cigrid-ui-412 new column types (#74) (major)

### CHANGED

- Types for method document and method version in the plate table were changed to string. 
- Added indexes to python models to match database schema.

---------

Co-authored-by: isakohlsson <isak.ohlsson@scilifelab.se>

alembic/env.py

@@ -1,10 +1,10 @@
 from __future__ import with_statement
 
-from sqlmodel import SQLModel
 
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 from logging.config import fileConfig
+from genotype_api.models import SQLModel
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -52,7 +52,9 @@ def run_migrations_online():
 
     """
     connectable = engine_from_config(
-        config.get_section(config.config_ini_section), prefix="sqlalchemy.", poolclass=pool.NullPool
+        config.get_section(config.config_ini_section),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
     )
 
     with connectable.connect() as connection:

alembic/versions/7f77cbc00305_change_version_field_type.py

@@ -0,0 +1,67 @@
+"""Change version field type
+
+Revision ID: 7f77cbc00305
+Revises: 21ef5ce15822
+Create Date: 2023-05-15 16:46:03.718794
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = "7f77cbc00305"
+down_revision = "21ef5ce15822"
+branch_labels = None
+depends_on = None
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index("plate_id", table_name="plate")
+    op.create_index(op.f("ix_plate_plate_id"), "plate", ["plate_id"], unique=True)
+    op.alter_column("user", "email", existing_type=mysql.VARCHAR(length=128), nullable=False)
+    op.drop_index("email", table_name="user")
+    op.drop_index("google_id", table_name="user")
+    op.create_index(op.f("ix_user_email"), "user", ["email"], unique=True)
+    op.drop_column("user", "avatar")
+    op.drop_column("user", "google_id")
+    op.alter_column(
+        "plate",
+        "method_document",
+        existing_type=mysql.INTEGER(),
+        type_=mysql.VARCHAR(length=128),
+    )
+    op.alter_column(
+        "plate",
+        "method_version",
+        existing_type=mysql.INTEGER(),
+        type_=mysql.VARCHAR(length=16),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "plate",
+        "method_version",
+        existing_type=mysql.VARCHAR(length=16),
+        type_=mysql.INTEGER(),
+    )
+    op.alter_column(
+        "plate",
+        "method_document",
+        existing_type=mysql.VARCHAR(length=128),
+        type_=mysql.INTEGER(),
+    )
+
+    op.add_column("user", sa.Column("google_id", mysql.VARCHAR(length=128), nullable=True))
+    op.add_column("user", sa.Column("avatar", mysql.TEXT(), nullable=True))
+    op.drop_index(op.f("ix_user_email"), table_name="user")
+    op.create_index("google_id", "user", ["google_id"], unique=False)
+    op.create_index("email", "user", ["email"], unique=False)
+    op.alter_column("user", "email", existing_type=mysql.VARCHAR(length=128), nullable=True)
+    op.drop_index(op.f("ix_plate_plate_id"), table_name="plate")
+    op.create_index("plate_id", "plate", ["plate_id"], unique=False)

genotype_api/api/endpoints/analyses.py

@@ -5,8 +5,15 @@
 from fastapi import APIRouter, Depends, status, Query, UploadFile, File
 from fastapi.responses import JSONResponse
 
-from genotype_api.crud.analyses import get_analysis, check_analyses_objects, create_analysis
-from genotype_api.crud.samples import create_analyses_sample_objects, refresh_sample_status
+from genotype_api.crud.analyses import (
+    get_analysis,
+    check_analyses_objects,
+    create_analysis,
+)
+from genotype_api.crud.samples import (
+    create_analyses_sample_objects,
+    refresh_sample_status,
+)
 from genotype_api.database import get_session
 from genotype_api.file_parsing.files import check_file
 from genotype_api.models import Analysis, AnalysisRead, AnalysisReadWithGenotype, User

genotype_api/api/endpoints/plates.py

@@ -12,7 +12,10 @@
     get_analyses_from_plate,
     check_analyses_objects,
 )
-from genotype_api.crud.samples import create_analyses_sample_objects, refresh_sample_status
+from genotype_api.crud.samples import (
+    create_analyses_sample_objects,
+    refresh_sample_status,
+)
 from genotype_api.crud.plates import create_plate, get_plate
 from genotype_api.crud.users import get_user_by_email
 from genotype_api.database import get_session
@@ -61,7 +64,9 @@ def upload_plate(
         )
 
