massbank 0.1.0 → 0.2.0

package/lib/validation/rules/accession-match-rule.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"accession-match-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/accession-match-rule.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACzE,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAE/E;;;;GAIG;AACH,qBAAa,kBAAmB,YAAW,eAAe;IACxD,QAAQ,CACN,MAAM,EAAE,MAAM,EACd,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,EAAE,qBAAqB,GAC9B,eAAe,EAAE;IAgBpB,WAAW,IAAI,iBAAiB,EAAE;CAGnC"}
+{"version":3,"file":"accession-match-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/accession-match-rule.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACzE,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAqB/E;;;;GAIG;AACH,qBAAa,kBAAmB,YAAW,eAAe;IACxD,QAAQ,CACN,MAAM,EAAE,MAAM,EACd,aAAa,EAAE,MAAM,EACrB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,EAAE,qBAAqB,GAC9B,eAAe,EAAE;IAgBpB,WAAW,IAAI,iBAAiB,EAAE;CAGnC"}

package/lib/validation/rules/accession-match-rule.js

@@ -1,4 +1,17 @@
-import path from 'node:path';
+/**
+ * Get the filename from a path (browser-compatible alternative to path.basename)
+ */
+function getBasename(filepath) {
+    const lastSlash = Math.max(filepath.lastIndexOf('/'), filepath.lastIndexOf('\\'));
+    return lastSlash >= 0 ? filepath.slice(lastSlash + 1) : filepath;
+}
+/**
+ * Remove the extension from a filename (browser-compatible alternative to path.extname)
+ */
+function removeExtension(filename) {
+    const lastDot = filename.lastIndexOf('.');
+    return lastDot > 0 ? filename.slice(0, lastDot) : filename;
+}
 /**
  * Validates that ACCESSION matches the filename
  * Only validates ACCESSION-filename matching.
@@ -9,12 +22,12 @@ export class AccessionMatchRule {
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
     _options) {
         const errors = [];
-        const basename = path.basename(filename, path.extname(filename));
+        const basename = removeExtension(getBasename(filename));
         if (record.ACCESSION !== basename) {
             errors.push({
                 file: filename,
                 line: 1,
-                message: `ACCESSION ${record.ACCESSION} does not match filename '${filename}'`,
+                message: `ACCESSION mismatch: File is named '${basename}.txt' but ACCESSION field is '${record.ACCESSION}'. Fix: Either rename the file to '${record.ACCESSION}.txt' or change ACCESSION field to '${basename}'.`,
                 type: 'validation',
             });
         }

package/lib/validation/rules/accession-match-rule.js.map

@@ -1 +1 @@
-{"version":3,"file":"accession-match-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/accession-match-rule.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAM7B;;;;GAIG;AACH,MAAM,OAAO,kBAAkB;IAC7B,QAAQ,CACN,MAAc,EACd,aAAqB,EACrB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,MAAM,GAAsB,EAAE,CAAC;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC,QAAQ,EAAE,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;QAEjE,IAAI,MAAM,CAAC,SAAS,KAAK,QAAQ,EAAE,CAAC;YAClC,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,QAAQ;gBACd,IAAI,EAAE,CAAC;gBACP,OAAO,EAAE,aAAa,MAAM,CAAC,SAAS,6BAA6B,QAAQ,GAAG;gBAC9E,IAAI,EAAE,YAAY;aACnB,CAAC,CAAC;QACL,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,WAAW;QACT,OAAO,EAAE,CAAC;IACZ,CAAC;CACF"}
+{"version":3,"file":"accession-match-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/accession-match-rule.ts"],"names":[],"mappings":"AAIA;;GAEG;AACH,SAAS,WAAW,CAAC,QAAgB;IACnC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CACxB,QAAQ,CAAC,WAAW,CAAC,GAAG,CAAC,EACzB,QAAQ,CAAC,WAAW,CAAC,IAAI,CAAC,CAC3B,CAAC;IACF,OAAO,SAAS,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;AACnE,CAAC;AAED;;GAEG;AACH,SAAS,eAAe,CAAC,QAAgB;IACvC,MAAM,OAAO,GAAG,QAAQ,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;IAC1C,OAAO,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;AAC7D,CAAC;AAED;;;;GAIG;AACH,MAAM,OAAO,kBAAkB;IAC7B,QAAQ,CACN,MAAc,EACd,aAAqB,EACrB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,MAAM,GAAsB,EAAE,CAAC;QACrC,MAAM,QAAQ,GAAG,eAAe,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;QAExD,IAAI,MAAM,CAAC,SAAS,KAAK,QAAQ,EAAE,CAAC;YAClC,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,QAAQ;gBACd,IAAI,EAAE,CAAC;gBACP,OAAO,EAAE,sCAAsC,QAAQ,iCAAiC,MAAM,CAAC,SAAS,sCAAsC,MAAM,CAAC,SAAS,uCAAuC,QAAQ,IAAI;gBACjN,IAAI,EAAE,YAAY;aACnB,CAAC,CAAC;QACL,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,WAAW;QACT,OAAO,EAAE,CAAC;IACZ,CAAC;CACF"}

