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fix: load raw bruker data #52

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merged 3 commits into from
Jun 28, 2024
Merged

fix: load raw bruker data #52

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98a376e
fix: remove possible black line in experiment
jobo322 Jun 28, 2024
c0779b8
fix: load raw Bruker data
jobo322 Jun 28, 2024
d69d481
fix: extract nucleus from tag
jobo322 Jun 28, 2024
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12 changes: 12 additions & 0 deletions src/converter/__tests__/nmredataToJSON.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
});
});
4 changes: 2 additions & 2 deletions src/converter/nmredataToJSON.js
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
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;
}

Expand All @@ -37,7 +37,7 @@

let nucleus = getNucleusFromTag(tag);

let dimension = ctag.replace(/([1|2]d)_.*/, '$1');

Check warning on line 40 in src/converter/nmredataToJSON.js

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GitHub Actions / nodejs / lint-eslint 

Capture group '([1|2]d)' should be converted to a named or non-capturing group
let signalProcessor =
dimension === '2d' ? getSignalData2D : getSignalData1D;

Expand All @@ -48,7 +48,7 @@
nucleus,
frequency: frequencyLine.value.larmor,
experiment: pulseProgramLine
? pulseProgramLine.value.pulseprogram
? pulseProgramLine.value.pulseprogram.trim()
: dimension,
headComment: nmredata[tag].headComment,
};
Expand Down
23 changes: 16 additions & 7 deletions src/converter/util/toJSON/getBrukerFiles.js
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Expand Up @@ -14,19 +14,18 @@

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]+\/).*/

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GitHub Actions / nodejs / lint-eslint 

Capture group '([.*/]*\w+\/[0-9]+\/)' should be converted to a named or non-capturing group
: /(.*\w+\/[0-9]+\/)pdata\/.*/;

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Capture group '(.*\w+\/[0-9]+\/)' should be converted to a named or non-capturing group
let toCheck = pathSpectrum.replace(regexRootPath, '$1');

let toCheck2 = pathSpectrum.replace(
/.*\/[0-9]+\/pdata\/([0-9]+)\/.*/,

Check warning on line 24 in src/converter/util/toJSON/getBrukerFiles.js

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GitHub Actions / nodejs / lint-eslint 

Capture group '([0-9]+)' should be converted to a named or non-capturing group
'$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 !==
Expand All @@ -35,8 +34,18 @@
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),
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4 changes: 2 additions & 2 deletions src/converter/util/toJSON/getNucleusFromTag.js
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Expand Up @@ -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;
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