No more server-side demo

Author: stephen-riggs

src/murfey/server/demo_api.py

@@ -555,7 +555,7 @@ def _release_refine_hold(message: dict, _db):
     _db.close()
 
 
-def _register_incomplete_2d_batch(message: dict, _db, demo: bool = False):
+def _register_incomplete_2d_batch(message: dict, _db):
     """Received first batch from particle selection service"""
     # the general parameters are stored using the preprocessing auto proc program ID
     logger.info("Registering incomplete particle batch for 2D classification")
@@ -664,24 +664,10 @@ def _register_incomplete_2d_batch(message: dict, _db, demo: bool = False):
             "processing_recipe", zocalo_message, new_connection=True
         )
         logger.info("2D classification requested")
-    if demo:
-        logger.info("Incomplete 2D batch registered in demo mode")
-        if not _db.exec(
-            select(func.count(db.Class2DParameters.particles_file)).where(
-                db.Class2DParameters.particles_file == class2d_message["particles_file"]
-                and db.Class2DParameters.pj_id == pj_id
-                and db.Class2DParameters.complete
-            )
-        ).one():
-            _register_complete_2d_batch(message, _db=_db, demo=demo)
-            message["class2d_message"]["particles_file"] = (
-                message["class2d_message"]["particles_file"] + "_new"
-            )
-            _register_complete_2d_batch(message, _db=_db, demo=demo)
     _db.close()
 
 
-def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
+def _register_complete_2d_batch(message: dict, _db):
     """Received full batch from particle selection service"""
     instrument_name = (
         _db.exec(select(db.Session).where(db.Session.id == message["session_id"]))
@@ -748,12 +734,6 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
             _murfey_class2ds(
                 murfey_ids, class2d_message["particles_file"], _app_id(pj_id, _db), _db
             )
-        if demo:
-            _register_class_selection(
-                {"session_id": message["session_id"], "class_selection_score": 0.5},
-                _db=_db,
-                demo=demo,
-            )
     elif not feedback_params.class_selection_score:
         # For the first batch, start a container and set the database to wait
         job_number_after_first_batch = (
@@ -1007,7 +987,7 @@ def _flush_class2d(
     _db.commit()
 
 
-def _register_class_selection(message: dict, _db, demo: bool = False):
+def _register_class_selection(message: dict, _db):
     """Received selection score from class selection service"""
     pj_id_params = _pj_id(message["program_id"], _db, recipe="em-spa-preprocess")
     pj_id = _pj_id(message["program_id"], _db, recipe="em-spa-class2d")
@@ -1039,57 +1019,13 @@ def _register_class_selection(message: dict, _db, demo: bool = False):
 
     feedback_params.class_selection_score = message.get("class_selection_score") or 0
     feedback_params.hold_class2d = False
-    next_job = feedback_params.next_job
-    if demo:
-        for saved_message in class2d_db:
-            # Send all held Class2D messages on with the selection score added
-            _db.expunge(saved_message)
-            particles_file = saved_message.particles_file
-            logger.info("Complete 2D classification registered in demo mode")
-            _register_3d_batch(
-                {
-                    "session_id": message["session_id"],
-                    "class3d_message": {
-                        "particles_file": particles_file,
-                        "class3d_dir": "Class3D",
-                        "batch_size": 50000,
-                    },
-                },
-                _db=_db,
-                demo=demo,
-            )
-            logger.info("3D classification registered in demo mode")
-            _register_3d_batch(
-                {
-                    "session_id": message["session_id"],
-                    "class3d_message": {
-                        "particles_file": particles_file + "_new",
-                        "class3d_dir": "Class3D",
-                        "batch_size": 50000,
-                    },
-                },
-                _db=_db,
-                demo=demo,
-            )
-            _register_initial_model(
-                {
-                    "session_id": message["session_id"],
-                    "initial_model": "InitialModel/job015/model.mrc",
-                },
-                _db=_db,
-                demo=demo,
-            )
-            next_job += 3 if default_spa_parameters.do_icebreaker_jobs else 2
-        feedback_params.next_job = next_job
-        _db.close()
-    else:
-        _flush_class2d(
-            message["session_id"],
-            message["program_id"],
-            _db,
-            relion_params=relion_params,
-            feedback_params=feedback_params,
-        )
+    _flush_class2d(
+        message["session_id"],
+        message["program_id"],
+        _db,
+        relion_params=relion_params,
+        feedback_params=feedback_params,
+    )
     _db.add(feedback_params)
     for sm in class2d_db:
         _db.delete(sm)
@@ -1225,7 +1161,7 @@ def _resize_intial_model(
     return None
 
