add metadata endpoint, context and hook (#4)

* add metadata endpoint, context and hook

* clean up junk test code

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

@@ -14,6 +14,7 @@
     add_new_standard,
     get_data,
     get_file,
+    get_metadata,
     get_standard,
     select_all,
     select_or_create_person,
@@ -25,6 +26,7 @@
     Edge,
     Element,
     LicenceType,
+    MetadataResponse,
     Review,
     XASStandard,
     XASStandardAdminResponse,
@@ -60,6 +62,11 @@ def get_session():
 add_pagination(app)
 
 
+@app.get("/api/metadata")
+def read_metadata(session: Session = Depends(get_session)) -> MetadataResponse:
+    return get_metadata(session)
+
+
 @app.get("/api/licences")
 def read_licences(session: Session = Depends(get_session)) -> List[LicenceType]:
     return list(LicenceType)

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

@@ -8,6 +8,9 @@
 
 from .schemas import (
     Beamline,
+    Edge,
+    Element,
+    LicenceType,
     Person,
     PersonInput,
     XASStandard,
@@ -30,6 +33,16 @@ def select_all(session, sql_model):
     return results.unique().all()
 
 
+def get_metadata(session):
+    output = {}
+    output["elements"] = select_all(session, Element)
+    output["edges"] = select_all(session, Edge)
+    output["beamlines"] = select_all(session, Beamline)
+    output["licences"] = list(LicenceType)
+
+    return output
+
+
 def get_standard(session, id) -> XASStandard:
     standard = session.get(XASStandard, id)
     if standard:

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

@@ -96,6 +96,13 @@ class BeamlineResponse(SQLModel):
     facility: FacilityResponse
 
 
+class MetadataResponse(SQLModel):
+    beamlines: List[BeamlineResponse]
+    elements: List[Element]
+    edges: List[Edge]
+    licences: List[str]
+
+
 class XASStandardDataInput(SQLModel):
     original_filename: str
     transmission: bool

xas-standards-client/src/App.test.tsx

@@ -1,11 +1,26 @@
-import { it, describe } from "vitest";
-import { render } from "@testing-library/react";
+import { it, describe, vi, expect } from "vitest";
+import { render, screen } from "@testing-library/react";
 
 import App from "./App";
 import { BrowserRouter } from "react-router-dom";
+import axios from "axios";
+
+vi.mock("axios");
 
 describe("App", () => {
-  it("renders welcome page", () => {
+  vi.mocked(axios.get).mockImplementation((url) => {
+    switch (url) {
+      case "/api/beamlines":
+        return Promise.resolve({});
+      default:
+        return Promise.resolve({});
+    }
+  });
+
+  it("renders welcome page", async () => {
     render(<App />, { wrapper: BrowserRouter });
+    expect(
+      await screen.findByText(/XAS Standards Database /i)
+    ).toBeInTheDocument();
   });
 });

xas-standards-client/src/App.tsx

@@ -6,16 +6,20 @@ import StandardViewer from "./components/StandardViewer.tsx";
 import StandardSubmission from "./components/StandardSubmission.tsx";
 import WelcomePage from "./components/WelcomePage.tsx";
 
+import { MetadataProvider } from "./contexts/MetadataContext.tsx";
+
 function App() {
   return (
     <div className="mainwindow">
       <Header />
-      <Routes>
-        <Route path="/" element={<WelcomePage />} />
-        <Route path="/view" element={<StandardViewer />} />
-        <Route path="/submit" element={<StandardSubmission />} />
-        {/* <Route path="/review" element={<ReviewPage />} /> */}
-      </Routes>
+      <MetadataProvider>
+        <Routes>
+          <Route path="/" element={<WelcomePage />} />
+          <Route path="/view" element={<StandardViewer />} />
+          <Route path="/submit" element={<StandardSubmission />} />
+          {/* <Route path="/review" element={<ReviewPage />} /> */}
+        </Routes>
+      </MetadataProvider>
     </div>
   );
 }

xas-standards-client/src/components/InstrumentForm.tsx

@@ -1,5 +1,3 @@
-import { s } from "vitest/dist/reporters-1evA5lom.js";
-
 function InstrumentForm(props) {
   const beamlines = props.beamlines;
   const beamlineHeader = props.beamlineHeader;

xas-standards-client/src/components/StandardSubmission.tsx

@@ -1,4 +1,6 @@
-import { useState, useEffect } from "react";
+import { useState, useContext } from "react";
+
+import { MetadataContext } from "../contexts/MetadataContext";
 
 import axios from "axios";
 import { AxiosResponse, AxiosError } from "axios";
@@ -12,17 +14,13 @@ import InstrumentForm from "./InstrumentForm";
 import CitationForm from "./CitationForm";
 import AdditionalInformationForm from "./AdditionalInfoForm";
 
-import { Edge, Element } from "../models";
-
 import { useNavigate } from "react-router-dom";
 
 const standards_url = "/api/standards";
-const beamlines_url = "/api/beamlines";
-const elements_url = "/api/elements";
-const edges_url = "/api/edges";
-const licences_url = "/api/licences";
 
 function StandardSubmission() {
+  const { elements, edges, beamlines, licences } = useContext(MetadataContext);
+
   const [file, setFile] = useState<File>();
   const [file2, setFile2] = useState<FileList>();
 
