diff --git a/tests/cli/test_query.py b/tests/cli/test_query.py
index d7eaad5..9421187 100644
--- a/tests/cli/test_query.py
+++ b/tests/cli/test_query.py
@@ -9,7 +9,7 @@
 import pytest
 
 from gambit.seq import SequenceFile
-from gambit.query import QueryInput, QueryResults
+from gambit.query import QueryResults
 from gambit.util.misc import zip_strict
 from gambit.util.io import write_lines, FilePath
 from gambit.cli.common import strip_seq_file_ext
@@ -20,13 +20,13 @@
 
 
 def make_args(testdb: TestDB, *,
-			  positional_files: Optional[Iterable[SequenceFile]] = None,
-			  list_file: Optional['FilePath'] = None,
-			  sig_file: bool = False,
-			  output: Optional['FilePath'] = None,
-			  outfmt: Optional[str] = None,
-			  strict: bool=False,
-			  ) -> list[str]:
+              positional_files: Optional[Iterable[SequenceFile]] = None,
+              list_file: Optional['FilePath'] = None,
+              sig_file: bool = False,
+              output: Optional['FilePath'] = None,
+              outfmt: Optional[str] = None,
+              strict: bool=False,
+              ) -> list[str]:
 	"""Make command line arguments for querying."""
 
 	args: list[str] = [f'--db={testdb.paths.root}', 'query']
@@ -50,16 +50,29 @@ def make_args(testdb: TestDB, *,
 	return args
 
 
-def make_ref_results(testdb: TestDB, inputs: Iterable[QueryInput], strict: bool, nqueries: Optional[int]):
+def make_ref_results(testdb: TestDB,
+                     labels: Iterable[str],
+                     strict: bool,
+                     files: Optional[Iterable[FilePath]],
+                     nqueries: Optional[int] = None,
+                     ):
 	"""
 	Make a copy of the reference query results to compare to, modifying to account for possibly
-	different query inputs and # of queries.
+	different query labels/files and # of queries.
 	"""
 	ref_results = copy(testdb.get_query_results(strict))
 	ref_results.items = ref_results.items[:nqueries]
 
-	for item, input in zip_strict(ref_results.items, inputs):
-		item.input = input
+	for item, label in zip_strict(ref_results.items, labels):
+		item.label = label
+
+	if files is None:
+		for item in ref_results.items:
+			item.file = None
+
+	if files is not None:
+		for item, file in zip_strict(ref_results.items, files):
+			item.file = Path(file)
 
 	return ref_results
 
@@ -94,21 +107,18 @@ def check_results(results_file: Path, out_fmt: str, ref_results: QueryResults):
 	],
 )
 def test_full_query(testdb: TestDB,
-					nqueries: Optional[int],
-					use_list_file: bool,
-					out_fmt: str,
-					strict: bool,
-					gzipped: bool,
-					tmp_path: Path,
-					):
+                    nqueries: Optional[int],
+                    use_list_file: bool,
+                    out_fmt: str,
+                    strict: bool,
+                    gzipped: bool,
+                    tmp_path: Path,
+                    ):
 	"""Run a full query using the command line interface."""
 
-	query_files = testdb.get_query_files(gzipped)[:nqueries]
-	inputs = [
-		QueryInput(strip_seq_file_ext(file.path.name), file)
-		for file in query_files
-	]
-	ref_results: QueryResults = make_ref_results(testdb, inputs, strict, nqueries)
+	query_files = [sigfile.path for sigfile in testdb.get_query_files(gzipped)[:nqueries]]
+	labels = [strip_seq_file_ext(file.name) for file in query_files]
+	ref_results: QueryResults = make_ref_results(testdb, labels, strict, query_files, nqueries=nqueries)
 
 	results_file = tmp_path / ('results.' + out_fmt)
 
@@ -137,8 +147,7 @@ def test_full_query(testdb: TestDB,
 def test_sigfile(testdb: TestDB, out_fmt: str, strict: bool, tmp_path: Path):
 	"""Test using signature file instead of parsing genome files."""
 
-	inputs = list(map(QueryInput, testdb.query_signatures.ids))
-	ref_results = make_ref_results(testdb, inputs, strict, None)
+	ref_results = make_ref_results(testdb, testdb.query_signatures.ids, strict, None)
 
 	results_file = tmp_path / ('results.' + out_fmt)
 
diff --git a/tests/results.py b/tests/results.py
index 88f27e0..33f0d0b 100644
--- a/tests/results.py
+++ b/tests/results.py
@@ -164,12 +164,12 @@ def cmp_genomematch_json(data, match: GenomeMatch):
 	cmp_taxon_json(data['matched_taxon'], match.matched_taxon)
 
 
-def check_json_results(file: TextIO,
-                       results: QueryResults,
-                       strict: bool = False,
-                       ):
+def check_json_results(file: TextIO, results: QueryResults, strict: bool = False):
 	"""Assert exported JSON data matches the given results object.
 
+	"Strict" mode also compares the ``timestamp``, ``gambit_version``, and ``extra`` attributes
+	at the top level and expects that full input file paths must match instead of just file names.
+
 	Parameters
 	----------
 	file