massbank 0.0.2 → 0.2.0

package/README.md

@@ -5,7 +5,7 @@
 [![test coverage](https://img.shields.io/codecov/c/github/cheminfo/massbank.svg)](https://codecov.io/gh/cheminfo/massbank)
 [![license](https://img.shields.io/npm/l/massbank.svg)](https://github.com/cheminfo/massbank/blob/main/LICENSE)
 
-Utilities to submit massbank data.
+A TypeScript/JavaScript library for validating MassBank record files. This library provides validation for MassBank format 2.6.0, ensuring compliance with MassBank standards for automated submission to the MassBank-data repository.
 
 ## Installation
 
@@ -15,13 +15,116 @@ npm install massbank
 
 ## Usage
 
-```js
-import { myModule } from 'massbank';
+### Basic File Validation
 
-const result = myModule(args);
-// result is ...
+```typescript
+import { validate } from 'massbank';
+
+// Validate a single file
+const result = await validate('path/to/MSBNK-test-TST00001.txt');
+
+if (result.success) {
+  console.log('Validation passed!');
+  console.log('Accession:', result.accessions[0]);
+} else {
+  console.error('❌ Validation failed:');
+  result.errors.forEach((error) => {
+    console.error(`  Line ${error.line}: ${error.message}`);
+  });
+}
+```
+
+### In-Memory Validation
+
+```typescript
+import { validateContent } from 'massbank';
+
+// Validate record text without file I/O
+const recordText = `ACCESSION: MSBNK-test-TST00001
+RECORD_TITLE: Test Record
+//`;
+
+const result = await validateContent(recordText, 'MSBNK-test-TST00001.txt');
+```
+
+### With Options
+
+```typescript
+import { validate } from 'massbank';
+import { FifoLogger } from 'fifo-logger';
+
+const logger = new FifoLogger({ level: 'info' });
+
+const result = await validate('record.txt', {
+  legacy: true, // Enable legacy mode for less strict validation
+  logger: logger, // Optional logger for validation messages
+});
+```
+
+## Validation Rules
+
+The validator performs the following checks:
+
+1. **Parse Validation** - Ensures the record can be parsed correctly according to MassBank format 2.6.0
+2. **ACCESSION Matching** - Validates that ACCESSION field matches the filename (CRITICAL for MassBank-data repository)
+   - Example: File `MSBNK-test-TST00001.txt` must contain `ACCESSION: MSBNK-test-TST00001`
+3. **Unrecognized Fields** - Warns about unrecognized field names (helps catch typos like `RECRD_TITLE` instead of `RECORD_TITLE`)
+4. **Non-Standard Characters** - Warns about non-standard ASCII characters (non-blocking)
+5. **Serialization Round-Trip** - Ensures parse → serialize → compare matches exactly (guarantees no data loss)
+
+## API Reference
+
+### `validate(filePath, options?)`
+
+Validate a single MassBank record file.
+
+**Parameters:**
+
+- `filePath: string` - Path to the .txt file to validate
+- `options?: ValidationOptions` - Optional validation options
+
+**Returns:** `Promise<ValidationResult>`
+
+**ValidationResult:**
+
+```typescript
+interface ValidationResult {
+  success: boolean; // true if no errors
+  errors: ValidationError[]; // Array of validation errors
+  warnings: ValidationWarning[]; // Array of warnings (non-blocking)
+  accessions: string[]; // Extracted ACCESSION values
+  filesProcessed: number; // Number of files processed (always 1)
+}
 ```
 
+### `validateContent(text, filename, options?)`
+
+Validate in-memory MassBank record content (no file I/O).
+
+**Parameters:**
+
+- `text: string` - The MassBank record text
+- `filename: string` - Logical filename for error reporting (e.g., 'user-upload.txt')
+- `options?: ValidationOptions` - Optional validation options
+
+**Returns:** `Promise<ValidationResult>`
+
+## MassBank Format 2.6.0 Compliance
+
+This library enforces MassBank format 2.6.0 standards, including:
+
+- **ACCESSION format:** `MSBNK-[ContributorID]-[RecordID]`
+  - Contributor ID: up to 32 characters (letters, digits, underscore)
+  - Record ID: up to 64 characters (capital letters, digits, underscore)
+- **Filename matching:** File must be named `{ACCESSION}.txt`
+- **Required fields:** ACCESSION, RECORD_TITLE, DATE, AUTHORS, LICENSE, and more
+- **SPLASH validation:** Optional spectral hash validation via API
+
+## Requirements
+
+- Node.js 18+ (for native fetch support in SPLASH validation)
