#52 repalce expected area by concentration

components/DaughterTable.vue

@@ -5,7 +5,7 @@ SPDX-License-Identifier: MIT
 -->
 <!-- 
     This component display in light version the table of metabolites of a calibration curve
-    of each daughter solution. It provide a input to indicate the expected area.
+    of each daughter solution. It provide a input to indicate the concentration.
     It is used in ManageCalibCurve.async.vue
  -->
 
@@ -27,12 +27,12 @@ const model = defineModel<{
   nameFile:string,
   nameMeta:string,
   area:number,
-  expectedArea:number}[]>({ required: true });
+  concentration:number}[]>({ required: true });
 // -- headers of the table
 const headers = ref([
     { title: t('header.nameMeta'), sortable:true, key: 'nameMeta' },
     { title: t('header.area'), sortable:true, key: 'area' },
-    { title: t('header.expectedArea'), sortable:true, key: 'expectedArea' },
+    { title: t('header.concentration'), sortable:true, key: 'concentration' },
 ]);
 // -- group by daughter solution
 const groupBy = ref([{ sortable:true, key: 'idFile' }]);
@@ -89,10 +89,10 @@ function delDaughterFile(idFile: string) {
         </td>
       </tr>
     </template>
-    <!-- input for expected area -->
-    <template #[`item.expectedArea`]="{index}">
+    <!-- input for concentration -->
+    <template #[`item.concentration`]="{index}">
       <v-text-field
-        v-model="model[index].expectedArea"
+        v-model="model[index].concentration"
         type="number"
         variant="plain"
         :rules="[(v) => v >= 0 || t('message.positiveNumber')]"

components/ManageCalibCurve.async.vue

@@ -39,7 +39,7 @@ const rDaughterTable = ref<{
     nameFile: string;
     nameMeta: string;
     area: number;
-    expectedArea: number}[]>([]);
+    concentration: number}[]>([]);
 const rDaughterLoading = ref<boolean>(false);
 
 /**
@@ -94,7 +94,7 @@ async function sendFile() {
       nameFile: daughterFile.value?.name || "error",
       nameMeta: r[0],
       area: r[1],
-      expectedArea: 0,
+      concentration: 0,
   })));
   
   // reset file input
@@ -108,15 +108,15 @@ function createDaughterGroup() {
         idFile: string;
         nameMeta: string;
         area: number;
-        expectedArea: number;
+        concentration: number;
   }) => {
     if (!acc[cur.idFile]) {
       acc[cur.idFile] = [];
     }
     acc[cur.idFile].push({
       nameMeta:cur.nameMeta,
       area:cur.area,
-      expectedArea:cur.expectedArea
+      concentration:cur.concentration
     });
     return acc;
   }, {});
@@ -177,7 +177,7 @@ function openCalibCurve(item: {id: string, name: string}) {
       nameFile: row.name,
       nameMeta: row.mol,
       area: row.area,
-      expectedArea: row.expected,
+      concentration: row.concentration,
     }));
     // End loading
     rDaughterLoading.value = false;
@@ -404,7 +404,7 @@ function archiveCalibCurve(item: {id: string, name: string}){
                 prepend-icon="mdi-water-plus"
                 hide-input
               />
-              <!-- show metabolite of daughter solution and enter area expected
+              <!-- show metabolite of daughter solution and enter concentration
               -->
               <daughter-table
                 v-model="rDaughterTable"

db/init.sql

@@ -130,7 +130,7 @@ CREATE TABLE daughter
   id_file SERIAL REFERENCES file (id) ON DELETE CASCADE,
   id_mol VARCHAR(52),
   area FLOAT NOT NULL,
-  expected FLOAT NOT NULL,
+  concentration FLOAT NOT NULL,
   PRIMARY KEY (id_calib_curves, id_file, id_mol)
 );
 
@@ -185,7 +185,7 @@ GROUP BY calib_curves.id;
 
 CREATE VIEW view_daughter_file AS
 SELECT file.id AS id,  file.name AS name,
-       daughter.id_mol AS mol, area, expected, id_calib_curves 
+       daughter.id_mol AS mol, area, concentration, id_calib_curves 
 FROM daughter, file
 WHERE daughter.id_file = file.id;
 

server/api/AddCalibCurve.post.ts

@@ -31,13 +31,13 @@ export default defineEventHandler(async (event) => {
                     lPromises.push(  
                         client.query(`
                             INSERT INTO daughter(
-                                id_calib_curves, id_file, id_mol, area, expected) 
+                                id_calib_curves, id_file, id_mol, area, concentration) 
                             VALUES (
                             '${idCalibCurve}',
                             '${idFile}',
                             '${metabo.nameMeta}',
                             '${metabo.area}',
-                            '${metabo.expectedArea}')`
+                            '${metabo.concentration}')`
                         )
                     );
                 }