package/lib/validation/rules/non-standard-chars-rule.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"non-standard-chars-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/non-standard-chars-rule.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACzE,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAa/E;;;;GAIG;AACH,qBAAa,oBAAqB,YAAW,eAAe;IAC1D,QAAQ,CACN,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,MAAM,EACrB,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,qBAAqB,GAC9B,eAAe,EAAE;IAQpB,WAAW,CACT,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,EAAE,qBAAqB,GAC9B,iBAAiB,EAAE;CAyBvB"}
+{"version":3,"file":"non-standard-chars-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/non-standard-chars-rule.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACzE,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAa/E;;;;GAIG;AACH,qBAAa,oBAAqB,YAAW,eAAe;IAC1D,QAAQ,CACN,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,MAAM,EACrB,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,qBAAqB,GAC9B,eAAe,EAAE;IAQpB,WAAW,CACT,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,EAAE,qBAAqB,GAC9B,iBAAiB,EAAE;CA4CvB"}

package/lib/validation/rules/non-standard-chars-rule.js

@@ -32,11 +32,27 @@ export class NonStandardCharsRule {
         const match = NON_STANDARD_CHARS_PATTERN.exec(originalText);
         if (match?.index !== undefined) {
             const { line, column } = PositionUtils.getLineColumn(originalText, match.index);
+            const char = match[0] || '';
+            const codePoint = char.codePointAt(0);
+            const hex = codePoint
+                ? `U+${codePoint.toString(16).toUpperCase().padStart(4, '0')}`
+                : '';
+            // Common replacements
+            const suggestions = new Map([
+                ['\u2014', 'Replace em-dash with hyphen'],
+                ['\u201C', 'Replace fancy opening quote with straight quote (")'],
+                ['\u201D', 'Replace fancy closing quote with straight quote (")'],
+                ['\u2018', "Replace fancy opening apostrophe with straight quote (')"],
+                ['\u2019', "Replace fancy closing apostrophe with straight quote (')"],
+                ['\u2022', 'Replace bullet point with hyphen (-)'],
+                ['\u00AE', 'Replace registered symbol with (R)'],
+            ]);
+            const suggestion = suggestions.get(char) || 'Replace with standard ASCII character';
             warnings.push({
                 file: filename,
                 line,
                 column,
-                message: 'Non standard ASCII character found. This might be an error. Please check carefully.',
+                message: `Non-standard character '${char}' (${hex}) found. ${suggestion}`,
             });
         }
         return warnings;

