feat: validate OPAl format during import

nfdi4health · Sep 11, 2023 · 9b98e02 · 9b98e02
1 parent 5508096
commit 9b98e02
Show file tree

Hide file tree

Showing 2 changed files with 70 additions and 1 deletion.
diff --git a/backend/restapi/__init__.py b/backend/restapi/__init__.py
@@ -228,7 +228,33 @@ def get_columns():
         except OSError:
             pass
 
-        return jsonify(list(df.columns.values))
+        return(jsonify(list(df.columns.values)))
+
+    @app.route('/api/instrument/columnCheck', methods=["POST"])
+    def column_check():
+        file_to_import = request.files.get("file", None)
+
+        if not os.path.exists(INSTRUMENTS + "/tmp"):
+            os.makedirs(INSTRUMENTS + "/tmp")
+
+        file_to_import.save(INSTRUMENTS + "/tmp/" + file_to_import.filename)
+
+        if file_to_import.filename.split(".")[-1] == "xlsx":
+            df = pd.read_excel(INSTRUMENTS + "/tmp/" + file_to_import.filename)
+        if file_to_import.filename.split(".")[-1] == "csv":
+            df = pd.read_csv(INSTRUMENTS + "/tmp/" + file_to_import.filename)
+
+        required_opal_columns = ["index", "table", "name", "valueType", "unit", "label:en", "label:la", "label:de",
+                                 "alias"]
+        actual_columns = df.columns.values
+        missing_columns = [i for i in required_opal_columns if i not in actual_columns]
+
+        try:
+            os.remove(INSTRUMENTS + "/tmp/" + file_to_import.filename)
+        except OSError:
+            pass
+
+        return(jsonify(missing_columns))
 
     @app.route('/api/instrument', methods=["POST"])
     def import_instrument():

diff --git a/frontend/src/components/import/ImportExcel.tsx b/frontend/src/components/import/ImportExcel.tsx
@@ -44,12 +44,45 @@ export default (props: {
         }).then((res) => res.json());
     });
 
+    const {
+        data: columnCheck,
+        mutate: checkColumns,
+        isSuccess: isSuccessColumnCheck,
+        isLoading: isLoadingColumnCheck,
+        isError: isErrorColumnCheck
+    } = useMutation(() => {
+        const file = new FormData();
+        file.append("file", props.files);
+        return fetch(`/api/instrument/columnCheck`, {
+            method: "POST",
+            body: file,
+        }).then((res) => res.json());
+    });
+
     const pick = () => {
         if (props.hasFile) {
             get_columns();
         }
     };
 
+    const check_columns = () => {
+        if (props.hasFile) {
+            checkColumns();
+        }
+    };
+
+    const displayColumnCheck = (item: any) => {
+        return (
+            item ?
+                item.length > 1 ?
+                    item.map((element: string, i: any) =>
+                        <dd key={i}>{element}</dd>)
+                    : item
+                : "-"
+        )
+    }
+    console.log(columnCheck)
+
     return (
         <>
             <EuiDescribedFormGroup
@@ -94,6 +127,8 @@ export default (props: {
                         <EuiButton
                             onClick={() => {
                                 pick();
+                                check_columns()
+                                console.log(columnCheck)
                             }}
                             isDisabled={!props.hasFile}
                         >
@@ -104,6 +139,14 @@ export default (props: {
                         {isError &&
                             <EuiTextColor color="danger">The file could not be validated. Try again, use another format
                                 or report via the blue feedback button.</EuiTextColor>}
+                        {isLoadingColumnCheck && <EuiLoadingSpinner/>}
+
+                        {columnCheck && columnCheck.length == 0 &&
+                            <EuiTextColor color="success">OPAL format validated</EuiTextColor>
+                        }
+                        {columnCheck && columnCheck.length != 0 &&
+                            <EuiTextColor color="danger">The following columns are required for the OPAL
+                                format: {displayColumnCheck(columnCheck)}</EuiTextColor>}
                     </>
                 </EuiFormRow>
             </EuiDescribedFormGroup>