diff --git a/.gitignore b/.gitignore index 118f812c..71244524 100644 --- a/.gitignore +++ b/.gitignore @@ -38,3 +38,5 @@ ENV/ env.bak/ venv.bak/ .DS_store + +ui/package-lock.json diff --git a/bedhost/helpers.py b/bedhost/helpers.py index d67de925..7d8e44d2 100644 --- a/bedhost/helpers.py +++ b/bedhost/helpers.py @@ -6,6 +6,7 @@ from bbconf.bbagent import BedBaseAgent from bbconf.models.base_models import UsageModel from starlette.responses import FileResponse, JSONResponse, RedirectResponse +from fastapi import Query from . import _LOGGER from .exceptions import BedHostException @@ -80,6 +81,13 @@ def drs_response(status_code, msg): return JSONResponse(status_code=status_code, content=content) +test_query_parameter = Query( + False, + description="Internal parameter for testing purposes. If true, the request will not be counted.", + include_in_schema=False, +) + + def count_requests( usage_data: UsageModel, event: Literal["bed_search", "bedset_search", "bed_meta", "bedset_meta", "files"], @@ -96,7 +104,11 @@ def decorator(func): async def wrapper(*args, **kwargs): function_result = await func(*args, **kwargs) - + if "test_request" in kwargs and kwargs["test_request"]: + _LOGGER.info( + f"Test request was executed. For '{event}' event with: {args}, {kwargs}. No results saved." + ) + return function_result if event == "files": file_path = kwargs.get("file_path") if "bed" in file_path or "bigbed" in file_path.lower(): diff --git a/bedhost/routers/base_api.py b/bedhost/routers/base_api.py index da924b2d..bcbb48ba 100644 --- a/bedhost/routers/base_api.py +++ b/bedhost/routers/base_api.py @@ -21,7 +21,7 @@ Type, ) from ..dependencies import fetch_detailed_stats -from ..helpers import get_openapi_version, count_requests +from ..helpers import get_openapi_version, count_requests, test_query_parameter from ..main import app, bbagent, usage_data router = APIRouter(prefix="/v1", tags=["base"]) @@ -144,6 +144,8 @@ async def service_info(): @router.get("/files/{file_path:path}") @count_requests(usage_data, event="files") -async def redirect_to_download(file_path: str, request: Request): +async def redirect_to_download( + file_path: str, request: Request, test_request: bool = test_query_parameter +): download_url = f"https://data2.bedbase.org/{file_path}" return RedirectResponse(url=download_url) diff --git a/bedhost/routers/bed_api.py b/bedhost/routers/bed_api.py index 6a9531d7..5cbd9b5a 100644 --- a/bedhost/routers/bed_api.py +++ b/bedhost/routers/bed_api.py @@ -38,7 +38,7 @@ from ..const import EXAMPLE_BED, MAX_FILE_SIZE, MAX_REGION_NUMBER, MIN_REGION_WIDTH from ..data_models import CROM_NUMBERS, BaseListResponse, BedDigest from ..main import bbagent, usage_data -from ..helpers import count_requests +from ..helpers import count_requests, test_query_parameter router = APIRouter(prefix="/v1/bed", tags=["bed"]) @@ -95,6 +95,7 @@ async def get_bed_metadata( full: Optional[bool] = Query( False, description="Return full record with stats, plots, files and metadata" ), + test_request: bool = test_query_parameter, ): """ Returns metadata for a single BED record. if full=True, returns full record with stats, plots, files and metadata. @@ -261,6 +262,32 @@ async def embed_bed_file( return embedding.tolist()[0] +@router.post( + "/umap", + summary="Get embeddings for a bed file.", + response_model=List[float], +) +async def embed_bed_file( + file: UploadFile = File(None), +): + """ + Create embedding for bed file + """ + _LOGGER.info("Embedding file..") + + if file is not None: + with tempfile.TemporaryDirectory() as dirpath: + file_path = os.path.join(dirpath, file.filename) + + with open(file_path, "wb") as bed_file: + shutil.copyfileobj(file.file, bed_file) + + region_set = RegionSet(file_path) + + embedding = bbagent.bed._get_umap_file(region_set) + return embedding.tolist()[0] + + @router.get( "/missing_plots", summary="Get missing plots for a bed file.", @@ -361,6 +388,7 @@ async def text_to_bed_search( assay: Optional[Union[str, None]] = None, limit: int = 10, offset: int = 0, + test_request: bool = test_query_parameter, ): """ Search for a BedFile by a text query. diff --git a/bedhost/routers/bedset_api.py b/bedhost/routers/bedset_api.py index 1fd8ffd1..0d7a4910 100644 --- a/bedhost/routers/bedset_api.py +++ b/bedhost/routers/bedset_api.py @@ -15,7 +15,7 @@ from ..main import bbagent, usage_data from ..data_models import CreateBEDsetRequest from ..utils import zip_pep -from ..helpers import count_requests +from ..helpers import count_requests, test_query_parameter router = APIRouter(prefix="/v1/bedset", tags=["bedset"]) @@ -46,6 +46,7 @@ async def list_bedsets( query: str = None, limit: int = 1000, offset: int = 0, + test_request: bool = test_query_parameter, ): """ Returns a list of BEDset records in the database with optional filters and search. @@ -64,6 +65,7 @@ async def list_bedsets( async def get_bedset_metadata( bedset_id: str, full: bool = True, + test_request: bool = test_query_parameter, ): # TODO: fix error with not found try: diff --git a/deployment/config/api-dev.bedbase.org.yaml b/deployment/config/api-dev.bedbase.org.yaml index f3bba70e..ab3ab944 100644 --- a/deployment/config/api-dev.bedbase.org.yaml +++ b/deployment/config/api-dev.bedbase.org.yaml @@ -4,6 +4,7 @@ path: # region2vec: databio/r2v-pretrained-for-search region2vec: databio/r2v-encode-hg38 vec2vec: 'databio/v2v-sentencetransformers-encode' + umap_model: "https://github.com/databio/bedbase-loader/raw/refs/heads/master/umap/hg38_umap_umap_model.joblib" database: host: $POSTGRES_HOST port: 5432 diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt index 580bd04f..cba08d95 100644 --- a/requirements/requirements-all.txt +++ b/requirements/requirements-all.txt @@ -1,5 +1,5 @@ -# bbconf @ git+https://github.com/databio/bbconf.git@comp_search#egg=bbconf -bbconf>=0.12.0 +bbconf @ git+https://github.com/databio/bbconf.git@umap#egg=bbconf +# bbconf>=0.12.0 fastapi>=0.103.0 logmuse>=0.2.7 markdown diff --git a/ui/.eslintrc.cjs b/ui/.eslintrc.cjs index d6c95379..172ad0d1 100644 --- a/ui/.eslintrc.cjs +++ b/ui/.eslintrc.cjs @@ -1,18 +1,11 @@ module.exports = { root: true, env: { browser: true, es2020: true }, - extends: [ - 'eslint:recommended', - 'plugin:@typescript-eslint/recommended', - 'plugin:react-hooks/recommended', - ], + extends: ['eslint:recommended', 'plugin:@typescript-eslint/recommended', 'plugin:react-hooks/recommended'], ignorePatterns: ['dist', '.eslintrc.cjs'], parser: '@typescript-eslint/parser', plugins: ['react-refresh'], rules: { - 'react-refresh/only-export-components': [ - 'warn', - { allowConstantExport: true }, - ], + 'react-refresh/only-export-components': ['warn', { allowConstantExport: true }], }, -} +}; diff --git a/ui/bedbase-types.d.ts b/ui/bedbase-types.d.ts index 95a5be88..e449f356 100644 --- a/ui/bedbase-types.d.ts +++ b/ui/bedbase-types.d.ts @@ -4,3069 +4,3069 @@ */ export interface paths { - "/v1": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * API intro page - * @description Display the index UI page - */ - get: operations["index_v1_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/docs/changelog": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** Release notes */ - get: operations["changelog_v1_docs_changelog_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** Lending Page */ - get: operations["lending_page__get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/stats": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get summary statistics for BEDbase platform - * @description Returns statistics - */ - get: operations["get_bedbase_db_stats_v1_stats_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/detailed-stats": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get detailed statistics for BEDbase platform, including number of files for each genome - * @description Returns detailed statistics - */ - get: operations["get_detailed_stats_v1_detailed_stats_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/detailed-usage": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get detailed usage statistics for BEDbase platform - * @description Returns detailed usage statistics - */ - get: operations["get_detailed_usage_v1_detailed_usage_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/genomes": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get available genomes - * @description Returns statistics - */ - get: operations["get_bedbase_db_stats_v1_genomes_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/assays": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get available assays - * @description Returns statistics - */ - get: operations["get_bedbase_db_stats_v1_assays_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/service-info": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * GA4GH service info - * @description Returns information about this service, such as versions, name, etc. - */ - get: operations["service_info_v1_service_info_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/files/{file_path}": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** Redirect To Download */ - get: operations["redirect_to_download_v1_files__file_path__get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/example": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get example BED record metadata - * @description Get metadata for an example BED record. - */ - get: operations["get_example_bed_record_v1_bed_example_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/list": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Paged list of all BED records - * @description Returns list of BED files in the database with optional filters. - */ - get: operations["list_beds_v1_bed_list_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/metadata": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get metadata for a single BED record - * @description Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_metadata_v1_bed__bed_id__metadata_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/metadata/plots": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get plots for a single BED record - * @description Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_plots_v1_bed__bed_id__metadata_plots_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/metadata/files": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get metadata for a single BED record - * @description Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_files_v1_bed__bed_id__metadata_files_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/metadata/stats": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get stats for a single BED record - * @description Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_stats_v1_bed__bed_id__metadata_stats_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/metadata/classification": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get classification of single BED file - * @description Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_classification_v1_bed__bed_id__metadata_classification_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/metadata/raw": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get raw metadata for a single BED record - * @description Returns raw metadata for a single BED record. This metadata is stored in PEPHub. And is not verified.Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_pephub_v1_bed__bed_id__metadata_raw_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/neighbours": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get nearest neighbours for a single BED record - * @description Returns most similar BED files in the database. Example - * bed_id: bbad85f21962bb8d972444f7f9a3a932 - */ - get: operations["get_bed_neighbours_v1_bed__bed_id__neighbours_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/embedding": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get embeddings for a single BED record - * @description Returns embeddings for a single BED record. - */ - get: operations["get_bed_embedding_v1_bed__bed_id__embedding_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/embed": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - get?: never; - put?: never; - /** - * Get embeddings for a bed file. - * @description Create embedding for bed file - */ - post: operations["embed_bed_file_v1_bed_embed_post"]; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/missing_plots": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get missing plots for a bed file. - * @description Get missing plots for a bed file - * - * example -> plot_id: gccontent - */ - get: operations["missing_plots_v1_bed_missing_plots_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/regions/{chr_num}": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get regions from a BED file that overlap a query region. - * @description Returns the queried regions with provided ID and optional query parameters - */ - get: operations["get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/search/text": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - get?: never; - put?: never; - /** - * Search for a BedFile - * @description Search for a BedFile by a text query. - * - * By default, it searches in the 'hg38' genome. To search in a different genome, specify the `genome` parameter. eg. mm10 - * Example: query="cancer" - */ - post: operations["text_to_bed_search_v1_bed_search_text_post"]; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/search/exact": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - get?: never; - put?: never; - /** Search for exact match of metadata in bed files */ - post: operations["text_to_bed_search_v1_bed_search_exact_post"]; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/search/bed": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - get?: never; - put?: never; - /** Search for similar bed files */ - post: operations["bed_to_bed_search_v1_bed_search_bed_post"]; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/tokens/{universe_id}": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get tokenized of bed file - * @description Return univers of bed file - * Example: bed: 0dcdf8986a72a3d85805bbc9493a1302 | universe: 58dee1672b7e581c8e1312bd4ca6b3c7 - */ - get: operations["get_tokens_v1_bed__bed_id__tokens__universe_id__get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/tokens/{universe_id}/info": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get link to tokenized bed file - * @description Return link to tokenized bed file - * Example: bed: 0dcdf8986a72a3d85805bbc9493a1302 | universe: 58dee1672b7e581c8e1312bd4ca6b3c7 - */ - get: operations["get_tokens_v1_bed__bed_id__tokens__universe_id__info_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bed/{bed_id}/genome-stats": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get reference genome validation results - * @description Return reference genome validation results for a bed file - * Example: bed: 0dcdf8986a72a3d85805bbc9493a1302 - */ - get: operations["get_ref_gen_results_v1_bed__bed_id__genome_stats_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/example": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** Get metadata for an example BEDset record */ - get: operations["get_example_bedset_record_v1_bedset_example_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/list": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Paged list of all BEDset records - * @description Returns a list of BEDset records in the database with optional filters and search. - */ - get: operations["list_bedsets_v1_bedset_list_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/{bedset_id}/metadata": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get all metadata for a single BEDset record - * @description Example - * bed_id: gse218680 - */ - get: operations["get_bedset_metadata_v1_bedset__bedset_id__metadata_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/{bedset_id}/pep": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Download PEP project for a single BEDset record - * @description Example - * bed_id: gse218680 - */ - get: operations["get_bedset_pep_v1_bedset__bedset_id__pep_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/{bedset_id}/metadata/plots": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get plots for single bedset record - * @description Example - * bed_id: gse218680 - */ - get: operations["get_bedset_metadata_v1_bedset__bedset_id__metadata_plots_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/{bedset_id}/metadata/stats": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get stats for a single BEDSET record - * @description Example - * bed_id: gse218680 - */ - get: operations["get_bedset_metadata_v1_bedset__bedset_id__metadata_stats_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/{bedset_id}/bedfiles": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get Bedfiles In Bedset - * @description Example - * bed_id: gse218680 - */ - get: operations["get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/bedset/{bedset_id}/track_hub": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get Track Hub Bedset - * @description Generate track hub files for the BED set - */ - get: operations["get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - /** - * Get Track Hub Bedset - * @description Generate track hub files for the BED set - */ - head: operations["get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head"]; - patch?: never; - trace?: never; - }; - "/v1/bedset/create": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - get?: never; - put?: never; - /** - * Create Bedset - * @description Create a new bedset by providing registry path to the PEPhub project - */ - post: operations["create_bedset_v1_bedset_create_post"]; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/objects/{object_id}": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get DRS object metadata - * @description Returns metadata about a DrsObject. - */ - get: operations["get_drs_object_metadata_v1_objects__object_id__get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/objects/{object_id}/access/{access_id}": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Get URL where you can retrieve files - * @description Returns a URL that can be used to fetch the bytes of a DrsObject. - */ - get: operations["get_object_bytes_url_v1_objects__object_id__access__access_id__get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/objects/{object_id}/access/{access_id}/bytes": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Download actual file - * @description Returns the bytes of a DrsObject. - */ - get: operations["get_object_bytes_v1_objects__object_id__access__access_id__bytes_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; - "/v1/objects/{object_id}/access/{access_id}/thumbnail": { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - /** - * Download thumbnail file - * @description Returns the bytes of a thumbnail of a DrsObject - */ - get: operations["get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get"]; - put?: never; - post?: never; - delete?: never; - options?: never; - head?: never; - patch?: never; - trace?: never; - }; + '/v1': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * API intro page + * @description Display the index UI page + */ + get: operations['index_v1_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/docs/changelog': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** Release notes */ + get: operations['changelog_v1_docs_changelog_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** Lending Page */ + get: operations['lending_page__get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/stats': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get summary statistics for BEDbase platform + * @description Returns statistics + */ + get: operations['get_bedbase_db_stats_v1_stats_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/detailed-stats': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get detailed statistics for BEDbase platform, including number of files for each genome + * @description Returns detailed statistics + */ + get: operations['get_detailed_stats_v1_detailed_stats_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/detailed-usage': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get detailed usage statistics for BEDbase platform + * @description Returns detailed usage statistics + */ + get: operations['get_detailed_usage_v1_detailed_usage_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/genomes': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get available genomes + * @description Returns statistics + */ + get: operations['get_bedbase_db_stats_v1_genomes_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/assays': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get available assays + * @description Returns statistics + */ + get: operations['get_bedbase_db_stats_v1_assays_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/service-info': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * GA4GH service info + * @description Returns information about this service, such as versions, name, etc. + */ + get: operations['service_info_v1_service_info_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/files/{file_path}': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** Redirect To Download */ + get: operations['redirect_to_download_v1_files__file_path__get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/example': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get example BED record metadata + * @description Get metadata for an example BED record. + */ + get: operations['get_example_bed_record_v1_bed_example_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/list': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Paged list of all BED records + * @description Returns list of BED files in the database with optional filters. + */ + get: operations['list_beds_v1_bed_list_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/metadata': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get metadata for a single BED record + * @description Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_metadata_v1_bed__bed_id__metadata_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/metadata/plots': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get plots for a single BED record + * @description Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_plots_v1_bed__bed_id__metadata_plots_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/metadata/files': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get metadata for a single BED record + * @description Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_files_v1_bed__bed_id__metadata_files_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/metadata/stats': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get stats for a single BED record + * @description Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_stats_v1_bed__bed_id__metadata_stats_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/metadata/classification': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get classification of single BED file + * @description Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_classification_v1_bed__bed_id__metadata_classification_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/metadata/raw': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get raw metadata for a single BED record + * @description Returns raw metadata for a single BED record. This metadata is stored in PEPHub. And is not verified.Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_pephub_v1_bed__bed_id__metadata_raw_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/neighbours': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get nearest neighbours for a single BED record + * @description Returns most similar BED files in the database. Example + * bed_id: bbad85f21962bb8d972444f7f9a3a932 + */ + get: operations['get_bed_neighbours_v1_bed__bed_id__neighbours_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/embedding': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get embeddings for a single BED record + * @description Returns embeddings for a single BED record. + */ + get: operations['get_bed_embedding_v1_bed__bed_id__embedding_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/embed': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + get?: never; + put?: never; + /** + * Get embeddings for a bed file. + * @description Create embedding for bed file + */ + post: operations['embed_bed_file_v1_bed_embed_post']; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/missing_plots': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get missing plots for a bed file. + * @description Get missing plots for a bed file + * + * example -> plot_id: gccontent + */ + get: operations['missing_plots_v1_bed_missing_plots_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/regions/{chr_num}': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get regions from a BED file that overlap a query region. + * @description Returns the queried regions with provided ID and optional query parameters + */ + get: operations['get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/search/text': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + get?: never; + put?: never; + /** + * Search for a BedFile + * @description Search for a BedFile by a text query. + * + * By default, it searches in the 'hg38' genome. To search in a different genome, specify the `genome` parameter. eg. mm10 + * Example: query="cancer" + */ + post: operations['text_to_bed_search_v1_bed_search_text_post']; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/search/exact': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + get?: never; + put?: never; + /** Search for exact match of metadata in bed files */ + post: operations['text_to_bed_search_v1_bed_search_exact_post']; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/search/bed': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + get?: never; + put?: never; + /** Search for similar bed files */ + post: operations['bed_to_bed_search_v1_bed_search_bed_post']; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/tokens/{universe_id}': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get tokenized of bed file + * @description Return univers of bed file + * Example: bed: 0dcdf8986a72a3d85805bbc9493a1302 | universe: 58dee1672b7e581c8e1312bd4ca6b3c7 + */ + get: operations['get_tokens_v1_bed__bed_id__tokens__universe_id__get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/tokens/{universe_id}/info': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get link to tokenized bed file + * @description Return link to tokenized bed file + * Example: bed: 0dcdf8986a72a3d85805bbc9493a1302 | universe: 58dee1672b7e581c8e1312bd4ca6b3c7 + */ + get: operations['get_tokens_v1_bed__bed_id__tokens__universe_id__info_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bed/{bed_id}/genome-stats': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get reference genome validation results + * @description Return reference genome validation results for a bed file + * Example: bed: 0dcdf8986a72a3d85805bbc9493a1302 + */ + get: operations['get_ref_gen_results_v1_bed__bed_id__genome_stats_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/example': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** Get metadata for an example BEDset record */ + get: operations['get_example_bedset_record_v1_bedset_example_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/list': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Paged list of all BEDset records + * @description Returns a list of BEDset records in the database with optional filters and search. + */ + get: operations['list_bedsets_v1_bedset_list_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/{bedset_id}/metadata': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get all metadata for a single BEDset record + * @description Example + * bed_id: gse218680 + */ + get: operations['get_bedset_metadata_v1_bedset__bedset_id__metadata_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/{bedset_id}/pep': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Download PEP project for a single BEDset record + * @description Example + * bed_id: gse218680 + */ + get: operations['get_bedset_pep_v1_bedset__bedset_id__pep_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/{bedset_id}/metadata/plots': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get plots for single bedset record + * @description Example + * bed_id: gse218680 + */ + get: operations['get_bedset_metadata_v1_bedset__bedset_id__metadata_plots_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/{bedset_id}/metadata/stats': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get stats for a single BEDSET record + * @description Example + * bed_id: gse218680 + */ + get: operations['get_bedset_metadata_v1_bedset__bedset_id__metadata_stats_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/{bedset_id}/bedfiles': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get Bedfiles In Bedset + * @description Example + * bed_id: gse218680 + */ + get: operations['get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/bedset/{bedset_id}/track_hub': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get Track Hub Bedset + * @description Generate track hub files for the BED set + */ + get: operations['get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + /** + * Get Track Hub Bedset + * @description Generate track hub files for the BED set + */ + head: operations['get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head']; + patch?: never; + trace?: never; + }; + '/v1/bedset/create': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + get?: never; + put?: never; + /** + * Create Bedset + * @description Create a new bedset by providing registry path to the PEPhub project + */ + post: operations['create_bedset_v1_bedset_create_post']; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/objects/{object_id}': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get DRS object metadata + * @description Returns metadata about a DrsObject. + */ + get: operations['get_drs_object_metadata_v1_objects__object_id__get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/objects/{object_id}/access/{access_id}': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Get URL where you can retrieve files + * @description Returns a URL that can be used to fetch the bytes of a DrsObject. + */ + get: operations['get_object_bytes_url_v1_objects__object_id__access__access_id__get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/objects/{object_id}/access/{access_id}/bytes': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Download actual file + * @description Returns the bytes of a DrsObject. + */ + get: operations['get_object_bytes_v1_objects__object_id__access__access_id__bytes_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; + '/v1/objects/{object_id}/access/{access_id}/thumbnail': { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + /** + * Download thumbnail file + * @description Returns the bytes of a thumbnail of a DrsObject + */ + get: operations['get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get']; + put?: never; + post?: never; + delete?: never; + options?: never; + head?: never; + patch?: never; + trace?: never; + }; } export type webhooks = Record; export interface components { - schemas: { - /** AccessMethod */ - AccessMethod: { - /** Type */ - type: string; - access_url?: components["schemas"]["AccessURL"] | null; - /** Access Id */ - access_id?: string | null; - /** Region */ - region?: string | null; - }; - /** AccessURL */ - AccessURL: { - /** Url */ - url: string; - /** Headers */ - headers?: Record | null; - }; - /** BaseListResponse */ - BaseListResponse: { - /** Count */ - count: number; - /** Limit */ - limit: number; - /** Offset */ - offset: number; - /** Results */ - results: unknown[]; - }; - /** BedClassification */ - BedClassification: { - /** Name */ - name?: string | null; - /** Genome Alias */ - genome_alias?: string; - /** Genome Digest */ - genome_digest?: string | null; - /** - * Bed Compliance - * @default bed3 - */ - bed_compliance: string; - /** Data Format */ - data_format?: string | null; - /** - * Compliant Columns - * @default 3 - */ - compliant_columns: number; - /** - * Non Compliant Columns - * @default 0 - */ - non_compliant_columns: number; - /** Header */ - header?: string | null; - }; - /** BedEmbeddingResult */ - BedEmbeddingResult: { - /** Identifier */ - identifier: string; - /** Payload */ - payload: Record; - /** Embedding */ - embedding: number[]; - }; - /** BedFiles */ - BedFiles: { - bed_file?: components["schemas"]["FileModel"] | null; - bigbed_file?: components["schemas"]["FileModel"] | null; - }; - /** BedListResult */ - BedListResult: { - /** Count */ - count: number; - /** Limit */ - limit: number; - /** Offset */ - offset: number; - /** Results */ - results: components["schemas"]["BedMetadataBasic"][]; - }; - /** BedListSearchResult */ - BedListSearchResult: { - /** Count */ - count: number; - /** Limit */ - limit: number; - /** Offset */ - offset: number; - /** Results */ - results?: components["schemas"]["QdrantSearchResult"][]; - }; - /** BedMetadataAll */ - BedMetadataAll: { - /** - * Name - * @default - */ - name: string | null; - /** Genome Alias */ - genome_alias?: string; - /** Genome Digest */ - genome_digest?: string | null; - /** - * Bed Compliance - * @default bed3 - */ - bed_compliance: string; - /** Data Format */ - data_format?: string | null; - /** - * Compliant Columns - * @default 3 - */ - compliant_columns: number; - /** - * Non Compliant Columns - * @default 0 - */ - non_compliant_columns: number; - /** Header */ - header?: string | null; - /** Id */ - id: string; - /** Description */ - description?: string | null; - /** - * Submission Date - * Format: date-time - */ - submission_date?: string; - /** Last Update Date */ - last_update_date?: string | null; - /** - * Is Universe - * @default false - */ - is_universe: boolean | null; - /** - * License Id - * @default DUO:0000042 - */ - license_id: string | null; - annotation?: components["schemas"]["StandardMeta"] | null; - /** - * Processed - * @default true - */ - processed: boolean | null; - stats?: components["schemas"]["BedStatsModel"] | null; - plots?: components["schemas"]["BedPlots"] | null; - files?: components["schemas"]["BedFiles"] | null; - universe_metadata?: components["schemas"]["UniverseMetadata"] | null; - /** Raw Metadata */ - raw_metadata?: components["schemas"]["BedPEPHub"] | components["schemas"]["BedPEPHubRestrict"] | null; - /** Bedsets */ - bedsets?: components["schemas"]["BedSetMinimal"][] | null; - }; - /** BedMetadataBasic */ - BedMetadataBasic: { - /** - * Name - * @default - */ - name: string | null; - /** Genome Alias */ - genome_alias?: string; - /** Genome Digest */ - genome_digest?: string | null; - /** - * Bed Compliance - * @default bed3 - */ - bed_compliance: string; - /** Data Format */ - data_format?: string | null; - /** - * Compliant Columns - * @default 3 - */ - compliant_columns: number; - /** - * Non Compliant Columns - * @default 0 - */ - non_compliant_columns: number; - /** Header */ - header?: string | null; - /** Id */ - id: string; - /** Description */ - description?: string | null; - /** - * Submission Date - * Format: date-time - */ - submission_date?: string; - /** Last Update Date */ - last_update_date?: string | null; - /** - * Is Universe - * @default false - */ - is_universe: boolean | null; - /** - * License Id - * @default DUO:0000042 - */ - license_id: string | null; - annotation?: components["schemas"]["StandardMeta"] | null; - /** - * Processed - * @default true - */ - processed: boolean | null; - }; - /** BedPEPHub */ - BedPEPHub: { - /** - * Sample Name - * @default - */ - sample_name: string; - /** - * Genome - * @default - */ - genome: string; - /** - * Organism - * @default - */ - organism: string; - /** - * Species Id - * @default - */ - species_id: string; - /** - * Cell Type - * @default - */ - cell_type: string; - /** - * Cell Line - * @default - */ - cell_line: string; - /** - * Assay - * @description Experimental protocol (e.g. ChIP-seq) - * @default - */ - assay: string; - /** - * Library Source - * @description Library source (e.g. genomic, transcriptomic) - * @default - */ - library_source: string; - /** - * Genotype - * @description Genotype of the sample - * @default - */ - genotype: string; - /** - * Target - * @description Target of the assay (e.g. H3K4me3) - * @default - */ - target: string; - /** - * Antibody - * @description Antibody used in the assay - * @default - */ - antibody: string; - /** - * Treatment - * @description Treatment of the sample (e.g. drug treatment) - * @default - */ - treatment: string; - /** - * Tissue - * @description Tissue type - * @default - */ - tissue: string; - /** - * Global Sample Id - * @description Global sample identifier - * @default - */ - global_sample_id: string; - /** - * Global Experiment Id - * @description Global experiment identifier - * @default - */ - global_experiment_id: string; - /** - * Description - * @description Description of the sample - * @default - */ - description: string; - } & { - [key: string]: unknown; - }; - /** BedPEPHubRestrict */ - BedPEPHubRestrict: { - /** - * Sample Name - * @default - */ - sample_name: string; - /** - * Genome - * @default - */ - genome: string; - /** - * Organism - * @default - */ - organism: string; - /** - * Species Id - * @default - */ - species_id: string; - /** - * Cell Type - * @default - */ - cell_type: string; - /** - * Cell Line - * @default - */ - cell_line: string; - /** - * Assay - * @description Experimental protocol (e.g. ChIP-seq) - * @default - */ - assay: string; - /** - * Library Source - * @description Library source (e.g. genomic, transcriptomic) - * @default - */ - library_source: string; - /** - * Genotype - * @description Genotype of the sample - * @default - */ - genotype: string; - /** - * Target - * @description Target of the assay (e.g. H3K4me3) - * @default - */ - target: string; - /** - * Antibody - * @description Antibody used in the assay - * @default - */ - antibody: string; - /** - * Treatment - * @description Treatment of the sample (e.g. drug treatment) - * @default - */ - treatment: string; - /** - * Tissue - * @description Tissue type - * @default - */ - tissue: string; - /** - * Global Sample Id - * @description Global sample identifier - * @default - */ - global_sample_id: string; - /** - * Global Experiment Id - * @description Global experiment identifier - * @default - */ - global_experiment_id: string; - /** - * Description - * @description Description of the sample - * @default - */ - description: string; - }; - /** BedPlots */ - BedPlots: { - chrombins?: components["schemas"]["FileModel"]; - gccontent?: components["schemas"]["FileModel"]; - partitions?: components["schemas"]["FileModel"]; - expected_partitions?: components["schemas"]["FileModel"]; - cumulative_partitions?: components["schemas"]["FileModel"]; - widths_histogram?: components["schemas"]["FileModel"]; - neighbor_distances?: components["schemas"]["FileModel"]; - open_chromatin?: components["schemas"]["FileModel"]; - tss_distance?: components["schemas"]["FileModel"]; - }; - /** BedSetBedFiles */ - BedSetBedFiles: { - /** Count */ - count: number; - /** Results */ - results: components["schemas"]["BedMetadataBasic"][]; - }; - /** BedSetListResult */ - BedSetListResult: { - /** Count */ - count: number; - /** Limit */ - limit: number; - /** Offset */ - offset: number; - /** Results */ - results: components["schemas"]["BedSetMetadata"][]; - }; - /** BedSetMetadata */ - BedSetMetadata: { - /** Id */ - id: string; - /** Name */ - name: string; - /** Md5Sum */ - md5sum: string; - /** - * Submission Date - * Format: date-time - */ - submission_date?: string; - /** - * Last Update Date - * Format: date-time - */ - last_update_date?: string; - statistics?: components["schemas"]["BedSetStats"] | null; - plots?: components["schemas"]["BedSetPlots"] | null; - /** Description */ - description?: string; - /** Summary */ - summary?: string; - /** Bed Ids */ - bed_ids?: string[]; - /** Author */ - author?: string | null; - /** Source */ - source?: string | null; - }; - /** BedSetMinimal */ - BedSetMinimal: { - /** Id */ - id: string; - /** Name */ - name?: string | null; - /** Description */ - description?: string | null; - }; - /** BedSetPlots */ - BedSetPlots: { - region_commonality?: components["schemas"]["FileModel"]; - }; - /** BedSetStats */ - BedSetStats: { - mean?: components["schemas"]["BedStatsModel"]; - sd?: components["schemas"]["BedStatsModel"]; - }; - /** BedStatsModel */ - BedStatsModel: { - /** Number Of Regions */ - number_of_regions?: number | null; - /** Gc Content */ - gc_content?: number | null; - /** Median Tss Dist */ - median_tss_dist?: number | null; - /** Mean Region Width */ - mean_region_width?: number | null; - /** Exon Frequency */ - exon_frequency?: number | null; - /** Exon Percentage */ - exon_percentage?: number | null; - /** Intron Frequency */ - intron_frequency?: number | null; - /** Intron Percentage */ - intron_percentage?: number | null; - /** Intergenic Percentage */ - intergenic_percentage?: number | null; - /** Intergenic Frequency */ - intergenic_frequency?: number | null; - /** Promotercore Frequency */ - promotercore_frequency?: number | null; - /** Promotercore Percentage */ - promotercore_percentage?: number | null; - /** Fiveutr Frequency */ - fiveutr_frequency?: number | null; - /** Fiveutr Percentage */ - fiveutr_percentage?: number | null; - /** Threeutr Frequency */ - threeutr_frequency?: number | null; - /** Threeutr Percentage */ - threeutr_percentage?: number | null; - /** Promoterprox Frequency */ - promoterprox_frequency?: number | null; - /** Promoterprox Percentage */ - promoterprox_percentage?: number | null; - }; - /** BinValues */ - BinValues: { - /** Bins */ - bins: (number | string)[]; - /** Counts */ - counts: number[]; - /** Mean */ - mean: number; - /** Median */ - median: number; - }; - /** Body_bed_to_bed_search_v1_bed_search_bed_post */ - Body_bed_to_bed_search_v1_bed_search_bed_post: { - /** - * File - * Format: binary - */ - file?: string; - }; - /** Body_embed_bed_file_v1_bed_embed_post */ - Body_embed_bed_file_v1_bed_embed_post: { - /** - * File - * Format: binary - */ - file?: string; - }; - /** ComponentVersions */ - ComponentVersions: { - /** Bedhost Version */ - bedhost_version: string; - /** Bbconf Version */ - bbconf_version: string; - /** Python Version */ - python_version: string; - /** Geniml Version */ - geniml_version: string; - /** Openapi Version */ - openapi_version: string; - }; - /** CreateBEDsetRequest */ - CreateBEDsetRequest: { - /** Registry Path */ - registry_path: string; - }; - /** DRSModel */ - DRSModel: { - /** Id */ - id: string; - /** Name */ - name?: string | null; - /** Self Uri */ - self_uri: string; - /** Size */ - size?: number | null; - /** Created Time */ - created_time?: string | null; - /** Updated Time */ - updated_time?: string | null; - /** Checksums */ - checksums: string; - /** Access Methods */ - access_methods: components["schemas"]["AccessMethod"][]; - /** Description */ - description?: string | null; - }; - /** EmbeddingModels */ - EmbeddingModels: { - /** Region2Vec */ - region2vec: string; - /** Text2Vec */ - text2vec: string; - }; - /** FileModel */ - FileModel: { - /** Name */ - name: string; - /** Title */ - title?: string | null; - /** Path */ - path: string; - /** File Digest */ - file_digest?: string | null; - /** Thumbnail Path */ - thumbnail_path?: string | null; - /** Description */ - description?: string | null; - /** Size */ - size?: number | null; - /** Object Id */ - object_id?: string | null; - /** Access Methods */ - access_methods?: components["schemas"]["AccessMethod"][]; - }; - /** FileStats */ - FileStats: { - /** Bed Compliance */ - bed_compliance: { - [key: string]: number; - }; - /** Data Format */ - data_format: { - [key: string]: number; - }; - /** File Genome */ - file_genome: { - [key: string]: number; - }; - /** File Organism */ - file_organism: { - [key: string]: number; - }; - /** File Assay */ - file_assay: { - [key: string]: number; - }; - /** Geo Status */ - geo_status: { - [key: string]: number; - }; - /** Bed Comments */ - bed_comments: { - [key: string]: number; - }; - mean_region_width: components["schemas"]["BinValues"]; - file_size: components["schemas"]["BinValues"]; - number_of_regions: components["schemas"]["BinValues"]; - geo: components["schemas"]["GEOStatistics"]; - }; - /** - * GEOStatistics - * @description GEO statistics for files. - */ - GEOStatistics: { - /** Number Of Files */ - number_of_files: { - [key: string]: number; - }; - /** Cumulative Number Of Files */ - cumulative_number_of_files: { - [key: string]: number; - }; - file_sizes: components["schemas"]["BinValues"]; - }; - /** HTTPValidationError */ - HTTPValidationError: { - /** Detail */ - detail?: components["schemas"]["ValidationError"][]; - }; - /** Organization */ - Organization: { - /** Name */ - name: string; - /** Url */ - url: string; - }; - /** QdrantSearchResult */ - QdrantSearchResult: { - /** Id */ - id: string; - /** Payload */ - payload?: Record; - /** Score */ - score?: number; - metadata?: components["schemas"]["BedMetadataBasic"] | null; - }; - /** RefGenValidModel */ - RefGenValidModel: { - /** Provided Genome */ - provided_genome: string; - /** Compared Genome */ - genome_digest: string; - compared_genome: string; - /** - * Xs - * @default 0 - */ - xs: number; - /** Oobr */ - oobr?: number | null; - /** Sequence Fit */ - sequence_fit?: number | null; - /** Assigned Points */ - assigned_points: number; - /** Tier Ranking */ - tier_ranking: number; - }; - /** RefGenValidReturnModel */ - RefGenValidReturnModel: { - /** Id */ - id: string; - /** Provided Genome */ - provided_genome?: string | null; - /** Compared Genome */ - compared_genome: components["schemas"]["RefGenValidModel"][]; - }; - /** ServiceInfoResponse */ - ServiceInfoResponse: { - /** Id */ - id: string; - /** Name */ - name: string; - type: components["schemas"]["Type"]; - /** Description */ - description: string; - organization: components["schemas"]["Organization"]; - /** Contacturl */ - contactUrl: string; - /** Documentationurl */ - documentationUrl: string; - /** Updatedat */ - updatedAt: string; - /** Environment */ - environment: string; - /** Version */ - version: string; - component_versions: components["schemas"]["ComponentVersions"]; - embedding_models: components["schemas"]["EmbeddingModels"]; - }; - /** - * StandardMeta - * @description Standardized Bed file metadata - */ - StandardMeta: { - /** - * Organism - * @description Name of species. e.g. Homo sapiens. - * @default - */ - organism: string; - /** - * Species Id - * @default - */ - species_id: string; - /** - * Genotype - * @description Genotype of the sample - * @default - */ - genotype: string; - /** - * Phenotype - * @description Phenotype of the sample - * @default - */ - phenotype: string; - /** - * Description - * @default - */ - description: string | null; - /** - * Cell Type - * @description specific kind of cell with distinct characteristics found in an organism. e.g. Neurons, Hepatocytes, Adipocytes - * @default - */ - cell_type: string; - /** - * Cell Line - * @description population of cells derived from a single cell and cultured in the lab for extended use, e.g. HeLa, HepG2, k562 - * @default - */ - cell_line: string; - /** - * Tissue - * @description Tissue type - * @default - */ - tissue: string; - /** - * Library Source - * @description Library source (e.g. genomic, transcriptomic) - * @default - */ - library_source: string; - /** - * Assay - * @description Experimental protocol (e.g. ChIP-seq) - * @default - */ - assay: string; - /** - * Antibody - * @description Antibody used in the assay - * @default - */ - antibody: string; - /** - * Target - * @description Target of the assay (e.g. H3K4me3) - * @default - */ - target: string; - /** - * Treatment - * @description Treatment of the sample (e.g. drug treatment) - * @default - */ - treatment: string; - /** - * Global Sample Id - * @description Global sample identifier. e.g. GSM000 - * @default - */ - global_sample_id: string[] | null; - /** - * Global Experiment Id - * @description Global experiment identifier. e.g. GSE000 - * @default - */ - global_experiment_id: string[] | null; - /** - * Original File Name - * @description Original file name - * @default - */ - original_file_name: string; - }; - /** StatsReturn */ - StatsReturn: { - /** - * Bedfiles Number - * @default 0 - */ - bedfiles_number: number; - /** - * Bedsets Number - * @default 0 - */ - bedsets_number: number; - /** - * Genomes Number - * @default 0 - */ - genomes_number: number; - }; - /** TokenizedBedResponse */ - TokenizedBedResponse: { - /** Universe Id */ - universe_id: string; - /** Bed Id */ - bed_id: string; - /** Tokenized Bed */ - tokenized_bed: number[]; - }; - /** TokenizedPathResponse */ - TokenizedPathResponse: { - /** Bed Id */ - bed_id: string; - /** Universe Id */ - universe_id: string; - /** File Path */ - file_path: string; - /** Endpoint Url */ - endpoint_url: string; - }; - /** Type */ - Type: { - /** Group */ - group: string; - /** Artifact */ - artifact: string; - /** Version */ - version: string; - }; - /** UniverseMetadata */ - UniverseMetadata: { - /** Construct Method */ - construct_method?: string | null; - /** Bedset Id */ - bedset_id?: string | null; - }; - /** UsageStats */ - UsageStats: { - /** Bed Metadata */ - bed_metadata: { - [key: string]: number; - }; - /** Bedset Metadata */ - bedset_metadata: { - [key: string]: number; - }; - /** Bed Search Terms */ - bed_search_terms: { - [key: string]: number; - }; - /** Bedset Search Terms */ - bedset_search_terms: { - [key: string]: number; - }; - /** Bed Downloads */ - bed_downloads: { - [key: string]: number; - }; - }; - /** ValidationError */ - ValidationError: { - /** Location */ - loc: (string | number)[]; - /** Message */ - msg: string; - /** Error Type */ - type: string; - }; - }; - responses: never; - parameters: never; - requestBodies: never; - headers: never; - pathItems: never; + schemas: { + /** AccessMethod */ + AccessMethod: { + /** Type */ + type: string; + access_url?: components['schemas']['AccessURL'] | null; + /** Access Id */ + access_id?: string | null; + /** Region */ + region?: string | null; + }; + /** AccessURL */ + AccessURL: { + /** Url */ + url: string; + /** Headers */ + headers?: Record | null; + }; + /** BaseListResponse */ + BaseListResponse: { + /** Count */ + count: number; + /** Limit */ + limit: number; + /** Offset */ + offset: number; + /** Results */ + results: unknown[]; + }; + /** BedClassification */ + BedClassification: { + /** Name */ + name?: string | null; + /** Genome Alias */ + genome_alias?: string; + /** Genome Digest */ + genome_digest?: string | null; + /** + * Bed Compliance + * @default bed3 + */ + bed_compliance: string; + /** Data Format */ + data_format?: string | null; + /** + * Compliant Columns + * @default 3 + */ + compliant_columns: number; + /** + * Non Compliant Columns + * @default 0 + */ + non_compliant_columns: number; + /** Header */ + header?: string | null; + }; + /** BedEmbeddingResult */ + BedEmbeddingResult: { + /** Identifier */ + identifier: string; + /** Payload */ + payload: Record; + /** Embedding */ + embedding: number[]; + }; + /** BedFiles */ + BedFiles: { + bed_file?: components['schemas']['FileModel'] | null; + bigbed_file?: components['schemas']['FileModel'] | null; + }; + /** BedListResult */ + BedListResult: { + /** Count */ + count: number; + /** Limit */ + limit: number; + /** Offset */ + offset: number; + /** Results */ + results: components['schemas']['BedMetadataBasic'][]; + }; + /** BedListSearchResult */ + BedListSearchResult: { + /** Count */ + count: number; + /** Limit */ + limit: number; + /** Offset */ + offset: number; + /** Results */ + results?: components['schemas']['QdrantSearchResult'][]; + }; + /** BedMetadataAll */ + BedMetadataAll: { + /** + * Name + * @default + */ + name: string | null; + /** Genome Alias */ + genome_alias?: string; + /** Genome Digest */ + genome_digest?: string | null; + /** + * Bed Compliance + * @default bed3 + */ + bed_compliance: string; + /** Data Format */ + data_format?: string | null; + /** + * Compliant Columns + * @default 3 + */ + compliant_columns: number; + /** + * Non Compliant Columns + * @default 0 + */ + non_compliant_columns: number; + /** Header */ + header?: string | null; + /** Id */ + id: string; + /** Description */ + description?: string | null; + /** + * Submission Date + * Format: date-time + */ + submission_date?: string; + /** Last Update Date */ + last_update_date?: string | null; + /** + * Is Universe + * @default false + */ + is_universe: boolean | null; + /** + * License Id + * @default DUO:0000042 + */ + license_id: string | null; + annotation?: components['schemas']['StandardMeta'] | null; + /** + * Processed + * @default true + */ + processed: boolean | null; + stats?: components['schemas']['BedStatsModel'] | null; + plots?: components['schemas']['BedPlots'] | null; + files?: components['schemas']['BedFiles'] | null; + universe_metadata?: components['schemas']['UniverseMetadata'] | null; + /** Raw Metadata */ + raw_metadata?: components['schemas']['BedPEPHub'] | components['schemas']['BedPEPHubRestrict'] | null; + /** Bedsets */ + bedsets?: components['schemas']['BedSetMinimal'][] | null; + }; + /** BedMetadataBasic */ + BedMetadataBasic: { + /** + * Name + * @default + */ + name: string | null; + /** Genome Alias */ + genome_alias?: string; + /** Genome Digest */ + genome_digest?: string | null; + /** + * Bed Compliance + * @default bed3 + */ + bed_compliance: string; + /** Data Format */ + data_format?: string | null; + /** + * Compliant Columns + * @default 3 + */ + compliant_columns: number; + /** + * Non Compliant Columns + * @default 0 + */ + non_compliant_columns: number; + /** Header */ + header?: string | null; + /** Id */ + id: string; + /** Description */ + description?: string | null; + /** + * Submission Date + * Format: date-time + */ + submission_date?: string; + /** Last Update Date */ + last_update_date?: string | null; + /** + * Is Universe + * @default false + */ + is_universe: boolean | null; + /** + * License Id + * @default DUO:0000042 + */ + license_id: string | null; + annotation?: components['schemas']['StandardMeta'] | null; + /** + * Processed + * @default true + */ + processed: boolean | null; + }; + /** BedPEPHub */ + BedPEPHub: { + /** + * Sample Name + * @default + */ + sample_name: string; + /** + * Genome + * @default + */ + genome: string; + /** + * Organism + * @default + */ + organism: string; + /** + * Species Id + * @default + */ + species_id: string; + /** + * Cell Type + * @default + */ + cell_type: string; + /** + * Cell Line + * @default + */ + cell_line: string; + /** + * Assay + * @description Experimental protocol (e.g. ChIP-seq) + * @default + */ + assay: string; + /** + * Library Source + * @description Library source (e.g. genomic, transcriptomic) + * @default + */ + library_source: string; + /** + * Genotype + * @description Genotype of the sample + * @default + */ + genotype: string; + /** + * Target + * @description Target of the assay (e.g. H3K4me3) + * @default + */ + target: string; + /** + * Antibody + * @description Antibody used in the assay + * @default + */ + antibody: string; + /** + * Treatment + * @description Treatment of the sample (e.g. drug treatment) + * @default + */ + treatment: string; + /** + * Tissue + * @description Tissue type + * @default + */ + tissue: string; + /** + * Global Sample Id + * @description Global sample identifier + * @default + */ + global_sample_id: string; + /** + * Global Experiment Id + * @description Global experiment identifier + * @default + */ + global_experiment_id: string; + /** + * Description + * @description Description of the sample + * @default + */ + description: string; + } & { + [key: string]: unknown; + }; + /** BedPEPHubRestrict */ + BedPEPHubRestrict: { + /** + * Sample Name + * @default + */ + sample_name: string; + /** + * Genome + * @default + */ + genome: string; + /** + * Organism + * @default + */ + organism: string; + /** + * Species Id + * @default + */ + species_id: string; + /** + * Cell Type + * @default + */ + cell_type: string; + /** + * Cell Line + * @default + */ + cell_line: string; + /** + * Assay + * @description Experimental protocol (e.g. ChIP-seq) + * @default + */ + assay: string; + /** + * Library Source + * @description Library source (e.g. genomic, transcriptomic) + * @default + */ + library_source: string; + /** + * Genotype + * @description Genotype of the sample + * @default + */ + genotype: string; + /** + * Target + * @description Target of the assay (e.g. H3K4me3) + * @default + */ + target: string; + /** + * Antibody + * @description Antibody used in the assay + * @default + */ + antibody: string; + /** + * Treatment + * @description Treatment of the sample (e.g. drug treatment) + * @default + */ + treatment: string; + /** + * Tissue + * @description Tissue type + * @default + */ + tissue: string; + /** + * Global Sample Id + * @description Global sample identifier + * @default + */ + global_sample_id: string; + /** + * Global Experiment Id + * @description Global experiment identifier + * @default + */ + global_experiment_id: string; + /** + * Description + * @description Description of the sample + * @default + */ + description: string; + }; + /** BedPlots */ + BedPlots: { + chrombins?: components['schemas']['FileModel']; + gccontent?: components['schemas']['FileModel']; + partitions?: components['schemas']['FileModel']; + expected_partitions?: components['schemas']['FileModel']; + cumulative_partitions?: components['schemas']['FileModel']; + widths_histogram?: components['schemas']['FileModel']; + neighbor_distances?: components['schemas']['FileModel']; + open_chromatin?: components['schemas']['FileModel']; + tss_distance?: components['schemas']['FileModel']; + }; + /** BedSetBedFiles */ + BedSetBedFiles: { + /** Count */ + count: number; + /** Results */ + results: components['schemas']['BedMetadataBasic'][]; + }; + /** BedSetListResult */ + BedSetListResult: { + /** Count */ + count: number; + /** Limit */ + limit: number; + /** Offset */ + offset: number; + /** Results */ + results: components['schemas']['BedSetMetadata'][]; + }; + /** BedSetMetadata */ + BedSetMetadata: { + /** Id */ + id: string; + /** Name */ + name: string; + /** Md5Sum */ + md5sum: string; + /** + * Submission Date + * Format: date-time + */ + submission_date?: string; + /** + * Last Update Date + * Format: date-time + */ + last_update_date?: string; + statistics?: components['schemas']['BedSetStats'] | null; + plots?: components['schemas']['BedSetPlots'] | null; + /** Description */ + description?: string; + /** Summary */ + summary?: string; + /** Bed Ids */ + bed_ids?: string[]; + /** Author */ + author?: string | null; + /** Source */ + source?: string | null; + }; + /** BedSetMinimal */ + BedSetMinimal: { + /** Id */ + id: string; + /** Name */ + name?: string | null; + /** Description */ + description?: string | null; + }; + /** BedSetPlots */ + BedSetPlots: { + region_commonality?: components['schemas']['FileModel']; + }; + /** BedSetStats */ + BedSetStats: { + mean?: components['schemas']['BedStatsModel']; + sd?: components['schemas']['BedStatsModel']; + }; + /** BedStatsModel */ + BedStatsModel: { + /** Number Of Regions */ + number_of_regions?: number | null; + /** Gc Content */ + gc_content?: number | null; + /** Median Tss Dist */ + median_tss_dist?: number | null; + /** Mean Region Width */ + mean_region_width?: number | null; + /** Exon Frequency */ + exon_frequency?: number | null; + /** Exon Percentage */ + exon_percentage?: number | null; + /** Intron Frequency */ + intron_frequency?: number | null; + /** Intron Percentage */ + intron_percentage?: number | null; + /** Intergenic Percentage */ + intergenic_percentage?: number | null; + /** Intergenic Frequency */ + intergenic_frequency?: number | null; + /** Promotercore Frequency */ + promotercore_frequency?: number | null; + /** Promotercore Percentage */ + promotercore_percentage?: number | null; + /** Fiveutr Frequency */ + fiveutr_frequency?: number | null; + /** Fiveutr Percentage */ + fiveutr_percentage?: number | null; + /** Threeutr Frequency */ + threeutr_frequency?: number | null; + /** Threeutr Percentage */ + threeutr_percentage?: number | null; + /** Promoterprox Frequency */ + promoterprox_frequency?: number | null; + /** Promoterprox Percentage */ + promoterprox_percentage?: number | null; + }; + /** BinValues */ + BinValues: { + /** Bins */ + bins: (number | string)[]; + /** Counts */ + counts: number[]; + /** Mean */ + mean: number; + /** Median */ + median: number; + }; + /** Body_bed_to_bed_search_v1_bed_search_bed_post */ + Body_bed_to_bed_search_v1_bed_search_bed_post: { + /** + * File + * Format: binary + */ + file?: string; + }; + /** Body_embed_bed_file_v1_bed_embed_post */ + Body_embed_bed_file_v1_bed_embed_post: { + /** + * File + * Format: binary + */ + file?: string; + }; + /** ComponentVersions */ + ComponentVersions: { + /** Bedhost Version */ + bedhost_version: string; + /** Bbconf Version */ + bbconf_version: string; + /** Python Version */ + python_version: string; + /** Geniml Version */ + geniml_version: string; + /** Openapi Version */ + openapi_version: string; + }; + /** CreateBEDsetRequest */ + CreateBEDsetRequest: { + /** Registry Path */ + registry_path: string; + }; + /** DRSModel */ + DRSModel: { + /** Id */ + id: string; + /** Name */ + name?: string | null; + /** Self Uri */ + self_uri: string; + /** Size */ + size?: number | null; + /** Created Time */ + created_time?: string | null; + /** Updated Time */ + updated_time?: string | null; + /** Checksums */ + checksums: string; + /** Access Methods */ + access_methods: components['schemas']['AccessMethod'][]; + /** Description */ + description?: string | null; + }; + /** EmbeddingModels */ + EmbeddingModels: { + /** Region2Vec */ + region2vec: string; + /** Text2Vec */ + text2vec: string; + }; + /** FileModel */ + FileModel: { + /** Name */ + name: string; + /** Title */ + title?: string | null; + /** Path */ + path: string; + /** File Digest */ + file_digest?: string | null; + /** Thumbnail Path */ + thumbnail_path?: string | null; + /** Description */ + description?: string | null; + /** Size */ + size?: number | null; + /** Object Id */ + object_id?: string | null; + /** Access Methods */ + access_methods?: components['schemas']['AccessMethod'][]; + }; + /** FileStats */ + FileStats: { + /** Bed Compliance */ + bed_compliance: { + [key: string]: number; + }; + /** Data Format */ + data_format: { + [key: string]: number; + }; + /** File Genome */ + file_genome: { + [key: string]: number; + }; + /** File Organism */ + file_organism: { + [key: string]: number; + }; + /** File Assay */ + file_assay: { + [key: string]: number; + }; + /** Geo Status */ + geo_status: { + [key: string]: number; + }; + /** Bed Comments */ + bed_comments: { + [key: string]: number; + }; + mean_region_width: components['schemas']['BinValues']; + file_size: components['schemas']['BinValues']; + number_of_regions: components['schemas']['BinValues']; + geo: components['schemas']['GEOStatistics']; + }; + /** + * GEOStatistics + * @description GEO statistics for files. + */ + GEOStatistics: { + /** Number Of Files */ + number_of_files: { + [key: string]: number; + }; + /** Cumulative Number Of Files */ + cumulative_number_of_files: { + [key: string]: number; + }; + file_sizes: components['schemas']['BinValues']; + }; + /** HTTPValidationError */ + HTTPValidationError: { + /** Detail */ + detail?: components['schemas']['ValidationError'][]; + }; + /** Organization */ + Organization: { + /** Name */ + name: string; + /** Url */ + url: string; + }; + /** QdrantSearchResult */ + QdrantSearchResult: { + /** Id */ + id: string; + /** Payload */ + payload?: Record; + /** Score */ + score?: number; + metadata?: components['schemas']['BedMetadataBasic'] | null; + }; + /** RefGenValidModel */ + RefGenValidModel: { + /** Provided Genome */ + provided_genome: string; + /** Compared Genome */ + genome_digest: string; + compared_genome: string; + /** + * Xs + * @default 0 + */ + xs: number; + /** Oobr */ + oobr?: number | null; + /** Sequence Fit */ + sequence_fit?: number | null; + /** Assigned Points */ + assigned_points: number; + /** Tier Ranking */ + tier_ranking: number; + }; + /** RefGenValidReturnModel */ + RefGenValidReturnModel: { + /** Id */ + id: string; + /** Provided Genome */ + provided_genome?: string | null; + /** Compared Genome */ + compared_genome: components['schemas']['RefGenValidModel'][]; + }; + /** ServiceInfoResponse */ + ServiceInfoResponse: { + /** Id */ + id: string; + /** Name */ + name: string; + type: components['schemas']['Type']; + /** Description */ + description: string; + organization: components['schemas']['Organization']; + /** Contacturl */ + contactUrl: string; + /** Documentationurl */ + documentationUrl: string; + /** Updatedat */ + updatedAt: string; + /** Environment */ + environment: string; + /** Version */ + version: string; + component_versions: components['schemas']['ComponentVersions']; + embedding_models: components['schemas']['EmbeddingModels']; + }; + /** + * StandardMeta + * @description Standardized Bed file metadata + */ + StandardMeta: { + /** + * Organism + * @description Name of species. e.g. Homo sapiens. + * @default + */ + organism: string; + /** + * Species Id + * @default + */ + species_id: string; + /** + * Genotype + * @description Genotype of the sample + * @default + */ + genotype: string; + /** + * Phenotype + * @description Phenotype of the sample + * @default + */ + phenotype: string; + /** + * Description + * @default + */ + description: string | null; + /** + * Cell Type + * @description specific kind of cell with distinct characteristics found in an organism. e.g. Neurons, Hepatocytes, Adipocytes + * @default + */ + cell_type: string; + /** + * Cell Line + * @description population of cells derived from a single cell and cultured in the lab for extended use, e.g. HeLa, HepG2, k562 + * @default + */ + cell_line: string; + /** + * Tissue + * @description Tissue type + * @default + */ + tissue: string; + /** + * Library Source + * @description Library source (e.g. genomic, transcriptomic) + * @default + */ + library_source: string; + /** + * Assay + * @description Experimental protocol (e.g. ChIP-seq) + * @default + */ + assay: string; + /** + * Antibody + * @description Antibody used in the assay + * @default + */ + antibody: string; + /** + * Target + * @description Target of the assay (e.g. H3K4me3) + * @default + */ + target: string; + /** + * Treatment + * @description Treatment of the sample (e.g. drug treatment) + * @default + */ + treatment: string; + /** + * Global Sample Id + * @description Global sample identifier. e.g. GSM000 + * @default + */ + global_sample_id: string[] | null; + /** + * Global Experiment Id + * @description Global experiment identifier. e.g. GSE000 + * @default + */ + global_experiment_id: string[] | null; + /** + * Original File Name + * @description Original file name + * @default + */ + original_file_name: string; + }; + /** StatsReturn */ + StatsReturn: { + /** + * Bedfiles Number + * @default 0 + */ + bedfiles_number: number; + /** + * Bedsets Number + * @default 0 + */ + bedsets_number: number; + /** + * Genomes Number + * @default 0 + */ + genomes_number: number; + }; + /** TokenizedBedResponse */ + TokenizedBedResponse: { + /** Universe Id */ + universe_id: string; + /** Bed Id */ + bed_id: string; + /** Tokenized Bed */ + tokenized_bed: number[]; + }; + /** TokenizedPathResponse */ + TokenizedPathResponse: { + /** Bed Id */ + bed_id: string; + /** Universe Id */ + universe_id: string; + /** File Path */ + file_path: string; + /** Endpoint Url */ + endpoint_url: string; + }; + /** Type */ + Type: { + /** Group */ + group: string; + /** Artifact */ + artifact: string; + /** Version */ + version: string; + }; + /** UniverseMetadata */ + UniverseMetadata: { + /** Construct Method */ + construct_method?: string | null; + /** Bedset Id */ + bedset_id?: string | null; + }; + /** UsageStats */ + UsageStats: { + /** Bed Metadata */ + bed_metadata: { + [key: string]: number; + }; + /** Bedset Metadata */ + bedset_metadata: { + [key: string]: number; + }; + /** Bed Search Terms */ + bed_search_terms: { + [key: string]: number; + }; + /** Bedset Search Terms */ + bedset_search_terms: { + [key: string]: number; + }; + /** Bed Downloads */ + bed_downloads: { + [key: string]: number; + }; + }; + /** ValidationError */ + ValidationError: { + /** Location */ + loc: (string | number)[]; + /** Message */ + msg: string; + /** Error Type */ + type: string; + }; + }; + responses: never; + parameters: never; + requestBodies: never; + headers: never; + pathItems: never; } export type $defs = Record; export interface operations { - index_v1_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - }; - }; - changelog_v1_docs_changelog_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "text/html": string; - }; - }; - }; - }; - lending_page__get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - }; - }; - get_bedbase_db_stats_v1_stats_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["StatsReturn"]; - }; - }; - }; - }; - get_detailed_stats_v1_detailed_stats_get: { - parameters: { - query?: { - concise?: boolean; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["FileStats"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_detailed_usage_v1_detailed_usage_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["UsageStats"]; - }; - }; - }; - }; - get_bedbase_db_stats_v1_genomes_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BaseListResponse"]; - }; - }; - }; - }; - get_bedbase_db_stats_v1_assays_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BaseListResponse"]; - }; - }; - }; - }; - service_info_v1_service_info_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["ServiceInfoResponse"]; - }; - }; - }; - }; - redirect_to_download_v1_files__file_path__get: { - parameters: { - query?: never; - header?: never; - path: { - file_path: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_example_bed_record_v1_bed_example_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedMetadataAll"]; - }; - }; - }; - }; - list_beds_v1_bed_list_get: { - parameters: { - query?: { - limit?: number; - offset?: number; - /** @description filter by genome of the bed file. e.g. 'hg38' */ - genome?: string; - /** @description filter by bed type. e.g. 'bed6+4' */ - bed_compliance?: string; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedListResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_metadata_v1_bed__bed_id__metadata_get: { - parameters: { - query?: { - /** @description Return full record with stats, plots, files and metadata */ - full?: boolean | null; - }; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedMetadataAll"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_plots_v1_bed__bed_id__metadata_plots_get: { - parameters: { - query?: never; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedPlots"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_files_v1_bed__bed_id__metadata_files_get: { - parameters: { - query?: never; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedFiles"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_stats_v1_bed__bed_id__metadata_stats_get: { - parameters: { - query?: never; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedStatsModel"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_classification_v1_bed__bed_id__metadata_classification_get: { - parameters: { - query?: never; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedClassification"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_pephub_v1_bed__bed_id__metadata_raw_get: { - parameters: { - query?: never; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedPEPHubRestrict"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_neighbours_v1_bed__bed_id__neighbours_get: { - parameters: { - query?: { - limit?: number; - offset?: number; - }; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedListSearchResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bed_embedding_v1_bed__bed_id__embedding_get: { - parameters: { - query?: never; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedEmbeddingResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - embed_bed_file_v1_bed_embed_post: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: { - content: { - "multipart/form-data": components["schemas"]["Body_embed_bed_file_v1_bed_embed_post"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": number[]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - missing_plots_v1_bed_missing_plots_get: { - parameters: { - query: { - plot_id: string; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BaseListResponse"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get: { - parameters: { - query?: { - /** @description query range: start coordinate */ - start?: string | null; - /** @description query range: start coordinate */ - end?: string | null; - }; - header?: never; - path: { - /** @description BED digest */ - bed_id: string; - /** - * @description Chromosome number - * @example chr1 - */ - chr_num: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "text/plain": string; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - text_to_bed_search_v1_bed_search_text_post: { - parameters: { - query: { - query: string; - genome?: string | null; - assay?: string | null; - limit?: number; - offset?: number; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedListSearchResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - text_to_bed_search_v1_bed_search_exact_post: { - parameters: { - query: { - query: string; - genome?: string | null; - assay?: string | null; - limit?: number; - offset?: number; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedListSearchResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - bed_to_bed_search_v1_bed_search_bed_post: { - parameters: { - query?: { - limit?: number; - offset?: number; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: { - content: { - "multipart/form-data": components["schemas"]["Body_bed_to_bed_search_v1_bed_search_bed_post"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedListSearchResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_tokens_v1_bed__bed_id__tokens__universe_id__get: { - parameters: { - query?: never; - header?: never; - path: { - bed_id: string; - universe_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["TokenizedBedResponse"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_tokens_v1_bed__bed_id__tokens__universe_id__info_get: { - parameters: { - query?: never; - header?: never; - path: { - bed_id: string; - universe_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["TokenizedPathResponse"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_ref_gen_results_v1_bed__bed_id__genome_stats_get: { - parameters: { - query?: never; - header?: never; - path: { - bed_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["RefGenValidReturnModel"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_example_bedset_record_v1_bedset_example_get: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedSetMetadata"]; - }; - }; - }; - }; - list_bedsets_v1_bedset_list_get: { - parameters: { - query?: { - query?: string; - limit?: number; - offset?: number; - }; - header?: never; - path?: never; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedSetListResult"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bedset_metadata_v1_bedset__bedset_id__metadata_get: { - parameters: { - query?: { - full?: boolean; - }; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedSetMetadata"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bedset_pep_v1_bedset__bedset_id__pep_get: { - parameters: { - query?: never; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bedset_metadata_v1_bedset__bedset_id__metadata_plots_get: { - parameters: { - query?: never; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedSetPlots"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bedset_metadata_v1_bedset__bedset_id__metadata_stats_get: { - parameters: { - query?: never; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedSetStats"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get: { - parameters: { - query?: never; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["BedSetBedFiles"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get: { - parameters: { - query?: never; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head: { - parameters: { - query?: never; - header?: never; - path: { - bedset_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - create_bedset_v1_bedset_create_post: { - parameters: { - query?: never; - header?: never; - path?: never; - cookie?: never; - }; - requestBody: { - content: { - "application/json": components["schemas"]["CreateBEDsetRequest"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_drs_object_metadata_v1_objects__object_id__get: { - parameters: { - query?: never; - header?: never; - path: { - object_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["DRSModel"]; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_object_bytes_url_v1_objects__object_id__access__access_id__get: { - parameters: { - query?: never; - header?: never; - path: { - object_id: string; - access_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": string; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_object_bytes_v1_objects__object_id__access__access_id__bytes_get: { - parameters: { - query?: never; - header?: never; - path: { - object_id: string; - access_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": string; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get: { - parameters: { - query?: never; - header?: never; - path: { - object_id: string; - access_id: string; - }; - cookie?: never; - }; - requestBody?: never; - responses: { - /** @description Successful Response */ - 200: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": string; - }; - }; - /** @description Validation Error */ - 422: { - headers: { - [name: string]: unknown; - }; - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; + index_v1_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + }; + }; + changelog_v1_docs_changelog_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'text/html': string; + }; + }; + }; + }; + lending_page__get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + }; + }; + get_bedbase_db_stats_v1_stats_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['StatsReturn']; + }; + }; + }; + }; + get_detailed_stats_v1_detailed_stats_get: { + parameters: { + query?: { + concise?: boolean; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['FileStats']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_detailed_usage_v1_detailed_usage_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['UsageStats']; + }; + }; + }; + }; + get_bedbase_db_stats_v1_genomes_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BaseListResponse']; + }; + }; + }; + }; + get_bedbase_db_stats_v1_assays_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BaseListResponse']; + }; + }; + }; + }; + service_info_v1_service_info_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['ServiceInfoResponse']; + }; + }; + }; + }; + redirect_to_download_v1_files__file_path__get: { + parameters: { + query?: never; + header?: never; + path: { + file_path: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_example_bed_record_v1_bed_example_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedMetadataAll']; + }; + }; + }; + }; + list_beds_v1_bed_list_get: { + parameters: { + query?: { + limit?: number; + offset?: number; + /** @description filter by genome of the bed file. e.g. 'hg38' */ + genome?: string; + /** @description filter by bed type. e.g. 'bed6+4' */ + bed_compliance?: string; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedListResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_metadata_v1_bed__bed_id__metadata_get: { + parameters: { + query?: { + /** @description Return full record with stats, plots, files and metadata */ + full?: boolean | null; + }; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedMetadataAll']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_plots_v1_bed__bed_id__metadata_plots_get: { + parameters: { + query?: never; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedPlots']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_files_v1_bed__bed_id__metadata_files_get: { + parameters: { + query?: never; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedFiles']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_stats_v1_bed__bed_id__metadata_stats_get: { + parameters: { + query?: never; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedStatsModel']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_classification_v1_bed__bed_id__metadata_classification_get: { + parameters: { + query?: never; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedClassification']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_pephub_v1_bed__bed_id__metadata_raw_get: { + parameters: { + query?: never; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedPEPHubRestrict']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_neighbours_v1_bed__bed_id__neighbours_get: { + parameters: { + query?: { + limit?: number; + offset?: number; + }; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedListSearchResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bed_embedding_v1_bed__bed_id__embedding_get: { + parameters: { + query?: never; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedEmbeddingResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + embed_bed_file_v1_bed_embed_post: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: { + content: { + 'multipart/form-data': components['schemas']['Body_embed_bed_file_v1_bed_embed_post']; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': number[]; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + missing_plots_v1_bed_missing_plots_get: { + parameters: { + query: { + plot_id: string; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BaseListResponse']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get: { + parameters: { + query?: { + /** @description query range: start coordinate */ + start?: string | null; + /** @description query range: start coordinate */ + end?: string | null; + }; + header?: never; + path: { + /** @description BED digest */ + bed_id: string; + /** + * @description Chromosome number + * @example chr1 + */ + chr_num: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'text/plain': string; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + text_to_bed_search_v1_bed_search_text_post: { + parameters: { + query: { + query: string; + genome?: string | null; + assay?: string | null; + limit?: number; + offset?: number; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedListSearchResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + text_to_bed_search_v1_bed_search_exact_post: { + parameters: { + query: { + query: string; + genome?: string | null; + assay?: string | null; + limit?: number; + offset?: number; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedListSearchResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + bed_to_bed_search_v1_bed_search_bed_post: { + parameters: { + query?: { + limit?: number; + offset?: number; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: { + content: { + 'multipart/form-data': components['schemas']['Body_bed_to_bed_search_v1_bed_search_bed_post']; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedListSearchResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_tokens_v1_bed__bed_id__tokens__universe_id__get: { + parameters: { + query?: never; + header?: never; + path: { + bed_id: string; + universe_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['TokenizedBedResponse']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_tokens_v1_bed__bed_id__tokens__universe_id__info_get: { + parameters: { + query?: never; + header?: never; + path: { + bed_id: string; + universe_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['TokenizedPathResponse']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_ref_gen_results_v1_bed__bed_id__genome_stats_get: { + parameters: { + query?: never; + header?: never; + path: { + bed_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['RefGenValidReturnModel']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_example_bedset_record_v1_bedset_example_get: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedSetMetadata']; + }; + }; + }; + }; + list_bedsets_v1_bedset_list_get: { + parameters: { + query?: { + query?: string; + limit?: number; + offset?: number; + }; + header?: never; + path?: never; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedSetListResult']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bedset_metadata_v1_bedset__bedset_id__metadata_get: { + parameters: { + query?: { + full?: boolean; + }; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedSetMetadata']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bedset_pep_v1_bedset__bedset_id__pep_get: { + parameters: { + query?: never; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bedset_metadata_v1_bedset__bedset_id__metadata_plots_get: { + parameters: { + query?: never; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedSetPlots']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bedset_metadata_v1_bedset__bedset_id__metadata_stats_get: { + parameters: { + query?: never; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedSetStats']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get: { + parameters: { + query?: never; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['BedSetBedFiles']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get: { + parameters: { + query?: never; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head: { + parameters: { + query?: never; + header?: never; + path: { + bedset_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + create_bedset_v1_bedset_create_post: { + parameters: { + query?: never; + header?: never; + path?: never; + cookie?: never; + }; + requestBody: { + content: { + 'application/json': components['schemas']['CreateBEDsetRequest']; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': unknown; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_drs_object_metadata_v1_objects__object_id__get: { + parameters: { + query?: never; + header?: never; + path: { + object_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['DRSModel']; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_object_bytes_url_v1_objects__object_id__access__access_id__get: { + parameters: { + query?: never; + header?: never; + path: { + object_id: string; + access_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': string; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_object_bytes_v1_objects__object_id__access__access_id__bytes_get: { + parameters: { + query?: never; + header?: never; + path: { + object_id: string; + access_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** @description Successful Response */ + 200: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': string; + }; + }; + /** @description Validation Error */ + 422: { + headers: { + [name: string]: unknown; + }; + content: { + 'application/json': components['schemas']['HTTPValidationError']; + }; + }; + }; + }; + get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get: { + parameters: { + query?: never; + header?: never; + path: { + object_id: string; + access_id: string; + }; + cookie?: never; + }; + requestBody?: never; + responses: { + /** 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"dependencies": { + "@databio/gtars": "^0.5.2", "@tanstack/react-query": "^5.28.0", "@tanstack/react-query-devtools": "^5.28.0", "@tanstack/react-table": "^8.15.3", + "@types/pako": "^2.0.4", "@uidotdev/usehooks": "^2.4.1", "axios": "^1.12.0", "bootstrap": "^5.3.3", @@ -22,8 +24,10 @@ "chart.js": "^4.4.2", "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", + "embedding-atlas": "^0.12.0", "framer-motion": "^11.0.20", "js-yaml": "^4.1.0", + "pako": "^2.1.0", "react": "^18.2.0", "react-bootstrap": "^2.10.1", "react-chartjs-2": "^5.2.0", @@ -35,8 +39,10 @@ "react-markdown": "^9.0.1", "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", + "three": "^0.177.0", "vega-embed": "^7.0.2", - "three": "^0.177.0" + "vite-plugin-top-level-await": "^1.6.0", + "vite-plugin-wasm": "^3.5.0" }, "devDependencies": { "@types/js-yaml": "^4.0.9", @@ -51,6 +57,6 @@ "eslint-plugin-react-refresh": "^0.4.5", "sass": "^1.72.0", "typescript": "^5.2.2", - "vite": "^6.3.6" + "vite": "^6.4.1" } } diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx new file mode 100644 index 00000000..b18b9837 --- /dev/null +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -0,0 +1,186 @@ +import { useEffect, useRef, useState } from 'react'; +import embed from 'vega-embed'; + +const COLOR = 'rgba(0, 128, 128, 1)'; + +type DistributionSpecDataPoint = { + chr: string; + start: number; + end: number; + n: number; + rid: number; +}; + +interface BedPlotsProps { + data: DistributionSpecDataPoint[]; +} + +const distributionSpec = (data: DistributionSpecDataPoint[]) => { + const transformedData = data.map((item: DistributionSpecDataPoint) => ({ + chr: item.chr, + withinGroupID: item.rid, + N: item.n, + start: item.start, + end: item.end, + })); + return { + $schema: 'https://vega-github.io/schema/vega-lite/v6.json', + // title: { + // text: 'Region Distribution Plot', + // fontSize: 24, + // fontWeight: 'bold', + // anchor: 'middle', + // offset: 10, + // }, + config: { + axis: { + grid: false, + }, + facet: { + spacing: -1, + }, + view: { + strokeWidth: 0, + cursor: 'inherit', + }, + // bar: { + // continuousBandSize: 2.5, + // }, + }, + data: { + values: transformedData, + }, + encoding: { + row: { + title: 'Chromosome', + field: 'chr', + header: { + labelAlign: 'left', + labelAngle: 0, + labelOrient: 'left', + labelPadding: 5, + labelBaseline: 'top', + labelFontSize: 9, + }, + sort: [ + 'chr1', + 'chr2', + 'chr3', + 'chr4', + 'chr5', + 'chr6', + 'chr7', + 'chr8', + 'chr9', + 'chr10', + 'chr11', + 'chr12', + 'chr13', + 'chr14', + 'chr15', + 'chr16', + 'chr17', + 'chr18', + 'chr19', + 'chr20', + 'chr21', + 'chr22', + 'chrX', + 'chrY', + 'chrM', + ], + type: 'ordinal', + color: { + value: COLOR, + }, + }, + x: { + axis: { + labelExpr: "datum.value == 0 ? 'start' : datum.value == 300 ? 'end' : ''", + values: [0, 300.0], + }, + field: 'withinGroupID', + scale: { + domain: [0, 300.0], + }, + title: 'Genome', + type: 'quantitative', + }, + y: { + axis: { + labels: false, + ticks: false, + }, + field: 'N', + title: '', + type: 'quantitative', + }, + }, + height: 25, + mark: { + cornerRadiusEnd: 0.5, + type: 'bar', + width: 2.5, + color: COLOR, + }, + }; +}; + +export const RegionDistributionPlot = (props: BedPlotsProps) => { + const { data } = props; + + const plotRef = useRef(null); + const [containerWidth, setContainerWidth] = useState(0); + + useEffect(() => { + const updateWidth = () => { + if (plotRef.current) { + const width = plotRef.current.offsetWidth * 0.8; + setContainerWidth(width); + } + }; + + updateWidth(); + window.addEventListener('resize', updateWidth); + return () => window.removeEventListener('resize', updateWidth); + }, []); + + useEffect(() => { + const element = plotRef.current; + if (element && containerWidth > 0) { + const spec = { + ...distributionSpec(data), + width: containerWidth, + }; + + try { + // eslint-disable-next-line @typescript-eslint/no-explicit-any + embed(element, spec as any, { + actions: { export: true, source: false, compiled: false }, + renderer: 'svg', + }).catch((error) => { + console.error('Embed error after parsing:', error); + }); + } catch (error) { + console.error(error); + } + } + + return () => { + if (element) { + element.innerHTML = ''; + } + }; + }, [containerWidth, data]); + + return ( +
+
+
+ ); +}; + +export default RegionDistributionPlot; diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx new file mode 100644 index 00000000..49046ecf --- /dev/null +++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx @@ -0,0 +1,144 @@ +import { useState, useEffect, useRef } from 'react'; +import { ChromosomeStatistics, RegionSet } from '@databio/gtars'; +import { RegionCountsPlot } from './region-counts-plot'; + +interface Props { + rs: RegionSet; + selectedFile: File | undefined; +} + +const ChromosomeStatsPanel = ({ rs, selectedFile }: Props) => { + const calc = rs.chromosomeStatistics(); + if (!calc) return null; + + const plotRef = useRef(null); + const [containerWidth, setContainerWidth] = useState(0); + + useEffect(() => { + const updateWidth = () => { + if (plotRef.current) { + const width = plotRef.current.offsetWidth - 120; + setContainerWidth(width); + } + }; + + updateWidth(); + window.addEventListener('resize', updateWidth); + return () => window.removeEventListener('resize', updateWidth); + }, []); + + const statsEntries = Array.from(calc.entries()).map((entry) => { + const [chrom, stats] = entry as [unknown, ChromosomeStatistics]; + const cs = stats as ChromosomeStatistics; + const row = { + chromosome: String(chrom), + count: cs.number_of_regions, + minimum: cs.minimum_region_length, + maximum: cs.maximum_region_length, + mean: cs.mean_region_length.toFixed(2), + median: cs.median_region_length.toFixed(2), + start: cs.start_nucleotide_position, + end: cs.end_nucleotide_position, + }; + try { + (cs as unknown as { free?: () => void }).free?.(); + } catch (e) { + /* ignore */ + } + return row; + }); + + return ( +
+
+
Number of regions per chromosome:
+
+
+ {containerWidth > 0 && } +
+
+
+ +
+
+
Chromosome regions statistics:
+
+ +
+
+
+
+ + + + + + + + + + + + + + + {statsEntries.map((s) => ( + + + + + + + + + + + ))} + +
Chromosome nameNumber of regionsStart positionEnd positionMin lengthMax lengthMean lengthMedian length
{s.chromosome}{s.count}{s.start}{s.end}{s.minimum}{s.maximum}{s.mean}{s.median}
+
+
+
+
+ ); +}; + +export default ChromosomeStatsPanel; diff --git a/ui/src/components/bed-analytics-components/region-counts-plot.tsx b/ui/src/components/bed-analytics-components/region-counts-plot.tsx new file mode 100644 index 00000000..d78ad9d9 --- /dev/null +++ b/ui/src/components/bed-analytics-components/region-counts-plot.tsx @@ -0,0 +1,138 @@ +import { useEffect, useRef } from 'react'; +import embed from 'vega-embed'; + +type StatsEntry = { + chromosome: string; + count: number; + end: number; + maximum: number; + mean: string; + median: string; + minimum: number; + start: number; +}; + +type Props = { + statsEntries: StatsEntry[]; + width: number; +}; + +const COLOR = 'rgba(0, 128, 128, 1)'; + +const RegionCountsPlot = ({ statsEntries, width }: Props) => { + const plotRef = useRef(null); + + const regionCountsSpec = (statsEntries: StatsEntry[]) => { + return { + $schema: 'https://vega.github.io/schema/vega-lite/v6.json', + data: { + values: statsEntries, + }, + layer: [ + { + mark: { + type: 'bar', + fill: COLOR, + cornerRadiusEnd: 2, + height: { + band: 0.8, + }, + }, + encoding: { + x: { + field: 'count', + type: 'quantitative', + title: 'Count', + sort: false, + axis: { + orient: 'bottom', + }, + }, + y: { + field: 'chromosome', + type: 'nominal', + title: 'Chromosome', + sort: [ + 'chr1', + 'chr2', + 'chr3', + 'chr4', + 'chr5', + 'chr6', + 'chr7', + 'chr8', + 'chr9', + 'chr10', + 'chr11', + 'chr12', + 'chr13', + 'chr14', + 'chr15', + 'chr16', + 'chr17', + 'chr18', + 'chr19', + 'chr20', + 'chr21', + 'chr22', + 'chrX', + 'chrY', + 'chrM', + ], + axis: { + labelFontSize: 9, + }, + }, + }, + }, + { + mark: { + type: 'rule', + opacity: 0, + }, + encoding: { + x: { + field: 'count', + type: 'quantitative', + title: null, + axis: { + orient: 'top', + labels: true, + ticks: true, + domain: true, + }, + }, + }, + }, + ], + width: width * 0.91, + height: statsEntries.length * 11, + }; + }; + + useEffect(() => { + if (plotRef.current && statsEntries) { + const spec = regionCountsSpec(statsEntries); + try { + embed(plotRef.current, spec as any, { + actions: true, + config: {}, + }).catch((error) => { + console.error('Embed error after parsing:', error); + }); + } catch (error) { + console.error(error); + } + } + + return () => { + if (plotRef.current) { + plotRef.current.innerHTML = ''; + } + }; + }, [statsEntries]); + + return
; +}; + +export { RegionCountsPlot }; diff --git a/ui/src/components/bed-splash-components/cards/gc-content-card.tsx b/ui/src/components/bed-splash-components/cards/gc-content-card.tsx index 690b9df4..98919c4e 100644 --- a/ui/src/components/bed-splash-components/cards/gc-content-card.tsx +++ b/ui/src/components/bed-splash-components/cards/gc-content-card.tsx @@ -12,9 +12,9 @@ export const GCContentCard = (props: Props) => { return ( ); }; diff --git a/ui/src/components/bed-splash-components/cards/mean-region-width-card.tsx b/ui/src/components/bed-splash-components/cards/mean-region-width-card.tsx index f094631b..1c9de401 100644 --- a/ui/src/components/bed-splash-components/cards/mean-region-width-card.tsx +++ b/ui/src/components/bed-splash-components/cards/mean-region-width-card.tsx @@ -12,9 +12,9 @@ export const MeanRegionWidthCard = (props: Props) => { return ( ); }; diff --git a/ui/src/components/bed-splash-components/cards/median-tss-dist-card.tsx b/ui/src/components/bed-splash-components/cards/median-tss-dist-card.tsx index 65bbd64b..b1579377 100644 --- a/ui/src/components/bed-splash-components/cards/median-tss-dist-card.tsx +++ b/ui/src/components/bed-splash-components/cards/median-tss-dist-card.tsx @@ -11,9 +11,9 @@ export const MedianTssDistCard = (props: Props) => { const { metadata } = props; return ( ); }; diff --git a/ui/src/components/bed-splash-components/cards/no-regions-card.tsx b/ui/src/components/bed-splash-components/cards/no-regions-card.tsx index b38836ca..72fb9bd0 100644 --- a/ui/src/components/bed-splash-components/cards/no-regions-card.tsx +++ b/ui/src/components/bed-splash-components/cards/no-regions-card.tsx @@ -11,9 +11,9 @@ export const NoRegionsCard = (props: Props) => { const { metadata } = props; return ( ); }; diff --git a/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx b/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx index 7b1b5b46..b8c98b35 100644 --- a/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx +++ b/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx @@ -12,18 +12,15 @@ export const StatCard = (props: Props) => { const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( -
-
-

{title}

-
-

{stat}

-
-
- - - + +
+
+
{title}
+
+

{stat}

+
-
+ ); }; diff --git a/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx index 59342828..950c37f6 100644 --- a/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx @@ -24,6 +24,11 @@ const chartOptions = { display: false, }, }, + layout: { + padding: { + bottom: 25, + }, + }, }; export const GenomicFeatureBar = (props: Props) => { @@ -98,29 +103,29 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
-
-
-

Genomic Features

-
-
-
- -
+
+
+
+

Genomic Features

+
+
+
+ +
setDisplayAsPercentage(!displayAsPercentage)} /> - +
- +
-
+
{ const [copiedId, setCopiedId] = useState(false); const [showRefGenomeModal, setShowRefGenomeModal] = useState(false); - const noFilesToDownload = !metadata.files?.bed_file && !metadata.files?.bigbed_file; return ( -
-
-
-

- - {metadata?.id || 'No ID available'} +
+
+
+
+ {metadata?.id || 'No ID available'} -
+

{!metadata?.processed && ( -

+

- This file has not been processed by the BedBoss pipeline yet. - + This file has not been processed by the BedBoss pipeline yet. } > - - - Not Processed - + + + Not Processed +

)} -
- - {(metadata?.processed && metadata?.genome_alias == 'hg38') && +
+ {metadata?.processed && metadata?.genome_alias == 'hg38' && ( - - } + )} + + + - {!addedToCart && cart[record_identifier || ''] ? ( ) : ( )} - - + + Downloads { // If there are no files to download, disable the dropdown noFilesToDownload ? ( - + There are no files to download ) : ( - + {metadata.files?.bed_file && ( - {(metadata.files?.bed_file?.access_methods || []).map((method) => { + {(metadata.files?.bed_file?.access_methods || []).map((method, index) => { if (method.type === 'local' || method.type === 's3') { return null; } return ( - + {method.access_id ? 'BED file' : 'No download link available'} ( - {bytesToSize(metadata.files?.bed_file?.size || 0)}) + {bytesToSize(metadata.files?.bed_file?.size || 0)}) ); })} @@ -168,14 +167,14 @@ export const BedSplashHeader = (props: Props) => { )} {metadata.files?.bigbed_file && ( - {(metadata.files?.bigbed_file?.access_methods || []).map((method) => { + {(metadata.files?.bigbed_file?.access_methods || []).map((method, index) => { if (method.type === 'local' || method.type === 's3') { return null; } return ( - + {method.access_id ? 'BigBED file' : 'No download link available'} ( - {bytesToSize(metadata.files?.bigbed_file?.size || 0)}) + {bytesToSize(metadata.files?.bigbed_file?.size || 0)}) ); })} @@ -188,121 +187,123 @@ export const BedSplashHeader = (props: Props) => {
-
{metadata.name}
-

{metadata?.description || 'No description available'}

+
{metadata.name}
+

{metadata?.description || 'No description available'}

-
-
-
-
+
+
+
+
-
-
Genome assembly
+
+
+
Genome assembly
} > {metadata?.genome_digest ? ( <> - +
- + className={genomeStats?.compared_genome ? 'badge bg-primary rounded-end-0' : 'badge bg-primary'} + > + {metadata.genome_alias || 'No assembly available'}
) : ( <> -
- +
+ {metadata.genome_alias || 'No assembly available'}
)} - {genomeStats?.compared_genome && + {genomeStats?.compared_genome && ( -
-
Genome compatibility details
+
+
+
Genome compatibility details
} >
{ if (showRefGenomeModal !== true) { setShowRefGenomeModal(true); } }} > - +
- } + )}
-
-
+
+
-
-
BED compliance
+
+
+
BED compliance
} > -
- +
+ {metadata?.bed_compliance || 'No compliance available'}
-
-
+
+
-
-
Data Format
+
+
+
Data Format
} > -
- +
+ {metadata?.data_format || 'No data format available'}
-
-
+
+
-
-
License
+
+
+
License
} > -
- +
+ {metadata?.license_id || 'DUO:0000042'}
@@ -310,19 +311,19 @@ export const BedSplashHeader = (props: Props) => {
{metadata?.is_universe && ( -
-
+
+
-
-
This BED file is part of the Universe
+
+
+
This BED file is part of the Universe
} > -
- +
+ Universe
@@ -330,26 +331,8 @@ export const BedSplashHeader = (props: Props) => {
)}
-
-
- -

- Created:{' '} - {metadata?.submission_date ? formatDateTime(metadata?.submission_date) : 'No date available'} -

-
- -
- -

- Updated:{' '} - {metadata?.last_update_date ? formatDateTime(metadata?.last_update_date) : 'No date available'} -

-
-
- {genomeStats?.compared_genome && + {genomeStats?.compared_genome && ( { @@ -357,7 +340,7 @@ export const BedSplashHeader = (props: Props) => { }} genomeStats={genomeStats} /> - } + )}
); }; diff --git a/ui/src/components/bed-splash-components/plots.tsx b/ui/src/components/bed-splash-components/plots.tsx index d04546ee..072c5968 100644 --- a/ui/src/components/bed-splash-components/plots.tsx +++ b/ui/src/components/bed-splash-components/plots.tsx @@ -30,16 +30,16 @@ const Plot = (props: PlotProps) => { setShow(true); } }} - className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all" + className='h-100 border rounded p-2 hover-border-primary transition-all bg-white' > -
- {title} - {/* */}
-
- {alt} +
+ {alt}
{ export const Plots = (props: PlotsProps) => { const { metadata } = props; - const plotNames = metadata.plots ? Object.keys(metadata.plots) : []; + // comment out partitions because we already have it in statistics section + const plotNames = metadata.plots ? Object.keys(metadata.plots).filter((name: string) => name != 'partitions') : []; return ( - + {metadata.plots && chunkArray(plotNames, 3).map((chunk, idx) => ( @@ -73,10 +74,10 @@ export const Plots = (props: PlotsProps) => { const title = plotExists ? metadata.plots[plotNameKey]?.title : plotName; const alt = plotExists ? // @ts-expect-error: type checking here is just too much - metadata.plots[plotNameKey]?.description || metadata.plots[plotNameKey].title + metadata.plots[plotNameKey]?.description || metadata.plots[plotNameKey].title : plotName; return ( - + { const { show, onHide, genomeStats } = props; - console.log(genomeStats?.compared_genome) - return ( onHide()} - size="lg" - aria-labelledby="contained-modal-title-vcenter" + size='lg' + aria-labelledby='contained-modal-title-vcenter' centered > Reference Genome Compatibility -

+

Note: Below is a ranking of the compatibility various reference genomes to this BED file - (tier 1 is best). - The ranking is based on the following metrics: + (tier 1 is best). The ranking is based on the following metrics:

-
- +
{CODE_SNIPPETS.map((snippet) => ( - - +
+ {snippet.code} -
- -
- +
))} - - -
- - - - -

BED Embedding Visualization

-

- BEDbase supports visualization of UMAP of hg38 BED embeddings. It allows users to explore the - similarity of genomic regions based on their embeddings, and - providing insights into the relationships between different BED files. - The visualization is available on the UMAP visualization. -

- - - UMAP visualization - - - - -

Search for BED Files

-

- BEDbase offers three search endpoints for discovering BED files and BEDsets, distinguishing itself from - other platforms by utilizing vector search to index and search through bed file regions. This approach - enhances search accuracy and efficiency compared to platforms relying on unstructured user-provided - metadata, which can be ambiguous and less reliable. User can search for BED files by providing a query - string, or a BED file. -

- - -
- setSearchTermSmall(e.target.value)} - onKeyDown={(e) => { - if (e.key === 'Enter') { - if (searchTermSmall.length === 0) { - return; - } - navigate(`/search?q=${searchTermSmall}`); - } - }} - className="p-2 rounded border w-100 shadow-sm" - /> - +
+
+ +
+
+
+
+ +
REST API
+
+

+ Programmatic access to the BEDbase web server with a RESTful API. Query, retrieve, and analyze + genomic regions with simple HTTP requests from any language. +

+ + API Docs + +
- - - {/*
*/} - - -

BEDbase Client

-

- BEDbase provides a Python an R client for interacting with the BEDbase API. The client allows users to - download, cache, and analyze BED files and BED sets programmatically, without the need to interact with - the native API. BBclient is available on PyPI in geniml package with other useful tools for genomic data - analysis. Python Geniml package:{' '} - - {' '} - PyPI geniml - - . - R package:{' '} - - {' '} - BEDbaser - - . -

- +
- -
- -
- +
- +
{BBCONF_SNIPPETS.map((snippet) => ( - - +
+ {snippet.code} -
- -
- +
))} - - -
- - - - -

Data Availability Summary

-

- Comprehensive metrics about BEDbase file statistics is available on the {' '} - metrics page. -

- - -
-
    -
  • - Number of bed files available: - {(bedbaseStats?.bedfiles_number || 0).toLocaleString()} -
    • -
  • - Number of bed sets available: - {(bedbaseStats?.bedsets_number || 0).toLocaleString()} -
    • -
  • - Number of genomes available: - {(bedbaseStats?.genomes_number || 0).toLocaleString()} -
    • -
+
+
+ +
+
+
+
+ +
BEDbase Clients
+
+

+ Download, cache, and analyze BED files programmatically with native Python and R packages. + Simplifies API interaction through high-level interfaces. +

+ +
- - +
+
diff --git a/ui/src/pages/metrics.tsx b/ui/src/pages/metrics.tsx index b3d2757b..f46814b2 100644 --- a/ui/src/pages/metrics.tsx +++ b/ui/src/pages/metrics.tsx @@ -1,14 +1,19 @@ import { useState } from 'react'; import { Layout } from '../components/layout.tsx'; -import { Col, Row, Container } from 'react-bootstrap'; import { useStats } from '../queries/useStats.ts'; import { useDetailedStats } from '../queries/useDetailedStats.ts'; import { useDetailedUsage } from '../queries/useDetailedUsage.ts'; -import { MetricPlot, MetricPlotType } from '../components/metrics/metric-plot.tsx'; +import { MetricPlotType } from '../components/metrics/metric-plot.tsx'; import { MetricModal } from '../components/modals/metric-modal.tsx'; import { CardSkeleton } from '../components/skeletons/card-skeleton'; import { EndpointsModal } from '../components/modals/endpoints-modal.tsx'; +import { MetricsSelector } from '../components/metrics/metrics-selector.tsx'; +import { FileStatistics } from '../components/metrics/file-statistics.tsx'; +import { GeoStatistics } from '../components/metrics/geo-statistics.tsx'; +import { UsageStatistics } from '../components/metrics/usage-statistics.tsx'; + +type MetricsView = 'file' | 'geo' | 'usage'; const API_BASE = import.meta.env.VITE_API_BASE || ''; export const PRIMARY_COLOR = 'rgba(0, 128, 128,0.6)'; @@ -25,14 +30,8 @@ interface MetricModalProps { angle?: boolean; } -const transformHistogramData = (bins: (string | number)[], counts: number[]): [string, number][] => { - return counts.map((count, index) => { - const binLabel = typeof bins[index] === 'number' ? String(bins[index]) : ''; - return [binLabel, Number(count)]; - }); -}; - export const Metrics = () => { + const [metricsView, setMetricsView] = useState('file'); const [showMetricModal, setShowMetricModal] = useState(false); const [metricModalTitle, setMetricModalTitle] = useState(''); const [metricModalType, setMetricModalType] = useState('bar'); @@ -46,16 +45,16 @@ export const Metrics = () => { const [endpointsModalShow, setEndpointsModalShow] = useState(false); const setMetricModalProps = ({ - title, - type, - data, - median = 0, - xlab = '', - ylab = '', - height = 400, - color = 1, - angle = true, - }: MetricModalProps): void => { + title, + type, + data, + median = 0, + xlab = '', + ylab = '', + height = 400, + color = 1, + angle = true, + }: MetricModalProps): void => { setMetricModalTitle(title); setMetricModalType(type); setMetricModalData(data); @@ -68,554 +67,76 @@ export const Metrics = () => { setShowMetricModal(true); }; - const { data: bedbaseStats } = useStats(); const { data: detailedStats, isLoading: statsIsLoading } = useDetailedStats(); const { data: usageStats, isLoading: usageIsLoading } = useDetailedUsage(); - console.log(detailedStats); - if (statsIsLoading || usageIsLoading) { return ( - -
- - -
- -
- - - - -
- -
-
- -
- - - - - + +
+
+
+
+ +
+
+
+
+
+
+ +
+
+ +
+
+
+ +
+
); } - ; return ( - - - - -

Metrics

- - - - - - - - - -

BEDbase File Statistics

- -
    -
  • - Number of bed files available: - {(bedbaseStats?.bedfiles_number || 0).toLocaleString()} -
    • -
  • - Number of bed sets available: - {(bedbaseStats?.bedsets_number || 0).toLocaleString()} -
    • -
  • - Number of genomes available: - {(bedbaseStats?.genomes_number || 0).toLocaleString()} -
    • -
- - - - {detailedStats && ( - - -
setMetricModalProps({ - title: 'BED Files by Genome', - type: 'bar', - data: Object.entries(detailedStats?.file_genome || {}), - xlab: 'Reference Genome', - ylab: 'Number of BED Files', - color: 0, - })} - > -
BED Files by Genome
- -
-
setMetricModalProps({ - title: 'BED Files by BED Compliance', - type: 'bar', - data: Object.entries(detailedStats?.bed_compliance || {}), - xlab: 'Compliance Type', - ylab: 'Number of BED Files', - color: 2, - })} - > -
BED Files by BED Compliance
- -
-
setMetricModalProps({ - title: 'BED Files by Assay Type', - type: 'bar', - data: Object.entries(detailedStats?.file_assay || {}), - xlab: 'Assay Type', - ylab: 'Number of BED Files', - color: 3, - })} - > -
BED Files by Assay Type
- -
-
setMetricModalProps({ - title: 'BED Comments', - type: 'bar', - data: Object.entries(detailedStats?.bed_comments || {}), - xlab: 'Comment Type', - ylab: 'Number of BED Files', - color: 4, - })} - > -
BED Files by BED Comments
- -
-
setMetricModalProps({ - title: 'BED File Size Histogram', - type: 'hist', - data: transformHistogramData( - Array.isArray(detailedStats?.file_size?.bins) ? detailedStats.file_size.bins : [], - Array.isArray(detailedStats?.file_size?.counts) ? detailedStats.file_size.counts : [], - ), - median: detailedStats?.file_size?.median, - xlab: 'File Size (MB)', - ylab: 'Counts', - color: 6, - angle: false, - })} - > -
BED File Size Histogram
- -
- - - - -
setMetricModalProps({ - title: 'BED Files by Data Format', - type: 'pie', - data: Object.entries(detailedStats?.data_format || {}), - xlab: 'Data Format', - ylab: 'Number of BED Files', - color: 1, - })} - > -
BED Files by Data Format
- -
- -
setMetricModalProps({ - title: 'BED Files by Organism', - type: 'bar', - data: Object.entries(detailedStats?.file_organism || {}), - xlab: 'Organism', - ylab: 'Number of BED Files', - color: 3, - })} - > -
BED Files by Organism
- -
-
setMetricModalProps({ - title: 'BED GEO processing status', - type: 'bar', - data: Object.entries(detailedStats?.geo_status || {}), - xlab: 'BED GEO processing status', - ylab: 'Number of BED Files', - color: 5, - })} - > -
BED GEO processing status
- -
-
setMetricModalProps({ - title: 'BED Number of Regions Histogram', - type: 'hist', - data: transformHistogramData( - Array.isArray(detailedStats?.number_of_regions?.bins) ? detailedStats.number_of_regions.bins : [], - Array.isArray(detailedStats?.number_of_regions?.counts) ? detailedStats.number_of_regions.counts : [], - ), - median: detailedStats?.number_of_regions?.median, - xlab: 'Number of Regions', - ylab: 'Counts', - color: 7, - angle: false, - })} - > -
BED Number of Regions Histogram
- -
-
setMetricModalProps({ - title: 'BED Mean Region Width Histogram', - type: 'hist', - data: transformHistogramData( - Array.isArray(detailedStats?.mean_region_width?.bins) ? detailedStats.mean_region_width.bins : [], - Array.isArray(detailedStats?.mean_region_width?.counts) ? detailedStats.mean_region_width.counts : [], - ), - median: detailedStats?.mean_region_width?.median, - xlab: 'Mean Region Width', - ylab: 'Counts', - color: 8, - angle: false, - })} - > -
BED Mean Region Width Histogram
- -
- - - - Data Format and BED compliance are calculated based on BED classification pipeline. -
BED compliance refers to the representation of a BED file as `bedn+m`. -
Data Format is assignment of region set files to one of the formats: `bed`, `narrow_peak`, - `broadpeak - and others`. -
More information: BEDbase - Docs - - -
-

GEO statistics

- - - -
setMetricModalProps({ - title: 'Cumulative number of bed files in GEO', - type: 'bar', - data: Object.entries(detailedStats?.geo?.cumulative_number_of_files || {}), - xlab: 'Year', - ylab: 'Number of BED Files', - color: 4, - })} - > -
Cumulative number of bed files in GEO
- -
-
setMetricModalProps({ - title: 'BED file size in GEO', - type: 'hist', - data: transformHistogramData( - Array.isArray(detailedStats?.geo?.file_sizes?.bins) ? detailedStats?.geo?.file_sizes?.bins : [], - Array.isArray(detailedStats?.geo?.file_sizes?.counts) ? detailedStats?.geo?.file_sizes?.counts : [], - ), - // median: detailedStats?.geo?.file_sizes?.median, // median is too big - xlab: 'File Size (MB)', - ylab: 'Counts', - color: 8, - angle: false, - })} - > -
BED File size in GEO
- -
- - - - -
setMetricModalProps({ - title: 'Number of bed files in GEO', - type: 'bar', - data: Object.entries(detailedStats?.geo?.number_of_files || {}), - xlab: 'Year', - ylab: 'Number of BED Files', - color: 1, - })} - > -
Number of bed files in GEO
- -
- - - - Some small inconsistencies in GEO data may occur due to the way BEDbase is processing GEO data. - - - + + +
+
+
+ {metricsView === 'file' && ( + )} - {usageStats && ( - -
-

BEDbase Usage Statistics

- -
setMetricModalProps({ - title: 'BED Files Popularity', - type: 'bar', - data: Object.entries(usageStats?.bed_metadata || {}), - xlab: 'BED ID', - ylab: 'Times Accessed', - color: 3, - })} - > -
BED File Popularity
- -
-
setMetricModalProps({ - title: 'BED Search Terms', - type: 'bar', - data: Object.entries(usageStats?.bed_search_terms || {}), - xlab: 'BED Search Query', - ylab: 'Number of BED Files', - color: 8, - })} - > -
BED Search Terms
- -
-
setMetricModalProps({ - title: 'BED file downloads', - type: 'bar', - data: Object.entries(usageStats?.bed_downloads || {}), - xlab: 'BED file id', - ylab: 'Number of Downloads', - color: 2, - })} - > -
BED file downloads
- -
- - - -
setMetricModalProps({ - title: 'BEDset Popularity', - type: 'bar', - data: Object.entries(usageStats?.bedset_metadata || {}), - xlab: 'BEDset ID', - ylab: 'Number of BED Files', - color: 7, - })} - > -
BEDset Popularity
- -
- -
setMetricModalProps({ - title: 'BEDset Search Term', - type: 'bar', - data: Object.entries(usageStats?.bedset_search_terms || {}), - xlab: 'BEDset Search Query', - ylab: 'Number of BED Files', - color: 9, - })} - > -
BEDset Search Terms
- -
- - + {metricsView === 'geo' && ( + )} + {metricsView === 'usage' && } + {showMetricModal && ( { show={endpointsModalShow} onHide={() => setEndpointsModalShow(false)} /> - - +
); }; diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx index d2c2f49b..ba6db725 100644 --- a/ui/src/pages/search.tsx +++ b/ui/src/pages/search.tsx @@ -1,36 +1,128 @@ -import { Layout } from '../components/layout'; - -import { useState } from 'react'; -import { useSearchParams } from 'react-router-dom'; +import { useState, useEffect, useRef } from 'react'; +import { useSearchParams, useLocation } from 'react-router-dom'; import { SearchSelector } from '../components/search/search-selector'; +import { SearchBar } from '../components/search/search-bar.tsx'; import { Text2Bed } from '../components/search/text2bed/text2bed'; import { Bed2Bed } from '../components/search/bed2bed/bed2bed'; -import { Text2BedSet } from '../components/search/text2bedset'; - +import { Text2BedSet } from '../components/search/text2bedset/text2bedset.tsx'; +import { Layout } from '../components/layout'; import { SearchViewProvider } from '../contexts/search-view-context.tsx'; +import { useBedUmap } from '../queries/useBedUmap.ts'; +import { BEDEmbeddingPlotRef } from '../components/umap/bed-embedding-plot.tsx'; type SearchView = 't2b' | 'b2b' | 't2bs'; export const SearchPage = () => { - const [searchParams] = useSearchParams(); + const location = useLocation(); + const embeddingPlotRef = useRef(null); + const uploadedFile = location.state?.file as File | undefined; + + const [searchParams, setSearchParams] = useSearchParams(); const [searchView, setSearchView] = useState((searchParams.get('view') as SearchView) || 't2b'); + const [searchTerm, setSearchTerm] = useState(searchParams.get('q') || ''); + const [genome, setGenome] = useState(searchParams.get('genome') || ''); + const [assay, setAssay] = useState(searchParams.get('assay') || ''); + + const [t2bLayout, setT2bLayout] = useState('table'); + const [t2bOffset, setT2bOffset] = useState(0); + const [t2bLimit, setT2bLimit] = useState(20); + + const [b2bLayout, setB2bLayout] = useState('split'); + const [b2bOffset, setB2bOffset] = useState(0); + const [b2bLimit, setB2bLimit] = useState(20); + + const [t2bsOffset, setT2bsOffset] = useState(0); + const [t2bsLimit, setT2bsLimit] = useState(20); + + const [triggerSearch, setTriggerSearch] = useState(0); + const [file, setFile] = useState(uploadedFile || null); + const [customCoordinates, setCustomCoordinates] = useState(null); + + const { mutateAsync: getUmapCoordinates } = useBedUmap(); + + const handleSearch = () => { + setT2bOffset(0); + setTriggerSearch((prev) => prev + 1); + }; + + useEffect(() => { + const params = new URLSearchParams(); + if (searchView) params.set('view', searchView); + if (searchView !== 'b2b') { + if (searchTerm) params.set('q', searchTerm); + } + if (searchView === 't2b') { + if (genome) params.set('genome', genome); + if (assay) params.set('assay', assay); + } + setSearchParams(params); + }, [searchTerm, genome, assay, searchView, setSearchParams]); + + useEffect(() => { + if (!file) return; + (async () => { + const coordinates = await getUmapCoordinates(file); + setCustomCoordinates(coordinates); + })(); + }, [file]); return ( - + { setSearchView(view); }} + // setOffset={searchView === 't2b' ? setT2bOffset : searchView === 'b2b' ? setB2bOffset : setT2bsOffset} + /> + null} + onSearch={handleSearch} + file={file} + setFile={setFile} + embeddingPlotRef={embeddingPlotRef} /> {searchView === 't2b' ? ( - + ) : searchView === 'b2b' ? ( - + ) : searchView === 't2bs' ? ( - + ) : (
Unknown searchView selected.
)} diff --git a/ui/src/pages/visualization.tsx b/ui/src/pages/visualization.tsx deleted file mode 100644 index fa5434df..00000000 --- a/ui/src/pages/visualization.tsx +++ /dev/null @@ -1,177 +0,0 @@ -import React, { useRef, useState, useEffect } from 'react'; -import ForceGraph3D from 'react-force-graph-3d'; -// import graphData from './output.json'; -import { Link } from 'react-router-dom'; -import { useUmapEmbeddings } from '../queries/useUmapEmbeddings.ts'; -import { useNavigate, useLocation } from 'react-router-dom'; - -export interface GraphNode { - id: string; - name: string; - description: string; - cell_line: string; - assay?: string; - x: number; - y: number; - z: number; -} - -type ColorBy = 'cell_line' | 'assay'; - -export const UMAPGraph: React.FC = () => { - const { data: umap_data, isLoading, error } = useUmapEmbeddings(); - const fgRef = useRef(); - const [searchId, setSearchId] = useState(''); - const [message, setMessage] = useState(''); - const navigate = useNavigate(); - const location = useLocation(); - const [colorByOption, setColorByOption] = useState('cell_line'); - - - useEffect(() => { - const queryParams = new URLSearchParams(location.search); - const initialSearchId = queryParams.get('searchId'); - if (initialSearchId) { - setSearchId(initialSearchId); - const timer = setTimeout(() => { - handleSearch(); - }, 1000); // Give time for the graph to initialize - return () => clearTimeout(timer); - } - }, [location.search, umap_data]); - - const handleSearch = () => { - - if (!umap_data) return; - const node = graphDataWithoutLinks.nodes.find((n: GraphNode) => n.id === searchId); - - if (node && fgRef.current) { - fgRef.current.cameraPosition( - { x: node.x, y: node.y, z: node.z + 300 }, // zoom in 300 units away - node, - 2000, // animate over 2 seconds - ); - setMessage(`Found: ${node.id}`); - navigate(`?searchId=${node.id}`); - } else { - - fgRef.current.cameraPosition( - { x: 0, y: 0, z: 1000 }, // reset to default center position - { x: 0, y: 0, z: 0 }, // look at the center - 2000, // animate over 2 seconds - ); - if (!searchId) { - setMessage(''); - } else { - setMessage(`Node with ID ${searchId} not found.`); - } - // setMessage('BED file not found or search is empty.'); - navigate(`?searchId=${node.id}`); - } - }; - - if (isLoading) { - return
Loading data...
; - } - - if (error) { - return
Error loading data: {error.message}
; - } - - const graphDataWithoutLinks = { - nodes: umap_data.nodes.map((node: GraphNode) => ({ - ...node, - x: node.x, - y: node.y, - z: node.z, - })), - links: [], - }; - - return ( -
- -
-
-
- setColorByOption('cell_line')} - /> - - - setColorByOption('assay')} - /> - -
-
-
- setSearchId(e.target.value)} - onKeyDown={e => e.key === 'Enter' && handleSearch()} - className="form-control me-2" - /> - -
- -
- {message &&

{message}

} -
-
- - ( - `
${node.id}
cell_line: ${node.cell_line}
assay: ${node.assay}
${node.description}
` - )} - nodeAutoColorBy={colorByOption} - nodeRelSize={60} - enableNodeDrag={false} - onNodeClick={(node: GraphNode) => { - if (node.id) { - // const url = `https://bedbase.org/bed/${node.id}`; - // window.open(url, '_blank'); - // navigator.clipboard.writeText(url).catch(console.error); - setSearchId(node.id); - handleSearch(); - setMessage(`Clicked on: ${node.id} \n ${node.cell_line} <\n ${node.assay}`); - } - }} - /> -
- - BEDbase Logo - - -
-
- - ); -}; \ No newline at end of file diff --git a/ui/src/queries/useBed2BedSearchPaginate.ts b/ui/src/queries/useBed2BedSearchPaginate.ts new file mode 100644 index 00000000..4966bae4 --- /dev/null +++ b/ui/src/queries/useBed2BedSearchPaginate.ts @@ -0,0 +1,46 @@ +import { useQuery } from '@tanstack/react-query'; +import { useBedbaseApi } from '../contexts/api-context'; +import { components } from '../../bedbase-types'; + +type SearchResponse = components['schemas']['BedListSearchResult']; +type SearchQuery = { + q: File | null; + limit?: number; + offset?: number; + autoRun?: boolean; +}; + +export const useBed2BedSearchPaginate = (query: SearchQuery) => { + const { api } = useBedbaseApi(); + const { q, limit, offset, autoRun } = query; + let enabled = false; + if (autoRun !== undefined && autoRun === true && !!q) { + enabled = true; + } + + return useQuery({ + queryKey: ['search', q, limit, offset], + queryFn: async () => { + if (!q) { + return { + count: 0, + results: [], + }; + } + const formData = new FormData(); + formData.append('file', q); + const { data } = await api.post( + `/bed/search/bed?limit=${limit || 20}&offset=${offset || 0}`, + formData, + { + headers: { + 'Content-Type': 'multipart/form-data', + }, + }, + ); + return data; + }, + enabled: enabled, + staleTime: 0, + }); +}; diff --git a/ui/src/queries/useBedUmap.ts b/ui/src/queries/useBedUmap.ts new file mode 100644 index 00000000..6d9c8ed1 --- /dev/null +++ b/ui/src/queries/useBedUmap.ts @@ -0,0 +1,29 @@ +import { useMutation, useQueryClient } from '@tanstack/react-query'; +import { AxiosInstance } from 'axios'; +import { useBedbaseApi } from '../contexts/api-context'; + +type UmapResponse = number[]; + +const getBedUmap = async (file: File, axiosInstance: AxiosInstance) => { + const formData = new FormData(); + formData.append('file', file); + + const { data } = await axiosInstance.post('/bed/umap', formData, { + headers: { + 'Content-Type': 'multipart/form-data', + }, + }); + return data; +}; + +export const useBedUmap = () => { + const queryClient = useQueryClient(); + const { api } = useBedbaseApi(); + + return useMutation({ + mutationFn: (file: File) => getBedUmap(file, api), + onSuccess: () => { + queryClient.invalidateQueries({ queryKey: ['bed-umap'] }); + }, + }); +}; diff --git a/ui/src/queries/useDetailedStats.ts b/ui/src/queries/useDetailedStats.ts index eedb9349..68552864 100644 --- a/ui/src/queries/useDetailedStats.ts +++ b/ui/src/queries/useDetailedStats.ts @@ -1,16 +1,16 @@ -import {useQuery} from '@tanstack/react-query'; -import {components} from '../../bedbase-types'; -import {useBedbaseApi} from '../contexts/api-context'; +import { useQuery } from '@tanstack/react-query'; +import { components } from '../../bedbase-types'; +import { useBedbaseApi } from '../contexts/api-context'; type BEDBASEStatistics = components['schemas']['FileStats']; export const useDetailedStats = () => { - const {api} = useBedbaseApi(); - return useQuery({ - queryKey: ['detailed-stats'], - queryFn: async () => { - const {data} = await api.get('/detailed-stats?concise=true'); - return data; - }, - }); + const { api } = useBedbaseApi(); + return useQuery({ + queryKey: ['detailed-stats'], + queryFn: async () => { + const { data } = await api.get('/detailed-stats?concise=true'); + return data; + }, + }); }; diff --git a/ui/src/queries/useDetailedUsage.ts b/ui/src/queries/useDetailedUsage.ts index 7db8b83e..5c90d77e 100644 --- a/ui/src/queries/useDetailedUsage.ts +++ b/ui/src/queries/useDetailedUsage.ts @@ -1,16 +1,16 @@ -import {useQuery} from '@tanstack/react-query'; -import {components} from '../../bedbase-types'; -import {useBedbaseApi} from '../contexts/api-context'; +import { useQuery } from '@tanstack/react-query'; +import { components } from '../../bedbase-types'; +import { useBedbaseApi } from '../contexts/api-context'; type BEDBASEStatistics = components['schemas']['UsageStats']; export const useDetailedUsage = () => { - const {api} = useBedbaseApi(); - return useQuery({ - queryKey: ['detailed-usage'], - queryFn: async () => { - const {data} = await api.get('/detailed-usage'); - return data; - }, - }); + const { api } = useBedbaseApi(); + return useQuery({ + queryKey: ['detailed-usage'], + queryFn: async () => { + const { data } = await api.get('/detailed-usage'); + return data; + }, + }); }; diff --git a/ui/src/queries/useStats.ts b/ui/src/queries/useStats.ts index ec90b47b..02081947 100644 --- a/ui/src/queries/useStats.ts +++ b/ui/src/queries/useStats.ts @@ -1,16 +1,16 @@ -import {useQuery} from '@tanstack/react-query'; -import {components} from '../../bedbase-types'; -import {useBedbaseApi} from '../contexts/api-context'; +import { useQuery } from '@tanstack/react-query'; +import { components } from '../../bedbase-types'; +import { useBedbaseApi } from '../contexts/api-context'; type BEDBASEStatistics = components['schemas']['StatsReturn']; export const useStats = () => { - const {api} = useBedbaseApi(); - return useQuery({ - queryKey: ['stats'], - queryFn: async () => { - const {data} = await api.get('/stats'); - return data; - }, - }); + const { api } = useBedbaseApi(); + return useQuery({ + queryKey: ['stats'], + queryFn: async () => { + const { data } = await api.get('/stats'); + return data; + }, + }); }; diff --git a/ui/src/queries/useText2BedSearch.ts b/ui/src/queries/useText2BedSearch.ts index 229eb7e6..3547f114 100644 --- a/ui/src/queries/useText2BedSearch.ts +++ b/ui/src/queries/useText2BedSearch.ts @@ -13,7 +13,6 @@ type SearchQuery = { }; export const useText2BedSearch = (query: SearchQuery) => { - const { api } = useBedbaseApi(); const { q, limit, offset, autoRun, genome, assay } = query; @@ -21,15 +20,16 @@ export const useText2BedSearch = (query: SearchQuery) => { if (autoRun !== undefined && autoRun === true && !!q) { enabled = true; } - console.log(assay) return useQuery({ queryKey: ['search', q, limit, offset, genome, assay], queryFn: async () => { - const { data } = await api.get(`/bed/search/text?query=${q}&limit=${limit}&offset=${offset}&genome=${genome}&assay=${assay}`); + const { data } = await api.get( + `/bed/search/text?query=${q}&limit=${limit}&offset=${offset}&genome=${genome}&assay=${assay}`, + ); return data; }, enabled: enabled, staleTime: 0, - placeholderData: (previousData) => previousData, + // placeholderData: (previousData) => previousData, }); }; diff --git a/ui/src/queries/useUmapEmbeddings.ts b/ui/src/queries/useUmapEmbeddings.ts index 11ad0bbe..56525b0c 100644 --- a/ui/src/queries/useUmapEmbeddings.ts +++ b/ui/src/queries/useUmapEmbeddings.ts @@ -4,7 +4,6 @@ export const useUmapEmbeddings = () => { return useQuery({ queryKey: ['umapData'], queryFn: async () => { - const cachedDataString = localStorage.getItem('umapData'); if (cachedDataString) { try { @@ -14,7 +13,9 @@ export const useUmapEmbeddings = () => { } } - const response = await fetch('https://raw.githubusercontent.com/databio/bedbase-loader/refs/heads/master/umap/hg38_umap.json'); + const response = await fetch( + 'https://raw.githubusercontent.com/databio/bedbase-loader/refs/heads/master/umap/hg38_umap.json', + ); if (!response.ok) { throw new Error('Failed to fetch UMAP data'); } @@ -26,8 +27,7 @@ export const useUmapEmbeddings = () => { console.warn('Failed to cache UMAP data in localStorage:', e); } return data; - }, staleTime: 1000 * 60 * 60, }); -}; \ No newline at end of file +}; diff --git a/ui/src/utils.ts b/ui/src/utils.ts index 4cc01e5b..9745207f 100644 --- a/ui/src/utils.ts +++ b/ui/src/utils.ts @@ -1,3 +1,5 @@ +import * as pako from 'pako'; + type ObjectType = 'bed' | 'bedset'; export const makeHttpDownloadLink = (md5: string) => { @@ -29,7 +31,26 @@ export const makePDFImageLink = (md5: string, plotName: string, type: ObjectType }; export const formatDateTime = (date: string) => { - return new Date(date).toLocaleString(); + const d = new Date(date); + const day = String(d.getDate()).padStart(2, '0'); + const months = [ + 'January', + 'February', + 'March', + 'April', + 'May', + 'June', + 'July', + 'August', + 'Sepptember', + 'October', + 'November', + 'December', + ]; + const month = months[d.getMonth()]; + const year = d.getFullYear(); + const time = d.toLocaleTimeString('en-US', { hour: '2-digit', minute: '2-digit', second: '2-digit', hour12: true }); + return `${month} ${day}, ${year} at ${time}`; }; export const bytesToSize = (bytes: number) => { @@ -53,7 +74,6 @@ export const generateBEDsetPEPDownloadRaw = (md5List: string[]) => { return script; }; - export const generateCurlScriptForCartDownloadMd = (md5List: string[]) => { const wgetCommands = md5List.map((md5, index) => { const downloadLink = makeHttpDownloadLink(md5); @@ -118,6 +138,14 @@ export const snakeToTitleCase = (str: string) => { .join(' '); }; +export const toTitleCase = (str: string): string => { + return str + .toLowerCase() + .split(' ') + .map((word) => word.charAt(0).toUpperCase() + word.slice(1)) + .join(' '); +}; + export const convertStatusCodeToMessage = (statusCode: number | undefined) => { if (statusCode === undefined) { return 'Unknown Error'; @@ -135,3 +163,99 @@ export const convertStatusCodeToMessage = (statusCode: number | undefined) => { return 'Unknown Error'; } }; + +export const tableau20 = [ + '#1f77b4', + '#aec7e8', + '#ff7f0e', + '#ffbb78', + '#2ca02c', + '#98df8a', + '#d62728', + '#ff9896', + '#9467bd', + '#c5b0d5', + '#8c564b', + '#c49c94', + '#e377c2', + '#f7b6d3', + '#7f7f7f', + '#c7c7c7', + '#bcbd22', + '#dbdb8d', + '#17becf', + '#9edae5', +]; + +// Point-in-polygon test using ray casting algorithm +export const isPointInPolygon = (point: { x: number; y: number }, polygon: { x: number; y: number }[]) => { + let inside = false; + for (let i = 0, j = polygon.length - 1; i < polygon.length; j = i++) { + const xi = polygon[i].x, + yi = polygon[i].y; + const xj = polygon[j].x, + yj = polygon[j].y; + + const intersect = yi > point.y !== yj > point.y && point.x < ((xj - xi) * (point.y - yi)) / (yj - yi) + xi; + if (intersect) inside = !inside; + } + return inside; +}; +// gtars bedfile handler +export type BedEntry = [string, number, number, string]; + +export async function parseBedFile(file: File): Promise { + let text: string; + if (file.name.endsWith('.gz')) { + const arrayBuffer = await file.arrayBuffer(); + const decompressed = pako.ungzip(new Uint8Array(arrayBuffer), { to: 'string' }); + text = decompressed; + } else { + text = await file.text(); + } + const lines = text.split('\n'); + const bedEntries: BedEntry[] = []; + + // export async function parseBedFile(file: File): Promise { + // const text = await file.text(); + // const lines = text.split('\n'); + // const bedEntries: BedEntry[] = []; + + for (const line of lines) { + const trimmedLine = line.trim(); + + // skip! + if (!trimmedLine || trimmedLine.startsWith('#')) { + continue; + } + + const columns = trimmedLine.split('\t'); + + // check for at least 3 columns (chr, start, end) + if (columns.length >= 3) { + const chr = columns[0]; + const start = parseInt(columns[1], 10); + const end = parseInt(columns[2], 10); + const rest = columns.slice(3).join('\t'); // join remaining columns if any + + // Validate that start and end are valid numbers + if (!isNaN(start) && !isNaN(end)) { + bedEntries.push([chr, start, end, rest]); + } + } + } + + return bedEntries; +} + +// helper function to handle file input change event +export function handleBedFileInput(event: Event, callback: (entries: BedEntry[]) => void): void { + const input = event.target as HTMLInputElement; + const file = input.files?.[0]; + + if (file) { + parseBedFile(file) + .then(callback) + .catch((error) => console.error('Error parsing BED file:', error)); + } +} diff --git a/ui/vite.config.ts b/ui/vite.config.ts index 5a33944a..97a14d9a 100644 --- a/ui/vite.config.ts +++ b/ui/vite.config.ts @@ -1,7 +1,25 @@ -import { defineConfig } from 'vite' -import react from '@vitejs/plugin-react' +import { defineConfig } from 'vite'; +import react from '@vitejs/plugin-react'; +import topLevelAwait from 'vite-plugin-top-level-await'; +import wasm from 'vite-plugin-wasm'; // https://vitejs.dev/config/ export default defineConfig({ - plugins: [react()], -}) + plugins: [wasm(), topLevelAwait(), react()], + build: { + target: 'esnext', // Ensure ESNext target for WASM support + }, + server: { + fs: { + allow: ['..'], // Allow serving files from one level up to the project root + }, + proxy: { + '/api': { + target: 'https://api-dev.bedbase.org/v1', + changeOrigin: true, + rewrite: (path) => path.replace(/^\/api/, ''), + secure: false, + }, + }, + }, +});