package/lib/validation/rules/non-standard-chars-rule.js.map

@@ -1 +1 @@
-{"version":3,"file":"non-standard-chars-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/non-standard-chars-rule.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAKtD;;;;;;;GAOG;AACH,MAAM,0BAA0B,GAC9B,yDAAyD,CAAC;AAE5D;;;;GAIG;AACH,MAAM,OAAO,oBAAoB;IAC/B,QAAQ,CACN,OAAe,EACf,aAAqB,EACrB,SAAiB,EACjB,QAA+B;QAE/B,KAAK,OAAO,CAAC;QACb,KAAK,aAAa,CAAC;QACnB,KAAK,SAAS,CAAC;QACf,KAAK,QAAQ,CAAC;QACd,OAAO,EAAE,CAAC;IACZ,CAAC;IAED,WAAW,CACT,MAAc,EACd,YAAoB,EACpB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,QAAQ,GAAwB,EAAE,CAAC;QAEzC,0BAA0B;QAC1B,IAAI,MAAM,CAAC,UAAU,EAAE,CAAC;YACtB,OAAO,QAAQ,CAAC;QAClB,CAAC;QAED,MAAM,KAAK,GAAG,0BAA0B,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;QAC5D,IAAI,KAAK,EAAE,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/B,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,aAAa,CAAC,aAAa,CAClD,YAAY,EACZ,KAAK,CAAC,KAAK,CACZ,CAAC;YACF,QAAQ,CAAC,IAAI,CAAC;gBACZ,IAAI,EAAE,QAAQ;gBACd,IAAI;gBACJ,MAAM;gBACN,OAAO,EACL,qFAAqF;aACxF,CAAC,CAAC;QACL,CAAC;QAED,OAAO,QAAQ,CAAC;IAClB,CAAC;CACF"}
+{"version":3,"file":"non-standard-chars-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/non-standard-chars-rule.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAKtD;;;;;;;GAOG;AACH,MAAM,0BAA0B,GAC9B,yDAAyD,CAAC;AAE5D;;;;GAIG;AACH,MAAM,OAAO,oBAAoB;IAC/B,QAAQ,CACN,OAAe,EACf,aAAqB,EACrB,SAAiB,EACjB,QAA+B;QAE/B,KAAK,OAAO,CAAC;QACb,KAAK,aAAa,CAAC;QACnB,KAAK,SAAS,CAAC;QACf,KAAK,QAAQ,CAAC;QACd,OAAO,EAAE,CAAC;IACZ,CAAC;IAED,WAAW,CACT,MAAc,EACd,YAAoB,EACpB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,QAAQ,GAAwB,EAAE,CAAC;QAEzC,0BAA0B;QAC1B,IAAI,MAAM,CAAC,UAAU,EAAE,CAAC;YACtB,OAAO,QAAQ,CAAC;QAClB,CAAC;QAED,MAAM,KAAK,GAAG,0BAA0B,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;QAC5D,IAAI,KAAK,EAAE,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/B,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,aAAa,CAAC,aAAa,CAClD,YAAY,EACZ,KAAK,CAAC,KAAK,CACZ,CAAC;YACF,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YAC5B,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;YACtC,MAAM,GAAG,GAAG,SAAS;gBACnB,CAAC,CAAC,KAAK,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE;gBAC9D,CAAC,CAAC,EAAE,CAAC;YAEP,sBAAsB;YACtB,MAAM,WAAW,GAAG,IAAI,GAAG,CAAiB;gBAC1C,CAAC,QAAQ,EAAE,6BAA6B,CAAC;gBACzC,CAAC,QAAQ,EAAE,qDAAqD,CAAC;gBACjE,CAAC,QAAQ,EAAE,qDAAqD,CAAC;gBACjE,CAAC,QAAQ,EAAE,0DAA0D,CAAC;gBACtE,CAAC,QAAQ,EAAE,0DAA0D,CAAC;gBACtE,CAAC,QAAQ,EAAE,sCAAsC,CAAC;gBAClD,CAAC,QAAQ,EAAE,oCAAoC,CAAC;aACjD,CAAC,CAAC;YAEH,MAAM,UAAU,GACd,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,uCAAuC,CAAC;YAEnE,QAAQ,CAAC,IAAI,CAAC;gBACZ,IAAI,EAAE,QAAQ;gBACd,IAAI;gBACJ,MAAM;gBACN,OAAO,EAAE,2BAA2B,IAAI,MAAM,GAAG,YAAY,UAAU,EAAE;aAC1E,CAAC,CAAC;QACL,CAAC;QAED,OAAO,QAAQ,CAAC;IAClB,CAAC;CACF"}

package/lib/validation/rules/serialization-rule.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"serialization-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/serialization-rule.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAE9C,OAAO,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACzE,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAE/E;;;;GAIG;AACH,qBAAa,iBAAkB,YAAW,eAAe;IACvD,QAAQ,CACN,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,EAAE,qBAAqB,GAC9B,eAAe,EAAE;IAuCpB,WAAW,IAAI,iBAAiB,EAAE;IAIlC,OAAO,CAAC,mBAAmB;CAY5B"}
+{"version":3,"file":"serialization-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/serialization-rule.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAE9C,OAAO,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACzE,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAE/E;;;;GAIG;AACH,qBAAa,iBAAkB,YAAW,eAAe;IACvD,QAAQ,CACN,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,EAAE,qBAAqB,GAC9B,eAAe,EAAE;IAkEpB,WAAW,IAAI,iBAAiB,EAAE;IAIlC,OAAO,CAAC,mBAAmB;CAY5B"}

