Initial review workflow

compose.yaml

@@ -0,0 +1,17 @@
+services:
+  postgres:
+    image: postgres:12
+    restart: always
+    user: root
+    environment:
+        POSTGRES_USER: xasadmin
+        POSTGRES_PASSWORD: password
+        POSTGRES_DB: xasstandarddb
+    ports:
+        - '5432:5432'
+    volumes:
+        - postgres-data:/var/lib/postgresql/data
+        - ./database/tables.sql:/docker-entrypoint-initdb.d/create_tables.sql
+
+volumes:
+    postgres-data:

database/tables.sql

@@ -182,7 +182,7 @@ CREATE TABLE beamline (
 	xray_source TEXT,
 	facility_id INTEGER,
 	PRIMARY KEY (id),
-	UNIQUE (name),
+    UNIQUE (facility_id, name),
 	FOREIGN KEY(facility_id) REFERENCES facility (id)
 );
 
@@ -203,22 +203,22 @@ INSERT INTO "beamline" VALUES(12,'I18','The Microfocus Beamline','I18 Undulator'
 INSERT INTO "beamline" VALUES(13,'I20-scanning','Versatile X-ray Spectroscopy','I20 Wiggler', 8);
 
 CREATE TABLE person (
-	id SERIAL,
+	id INTEGER PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
 	identifier TEXT NOT NULL,
-	PRIMARY KEY (id),
+    admin BOOLEAN NOT NULL DEFAULT FALSE,
 	UNIQUE (identifier)
 );
 
 COMMENT ON TABLE person IS 'Table to store unique identifier of user';
 
 CREATE TABLE xas_standard_data (
-    id SERIAL,
+    id INTEGER PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
 	original_filename TEXT NOT NULL,
     transmission BOOLEAN NOT NULL,
     fluorescence BOOLEAN NOT NULL,
+    emission BOOLEAN NOT NULL,
     reference BOOLEAN NOT NULL,
-    location TEXT NOT NULL,
-	PRIMARY KEY (id)
+    location TEXT NOT NULL
 );
 
 COMMENT ON TABLE xas_standard_data IS 'Data file storing the standard data';
@@ -227,7 +227,7 @@ CREATE TYPE review_status_enum AS ENUM('pending', 'approved', 'rejected');
 CREATE TYPE licence_enum AS ENUM('cc_by', 'cc_0', 'logged_in_only');
 
 CREATE Table xas_standard (
-    id SERIAL,
+    id INTEGER PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
     submitter_id INTEGER NOT NULL,
     reviewer_id INTEGER,
     submission_date TIMESTAMP,
@@ -240,12 +240,13 @@ CREATE Table xas_standard (
     edge_id INTEGER,
     sample_name TEXT,
     sample_prep TEXT,
+    sample_comp TEXT,
     beamline_id INTEGER,
     mono_name TEXT,
     mono_dspacing TEXT,
     additional_metadata TEXT,
+    citation TEXT,
     licence licence_enum NOT NULL,
-    PRIMARY KEY (id),
     FOREIGN KEY(submitter_id) REFERENCES person (id),
     FOREIGN KEY(reviewer_id) REFERENCES person (id),
     FOREIGN KEY(data_id) REFERENCES xas_standard_data (id),
@@ -257,11 +258,10 @@ CREATE Table xas_standard (
 COMMENT ON TABLE xas_standard IS 'Metadata relating to an xas standard measurement';
 
 CREATE Table xas_standard_attachment (
-    id SERIAL,
+    id INTEGER PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
     xas_standard_id INTEGER NOT NULL,
     location TEXT NOT NULL,
     description TEXT,
-    PRIMARY KEY (id),
     FOREIGN KEY(xas_standard_id) REFERENCES xas_standard (id)
 );
 

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

@@ -1,6 +1,6 @@
 import datetime
 import os
-from typing import Annotated, List, Optional, Union
+from typing import Annotated, List, Optional
 
 import requests
 from fastapi import (
@@ -33,15 +33,17 @@
     update_review,
 )
 from .schemas import (
+    AdminXASStandardResponse,
     Beamline,
     BeamlineResponse,
     Edge,
     Element,
     LicenceType,
     MetadataResponse,
-    Review,
+    Person,
+    ReviewStatus,
     XASStandard,
-    XASStandardAdminResponse,
+    XASStandardAdminReviewInput,
     XASStandardInput,
     XASStandardResponse,
 )
@@ -121,8 +123,16 @@ async def get_current_user(
 
