add code for sample form enum

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/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-client/src/components/submission/SampleForm.tsx

@@ -1,4 +1,11 @@
-import { Grid, TextField } from "@mui/material";
+import {
+  Grid,
+  TextField,
+  FormControl,
+  InputLabel,
+  Select,
+  MenuItem,
+} from "@mui/material";
 
 function SampleForm(props: {
   sampleName: string;
@@ -7,6 +14,9 @@ function SampleForm(props: {
   setSampleComp: (composition: string) => void;
   samplePrep: string;
   setSamplePrep: (preparation: string) => void;
+  sampleForm: string;
+  setSampleForm: (preparation: string) => void;
+  sampleFormOptions: string[];
 }) {
   const sampleName = props.sampleName;
   const setSampleName = props.setSampleName;
@@ -49,12 +59,24 @@ function SampleForm(props: {
         />
       </Grid>
       <Grid item xs={6}>
-        <TextField
-          margin="dense"
-          id="sampleform"
-          label="Sample Form"
-          variant="outlined"
-        />
+        <FormControl fullWidth>
+          <InputLabel margin="dense" id="sampleform">
+            Sample Form
+          </InputLabel>
+          <Select
+            name="sampleform"
+            id="sampleform"
+            label="Sample Form"
+            value={props.sampleForm}
+            onChange={(e) => props.setSampleForm(e.target.value)}
+          >
+            {props.sampleFormOptions.map((x, y) => (
+              <MenuItem key={y} value={x}>
+                {x}
+              </MenuItem>
+            ))}
+          </Select>
+        </FormControl>
       </Grid>
     </Grid>
   );

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

@@ -32,7 +32,8 @@ import {
 const standards_url = "/api/standards";
 
 function StandardSubmission() {
-  const { elements, edges, beamlines, licences } = useContext(MetadataContext);
+  const { elements, edges, beamlines, licences, sample_forms } =
+    useContext(MetadataContext);
 
   const [file, setFile] = useState<File>();
   // const [file2, setFile2] = useState<FileList>();
@@ -42,6 +43,7 @@ function StandardSubmission() {
   const [sampleName, setSampleName] = useState("");
   const [sampleComp, setSampleComp] = useState("");
   const [samplePrep, setSamplePrep] = useState("");
+  const [sampleForm, setSampleForm] = useState(sample_forms[0]);
   const [beamlineId, setBeamlineId] = useState(1);
   const [beamlineHeader, setBeamlineHeader] = useState("");
   const [doi, setDOI] = useState("");
@@ -72,6 +74,7 @@ function StandardSubmission() {
     form.append("sample_name", sampleName);
     form.append("sample_comp", sampleComp);
     form.append("sample_prep", samplePrep);
+    form.append("sample_form", sampleForm);
     form.append("doi", doi);
     form.append("citation", citation);
     form.append("comments", comments);
@@ -203,6 +206,9 @@ function StandardSubmission() {
               setSampleComp={setSampleComp}
               samplePrep={samplePrep}
               setSamplePrep={setSamplePrep}
+              sampleForm={sampleForm}
+              setSampleForm={setSampleForm}
+              sampleFormOptions={sample_forms}
             />
           </Grid>
           <Grid item xs={6}>

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

@@ -11,6 +11,7 @@ function useMetadata(): AppMetadata {
     elements: [],
     edges: [],
     licences: [],
+    sample_forms: []
   });
 
   useEffect(() => {

xas-standards-client/src/models.ts

@@ -57,6 +57,7 @@ export interface AppMetadata {
   elements: Element[];
   edges: Edge[];
   licences: string[];
+  sample_forms: string[];
 }
 
 export interface User {