docs

src/oaklib/cli.py

@@ -3503,7 +3503,7 @@ def _is_uri_or_curie(v):
 
  # batch query results: this allows us to produce buffered output
  # for a long-running query
- for row_it in chunk(impl.onto_query(query, prefixes=prefixes)):
+ for row_it in chunk(impl.query(query, prefixes=prefixes)):
  rows = []
  # collect rows in batch, and set label_fields if not already set
  for r in row_it:

src/oaklib/query.py

@@ -1,3 +1,8 @@
+"""Representation and execution of complex boolean queries.
+
+See also `<https://incatools.github.io/ontology-access-kit/howtos/use-oak-expression-language.html>`_.
+"""
+
 import itertools
 import logging
 import re
@@ -38,13 +43,19 @@
 
 
 class OperatorEnum(str, Enum):
+ """Boolean operators for queries."""
+
  AND = "and"
  OR = "or"
  NOT = "not"
 
 
 class FunctionEnum(str, Enum):
+ """Enumeration of types of functions for queries."""
+
  ANCESTOR = "anc"
+ """Ancestor query."""
+
  DESCENDANT = "desc"
  SUBCLASS = "sub"
  CHILD = "child"
@@ -53,6 +64,7 @@ class FunctionEnum(str, Enum):
  MRCA = "mrca"
  NON_REDUNDANT = "nr"
  GAP_FILL = "gap_fill"
+ QUERY = "query"
 
 
 class Query(BaseModel):
@@ -576,7 +588,7 @@ def chain_results(v):
  query_terms = query_terms[1:]
  chain_results(eval(expr, {"impl": adapter, "terms": results})) # noqa
  elif term.startswith(".query"):
- # arbitrary SPARQL query
+ # arbitrary SPARQL or SQL query (implementation specific)
  params = _parse_params(term)
  prefixes = params.get("prefixes", None)
  query = query_terms[0]

tests/test_cli.py

@@ -1030,7 +1030,9 @@ def test_query(self):
  reader = csv.DictReader(file, delimiter="\t")
  rows = [row for row in reader]
  for e in expected:
- self.assertIn(e, rows)
+ self.assertIn(
+ e, rows, f"Expected {expected} for {query} in {adapter} with args {args}"
+ )
  # for case in cases:
  # self.assertIn(case, rows)