package/lib/validation/rules/serialization-rule.js

@@ -18,11 +18,34 @@ export class SerializationRule {
             const diffPosition = this.findFirstDifference(normalizedOriginal, serialized);
             if (diffPosition !== -1) {
                 const { line, column } = PositionUtils.getLineColumn(normalizedOriginal, diffPosition);
+                // Get context around the difference for better error message
+                const originalLine = normalizedOriginal.split('\n')[line - 1] || '';
+                const serializedLine = serialized.split('\n')[line - 1] || '';
+                let message = 'File formatting issue detected (round-trip validation failed).';
+                // Provide specific guidance based on common issues
+                if (originalLine !== serializedLine) {
+                    if (originalLine.includes('  ') && serializedLine.includes(' ')) {
+                        message += ' Check for extra spaces or inconsistent spacing.';
+                    }
+                    else if (!serializedLine.trim()) {
+                        message +=
+                            ' This line may contain unrecognized fields that were ignored during parsing.';
+                    }
+                    else {
+                        const expectedPreview = serializedLine.length > 80
+                            ? `${serializedLine.slice(0, 77)}...`
+                            : serializedLine;
+                        const foundPreview = originalLine.length > 80
+                            ? `${originalLine.slice(0, 77)}...`
+                            : originalLine;
+                        message += ` Expected (${serializedLine.length} chars): "${expectedPreview}" but found (${originalLine.length} chars): "${foundPreview}"`;
+                    }
+                }
                 errors.push({
                     file: filename,
                     line,
                     column,
-                    message: 'File content differs from generated record string. This might be a code problem. Please Report!',
+                    message,
                     type: 'serialization',
                 });
             }

