Kemal Yaylali
3ab404ebe5
From clicking through the redesigned UI: - scoring a case without a model registry painted a red failure across a case that had in fact analysed fine. It is now a quiet note saying the model term contributes 0, because scoring is an optional fourth of the rank, not the analysis. - the MLflow default moves to port 5001. On macOS, AirPlay Receiver owns 5000, which is why the registry answered "403" rather than refusing the connection; docker-compose publishes 5001 to match. - a funnel step that kept nothing drew a visible bar. Zero now draws zero. - "1 candidates". - the funnel's fixed grid columns forced a horizontal scrollbar on the report. The report also lists the top undecided candidates now: the first thing anyone opens has no decisions in it, and "Shortlisted (0)" alone said nothing about what the tool found. Tests: api 77, web 32; ruff, mypy, svelte-check clean.
38 lines
1.8 KiB
Python
38 lines
1.8 KiB
Python
from pathlib import Path
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from pydantic_settings import BaseSettings, SettingsConfigDict
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# api/app/config.py -> repo root locally; "/" in the API image, where compose mounts /pipeline.
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REPO_ROOT = Path(__file__).resolve().parents[2]
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class Settings(BaseSettings):
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model_config = SettingsConfigDict(env_file=".env", extra="ignore")
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database_url: str = "postgresql+asyncpg://rarelens:rarelens@localhost:5432/rarelens"
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# docker-compose publishes MLflow on 5001; macOS AirPlay Receiver owns 5000.
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mlflow_tracking_uri: str = "http://localhost:5001"
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model_name: str = "rarelens-pathogenicity"
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# Registry alias set by `rarelens_ml.train --register` (stages are deprecated in MLflow 3).
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model_alias: str = "production"
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# A model artifact URI (gs://...) scores without an MLflow server running; wins over the registry.
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model_uri: str | None = None
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gcs_bucket: str | None = None # set in GCP; local uses ./data
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pubsub_topic: str | None = None # "vcf-uploaded" in GCP; local runs pipeline inline
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# Serverless track: run the Nextflow driver as a Cloud Run job instead of Argo + Pub/Sub.
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cloudrun_job: str | None = None
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gcp_project: str | None = None # required with pubsub_topic or cloudrun_job
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gcp_region: str = "europe-west2"
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pipeline_dir: Path = REPO_ROOT / "pipeline"
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# Handed to the pipeline when it differs from the API's own: the loader runs inside a
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# container, where the API's localhost would be the container itself.
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pipeline_database_url: str | None = None
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nextflow_profile: str = "docker"
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# Local (non-gs://) VCFs must live under this directory.
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local_data_root: Path = Path("/data")
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# Browsers calling the API cross-origin; behind the ingress the UI is same-origin.
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cors_origins: list[str] = ["http://localhost:5173"]
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settings = Settings()
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