feat: add TGA zone to zones migration and extract migrations to separate file

Author: lpatiny

.gitignore

@@ -3,3 +3,4 @@ node_modules
 .DS_Store
 build
 .eslintcache
+.claude

eln/Sample.js

@@ -12,6 +12,7 @@ import { createVar } from './jpaths';
 import convertToJcamp from './libs/convertToJcamp';
 import elnPlugin from './libs/elnPlugin';
 import { splitJcamp } from './sample/splitJcamp';
+import { updateSample } from './sampleMigrations';
 
 const DataObject = Datas.DataObject;
 
@@ -916,35 +917,4 @@ async function copyAnalysis(sample, original) {
   UI.showNotification('Analysis copied to clipboard', 'success');
 }
 
-function updateSample(sample) {
-  if (!sample.$content.general) {
-    sample.$content.general = {};
-  }
-
-  /** This is the old place we used to put the sequence.
-   * By default we expect it is a peptidic sequence
-   */
-  if (sample.$content.general.sequence) {
-    // eslint-disable-next-line no-console
-    console.log('Migrating sequence', sample.$content.general.sequence);
-    if (!sample.$content.biology) sample.$content.biology = {};
-    if (!sample.$content.biology.peptidic) {
-      sample.$content.biology.peptidic = [];
-    }
-    if (!sample.$content.biology.peptidic.length > 0) {
-      sample.$content.biology.peptidic[0] = {};
-    }
-    if (!sample.$content.biology.peptidic[0].seq) {
-      sample.$content.biology.peptidic[0].seq = [];
-    }
-    if (!sample.$content.biology.peptidic[0].seq.length > 0) {
-      sample.$content.biology.peptidic[0].seq[0] = {};
-    }
-    sample.setChildSync(
-      ['$content', 'biology', 'peptidic', 0, 'seq', 0, 'sequence'],
-      sample.$content.general.sequence,
-    );
-    sample.$content.general.sequence = undefined;
-  }
-}
 module.exports = Sample;

eln/sampleMigrations.js

@@ -0,0 +1,73 @@
+/**
+ * Migrations for sample data structure changes
+ */
+
+/**
+ * Migrates sequence data from the old location to the new biology structure.
+ * Old location: $content.general.sequence
+ * New location: $content.biology.peptidic[0].seq[0].sequence
+ * By default we expect it is a peptidic sequence.
+ *
+ * @param {object} sample - The sample object to migrate
+ */
+function migrateSequence(sample) {
+  if (!sample.$content.general) {
+    sample.$content.general = {};
+  }
+
+  if (sample.$content.general.sequence) {
+    // eslint-disable-next-line no-console
+    console.log('Migrating sequence', sample.$content.general.sequence);
+    if (!sample.$content.biology) sample.$content.biology = {};
+    if (!sample.$content.biology.peptidic) {
+      sample.$content.biology.peptidic = [];
+    }
+    if (!sample.$content.biology.peptidic.length > 0) {
+      sample.$content.biology.peptidic[0] = {};
+    }
+    if (!sample.$content.biology.peptidic[0].seq) {
+      sample.$content.biology.peptidic[0].seq = [];
+    }
+    if (!sample.$content.biology.peptidic[0].seq.length > 0) {
+      sample.$content.biology.peptidic[0].seq[0] = {};
+    }
+    sample.setChildSync(
+      ['$content', 'biology', 'peptidic', 0, 'seq', 0, 'sequence'],
+      sample.$content.general.sequence,
+    );
+    sample.$content.general.sequence = undefined;
+  }
+}
+
+/**
+ * Migrates thermogravimetric analysis metadata from "zone" to "zones".
+ * Old location: $content.spectra.thermogravimetricAnalysis[].meta.zone
+ * New location: $content.spectra.thermogravimetricAnalysis[].meta.zones
+ *
+ * @param {object} sample - The sample object to migrate
+ */
+function migrateTGAZones(sample) {
+  const tgaEntries = sample.$content?.spectra?.thermogravimetricAnalysis;
+  if (!Array.isArray(tgaEntries)) return;
+
+  for (const entry of tgaEntries) {
+    if (entry.zone && !entry.zones) {
+      // eslint-disable-next-line no-console
+      console.log('Migrating TGA zone to zones');
+      entry.zones = entry.zone;
+      delete entry.zone;
+    }
+  }
+}
+
+/**
+ * Run all migrations on a sample
+ *
+ * @param {object} sample - The sample object to migrate
+ */
+function updateSample(sample) {
+  migrateSequence(sample);
+  migrateTGAZones(sample);
+}
+
+module.exports = { updateSample };