Merge pull request #273 from Clinical-Genomics/accept_http_forms

Modify pydantic model so report endpoints accept either JSON or form data

CHANGELOG.md

@@ -1,4 +1,6 @@
 ## [unreleased]
+### Added
+- Coverage report and genes coverage overview endpoints now accept also requests with application/x-www-form-urlencoded data
 ### Fixed
 - Faster genes overview report loading
 - Broken GitHub action due to d4tools failing to install using cargo

src/chanjo2/demo/__init__.py

@@ -2,7 +2,7 @@
 
 from importlib_resources import files
 
-from chanjo2.constants import BUILD_37
+from chanjo2.constants import BUILD_37, DEFAULT_COMPLETENESS_LEVELS
 
 BASE_PATH: str = "chanjo2.demo"
 
@@ -25,16 +25,17 @@
 
 HTTP_SERVER_D4_file = "https://d4-format-testing.s3.us-west-1.amazonaws.com/hg002.d4"
 DEMO_HGNC_GENE_SYMBOLS = ["MTHFR", "DHFR", "FOLR1", "SLC46A1", "LAMA1", "PIPPI6"]
+ANALYSIS_DATE = "2023-04-23T10:20:30.400+02:30"
 
-# Data for generating a demo coverage report
+# JSON Data for generating a demo coverage report
 DEMO_COVERAGE_QUERY_DATA = {
     "build": BUILD_37,
     "samples": [
         {
             "name": DEMO_SAMPLE["name"],
             "case_name": DEMO_CASE["name"],
             "coverage_file_path": d4_demo_path,
-            "analysis_date": "2023-04-23T10:20:30.400+02:30",
+            "analysis_date": ANALYSIS_DATE,
         }
     ],
     "case_display_name": "643594",
@@ -45,3 +46,19 @@
     "hgnc_gene_symbols": DEMO_HGNC_GENE_SYMBOLS,
     "default_level": 20,
 }
+
+# HTTP FORM-like data for generating a demo coverage report
+DEMO_COVERAGE_QUERY_FORM = {
+    "build": BUILD_37,
+    "samples": f"[{{'name': '{DEMO_SAMPLE['name']}', 'coverage_file_path': '{d4_demo_path}', 'case_name': '{DEMO_CASE['name']}', 'analysis_date': '{ANALYSIS_DATE}'}}]",
+    "case_display_name": DEMO_CASE["name"],
+    "gene_panel": "A test Panel 1.0",
+    "interval_type": "transcripts",
+    "ensembl_gene_ids": [],
+    "hgnc_gene_ids": [],
+    "hgnc_gene_symbols": ",".join(DEMO_HGNC_GENE_SYMBOLS),
+    "default_level": "20",
+    "completeness_thresholds": ",".join(
+        [str(threshold) for threshold in DEFAULT_COMPLETENESS_LEVELS]
+    ),
+}

src/chanjo2/endpoints/overview.py

@@ -1,10 +1,11 @@
 import logging
 from os import path
 
-from fastapi import APIRouter, Depends, Request
+from fastapi import APIRouter, Depends, HTTPException, Request, status
 from fastapi.encoders import jsonable_encoder
 from fastapi.responses import HTMLResponse
 from fastapi.templating import Jinja2Templates
+from pydantic_core._pydantic_core import ValidationError
 from sqlalchemy.orm import Session
 from starlette.datastructures import FormData
 
@@ -50,12 +51,25 @@ async def demo_overview(request: Request, db: Session = Depends(get_session)):
 