package/lib/validation/rules/serialization-rule.js.map

@@ -1 +1 @@
-{"version":3,"file":"serialization-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/serialization-rule.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAI5D;;;;GAIG;AACH,MAAM,OAAO,iBAAiB;IAC5B,QAAQ,CACN,MAAc,EACd,YAAoB,EACpB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,MAAM,GAAsB,EAAE,CAAC;QAErC,IAAI,CAAC;YACH,MAAM,UAAU,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC;YAC3C,6DAA6D;YAC7D,MAAM,kBAAkB,GAAG,YAAY,CAAC,OAAO,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC;YAEhE,wBAAwB;YACxB,MAAM,YAAY,GAAG,IAAI,CAAC,mBAAmB,CAC3C,kBAAkB,EAClB,UAAU,CACX,CAAC;YAEF,IAAI,YAAY,KAAK,CAAC,CAAC,EAAE,CAAC;gBACxB,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,aAAa,CAAC,aAAa,CAClD,kBAAkB,EAClB,YAAY,CACb,CAAC;gBACF,MAAM,CAAC,IAAI,CAAC;oBACV,IAAI,EAAE,QAAQ;oBACd,IAAI;oBACJ,MAAM;oBACN,OAAO,EACL,iGAAiG;oBACnG,IAAI,EAAE,eAAe;iBACtB,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,QAAQ;gBACd,OAAO,EAAE,yBAAyB,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,eAAe,EAAE;gBAC5F,IAAI,EAAE,eAAe;aACtB,CAAC,CAAC;QACL,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,WAAW;QACT,OAAO,EAAE,CAAC;IACZ,CAAC;IAEO,mBAAmB,CAAC,IAAY,EAAE,IAAY;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QACrD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;YACnC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;gBACxB,OAAO,CAAC,CAAC;YACX,CAAC;QACH,CAAC;QACD,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,EAAE,CAAC;YAChC,OAAO,SAAS,CAAC;QACnB,CAAC;QACD,OAAO,CAAC,CAAC,CAAC;IACZ,CAAC;CACF"}
+{"version":3,"file":"serialization-rule.js","sourceRoot":"","sources":["../../../src/validation/rules/serialization-rule.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAI5D;;;;GAIG;AACH,MAAM,OAAO,iBAAiB;IAC5B,QAAQ,CACN,MAAc,EACd,YAAoB,EACpB,QAAgB;IAChB,6DAA6D;IAC7D,QAA+B;QAE/B,MAAM,MAAM,GAAsB,EAAE,CAAC;QAErC,IAAI,CAAC;YACH,MAAM,UAAU,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC;YAC3C,6DAA6D;YAC7D,MAAM,kBAAkB,GAAG,YAAY,CAAC,OAAO,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC;YAEhE,wBAAwB;YACxB,MAAM,YAAY,GAAG,IAAI,CAAC,mBAAmB,CAC3C,kBAAkB,EAClB,UAAU,CACX,CAAC;YAEF,IAAI,YAAY,KAAK,CAAC,CAAC,EAAE,CAAC;gBACxB,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,aAAa,CAAC,aAAa,CAClD,kBAAkB,EAClB,YAAY,CACb,CAAC;gBAEF,6DAA6D;gBAC7D,MAAM,YAAY,GAAG,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBACpE,MAAM,cAAc,GAAG,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAE9D,IAAI,OAAO,GACT,gEAAgE,CAAC;gBAEnE,mDAAmD;gBACnD,IAAI,YAAY,KAAK,cAAc,EAAE,CAAC;oBACpC,IAAI,YAAY,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;wBAChE,OAAO,IAAI,kDAAkD,CAAC;oBAChE,CAAC;yBAAM,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,EAAE,CAAC;wBAClC,OAAO;4BACL,8EAA8E,CAAC;oBACnF,CAAC;yBAAM,CAAC;wBACN,MAAM,eAAe,GACnB,cAAc,CAAC,MAAM,GAAG,EAAE;4BACxB,CAAC,CAAC,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;4BACrC,CAAC,CAAC,cAAc,CAAC;wBACrB,MAAM,YAAY,GAChB,YAAY,CAAC,MAAM,GAAG,EAAE;4BACtB,CAAC,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;4BACnC,CAAC,CAAC,YAAY,CAAC;wBACnB,OAAO,IAAI,cAAc,cAAc,CAAC,MAAM,aAAa,eAAe,gBAAgB,YAAY,CAAC,MAAM,aAAa,YAAY,GAAG,CAAC;oBAC5I,CAAC;gBACH,CAAC;gBAED,MAAM,CAAC,IAAI,CAAC;oBACV,IAAI,EAAE,QAAQ;oBACd,IAAI;oBACJ,MAAM;oBACN,OAAO;oBACP,IAAI,EAAE,eAAe;iBACtB,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,CAAC,IAAI,CAAC;gBACV,IAAI,EAAE,QAAQ;gBACd,OAAO,EAAE,yBAAyB,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,eAAe,EAAE;gBAC5F,IAAI,EAAE,eAAe;aACtB,CAAC,CAAC;QACL,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,WAAW;QACT,OAAO,EAAE,CAAC;IACZ,CAAC;IAEO,mBAAmB,CAAC,IAAY,EAAE,IAAY;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QACrD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;YACnC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;gBACxB,OAAO,CAAC,CAAC;YACX,CAAC;QACH,CAAC;QACD,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,EAAE,CAAC;YAChC,OAAO,SAAS,CAAC;QACnB,CAAC;QACD,OAAO,CAAC,CAAC,CAAC;IACZ,CAAC;CACF"}

package/lib/validation/rules/unrecognized-field-rule.d.ts

@@ -12,5 +12,14 @@ export declare class UnrecognizedFieldRule implements IValidationRule {
     private readonly recognizedFields;
     validate(_record: Record, _originalText: string, _filename: string, _options?: ValidationRuleOptions): never[];
     getWarnings(_record: Record, originalText: string, filename: string, _options?: ValidationRuleOptions): ValidationWarning[];
+    /**
+     * Find a similar field name for typo suggestions
+     * Uses simple Levenshtein distance for similarity
+     */
+    private findSimilarField;
+    /**
+     * Calculate Levenshtein distance between two strings
+     */
+    private levenshteinDistance;
 }
 //# sourceMappingURL=unrecognized-field-rule.d.ts.map

