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Merged
NishaSharma14 merged 3 commits into from
Sep 1, 2026
Merged

fix(nmr): handle nested arrays when extracting spectra metadata #1530

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87b1039
fix(nmr): handle nested arrays when extracting spectra metadata
vcnainala Aug 20, 2026
222c902
Merge branch 'development' into fix/spectra-info-array-to-string
vcnainala Aug 20, 2026
451569b
Merge branch 'development' into fix/spectra-info-array-to-string
NishaSharma14 Sep 1, 2026
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123 changes: 105 additions & 18 deletions app/Support/Nmr/DatasetSpectraInfoExtractor.php
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Original file line number Diff line number Diff line change
Expand Up @@ -156,15 +156,12 @@ private function buildSearchText(array $info): string
$parts = [];

foreach ($info as $key => $value) {
if ($value === null || $value === '') {
$flattened = $this->flattenForSearch($value);
if ($flattened === '') {
continue;
}

if (is_array($value)) {
$parts[] = $key.' '.implode(' ', array_map('strval', $value));
} else {
$parts[] = $key.' '.(string) $value;
}
$parts[] = $key.' '.$flattened;
}

$parts[] = json_encode($info, JSON_UNESCAPED_UNICODE) ?: '';
Expand All @@ -174,6 +171,39 @@ private function buildSearchText(array $info): string
return $normalized ?? '';
}

/**
* Recursively stringify scalars so nested NMRium arrays (2D frequencies,
* filters, meta) never trigger "Array to string conversion".
*/
private function flattenForSearch(mixed $value): string
{
if ($value === null || $value === '') {
return '';
}

if (is_bool($value)) {
return $value ? '1' : '';
}

if (is_array($value)) {
$parts = [];
foreach ($value as $item) {
$flattened = $this->flattenForSearch($item);
if ($flattened !== '') {
$parts[] = $flattened;
}
}

return implode(' ', $parts);
}

if (! is_scalar($value)) {
return '';
}

return trim((string) $value);
}

private function property(array $info, string $key): mixed
{
return $info[$key] ?? null;
Expand All @@ -185,20 +215,56 @@ private function normalizeString(mixed $value): ?string
return null;
}

if (is_array($value)) {
foreach ($this->scalarLeaves($value) as $leaf) {
$normalized = $this->normalizeString($leaf);
if ($normalized !== null) {
return $normalized;
}
}

return null;
}

if (is_bool($value) || ! is_scalar($value)) {
return null;
}

$string = trim((string) $value);

return $string === '' ? null : $string;
}

/**
* @return list<int|float|string|bool>
*/
private function scalarLeaves(array $value): array
{
$leaves = [];

array_walk_recursive($value, function (mixed $item) use (&$leaves): void {
if (is_scalar($item)) {
$leaves[] = $item;
}
});

return $leaves;
}

private function normalizeNucleus(mixed $value): ?string
{
return $this->normalizeString($value);
}

private function normalizeDecimal(mixed $value): ?string
{
if ($value === null || $value === '') {
return null;
}

if (is_array($value)) {
foreach ($value as $item) {
$normalized = $this->normalizeString($item);
foreach ($this->scalarLeaves($value) as $leaf) {
$normalized = $this->normalizeDecimal($leaf);
if ($normalized !== null) {
return $normalized;
}
Expand All @@ -207,15 +273,6 @@ private function normalizeNucleus(mixed $value): ?string
return null;
}

return $this->normalizeString($value);
}

private function normalizeDecimal(mixed $value): ?string
{
if ($value === null || $value === '') {
return null;
}

if (! is_numeric($value)) {
return null;
}
Expand All @@ -229,6 +286,17 @@ private function normalizeInteger(mixed $value): ?int
return null;
}

if (is_array($value)) {
foreach ($this->scalarLeaves($value) as $leaf) {
$normalized = $this->normalizeInteger($leaf);
if ($normalized !== null) {
return $normalized;
}
}

return null;
}

if (! is_numeric($value)) {
return null;
}
Expand All @@ -245,7 +313,7 @@ private function normalizeSmallInteger(mixed $value): ?int

private function normalizeBoolean(mixed $value): ?bool
{
if ($value === null || $value === '') {
if ($value === null || $value === '' || is_array($value)) {
return null;
}

Expand All @@ -257,6 +325,10 @@ private function normalizeBoolean(mixed $value): ?bool
return (bool) $value;
}

if (! is_scalar($value)) {
return null;
}

$normalized = strtolower(trim((string) $value));

return match ($normalized) {
Expand Down Expand Up @@ -365,10 +437,25 @@ private function normalizeTubeDiameter(mixed $value): ?string
return null;
}

if (is_array($value)) {
foreach ($this->scalarLeaves($value) as $leaf) {
$normalized = $this->normalizeTubeDiameter($leaf);
if ($normalized !== null) {
return $normalized;
}
}

return null;
}

if (is_numeric($value)) {
return (string) (int) round((float) $value);
}

if (! is_scalar($value)) {
return null;
}

$string = strtolower(trim((string) $value));

if (preg_match('/(\d+(?:\.\d+)?)\s*mm?/', $string, $matches) === 1) {
Expand Down
51 changes: 51 additions & 0 deletions tests/Unit/Support/DatasetSpectraInfoExtractorTest.php
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Original file line number Diff line number Diff line change
Expand Up @@ -303,6 +303,57 @@ public function test_extract_falls_back_to_jcamp_when_no_vendor_metadata(): void
$this->assertSame('JCAMP', $payload['spectra_manufacturer']);
}

public function test_extract_handles_nested_arrays_without_array_to_string_error(): void
{
$dataset = $this->makeDataset();

NMRium::factory()->forDataset($dataset)->create([
'nmrium_info' => [
'data' => [
'spectra' => [
[
'info' => [
'solvent' => 'CDCl3',
'nucleus' => ['1H', '13C'],
'experiment' => ['HSQC'],
'probeName' => ['name' => 'BBO'],
'originFrequency' => [600.13, 150.9],
'baseFrequency' => [600.13, 150.9],
'spectralWidth' => [16.02, 220.0],
'numberOfPoints' => [2048, 512],
'filters' => [
[
'name' => 'shift2D',
'value' => ['shift' => [0, 0]],
],
],
'meta' => [
'instrument' => ['vendor' => 'Bruker'],
],
],
],
],
],
],
]);

$dataset->refresh();

$payload = $this->extractor->extractForDataset($dataset);

$this->assertSame('CDCl3', $payload['spectra_solvent']);
$this->assertSame('1H', $payload['spectra_nucleus']);
$this->assertSame('HSQC', $payload['spectra_experiment']);
$this->assertSame('BBO', $payload['spectra_probe_name']);
$this->assertSame('600.13', $payload['spectra_origin_frequency']);
$this->assertSame('600.13', $payload['spectra_base_frequency']);
$this->assertSame('16.02', $payload['spectra_spectral_width']);
$this->assertSame(2048, $payload['spectra_number_of_points']);
$this->assertNotNull($payload['spectra_info_extracted_at']);
$this->assertStringContainsString('bruker', strtolower($payload['spectra_search_text']));
$this->assertStringContainsString('hsqc', $payload['spectra_search_text']);
}

public function test_extract_returns_empty_payload_when_no_nmrium_info(): void
{
$dataset = $this->makeDataset();
Expand Down
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