text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
values | hash stringlengths 16 16 | score float64 7 8.5 | stars int64 0 237k |
|---|---|---|---|---|---|---|
"""Provide core typing/structure for categorical variants."""
import logging
from ga4gh.cat_vrs import models as cat_vrs_models
from ga4gh.vrs import models as vrs_models
from ga4gh.vrs.dataproxy import _DataProxy
from pydantic import Field, field_validator
_logger = logging.getLogger(__name__)
_seqrepo_seqtype_to... | biocommons/anyvar | src/anyvar/core/categorical_variants.py | .py | 43676da16ad311cb | 7.63 | 17 |
"""Define types and classes for *metadata*, i.e. additional descriptions on top of stored objects.
This currently includes
* **Extensions**: free-text key-value descriptions of an object
* **Mappings**: directed associations between objects
"""
from enum import StrEnum
from pydantic import BaseModel, JsonValue
cl... | biocommons/anyvar | src/anyvar/core/metadata.py | .py | 11a8b3f65be69bb5 | 7.63 | 17 |
"""Defines functions used to lift over variants between GRCh37 & GRCh38"""
import logging
from enum import Enum
from typing import TypeVar
from agct import (
Assembly,
Converter,
Strand,
get_converter,
get_refget_id_from_seqinfo,
get_seqinfo_from_refget_id,
)
from ga4gh.core import ga4gh_ident... | biocommons/anyvar | src/anyvar/mapping/liftover.py | .py | b2c013c367fe7b57 | 7.63 | 17 |
"""Define data models for use in variant projection"""
from dataclasses import dataclass, field
from typing import TypeAlias
from ga4gh.vrs import models
from anyvar.core.metadata import VariationMapping
from anyvar.core.objects import SupportedVrsVariation
class ProjectionError(Exception):
"""Indicates a fail... | biocommons/anyvar | src/anyvar/mapping/projection_models.py | .py | e594f8bb3a9dd628 | 7.63 | 17 |
"""Provide a public interface to mapping models and functions"""
from typing import Protocol
from anyvar.core.objects import SupportedVrsVariation
from anyvar.mapping.projection_models import ProjectionResults
from anyvar.storage.base import Storage
class VariantProjectorProtocol(Protocol):
"""Protocol for vari... | biocommons/anyvar | src/anyvar/mapping/protocols.py | .py | 6008f5c221c28b40 | 7.63 | 17 |
"""Define the Celery app and tasks for asynchronous request-response support"""
import datetime
import logging
import os
import threading
from pathlib import Path
import celery.signals
from celery import Celery, Task
from celery.result import AsyncResult
from dotenv import load_dotenv
import anyvar
from anyvar.resta... | biocommons/anyvar | src/anyvar/queueing/celery_worker.py | .py | 58773bafc6e8065d | 7.63 | 17 |
"""Shared helpers for asynchronous request-response endpoints."""
import asyncio
import logging
import os
from collections.abc import Awaitable, Callable
from fastapi import Response, status
from fastapi.responses import FileResponse, JSONResponse
from anyvar.restapi import has_async_imports
from anyvar.restapi.sche... | biocommons/anyvar | src/anyvar/restapi/async_utils.py | .py | dd8027cf3b5caafa | 7.63 | 17 |
"""Bearer token authentication implementation that can be enabled via environment variables."""
import logging
import os
import time
from collections.abc import Awaitable, Callable
from dataclasses import dataclass, field
import jwt
from fastapi import Depends, HTTPException
from fastapi.security import HTTPAuthoriza... | biocommons/anyvar | src/anyvar/restapi/auth.py | .py | 36ddfefb88510b89 | 7.63 | 17 |
"""Provide API routes related to categorical variants"""
import contextlib
from http import HTTPStatus
from typing import Annotated
from fastapi import APIRouter, Body, HTTPException, Query, Request
from ga4gh.cat_vrs import models as cat_vrs
from ga4gh.vrs import models as vrs
from anyvar.anyvar import AnyVar, Inva... | biocommons/anyvar | src/anyvar/restapi/categorical_variants_router.py | .py | a27d642d123d27a8 | 7.63 | 17 |
"""Provide core route definitions for REST service."""
import logging
import logging.config
import os
import pathlib
from contextlib import asynccontextmanager
import anyio
import yaml
from dotenv import load_dotenv
from fastapi import (
Depends,
FastAPI,
)
import anyvar
from anyvar import AnyVar
from anyvar... | biocommons/anyvar | src/anyvar/restapi/main.py | .py | 366df40687d25757 | 7.63 | 17 |
"""Provide PostgreSQL-based storage implementation."""
import base64
import json
from abc import ABC, abstractmethod
from collections.abc import Iterable
from dataclasses import dataclass
from ga4gh.vrs import models as vrs_models
from pydantic import JsonValue
from anyvar.core import metadata
from anyvar.core impor... | biocommons/anyvar | src/anyvar/storage/base.py | .py | 4ae79e58b7aa3ce0 | 7.63 | 17 |
"""Provide DuckDB-based storage implementation.
Most live, persistent variant registration and search services will want to employ the
PostgreSQL storage option for its performance, particularly for concurrent writes and
large-scale datasets. However, DuckDB may be better in certain use cases:
* The DuckDB file-based... | biocommons/anyvar | src/anyvar/storage/duckdb.py | .py | dd88c7a1ffd3e20f | 7.63 | 17 |
"""Central registry for all object mappers."""
from typing import TypeVar
from ga4gh.vrs import models as vrs_models
from anyvar.core import metadata
from anyvar.core.categorical_variants import CanonicalAllele, ProteinSequenceConsequence
from anyvar.storage import orm
from anyvar.storage.mappers import (
Allele... | biocommons/anyvar | src/anyvar/storage/mapper_registry.py | .py | c1be9247a158c9b4 | 7.63 | 17 |
# ruff: noqa: D101 D102 D107
"""Object mappers for converting between VRS models and database entities."""
from abc import ABC, abstractmethod
from typing import Generic, TypeVar
from ga4gh.cat_vrs import models as cat_vrs_models
from ga4gh.vrs import models as vrs_models
from anyvar.core import metadata
from anyvar... | biocommons/anyvar | src/anyvar/storage/mappers.py | .py | 0b5b19f08aefbb0c | 7.63 | 17 |
"""Stateless storage implementation (no persistence).
