From 97afbd5403c0d96dc2f45db43ecd2473e600d555 Mon Sep 17 00:00:00 2001
From: Jose Alejandro Bolanos Arroyave <jose.bolanos@correounivalle.edu.co>
Date: Fri, 28 Jun 2024 10:32:35 -0500
Subject: [PATCH] fix: load raw bruker data (#52)

* fix: remove possible black line in experiment

* fix: load raw Bruker data

* fix: extract nucleus from tag
---
 .../__tests__/nmredataToJSON.test.js          | 12 ++++++++++
 src/converter/nmredataToJSON.js               |  4 ++--
 src/converter/util/toJSON/getBrukerFiles.js   | 23 +++++++++++++------
 .../util/toJSON/getNucleusFromTag.js          |  4 ++--
 4 files changed, 32 insertions(+), 11 deletions(-)

diff --git a/src/converter/__tests__/nmredataToJSON.test.js b/src/converter/__tests__/nmredataToJSON.test.js
index 55b3428..1c3ba3e 100644
--- a/src/converter/__tests__/nmredataToJSON.test.js
+++ b/src/converter/__tests__/nmredataToJSON.test.js
@@ -50,4 +50,16 @@ describe('NMReData to nmrium', () => {
       'AN-menthol/10/specpar',
     ]);
   });
+
+  it('1D data with more than one carbon spectra', async () => {
+    const nmrRecord = await readNmrRecord(
+      await getData('3,5-Bis(trifluoromethyl)aniline-sym.zip'),
+    );
+    let jsonData = await nmrRecord.toJSON();
+
+    //dept135 is under tag #2 so it is what is testing.
+    expect(
+      jsonData.spectra.some((s) => s.experiment === 'dept135'),
+    ).toBeTruthy();
+  });
 });
diff --git a/src/converter/nmredataToJSON.js b/src/converter/nmredataToJSON.js
index 0f629bc..67b6057 100644
--- a/src/converter/nmredataToJSON.js
+++ b/src/converter/nmredataToJSON.js
@@ -19,7 +19,7 @@ export async function nmredataToJSON(nmredata, options) {
   let spectra = data.spectra;
   let molecules = data.molecules;
 
-  if (nmredata.SMILES) {
+  if (nmredata.SMILES?.data.length > 0) {
     molecules[0].smiles = nmredata.SMILES.data[0].value;
   }
 
@@ -48,7 +48,7 @@ export async function nmredataToJSON(nmredata, options) {
       nucleus,
       frequency: frequencyLine.value.larmor,
       experiment: pulseProgramLine
-        ? pulseProgramLine.value.pulseprogram
+        ? pulseProgramLine.value.pulseprogram.trim()
         : dimension,
       headComment: nmredata[tag].headComment,
     };
diff --git a/src/converter/util/toJSON/getBrukerFiles.js b/src/converter/util/toJSON/getBrukerFiles.js
index 359fd09..952cf48 100644
--- a/src/converter/util/toJSON/getBrukerFiles.js
+++ b/src/converter/util/toJSON/getBrukerFiles.js
@@ -14,19 +14,18 @@ export async function getBrukerFiles(tag, options) {
 
     let relativePath = locationLine.value.spectrum_location;
     if (relativePath.match(/file:/s)) {
-      let pathSpectrum = root + relativePath.replace(/file:/s, '');
-      let toCheck = pathSpectrum.replace(/(.*\w+\/[0-9]+\/)pdata\/.*/, '$1');
+      let pathSpectrum = root + relativePath.replace(/file:[./]*/s, '');
+      const regexRootPath = pathSpectrum.match(/[ser|fid]/s)
+        ? /([.*/]*\w+\/[0-9]+\/).*/
+        : /(.*\w+\/[0-9]+\/)pdata\/.*/;
+      let toCheck = pathSpectrum.replace(regexRootPath, '$1');
+
       let toCheck2 = pathSpectrum.replace(
         /.*\/[0-9]+\/pdata\/([0-9]+)\/.*/,
         '$1',
       );
       let brukerFolder = [];
       for (let file of fileCollection) {
-        if (
-          toCheck !== file.relativePath.replace(/([.*/]*\w+\/[0-9]+\/).*/, '$1')
-        ) {
-          continue;
-        }
         if (file.relativePath.match('pdata')) {
           if (
             toCheck2 !==
@@ -35,8 +34,18 @@ export async function getBrukerFiles(tag, options) {
             continue;
           }
         }
+
+        const path = file.relativePath.replace(/([.*/]*\w+\/[0-9]+\/).*/, '$1');
+        if (
+          toCheck !== path &&
+          !['ser', 'fid'].some((e) => pathSpectrum === `${path}${e}`)
+        ) {
+          continue;
+        }
+
         brukerFolder.push(file);
       }
+
       sources.push({
         type: 'brukerFiles',
         fileCollection: new FileCollection(brukerFolder),
diff --git a/src/converter/util/toJSON/getNucleusFromTag.js b/src/converter/util/toJSON/getNucleusFromTag.js
index 68a8818..1cf19f0 100644
--- a/src/converter/util/toJSON/getNucleusFromTag.js
+++ b/src/converter/util/toJSON/getNucleusFromTag.js
@@ -4,11 +4,11 @@ export function getNucleusFromTag(label) {
   if (dimensions === '1') {
     nucleus = label
       .substring(3, label.length)
-      .replace(/(?<nucleus>[0-9]+\w+)#\w+/g, '$nucleus');
+      .replace(/(?<nucleus>[0-9]+\w+)#\w+/g, '$<nucleus>');
   } else if (dimensions === '2') {
     let data = label.substring(12, label.length).split('_');
     for (let i = 0; i < data.length; i += 2) {
-      nucleus.push(data[i].replace(/(?<nucleus>[0-9]+\w+)#\w+/g, '$nucleus'));
+      nucleus.push(data[i].replace(/(?<nucleus>[0-9]+\w+)#\w+/g, '$<nucleus>'));
     }
   }
   return nucleus;