Make analysis config_path optional (#523)

## Description

The `config_path` of an Analysis is only used when the workflow manager is Slurm and no such file is longer being created for most Nextflow pipelines, therefore it should not be required for analyses that does not have Slurm set as workflow manager. 

### Added

- Validation that checks that a config_path is set when Slurm is the workflow manager

### Changed

- Made config_path optional when adding and persisting analyses in Trailblazer and the workflow manager is not Slurm.

---------

Co-authored-by: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>

Author: mogmi

tests/integration/endpoints/test_add_pending_analysis.py

@@ -1,34 +1,103 @@
+import json
 from http import HTTPStatus
 
 from flask.testing import FlaskClient
+from werkzeug.test import TestResponse
 
-from trailblazer.constants import TrailblazerPriority, TrailblazerTypes
-from trailblazer.dto.create_analysis_request import CreateAnalysisRequest
+from trailblazer.store.models import Analysis
 from trailblazer.store.store import Store
 
 TYPE_JSON = "application/json"
 
 
 def test_adding_analysis(client: FlaskClient, store: Store):
     # GIVEN a valid request to add an analysis
-    create_analysis_request = CreateAnalysisRequest(
-        case_id="case_id",
-        config_path="config_path",
-        workflow=TrailblazerTypes.WGS,
-        priority=TrailblazerPriority.NORMAL,
-        out_dir="out_dir",
-        ticket="ticket_id",
-        type=TrailblazerTypes.WGS,
-        order_id=123,
+    data: str = json.dumps(
+        {
+            "case_id": "case_id",
+            "config_path": "config_path",
+            "order_id": 123,
+            "out_dir": "out_dir",
+            "priority": "normal",
+            "ticket": "ticket_id",
+            "tower_workflow_id": None,
+            "type": "wgs",
+            "workflow": "wgs",
+        }
     )
-    data: str = create_analysis_request.model_dump_json()
 
     # WHEN sending the request
-    response = client.post("/api/v1/add-pending-analysis", data=data, content_type=TYPE_JSON)
+    response: TestResponse = client.post(
+        "/api/v1/add-pending-analysis", data=data, content_type=TYPE_JSON
+    )
 
-    # THEN it gives a success response
+    # THEN it gives a success response with json contents
     assert response.status_code == HTTPStatus.CREATED
+    assert response.json
 
     # THEN the analysis was persisted
     analysis_id = int(response.json["id"])
     assert store.get_analysis_with_id(analysis_id)
+
+
+def test_adding_analysis_without_config_path(client: FlaskClient, store: Store):
+    # GIVEN a request to add an analysis with tower as workflow manager and no config_path
+    data: str = json.dumps(
+        {
+            "case_id": "case_id",
+            "config_path": None,
+            "order_id": 123,
+            "out_dir": "out_dir",
+            "priority": "normal",
+            "ticket": "ticket_id",
+            "tower_workflow_id": None,
+            "type": "wgs",
+            "workflow": "wgs",
+            "workflow_manager": "nf_tower",
+        }
+    )
+
+    # WHEN sending the request
+    response: TestResponse = client.post(
+        "/api/v1/add-pending-analysis", data=data, content_type=TYPE_JSON
+    )
+
+    # THEN it gives a success response with json contents
+    assert response.status_code == HTTPStatus.CREATED
+    assert response.json
+
+    # THEN the analysis was persisted without a config_path
+    analysis_id = int(response.json["id"])
+    analysis: Analysis = store.get_analysis_with_id(analysis_id)
+    assert analysis.config_path is None
+
+
+def test_adding_analysis_without_config_path_and_slurm_workflow_manager_fails(
+    client: FlaskClient,
+):
+    # GIVEN a request to add an analysis with slurm as workflow manager and no config_path
+    data: str = json.dumps(
+        {
+            "case_id": "case_id",
+            "email": None,
+            "is_hidden": None,
+            "order_id": 123,
+            "out_dir": "out_dir",
+            "priority": "normal",
+            "ticket": "ticket_id",
+            "tower_workflow_id": None,
+            "type": "wgs",
+            "workflow": "wgs",
+            "workflow_manager": "slurm",
+        }
+    )
+
+    # WHEN sending the request
+    response: TestResponse = client.post(
+        "/api/v1/add-pending-analysis", data=data, content_type=TYPE_JSON
+    )
+
+    # THEN an error response is returned
+    assert response.status_code == HTTPStatus.BAD_REQUEST
+    assert response.json
+    assert response.json["error"]