Use for processing-only deployments (e.g., variation translation, VCF annotation);
writes are discarded and reads always miss.
"""
from collections.abc import Iterable
from pydantic import JsonValue
from anyvar.core import metadata
from anyvar.core import object... | biocommons/anyvar | src/anyvar/storage/no_db.py | .py | 5feec4f4d56d717a | 7.63 | 17 |
"""SQLAlchemy ORM models for AnyVar database schema."""
import os
import re
from collections.abc import Iterator
from ga4gh.vrs.models import MoleculeType
from sqlalchemy import (
JSON,
Enum,
ForeignKey,
Integer,
Sequence,
String,
create_engine,
inspect,
)
from sqlalchemy.dialects.post... | biocommons/anyvar | src/anyvar/storage/orm.py | .py | 50883b34173964e6 | 7.63 | 17 |
"""Provide PostgreSQL-based storage implementation."""
import json
from pydantic import JsonValue
from sqlalchemy import (
ColumnElement,
Engine,
Index,
create_engine,
delete,
func,
)
from sqlalchemy.dialects.postgresql import insert
from sqlalchemy.orm import Session, sessionmaker
from anyva... | biocommons/anyvar | src/anyvar/storage/postgres.py | .py | 865476abe7039e51 | 7.63 | 17 |
"""Provide base properties for Translator classes."""
from abc import ABC, abstractmethod
from ga4gh.vrs.dataproxy import _DataProxy
from anyvar.core.objects import SupportedVrsVariation
class TranslatorSetupError(Exception):
"""Indicates failure to create translator instance (e.g. invalid params provided)"""
... | biocommons/anyvar | src/anyvar/translate/base.py | .py | 4878c1422b1f5cc3 | 7.63 | 17 |
"""Provide shared variation registration logic for use by REST API and Celery workers."""
import logging
from ga4gh.vrs.dataproxy import DataProxyValidationError
from hgvs.exceptions import HGVSParseError
from anyvar.anyvar import AnyVar
from anyvar.core import objects
from anyvar.mapping import liftover
from anyvar... | biocommons/anyvar | src/anyvar/translate/register.py | .py | 79c373a1e4be9d72 | 7.63 | 17 |
"""Normalize incoming variation descriptions with the VRS-Python library."""
import logging
from os import environ
from warnings import warn
from biocommons.seqrepo import SeqRepo
from bioutils.accessions import coerce_namespace
from ga4gh.vrs import models
from ga4gh.vrs.dataproxy import SeqRepoDataProxy, _DataProxy... | biocommons/anyvar | src/anyvar/translate/vrs_python.py | .py | 78f53650845f3119 | 7.63 | 17 |
"""Support processing and manipulation of VCF objects."""
import logging
from contextlib import nullcontext
from pathlib import Path
import pysam
from ga4gh.core import ga4gh_identify
from ga4gh.vrs import models as vrs_models
from ga4gh.vrs import normalize
from ga4gh.vrs.dataproxy import _DataProxy
from ga4gh.vrs.e... | biocommons/anyvar | src/anyvar/vcf/ingest.py | .py | c4b85c090819ad01 | 7.63 | 17 |
import json
import os
from pathlib import Path
import pytest
from dotenv import load_dotenv
from fastapi.testclient import TestClient
from ga4gh.vrs import models
from pydantic import BaseModel
from anyvar.anyvar import AnyVar, create_projector, create_storage, create_translator
from anyvar.core import objects
from a... | biocommons/anyvar | tests/conftest.py | .py | 21421255a0133d36 | 8.13 | 17 |
import contextlib
import os
import shutil
from typing import Any, cast
import pytest
from celery.contrib.testing.worker import start_worker
from celery.result import AsyncResult
from fastapi.testclient import TestClient
from pytest_mock import MockerFixture
from tests.conftest import build_vrs_variant_from_dict
impor... | biocommons/anyvar | tests/integration/restapi/conftest.py | .py | 52a21f4d9d040372 | 8.13 | 17 |
from http import HTTPStatus
import pytest
from fastapi.testclient import TestClient
@pytest.fixture(scope="session")
def braf_extension_payload() -> dict:
return {
"name": "clinvar_somatic_classification",
"value": "Oncogenic",
}
def test_extension_crud(
restapi_client: TestClient,
... | biocommons/anyvar | tests/integration/restapi/objects_router/test_extension.py | .py | 28e8401918c155e9 | 8.13 | 17 |
"""Test location lookup endpoint"""
from http import HTTPStatus
from fastapi.testclient import TestClient
def test_location(restapi_client: TestClient, preloaded_alleles: dict):
"""Perform basic location tests"""
for allele in preloaded_alleles.values():
key = allele["variation"]["location"]["id"]
... | biocommons/anyvar | tests/integration/restapi/objects_router/test_location.py | .py | aba21d7a64b5b229 | 7.13 | 17 |
"""Test mapping endpoints"""
from http import HTTPStatus
import pytest
from anyvar.core import metadata
from anyvar.storage.base import Storage
@pytest.fixture
def preloaded_allele_pairs(preloaded_alleles: dict):
"""Get preloaded allele pairs"""
preloaded_alleles_l = [allele["variation"] for allele in prel... | biocommons/anyvar | tests/integration/restapi/objects_router/test_mappings.py | .py | 94739817968d3f8c | 7.13 | 17 |
from collections import defaultdict
import importlib
BINDING_DB = 'BINDING-DB'
BGEE_HUMAN = 'BgeeHuman'
BGEE_MOUSE = 'BgeeMouse'
CAM_KP = 'CAM-KP'
CCIDB = 'CCIDB'
CEBS = 'CEBS'
CHEBI_PROPERTIES = 'CHEBIProps'
CLINICAL_TRIALS_KP = 'ClinicalTrialsKP'
CLINGEN_DOSAGE_SENSITIVITY = 'ClinGenDosageSensitivity'
CLINGEN_GENE_D... | RobokopU24/ORION | orion/data_sources.py | .py | 7d589ad87202558f | 7.64 | 18 |
import os
import shutil
import requests
from orion.config import config
from orion.logging import get_orion_logger
logger = get_orion_logger(__name__)
class GraphRegistryError(Exception):
pass
class GraphRegistryClient:
def __init__(self, base_url: str = config.ORION_GRAPH_REGISTRY_URL, timeout: float =... | RobokopU24/ORION | orion/graph_registry.py | .py | 757b76f15893d247 | 7.64 | 18 |
"""Semantic versioning for graph releases.
