Release v1.6.0

CHANGELOG.rst

@@ -2,6 +2,14 @@
 Changelog
 ==========
 
++++++++++
+v1.6.0 (14/05/2024)
++++++++++
+
+**Added**
+
+- B Factor fit plot (:code:`/{autoProcId}/bFactorFit`)
+
 +++++++++
 v1.5.0 (25/03/2024)
 +++++++++

src/pato/auth/template.py

@@ -15,8 +15,8 @@ def movie(movieId: int) -> int:
         return movieId
 
     @staticmethod
-    def autoproc_program(autoProcProgramId: int) -> int:
-        return autoProcProgramId
+    def autoproc_program(autoProcId: int) -> int:
+        return autoProcId
 
     @staticmethod
     def processing_job(processingJobId: int) -> int:

src/pato/crud/autoproc.py

@@ -5,6 +5,7 @@
 from lims_utils.models import Paged
 from lims_utils.tables import (
     CTF,
+    BFactorFit,
     CryoemInitialModel,
     MotionCorrection,
     Movie,
@@ -17,7 +18,7 @@
 from lims_utils.tables import (
     t_ParticleClassification_has_CryoemInitialModel as ParticleClassificationHasCryoem,
 )
-from sqlalchemy import UnaryExpression, and_, or_, select
+from sqlalchemy import UnaryExpression, and_, func, or_, select
 
 from ..models.response import (
     Classification,
@@ -102,6 +103,23 @@ def get_particle_picker(autoProcId: int, filterNull: bool, limit: int, page: int
 }
 
 
+def get_b_factor_fit(autoProcId: int):
+    query = (
+        (
+            select(
+                func.ln(BFactorFit.numberOfParticles).label("numberOfParticles"),
+                (1 / func.pow(BFactorFit.resolution, 2)).label("resolution"),
+            )
+            .select_from(ParticleClassificationGroup)
+            .filter(ParticleClassificationGroup.programId == autoProcId)
+        )
+        .join(ParticleClassification)
+        .join(BFactorFit)
+    )
+
+    return db.session.execute(query).all()
+
+
 def get_classification(
     autoProcId: int,
     limit: int,

src/pato/models/response.py

@@ -461,3 +461,8 @@ class IceThicknessWithAverage(OrmBaseModel):
 
 class ReprocessingResponse(BaseModel):
     processingJobId: int
+
+
+class BFactorFitOut(BaseModel):
+    numberOfParticles: float
+    resolution: float

src/pato/routes/autoproc.py

@@ -8,6 +8,7 @@
 from ..crud import autoproc as crud
 from ..crud import generic
 from ..models.response import (
+    BFactorFitOut,
     Classification,
     CtfBaseSpa,
     FullMovie,
@@ -151,3 +152,9 @@ def get_particle_count(
     return generic.get_particle_count(
         parent_type="autoProc", parent_id=autoProcId, minimum=minimum, dataBin=dataBin
     )
+
+
+@router.get("/{autoProcId}/bFactorFit", response_model=ItemList[BFactorFitOut])
+def get_b_factor_fit(autoProcId: int = Depends(auth)):
+    """Get B factor fit data"""
+    return ItemList(items=crud.get_b_factor_fit(autoProcId=autoProcId))

tests/autoproc/test_b_factor.py

@@ -0,0 +1,13 @@
+def test_get_user(mock_permissions, client):
+    """Get B factor fit data for an autoprocessing program"""
+    resp = client.get("/autoProc/56986680/bFactorFit")
+    assert resp.status_code == 200
+    assert len(resp.json()["items"]) == 1
+
+
+def test_get_minimum(mock_permissions, client):
+    """Get B Factor fit data for an autoprocessing program that does not have
+    B factor fit data"""
+    resp = client.get("/autoProc/56425592/bFactorFit")
+    assert resp.status_code == 200
+    assert len(resp.json()["items"]) == 0