 @router.post("/overview", response_class=HTMLResponse)
 async def overview(
-    request: Request, report_query: ReportQuery, db: Session = Depends(get_session)
+    request: Request,
+    db: Session = Depends(get_session),
 ):
     """Return the genes overview page over a list of genes for a list of samples."""
+    request_headers: str = request.headers.get("Content-Type")
+    try:
+        if request_headers == "application/json":
+            overview_query = ReportQuery(**await request.json())
+        else:
+            overview_query = ReportQuery.as_form(await request.form())
+
+    except ValidationError as ve:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=ve.json(),
+        )
 
     overview_content: dict = get_report_data(
-        query=report_query, session=db, is_overview=True
+        query=overview_query, session=db, is_overview=True
     )
     return templates.TemplateResponse(
         "overview.html",

src/chanjo2/endpoints/report.py

@@ -3,9 +3,10 @@
 from os import path
 from typing import Dict
 
-from fastapi import APIRouter, Depends, Request
+from fastapi import APIRouter, Depends, HTTPException, Request, status
 from fastapi.responses import HTMLResponse
 from fastapi.templating import Jinja2Templates
+from pydantic_core._pydantic_core import ValidationError
 from sqlalchemy.orm import Session
 
 from chanjo2.dbutil import get_session
@@ -50,11 +51,25 @@ async def demo_report(request: Request, db: Session = Depends(get_session)):
 
 @router.post("/report", response_class=HTMLResponse)
 async def report(
-    request: Request, report_query: ReportQuery, db: Session = Depends(get_session)
+    request: Request,
+    db: Session = Depends(get_session),
 ):
     """Return a coverage report over a list of genes for a list of samples."""
 
     start_time = time.time()
+    request_headers: str = request.headers.get("Content-Type")
+
+    try:
+        if request_headers == "application/json":
+            report_query = ReportQuery(**await request.json())
+        else:
+            report_query = ReportQuery.as_form(await request.form())
+    except ValidationError as ve:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=ve.json(),
+        )
+
     report_content: dict = get_report_data(query=report_query, session=db)
     LOG.debug(f"Time to compute stats: {time.time() - start_time} seconds.")
     return templates.TemplateResponse(

src/chanjo2/models/pydantic_models.py

@@ -3,11 +3,12 @@
 from datetime import datetime
 from enum import Enum
 from pathlib import Path
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Union
 
 import validators
 from pydantic import BaseModel, Field, field_validator, model_validator
 from pydantic_settings import SettingsConfigDict
+from starlette.datastructures import FormData
 
 from chanjo2.constants import (
     AMBIGUOUS_SAMPLES_INPUT,
@@ -232,6 +233,44 @@ class ReportQuery(BaseModel):
     case_display_name: Optional[str] = None
     samples: List[ReportQuerySample]
 
+    @staticmethod
+    def comma_sep_values_to_list(
+        comma_sep_values: Optional[str], items_format: Union[str, int]
+    ) -> Optional[List[Union[str, int]]]:
+        """Helper function that formats list of strings or integers passed by a form as comma separated values."""
+        if comma_sep_values is None:
+            return
+        if items_format == str:
+            return [item.strip() for item in comma_sep_values.split(",")]
+        else:
+            return [int(item.strip()) for item in comma_sep_values.split(",")]
+
+    @classmethod
+    def as_form(cls, form_data: FormData) -> "ReportQuery":
+        report_query = cls(
+            build=form_data.get("build"),
+            completeness_thresholds=cls.comma_sep_values_to_list(
+                comma_sep_values=form_data.get("completeness_thresholds"),
+                items_format=int,
+            )
+            or DEFAULT_COMPLETENESS_LEVELS,
+            ensembl_gene_ids=cls.comma_sep_values_to_list(
+                comma_sep_values=form_data.get("ensembl_gene_ids"), items_format=str
+            ),
+            hgnc_gene_ids=cls.comma_sep_values_to_list(
+                comma_sep_values=form_data.get("hgnc_gene_ids"), items_format=int
+            ),
+            hgnc_gene_symbols=cls.comma_sep_values_to_list(
+                comma_sep_values=form_data.get("hgnc_gene_symbols"), items_format=str
+            ),
+            interval_type=form_data.get("interval_type"),
+            default_level=form_data.get("default_level"),
+            panel_name=form_data.get("panel_name"),
+            case_display_name=form_data.get("case_display_name"),
+            samples=form_data.get("samples"),
+        )
+        return report_query
+
     @field_validator("samples", mode="before")
     def samples_validator(cls, sample_list):
         if isinstance(sample_list, str):