package/lib/validation/rules/unrecognized-field-rule.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"unrecognized-field-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/unrecognized-field-rule.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAE/E;;;GAGG;AACH,qBAAa,qBAAsB,YAAW,eAAe;IAC3D;;OAEG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAsC9B;IAEH,QAAQ,CAEN,OAAO,EAAE,MAAM,EAEf,aAAa,EAAE,MAAM,EAErB,SAAS,EAAE,MAAM,EAEjB,QAAQ,CAAC,EAAE,qBAAqB,GAC/B,KAAK,EAAE;IAKV,WAAW,CACT,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,CAAC,EAAE,qBAAqB,GAC/B,iBAAiB,EAAE;CA6BvB"}
+{"version":3,"file":"unrecognized-field-rule.d.ts","sourceRoot":"","sources":["../../../src/validation/rules/unrecognized-field-rule.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,KAAK,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAE/E;;;GAGG;AACH,qBAAa,qBAAsB,YAAW,eAAe;IAC3D;;OAEG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAsC9B;IAEH,QAAQ,CAEN,OAAO,EAAE,MAAM,EAEf,aAAa,EAAE,MAAM,EAErB,SAAS,EAAE,MAAM,EAEjB,QAAQ,CAAC,EAAE,qBAAqB,GAC/B,KAAK,EAAE;IAKV,WAAW,CACT,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAEhB,QAAQ,CAAC,EAAE,qBAAqB,GAC/B,iBAAiB,EAAE;IA0CtB;;;OAGG;IACH,OAAO,CAAC,gBAAgB;IAgBxB;;OAEG;IACH,OAAO,CAAC,mBAAmB;CAkC5B"}

package/lib/validation/rules/unrecognized-field-rule.js

@@ -74,14 +74,76 @@ export class UnrecognizedFieldRule {
             const key = line.slice(0, colonIndex).trim();
             // Check if this is an unrecognized field
             if (!this.recognizedFields.has(key)) {
+                // Suggest similar field names for common typos
+                // Normalize to uppercase for comparison to catch case errors
+                const suggestion = this.findSimilarField(key.toUpperCase());
+                let message = `Unrecognized field '${key}'. Not a valid MassBank 2.6.0 field.`;
+                if (suggestion) {
+                    message += ` Did you mean '${suggestion}'?`;
+                }
+                else {
+                    message +=
+                        ' Remove this line or check the MassBank format specification.';
+                }
                 warnings.push({
                     file: filename,
                     line: i + 1,
-                    message: `Unrecognized field '${key}'. This may be a typo or an unsupported field.`,
+                    message,
                 });
             }
         }
         return warnings;
     }
+    /**
+     * Find a similar field name for typo suggestions
+     * Uses simple Levenshtein distance for similarity
+     */
+    findSimilarField(input) {
+        let bestMatch = null;
+        let bestDistance = Number.POSITIVE_INFINITY;
+        for (const field of this.recognizedFields) {
+            const distance = this.levenshteinDistance(input, field);
+            // Only suggest if very similar (distance <= 2)
+            if (distance <= 2 && distance < bestDistance) {
+                bestDistance = distance;
+                bestMatch = field;
+            }
+        }
+        return bestMatch;
+    }
+    /**
+     * Calculate Levenshtein distance between two strings
+     */
+    levenshteinDistance(a, b) {
+        const matrix = [];
+        for (let i = 0; i <= b.length; i++) {
+            matrix[i] = [i];
+        }
+        const firstRow = matrix[0];
+        if (firstRow) {
+            for (let j = 0; j <= a.length; j++) {
+                firstRow[j] = j;
+            }
+        }
+        for (let i = 1; i <= b.length; i++) {
+            const currentRow = matrix[i];
+            const prevRow = matrix[i - 1];
+            if (!currentRow || !prevRow)
+                continue;
+            for (let j = 1; j <= a.length; j++) {
+                if (b.charAt(i - 1) === a.charAt(j - 1)) {
+                    currentRow[j] = prevRow[j - 1] ?? 0;
+                }
+                else {
+                    const substitution = (prevRow[j - 1] ?? 0) + 1;
+                    const insertion = (currentRow[j - 1] ?? 0) + 1;
+                    const deletion = (prevRow[j] ?? 0) + 1;
+                    currentRow[j] = Math.min(substitution, insertion, deletion);
+                }
+            }
+        }
+        const lastRow = matrix[b.length];
+        return lastRow?.[a.length] ?? Number.POSITIVE_INFINITY;
+    }
 }
 //# sourceMappingURL=unrecognized-field-rule.js.map

package/lib/validation/rules/unrecognized-field-rule.js.map

@@ -1 +1 @@
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package/lib/validator/validator.d.ts.map

@@ -1 +1 @@
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package/lib/validator/validator.js