+- No external runtime dependencies (only optional `fifo-logger`)
+
 ## License
 
 [MIT](./LICENSE)

package/lib/index.d.ts

@@ -1,6 +1,7 @@
 /**
- * My module
- * @returns A very important number
+ * MassBank validation library
+ * Main entry point for the package
  */
-export declare function myModule(): number;
+export { validate, validateContent } from './validator/index.js';
+export type { ValidationError, ValidationOptions, ValidationResult, ValidationWarning, } from './types.js';
 //# sourceMappingURL=index.d.ts.map

package/lib/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAGH,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AAGjE,YAAY,EACV,eAAe,EACf,iBAAiB,EACjB,gBAAgB,EAChB,iBAAiB,GAClB,MAAM,YAAY,CAAC"}

package/lib/index.js

@@ -1,8 +1,7 @@
 /**
- * My module
- * @returns A very important number
+ * MassBank validation library
+ * Main entry point for the package
  */
-export function myModule() {
-    return 42;
-}
+// Validation functions
+export { validate, validateContent } from './validator/index.js';
 //# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,uBAAuB;AACvB,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC"}

package/lib/parser/exceptions.d.ts

@@ -0,0 +1,9 @@
+import type { ParseError } from '../types.js';
+/**
+ * Exception thrown when parsing fails
+ */
+export declare class ParseException extends Error {
+    readonly parseError: ParseError;
+    constructor(parseError: ParseError, message?: string);
+}
+//# sourceMappingURL=exceptions.d.ts.map

package/lib/parser/exceptions.d.ts.map

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package/lib/parser/exceptions.js

@@ -0,0 +1,17 @@
+/**
+ * Exception thrown when parsing fails
+ */
+export class ParseException extends Error {
+    parseError;
+    constructor(parseError, message) {
+        super(message || parseError.message);
+        this.parseError = parseError;
+        this.name = 'ParseException';
+        // Maintains proper stack trace for where our error was thrown (only available on V8)
+        const ErrorConstructor = Error;
+        if (typeof ErrorConstructor.captureStackTrace === 'function') {
+            ErrorConstructor.captureStackTrace(this, ParseException);
+        }
+    }
+}
+//# sourceMappingURL=exceptions.js.map

package/lib/parser/exceptions.js.map

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package/lib/parser/field-parsers.d.ts

@@ -0,0 +1,53 @@
+import type { Record } from '../record.js';
+import type { IFieldParser } from './interfaces.js';
+/**
+ * Base class for field parsers
+ */
+declare abstract class BaseFieldParser implements IFieldParser {
+    abstract canParse(key: string): boolean;
+    abstract parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Header field parser
+ */
+export declare class HeaderFieldParser extends BaseFieldParser {
+    canParse(key: string): boolean;
+    parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Compound (CH$) field parser
+ */
+export declare class CompoundFieldParser extends BaseFieldParser {
+    canParse(key: string): boolean;
+    parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Analytical conditions (AC$) field parser
+ */
+export declare class AnalyticalConditionsFieldParser extends BaseFieldParser {
+    canParse(key: string): boolean;
+    parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Mass spectrometry (MS$) field parser
+ */
+export declare class MassSpectrometryFieldParser extends BaseFieldParser {
+    canParse(key: string): boolean;
+    parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Peak (PK$) field parser (non-table fields)
+ */
+export declare class PeakFieldParser extends BaseFieldParser {
+    canParse(key: string): boolean;
+    parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Species (SP$) field parser
+ */
+export declare class SpeciesFieldParser extends BaseFieldParser {
+    canParse(key: string): boolean;
+    parse(key: string, value: string, record: Record): void;
+}
+export {};
+//# sourceMappingURL=field-parsers.d.ts.map

package/lib/parser/field-parsers.d.ts.map

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package/lib/parser/field-parsers.js

@@ -0,0 +1,218 @@
+/**
