@toxplanet/pegasus-sdk 1.1.24 → 1.1.25

package/lib/chemicals.js

@@ -39,6 +39,42 @@ function parsePostgresArray(str) {
   return result;
 }
 
+function transformChemicalMeta(meta) {
+  if (!meta || typeof meta !== 'object') return [];
+  if (Array.isArray(meta)) {
+    // If it's already in new format, return as-is
+    if (meta.length > 0 && meta[0].key !== undefined) {
+      return meta;
+    }
+    // Transform from old format { meta_key, meta_value_text, meta_value_type, ... } to new format { key, value, [unit] }
+    return meta.map(item => {
+      const transformed = {
+        key: item.meta_key || item.key,
+        value: item.meta_value_text || item.value || []
+      };
+      if (item.unit) transformed.unit = item.unit;
+      return transformed;
+    });
+  }
+  return [];
+}
+
+function transformChemicalIdentifiers(identifiers) {
+  if (!identifiers || typeof identifiers !== 'object') return [];
+  if (Array.isArray(identifiers)) {
+    // If it's already in new format, return as-is
+    if (identifiers.length > 0 && identifiers[0].type !== undefined) {
+      return identifiers;
+    }
+    // Transform from old format { identifier_key, identifier_value, ... } to new format { type, value }
+    return identifiers.map(item => ({
+      type: item.identifier_key || item.type,
+      value: Array.isArray(item.identifier_value) ? item.identifier_value[0] : (item.value || item.identifier_value)
+    }));
+  }
+  return [];
+}
+
 class ChemicalsService {
   constructor(connection) {
     this.connection = connection;
@@ -64,8 +100,8 @@ class ChemicalsService {
       chemicalId: row.chemical_id,
       sourceId: row.source_id,
       chemicalName: row.chemical_name,
-      chemicalMeta: row.chemical_meta ? JSON.parse(row.chemical_meta) : null,
-      chemicalIdentifiers: row.chemical_identifiers ? JSON.parse(row.chemical_identifiers) : null,
+      chemicalMeta: row.chemical_meta ? (Array.isArray(row.chemical_meta) ? row.chemical_meta : JSON.parse(row.chemical_meta)) : null,
+      chemicalIdentifiers: row.chemical_identifiers ? (Array.isArray(row.chemical_identifiers) ? row.chemical_identifiers : JSON.parse(row.chemical_identifiers)) : null,
       chemicalSynonyms: this._parsePostgresArray(row.chemical_synonyms),
       chemicalCategories: this._parsePostgresArray(row.chemical_categories),
       createdAt: row.created_at,
@@ -132,11 +168,14 @@ class ChemicalsService {
       'RETURNING chemical_id, source_id'
     ].join('\n');
 
+    const transformedMeta = transformChemicalMeta(chemical.chemicalMeta);
+    const transformedIdentifiers = transformChemicalIdentifiers(chemical.chemicalIdentifiers);
+
     const parameters = [
       { name: 'source_id', value: { stringValue: chemical.sourceId } },
       { name: 'chemical_name', value: { stringValue: chemical.chemicalName } },
-      { name: 'chemical_meta', value: { stringValue: JSON.stringify(chemical.chemicalMeta ?? {}) }, typeHint: 'JSON' },
-      { name: 'chemical_identifiers', value: { stringValue: JSON.stringify(chemical.chemicalIdentifiers ?? {}) }, typeHint: 'JSON' },
+      { name: 'chemical_meta', value: { stringValue: JSON.stringify(transformedMeta) }, typeHint: 'JSON' },
+      { name: 'chemical_identifiers', value: { stringValue: JSON.stringify(transformedIdentifiers) }, typeHint: 'JSON' },
       { name: 'chemical_synonyms', value: { stringValue: this._toPostgresArray(chemical.chemicalSynonyms ?? []) } },
       { name: 'chemical_categories', value: { stringValue: this._toPostgresArray(chemical.chemicalCategories ?? []) } },
       { name: 'created_at', value: { stringValue: this._serializeDate(chemical.createdAt) } },
@@ -326,13 +365,16 @@ class ChemicalsService {
     try {
       await this.connection.ensureConnected();
       
+      const transformedMeta = transformChemicalMeta(chemical.chemical_meta);
+      const transformedIdentifiers = transformChemicalIdentifiers(chemical.chemical_identifiers);
+
       const columns = ['source_id', 'chemical_name', 'chemical_meta', 'chemical_identifiers', 'chemical_synonyms', 'chemical_categories', 'created_at', 'updated_at'];
       const values = [':source_id', ':chemical_name', ':chemical_meta::jsonb', ':chemical_identifiers::jsonb', ':chemical_synonyms::text[]', ':chemical_categories::text[]', ':created_at::timestamp', ':updated_at::timestamp'];
       const params = [
         { name: 'source_id', value: { stringValue: chemical.source_id } },
         { name: 'chemical_name', value: { stringValue: chemical.chemical_name } },
-        { name: 'chemical_meta', value: { stringValue: JSON.stringify(chemical.chemical_meta || {}) }, typeHint: 'JSON' },
-        { name: 'chemical_identifiers', value: { stringValue: JSON.stringify(chemical.chemical_identifiers || {}) }, typeHint: 'JSON' },
+        { name: 'chemical_meta', value: { stringValue: JSON.stringify(transformedMeta) }, typeHint: 'JSON' },
+        { name: 'chemical_identifiers', value: { stringValue: JSON.stringify(transformedIdentifiers) }, typeHint: 'JSON' },
         { name: 'chemical_synonyms', value: { stringValue: this._toPostgresArray(chemical.chemical_synonyms || []) } },
         { name: 'chemical_categories', value: { stringValue: this._toPostgresArray(chemical.chemical_categories || []) } },
         { name: 'created_at', value: { stringValue: this._serializeDate(chemical.created_at || new Date()) } },
@@ -372,12 +414,14 @@ class ChemicalsService {
         params.push({ name: 'chemical_name', value: { stringValue: updates.chemical_name } });
       }
       if (updates.chemical_meta) {
+        const transformedMeta = transformChemicalMeta(updates.chemical_meta);
         setClauses.push('chemical_meta = :chemical_meta::jsonb');
-        params.push({ name: 'chemical_meta', value: { stringValue: JSON.stringify(updates.chemical_meta) }, typeHint: 'JSON' });
+        params.push({ name: 'chemical_meta', value: { stringValue: JSON.stringify(transformedMeta) }, typeHint: 'JSON' });
       }
       if (updates.chemical_identifiers) {
+        const transformedIdentifiers = transformChemicalIdentifiers(updates.chemical_identifiers);
         setClauses.push('chemical_identifiers = :chemical_identifiers::jsonb');
-        params.push({ name: 'chemical_identifiers', value: { stringValue: JSON.stringify(updates.chemical_identifiers) }, typeHint: 'JSON' });
+        params.push({ name: 'chemical_identifiers', value: { stringValue: JSON.stringify(transformedIdentifiers) }, typeHint: 'JSON' });
       }
       if (updates.chemical_synonyms) {
         setClauses.push('chemical_synonyms = :chemical_synonyms::text[]');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@toxplanet/pegasus-sdk",
-  "version": "1.1.24",
+  "version": "1.1.25",
   "description": "SDK for migrating chemical data to Pegasus PostgreSQL + OpenSearch architecture with Elasticsearch client compatibility",
   "main": "index.js",
   "type": "commonjs",