fix alembic not detecting the medical history fulltext index

Author: rbuels

backend/app/alembic/versions/60300545fecf_add_fulltext_index_for_patient_medical_.py

@@ -18,17 +18,16 @@
 
 
 def upgrade() -> None:
-    # Create GIN index on medical_history column
-    op.execute("""
-        CREATE EXTENSION IF NOT EXISTS pg_trgm;
-        CREATE INDEX IF NOT EXISTS ix_patient_medical_history_gin 
-        ON patient 
-        USING GIN (medical_history gin_trgm_ops);
-    """)
-
+    op.execute("CREATE EXTENSION IF NOT EXISTS pg_trgm;")
+    op.create_index(
+        'ix_patient_medical_history_gin',
+        'patient',
+        ['medical_history'],
+        unique=False,
+        postgresql_using='gin',
+        postgresql_ops={'medical_history': 'gin_trgm_ops'}
+    )
 
 def downgrade() -> None:
-    # Drop the GIN index
-    op.execute("""
-        DROP INDEX IF EXISTS ix_patient_medical_history_gin;
-    """)
+    op.drop_index('ix_patient_medical_history_gin', table_name='patient')
+

backend/app/alembic/versions/da61fe01b001_drop_storage_path_column.py

@@ -0,0 +1,29 @@
+"""drop storage_path column
+
+Revision ID: da61fe01b001
+Revises: e62dc93fe967
+Create Date: 2025-02-23 20:49:29.015113
+
+"""
+from alembic import op
+import sqlalchemy as sa
+import sqlmodel.sql.sqltypes
+
+
+# revision identifiers, used by Alembic.
+revision = 'da61fe01b001'
+down_revision = 'e62dc93fe967'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('attachment', 'storage_path')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('attachment', sa.Column('storage_path', sa.VARCHAR(length=1024), autoincrement=False, nullable=False))
+    # ### end Alembic commands ###

backend/app/models/patients.py

@@ -1,7 +1,8 @@
-
 from typing import TYPE_CHECKING
 from datetime import datetime
-from sqlmodel import Field, Relationship, SQLModel
+
+from sqlmodel import Field, Relationship, SQLModel, create_engine, Session, select
+from sqlalchemy import Index
 import uuid
 
 if TYPE_CHECKING:
@@ -27,6 +28,16 @@ class Patient(PatientBase, table=True):
     id: uuid.UUID = Field(default_factory=uuid.uuid4, primary_key=True)
     attachments: list["Attachment"] = Relationship(back_populates="patient", cascade_delete=True)
 
+    __table_args__ = (
+        # define a fulltext index on medical_history
+        Index(
+            'ix_patient_medical_history_gin',
+            'medical_history',
+            postgresql_using='gin',
+            postgresql_ops={'medical_history': 'gin_trgm_ops'}
+        ),
+    )
+
 # Properties to return via API, id is always required
 class PatientPublic(PatientBase):
     id: uuid.UUID

backend/app/tests/api/routes/test_attachments.py

@@ -25,7 +25,6 @@ def test_create_attachment(
     data = {
         "file_name": "test.pdf",
         "mime_type": "application/pdf",
-        "storage_path": "patients/attachments/test.pdf",
         "description": "Test attachment",
         "patient_id": str(patient.id)
     }
@@ -58,7 +57,6 @@ def test_read_attachment_details(
     attachment = Attachment(
         file_name="test.pdf",
         mime_type="application/pdf",
-        storage_path="patients/attachments/test.pdf",
         description="Test attachment",
         patient_id=patient.id
     )
@@ -94,13 +92,11 @@ def test_list_attachments(
     attachment1 = Attachment(
         file_name="test1.pdf",
         mime_type="application/pdf",
-        storage_path="patients/attachments/test1.pdf",
         patient_id=patient.id
     )
     attachment2 = Attachment(
         file_name="test2.pdf",
         mime_type="application/pdf",
-        storage_path="patients/attachments/test2.pdf",
         patient_id=patient.id
     )
     db.add(attachment1)

backend/app/tests/api/routes/test_patients.py

@@ -210,13 +210,11 @@ def test_read_patients_attachment_filter(
     attachment1 = Attachment(
         file_name="test1.bam",
         mime_type="application/x-bam",
-        storage_path="patients/attachments/test1.bam",
         patient_id=patient1.id
     )
     attachment2 = Attachment(
         file_name="test.cram",
         mime_type="application/x-cram",
-        storage_path="patients/attachments/test.cram",
         patient_id=patient2.id
     )
     db.add(attachment1)