Sampleform

database/tables.sql

@@ -224,7 +224,8 @@ CREATE TABLE xas_standard_data (
 COMMENT ON TABLE xas_standard_data IS 'Data file storing the standard data';
 
 CREATE TYPE review_status_enum AS ENUM('pending', 'approved', 'rejected');
-CREATE TYPE licence_enum AS ENUM('cc_by', 'cc_0', 'logged_in_only');
+CREATE TYPE licence_enum AS ENUM('cc_by', 'cc_0');
+CREATE TYPE sample_form_enum AS ENUM('other', 'foil', 'pellet');
 
 CREATE Table xas_standard (
     id INTEGER PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
@@ -241,6 +242,7 @@ CREATE Table xas_standard (
     sample_name TEXT,
     sample_prep TEXT,
     sample_comp TEXT,
+    sample_form sample_form_enum,
     beamline_id INTEGER,
     mono_name TEXT,
     mono_dspacing TEXT,

xas-standards-api/Dockerfile

@@ -1,25 +1,15 @@
-# This file is for use as a devcontainer and a runtime container
-#
-# The devcontainer should use the build target and run as root with podman
-# or docker with user namespaces.
-#
+#build api
+#copy to runtime
 FROM python:3.11 as build
 
 ARG PIP_OPTIONS=.
 
-# Add any system dependencies for the developer/build environment here e.g.
-# RUN apt-get update && apt-get upgrade -y && \
-#     apt-get install -y --no-install-recommends \
-#     desired-packages \
-#     && rm -rf /var/lib/apt/lists/*
-
 # set up a virtual environment and put it in PATH
 RUN python -m venv /venv
 ENV PATH=/venv/bin:$PATH
 
-# Copy any required context for the pip install over
-COPY . /context
-WORKDIR /context
+WORKDIR /api
+COPY . .
 
 # install python package into /venv
 RUN pip install ${PIP_OPTIONS}
@@ -32,6 +22,9 @@ FROM python:3.11-slim as runtime
 COPY --from=build /venv/ /venv/
 ENV PATH=/venv/bin:$PATH
 
+RUN apt-get update && apt-get install libpq5 -y
+
+EXPOSE 5000
+
 # change this entrypoint if it is not the same as the repo
 ENTRYPOINT ["xas-standards-api"]
-CMD ["--version"]

xas-standards-api/src/xas_standards_api/app.py

@@ -1,39 +1,12 @@
-import os
-
-from fastapi import (
-    FastAPI,
-)
-from fastapi.staticfiles import StaticFiles
+from fastapi import FastAPI
 from fastapi_pagination import add_pagination
-from starlette.responses import RedirectResponse
 
 from .routers import admin, open, protected
 
-dev = False
-
-env_value = os.environ.get("FASTAPI_APP_ENV")
-
-if env_value and env_value == "development":
-    print("RUNNING IN DEV MODE")
-    dev = True
-
-
-build_dir = os.environ.get("FRONTEND_BUILD_DIR")
-
 app = FastAPI()
 
 app.include_router(open.router)
 app.include_router(protected.router)
 app.include_router(admin.router)
 
 add_pagination(app)
-
-
-@app.get("/login", response_class=RedirectResponse)
-async def redirect_home():
-    # proxy handles log in so if you reach here go home
-    return "/"
-
-
-if build_dir:
-    app.mount("/", StaticFiles(directory="/client/dist", html=True), name="site")

xas-standards-api/src/xas_standards_api/crud.py

@@ -17,6 +17,7 @@
     Person,
     PersonInput,
     ReviewStatus,
+    SampleForm,
     XASStandard,
     XASStandardAdminReviewInput,
     XASStandardData,
@@ -82,6 +83,7 @@ def get_metadata(session):
     output["edges"] = select_all(session, Edge)
     output["beamlines"] = select_all(session, Beamline)
     output["licences"] = list(LicenceType)
+    output["sample_forms"] = list(SampleForm)
 
     return output
 
@@ -260,3 +262,13 @@ def is_admin_user(session: Session, user_id: str):
         raise HTTPException(status_code=401, detail=f"User {user_id} not admin")
 
     return True
+
+
+def get_registered_elements(session: Session):
+    statement = (
+        select(Element)
+        .where(XASStandard.element_z == Element.z)
+        .where(XASStandard.review_status == ReviewStatus.approved)
+    )
+    results = session.exec(statement)
+    return results.unique().all()

xas-standards-api/src/xas_standards_api/models/models.py

@@ -14,7 +14,12 @@ class ReviewStatus(enum.Enum):
 class LicenceType(enum.Enum):
     cc_by = "cc_by"
     cc_0 = "cc_0"
-    logged_in_only = "logged_in_only"
+
+
+class SampleForm(enum.Enum):
+    other = "other"
+    foil = "foil"
+    pellet = "pellet"
 
 
 class PersonInput(SQLModel):
@@ -102,6 +107,7 @@ class XASStandardInput(SQLModel):
     sample_name: str
     sample_prep: Optional[str]
     sample_comp: Optional[str]
+    sample_form: SampleForm = Field(sa_column=Column(Enum(SampleForm)))
     beamline_id: int = Field(foreign_key="beamline.id")
     licence: LicenceType = Field(sa_column=Column(Enum(LicenceType)))
 

xas-standards-api/src/xas_standards_api/models/response_models.py

@@ -36,3 +36,4 @@ class MetadataResponse(SQLModel):
     elements: List[Element]
     edges: List[Edge]
     licences: List[str]
+    sample_forms: List[str]

xas-standards-api/src/xas_standards_api/routers/open.py

@@ -4,7 +4,14 @@
 from fastapi_pagination.cursor import CursorPage
 from sqlmodel import Session
 
