Fix GenericFilter creating conditional with empty list (#744)

* Test that fails

* Add fix to check empty IN in the GenericFilters

* Linting

* Better logic for FilterModel.is_false

---------

Co-authored-by: Michael Franklin <[email protected]>

db/python/tables/sequencing_group.py

@@ -61,6 +61,9 @@ async def query(
         self, filter_: SequencingGroupFilter
     ) -> tuple[set[ProjectId], list[SequencingGroupInternal]]:
         """Query samples"""
+        if filter_.is_false():
+            return set(), []
+
         sql_overrides = {
             'project': 's.project',
             'sample_id': 'sg.sample_id',
@@ -166,9 +169,9 @@ async def get_all_sequencing_group_ids_by_sample_ids_by_type(
         WHERE project = :project
         """
         rows = await self.connection.fetch_all(_query, {'project': self.project})
-        sequencing_group_ids_by_sample_ids_by_type: dict[
-            int, dict[str, list[int]]
-        ] = defaultdict(lambda: defaultdict(list))
+        sequencing_group_ids_by_sample_ids_by_type: dict[int, dict[str, list[int]]] = (
+            defaultdict(lambda: defaultdict(list))
+        )
         for row in rows:
             sample_id = row['sid']
             sg_id = row['sgid']

db/python/utils.py

@@ -146,6 +146,12 @@ def generate_field_name(name):
         """
         return NONFIELD_CHARS_REGEX.sub('_', name)
 
+    def is_false(self) -> bool:
+        """
+        The filter will resolve to False (usually because the in_ is an empty list)
+        """
+        return self.in_ is not None and len(self.in_) == 0
+
     def to_sql(
         self, column: str, column_name: str = None
     ) -> tuple[str, dict[str, T | list[T]]]:
@@ -161,6 +167,9 @@ def to_sql(
             conditionals.append(f'{column} = :{k}')
             values[k] = self._sql_value_prep(self.eq)
         if self.in_ is not None:
+            if len(self.in_) == 0:
+                # in an empty list is always false
+                return 'FALSE', {}
             if not isinstance(self.in_, list):
                 raise ValueError('IN filter must be a list')
             if len(self.in_) == 1:
@@ -171,7 +180,8 @@ def to_sql(
                 k = self.generate_field_name(_column_name + '_in')
                 conditionals.append(f'{column} IN :{k}')
                 values[k] = self._sql_value_prep(self.in_)
-        if self.nin is not None:
+        if self.nin is not None and len(self.nin) > 0:
+            # not in an empty list is always true
             if not isinstance(self.nin, list):
                 raise ValueError('NIN filter must be a list')
             k = self.generate_field_name(column + '_nin')
@@ -223,6 +233,21 @@ def __hash__(self):
         """Hash the GenericFilterModel, this doesn't override well"""
         return hash(dataclasses.astuple(self))
 
+    def is_false(self) -> bool:
+        """
+        Returns False if any of the internal filters is FALSE
+        """
+        for field in dataclasses.fields(self):
+            value = getattr(self, field.name)
+            if isinstance(value, GenericFilter) and value.is_false():
+                return True
+
+            if isinstance(value, dict):
+                if any(f.is_false() for f in value.values()):
+                    return True
+
+        return False
+
     def __post_init__(self):
         for field in dataclasses.fields(self):
             value = getattr(self, field.name)
@@ -259,6 +284,9 @@ def to_sql(
         self, field_overrides: dict[str, str] = None
     ) -> tuple[str, dict[str, Any]]:
         """Convert the model to SQL, and avoid SQL injection"""
+        if self.is_false():
+            return 'FALSE', {}
+
         _foverrides = field_overrides or {}
 
         # check for bad field_overrides

test/test_analysis.py

@@ -95,6 +95,14 @@ async def test_get_analysis_by_id(self):
         self.assertEqual('cram', analysis.type)
         self.assertEqual(AnalysisStatus.COMPLETED, analysis.status)
 
+    @run_as_sync
+    async def test_empty_query(self):
+        """
+        Test empty IDs to see the query construction
+        """
+        analyses = await self.al.query(AnalysisFilter(id=GenericFilter(in_=[])))
+        self.assertEqual(len(analyses), 0)
+
     @run_as_sync
     async def test_add_cram(self):
         """

test/test_sequencing_groups.py

@@ -52,6 +52,14 @@ async def setUp(self) -> None:
         self.sglayer = SequencingGroupLayer(self.connection)
         self.slayer = SampleLayer(self.connection)
 
+    @run_as_sync
+    async def test_empty_query(self):
+        """
+        Test empty IDs to see the query construction
+        """
+        sgs = await self.sglayer.query(SequencingGroupFilter(id=GenericFilter(in_=[])))
+        self.assertEqual(len(sgs), 0)
+
     @run_as_sync
     async def test_insert_sequencing_group(self):
         """Test inserting and fetching a sequencing group"""