Release 0.12.0

.gitignore

@@ -38,3 +38,5 @@ ENV/
 env.bak/
 venv.bak/
 .DS_store
+
+ui/package-lock.json

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():

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)

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.

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:

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

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

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 }],
   },
-}
+};