@@ -39,32 +37,8 @@ function StandardSubmission() {
   const [citation, setCitation] = useState("");
   const [comments, setComments] = useState("");
 
-  const [beamlines, setBeamlines] = useState([]);
-  const [elements, setElements] = useState<Element[]>([]);
-  const [edges, setEdges] = useState<Edge[]>([]);
-  const [licences, setLicences] = useState([]);
-
   const navigate = useNavigate();
 
-  useEffect(() => {
-    axios.get(beamlines_url).then((res) => {
-      setBeamlines(res.data);
-    });
-
-    axios.get(elements_url).then((res) => {
-      setElements(res.data);
-    });
-
-    axios.get(edges_url).then((res) => {
-      setEdges(res.data);
-    });
-
-    axios.get(licences_url).then((res) => {
-      setLicences(res.data);
-      setLicence(res.data[0]);
-    });
-  }, []);
-
   const handleSubmit = (event: React.FormEvent<HTMLFormElement>) => {
     event.preventDefault();
 

xas-standards-client/src/components/StandardViewer.tsx

@@ -1,25 +1,25 @@
-import { useState, useEffect } from "react";
+import { useState, useContext } from "react";
 
 import XASChart from "./StandardsChart.tsx";
 import axios from "axios";
 import StandardsTable from "./StandardsTable.tsx";
-import { Element } from "../models.ts";
 
 import { XASStandard, XASData } from "../models.ts";
+import { MetadataContext } from "../contexts/MetadataContext.tsx";
 
 const data_url = "/api/data";
-const elements_url = "/api/elements";
 
 function StandardViewer() {
   const [standards, setStandardsList] = useState<XASStandard[]>([]);
 
   const [xasdata, setXASData] = useState<XASData | null>(null);
-  const [elements, setElements] = useState<Element[]>([]);
   const [showTrans, setShowTrans] = useState(false);
   const [showFluor, setShowFluor] = useState(false);
   const [showRef, setShowRef] = useState(false);
   const [contains, setContains] = useState([false, false, false]);
 
+  const { elements } = useContext(MetadataContext);
+
   function getData(setXASData: React.Dispatch<XASData>) {
     return (id: number) => {
       axios.get(data_url + "/" + id).then((response) => {
@@ -40,12 +40,6 @@ function StandardViewer() {
 
   const onClick = getData(setXASData);
 
-  useEffect(() => {
-    axios.get(elements_url).then((res) => {
-      setElements(res.data);
-    });
-  }, []);
-
   return (
     <div className="mainbody">
       <StandardsTable

xas-standards-client/src/contexts/MetadataContext.tsx

@@ -0,0 +1,23 @@
+import { createContext } from "react";
+import { AppMetadata } from "../models";
+import useMetadata from "../hooks/useMetadata";
+
+const MetadataContext = createContext<AppMetadata>({
+  elements: [],
+  edges: [],
+  beamlines: [],
+  licences: [],
+});
+
+function MetadataProvider(props: { children: React.ReactNode }) {
+  const { children } = props;
+  const appMetadata = useMetadata();
+
+  return (
+    <MetadataContext.Provider value={appMetadata}>
+      {children}
+    </MetadataContext.Provider>
+  );
+}
+
+export { MetadataContext, MetadataProvider };

xas-standards-client/src/hooks/useMetadata.ts

@@ -0,0 +1,26 @@
+import { useEffect, useState } from "react";
+import axios from "axios";
+
+const metadata_url = "/api/metadata";
+
+import { AppMetadata } from "../models";
+
+function useMetadata(): AppMetadata {
+  const [appMetadata, setAppMetdata] = useState<AppMetadata>({
+    beamlines: [],
+    elements: [],
+    edges: [],
+    licences: [],
+  });
+
+  useEffect(() => {
+    axios.get(metadata_url).then((res) => {
+      //   console.log("BEAMLINE! " + res.data.name);
+      setAppMetdata(res.data);
+    });
+  }, []);
+
+  return appMetadata;
+}
+
+export default useMetadata;

xas-standards-client/src/models.ts

@@ -43,35 +43,9 @@ export interface XASStandardInput {
   licence: string;
 }
 
-
-
-const emptyElement: Element = {
-    symbol: "",
-    z: -1
+export interface AppMetadata {
+  beamlines: Beamline[];
+  elements: Element[];
+  edges: Edge[];
+  licences: string[];
 }
-
-const emptyEdge: Edge = {
-    name: "",
-    id: -1
-}
-
-const emptyBeamline: Beamline = {
-  name: "";
-  facility: "";
-}
-}
-
-
-    const empty: XASStandard = {
-        id: -1,
-
-  edge: Edge;
-  sample_name: string;
-  sample_prep: string;
-  sample_comp: string;
-  doi: string;
-  citation: string;
-  facility: string;
-  collection_date: string;
-  beamline: Beamline;
-    }

xas-standards-client/src/xdifile.test.ts

@@ -5,7 +5,7 @@ import XDIFile from "./xdifile";
 
 describe("Parse info from xdi file", () =>
   new Promise((done) => {
-    fs.readFile("test.xdi", "utf8", (err, data) => {
+    fs.readFile("test.xdi", "utf8", (err: any, data: string) => {
       if (err) throw err;
       const xdi = XDIFile.parseFile(data);