 
-def _register_3d_batch(message: dict, _db, demo: bool = False):
+def _register_3d_batch(message: dict, _db):
     """Received 3d batch from class selection service"""
     class3d_message = message.get("class3d_message")
     assert isinstance(class3d_message, dict)
@@ -1419,7 +1355,7 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
         _db.close()
 
 
-def _register_initial_model(message: dict, _db, demo: bool = False):
+def _register_initial_model(message: dict, _db):
     """Received initial model from 3d classification service"""
     pj_id_params = _pj_id(message["program_id"], _db, recipe="em-spa-preprocess")
     # Add the initial model file to the database
@@ -1551,7 +1487,7 @@ def _flush_tomography_preprocessing(message: dict, _db):
         _db.close()
 
 
-def _flush_grid_square_records(message: dict, _db, demo: bool = False):
+def _flush_grid_square_records(message: dict, _db):
     tag = message["tag"]
     session_id = message["session_id"]
     gs_ids = []
@@ -1561,21 +1497,19 @@ def _flush_grid_square_records(message: dict, _db, demo: bool = False):
         .where(db.GridSquare.tag == tag)
     ).all():
         gs_ids.append(gs.id)
-        if demo:
-            logger.info(f"Flushing grid square {gs.name}")
+        logger.info(f"Flushing grid square {gs.name}")
     for i in gs_ids:
-        _flush_foil_hole_records(i, _db=_db, demo=demo)
+        _flush_foil_hole_records(i, _db=_db)
 
 
-def _flush_foil_hole_records(grid_square_id: int, _db, demo: bool = False):
+def _flush_foil_hole_records(grid_square_id: int, _db):
     for fh in _db.exec(
         select(db.FoilHole).where(db.FoilHole.grid_square_id == grid_square_id)
     ).all():
-        if demo:
-            logger.info(f"Flushing foil hole: {fh.name}")
+        logger.info(f"Flushing foil hole: {fh.name}")
 
 
-def _register_refinement(message: dict, _db, demo: bool = False):
+def _register_refinement(message: dict, _db):
     """Received class to refine from 3D classification"""
     instrument_name = (
         _db.exec(select(db.Session).where(db.Session.id == message["session_id"]))
@@ -1725,7 +1659,7 @@ def _register_refinement(message: dict, _db, demo: bool = False):
         _db.close()
 
 
-def _register_bfactors(message: dict, _db, demo: bool = False):
+def _register_bfactors(message: dict, _db):
     """Received refined class to calculate b-factor"""
     instrument_name = (
         _db.exec(select(db.Session).where(db.Session.id == message["session_id"]))
@@ -1846,7 +1780,7 @@ def _register_bfactors(message: dict, _db, demo: bool = False):
     return True
 
 
-def _save_bfactor(message: dict, _db, demo: bool = False):
+def _save_bfactor(message: dict, _db):
     """Received b-factor from refinement run"""
     pj_id = _pj_id(message["program_id"], _db, recipe="em-spa-refine")
     bfactor_run = _db.exec(

src/murfey/server/feedback.py

@@ -2,7 +2,6 @@
 
 import argparse
 import logging
-import os
 from threading import Thread
 from typing import Literal
 
