PR feedback

cumulus_library/base_table_builder.py

@@ -119,14 +119,10 @@ def comment_queries(self, doc_str=None):
         commented_queries.pop()
         self.queries = commented_queries
 
-    def write_queries(
-        self, filename: str = "output.sql", dir_path: pathlib.Path = None
-    ):
+    def write_queries(self, path: pathlib.Path = pathlib.Path.cwd() / "output.sql"):
+        path.parents[0].mkdir(parents=True, exist_ok=True)
         """writes all queries constructed by prepare_queries to disk"""
-        if dir_path:
-            dir_path.mkdir(exist_ok=True)
-            filename = dir_path / filename
-        with open(filename, "w", encoding="utf-8") as file:
+        with open(path, "w", encoding="utf-8") as file:
             for query in self.queries:
                 file.write(query)
                 file.write("\n")

cumulus_library/cli.py

@@ -297,7 +297,6 @@ def get_studies_by_manifest_path(path: pathlib.Path) -> dict:
 
 def run_cli(args: Dict):
     """Controls which library tasks are run based on CLI arguments"""
-    print(args)
     if args["action"] == "create":
         create_template(args["create_dir"])
 
@@ -308,11 +307,11 @@ def run_cli(args: Dict):
     else:
         db_backend = databases.create_db_backend(args)
         try:
-            builder = StudyRunner(db_backend, data_path=args.get("data_path"))
-            if "verbose" in args and args["verbose"]:
-                builder.verbose = True
+            runner = StudyRunner(db_backend, data_path=args.get("data_path"))
+            if args.get("verbose"):
+                runner.verbose = True
             print("Testing connection to database...")
-            builder.cursor.execute("SHOW DATABASES")
+            runner.cursor.execute("SHOW DATABASES")
 
             study_dict = get_study_dict(args["study_dir"])
             if "prefix" not in args.keys():
@@ -326,42 +325,42 @@ def run_cli(args: Dict):
                                 "you include `-s path/to/study/dir` as an arugment."
                             )
             if args["action"] == "clean":
-                builder.clean_study(
+                runner.clean_study(
                     args["target"],
                     study_dict,
                     stats_clean=args["stats_clean"],
                     prefix=args["prefix"],
                 )
             elif args["action"] == "build":
                 if "all" in args["target"]:
-                    builder.clean_and_build_all(study_dict, args["stats_build"])
+                    runner.clean_and_build_all(study_dict, args["stats_build"])
                 else:
                     for target in args["target"]:
                         if args["builder"]:
-                            builder.run_single_table_builder(
+                            runner.run_single_table_builder(
                                 study_dict[target], args["builder"]
                             )
                         else:
-                            builder.clean_and_build_study(
+                            runner.clean_and_build_study(
                                 study_dict[target],
                                 stats_build=args["stats_build"],
                                 continue_from=args["continue_from"],
                             )
 
             elif args["action"] == "export":
                 if "all" in args["target"]:
-                    builder.export_all(study_dict, args["data_path"])
+                    runner.export_all(study_dict, args["data_path"])
                 else:
                     for target in args["target"]:
-                        builder.export_study(study_dict[target], args["data_path"])
+                        runner.export_study(study_dict[target], args["data_path"])
 
             elif args["action"] == "generate-sql":
                 if "all" in args["target"]:
                     for target in study_dict.keys():
-                        builder.generate_all_sql(study_dict[target])
+                        runner.generate_all_sql(study_dict[target])
                 else:
                     for target in args["target"]:
-                        builder.generate_study_sql(study_dict[target])
+                        runner.generate_study_sql(study_dict[target])
         finally:
             db_backend.close()
 

cumulus_library/study_parser.py

@@ -322,7 +322,7 @@ def _load_and_execute_builder(
         verbose: bool = False,
         drop_table: bool = False,
         parser: databases.DatabaseParser = None,
-        generate_sql: bool = False,
+        write_reference_sql: bool = False,
         doc_str: str = None,
     ) -> None:
         """Loads a table builder from a file.
@@ -371,12 +371,12 @@ def _load_and_execute_builder(
         # execute, since the subclass would otherwise hang around.
         table_builder_class = table_builder_subclasses[0]
         table_builder = table_builder_class()
-        if generate_sql:
+        if write_reference_sql:
             table_builder.prepare_queries(cursor, schema, parser=parser)
             table_builder.comment_queries(doc_str=doc_str)
+            new_filename = pathlib.Path(f"{filename}").stem + ".sql"
             table_builder.write_queries(
-                filename=f"{filename.split('.')[0]}.sql",
-                dir_path=pathlib.Path(f"{self._study_path}/reference_sql"),
+                path=pathlib.Path(f"{self._study_path}/reference_sql/" + new_filename)
             )
         else:
             table_builder.execute_queries(
@@ -525,7 +525,7 @@ def run_generate_sql(
         parser: databases.DatabaseParser = None,
         **kwargs,
     ) -> None:
-        """Loads modules from a manifest and executes code via BaseTableBuilder
+        """Generates reference SQL from all BaseTableBuilder-derived classes in the manifest
 
         :param cursor: A DatabaseCursor object
         :param schema: The name of the schema to write tables to
@@ -544,7 +544,12 @@ def run_generate_sql(
         )
         for file in all_generators:
             self._load_and_execute_builder(
-                file, cursor, schema, parser=parser, generate_sql=True, doc_str=doc_str
+                file,
+                cursor,
+                schema,
+                parser=parser,
+                write_reference_sql=True,
+                doc_str=doc_str,
             )
 
     def build_study(