Merged recent changes from 'main'

Author: tieneupin

src/murfey/server/api/file_io_frontend.py

@@ -1,6 +1,9 @@
 from logging import getLogger
+from pathlib import Path
 
 from fastapi import APIRouter, Depends
+from pydantic import BaseModel
+from sqlmodel import Session, select
 
 from murfey.server.api.auth import (
     MurfeySessionIDFrontend as MurfeySessionID,
@@ -11,6 +14,7 @@
     process_gain as _process_gain,
 )
 from murfey.server.murfey_db import murfey_db
+from murfey.util.config import get_machine_config
 
 logger = getLogger("murfey.server.api.file_io_frontend")
 
@@ -28,3 +32,27 @@ async def process_gain(
 ):
     result = await _process_gain(session_id, gain_reference_params, db)
     return result
+
+
+class SymlinkParameters(BaseModel):
+    target: Path  # these are the paths without the rsync basepath as that is what the frontend has access to
+    symlink: Path
+    override: bool = False
+
+
+@router.post("/sessions/{session_id}/symlink")
+async def create_symlink(
+    session_id: MurfeySessionID, symlink_params: SymlinkParameters, db=murfey_db
+) -> str:
+    murfey_session = db.exec(select(Session).where(Session.id == session_id)).one()
+    instrument_name = murfey_session.instrument_name
+    machine_config = get_machine_config(instrument_name=instrument_name)[
+        instrument_name
+    ]
+    symlink_full_path = machine_config.rsync_basepath / symlink_params.symlink
+    if symlink_full_path.is_symlink() and symlink_params.override:
+        symlink_full_path.unlink()
+    if symlink_full_path.exists():
+        return ""
+    symlink_full_path.symlink_to(symlink_params.target)
+    return str(symlink_params.symlink)

src/murfey/server/feedback.py

@@ -241,6 +241,8 @@ def _2d_class_murfey_ids(particles_file: str, app_id: int, _db) -> Dict[str, int
             db.Class2D.particles_file == particles_file and db.Class2D.pj_id == pj_id
         )
     ).all()
+    if not classes:
+        raise ValueError(f"No 2D classification IDs found for {particles_file}")
     return {str(cl.class_number): cl.murfey_id for cl in classes}
 
 
@@ -256,6 +258,8 @@ def _3d_class_murfey_ids(particles_file: str, app_id: int, _db) -> Dict[str, int
             and db.Class3D.pj_id == pj_id
         )
     ).all()
+    if not classes:
+        raise ValueError(f"No 3D classification IDs found for {particles_file}")
     return {str(cl.class_number): cl.murfey_id for cl in classes}
 
 
@@ -623,7 +627,9 @@ def _register_incomplete_2d_batch(message: dict, _db, demo: bool = False):
         )
         _db.add(class2d_params)
         _db.commit()
-        murfey_ids = _murfey_id(message["program_id"], _db, number=50)
+        murfey_ids = _murfey_id(
+            message["program_id"], _db, number=default_spa_parameters.nr_classes_2d
+        )
         _murfey_class2ds(
             murfey_ids, class2d_message["particles_file"], message["program_id"], _db
         )
@@ -747,7 +753,9 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
             _db.add(class2d_params)
             _db.commit()
             _db.close()
-            murfey_ids = _murfey_id(_app_id(pj_id, _db), _db, number=50)
+            murfey_ids = _murfey_id(
+                _app_id(pj_id, _db), _db, number=default_spa_parameters.nr_classes_2d
+            )
             _murfey_class2ds(
                 murfey_ids, class2d_message["particles_file"], _app_id(pj_id, _db), _db
             )
@@ -796,7 +804,13 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
         else:
             class_uuids = {
                 str(i + 1): m
-                for i, m in enumerate(_murfey_id(_app_id(pj_id, _db), _db, number=50))
+                for i, m in enumerate(
+                    _murfey_id(
+                        _app_id(pj_id, _db),
+                        _db,
+                        number=default_spa_parameters.nr_classes_2d,
+                    )
+                )
             }
             class2d_grp_uuid = _murfey_id(_app_id(pj_id, _db), _db)[0]
         zocalo_message: dict = {
@@ -865,7 +879,13 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
         else:
             class_uuids = {
                 str(i + 1): m
-                for i, m in enumerate(_murfey_id(_app_id(pj_id, _db), _db, number=50))
+                for i, m in enumerate(
+                    _murfey_id(
+                        _app_id(pj_id, _db),
+                        _db,
+                        number=default_spa_parameters.nr_classes_2d,
+                    )
+                )
             }
             class2d_grp_uuid = _murfey_id(_app_id(pj_id, _db), _db)[0]
         zocalo_message = {

src/murfey/util/route_manifest.yaml

@@ -477,6 +477,13 @@ murfey.server.api.file_io_frontend.router:
         type: int
     methods:
       - POST
+  - path: /file_io/frontend/sessions/{session_id}/symlink
+    function: create_symlink
+    path_params:
+      - name: session_id
+        type: int
+    methods:
+      - POST
 murfey.server.api.file_io_instrument.router:
   - path: /file_io/instrument/visits/{visit_name}/sessions/{session_id}/suggested_path
     function: suggest_path