check dbkey: [".."] as well, fix mypy errors

ahmedhamidawan · Jan 30, 2024 · 3e94c4d · 3e94c4d
1 parent 38b1107
commit 3e94c4d
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
@@ -78,6 +78,7 @@ def _get_index_filename(self, id, tbl_entries, ext, index_type):
 
 class GenomeFilterMixin:
     orm_filter_parsers: "OrmFilterParsersType"
+    database_connection: str
     valid_ops = ("eq", "contains", "has")
 
     def create_genome_filter(self, attr, op, val):
@@ -89,19 +90,21 @@ def _create_genome_filter(model_class=None):
             # Doesn't filter genome_build for collections
             if model_class.__name__ == "HistoryDatasetCollectionAssociation":
                 return False
-            # TODO: should use is_postgres(self.app.config.database_connection) in 23.2
-            if self.app.config.database_connection.startswith("postgres"):
+            # TODO: should use is_postgres(self.database_connection) in 23.2
+            if self.database_connection.startswith("postgres"):
                 column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")
             else:
                 column = func.json_extract(model_class.table.c._metadata, "$.dbkey")
             lower_val = val.lower()  # Ignore case
+            # dbkey can either be "hg38" or '["hg38"]', so we need to check both
             if op == "eq":
-                cond = func.lower(column) == lower_val
+                cond = func.lower(column) == lower_val or func.lower(column) == f'["{lower_val}"]'
             else:
                 cond = func.lower(column).contains(lower_val, autoescape=True)
             return cond
 
         return _create_genome_filter
 
-    def _add_parsers(self):
+    def _add_parsers(self, database_connection: str):
+        self.database_connection = database_connection
         self.orm_filter_parsers.update({"genome_build": self.create_genome_filter})
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
@@ -631,9 +631,10 @@ def parse_type_id_list(self, type_id_list_string, sep=","):
         return [self.decode_type_id(type_id) for type_id in type_id_list_string.split(sep)]
 
     def _add_parsers(self):
+        database_connection: str = self.app.config.database_connection
         super()._add_parsers()
         annotatable.AnnotatableFilterMixin._add_parsers(self)
-        genomes.GenomeFilterMixin._add_parsers(self)
+        genomes.GenomeFilterMixin._add_parsers(self, database_connection)
         deletable.PurgableFiltersMixin._add_parsers(self)
         taggable.TaggableFilterMixin._add_parsers(self)
         tools.ToolFilterMixin._add_parsers(self)