Populate electrical_cell_recording ids (#364)

Add missing records into electrical_cell_recording
caused by migrations d58bc70ec10f and b352b28dae67

Unrelated: remove mesh type from EntityType.

Author: GianlucaFicarelli

alembic/versions/20250912_172025_06af11530839_populate_electrical_cell_recording_ids.py

@@ -0,0 +1,129 @@
+"""Populate electrical_cell_recording ids.
+
+Revision ID: 06af11530839
+Revises: de87a4c88ded
+Create Date: 2025-09-12 17:20:25.828230
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from alembic_postgresql_enum import TableReference
+
+from sqlalchemy import Text
+import app.db.types
+
+# revision identifiers, used by Alembic.
+revision: str = "06af11530839"
+down_revision: Union[str, None] = "de87a4c88ded"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # add missing records into electrical_cell_recording
+    # caused by migrations d58bc70ec10f and b352b28dae67
+    op.execute(
+        """
+        INSERT INTO electrical_cell_recording (id)
+        SELECT e.id
+        FROM entity e
+        JOIN electrical_recording er ON e.id = er.id
+        WHERE e.type = 'electrical_cell_recording'
+        ON CONFLICT (id) DO NOTHING
+        """
+    )
+    # remove mesh type
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "brain_atlas_region",
+            "cell_composition",
+            "electrical_cell_recording",
+            "electrical_recording",
+            "electrical_recording_stimulus",
+            "emodel",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "external_url",
+            "ion_channel",
+            "ion_channel_model",
+            "ion_channel_recording",
+            "memodel",
+            "memodel_calibration_result",
+            "me_type_density",
+            "reconstruction_morphology",
+            "simulation",
+            "simulation_campaign",
+            "simulation_campaign_generation",
+            "simulation_execution",
+            "simulation_result",
+            "scientific_artifact",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "subject",
+            "validation_result",
+            "circuit",
+            "em_dense_reconstruction_dataset",
+            "em_cell_mesh",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )
+
+
+def downgrade() -> None:
+    # restore mesh type
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "brain_atlas_region",
+            "cell_composition",
+            "electrical_cell_recording",
+            "electrical_recording",
+            "electrical_recording_stimulus",
+            "emodel",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "external_url",
+            "ion_channel",
+            "ion_channel_model",
+            "ion_channel_recording",
+            "memodel",
+            "mesh",
+            "memodel_calibration_result",
+            "me_type_density",
+            "reconstruction_morphology",
+            "simulation",
+            "simulation_campaign",
+            "simulation_campaign_generation",
+            "simulation_execution",
+            "simulation_result",
+            "scientific_artifact",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "subject",
+            "validation_result",
+            "circuit",
+            "em_dense_reconstruction_dataset",
+            "em_cell_mesh",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )

app/db/types.py

@@ -71,7 +71,6 @@ class EntityType(StrEnum):
     ion_channel_model = auto()
     ion_channel_recording = auto()
     memodel = auto()
-    mesh = auto()
     memodel_calibration_result = auto()
     me_type_density = auto()
     reconstruction_morphology = auto()