tests/store/crud/test_create.py

@@ -1,6 +1,10 @@
+from sqlalchemy import inspect
+
 from tests.mocks.store_mock import MockStore
+from trailblazer.constants import TrailblazerPriority, TrailblazerTypes
+from trailblazer.dto.create_analysis_request import CreateAnalysisRequest
 from trailblazer.store.filters.user_filters import UserFilter, apply_user_filter
-from trailblazer.store.models import User
+from trailblazer.store.models import Analysis, User
 
 
 def test_add_user(store: MockStore, user_email: str, username: str):
@@ -19,3 +23,19 @@ def test_add_user(store: MockStore, user_email: str, username: str):
     ).first()
     assert new_user
     assert user == new_user
+
+
+def test_add_pending_analysis(store: MockStore):
+    # GIVEN a valid CreateAnalysisRequest
+    analysis_data = CreateAnalysisRequest(
+        case_id="pending_analysis_case_id",
+        out_dir="/out/dir",
+        priority=TrailblazerPriority.LOW,
+        type=TrailblazerTypes.WGS,
+    )
+
+    # WHEN creating and storing a pending analysis
+    analysis: Analysis = store.add_pending_analysis(analysis_data)
+
+    # THEN an analysis has been created and persisted to the database
+    assert inspect(analysis).persistent

trailblazer/constants.py

@@ -26,8 +26,8 @@ class FileExtension(StrEnum):
 class WorkflowManager(StrEnum):
     """Supported task managers."""
 
-    SLURM: str = "slurm"
-    TOWER: str = "nf_tower"
+    SLURM = "slurm"
+    TOWER = "nf_tower"
 
     @classmethod
     def list(cls) -> list:
@@ -89,22 +89,22 @@ class CharacterFormat(StrEnum):
 class TrailblazerTypes(StrEnum):
     """Trailblazer analysis types."""
 
-    OTHER: str = "other"
-    RNA: str = "rna"
-    TGS: str = "tgs"
-    WES: str = "wes"
-    WGS: str = "wgs"
-    WTS: str = "wts"
+    OTHER = "other"
+    RNA = "rna"
+    TGS = "tgs"
+    WES = "wes"
+    WGS = "wgs"
+    WTS = "wts"
 
 
 class TrailblazerPriority(StrEnum):
     """Trailblazer analysis priorities."""
 
-    LOW: str = "low"
-    NORMAL: str = "normal"
-    HIGH: str = "high"
-    EXPRESS: str = "express"
-    MAINTENANCE: str = "maintenance"
+    LOW = "low"
+    NORMAL = "normal"
+    HIGH = "high"
+    EXPRESS = "express"
+    MAINTENANCE = "maintenance"
 
 
 class TrailblazerStatus(StrEnum):

trailblazer/dto/create_analysis_request.py

@@ -1,11 +1,13 @@
-from pydantic import BaseModel
+from typing import Self
+
+from pydantic import BaseModel, model_validator
 
 from trailblazer.constants import TrailblazerPriority, TrailblazerTypes, WorkflowManager
 
 
 class CreateAnalysisRequest(BaseModel):
     case_id: str
-    config_path: str
+    config_path: str | None = None
     email: str | None = None
     is_hidden: bool | None = None
     order_id: int | None = None
@@ -16,3 +18,9 @@ class CreateAnalysisRequest(BaseModel):
     type: TrailblazerTypes
     workflow: str | None = None
     workflow_manager: WorkflowManager | None = None
+
+    @model_validator(mode="after")
+    def check_config_path_set_for_slurm_workflow_manager(self) -> Self:
+        if (self.workflow_manager == WorkflowManager.SLURM) and (not self.config_path):
+            raise ValueError("config_path needs to be set when SLURM is workflow manager")
+        return self

trailblazer/store/models.py

@@ -75,7 +75,7 @@ class Analysis(Model):
     case_id = Column(types.String(128), nullable=False)
     comment = Column(types.Text)
     completed_at = Column(types.DateTime)
-    config_path = Column(types.Text)
+    config_path = Column(types.Text, nullable=True, default=None)
     id = Column(types.Integer, primary_key=True)
     is_visible = Column(types.Boolean, default=True)
     logged_at = Column(types.DateTime, default=datetime.datetime.now)