@@ -105,10 +104,6 @@ def run():
     parser.add_argument(
         "--workers", help="Number of workers for Uvicorn server", type=int, default=2
     )
-    parser.add_argument(
-        "--demo",
-        action="store_true",
-    )
     parser.add_argument(
         "--feedback",
         action="store_true",
@@ -154,22 +149,16 @@ def run():
     # Install a log filter to all existing handlers.
     LogFilter.install()
 
-    if args.demo:
-        # Run in demo mode with no connections set up
-        os.environ["MURFEY_DEMO"] = "1"
-    else:
-        # Load RabbitMQ configuration and set up the connection
-        try:
-            PikaTransport().load_configuration_file(
-                security_config.rabbitmq_credentials
-            )
-            _set_up_transport("PikaTransport")
-            logger.info("Set up message transport manager")
-        except WorkflowsError:
-            logger.error(
-                "Error encountered setting up RabbitMQ connection",
-                exc_info=True,
-            )
+    # Load RabbitMQ configuration and set up the connection
+    try:
+        PikaTransport().load_configuration_file(security_config.rabbitmq_credentials)
+        _set_up_transport("PikaTransport")
+        logger.info("Set up message transport manager")
+    except WorkflowsError:
+        logger.error(
+            "Error encountered setting up RabbitMQ connection",
+            exc_info=True,
+        )
 
     # Set up logging now that the desired verbosity is known
     _set_up_logging(quiet=args.quiet, verbosity=args.verbose)

src/murfey/server/run.py

@@ -42,7 +42,7 @@ def parse_stringified_list(cls, value):
 
 
 def register_align_and_merge_result(
-    message: dict, murfey_db: Session, demo: bool = False
+    message: dict, murfey_db: Session
 ) -> dict[str, bool]:
     """
     session_id (recipe)

src/murfey/workflows/clem/register_align_and_merge_results.py

@@ -481,7 +481,7 @@ def _register_grid_square(
     return
 
 
-def run(message: dict, murfey_db: Session, demo: bool = False) -> dict[str, bool]:
+def run(message: dict, murfey_db: Session) -> dict[str, bool]:
     session_id: int = (
         int(message["session_id"])
         if not isinstance(message["session_id"], int)

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -11,7 +11,6 @@
 def run(
     message: dict,
     murfey_db: SQLModelSession,  # Defined for compatibility but unused
-    demo: bool = False,
 ):
     if _transport_object is None:
         logger.error("Unable to find transport manager")

src/murfey/workflows/register_atlas_update.py

@@ -12,9 +12,7 @@
 logger = logging.getLogger("murfey.workflows.register_data_collection")
 
 
-def run(
-    message: dict, murfey_db: SQLModelSession, demo: bool = False
-) -> dict[str, bool]:
+def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
     # Fail immediately if transport manager was not provided
     if _transport_object is None:
         logger.error("Unable to find transport manager")

src/murfey/workflows/register_data_collection.py

@@ -13,9 +13,7 @@
 logger = logging.getLogger("murfey.workflows.register_data_collection_group")
 
 
-def run(
-    message: dict, murfey_db: SQLModelSession, demo: bool = False
-) -> dict[str, bool]:
+def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
     # Fail immediately if no transport wrapper is found
     if _transport_object is None:
         logger.error("Unable to find transport manager")

src/murfey/workflows/register_data_collection_group.py

@@ -9,9 +9,7 @@
 logger = logging.getLogger("murfey.workflows.register_data_collection_group")
 
 
-def run(
-    message: dict, murfey_db: SQLModelSession, demo: bool = False
-) -> dict[str, bool]:
+def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
     # Fail immediately if no transport wrapper is found
     if _transport_object is None:
         logger.error("Unable to find transport manager")

src/murfey/workflows/register_experiment_type_update.py

@@ -14,7 +14,7 @@
 logger = logging.getLogger("murfey.workflows.register_processing_job")
 
 
-def run(message: dict, murfey_db: SQLModelSession, demo: bool = False):
+def run(message: dict, murfey_db: SQLModelSession):
     # Faill immediately if not transport manager is set
     if _transport_object is None:
         logger.error("Unable to find transport manager")