#48 read excel file. List Metabo and thier area not empty

components/ManageSerie.async.vue

@@ -45,12 +45,15 @@ async function sendFile() {
   // send file to the server
   // - TODO: show loading spinner
 
+  // - Put file in a FormData object to send all format file 
+  //   (ex: csv, xls, xlsx, ...)
+  const formData = new FormData();
+  formData.append('file', daughterFile.value);
+
   await $fetch('/api/extractFromFile', {
     method: 'POST',
-    body: daughterFile.value,
+    body: formData,
   });
-  console.log("sendFile");
-  console.log(daughterFile.value?.name);
 
 }
 </script>

server/api/extractFromFile.ts

@@ -10,19 +10,23 @@
 
 import fs from "fs";
 import path from "path";
+import { P2M2ToolsApi, P2M2ToolsApiFill } from "@/types/p2m2Api";
 
 export default defineEventHandler(async(event) => {
     // Read the form data from the event
-    const formData = await readBody(event);
+    const formData = await readMultipartFormData(event);
+
     // Get the file from the form data
     if(!formData){
         return 2;
     }
-
+
+    const rFile = formData[0].data;
+
     // wrtie the file on disk
     const id = crypto.randomUUID();
     const filePath = path.join("/shareFile", id);
-    fs.writeFileSync(filePath, formData);
+    fs.writeFileSync(filePath, rFile);
 
 
     // Send the file to the parser
@@ -35,14 +39,14 @@ export default defineEventHandler(async(event) => {
             body: fs.readFileSync(filePath),
         })
         .then((resp) => {
-            return resp.json() as Promise<{}|{ header : string[], samples : string[][]}>;
+            return resp.json() as Promise<P2M2ToolsApi>;
         })
         .then((jsonResp) => {
             // If the file is unknown, delete it
             if(JSON.stringify(jsonResp) === JSON.stringify({})){
                 return 1;
             }
-            return jsonResp;
+            return extractMetabolites(jsonResp as P2M2ToolsApiFill);
         })
         .catch(()=>{
             // If an error occurs, delete the file
@@ -51,10 +55,36 @@ export default defineEventHandler(async(event) => {
         .finally(()=>{
             // Delete the file
             fs.rmSync(filePath);
-            console.log("File deleted");
 
         });
+
+})
+
 
-    // console.log(resp);
-
-})
+/**
+ * We extract name and area of metabolites from the file.
+ * @param jsonResp  The response from the parser
+ * @returns The list of tupple metabolites and their area
+ */
+function extractMetabolites(jsonResp: P2M2ToolsApiFill): [string, number][] {
+    // Check if the response contains the header and the samples
+    if(jsonResp.header && jsonResp.samples){
+        // Get the index of the name and the area
+        const idxMeta = jsonResp.header.indexOf("metabolite");
+        const idxArea = jsonResp.header.indexOf("area");
+        // If the name and the area are found, return the list of metabolites 
+        // and their area
+        if(idxMeta != -1 && idxArea != -1){
+
+            const metaArea = jsonResp.samples.filter(x => 
+                // keep the metabolite and the area are not empty
+                x[idxMeta] !== "" && x[idxArea] !== "" && 
+                // keep if the area is a number
+                !isNaN(parseFloat(x[idxArea])));
+
+            return metaArea.map(x => [x[idxMeta], parseFloat(x[idxArea])]
+            );
+        }
+    }
+    return [];
+}

types/p2m2Api.ts

@@ -0,0 +1,9 @@
+// SPDX-FileCopyrightText: 2024 Marcellino Palerme <[email protected]>
+//
+// SPDX-License-Identifier: MIT
+
+// We declare type of response of the p2m2ToolsApi
+
+export type P2M2ToolsApi = {}|{ header : string[], samples : string[][]};
+
+export type P2M2ToolsApiFill = { header : string[], samples : string[][]};