refact(db): move some db calls into methods in class

bento_wes/backends/_wes_backend.py

@@ -354,11 +354,7 @@ def _initialize_run_and_get_command(
             self.log_error("Could not find workflow name in workflow file")
             return self._finish_run_and_clean_up(run, states.STATE_SYSTEM_ERROR)
 
-        c = self.db.cursor()
-
-        # TODO: To avoid having multiple names, we should maybe only set this once?
-        c.execute("UPDATE runs SET run_log__name = ? WHERE id = ?", (workflow_name, run.run_id))
-        self.db.commit()
+        self.db.set_run_log_name(run, workflow_name)
 
         # -- Store input for the workflow in a file in the temporary folder --------------------------------------------
         with open(self._params_path(run), "w") as pf:
@@ -368,10 +364,7 @@ def _initialize_run_and_get_command(
         cmd = self._get_command(self.workflow_path(run), self._params_path(run), self.run_dir(run))
 
         # -- Update run log with command and Celery ID -----------------------------------------------------------------
-        c.execute(
-            "UPDATE runs SET run_log__cmd = ?, run_log__celery_id = ? WHERE id = ?",
-            (" ".join(cmd), celery_id, run.run_id))
-        self.db.commit()
+        self.db.set_run_log_command_and_celery_id(run, cmd, celery_id)
 
         return cmd, workflow_params_with_secrets
 

bento_wes/db.py

@@ -11,6 +11,7 @@
 from urllib.parse import urljoin
 
 from . import states
+from .backends.backend_types import Command
 from .constants import SERVICE_ARTIFACT
 from .events import get_flask_event_bus
 from .models import RunLog, RunRequest, Run, RunWithDetailsAndOutput
@@ -95,10 +96,8 @@ def close(self):
         self._conn.close()
 
     def init(self):
-        c = self.cursor()
-
         with current_app.open_resource("schema.sql") as sf:
-            c.executescript(sf.read().decode("utf-8"))
+            self.cursor().executescript(sf.read().decode("utf-8"))
 
         self.commit()
 
@@ -113,10 +112,10 @@ def finish_run(
         """
         Updates a run's state, sets the run log's end time, and publishes an event corresponding with a run failure
         or a run success, depending on the state.
-        :param c: An SQLite connection cursor
         :param event_bus: A bento_lib-defined event bus implementation for sending events
         :param run: The run which just finished
         :param state: The terminal state for the finished run
+        :param cursor: An SQLite connection cursor to re-use (optional)
         :param logger: An optionally-provided logger object.
         :return:
         """
@@ -224,6 +223,17 @@ def get_run_with_details(
             return cls.run_with_details_and_output_from_row(c, run, stream_content)
         return None
 
+    def set_run_log_name(self, run: Run, workflow_name: str):
+        # TODO: To avoid having multiple names, we should maybe only set this once?
+        self.cursor().execute("UPDATE runs SET run_log__name = ? WHERE id = ?", (workflow_name, run.run_id))
+        self.commit()
+
+    def set_run_log_command_and_celery_id(self, run: Run, cmd: Command, celery_id: int):
+        self.cursor().execute(
+            "UPDATE runs SET run_log__cmd = ?, run_log__celery_id = ? WHERE id = ?",
+            (" ".join(cmd), celery_id, run.run_id))
+        self.commit()
+
     @staticmethod
     def set_run_outputs(c: sqlite3.Cursor, run_id: str, outputs: dict[str, Any]):
         c.execute("UPDATE runs SET outputs = ? WHERE id = ?", (json.dumps(outputs), str(run_id)))