Store job information

- add Job model and /admin/jobs endpoint
- start/end times, status and error messages are now stored for each job
- admins can view the list of jobs
- resolves #20

backend/src/predicTCR_server/app.py

@@ -13,10 +13,13 @@
 from flask_jwt_extended import JWTManager
 from flask_cors import cross_origin
 from predicTCR_server.logger import get_logger
+from predicTCR_server.utils import timestamp_now
 from predicTCR_server.model import (
     db,
     Sample,
     User,
+    Job,
+    Status,
     Settings,
     add_new_user,
     add_new_runner_user,
@@ -281,6 +284,16 @@ def admin_users():
         )
         return jsonify(users=[user.as_dict() for user in users])
 
+    @app.route("/api/admin/jobs", methods=["GET"])
+    @jwt_required()
+    def admin_jobs():
+        if not current_user.is_admin:
+            return jsonify(message="Admin account required"), 400
+        jobs = (
+            db.session.execute(db.select(Job).order_by(db.desc(Job.id))).scalars().all()
+        )
+        return jsonify(jobs=[job.as_dict() for job in jobs])
+
     @app.route("/api/admin/runner_token", methods=["GET"])
     @jwt_required()
     def admin_runner_token():
@@ -305,7 +318,17 @@ def runner_request_job():
         sample_id = request_job()
         if sample_id is None:
             return jsonify(message="No job available"), 204
-        return {"sample_id": sample_id}
+        new_job = Job(
+            id=None,
+            sample_id=sample_id,
+            timestamp_start=timestamp_now(),
+            timestamp_end=0,
+            status=Status.RUNNING,
+            error_message="",
+        )
+        db.session.add(new_job)
+        db.session.commit()
+        return {"job_id": new_job.id, "sample_id": sample_id}
 
     @app.route("/api/runner/result", methods=["POST"])
     @cross_origin()
@@ -317,6 +340,9 @@ def runner_result():
         sample_id = form_as_dict.get("sample_id", None)
         if sample_id is None:
             return jsonify(message="Missing key: sample_id"), 400
+        job_id = form_as_dict.get("job_id", None)
+        if job_id is None:
+            return jsonify(message="Missing key: job_id"), 400
         success = form_as_dict.get("success", None)
         if success is None or success.lower() not in ["true", "false"]:
             logger.info("  -> missing success key")
@@ -328,19 +354,22 @@ def runner_result():
             return jsonify(message="Result has success=True but no file"), 400
         runner_hostname = form_as_dict.get("runner_hostname", "")
         logger.info(
-            f"Result upload for '{sample_id}' from runner {current_user.email} / {runner_hostname}"
+            f"Job '{job_id}' uploaded result for '{sample_id}' from runner {current_user.email} / {runner_hostname}"
         )
-        error_message = form_as_dict.get("error_message", None)
-        if error_message is not None:
+        error_message = form_as_dict.get("error_message", "")
+        if error_message != "":
             logger.info(f"  -> error message: {error_message}")
-        message, code = process_result(sample_id, success, zipfile)
+        message, code = process_result(
+            int(job_id), int(sample_id), success, error_message, zipfile
+        )
         return jsonify(message=message), code
 
     with app.app_context():
         db.create_all()
         if db.session.get(Settings, 1) is None:
             db.session.add(
                 Settings(
+                    id=None,
                     default_personal_submission_quota=10,
                     default_personal_submission_interval_mins=30,
                     global_quota=1000,

backend/src/predicTCR_server/model.py

@@ -2,12 +2,14 @@
 
 import re
 import flask
-from enum import Enum
+import enum
 import argon2
 import pathlib
 from flask_sqlalchemy import SQLAlchemy
+from sqlalchemy.orm import DeclarativeBase, MappedAsDataclass, Mapped, mapped_column
 from werkzeug.datastructures import FileStorage
 from sqlalchemy.inspection import inspect
+from sqlalchemy import Integer, String, Boolean, Enum
 from dataclasses import dataclass
 from predicTCR_server.email import send_email
 from predicTCR_server.settings import predicTCR_url
@@ -20,12 +22,17 @@
     decode_password_reset_token,
 )
 
