Register FIB data in ISPyB (#805)

* Moved 'number_from_name' into new module 'murfey.util.fib'
* Adjust logic to register only the latest FIB atlas acquired for a FIB sample slot
* Updated registration logic so that 'add' and 'commit' always happen at the end of the function, and both new and old entries are populated or updated correctly
* Added logic to register data collection group and atlas rows in ISPyB using FIB atlas data
* Updated the FIB atlas registration workflow so that it is passed to and run through the RabbitMQ feedback queue instead of being loaded directly
* Add minimal logic needed to create, save, and register thumbnail images of the FIB atlases

Author: tieneupin

src/murfey/client/contexts/fib.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-import re
 import threading
 import xml.etree.ElementTree as ET
 from dataclasses import dataclass, field
@@ -11,6 +10,7 @@
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.util.client import capture_post
+from murfey.util.fib import number_from_name
 from murfey.util.models import (
     LamellaSiteInfo,
     MillingStepInfo,
@@ -24,22 +24,6 @@
 lock = threading.Lock()
 
 
-def _number_from_name(name: str) -> int:
-    """
-    In the AutoTEM and Maps workflows for the FIB, the sites and images are
-    auto-incremented with parenthesised numbers (e.g. "Lamella (2)"), with
-    the first site/image typically not having a number.
-
-    This function extracts the number from the file name, and returns 1 if
-    no such number is found.
-    """
-    return (
-        int(match.group(1))
-        if (match := re.search(r"^[\w\s]+\((\d+)\)$", name)) is not None
-        else 1
-    )
-
-
 T = TypeVar("T")
 
 
@@ -416,7 +400,7 @@ def _parse_autotem_metadata(self, file: Path):
             if (site_name := _parse_xml_text(site, "Name", str)) is None:
                 logger.warning("Current site doesn't have a name")
                 continue
-            site_num = _number_from_name(site_name)
+            site_num = number_from_name(site_name)
             site_info = LamellaSiteInfo(
                 project_name=project_name,
                 site_name=site_name,
@@ -555,7 +539,7 @@ def _make_drift_correction_gif(
         parts = file.parts
         try:
             lamella_name = parts[parts.index("Sites") + 1]
-            lamella_number = _number_from_name(lamella_name)
+            lamella_number = number_from_name(lamella_name)
         except Exception:
             logger.warning(
                 f"Could not extract metadata from file {file}", exc_info=True

src/murfey/server/api/workflow_fib.py

@@ -1,7 +1,6 @@
 import json
 import logging
 import os
-from importlib.metadata import entry_points
 from pathlib import Path
 
 import numpy as np
@@ -11,6 +10,7 @@
 from sqlmodel import Session, select
 
 import murfey.util.db as MurfeyDB
+from murfey.server import _transport_object
 from murfey.server.api.auth import validate_instrument_token
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise_path
@@ -26,30 +26,25 @@
 )
 
 
-class FIBAtlasInfo(BaseModel):
-    file: Path | None = None
+class FIBAtlasFile(BaseModel):
+    file: Path
 
 
 @router.post("/sessions/{session_id}/register_atlas")
 def register_fib_atlas(
     session_id: int,
-    fib_atlas_info: FIBAtlasInfo,
-    db: Session = murfey_db,
+    fib_atlas: FIBAtlasFile,
 ):
-    # See if the relevant workflow is available
-    if not (
-        workflow_search := list(
-            entry_points(group="murfey.workflows", name="fib.register_atlas")
-        )
-    ):
-        raise RuntimeError("Unable to find Murfey workflow to register FIB atlas")
-    workflow = workflow_search[0]
-
-    # Run the workflow
-    workflow.load()(
-        session_id=session_id,
-        file=fib_atlas_info.file,
-        murfey_db=db,
+    if _transport_object is None:
+        logger.error("No Transport Manager object was set up")
+        return None
+    _transport_object.send(
+        _transport_object.feedback_queue,
+        {
+            "register": "fib.register_atlas",
+            "session_id": session_id,
+            "atlas_file": str(fib_atlas.file),
+        },
     )
 
 

src/murfey/util/db.py

@@ -10,7 +10,9 @@
 from sqlmodel import Enum, Field, Relationship, SQLModel, create_engine
 
 """
+=======================================================================================
 GENERAL
+=======================================================================================
 """
 
 
@@ -173,7 +175,9 @@ class ImagingSite(SQLModel, table=True):  # type: ignore
 
 
 """
+=======================================================================================
 TEM SESSION AND PROCESSING WORKFLOW
+=======================================================================================
 """
 
 
@@ -1072,7 +1076,9 @@ class CryoemInitialModel(SQLModel, table=True):  # type: ignore
 
 
 """
+=======================================================================================
 FUNCTIONS
+=======================================================================================
 """
 
 

src/murfey/util/fib.py

@@ -0,0 +1,21 @@
+"""
+General functinos specific to the FIB workflow
+"""
+
+import re
+
+
+def number_from_name(name: str) -> int:
+    """
+    In the AutoTEM and Maps workflows for the FIB, the sites and images are
+    auto-incremented with parenthesised numbers (e.g. "Lamella (2)"), with
+    the first site/image typically not having a number.
+
+    This function extracts the number from the file name, and returns 1 if
+    no such number is found.
+    """
+    return (
+        int(match.group(1))
+        if (match := re.search(r"^[\w\s]+\((\d+)\)$", name)) is not None
+        else 1
+    )