server/api/UpdateCalibCurve.post.ts

@@ -1,7 +1,7 @@
 // SPDX-FileCopyrightText: 2024 Marcellino Palerme <[email protected]>
 //
 // SPDX-License-Identifier: MIT
-// this file is used to update the expected concentration of the daughters
+// this file is used to update the concentration of the daughters
 // of a calibration curve
 
 import pg from "pg";
@@ -16,10 +16,10 @@ export default defineEventHandler(async (event) => {
             for(const idFile in body.daughters){
                 // for each metabolite of the daughter solution
                 for(const daughter of body.daughters[idFile]){
-                   // update expected concentration
+                   // update concentration
                    lQueryPromises.push(client.query(`
                         UPDATE daughter
-                        SET expected = ${daughter.expectedArea}
+                        SET concentration = ${daughter.concentration}
                         WHERE id_file = ${idFile}
                         AND id_mol = '${daughter.nameMeta}'
                         AND id_calib_curves = ${body.idCalibCurve}`

server/api/extract.post.ts

@@ -27,20 +27,20 @@ async function exportFile(addressFile: {
 }
 
 /**
- * Calculate area of metabolite about calibration curves
+ * Calculate concentration of metabolite about calibration curves
  * 
  * @param sample one sample
  * @param lMolRatio list of ratio of metabolite associate to project
  * @param indexMeta index of name of metabolite in sample
  * @param indexArea index of area in sample
  */
-function CalculateArea(sample: string[], lMolRatio: { [key: string]: number }, indexMeta:number, indexArea:number): string[] {    
+function CalculateConcentration(sample: string[], lMolRatio: { [key: string]: number }, indexMeta:number, indexArea:number): string[] {    
     const tempSample = sample;
     // no metabolites in calibration curves associate of project 
     if(lMolRatio[tempSample[indexMeta]] === undefined){
         return [...tempSample, "0"];
     }
-    // calculate area
+    // calculate Concentration
     tempSample.push((parseFloat(tempSample[indexArea]) * lMolRatio[tempSample[indexMeta]]).toString());  
 
     return tempSample;
@@ -105,21 +105,21 @@ export default defineEventHandler(async (event) => {
         })
         .then((resp: any[]) => Promise.all(resp.map((x: { json: () => any; }) => x.json())))
         .then(async (resps: any) => {
-            // function to calculate area do nothing
+            // function to calculate concentration do nothing
             let funcCalcul = (x: any) => x;
             let temp = [resps[0].header];
             const lMolRatio = await GetRatio(client, idProject);
             // verify if we have calibration curves
             if (Object.keys(lMolRatio).length != 0) {
-                // affect function to calculate area
-                funcCalcul = (x: any) => CalculateArea(x, 
+                // affect function to calculate concentration
+                funcCalcul = (x: any) => CalculateConcentration(x, 
                                         lMolRatio,
                                         resps[0].header.indexOf("metabolite"),
                                         resps[0].header.indexOf("area"));
-                // add header for calculated area
-                temp = [[...resps[0].header, "CalculatedArea"]];                
+                // add header for calculated Concentration
+                temp = [[...resps[0].header, "Concentration"]];                
             }
-            // calculate area for all samples                        
+            // calculate concentration for all samples                        
             for(const sample of resps[0].samples){
 
                 temp.push(funcCalcul(sample));

server/api/function/RegCalibCurve.ts

@@ -14,31 +14,31 @@ export async function calculateRatioCalibCurve(idCalibCurve:string):Promise<numb
 
     return client.connect()
         .then(() => {
-            // Get the area and expected area of the metabolite of the calibration curve
+            // Get the area and concentration of the metabolite of the calibration curve
             return client.query(`
-                SELECT id_mol,area, expected FROM daughter
+                SELECT id_mol,area, concentration FROM daughter
                 WHERE id_calib_curves='${idCalibCurve}'
             `)
         })
         .then((res:{rows:any[]}) => {
-            // create array area/expected for each metabolite
-            const metaAreaExpected: {[key:string]:[number,number][]} = {}
+            // create array area/concentration for each metabolite
+            const metaConcentration: {[key:string]:[number,number][]} = {}
 
             for(const row of res.rows){
                 // if the metabolite is not in the array, create it
-                if(metaAreaExpected[row.id_mol]===undefined){
+                if(metaConcentration[row.id_mol]===undefined){
                     // initialize first element to position 0,0
                     // if no metabolits, machine return noting
-                    metaAreaExpected[row.id_mol] = [[0,0]]
+                    metaConcentration[row.id_mol] = [[0,0]]
                 }
-                metaAreaExpected[row.id_mol].push([row.area,row.expected]);
+                metaConcentration[row.id_mol].push([row.area,row.concentration]);
             }
 
             // caclulate director coefficient of each metabolite
             const metaRatio: {[key:string]:number}= {}
-            for(const key in metaAreaExpected){
+            for(const key in metaConcentration){
                 // calculate the linear regression
-                const {m} = linearRegression(metaAreaExpected[key]);
+                const {m} = linearRegression(metaConcentration[key]);
                 metaRatio[key] = m;
             }
             return metaRatio