-db = SQLAlchemy()
+
+class Base(DeclarativeBase, MappedAsDataclass):
+    pass
+
+
+db = SQLAlchemy(model_class=Base)
 ph = argon2.PasswordHasher()
 logger = get_logger()
 
 
-class Status(str, Enum):
+class Status(str, enum.Enum):
     QUEUED = "queued"
     RUNNING = "running"
     COMPLETED = "completed"
@@ -34,34 +41,45 @@ class Status(str, Enum):
 
 @dataclass
 class Settings(db.Model):
-    id: int = db.Column(db.Integer, primary_key=True)
-    default_personal_submission_quota: int = db.Column(db.Integer, nullable=False)
-    default_personal_submission_interval_mins: int = db.Column(
-        db.Integer, nullable=False
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    default_personal_submission_quota: Mapped[int] = mapped_column(
+        Integer, nullable=False
+    )
+    default_personal_submission_interval_mins: Mapped[int] = mapped_column(
+        Integer, nullable=False
     )
-    global_quota: int = db.Column(db.Integer, nullable=False)
-    tumor_types: str = db.Column(db.String, nullable=False)
-    sources: str = db.Column(db.String, nullable=False)
-    csv_required_columns: str = db.Column(db.String, nullable=False)
+    global_quota: Mapped[int] = mapped_column(Integer, nullable=False)
+    tumor_types: Mapped[str] = mapped_column(String, nullable=False)
+    sources: Mapped[str] = mapped_column(String, nullable=False)
+    csv_required_columns: Mapped[str] = mapped_column(String, nullable=False)
 
     def as_dict(self):
-        return {
-            c: getattr(self, c)
-            for c in inspect(self).attrs.keys()
-            if c != "password_hash"
-        }
+        return {c: getattr(self, c) for c in inspect(self).attrs.keys()}
+
+
+@dataclass
+class Job(db.Model):
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    sample_id: Mapped[int] = mapped_column(Integer, nullable=False)
+    timestamp_start: Mapped[int] = mapped_column(Integer, nullable=False)
+    timestamp_end: Mapped[int] = mapped_column(Integer, nullable=False)
+    status: Mapped[Status] = mapped_column(Enum(Status), nullable=False)
+    error_message: Mapped[str] = mapped_column(String, nullable=False)
+
+    def as_dict(self):
+        return {c: getattr(self, c) for c in inspect(self).attrs.keys()}
 
 
 @dataclass
 class Sample(db.Model):
-    id: int = db.Column(db.Integer, primary_key=True)
-    email: str = db.Column(db.String(256), nullable=False)
-    name: str = db.Column(db.String(128), nullable=False)
-    tumor_type: str = db.Column(db.String(128), nullable=False)
-    source: str = db.Column(db.String(128), nullable=False)
-    timestamp: int = db.Column(db.Integer, nullable=False)
-    status: Status = db.Column(db.Enum(Status), nullable=False)
-    has_results_zip: bool = db.Column(db.Boolean, nullable=False)
+    id: Mapped[int] = mapped_column(Integer, primary_key=True)
+    email: Mapped[str] = mapped_column(String(256), nullable=False)
+    name: Mapped[str] = mapped_column(String(128), nullable=False)
+    tumor_type: Mapped[str] = mapped_column(String(128), nullable=False)
+    source: Mapped[str] = mapped_column(String(128), nullable=False)
+    timestamp: Mapped[int] = mapped_column(Integer, nullable=False)
+    status: Mapped[Status] = mapped_column(Enum(Status), nullable=False)
+    has_results_zip: Mapped[bool] = mapped_column(Boolean, nullable=False)
 
     def _base_path(self) -> pathlib.Path:
         data_path = flask.current_app.config["PREDICTCR_DATA_PATH"]
@@ -79,17 +97,17 @@ def result_file_path(self) -> pathlib.Path:
 