 
 @app.get("/api/user")
-async def check(user_id: str = Depends(get_current_user)):
-    return {"user": user_id}
+async def check(
+    session: Session = Depends(get_session), user_id: str = Depends(get_current_user)
+):
+
+    statement = select(Person).where(Person.identifier == user_id)
+    person = session.exec(statement).first()
+
+    admin = person is not None and person.admin
+
+    return {"user": user_id, "admin": admin}
 
 
 @app.get("/api/metadata")
@@ -157,31 +167,44 @@ def read_edges(session: Session = Depends(get_session)) -> List[Edge]:
 def read_standards(
     session: Session = Depends(get_session),
     element: str | None = None,
-    admin: bool = False,
-    response_model=Union[XASStandardResponse, XASStandardAdminResponse],
-) -> CursorPage[XASStandardAdminResponse | XASStandardResponse]:
+) -> CursorPage[XASStandardResponse]:
 
-    statement = select(XASStandard)
+    statement = select(XASStandard).where(
+        XASStandard.review_status == ReviewStatus.approved
+    )
 
     if element:
         statement = statement.join(Element, XASStandard.element_z == Element.z).where(
             Element.symbol == element
         )
 
-    if admin:
+    return paginate(
+        session,
+        statement.order_by(XASStandard.id),
+    )
 
-        def transformer(x):
-            return [XASStandardAdminResponse.model_validate(i) for i in x]
 
-    else:
+@app.get("/api/admin/standards")
+def read_standards_admin(
+    session: Session = Depends(get_session),
+    user_id: str = Depends(get_current_user),
+) -> CursorPage[AdminXASStandardResponse]:
 
-        def transformer(x):
-            return [XASStandardResponse.model_validate(i) for i in x]
+    statement = select(Person).where(Person.identifier == user_id)
+    person = session.exec(statement).first()
 
-    return paginate(
-        session, statement.order_by(XASStandard.id), transformer=transformer
+    if person is None or not person.admin:
+        raise HTTPException(status_code=401, detail=f"No standard with id={user_id}")
+
+    if not person.admin:
+        raise HTTPException(status_code=401, detail=f"User {user_id} not admin")
+
+    statement = select(XASStandard).where(
+        XASStandard.review_status == ReviewStatus.pending
     )
 
+    return paginate(session, statement.order_by(XASStandard.id))
+
 
 @app.get("/api/standards/{id}")
 async def read_standard(
@@ -234,8 +257,21 @@ def add_standard_file(
 
 
 @app.patch("/api/standards")
-def submit_review(review: Review, session: Session = Depends(get_session)):
-    return update_review(session, review)
+def submit_review(
+    review: XASStandardAdminReviewInput,
+    session: Session = Depends(get_session),
+    user_id: str = Depends(get_current_user),
+):
+
+    statement = select(Person).where(Person.identifier == user_id)
+    person = session.exec(statement).first()
+
+    if person is None or not person.admin:
+        raise HTTPException(status_code=401, detail=f"No standard with id={user_id}")
+
+    if not person.admin:
+        raise HTTPException(status_code=401, detail=f"User {user_id} not admin")
+    return update_review(session, review, person.id)
 
 
 @app.get("/api/data/{id}")

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

@@ -51,9 +51,11 @@ def get_standard(session, id) -> XASStandard:
         raise HTTPException(status_code=404, detail=f"No standard with id={id}")
 
 
-def update_review(session, review):
-    standard = session.get(XASStandard, review.id)
+def update_review(session, review, reviewer_id):
+    standard = session.get(XASStandard, review.standard_id)
     standard.review_status = review.review_status
+    standard.reviewer_comments = review.reviewer_comments
+    standard.reviewer_id = reviewer_id
     session.add(standard)
     session.commit()
     session.refresh(standard)
@@ -89,6 +91,7 @@ def add_new_standard(session, file1, xs_input: XASStandardInput, additional_file
 
     fluorescence = "mufluor" in set_labels
     transmission = "mutrans" in set_labels
+    reference = "murefer" in set_labels
     emission = "mutey" in set_labels
 
     xsd = XASStandardDataInput(
@@ -97,6 +100,7 @@ def add_new_standard(session, file1, xs_input: XASStandardInput, additional_file
         original_filename=file1.filename,
         emission=emission,
         transmission=transmission,
+        reference=reference,
     )
 
     new_standard = XASStandard.model_validate(xs_input)

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

@@ -6,11 +6,6 @@
 from sqlmodel import Column, Enum, Field, Relationship, SQLModel
 
