From 4083bf174cbc8f6e7a49318eed69795d6923c49d Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 11 Dec 2023 15:33:21 +0100 Subject: [PATCH] feat: implementing ClinVar upload (#99) WIP --- backend/Pipfile | 1 + backend/Pipfile.lock | 571 +++++++++++++++--- .../api_v1/endpoints/clinvar_submission.py | 1 + backend/app/models/clinvar_submission.py | 78 +++ 4 files changed, 566 insertions(+), 85 deletions(-) create mode 100644 backend/app/api/api_v1/endpoints/clinvar_submission.py create mode 100644 backend/app/models/clinvar_submission.py diff --git a/backend/Pipfile b/backend/Pipfile index 7973f3bed..507711e0d 100644 --- a/backend/Pipfile +++ b/backend/Pipfile @@ -27,6 +27,7 @@ greenlet = "*" emails = "*" jinja2 = "*" sentry-sdk = {extras = ["fastapi"], version = "*"} +clinvar-this = "*" [dev-packages] aiosqlite = "*" diff --git a/backend/Pipfile.lock b/backend/Pipfile.lock index 1d996e449..4bf164e4c 100644 --- a/backend/Pipfile.lock +++ b/backend/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "3300e7c5ca69e8575acc5c6428468c5e7ce4b30443796eb6c37b9ce0b274901d" + "sha256": "bdf901568842992adb5c90a9aacb76e31be1e47956a8085d7d594b30f9f9bcc1" }, "pipfile-spec": 6, "requires": { @@ -18,12 +18,12 @@ "default": { "alembic": { "hashes": [ - "sha256:47d52e3dfb03666ed945becb723d6482e52190917fdb47071440cfdba05d92cb", - "sha256:bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f" + "sha256:a23974ea301c3ee52705db809c7413cecd165290c6679b9998dd6c74342ca23a", + "sha256:ab4b3b94d2e1e5f81e34be8a9b7b7575fc9dd5398fccb0bef351ec9b14872623" ], "index": "pypi", - "markers": "python_version >= '3.7'", - "version": "==1.12.1" + "markers": "python_version >= '3.8'", + "version": "==1.13.0" }, "annotated-types": { "hashes": [ @@ -97,6 +97,14 @@ "markers": "python_full_version >= '3.8.0'", "version": "==0.29.0" }, + "attrs": { + "hashes": [ + "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04", + "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015" + ], + "markers": "python_version >= '3.7'", + "version": "==23.1.0" + }, "bcrypt": { "hashes": [ "sha256:12611c4b0a8b1c461646228344784a1089bc0c49975680a2f54f516e71e9b79e", @@ -305,6 +313,14 @@ "markers": "python_version >= '3.7'", "version": "==8.1.7" }, + "clinvar-this": { + "hashes": [ + "sha256:cbefeb541767da2725e3c9c29481483b404bc8d8b3261b157c0013514c5ef402" + ], + "index": "pypi", + "markers": "python_version >= '3.6'", + "version": "==0.14.0" + }, "cryptography": { "hashes": [ "sha256:079b85658ea2f59c4f43b70f8119a52414cdb7be34da5d019a77bf96d473b960", @@ -412,67 +428,68 @@ }, "greenlet": { "hashes": [ - "sha256:0a02d259510b3630f330c86557331a3b0e0c79dac3d166e449a39363beaae174", - "sha256:0b6f9f8ca7093fd4433472fd99b5650f8a26dcd8ba410e14094c1e44cd3ceddd", - "sha256:100f78a29707ca1525ea47388cec8a049405147719f47ebf3895e7509c6446aa", - "sha256:1757936efea16e3f03db20efd0cd50a1c86b06734f9f7338a90c4ba85ec2ad5a", - 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+++ b/backend/app/api/api_v1/endpoints/clinvar_submission.py @@ -0,0 +1 @@ +"""Endpoints for the ClinVar submission API.""" diff --git a/backend/app/models/clinvar_submission.py b/backend/app/models/clinvar_submission.py new file mode 100644 index 000000000..9b3f35832 --- /dev/null +++ b/backend/app/models/clinvar_submission.py @@ -0,0 +1,78 @@ +"""Models for the ClinVar submission.""" + +import uuid as uuid_module +from typing import Optional, TYPE_CHECKING + +import clinvar_api.models as clinvar_models +from fastapi_users_db_sqlalchemy.generics import GUID # noqa +from sqlalchemy import ( + JSON, + Boolean, + Column, + Enum, + ForeignKey, + Integer, + String, + UniqueConstraint, + Uuid, +) +from sqlalchemy.orm import Mapped, mapped_column + +from app.db.session import Base + +UUID_ID = uuid_module.UUID + + +class ClinvarUserOrg(Base): + """Information to attach to a user for one organisation.""" + + __tablename__ = "clinvarsubmissionuserorg" + + if TYPE_CHECKING: # pragma: no cover + id: UUID_ID + user: UUID_ID + label: str + clinvar_api_token: str + + +class ClinvarSubmissionLogbook(Base): + """ + Container for the activity of one variant submission to ClinVar for + a single organisation. + + One variant submission corresponds to a genetic variant as submitted for + one condition and one organisation. The variant can be submitted and + on success an SCV identifier is returned. Deletion and resubmission + will lead to a new SCV identifier so we store the top-level identifier + only. + """ + + __tablename__ = "clinvarsubmissionlogbook" + + if TYPE_CHECKING: # pragma: no cover + id: UUID_ID + clinvaruserorg: UUID_ID + primary_id: str + status_presence: str + status_success: str + + +class ClinvarSubmissionEntry(Base): + """One entry in a :ref:`ClinvarSubmissionLookbook`. + + This corresponds to a submission sent to ClinVar and the corresponding + response. + """ + + __tablename__ = "clinvarsubmissionentry" + + if TYPE_CHECKING: # pragma: no cover + id: UUID_ID + clinvarsubmissionlogbook: UUID_ID + kind: str + status: str + send_payload: str + send_timestamp: str + response_status: str + response_payload: str + response_timestamp: str