tests/src/chanjo2/endpoints/test_overview.py

@@ -1,11 +1,12 @@
+import json
 from typing import Dict, List, Type
 
 from fastapi import status
 from fastapi.testclient import TestClient
 from requests.models import Response
 
 from chanjo2.constants import BUILD_37, DEFAULT_COMPLETENESS_LEVELS
-from chanjo2.demo import DEMO_COVERAGE_QUERY_DATA
+from chanjo2.demo import DEMO_COVERAGE_QUERY_DATA, DEMO_COVERAGE_QUERY_FORM
 
 
 def test_demo_overview(client: TestClient, endpoints: Type):
@@ -22,7 +23,7 @@ def test_demo_overview(client: TestClient, endpoints: Type):
 
 
 def test_overview_json_data(client: TestClient, endpoints: Type):
-    """Test the endpoint that creates the genes coverage overview page by providing json data in POST request."""
+    """Test the endpoint that creates the genes coverage overview page by providing json data in the POST request."""
 
     # GIVEN a query with json data to the genes coverage overview endpoint
     response: Response = client.post(
@@ -37,6 +38,22 @@ def test_overview_json_data(client: TestClient, endpoints: Type):
     assert response.template.name == "overview.html"
 
 
+def test_overview_form_data(client: TestClient, endpoints: Type):
+    """Test the endpoint that creates the genes coverage overview page by providing application/x-www-form-urlencoded data in the POST request."""
+
+    # GIVEN a query with application/x-www-form-urlencoded data to the genes coverage overview endpoint
+    response: Response = client.post(
+        endpoints.OVERVIEW,
+        data=DEMO_COVERAGE_QUERY_FORM,
+        headers={"Content-Type": "application/x-www-form-urlencoded"},
+    )
+    # Then the request should be successful
+    assert response.status_code == status.HTTP_200_OK
+
+    # And return an HTML page
+    assert response.template.name == "overview.html"
+
+
 def test_gene_overview(
     client: TestClient, endpoints: Type, genomic_ids_per_build: Dict[str, List]
 ):

tests/src/chanjo2/endpoints/test_report.py

@@ -6,7 +6,7 @@
 from requests.models import Response
 
 from chanjo2.constants import GENE_LISTS_NOT_SUPPORTED_MSG
-from chanjo2.demo import DEMO_COVERAGE_QUERY_DATA
+from chanjo2.demo import DEMO_COVERAGE_QUERY_DATA, DEMO_COVERAGE_QUERY_FORM
 
 
 def test_demo_report(client: TestClient, endpoints: Type):
@@ -38,11 +38,11 @@ def test_report_request_no_genes(client: TestClient, endpoints: Type):
     # THEN the response should return the expected error code and message
     assert response.status_code == status.HTTP_422_UNPROCESSABLE_ENTITY
     result = response.json()
-    assert GENE_LISTS_NOT_SUPPORTED_MSG in result["detail"][0]["msg"]
+    assert GENE_LISTS_NOT_SUPPORTED_MSG in result["detail"]
 
 
 def test_report_json_data(client: TestClient, endpoints: Type):
-    """Test the coverage report endpoint by providing json data in POST request."""
+    """Test the coverage report endpoint by providing json data in a POST request."""
 
     # GIVEN a query with json data to the report endpoint
     response: Response = client.post(
@@ -55,3 +55,19 @@ def test_report_json_data(client: TestClient, endpoints: Type):
 
     # And return an HTML page
     assert response.template.name == "report.html"
+
+
+def test_report_form_data(client: TestClient, endpoints: Type):
+    """Test the coverage report endpoint by providing application/x-www-form-urlencoded data in a POST request."""
+
+    # GIVEN a query with application/x-www-form-urlencoded data to the report endpoint
+    response: Response = client.post(
+        endpoints.REPORT,
+        data=DEMO_COVERAGE_QUERY_FORM,
+        headers={"Content-Type": "application/x-www-form-urlencoded"},
+    )
+    # Then the request should be successful
+    assert response.status_code == status.HTTP_200_OK
+
+    # And return an HTML page
+    assert response.template.name == "report.html"