 @dataclass
 class User(db.Model):
-    id: int = db.Column(db.Integer, primary_key=True)
-    email: str = db.Column(db.Text, nullable=False, unique=True)
-    password_hash: str = db.Column(db.Text, nullable=False)
-    activated: bool = db.Column(db.Boolean, nullable=False)
-    enabled: bool = db.Column(db.Boolean, nullable=False)
-    quota: int = db.Column(db.Integer, nullable=False)
-    submission_interval_minutes: int = db.Column(db.Integer, nullable=False)
-    last_submission_timestamp: int = db.Column(db.Integer, nullable=False)
-    is_admin: bool = db.Column(db.Boolean, nullable=False)
-    is_runner: bool = db.Column(db.Boolean, nullable=False)
-    full_results: bool = db.Column(db.Boolean, nullable=False)
+    id: int = mapped_column(Integer, primary_key=True)
+    email: str = mapped_column(String, nullable=False, unique=True)
+    password_hash: str = mapped_column(String, nullable=False)
+    activated: bool = mapped_column(Boolean, nullable=False)
+    enabled: bool = mapped_column(Boolean, nullable=False)
+    quota: int = mapped_column(Integer, nullable=False)
+    submission_interval_minutes: int = mapped_column(Integer, nullable=False)
+    last_submission_timestamp: int = mapped_column(Integer, nullable=False)
+    is_admin: bool = mapped_column(Boolean, nullable=False)
+    is_runner: bool = mapped_column(Boolean, nullable=False)
+    full_results: bool = mapped_column(Boolean, nullable=False)
 
     def set_password_nocheck(self, new_password: str):
         self.password_hash = ph.hash(new_password)
@@ -145,17 +163,26 @@ def request_job() -> int | None:
 
 
 def process_result(
-    sample_id: str, success: bool, result_zip_file: FileStorage | None
+    job_id: int,
+    sample_id: int,
+    success: bool,
+    error_message: str,
+    result_zip_file: FileStorage | None,
 ) -> tuple[str, int]:
-    sample = db.session.execute(
-        db.select(Sample).filter_by(id=sample_id)
-    ).scalar_one_or_none()
+    sample = db.session.get(Sample, sample_id)
     if sample is None:
         logger.warning(f" --> Unknown sample id {sample_id}")
         return f"Unknown sample id {sample_id}", 400
+    job = db.session.get(Job, job_id)
+    if job is None:
+        logger.warning(f" --> Unknown job id {job_id}")
+        return f"Unknown job id {job_id}", 400
+    job.timestamp_end = timestamp_now()
     if success is False:
         sample.has_results_zip = False
         sample.status = Status.FAILED
+        job.status = Status.FAILED
+        job.error_message = error_message
         db.session.commit()
         return "Result processed", 200
     if result_zip_file is None:
@@ -165,6 +192,7 @@ def process_result(
     result_zip_file.save(sample.result_file_path())
     sample.has_results_zip = True
     sample.status = Status.COMPLETED
+    job.status = Status.COMPLETED
     db.session.commit()
     return "Result processed", 200
 
@@ -244,6 +272,7 @@ def add_new_user(email: str, password: str, is_admin: bool) -> tuple[str, int]:
     try:
         db.session.add(
             User(
+                id=None,
                 email=email,
                 password_hash=ph.hash(password),
                 activated=False,
@@ -282,6 +311,7 @@ def add_new_runner_user() -> User | None:
             runner_name = f"runner{runner_number}"
         db.session.add(
             User(
+                id=None,
                 email=runner_name,
                 password_hash="",
                 activated=False,
@@ -419,6 +449,7 @@ def add_new_sample(
     settings = db.session.get(Settings, 1)
     settings.global_quota -= 1
     new_sample = Sample(
+        id=None,
         email=email,
         name=name,
         tumor_type=tumor_type,