-from ..crud import get_data, get_file, get_metadata, get_standard, read_standards_page
+from ..crud import (
+    get_data,
+    get_file,
+    get_metadata,
+    get_registered_elements,
+    get_standard,
+    read_standards_page,
+)
 from ..database import get_session
 from ..models.models import ReviewStatus
 from ..models.response_models import (
@@ -48,3 +55,8 @@ async def read_data(
         return get_file(session, id)
 
     return get_data(session, id)
+
+
+@router.get("/api/elements/metrics")
+async def read_elements(session: Session = Depends(get_session)):
+    return get_registered_elements(session)

xas-standards-api/src/xas_standards_api/routers/protected.py

@@ -38,6 +38,7 @@ def add_standard_file(
     beamline_id: Annotated[int, Form()],
     sample_name: Annotated[str, Form()],
     sample_prep: Annotated[str, Form()],
+    sample_form: Annotated[str, Form()],
     doi: Annotated[str, Form()],
     citation: Annotated[str, Form()],
     comments: Annotated[str, Form()],
@@ -62,6 +63,7 @@ def add_standard_file(
         edge_id=edge_id,
         sample_name=sample_name,
         sample_prep=sample_prep,
+        sample_form=sample_form,
         submitter_comments=comments,
         citation=citation,
         licence=licence,

xas-standards-api/tests/test_protected_router.py

@@ -69,6 +69,7 @@ def get_admin_user():
             "beamline_id": 1,
             "sample_name": unique_sample_name,
             "sample_prep": "test",
+            "sample_form": "foil",
             "doi": "doi",
             "citation": "citation",
             "comments": "comments",

xas-standards-api/tests/utils.py

@@ -86,6 +86,7 @@ def build_test_database(session: Session):
             sample_name="sample",
             sample_prep="pellet",
             sample_comp="H",
+            sample_form="foil",
             beamline_id=1,
             licence=LicenceType.cc_0,
             id=1,
@@ -108,6 +109,7 @@ def build_test_database(session: Session):
             sample_name="sample",
             sample_prep="pellet",
             sample_comp="He",
+            sample_form="pellet",
             beamline_id=1,
             licence=LicenceType.cc_0,
             id=2,

xas-standards-client/Dockerfile

@@ -0,0 +1,25 @@
+#build client
+#build api
+#copy to runtime
+
+FROM node:18-bullseye-slim as build-web
+
+WORKDIR /client
+
+RUN yes | npm install -g pnpm
+
+RUN apt update 
+
+COPY . .
+
+RUN yes | pnpm install
+
+RUN pnpm vite build
+
+From nginx as host
+
+COPY --from=build-web /client/dist/ /usr/share/nginx/html
+COPY ./nginx/default.conf /etc/nginx/conf.d/default.conf
+
+# change this entrypoint if it is not the same as the repo
+ENTRYPOINT ["nginx","-g", "daemon off;"]

xas-standards-client/nginx/default.conf

@@ -0,0 +1,46 @@
+server {
+    listen       80;
+    server_name  localhost;
+
+    #access_log  /var/log/nginx/host.access.log  main;
+
+
+    location / {
+        root   /usr/share/nginx/html;
+        index  index.html index.htm;
+        try_files $uri /index.html =404;
+    }
+
+    #error_page  404              /404.html;
+
+    # redirect server error pages to the static page /50x.html
+    #
+    error_page   500 502 503 504  /50x.html;
+    location = /50x.html {
+        root   /usr/share/nginx/html;
+    }
+
+    # proxy the PHP scripts to Apache listening on 127.0.0.1:80
+    #
+    #location ~ \.php$ {
+    #    proxy_pass   http://127.0.0.1;
+    #}
+
+    # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
+    #
+    #location ~ \.php$ {
+    #    root           html;
+    #    fastcgi_pass   127.0.0.1:9000;
+    #    fastcgi_index  index.php;
+    #    fastcgi_param  SCRIPT_FILENAME  /scripts$fastcgi_script_name;
+    #    include        fastcgi_params;
+    #}
+
+    # deny access to .htaccess files, if Apache's document root
+    # concurs with nginx's one
+    #
+    #location ~ /\.ht {
+    #    deny  all;
+    #}
+}
+

xas-standards-client/src/App.tsx

@@ -17,7 +17,8 @@ import { useState, useMemo } from "react";
 import { Stack } from "@mui/material";
 import { createTheme, ThemeProvider } from "@mui/material/styles";
 
-import ReviewPage from "./components/ReviewPage.tsx";
+import ReviewPage from "./components/review/ReviewPage.tsx";
+import Terms from "./components/Terms.tsx";
 
 function App() {
   const prefersDarkMode = useMediaQuery("(prefers-color-scheme: dark)");
@@ -56,6 +57,7 @@ function App() {
             <Routes>
               <Route path="/" element={<WelcomePage />} />
               <Route path="/view" element={<StandardViewerMui />} />
+              <Route path="/terms" element={<Terms />} />
               <Route
                 path="/submit"
                 element={