Merge pull request #260 from gyorilab/fix-web-api

Fix web api

Author: bgyori

src/indra_cogex/apps/queries_web/__init__.py

@@ -181,6 +181,7 @@ def get_example_data():
         'namespace': literature_metadata_ns,
         'functions': [
             "get_pmids_for_mesh",
+            "get_pmids_for_stmt_hash",
             "get_mesh_ids_for_pmid",
             "get_mesh_ids_for_pmids",
             "get_publisher_for_journal",
@@ -546,6 +547,24 @@ def get_example_data():
 # Maps function names to the actual functions
 func_mapping = {fname: getattr(module, fname) for module, fname in module_functions}
 
+# Validate that all functions in func_mapping are registered in FUNCTION_CATEGORIES.
+# This catches the common mistake of adding a function to module_functions but forgetting
+# to add it to FUNCTION_CATEGORIES, which would cause a runtime error later.
+_registered_functions = set()
+for _category, _info in FUNCTION_CATEGORIES.items():
+    _registered_functions.update(_info['functions'])
+
+_unregistered_functions = set(func_mapping.keys()) - _registered_functions
+if _unregistered_functions:
+    logger.warning(
+        f"The following functions are in func_mapping but not registered in "
+        f"FUNCTION_CATEGORIES: {sorted(_unregistered_functions)}. "
+        f"Add them to FUNCTION_CATEGORIES to expose them via the API."
+    )
+
+# Clean up temporary variables
+del _registered_functions, _unregistered_functions
+
 # Create resource for each query function
 for module, func_name in module_functions:
     if not isfunction(getattr(module, func_name)) or func_name == "get_schema_graph":
@@ -570,9 +589,14 @@ def get_example_data():
             f"it to FUNCTION_CATEGORIES."
         )
 
-    short_doc, fixed_doc = get_docstring(
-        func, skip_params=SKIP_GLOBAL | SKIP_ARGUMENTS.get(func_name, set())
-    )
+    try:
+        short_doc, fixed_doc = get_docstring(
+            func, skip_params=SKIP_GLOBAL | SKIP_ARGUMENTS.get(func_name, set())
+        )
+    except ValueError as e:
+        raise ValueError(
+            f"Error processing docstring for function '{func_name}': {e}"
+        ) from e
 
     param_names = list(func_sig.parameters.keys())
     param_names.remove("client")

src/indra_cogex/apps/queries_web/helpers.py

@@ -132,7 +132,7 @@ def get_web_return_annotation(sig: Signature) -> Type:
     # Get the return annotation
     return_annotation = sig.return_annotation
     if return_annotation is sig.empty:
-        raise ValueError("Forgot to type annotate function")
+        raise ValueError("Forgot to type annotate function return value")
 
     # Translate the return annotation:
     # Iterable[Node] -> List[Dict[str, Any]]
@@ -233,7 +233,7 @@ def get_docstring(
         )
     sig = signature(fun)
     if sig.return_annotation is sig.empty:
-        raise ValueError("Forgot to type annotate function")
+        raise ValueError(f"Forgot to type annotate function return value of {fun.__name__}")
 
     full_docstr = """{title}
 {extra_description}

src/indra_cogex/client/queries.py

@@ -801,9 +801,9 @@ def get_pmids_for_mesh(
 
     return client.query_nodes(query, **query_param)
 
-@autoclient()
-def get_pmids_for_stmt_hash(stmt_hash: int, *, client: Neo4jClient):
 
+@autoclient()
+def get_pmids_for_stmt_hash(stmt_hash: int, *, client: Neo4jClient) -> List[str]:
     """Return the PubMed IDs for the given statement hash.
 
     Parameters
@@ -816,7 +816,7 @@ def get_pmids_for_stmt_hash(stmt_hash: int, *, client: Neo4jClient):
     Returns
     -------
     :
-        The PubMed IDs for the given MESH term
+        The PubMed IDs for the given statement hash.
     """
     query = """
         MATCH (e:Evidence {stmt_hash: $hash})-[:has_citation]-(p:Publication)
@@ -2701,7 +2701,7 @@ def get_projects_for_patent(
     )
 
 
-#interpro
+# interpro
 @autoclient()
 def get_domains_for_gene(
     gene: Tuple[str, str], *, client: Neo4jClient
@@ -2783,7 +2783,7 @@ def gene_has_domain(
     )
 
 
-#gwas
+# gwas
 @autoclient()
 def get_phenotypes_for_variant_gwas(
     variant: Tuple[str, str], *, client: Neo4jClient
@@ -3533,8 +3533,6 @@ def build_edges_from_graph(graph, statements, input_node_names, include_db_evide
     return edges
 
 
-
-
 def _get_edge_styling(stmt_type):
     """Return RGB base color, dash pattern, and arrow spec for statement type."""
     if 'Activation' in stmt_type:
@@ -3644,7 +3642,6 @@ def get_network(
         return {"nodes": [], "edges": [], "error": str(e)}
 
 
-
 if __name__ == "__main__":
     print(get_prefix_counter())
     print(get_node_counter())