@@ -1,6 +1,5 @@
 import { ParseException, parseRecord } from '../parser/index.js';
 import { RecordValidator } from '../validation/index.js';
-import { FileUtils } from './file-utils.js';
 /**
  * Validate a single MassBank record file
  * @param filePath - Path to the .txt file
@@ -15,6 +14,8 @@ export async function validate(filePath, options = {}) {
     if (options.logger) {
         options.logger.info(`Validating file: ${filePath}`);
     }
+    // Dynamic import to avoid pulling node:fs/promises into browser bundles
+    const { FileUtils } = await import('./file-utils.js');
     // Read file
     let fileContent;
     try {

package/lib/validator/validator.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "massbank",
-  "version": "0.1.0",
+  "version": "0.2.0",
   "license": "MIT",
   "description": "Utilities to submit massbank data",
   "keywords": [],

package/src/validation/rules/accession-match-rule.ts

@@ -1,9 +1,26 @@
-import path from 'node:path';
-
 import type { Record } from '../../record.js';
 import type { ValidationError, ValidationWarning } from '../../types.js';
 import type { IValidationRule, ValidationRuleOptions } from '../interfaces.js';
 
+/**
+ * Get the filename from a path (browser-compatible alternative to path.basename)
+ */
+function getBasename(filepath: string): string {
+  const lastSlash = Math.max(
+    filepath.lastIndexOf('/'),
+    filepath.lastIndexOf('\\'),
+  );
+  return lastSlash >= 0 ? filepath.slice(lastSlash + 1) : filepath;
+}
+
+/**
+ * Remove the extension from a filename (browser-compatible alternative to path.extname)
+ */
+function removeExtension(filename: string): string {
+  const lastDot = filename.lastIndexOf('.');
+  return lastDot > 0 ? filename.slice(0, lastDot) : filename;
+}
+
 /**
  * Validates that ACCESSION matches the filename
  * Only validates ACCESSION-filename matching.
@@ -18,13 +35,13 @@ export class AccessionMatchRule implements IValidationRule {
     _options: ValidationRuleOptions,
   ): ValidationError[] {
     const errors: ValidationError[] = [];
-    const basename = path.basename(filename, path.extname(filename));
+    const basename = removeExtension(getBasename(filename));
 
     if (record.ACCESSION !== basename) {
       errors.push({
         file: filename,
         line: 1,
-        message: `ACCESSION ${record.ACCESSION} does not match filename '${filename}'`,
+        message: `ACCESSION mismatch: File is named '${basename}.txt' but ACCESSION field is '${record.ACCESSION}'. Fix: Either rename the file to '${record.ACCESSION}.txt' or change ACCESSION field to '${basename}'.`,
         type: 'validation',
       });
     }

package/src/validation/rules/non-standard-chars-rule.ts

@@ -53,12 +53,31 @@ export class NonStandardCharsRule implements IValidationRule {
         originalText,
         match.index,
       );
+      const char = match[0] || '';
+      const codePoint = char.codePointAt(0);
+      const hex = codePoint
+        ? `U+${codePoint.toString(16).toUpperCase().padStart(4, '0')}`
+        : '';
+
+      // Common replacements
+      const suggestions = new Map<string, string>([
+        ['\u2014', 'Replace em-dash with hyphen'],
+        ['\u201C', 'Replace fancy opening quote with straight quote (")'],
+        ['\u201D', 'Replace fancy closing quote with straight quote (")'],
+        ['\u2018', "Replace fancy opening apostrophe with straight quote (')"],
+        ['\u2019', "Replace fancy closing apostrophe with straight quote (')"],
+        ['\u2022', 'Replace bullet point with hyphen (-)'],
+        ['\u00AE', 'Replace registered symbol with (R)'],
+      ]);
+
+      const suggestion =
+        suggestions.get(char) || 'Replace with standard ASCII character';
+
       warnings.push({
         file: filename,
         line,
         column,
-        message:
-          'Non standard ASCII character found. This might be an error. Please check carefully.',
+        message: `Non-standard character '${char}' (${hex}) found. ${suggestion}`,
       });
     }
 

