Merge pull request #107 from databio/dev

Release 0.4.1

.gitignore

@@ -27,4 +27,14 @@ geniml
 
 local_cache
 
-environment/
+environment/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.DS_store

README.md

@@ -8,13 +8,18 @@
 It needs a path to the *bedbase configuration file*, which can be provided either via `-c`/`--config` argument or read from `$BEDBASE_CONFIG` environment variable. 
 
 ---
-dfgeaf
 **Deployed public instance**: <a href="https://bedbase.org/" target="_blank">https://bedbase.org/</a>
 
 **Documentation**: <a href="https://docs.bedbase.org/" target="_blank">https://docs.bedbase.org/bedhost</a>
 
 **API**: <a href="https://api.bedbase.org/" target="_blank">https://api.bedbase.org/</a>
 
+**DEV API**: <a href="https://dev.bedbase.org/" target="_blank">https://api-dev.bedbase.org/</a>
+
+**UI**: <a href="https://bedbase.org/" target="_blank">https://bedbase.org/</a>
+
+**DEV UI**: <a href="https://dev.bedhost.pages.dev/" target="_blank">https://dev.bedhost.pages.dev/</a>
+
 **Source Code**: <a href="https://github.com/databio/bedhost/" target="_blank">https://github.com/databio/bedhost/</a>
 
 ---

bedhost/_version.py

@@ -1 +1 @@
-__version__ = "0.4.0"
+__version__ = "0.4.1"

bedhost/const.py

@@ -1,17 +1,7 @@
 import os
-from platform import python_version
-from bbconf import __version__ as bbconf_v
-
-from ._version import __version__ as SERVER_VERSION
 
 PKG_NAME = "bedhost"
 
-# for now bedstat version is hard coded
-ALL_VERSIONS = {
-    "bedhost_version": SERVER_VERSION,
-    "bbconf_version": bbconf_v,
-    "python_version": python_version(),
-}
 TEMPLATES_DIRNAME = "templates"
 STATIC_DIRNAME = "../docs"
 STATIC_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), STATIC_DIRNAME)

bedhost/data_models.py

@@ -47,9 +47,16 @@ class ComponentVersions(BaseModel):
     bedhost_version: str
     bbconf_version: str
     python_version: str
+    geniml_version: str
     openapi_version: str
 
 
+class EmbeddingModels(BaseModel):
+    vec2vec: str
+    region2vec: str
+    text2vec: str
+
+
 class ServiceInfoResponse(BaseModel):
     id: str
     name: str
@@ -62,3 +69,4 @@ class ServiceInfoResponse(BaseModel):
     environment: str
     version: str
     component_versions: ComponentVersions
+    embedding_models: EmbeddingModels

bedhost/main.py

@@ -4,14 +4,13 @@
 
 from fastapi import FastAPI, Request
 from fastapi.middleware.cors import CORSMiddleware
-from fastapi.responses import JSONResponse, HTMLResponse
+from fastapi.responses import HTMLResponse
 
 import markdown
 from fastapi.templating import Jinja2Templates
 from bbconf.exceptions import (
     MissingObjectError,
     MissingThumbnailError,
-    BadAccessMethodError,
     BEDFileNotFoundError,
     BedSetNotFoundError,
 )
@@ -24,11 +23,10 @@
     drs_response,
 )
 from .cli import build_parser
+from ._version import __version__ as bedhost_version
 from .const import (
-    ALL_VERSIONS,
     PKG_NAME,
     STATIC_PATH,
-    SERVER_VERSION,
 )
 
 
@@ -62,7 +60,7 @@
 app = FastAPI(
     title=PKG_NAME,
     description="BED file/sets statistics and image server API",
-    version=SERVER_VERSION,
+    version=bedhost_version,
     docs_url="/docs",
     openapi_tags=tags_metadata,
 )
@@ -72,7 +70,7 @@
     "http://localhost:8000",
     "http://localhost:5173",
     "https://bedbase.org",
-    "*",  # allow cross origin resource sharing, since this is a public API
+    "*",  # allow cross-origin resource sharing, since this is a public API
 ]
 
 app.add_middleware(

bedhost/routers/base_api.py

@@ -7,16 +7,21 @@
 from fastapi import APIRouter
 
 from bbconf.models.base_models import StatsReturn
-
+from platform import python_version
+from bbconf import __version__ as bbconf_version
+from geniml import __version__ as geniml_version
 
 from ..main import bbagent, app
-from ..const import ALL_VERSIONS
 from ..helpers import get_openapi_version
 from ..data_models import ServiceInfoResponse
+from .._version import __version__ as bedhost_version
 
 router = APIRouter(prefix="/v1", tags=["base"])
 
