updated service info

databio · Apr 11, 2024 · 6d34a4b · 6d34a4b
1 parent 5bc60f8
commit 6d34a4b
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Showing 5 changed files with 37 additions and 27 deletions.
diff --git a/bedhost/const.py b/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)

diff --git a/bedhost/data_models.py b/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
diff --git a/bedhost/main.py b/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(

diff --git a/bedhost/routers/base_api.py b/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,
+        },
     )
diff --git a/requirements/requirements-all.txt b/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