     excel_parser = GenotypeAnalysis(
-        excel_file=BytesIO(file.file.read()), file_name=str(file_name), include_key="-CG-"
+        excel_file=BytesIO(file.file.read()),
+        file_name=str(file_name),
+        include_key="-CG-",
     )
     analyses: List[Analysis] = list(excel_parser.generate_analyses())
     check_analyses_objects(session=session, analyses=analyses, analysis_type="genotype")
@@ -78,8 +83,8 @@ def upload_plate(
 @router.patch("/{plate_id}/sign-off", response_model=Plate)
 def sign_off_plate(
     plate_id: int,
-    method_document: int = Query(...),
-    method_version: int = Query(...),
+    method_document: str = Query(...),
+    method_version: str = Query(...),
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
@@ -106,7 +111,12 @@ def sign_off_plate(
     response_model_exclude={
         "analyses": {
             "__all__": {
-                "sample": {"analyses": True, "created_at": True, "sex": True, "id": True},
+                "sample": {
+                    "analyses": True,
+                    "created_at": True,
+                    "sex": True,
+                    "id": True,
+                },
                 "source": True,
                 "created_at": True,
                 "type": True,
@@ -165,5 +175,6 @@ def delete_plate(
     session.commit()
 
     return JSONResponse(
-        f"Deleted plate: {plate_id} and analyses: {analyse_ids}", status_code=status.HTTP_200_OK
+        f"Deleted plate: {plate_id} and analyses: {analyse_ids}",
+        status_code=status.HTTP_200_OK,
     )

genotype_api/api/endpoints/samples.py

@@ -214,7 +214,8 @@ def match(
         if count.get("match", 0) + count.get("unknown", 0) > 40:
             match_results.append(
                 MatchResult(
-                    sample_id=genotype.sample_id, match_results=MatchCounts.parse_obj(count)
+                    sample_id=genotype.sample_id,
+                    match_results=MatchCounts.parse_obj(count),
                 ),
             )
     return match_results

genotype_api/api/endpoints/snps.py

@@ -50,7 +50,8 @@ async def upload_snps(
 
 @router.delete("/")
 def delete_snps(
-    session: Session = Depends(get_session), current_user: User = Depends(get_active_user)
+    session: Session = Depends(get_session),
+    current_user: User = Depends(get_active_user),
 ):
     """Delete all SNPs"""
 

genotype_api/crud/analyses.py

@@ -52,7 +52,9 @@ def check_analyses_objects(
     """Raising 400 if any analysis in the list already exist in the database"""
     for analysis_obj in analyses:
         db_analysis: Analysis = get_analysis_type_sample(
-            session=session, sample_id=analysis_obj.sample_id, analysis_type=analysis_type
+            session=session,
+            sample_id=analysis_obj.sample_id,
+            analysis_type=analysis_type,
         )
         if db_analysis:
             session.delete(db_analysis)

genotype_api/file_parsing/vcf.py

@@ -54,7 +54,9 @@ def generate_analyses(self) -> Iterable[Analysis]:
             gt_info: Genotype
             for gt_info in variant_object.genotypes:
                 db_genotype = DBGenotype(
-                    rsnumber=variant_object.id, allele_1=gt_info.allele_1, allele_2=gt_info.allele_2
+                    rsnumber=variant_object.id,
+                    allele_1=gt_info.allele_1,
+                    allele_2=gt_info.allele_2,
                 )
                 analyses[gt_info.sample_id].genotypes.append(db_genotype)
         return [analysis for analysis in analyses.values()]

genotype_api/models.py

@@ -1,12 +1,12 @@
-from datetime import datetime
-from typing import Optional, List, Dict, Tuple, Type, Any
 from collections import Counter
+from datetime import datetime
+from typing import Any, Dict, List, Optional, Tuple, Type
 