 
+packages_versions = {}
+
+
 @router.get(
     "/stats",
     summary="Get summary statistics for the DRS object store",
@@ -36,24 +41,33 @@ async def service_info():
     """
     Returns information about this service, such as versions, name, etc.
     """
-    all_versions = ALL_VERSIONS
-    service_version = all_versions["bedhost_version"]
-    all_versions.update({"openapi_version": get_openapi_version(app)})
+    all_versions = {
+        "bedhost_version": bedhost_version,
+        "bbconf_version": bbconf_version,
+        "geniml_version": geniml_version,
+        "python_version": python_version(),
+        "openapi_version": get_openapi_version(app),
+    }
 
     return ServiceInfoResponse(
         id="org.bedbase.api",
         name="BEDbase API",
         type={
             "group": "org.databio",
             "artifact": "bedbase",
-            "version": service_version,
+            "version": bedhost_version,
         },
         description="An API providing genomic interval data and metadata",
         organization={"name": "Databio Lab", "url": "https://databio.org"},
         contactUrl="https://github.com/databio/bedbase/issues",
-        documentationUrl="https://bedbase.org",
+        documentationUrl="https://docs.bedbase.org",
         updatedAt="2023-10-25T00:00:00Z",
-        environment="dev",
-        version=service_version,
+        environment="main",
+        version=bedhost_version,
         component_versions=all_versions,
+        embedding_models={
+            "vec2vec": bbagent.config.config.path.vec2vec,
+            "region2vec": bbagent.config.config.path.region2vec,
+            "text2vec": bbagent.config.config.path.text2vec,
+        },
     )

bedhost/routers/bed_api.py

@@ -271,10 +271,10 @@ async def text_to_bed_search(query, limit: int = 10, offset: int = 0):
     tags=["search"],
     response_model=BedListSearchResult,
 )
-async def text_to_bed_search(
+async def bed_to_bed_search(
     file: UploadFile = File(None), limit: int = 10, offset: int = 0
 ):
-    _LOGGER.info(f"Searching for bedfiles...")
+    _LOGGER.info("Searching for bedfiles...")
 
     if file is not None:
         with tempfile.TemporaryDirectory() as dirpath:

bedhost/routers/bedset_api.py

@@ -101,13 +101,8 @@ async def get_bedset_metadata(
 )
 async def get_bedfiles_in_bedset(
     bedset_id: str,
-    limit: int = 100,
-    offset: int = 0,
-    full: bool = False,
 ):
-    return bbagent.bedset.get_bedset_bedfiles(
-        bedset_id, limit=limit, offset=offset, full=full
-    )
+    return bbagent.bedset.get_bedset_bedfiles(bedset_id)
 
 
 # TODO: how are we using it?

requirements/requirements-all.txt

@@ -1,12 +1,12 @@
 # bbconf @ git+https://github.com/databio/bbconf.git@dev#egg=bbconf
-bbconf>=0.5.0
+bbconf>=0.5.1
 fastapi>=0.103.0
 logmuse>=0.2.7
 markdown
 requests
 setuptools
 uvicorn
 yacman>=0.9.2
-pephubclient>=0.4.0
+pephubclient>=0.4.1
 psycopg[binary,pool]
 python-multipart>=0.0.9

ui/.env

@@ -1,2 +1,2 @@
 # VITE_API_BASE=http://localhost:8000/v1
-VITE_API_BASE=https://api.bedbase.org/v1
+# VITE_API_BASE=https://api-dev.bedbase.org/v1

ui/index.html

@@ -1,10 +1,10 @@
-<!doctype html>
+<!DOCTYPE html>
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
     <link rel="icon" type="image/svg+xml" href="/vite.svg" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Vite + React + TS</title>
+    <title>BEDbase.org</title>
   </head>
   <body>
     <div id="root"></div>