ queryparser.add_boolean_prefix("author", "A")
+ queryparser.add_boolean_prefix("species", species_prefix)
+ queryparser.add_boolean_prefix("group", "XG")
+ queryparser.add_boolean_prefix("tissue", "XI")
+ queryparser.add_boolean_prefix("dataset", "XDS")
+ queryparser.add_boolean_prefix("symbol", "XY")
+ queryparser.add_boolean_prefix("chr", chromosome_prefix)
+ queryparser.add_boolean_prefix("peakchr", "XPC")
+ queryparser.add_prefix("description", "XD")
+ range_prefixes = ["mean", "peak", "mb", "peakmb", "additive", "year"]
+ for i, prefix in enumerate(range_prefixes):
+ queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":"))
+
+ # Add field processors for synteny triplets.
+ species_shorthands = {"Hs": "human",
+ "Mm": "mouse"}
+ for shorthand, species in species_shorthands.items():
+ field_processors = [partial(parse_location_field,
+ xapian.Query(species_prefix + species),
+ chromosome_prefix,
+ range_prefixes.index("mb"),
+ Just)]
+ # With synteny search, we search for the same gene sequences
+ # across different species. But, the same gene sequences may be
+ # present in very different chromosomal positions in different
+ # species. So, we first liftover.
+ # TODO: Implement liftover and synteny search for species other than
+ # human.
+ if shorthand == "Hs":
+ chain_files = {"mouse": "hg19ToMm10-chains.over.chain.gz"}
+ for lifted_species, chain_file in chain_files.items():
+ field_processors.append(
+ partial(parse_location_field,
+ xapian.Query(species_prefix + lifted_species),
+ chromosome_prefix,
+ range_prefixes.index("mb"),
+ partial(liftover_interval,
+ synteny_files_directory / chain_file)))
+ queryparser.add_boolean_prefix(
+ shorthand,
+ FieldProcessor(field_processor_or(*field_processors)))
+ return queryparser.parse_query(query)
@search.route("/")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 22:16:55 +0000