ORION distinguishes two versions for every graph it builds:
- **build_version** — a deterministic ``xxh64`` hash of the graph's inputs (data
source versions, normalization schemes, merge strategies, and the build_versions
of any subgraphs). Two builds with identical inpu... | RobokopU24/ORION | orion/graph_versioning.py | .py | 3c6ab65dc1d5ea90 | 7.64 | 18 |
"""KGX graph bundle on disk: nodes, edges, graph-metadata, schema.
`KGXBundle` provides utilities for one KGX graph (nodes and edges files) and its metadata.
It manages the files - resolving paths (handling .gz or not), checking which files are
present, and loading the JSON metadata files.
"""
import gzip
import json... | RobokopU24/ORION | orion/kgx_bundle.py | .py | 725ad589efac0828 | 7.64 | 18 |
import os
import logging
from logging.handlers import RotatingFileHandler
from orion.config import config
ORION_LOG_FORMAT = '[%(asctime)s] %(name)s %(levelname)s: %(message)s'
def get_orion_logger(name):
"""Return a logger for ORION library code.
Follows the standard library convention (as used by reques... | RobokopU24/ORION | orion/logging.py | .py | cb3914cce0b18410 | 7.64 | 18 |
class TestModule(object):
'''Tenks tests.'''
def tests(self):
return {
# Libvirt tests.
'requires_libvirt_configuration': requires_libvirt_configuration,
}
def requires_libvirt_configuration(node):
"""Select nodes that require configuration in Libvirt."""
retur... | openstack/tenks | ansible/test_plugins/tenks.py | .py | 27537cb06a400161 | 7.54 | 11 |
# Copyright (c) 2018 StackHPC Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | openstack/tenks | tests/test_tenks_update_state.py | .py | 43768a0e36e6f1f0 | 7.04 | 11 |
"""Helper modules to parse docker compoose --help arguments"""
from __future__ import annotations
import logging
from collections.abc import Iterable, Iterator
from dataclasses import dataclass
logger = logging.getLogger(__name__)
OPTION = "OPTION"
_TYPE_CONVERSIONS = {
"CA_PATH": str,
"CLIENT_CERT_PATH": s... | schollm/docker-composer | src/docker_composer/_utils/argument.py | .py | 06da761203c20857 | 7.64 | 18 |
from __future__ import annotations
import logging
import subprocess
from collections import defaultdict
from collections.abc import Iterator, Mapping
from functools import lru_cache, reduce
from operator import add
from pathlib import Path
import black
import isort
from isort.exceptions import ISortError
from docker... | schollm/docker-composer | src/docker_composer/_utils/generate_class.py | .py | b60ced26ddfd0bf1 | 7.64 | 18 |
import subprocess
from functools import reduce
from operator import add
from typing import Iterable, Optional
import dataclasses as _dc
import logging
logger = logging.getLogger(__name__)
def _flatten(lists: Iterable[list]):
"""Flatten an iterable of lists"""
return reduce(add, lists, [])
@_dc.dataclass()... | schollm/docker-composer | src/docker_composer/base.py | .py | b53c0f2b764127b2 | 7.64 | 18 |
import pytest
from textwrap import dedent
from docker_composer._utils.generate_class import collect_help_lines
GEN1 = " General 1"
GEN2 = " general 2"
DETAIL1 = " Detail 1"
OPTION1 = " --foo NUMBER Foo number"
OPTION2 = " --verbose Verbose Plob"
OPTION3 = " -f, --file Input file"
OPTION3_2 = " file ... | schollm/docker-composer | tests/docker_composer/test_generate_class.py | .py | 50398b7e1fb1dfd9 | 7.14 | 18 |
#!/usr/bin/python3
# Copyright SUSE LLC
"""Verify qe-lsg NetBox machines with non-excluded statuses are not reachable via ping.
Exits 1 if any such machine responds to ping, indicating it is unexpectedly powered on.
By default machines with status active, unused, or staged are excluded from the check.
"""
from __futu... | os-autoinst/os-autoinst-scripts | check-netbox-machine-state.py | .py | 8cc187bf65cbe430 | 7.45 | 7 |
#!/usr/bin/python3
# Copyright SUSE LLC
# ruff: file-ignore[print]
"""Report QE machines that draw unexpected power via SNMP PDU queries.
Exits 1 if any machine not marked active in NetBox draws more than MAX_POWER Watts (default: 5),
indicating it may still be powered on despite being decommissioned or unused.
"""
f... | os-autoinst/os-autoinst-scripts | check-netbox-unused-machine-power.py | .py | 417de6d637b9de01 | 7.45 | 7 |
#!/usr/bin/python3
# Copyright SUSE LLC
"""Automate the rotation of GitLab Project Access Tokens and update CI/CD variables.