 
-class Review(BaseModel):
-    id: int
-    review_status: str
-
-
 class Mono(BaseModel):
     name: Optional[str] = None
     d_spacing: Optional[str] = None
@@ -27,6 +22,7 @@ class PersonInput(SQLModel):
 
 class Person(PersonInput, table=True):
     id: int | None = Field(primary_key=True, default=None)
+    admin: bool = False
 
 
 class ElementInput(SQLModel):
@@ -107,6 +103,7 @@ class XASStandardDataInput(SQLModel):
     original_filename: str
     transmission: bool
     fluorescence: bool
+    reference: bool
     emission: bool
     location: str
 
@@ -153,14 +150,20 @@ class XASStandard(XASStandardInput, table=True):
     data_id: int | None = Field(foreign_key="xas_standard_data.id", default=None)
     reviewer_id: Optional[int] = Field(foreign_key="person.id", default=None)
     reviewer_comments: Optional[str] = None
-    review_status: Optional[ReviewStatus] = Field(
+    review_status: ReviewStatus = Field(
         sa_column=Column(Enum(ReviewStatus)), default=ReviewStatus.pending
     )
 
     xas_standard_data: XASStandardData = Relationship(back_populates="xas_standard")
     element: Element = Relationship(sa_relationship_kwargs={"lazy": "joined"})
     edge: Edge = Relationship(sa_relationship_kwargs={"lazy": "joined"})
     beamline: Beamline = Relationship(sa_relationship_kwargs={"lazy": "selectin"})
+    submitter: Person = Relationship(
+        sa_relationship_kwargs={
+            "lazy": "selectin",
+            "foreign_keys": "[XASStandard.submitter_id]",
+        }
+    )
 
 
 class XASStandardResponse(XASStandardInput):
@@ -171,7 +174,12 @@ class XASStandardResponse(XASStandardInput):
     submitter_id: int
 
 
-class XASStandardAdminResponse(XASStandardResponse):
-    reviewer_id: Optional[int] = None
+class AdminXASStandardResponse(XASStandardResponse):
+    submitter: Person
+
+
+class XASStandardAdminReviewInput(SQLModel):
     reviewer_comments: Optional[str] = None
-    review_status: Optional[ReviewStatus] = None
+    review_status: ReviewStatus
+    standard_id: int
+    # get fedid from person table

xas-standards-client/src/App.tsx

@@ -1,9 +1,8 @@
 import Header from "./components/Header.tsx";
 import { Routes, Route } from "react-router-dom";
 import StandardViewerMui from "./components/StandardViewer.tsx";
-import StandardSubmission from "./components/StandardSubmission.tsx";
+import StandardSubmission from "./components/submission/StandardSubmission.tsx";
 import WelcomePage from "./components/WelcomePage.tsx";
-import BasicSelect from "./components/SelectTest.tsx";
 
 import { MetadataProvider } from "./contexts/MetadataContext.tsx";
 import { UserProvider } from "./contexts/UserContext.tsx";
@@ -18,6 +17,7 @@ import { Stack } from "@mui/material";
 import { createTheme, ThemeProvider } from "@mui/material/styles";
 
 import ColorModeContext from "./contexts/ColorModeContext.tsx";
+import ReviewPage from "./components/ReviewPage.tsx";
 
 function App() {
   const [mode, setMode] = useState<"light" | "dark">("light");
@@ -50,7 +50,6 @@ function App() {
             <MetadataProvider>
               <Routes>
                 <Route path="/" element={<WelcomePage />} />
-                <Route path="/test" element={<BasicSelect />} />
                 <Route path="/view" element={<StandardViewerMui />} />
                 <Route
                   path="/submit"
@@ -60,6 +59,7 @@ function App() {
                     </RequireAuth>
                   }
                 />
+                <Route path="/review" element={<ReviewPage />} />
                 <Route path="/login" element={<LogInPage />} />
                 {/* <Route path="/review" element={<ReviewPage />} /> */}
               </Routes>

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

@@ -44,6 +44,7 @@ export default function Header() {
   const user = useContext(UserContext);
   console.log(user);
   const loggedIn = user != null;
+  const admin = user != null && user.admin
   console.log(loggedIn);
 
   const navitems = {
@@ -82,6 +83,9 @@ export default function Header() {
           {loggedIn && (
             <NavListItem to="/submit" label="Submit" />
           ) }
+          {admin && (
+            <NavListItem to="/review" label="Review" />
+          ) }
         </List>
         </Stack>
         <Stack direction="row" alignItems={"center"}>