backend/tests/helpers/flask_test_utils.py

@@ -14,6 +14,7 @@ def add_test_users(app):
             email = f"{name}@abc.xy"
             db.session.add(
                 User(
+                    id=None,
                     email=email,
                     password_hash=ph.hash(name),
                     activated=True,
@@ -46,6 +47,7 @@ def add_test_samples(app, data_path: pathlib.Path):
                 with open(f"{ref_dir}/input.{input_file_type}", "w") as f:
                     f.write(input_file_type)
             new_sample = Sample(
+                id=None,
                 email="[email protected]",
                 name=name,
                 tumor_type=f"tumor_type{sample_id}",

backend/tests/test_app.py

@@ -210,12 +210,13 @@ def test_result_invalid(client):
     assert "No results available" in response.json["message"]
 
 
-def _upload_result(client, result_zipfile: pathlib.Path, sample_id: int):
+def _upload_result(client, result_zipfile: pathlib.Path, job_id: int, sample_id: int):
     headers = _get_auth_headers(client, "[email protected]", "runner")
     with open(result_zipfile, "rb") as f:
         response = client.post(
             "/api/runner/result",
             data={
+                "job_id": job_id,
                 "sample_id": sample_id,
                 "success": True,
                 "file": (io.BytesIO(f.read()), result_zipfile.name),
@@ -225,19 +226,57 @@ def _upload_result(client, result_zipfile: pathlib.Path, sample_id: int):
     return response
 
 
-def test_result_valid(client, result_zipfile):
-    headers = _get_auth_headers(client, "[email protected]", "user")
-    sample_id = 1
-    assert _upload_result(client, result_zipfile, sample_id).status_code == 200
+def test_runner_valid_success(client, result_zipfile):
+    headers = _get_auth_headers(client, "[email protected]", "runner")
+    # request job
+    request_job_response = client.post(
+        "/api/runner/request_job",
+        json={"runner_hostname": "me"},
+        headers=headers,
+    )
+    assert request_job_response.status_code == 200
+    assert request_job_response.json == {"sample_id": 1, "job_id": 1}
+    # upload successful result
+    assert _upload_result(client, result_zipfile, 1, 1).status_code == 200
     response = client.post(
         "/api/result",
-        json={"sample_id": sample_id},
-        headers=headers,
+        json={"sample_id": 1},
+        headers=_get_auth_headers(client, "[email protected]", "user"),
     )
     assert response.status_code == 200
     assert len(response.data) > 1
 
 
+def test_runner_valid_failure(client, result_zipfile):
+    headers = _get_auth_headers(client, "[email protected]", "runner")
+    # request job
+    request_job_response = client.post(
+        "/api/runner/request_job",
+        json={"runner_hostname": "me"},
+        headers=headers,
+    )
+    assert request_job_response.status_code == 200
+    assert request_job_response.json == {"sample_id": 1, "job_id": 1}
+    # upload failure result
+    result_response = client.post(
+        "/api/runner/result",
+        data={
+            "job_id": 1,
+            "sample_id": 1,
+            "success": False,
+            "error_message": "Something went wrong",
+        },
+        headers=headers,
+    )
+    assert result_response.status_code == 200
+    response = client.post(
+        "/api/result",
+        json={"sample_id": 1},
+        headers=_get_auth_headers(client, "[email protected]", "user"),
+    )
+    assert response.status_code == 400
+
+
 def test_admin_samples_valid(client):
     headers = _get_auth_headers(client, "[email protected]", "admin")
     response = client.get("/api/admin/samples", headers=headers)
@@ -288,12 +327,6 @@ def test_admin_users_valid(client):
     assert "users" in response.json
 
 
-def test_runner_result_valid(client, result_zipfile):
-    response = _upload_result(client, result_zipfile, 1)
-    assert response.status_code == 200
-    assert "result processed" in response.json["message"].lower()
-
-
 def test_admin_update_user_valid(client):
     headers = _get_auth_headers(client, "[email protected]", "admin")
     user = client.get("/api/admin/users", headers=headers).json["users"][0]