This script checks the expiration date of a specified GitLab Project Access Token.
If the token is scheduled to expire in 1 day or less, the script rotates the token,
extends its validity by 364... | os-autoinst/os-autoinst-scripts | rotate-gitlab-token.py | .py | 2b7e8ed34c3ac90b | 7.45 | 7 |
#!/usr/bin/env python3
# Copyright SUSE LLC
# ruff: file-ignore[print, suspicious-subprocess-import]
"""Automated openQA Zombie Reaper for s390x.
Checks s390x hypervisors for persistent zombie qemu processes and reboots the host
if any are found, while also retriggering the affected openQA jobs.
"""
from __future__ ... | os-autoinst/os-autoinst-scripts | s390x-qemu-zombie-reaper.py | .py | 03a1da1c7e65af25 | 7.45 | 7 |
# -*- coding: utf-8 -*-
"""
@author: Ken Mwaura
"""
from sqlalchemy import Column, String, Integer, Date
from datetime import date as dt
from base_sql import Base
class Player(Base):
__tablename__ = "players"
id = Column(Integer, primary_key=True)
username = Column(String(80))
place = Column(String... | KenMwaura1/simple-web-scraper | db/player_sql.py | .py | b22893e3f5168f4c | 7.5 | 9 |
"""
@author: Ken Mwaura
"""
from sqlalchemy import Column, String, Date, Integer, Float
from datetime import date as dt
from base_sql import Base
class Earning_Player(Base):
__tablename__ = "paid_players"
id = Column(Integer, primary_key=True)
username = Column(String(80))
place = Column(String())
... | KenMwaura1/simple-web-scraper | db/top_earning_players_sql.py | .py | 2315531c15f228c8 | 7.5 | 9 |
from django.db.models import F
from django.db.models.constants import LOOKUP_SEP
from djangorestframework_camel_case.settings import api_settings
from djangorestframework_camel_case.util import camel_to_underscore
from rest_framework import filters
class MaCantineOrderingFilter(filters.OrderingFilter):
"""
Al... | betagouv/ma-cantine | api/filters/utils.py | .py | 09c5c278ef077a3b | 7.65 | 19 |
from logging.config import fileConfig
import os
from pathlib import Path
from sqlalchemy import engine_from_config
from sqlalchemy import pool
from alembic import context
from antarest.dbmodel import Base
from antarest.core.config import Config
from antarest.core.utils import utils
# this is the Alembic Config obj... | AntaresSimulatorTeam/AntaREST | alembic/env.py | .py | 6cdb888f387e75d4 | 7.66 | 20 |
"""add_study_version_to_commands
Revision ID: 00a9ceb38842
Revises: b33e1f57a60c
Create Date: 2024-10-28 10:30:15.877468
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.sql import table, column
from sqlalchemy.orm import Session
# revision identifiers, used by Alembic.
revision = '00a9ceb38842'
d... | AntaresSimulatorTeam/AntaREST | alembic/versions/00a9ceb38842_add_study_version_to_commands.py | .py | 1157f42ae8cf35c1 | 7.66 | 20 |
"""Add solver_presets table
Revision ID: 04a098a4a38e
Revises: a9dfa0e1f23d
Create Date: 2025-10-23 11:17:03.210771
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "04a098a4a38e"
down_revision = "a9dfa0e1f23d"
branch_labels = None
depends_on = None
def upgra... | AntaresSimulatorTeam/AntaREST | alembic/versions/04a098a4a38e_add_solver_presets_table.py | .py | a594b53b52f5da54 | 7.66 | 20 |
"""add slurm_runtime_config
Revision ID: 06697016d057
Revises: 3855b61c3232
Create Date: 2026-08-03 11:24:03.839320
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "06697016d057"
down_revision = "3855b61c3232"
branch_labels = None
depends_on = None
def upgra... | AntaresSimulatorTeam/AntaREST | alembic/versions/06697016d057_add_slurm_runtime_config.py | .py | a636695935475089 | 7.66 | 20 |
"""merge directory management and solver presets branches
Revision ID: 0b2141573d50
Revises: f1ff6904ff9f, 04a098a4a38e
Create Date: 2025-10-29 00:00:00.000000
"""
# revision identifiers, used by Alembic.
revision = "0b2141573d50"
down_revision = ("f1ff6904ff9f", "04a098a4a38e")
branch_labels = None
depends_on = Non... | AntaresSimulatorTeam/AntaREST | alembic/versions/0b2141573d50_merge_directory_and_solver_presets.py | .py | 627ffb85be98809c | 7.16 | 20 |
"""create_link_table
Revision ID: 10318e5320f6
Revises: 6a6d36e3c6ed
Create Date: 2026-01-28 17:32:28.795223
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '10318e5320f6'
down_revision = '6a6d36e3c6ed'
branch_labels = None
depends_on = None
def upgrade():
... | AntaresSimulatorTeam/AntaREST | alembic/versions/10318e5320f6_create_link_table.py | .py | 4ddfcec5e7737bbf | 7.66 | 20 |
"""create_link_matrices
Revision ID: 124274d80f2e
Revises: 9c4e7f2a3b1d
Create Date: 2026-01-30 13:37:09.850694
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '124274d80f2e'
down_revision = '9c4e7f2a3b1d'
branch_labels = None
depends_on = None
def upgrade():... | AntaresSimulatorTeam/AntaREST | alembic/versions/124274d80f2e_create_link_matrices.py | .py | 1f37054d2fb34956 | 7.66 | 20 |
"""permission_fix
Revision ID: 15f3bce09264
Revises: bb2d1f638a3e
Create Date: 2021-07-29 14:12:36.116348
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '15f3bce09264'
down_revision = 'bb2d1f638a3e'
branch_labels = None
depends_on = None
def upgrade():
#... | AntaresSimulatorTeam/AntaREST | alembic/versions/15f3bce09264_permission_fix.py | .py | 66ac973638520764 | 7.66 | 20 |
"""grant permissions on study_data_id_seq
Revision ID: 17f8a36cbed6
Revises: 1f0c9b2e7a34
Create Date: 2026-08-18 16:09:22.062707
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "17f8a36cbed6"
down_revision = "1f0c9b2e7a34"
branch_labels = None
depends_on = No... | AntaresSimulatorTeam/AntaREST | alembic/versions/17f8a36cbed6_grant_permissions_on_study_data_id_seq.py | .py | 772abcfa6cd4f92b | 7.66 | 20 |
"""make studies path nullable
Revision ID: 1bb1c26c70d8
Revises: 40f4391430e7
Create Date: 2026-08-20 15:43:44.948640
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = '1bb1c26c70d8'
down_revision = '40f4391430e7'
branch_labels = None
depends_on = None
def upgr... | AntaresSimulatorTeam/AntaREST | alembic/versions/1bb1c26c70d8_make_studies_path_nullable.py | .py | a9387cf3efc868ef | 7.66 | 20 |
"""use_surrogate_study_data_key
Replace the 36 chars `study_id` carried by every study data table with the bigint surrogate
key `study_data.study_data_id`.
