nmdc-runtime 1.4.2__tar.gz → 1.5.0__tar.gz

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/.env.example

@@ -38,4 +38,6 @@ NEON_API_BASE_URL=https://data.neonscience.org/api/v0
 
 NERSC_USERNAME=replaceme
 ORCID_NMDC_CLIENT_ID=replaceme
-ORCID_NMDC_CLIENT_SECRET=replaceme
+ORCID_NMDC_CLIENT_SECRET=replaceme
+
+INFO_BANNER_INNERHTML='Announcement: Something important is about to happen. If you have questions, please contact <a href="mailto:support@microbiomedata.org">support@microbiomedata.org</a>.'

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmdc_runtime
-Version: 1.4.2
+Version: 1.5.0
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/nmdc_runtime/api/main.py

@@ -8,6 +8,7 @@ from typing import Annotated
 import fastapi
 import requests
 import uvicorn
+from bs4 import BeautifulSoup
 from fastapi import APIRouter, FastAPI, Cookie
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.openapi.docs import get_swagger_ui_html
@@ -483,10 +484,16 @@ def custom_swagger_ui_html(
         access_token = rv.json()["access_token"]
 
     swagger_ui_parameters = {"withCredentials": True}
+    onComplete = ""
     if access_token is not None:
+        onComplete += f"""ui.preauthorizeApiKey(<double-quote>bearerAuth</double-quote>, <double-quote>{access_token}</double-quote>); """
+    if os.getenv("INFO_BANNER_INNERHTML"):
+        info_banner_innerhtml = os.getenv("INFO_BANNER_INNERHTML")
+        onComplete += f"""banner = document.createElement(<double-quote>section</double-quote>); banner.classList.add(<double-quote>nmdc-info-banner</double-quote>); banner.classList.add(<double-quote>block</double-quote>); banner.classList.add(<double-quote>col-12</double-quote>); banner.innerHTML = `{info_banner_innerhtml.replace('"', '<double-quote>')}`; document.querySelector(<double-quote>.information-container</double-quote>).prepend(banner); """
+    if onComplete:
         swagger_ui_parameters.update(
             {
-                "onComplete": f"""<unquote-safe>() => {{ ui.preauthorizeApiKey(<double-quote>bearerAuth</double-quote>, <double-quote>{access_token}</double-quote>) }}</unquote-safe>""",
+                "onComplete": f"""<unquote-safe>() => {{ {onComplete} }}</unquote-safe>""",
             }
         )
     response = get_swagger_ui_html(
@@ -504,6 +511,10 @@ def custom_swagger_ui_html(
         .replace('</unquote-safe>"', "")
         .replace("<double-quote>", '"')
         .replace("</double-quote>", '"')
+        .replace(
+            "</head>",
+            "<style>.nmdc-info-banner { padding: 1em; background-color: #448aff1a; border: .075rem solid #448aff; }</style></head>",
+        )
     )
     return HTMLResponse(content=content)
 

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/nmdc_runtime.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmdc_runtime
-Version: 1.4.2
+Version: 1.5.0
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/nmdc_runtime.egg-info/SOURCES.txt

@@ -409,7 +409,6 @@ nmdc_runtime/lib/transform_nmdc_data.py
 nmdc_runtime/minter/__init__.py
 nmdc_runtime/minter/bootstrap.py
 nmdc_runtime/minter/config.py
-nmdc_runtime/minter/nmdc.schema.json
 nmdc_runtime/minter/adapters/__init__.py
 nmdc_runtime/minter/adapters/repository.py
 nmdc_runtime/minter/domain/__init__.py

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/requirements/main.in

@@ -24,7 +24,7 @@ mkdocs-jupyter
 mkdocs-material
 mkdocs-mermaid2-plugin
 motor
-nmdc-schema==10.1.4
+nmdc-schema==10.2.0
 openpyxl
 pandas
 passlib[bcrypt]

{nmdc_runtime-1.4.2 → nmdc_runtime-1.5.0}/requirements/main.txt

@@ -62,6 +62,8 @@ beautifulsoup4==4.12.3
     #   -r requirements/main.in
     #   mkdocs-mermaid2-plugin
     #   nbconvert
+bioregistry==0.10.158
+    # via nmdc-schema
 black==24.2.0
     # via shed
 bleach==6.1.0
@@ -95,6 +97,7 @@ click==8.1.7
     # via
     #   -r requirements/main.in
     #   beanie
+    #   bioregistry
     #   black
     #   dagster
     #   dagster-webserver
@@ -102,7 +105,9 @@ click==8.1.7
     #   linkml
     #   linkml-runtime
     #   mkdocs
+    #   more-click
     #   prefixcommons
+    #   pystow
     #   terminusdb-client
     #   uvicorn
 colorama==0.4.6
@@ -121,6 +126,7 @@ cryptography==42.0.5
     # via python-jose
 curies==0.7.7
     # via
+    #   bioregistry
     #   linkml-runtime
     #   prefixmaps
 dagit==1.6.8
@@ -435,6 +441,8 @@ mkdocs-mermaid2-plugin==0.6.0
     #   nmdc-schema
 mkdocs-redirects==1.2.1
     # via nmdc-schema
+more-click==0.1.2
+    # via bioregistry
 motor==3.3.2
     # via
     #   -r requirements/main.in
@@ -460,7 +468,7 @@ nbformat==5.9.2
     #   nbconvert
 nest-asyncio==1.6.0
     # via ipykernel
-nmdc-schema==10.1.4
+nmdc-schema==10.2.0
     # via -r requirements/main.in
 notebook==7.1.1
     # via jupyter
@@ -566,6 +574,7 @@ pydantic==2.6.3
     # via
     #   -r requirements/main.in
     #   beanie
+    #   bioregistry
     #   curies
     #   dagster
     #   fastapi
@@ -608,6 +617,8 @@ pyshexc==0.9.1
     # via
     #   linkml
     #   pyshex
+pystow==0.5.4
+    # via bioregistry
 pytest==8.0.2
     # via pytest-logging
 pytest-logging==2015.11.4
@@ -700,6 +711,7 @@ regex==2023.12.25
 requests==2.31.0
     # via
     #   -r requirements/main.in
+    #   bioregistry
     #   curies
     #   dagster
     #   dagster-graphql
@@ -711,6 +723,7 @@ requests==2.31.0
     #   mkdocs-mermaid2-plugin
     #   prefixcommons
     #   pyshex
+    #   pystow
     #   requests-cache
     #   requests-toolbelt
     #   sphinx
@@ -857,7 +870,9 @@ tornado==6.4
 tqdm==4.66.2
     # via
     #   -r requirements/main.in
+    #   bioregistry
     #   dagster
+    #   pystow
     #   terminusdb-client
 traitlets==5.14.1
     # via