Smartem grid square registration fixes (#818)

Changes to make grid square registration work for serialem

Author: stephen-riggs

src/murfey/client/analyser.py

@@ -243,11 +243,15 @@ def _find_context(self, file_path: Path) -> bool:
             )
             return True
 
-        if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
+        if (
+            "Metadata" in file_path.parts
+            or "gridsquares" in file_path.parts
+            or file_path.name == "EpuSession.dm"
+        ):
             if (context := _get_context("SPAMetadataContext")) is None:
                 return False
             self._context = context.load()(
-                "epu",
+                "serialem" if self._serialem else "epu",
                 self._basepath,
                 self._murfey_config,
                 self._token,
@@ -357,12 +361,13 @@ def _analyse(self, transferred_file: Path):
         if self._limited:
             if (
                 "Metadata" in transferred_file.parts
+                or "gridsquares" in transferred_file.parts
                 or transferred_file.name == "EpuSession.dm"
             ) and not self._context:
                 if not (context := _get_context("SPAMetadataContext")):
                     return None
                 self._context = context.load()(
-                    "epu",
+                    "serialem" if self._serialem else "epu",
                     self._basepath,
                     self._murfey_config,
                     self._token,

src/murfey/client/contexts/spa_metadata.py

@@ -138,6 +138,12 @@ def post_transfer_serialem(
                 visitless_source = _get_visitless_source(
                     source, environment, skip_search=True
                 )
+                destination_file = _file_transferred_to(
+                    environment,
+                    source,
+                    transferred_file,
+                    Path(self._machine_config.get("rsync_basepath", "")),
+                )
                 capture_post(
                     base_url=str(environment.url.geturl()),
                     router_name="session_control.spa_router",
@@ -148,7 +154,9 @@ def post_transfer_serialem(
                     gsid=transferred_file.stem,
                     data={
                         "tag": visitless_source,
+                        "image_path": str(destination_file),
                         "count": len(self._registered_squares_serialem) + 1,
+                        "serialem": self._acquisition_software == "serialem",
                     },
                 )
                 self._registered_squares_serialem.add(transferred_file.stem)

src/murfey/server/api/session_control.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 from typing import Dict, List, Optional
 
+import requests
 from fastapi import APIRouter, Depends
 from fastapi.responses import FileResponse
 from ispyb.sqlalchemy import AutoProcProgram as ISPyBAutoProcProgram
@@ -417,24 +418,31 @@ def register_atlas(
 
 class SquareRegistration(BaseModel):
     tag: str
+    image_path: str | None = None
     count: int | None = None
+    serialem: bool = False
 
 
 @spa_router.post("/sessions/{session_id}/register_square/{gsid}")
 def register_square(
     session_id: MurfeySessionID,
-    gsid: int,
+    gsid: int | str,
     square_registration_data: SquareRegistration,
     db=murfey_db,
 ):
     if SMARTEM_ACTIVE:
-        gs = db.exec(
-            select(GridSquare)
-            .where(GridSquare.name == gsid)
-            .where(GridSquare.tag == square_registration_data.tag)
-            .where(GridSquare.session_id == session_id)
-        ).one_or_none()
-        if gs and gs.smartem_uuid:
+        logger.info(f"smartem active for square {sanitise(str(gsid))}")
+        if square_registration_data.serialem:
+            smartem_uuid: int | str | None = gsid
+        else:
+            gs = db.exec(
+                select(GridSquare)
+                .where(GridSquare.name == gsid)
+                .where(GridSquare.tag == square_registration_data.tag)
+                .where(GridSquare.session_id == session_id)
+            ).one_or_none()
+            smartem_uuid = gs.smartem_uuid if gs else None
+        if smartem_uuid is not None:
             session = db.exec(select(Session).where(Session.id == session_id)).one()
             machine_config = get_machine_config(session.instrument_name)[
                 session.instrument_name
@@ -444,8 +452,16 @@ def register_square(
                     base_url=machine_config.smartem_api_url, logger=logger
                 )
                 smartem_client.gridsquare_registered(
-                    gs.smartem_uuid, count=square_registration_data.count
+                    smartem_uuid, count=square_registration_data.count
+                )
+                result = requests.put(
+                    f"{machine_config.smartem_api_url}/gridsquares/{smartem_uuid}",
+                    json={"image_path": square_registration_data.image_path},
                 )
+                if not result.status_code == 200:
+                    logger.warning(
+                        f"Post to smartem gridsquares returned {result.status_code}"
+                    )
     else:
         logger.info("smartem deactivated so did not register square")
 

src/murfey/util/route_manifest.yaml

@@ -920,7 +920,7 @@ murfey.server.api.session_control.spa_router:
     function: register_square
     path_params:
       - name: gsid
-        type: int
+        type: int | str
       - name: session_id
         type: int
     methods: