Merge pull request #149 from databio/dev

Release 0.8.0

bedhost/__init__.py

@@ -1,5 +1,7 @@
-import logmuse
 import logging
+
+import logmuse
+
 from .const import PKG_NAME
 
 _LOGGER = logmuse.init_logger(PKG_NAME)

bedhost/_version.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.8.0"

bedhost/cli.py

@@ -1,6 +1,7 @@
+from ubiquerg import VersionInHelpParser
+
 from . import PKG_NAME
 from ._version import __version__
-from ubiquerg import VersionInHelpParser
 
 
 def build_parser():

bedhost/data_models.py

@@ -1,6 +1,7 @@
+from enum import Enum
+
 from fastapi import Path
 from pydantic import BaseModel
-from enum import Enum
 
 RemoteClassEnum = Enum(
     "RemoteClassEnum",
@@ -69,3 +70,10 @@ class ServiceInfoResponse(BaseModel):
     version: str
     component_versions: ComponentVersions
     embedding_models: EmbeddingModels
+
+
+class BaseListResponse(BaseModel):
+    count: int
+    limit: int
+    offset: int
+    results: list

bedhost/helpers.py

@@ -1,7 +1,7 @@
-from starlette.responses import FileResponse, RedirectResponse, JSONResponse
+import os
 
 from bbconf.bbagent import BedBaseAgent
-import os
+from starlette.responses import FileResponse, JSONResponse, RedirectResponse
 
 from . import _LOGGER
 from .exceptions import BedHostException
@@ -50,7 +50,7 @@ def attach_routers(app):
     _LOGGER.info("Mounting routers...")
 
     # importing routers here avoids circular imports
-    from .routers import bed_api, bedset_api, objects_api, base_api
+    from .routers import base_api, bed_api, bedset_api, objects_api
 
     app.include_router(base_api.router)
     app.include_router(bed_api.router)

bedhost/main.py

@@ -1,34 +1,24 @@
 import os
 import sys
-import uvicorn
-
-from fastapi import FastAPI, Request
-from fastapi.middleware.cors import CORSMiddleware
-from fastapi.responses import HTMLResponse, RedirectResponse
 
 import markdown
-from fastapi.templating import Jinja2Templates
+import uvicorn
 from bbconf.exceptions import (
-    MissingObjectError,
-    MissingThumbnailError,
     BEDFileNotFoundError,
     BedSetNotFoundError,
+    MissingObjectError,
+    MissingThumbnailError,
 )
-
+from fastapi import FastAPI, Request
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import HTMLResponse, RedirectResponse
+from fastapi.templating import Jinja2Templates
 
 from . import _LOGGER
-from .helpers import (
-    configure,
-    attach_routers,
-    drs_response,
-)
-from .cli import build_parser
 from ._version import __version__ as bedhost_version
-from .const import (
-    PKG_NAME,
-    STATIC_PATH,
-)
-
+from .cli import build_parser
+from .const import PKG_NAME, STATIC_PATH
+from .helpers import attach_routers, configure, drs_response
 
 tags_metadata = [
     {

bedhost/routers/base_api.py

@@ -1,26 +1,27 @@
 try:
-    from typing import Annotated, Dict, Optional, List, Any
+    from typing import Annotated, Any, Dict, List, Optional
 except ImportError:
     from typing_extensions import Annotated
     from typing import Dict, Optional, List, Any
 
-from fastapi import APIRouter
-
-from bbconf.models.base_models import StatsReturn
 from platform import python_version
+
 from bbconf import __version__ as bbconf_version
+from bbconf.models.base_models import StatsReturn
+from fastapi import APIRouter
 from geniml import __version__ as geniml_version
 
-from ..main import bbagent, app
-from ..helpers import get_openapi_version
+from .._version import __version__ as bedhost_version
 from ..data_models import (
-    ServiceInfoResponse,
-    Type,
-    Organization,
+    BaseListResponse,
     ComponentVersions,
     EmbeddingModels,
+    Organization,
+    ServiceInfoResponse,
+    Type,
 )
-from .._version import __version__ as bedhost_version
+from ..helpers import get_openapi_version
+from ..main import app, bbagent
 
 router = APIRouter(prefix="/v1", tags=["base"])
 
@@ -39,6 +40,24 @@ async def get_bedbase_db_stats():
     return bbagent.get_stats()
 
 
+@router.get(
+    "/genomes",
+    summary="Get available genomes",
+    response_model=BaseListResponse,
+)
+async def get_bedbase_db_stats():
+    """
+    Returns statistics
+    """
+    genomes = bbagent.get_list_genomes()
+    return BaseListResponse(
+        count=len(genomes),
+        limit=100,
+        offset=0,
+        results=genomes,
+    )
+
+
 @router.get(
     "/service-info", summary="GA4GH service info", response_model=ServiceInfoResponse
 )

bedhost/routers/bed_api.py

@@ -1,43 +1,41 @@
 import subprocess
 
 try:
-    from typing import Annotated, Dict, Optional, List, Any
+    from typing import Annotated, Any, Dict, List, Optional
 except ImportError:
     from typing_extensions import Annotated
     from typing import Dict, Optional, List, Any
 
-from fastapi import APIRouter, HTTPException, Query, UploadFile, File
-from fastapi.responses import PlainTextResponse
-
-from gtars.tokenizers import RegionSet
-
-import tempfile
 import os
 import shutil
+import tempfile
 
+from bbconf.exceptions import (
+    BedBaseConfError,
+    BEDFileNotFoundError,
+    TokenizeFileNotExistError,
+)
 from bbconf.models.bed_models import (
+    BedClassification,  # BedPEPHub,
+    BedEmbeddingResult,
+    BedFiles,
     BedListResult,
+    BedListSearchResult,
     BedMetadataAll,
-    BedFiles,
-    BedStatsModel,
-    BedPlots,
-    BedClassification,
-    # BedPEPHub,
     BedPEPHubRestrict,
-    BedListSearchResult,
-    TokenizedPathResponse,
+    BedPlots,
+    BedStatsModel,
     TokenizedBedResponse,
-    BedEmbeddingResult,
+    TokenizedPathResponse,
 )
-from bbconf.exceptions import BEDFileNotFoundError, TokenizeFileNotExistError
+from fastapi import APIRouter, File, HTTPException, Query, UploadFile
+from fastapi.responses import PlainTextResponse
+from gtars.tokenizers import RegionSet
 
 from .. import _LOGGER
-from ..main import bbagent
-from ..data_models import (
-    BedDigest,
-    CROM_NUMBERS,
-)
 from ..const import EXAMPLE_BED
+from ..data_models import CROM_NUMBERS, BaseListResponse, BedDigest
+from ..main import bbagent
 
 router = APIRouter(prefix="/v1/bed", tags=["bed"])
 
@@ -52,7 +50,7 @@ async def get_example_bed_record():
     """
     Get metadata for an example BED record.
     """
-    result = bbagent.bed.get_ids_list(limit=1, offset=0).results
+    result = bbagent.bed.get_ids_list(limit=1, offset=0, genome="hg38").results
     if result:
         return result[0]
     raise HTTPException(status_code=404, detail="No records found")
@@ -238,6 +236,33 @@ async def embed_bed_file(
     return embedding.tolist()[0]
 
 
+@router.get(
+    "/missing_plots",
+    summary="Get missing plots for a bed file.",
+    response_model=BaseListResponse,
+)
+async def missing_plots(plot_id: str):
+    """
+    Get missing plots for a bed file
+
+    example ->  plot_id: gccontent
+    """
+
+    try:
+        bed_ids = bbagent.bed.get_missing_plots(plot_id, limit=100000, offset=0)
+    except BedBaseConfError as e:
+        raise HTTPException(
+            status_code=404,
+            detail=f"{e}",
+        )
+    return BaseListResponse(
+        count=len(bed_ids),
+        limit=100000,
+        offset=0,
+        results=bed_ids,
+    )
+
+
 @router.get(
     "/{bed_id}/regions/{chr_num}",
     summary="Get regions from a BED file that overlap a query region.",

bedhost/routers/bedset_api.py

@@ -1,20 +1,19 @@
-from fastapi import APIRouter, HTTPException, Request, Response
 import logging
 
+from bbconf.exceptions import BedSetNotFoundError
 from bbconf.models.bedset_models import (
-    BedSetMetadata,
-    BedSetListResult,
     BedSetBedFiles,
+    BedSetListResult,
+    BedSetMetadata,
     BedSetPlots,
     BedSetStats,
 )
-from bbconf.exceptions import BedSetNotFoundError
+from fastapi import APIRouter, HTTPException, Request, Response
 
+from ..const import EXAMPLE_BEDSET, PKG_NAME
 from ..main import bbagent
-from ..const import PKG_NAME, EXAMPLE_BEDSET
 from ..utils import zip_pep
 
-
 router = APIRouter(prefix="/v1/bedset", tags=["bedset"])
 
 _LOGGER = logging.getLogger(PKG_NAME)

bedhost/routers/objects_api.py

@@ -1,17 +1,16 @@
 try:
-    from typing import Annotated, Dict, Optional, List, Any
+    from typing import Annotated, Any, Dict, List, Optional
 except ImportError:
     from typing_extensions import Annotated
     from typing import Dict, Optional, List, Any
 
-from fastapi import APIRouter, HTTPException, Request
+from urllib.parse import urlparse
+
 from bbconf.models.drs_models import DRSModel
+from fastapi import APIRouter, HTTPException, Request
 
+from ..helpers import serve_file
 from ..main import bbagent
-from ..helpers import (
-    serve_file,
-)
-from urllib.parse import urlparse
 
 router = APIRouter(prefix="/v1/objects", tags=["objects"])
 

deployment/config/api-dev.bedbase.org.yaml

@@ -14,7 +14,7 @@ qdrant:
   host: $QDRANT_HOST
   port: 6333
   api_key: $QDRANT_API_KEY
-  file_collection: bedbase2
+  file_collection: bedbase
   text_collection: bed_text
 server:
   host: 0.0.0.0

deployment/config/api.bedbase.org.yaml

@@ -14,7 +14,7 @@ qdrant:
   host: $QDRANT_HOST
   port: 6333
   api_key: $QDRANT_API_KEY
-  file_collection: bedbase2
+  file_collection: bedbase
   text_collection: bed_text
 server:
   host: 0.0.0.0

requirements/requirements-all.txt

@@ -1,5 +1,5 @@
-#bbconf @ git+https://github.com/databio/bbconf.git@dev#egg=bbconf
-bbconf>=0.8.0
+# bbconf @ git+https://github.com/databio/bbconf.git@dev#egg=bbconf
+bbconf>=0.9.0
 fastapi>=0.103.0
 logmuse>=0.2.7
 markdown

tests/test_fastapi/test_api.py

@@ -1,6 +1,7 @@
-from fastapi.testclient import TestClient
 import os
+
 import pytest
+from fastapi.testclient import TestClient
 
 # os.environ.setdefault("BEDBASE_CONFIG", os.path.abspath("test_config.yaml"))
 # from bedhost.main import app

ui/bedbase-types.d.ts

@@ -1182,7 +1182,7 @@ export interface components {
              * @description Name of species. e.g. Homo sapiens.
              * @default
              */
-            organism: string;
+            species_name: string;
             /**
              * Species Id
              * @default
@@ -1234,7 +1234,7 @@ export interface components {
              * @description Experimental protocol (e.g. ChIP-seq)
              * @default
              */
-            exp_protocol: string;
+            assay: string;
             /**
              * Antibody
              * @description Antibody used in the assay