Revision ID: 1f0c9b2e7a34
Revises: 6012b0407e38
Create Date: 2026-08-11 09:00:00.000000
"""
import hashlib
import logging
from typing import Any, Callable, Dict... | AntaresSimulatorTeam/AntaREST | alembic/versions/1f0c9b2e7a34_use_surrogate_study_data_key.py | .py | b118cc7113340079 | 7.66 | 20 |
# noinspection SpellCheckingInspection
"""
Add indexes to Study tables
The goal of this migration is to add indexes on the `study`, `rawstudy` and `study_additional_data` tables,
in order to speed up data search queries for the search engine.
Revision ID: 1f5db5dfad80
Revises: 782a481f3414
Create Date: 2024-01-19 18:... | AntaresSimulatorTeam/AntaREST | alembic/versions/1f5db5dfad80_add_indexes_to_study_tables.py | .py | 79dec31285b84ecb | 7.66 | 20 |
"""add_task_type
Revision ID: 23ff8deddb4a
Revises: 298aecf6ea40
Create Date: 2022-01-25 09:50:17.304650
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '23ff8deddb4a'
down_revision = '298aecf6ea40'
branch_labels = None
depends_on = None
def upgrade():
# ... | AntaresSimulatorTeam/AntaREST | alembic/versions/23ff8deddb4a_add_task_type.py | .py | 1e1101103bcd9182 | 7.66 | 20 |
"""add_storage_mode_and_area_tables
Revision ID: 2572145aff71
Revises: 9770c0960334
Create Date: 2025-01-17 00:00:00.000000
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "2572145aff71"
down_revision = "9770c0960334"
branch_labels = None
depends_on = None
d... | AntaresSimulatorTeam/AntaREST | alembic/versions/2572145aff71_add_storage_mode_and_area_tables.py | .py | 1700bc894549f393 | 7.66 | 20 |
"""add_job_solver_stats
Revision ID: 26c50ef2a0e1
Revises: c9dcca887456
Create Date: 2022-06-08 18:19:30.858085
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '26c50ef2a0e1'
down_revision = 'c9dcca887456'
branch_labels = None
depends_on = None
def upgrade():... | AntaresSimulatorTeam/AntaREST | alembic/versions/26c50ef2a0e1_add_job_solver_stats.py | .py | d667fcdf05689010 | 7.66 | 20 |
"""add_configdata
Revision ID: 298aecf6ea40
Revises: a845d5eae88e
Create Date: 2022-01-07 17:07:21.389595
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '298aecf6ea40'
down_revision = 'a845d5eae88e'
branch_labels = None
depends_on = None
def upgrade():
#... | AntaresSimulatorTeam/AntaREST | alembic/versions/298aecf6ea40_add_configdata.py | .py | 2bfd7be079d796f4 | 7.66 | 20 |
"""fix_permissions
Revision ID: 2a8c5e41f214
Revises: 76dd045d12f4
Create Date: 2022-03-04 15:26:27.793630
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '2a8c5e41f214'
down_revision = '76dd045d12f4'
branch_labels = None
depends_on = None
def upgrade():
... | AntaresSimulatorTeam/AntaREST | alembic/versions/2a8c5e41f214_fix_permissions.py | .py | e267b45e905f61d8 | 7.66 | 20 |
"""add_tasks
Revision ID: 2ed6bf9f1690
Revises: ae61e887e309
Create Date: 2021-08-19 14:56:38.632677
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
from sqlalchemy import Sequence
from sqlalchemy.sql.ddl import CreateSequence, DropSequence
revision = "2ed6bf9f1690"
down... | AntaresSimulatorTeam/AntaREST | alembic/versions/2ed6bf9f1690_add_tasks.py | .py | 89530680c10be88f | 7.66 | 20 |
"""empty message
Revision ID: 3292cdb4557a
Revises: ae61e887e309
Create Date: 2021-08-19 18:05:58.413966
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = "3292cdb4557a"
down_revision = "2ed6bf9f1690"
branch_labels = None
depends_on = None
def upgrade():
# ... | AntaresSimulatorTeam/AntaREST | alembic/versions/3292cdb4557a_variantstudy.py | .py | 8a912d528ee70316 | 7.66 | 20 |
"""add schedule_at to job_result
Revision ID: 3855b61c3232
Revises: cbf69219c1b6
Create Date: 2026-07-28 17:02:49.701163
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "3855b61c3232"
down_revision = "cbf69219c1b6"
branch_labels = None
depends_on = None
def ... | AntaresSimulatorTeam/AntaREST | alembic/versions/3855b61c3232_add_schedule_at_to_job_result.py | .py | 26eefcb90edf37e3 | 7.66 | 20 |
"""Add tag and study_tag tables
Revision ID: 3c70366b10ea
Revises: 1f5db5dfad80
Create Date: 2024-02-02 13:06:47.627554
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = "3c70366b10ea"
down_revision = "1f5db5dfad80"
branch_labels = None
depends_on = None
def up... | AntaresSimulatorTeam/AntaREST | alembic/versions/3c70366b10ea_add_tag_and_study_tag_tables.py | .py | 6dda4e8bec5a85aa | 7.66 | 20 |
"""add_st_storage_tables_for_reserves
Revision ID: 40f4391430e7
Revises: 17f8a36cbed6
Create Date: 2026-08-11 15:49:32.314554
"""
from sqlalchemy import Column, Float, ForeignKeyConstraint, String
from alembic import op
from antarest.study.dao.database.models import study_data_id_col
# revision identifiers, used b... | AntaresSimulatorTeam/AntaREST | alembic/versions/40f4391430e7_add_st_storage_tables_for_reserves.py | .py | 28a8bd65fffc424b | 7.66 | 20 |
"""change_reserves_format
Revision ID: 4121d3b48393
Revises: rp986cf862cy
Create Date: 2026-05-21 10:36:43.512270
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "4121d3b48393"
down_revision = "rp986cf862cy"
branch_labels = None
depends_on = None
def upgrade... | AntaresSimulatorTeam/AntaREST | alembic/versions/4121d3b48393_change_reserves_format.py | .py | 3e0571952992a5a4 | 7.66 | 20 |
"""add_commandblock_index
Revision ID: 423fe2c8ee40
Revises: bae9c99bc42d
Create Date: 2025-02-27 14:08:50.413459
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = "423fe2c8ee40"
down_revision = "bae9c99bc42d"
branch_labels = None
depends_on = None
def upgrade():
with op.batch_alt... | AntaresSimulatorTeam/AntaREST | alembic/versions/423fe2c8ee40_add_commandblock_index.py | .py | f21ce0a6d912fa1e | 7.66 | 20 |
"""add_reserves_enabled_to_compatibility_parameters
Revision ID: 444b392eeaa6
Revises: 81typ5zz6v1y
Create Date: 2026-04-03 13:45:09.584335
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '444b392eeaa6'
down_revision = '81typ5zz6v1y'
branch_labels = None
depend... | AntaresSimulatorTeam/AntaREST | alembic/versions/444b392eeaa6_add_reserves_enabled_to_compatibility_.py | .py | 9602a9fed5b56003 | 7.66 | 20 |
"""add_dataset
Revision ID: 47ab888dc44d
Revises: 6a04e38b8704
Create Date: 2021-07-20 13:41:42.420567
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '47ab888dc44d'
down_revision = '6a04e38b8704'
branch_labels = None
depends_on = None
def upgrade():
# ##... | AntaresSimulatorTeam/AntaREST | alembic/versions/47ab888dc44d_add_dataset.py | .py | de8189e7b421942c | 7.66 | 20 |
"""add_cascade_delete_for_sqlite
Revision ID: 490b80a84bb5
Revises: c0c4aaf84861
Create Date: 2024-10-11 11:38:45.108227
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '490b80a84bb5'
down_revision = 'c0c4aaf84861'
branch_labels = None
depends_on = None
def up... | AntaresSimulatorTeam/AntaREST | alembic/versions/490b80a84bb5_add_cascade_delete_for_sqlite.py | .py | 5e2aecf944289e97 | 7.66 | 20 |
"""merge_heads
Revision ID: 4bbe4f165a05
Revises: f3a153a9a048
Create Date: 2026-01-28 15:10:18.927783
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '4bbe4f165a05'
down_revision = ("f3a153a9a048", "7b406752d80")
branch_labels = None
depends_on = None
def up... | AntaresSimulatorTeam/AntaREST | alembic/versions/4bbe4f165a05_merge_heads.py | .py | dcbdb6956b727fd4 | 7.16 | 20 |
"""sequence_creation
Revision ID: 512a751033dd
Revises: 47ab888dc44d
Create Date: 2021-07-26 10:41:33.033615
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.schema import Sequence, CreateSequence
# revision identifiers, used by Alembic.
from sqlalchemy.sql.ddl import DropSequence
revision = '512a... | AntaresSimulatorTeam/AntaREST | alembic/versions/512a751033dd_sequence_creation.py | .py | b1f9a5ab80a45027 | 7.66 | 20 |
"""service_refactoring
Revision ID: 55138d877c6a
Revises: c83b8bb38a7c
Create Date: 2021-09-15 19:56:51.554898
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '55138d877c6a'
down_revision = 'c83b8bb38a7c'
branch_labels = None
depends_on = None
def upgrade():
... | AntaresSimulatorTeam/AntaREST | alembic/versions/55138d877c6a_service_refactoring.py | .py | b5da3792d4945174 | 7.66 | 20 |
"""add_thematic_trimming_table
Revision ID: 562d4e1bd95d
Revises: c20d6b990db0
Create Date: 2026-02-24 17:18:50.260580
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '562d4e1bd95d'
down_revision = 'c20d6b990db0'
branch_labels = None
depends_on = None
def upg... | AntaresSimulatorTeam/AntaREST | alembic/versions/562d4e1bd95d_add_thematic_trimming_table.py | .py | f08230056900e8f0 | 7.66 | 20 |
"""add output table in db
Revision ID: 6012b0407e38
Revises: 06697016d057
Create Date: 2026-07-08 13:51:13.329059
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "6012b0407e38"
down_revision = "06697016d057"
branch_labels = None
depends_on = None
def upgrade... | AntaresSimulatorTeam/AntaREST | alembic/versions/6012b0407e38_add_output_table_in_db.py | .py | 22459c73b7a4467e | 7.66 | 20 |
"""rawstudies_folder_info
Revision ID: 63ed81e5ce6f
Revises: ab143a39c4db
Create Date: 2021-09-27 18:23:44.909595
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
from sqlalchemy import text
from sqlalchemy.engine import Connection
revision = '63ed81e5ce6f'
down_revision ... | AntaresSimulatorTeam/AntaREST | alembic/versions/63ed81e5ce6f_rawstudies_folder_info.py | .py | bf623db4d7d5602c | 7.66 | 20 |
"""add_thermal_reserve_tables
Revision ID: 665f7b1d7575
Revises: 80fdf2408ede
Create Date: 2026-06-23 13:41:03.310148
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '665f7b1d7575'
down_revision = '80fdf2408ede'
branch_labels = None
depends_on = None
def upgr... | AntaresSimulatorTeam/AntaREST | alembic/versions/665f7b1d7575_add_thermal_reserve_.py | .py | 127b6d9e93897f19 | 7.66 | 20 |
"""create_area_matrices_table
Revision ID: 6a6d36e3c6ed
Revises: 8f3d2a1b5c7e
Create Date: 2026-01-26 10:45:36.111886
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '6a6d36e3c6ed'
down_revision = "8f3d2a1b5c7e"
branch_labels = None
depends_on = None
def upgr... | AntaresSimulatorTeam/AntaREST | alembic/versions/6a6d36e3c6ed_create_area_matrices_table.py | .py | 5d9402c33fa05be2 | 7.66 | 20 |
"""resolves a divergence in the Alembic migration history by merging multiple head revisions
Revision ID: 6c3d9dbf678c
Revises: fa59340767b0, a8c6e9d47b12
Create Date: 2025-07-28 11:07:02.181937
"""
# revision identifiers, used by Alembic.
revision = "6c3d9dbf678c"
down_revision = ("fa59340767b0", "a8c6e9d47b12")
br... | AntaresSimulatorTeam/AntaREST | alembic/versions/6c3d9dbf678c_merge_divergent_heads.py | .py | c21dc9a0161c69ce | 7.16 | 20 |
"""add_launcher_job_logs
Revision ID: 76dd045d12f4
Revises: f5aed532a99c
Create Date: 2022-02-25 16:56:29.622137
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
from sqlalchemy import Sequence
from sqlalchemy.sql.ddl import CreateSequence, DropSequence
revision = '76dd04... | AntaresSimulatorTeam/AntaREST | alembic/versions/76dd045d12f4_add_launcher_job_logs.py | .py | 2c10f1154447f219 | 7.66 | 20 |
"""fix task_job cascade delete
Revision ID: 782a481f3414
Revises: d495746853cc
Create Date: 2023-12-16 14:26:30.035324
"""
import sqlalchemy as sa # type: ignore
from alembic import context, op
# revision identifiers, used by Alembic.
revision = "782a481f3414"
down_revision = "d495746853cc"
branch_labels = None
dep... | AntaresSimulatorTeam/AntaREST | alembic/versions/782a481f3414_fix_task_job_cascade_delete.py | .py | c6be2ff435432882 | 7.66 | 20 |
"""add_reserve_definition_table
Revision ID: 7a1e9c4d82f5
Revises: c61baf008ebd
Create Date: 2026-04-15 10:00:00.000000
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = "7a1e9c4d82f5"
down_revision = "c61baf008ebd"
branch_labels = None
depends_on = None
def up... | AntaresSimulatorTeam/AntaREST | alembic/versions/7a1e9c4d82f5_add_reserve_definition_table.py | .py | 665f3b514c12f468 | 7.66 | 20 |
"""adding favorite_study table
Revision ID: 7b406752d80
Revises: 0146b79f723c
Create Date: 2026-01-07 10:27:58.254977
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "7b406752d80"
down_revision = "0146b79f723c"
branch_labels = None
depends_on = None
def upgra... | AntaresSimulatorTeam/AntaREST | alembic/versions/7b406752d80_add_favorite_table.py | .py | 947d195da85d35c9 | 7.66 | 20 |
"""add_favorite_external_directory_table
Revision ID: 80fdf2408ede
Revises: rp986cf862cy
Create Date: 2026-06-10 13:33:16.721647
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '80fdf2408ede'
down_revision = 'f50e7ed59478'
branch_labels = None
depends_on = None... | AntaresSimulatorTeam/AntaREST | alembic/versions/80fdf2408ede_add_favorite_external_directory_table.py | .py | 6d2bc034b1ecbaf2 | 7.66 | 20 |
"""add_study_disk_space_analysis_table
Revises: c11cfe5728b0
Create Date: 2022-01-25 09:50:17.304650
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '81typ5zz6v1y'
down_revision = 'f9ecc0607cc5'
branch_labels = None
depends_on = None
def upgrade():
op.crea... | AntaresSimulatorTeam/AntaREST | alembic/versions/81typ5zz6v1y_add_study_disk_space_analysis_table.py | .py | 527df040bb15f177 | 7.66 | 20 |
"""create_intermediate_table
Revision ID: 844f4a7cd371
Revises: 4121d3b48393
Create Date: 2026-05-28 16:27:08.165716
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "844f4a7cd371"
down_revision = "4121d3b48393"
branch_labels = None
depends_on = None
INTERMED... | AntaresSimulatorTeam/AntaREST | alembic/versions/844f4a7cd371_create_intermediate_table.py | .py | c4f3b635a8ee32d4 | 7.66 | 20 |
"""
Sphinx Read the Docs theme.
From https://github.com/ryan-roemer/sphinx-bootstrap-theme.
"""
from os import path
from sphinx import version_info
from sphinx.locale import _
try:
# Avaliable from Sphinx 1.6
from sphinx.util.logging import getLogger
except ImportError:
from logging import getLogger
_... | viur-framework/viur-core | docs/rtdtemplate/__init__.py | .py | 29d13a0f04b0ccfe | 7.62 | 16 |
import typing as t
from viur.core import conf, db, utils
from viur.core.bones.base import BaseBone
DEFAULT_VALUE_T: t.TypeAlias = bool | None | list[bool] | dict[str, list[bool] | bool]
class BooleanBone(BaseBone):
"""
Represents a boolean data type, which can have two possible values: `True` or `False`.
... | viur-framework/viur-core | src/viur/core/bones/boolean.py | .py | 999cc8b3a2e08b4e | 7.62 | 16 |
import logging
import typing as t
import requests
from viur.core import conf, current
from viur.core.bones.base import BaseBone, ReadFromClientError, ReadFromClientErrorSeverity
if t.TYPE_CHECKING:
from viur.core.skeleton import SkeletonInstance
class CaptchaBone(BaseBone):
r"""
The CaptchaBone is used... | viur-framework/viur-core | src/viur/core/bones/captcha.py | .py | 0cbb4222d641adbb | 7.62 | 16 |
from viur.core.bones.base import ReadFromClientError, ReadFromClientErrorSeverity
from viur.core.bones.string import StringBone
class CredentialBone(StringBone):
"""
A bone for storing credentials. This bone is designed to store sensitive information like
passwords, API keys, or other secret strin... | viur-framework/viur-core | src/viur/core/bones/credential.py | .py | 910125ba72bec690 | 7.62 | 16 |
import re
import string
from encodings import idna
from viur.core.bones.string import StringBone
from viur.core import i18n
_DNS_LABEL_RE = re.compile(r"(?!-)[a-z0-9-]{1,63}(?<!-)", re.IGNORECASE)
"""A single DNS label per RFC 1035: 1-63 alphanumerics or hyphens, no leading or trailing hyphen."""
class EmailBone(Str... | viur-framework/viur-core | src/viur/core/bones/email.py | .py | 90f63461aa43becf | 7.62 | 16 |
"""
The FileBone is a subclass of the TreeLeafBone class, which is a relational bone that can reference
another entity's fields. FileBone provides additional file-specific properties and methods, such as
managing file derivatives, handling file size and mime type restrictions, and refreshing file
metadata.
"""
import h... | viur-framework/viur-core | src/viur/core/bones/file.py | .py | 4682f8150a0b57e0 | 7.62 | 16 |
import ast
import json
import jsonschema
import typing as t
from viur.core.bones.base import ReadFromClientError, ReadFromClientErrorSeverity
from viur.core.bones.raw import RawBone
from viur.core import utils
class JsonBone(RawBone):
"""
This bone saves its content as a JSON-string, but unpacks its content t... | viur-framework/viur-core | src/viur/core/bones/json.py | .py | 3e2beb738b02ed00 | 7.62 | 16 |
import copy
import logging
import typing as t
from viur.core import db, i18n
from viur.core.bones.base import BaseBone, ReadFromClientError, ReadFromClientErrorSeverity
class KeyBone(BaseBone):
"""
The KeyBone is used for managing keys in the database. It provides various methods for validating,
convertin... | viur-framework/viur-core | src/viur/core/bones/key.py | .py | 0f1f598cfbafb06b | 7.62 | 16 |
import logging
import numbers
import sys
import typing as t
import warnings
from viur.core import db, i18n
from viur.core.bones.base import BaseBone, ReadFromClientError, ReadFromClientErrorSeverity
if t.TYPE_CHECKING:
from viur.core.skeleton import SkeletonInstance
# Constants for Mne (MIN/MAX-never-exceed)
MIN... | viur-framework/viur-core | src/viur/core/bones/numeric.py | .py | 2f83c49673acf01a | 7.62 | 16 |
import re
import typing as t
from viur.core import i18n
from viur.core.bones.string import StringBone
from viur.core.bones.base import ReadFromClientError, ReadFromClientErrorSeverity
DEFAULT_REGEX = r"^\+?(\d{1,3})[-\s]?(\d{1,4})[-\s]?(\d{1,4})[-\s]?(\d{1,9})$"
class PhoneBone(StringBone):
"""
The PhoneBon... | viur-framework/viur-core | src/viur/core/bones/phone.py | .py | fd53cf9288458c91 | 7.62 | 16 |
import re
from viur.core.bones.base import BaseBone, ReadFromClientError, ReadFromClientErrorSeverity
SEARCH_TAGS = re.compile(r"[^\s]+")
class RawBone(BaseBone):
"""
Stores its data without applying any pre/post-processing or filtering.
Can be used to store any textual content.
Use the dot-notation... | viur-framework/viur-core | src/viur/core/bones/raw.py | .py | 4b5115fc4c652783 | 7.62 | 16 |
import json
import logging
import typing as t
from viur.core.bones.base import BaseBone, ReadFromClientError, ReadFromClientErrorSeverity
from viur.core import db, utils, tasks, i18n
if t.TYPE_CHECKING:
from ..skeleton import SkeletonInstance
class RecordBone(BaseBone):
"""
The RecordBone class is a spe... | viur-framework/viur-core | src/viur/core/bones/record.py | .py | 34f6e82d6a9f58c6 | 7.62 | 16 |
import enum
import typing as t
from collections import OrderedDict
from numbers import Number
from viur.core.config import conf
from viur.core.bones.base import BaseBone, ReadFromClientError, ReadFromClientErrorSeverity
from viur.core.i18n import translate
if t.TYPE_CHECKING:
from viur.core.skeleton import Skeleto... | viur-framework/viur-core | src/viur/core/bones/select.py | .py | f154ac07d2d17cda | 7.62 | 16 |
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