+from pydantic import BaseModel, EmailStr, constr, validator
+from sqlalchemy import Index
+from sqlmodel import Field, Relationship, SQLModel
 
-from pydantic import constr, EmailStr, BaseModel, validator
-from sqlmodel import SQLModel, Field, Relationship
-
-from genotype_api.constants import TYPES, SEXES, STATUS, CUTOFS
+from genotype_api.constants import CUTOFS, SEXES, STATUS, TYPES
 
 
 class PlateStatusCounts(BaseModel):
@@ -71,6 +71,8 @@ class GenotypeBase(SQLModel):
 
 
 class Genotype(GenotypeBase, table=True):
+    __tablename__ = "genotype"
+    __table_args__ = (Index("_analysis_rsnumber", "analysis_id", "rsnumber", unique=True),)
     id: Optional[int] = Field(default=None, primary_key=True)
 
     analysis: Optional["Analysis"] = Relationship(back_populates="genotypes")
@@ -105,6 +107,8 @@ class AnalysisBase(SQLModel):
 
 
 class Analysis(AnalysisBase, table=True):
+    __tablename__ = "analysis"
+    __table_args__ = (Index("_sample_type", "sample_id", "type", unique=True),)
     id: Optional[int] = Field(default=None, primary_key=True)
 
     sample: Optional["Sample"] = Relationship(back_populates="analyses")
@@ -136,6 +140,7 @@ class SampleBase(SampleSlim):
 
 
 class Sample(SampleBase, table=True):
+    __tablename__ = "sample"
     id: Optional[constr(max_length=32)] = Field(default=None, primary_key=True)
 
     analyses: Optional[List["Analysis"]] = Relationship(back_populates="sample")
@@ -176,6 +181,7 @@ class SNPBase(SQLModel):
 
 
 class SNP(SNPBase, table=True):
+    __tablename__ = "snp"
     """Represent a SNP position under investigation."""
 
     id: Optional[constr(max_length=32)] = Field(default=None, primary_key=True)
@@ -186,11 +192,12 @@ class SNPRead(SNPBase):
 
 
 class UserBase(SQLModel):
-    email: EmailStr = Field(index=True)
+    email: EmailStr = Field(index=True, unique=True)
     name: Optional[str] = ""
 
 
 class User(UserBase, table=True):
+    __tablename__ = "user"
     id: Optional[int] = Field(default=None, primary_key=True)
     plates: Optional[List["Plate"]] = Relationship(back_populates="user")
 
@@ -205,14 +212,15 @@ class UserCreate(UserBase):
 
 class PlateBase(SQLModel):
     created_at: Optional[datetime] = datetime.now()
-    plate_id: constr(max_length=16)
+    plate_id: constr(max_length=16) = Field(index=True, unique=True)
     signed_by: Optional[int] = Field(default=None, foreign_key="user.id")
     signed_at: Optional[datetime]
-    method_document: Optional[int] = 1477
-    method_version: Optional[int]
+    method_document: Optional[str]
+    method_version: Optional[str]
 
 
 class Plate(PlateBase, table=True):
+    __tablename__ = "plate"
     id: Optional[int] = Field(default=None, primary_key=True)
     user: Optional["User"] = Relationship(back_populates="plates")
     analyses: Optional[List["Analysis"]] = Relationship(back_populates="plate")

genotype_api/security.py

@@ -38,11 +38,13 @@ async def __call__(self, request: Request):
         credentials: HTTPAuthorizationCredentials = await super(JWTBearer, self).__call__(request)
         if not credentials:
             raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN, detail="Invalid authorization code."
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail="Invalid authorization code.",
             )
         if credentials.scheme != "Bearer":
             raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN, detail="Invalid authentication scheme."
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail="Invalid authentication scheme.",
             )
         self.verify_jwt(credentials.credentials)
 
@@ -53,7 +55,8 @@ def verify_jwt(self, jwtoken: str) -> Optional[dict]:
             return decode_id_token(jwtoken)
         except Exception:
             raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN, detail="Invalid token or expired token."
+                status_code=status.HTTP_403_FORBIDDEN,
+                detail="Invalid token or expired token.",
             )