package/src/validation/rules/serialization-rule.ts

@@ -35,12 +35,39 @@ export class SerializationRule implements IValidationRule {
           normalizedOriginal,
           diffPosition,
         );
+
+        // Get context around the difference for better error message
+        const originalLine = normalizedOriginal.split('\n')[line - 1] || '';
+        const serializedLine = serialized.split('\n')[line - 1] || '';
+
+        let message =
+          'File formatting issue detected (round-trip validation failed).';
+
+        // Provide specific guidance based on common issues
+        if (originalLine !== serializedLine) {
+          if (originalLine.includes('  ') && serializedLine.includes(' ')) {
+            message += ' Check for extra spaces or inconsistent spacing.';
+          } else if (!serializedLine.trim()) {
+            message +=
+              ' This line may contain unrecognized fields that were ignored during parsing.';
+          } else {
+            const expectedPreview =
+              serializedLine.length > 80
+                ? `${serializedLine.slice(0, 77)}...`
+                : serializedLine;
+            const foundPreview =
+              originalLine.length > 80
+                ? `${originalLine.slice(0, 77)}...`
+                : originalLine;
+            message += ` Expected (${serializedLine.length} chars): "${expectedPreview}" but found (${originalLine.length} chars): "${foundPreview}"`;
+          }
+        }
+
         errors.push({
           file: filename,
           line,
           column,
-          message:
-            'File content differs from generated record string. This might be a code problem. Please Report!',
+          message,
           type: 'serialization',
         });
       }

package/src/validation/rules/unrecognized-field-rule.ts

@@ -89,14 +89,84 @@ export class UnrecognizedFieldRule implements IValidationRule {
 
       // Check if this is an unrecognized field
       if (!this.recognizedFields.has(key)) {
+        // Suggest similar field names for common typos
+        // Normalize to uppercase for comparison to catch case errors
+        const suggestion = this.findSimilarField(key.toUpperCase());
+        let message = `Unrecognized field '${key}'. Not a valid MassBank 2.6.0 field.`;
+
+        if (suggestion) {
+          message += ` Did you mean '${suggestion}'?`;
+        } else {
+          message +=
+            ' Remove this line or check the MassBank format specification.';
+        }
+
         warnings.push({
           file: filename,
           line: i + 1,
-          message: `Unrecognized field '${key}'. This may be a typo or an unsupported field.`,
+          message,
         });
       }
     }
 
     return warnings;
   }
+
+  /**
+   * Find a similar field name for typo suggestions
+   * Uses simple Levenshtein distance for similarity
+   */
+  private findSimilarField(input: string): string | null {
+    let bestMatch: string | null = null;
+    let bestDistance = Number.POSITIVE_INFINITY;
+
+    for (const field of this.recognizedFields) {
+      const distance = this.levenshteinDistance(input, field);
+      // Only suggest if very similar (distance <= 2)
+      if (distance <= 2 && distance < bestDistance) {
+        bestDistance = distance;
+        bestMatch = field;
+      }
+    }
+
+    return bestMatch;
+  }
+
+  /**
+   * Calculate Levenshtein distance between two strings
+   */
+  private levenshteinDistance(a: string, b: string): number {
+    const matrix: number[][] = [];
+
+    for (let i = 0; i <= b.length; i++) {
+      matrix[i] = [i];
+    }
+
+    const firstRow = matrix[0];
+    if (firstRow) {
+      for (let j = 0; j <= a.length; j++) {
+        firstRow[j] = j;
+      }
+    }
+
+    for (let i = 1; i <= b.length; i++) {
+      const currentRow = matrix[i];
+      const prevRow = matrix[i - 1];
+      if (!currentRow || !prevRow) continue;
+
+      for (let j = 1; j <= a.length; j++) {
+        if (b.charAt(i - 1) === a.charAt(j - 1)) {
+          currentRow[j] = prevRow[j - 1] ?? 0;
+        } else {
+          const substitution = (prevRow[j - 1] ?? 0) + 1;
+          const insertion = (currentRow[j - 1] ?? 0) + 1;
+          const deletion = (prevRow[j] ?? 0) + 1;
+          currentRow[j] = Math.min(substitution, insertion, deletion);
+        }
+      }
+    }
+
+    const lastRow = matrix[b.length];
+    return lastRow?.[a.length] ?? Number.POSITIVE_INFINITY;
+  }
 }

package/src/validator/validator.ts

@@ -7,8 +7,6 @@ import type {
 } from '../types.js';
 import { RecordValidator } from '../validation/index.js';
 
-import { FileUtils } from './file-utils.js';
-
 /**
  * Validate a single MassBank record file
  * @param filePath - Path to the .txt file
@@ -28,6 +26,9 @@ export async function validate(
     options.logger.info(`Validating file: ${filePath}`);
   }
 
+  // Dynamic import to avoid pulling node:fs/promises into browser bundles
+  const { FileUtils } = await import('./file-utils.js');
+
   // Read file
   let fileContent: string;
   try {