+ * Base class for field parsers
+ */
+class BaseFieldParser {
+}
+/**
+ * Header field parser
+ */
+export class HeaderFieldParser extends BaseFieldParser {
+    canParse(key) {
+        const headerFields = [
+            'ACCESSION',
+            'RECORD_TITLE',
+            'DATE',
+            'AUTHORS',
+            'LICENSE',
+            'COPYRIGHT',
+            'PUBLICATION',
+            'PROJECT',
+            'COMMENT',
+            'DEPRECATED',
+        ];
+        return headerFields.includes(key);
+    }
+    parse(key, value, record) {
+        switch (key) {
+            case 'ACCESSION':
+                record.ACCESSION = value;
+                break;
+            case 'RECORD_TITLE':
+                record.RECORD_TITLE = value;
+                break;
+            case 'DATE':
+                record.DATE = value;
+                break;
+            case 'AUTHORS':
+                record.AUTHORS = value;
+                break;
+            case 'LICENSE':
+                record.LICENSE = value;
+                break;
+            case 'COPYRIGHT':
+                record.COPYRIGHT = value;
+                break;
+            case 'PUBLICATION':
+                record.PUBLICATION = value;
+                break;
+            case 'PROJECT':
+                record.PROJECT = value;
+                break;
+            case 'COMMENT':
+                if (!record.COMMENT) {
+                    record.COMMENT = [];
+                }
+                record.COMMENT.push(value);
+                break;
+            case 'DEPRECATED':
+                record.DEPRECATED = value;
+                break;
+            default:
+                break;
+        }
+    }
+}
+/**
+ * Compound (CH$) field parser
+ */
+export class CompoundFieldParser extends BaseFieldParser {
+    canParse(key) {
+        return key.startsWith('CH$');
+    }
+    parse(key, value, record) {
+        switch (key) {
+            case 'CH$NAME':
+                if (!record.CH$NAME) {
+                    record.CH$NAME = [];
+                }
+                record.CH$NAME.push(value);
+                break;
+            case 'CH$COMPOUND_CLASS':
+                record.CH$COMPOUND_CLASS = value;
+                break;
+            case 'CH$FORMULA':
+                record.CH$FORMULA = value;
+                break;
+            case 'CH$EXACT_MASS':
+                record.CH$EXACT_MASS = value;
+                break;
+            case 'CH$SMILES':
+                record.CH$SMILES = value;
+                break;
+            case 'CH$IUPAC':
+                record.CH$IUPAC = value;
+                break;
+            case 'CH$LINK':
+                if (!record.CH$LINK) {
+                    record.CH$LINK = [];
+                }
+                record.CH$LINK.push(value);
+                break;
+            default:
+                break;
+        }
+    }
+}
+/**
+ * Analytical conditions (AC$) field parser
+ */
+export class AnalyticalConditionsFieldParser extends BaseFieldParser {
+    canParse(key) {
+        return key.startsWith('AC$');
+    }
+    parse(key, value, record) {
+        switch (key) {
+            case 'AC$INSTRUMENT':
+                record.AC$INSTRUMENT = value;
+                break;
+            case 'AC$INSTRUMENT_TYPE':
+                record.AC$INSTRUMENT_TYPE = value;
+                break;
+            case 'AC$MASS_SPECTROMETRY':
+                if (!record.AC$MASS_SPECTROMETRY) {
+                    record.AC$MASS_SPECTROMETRY = [];
+                }
+                record.AC$MASS_SPECTROMETRY.push(value);
+                break;
+            case 'AC$CHROMATOGRAPHY':
+                if (!record.AC$CHROMATOGRAPHY) {
+                    record.AC$CHROMATOGRAPHY = [];
+                }
+                record.AC$CHROMATOGRAPHY.push(value);
+                break;
+            default:
+                break;
+        }
+    }
+}
+/**
+ * Mass spectrometry (MS$) field parser
+ */
+export class MassSpectrometryFieldParser extends BaseFieldParser {
+    canParse(key) {
+        return key.startsWith('MS$');
+    }
+    parse(key, value, record) {
+        switch (key) {
+            case 'MS$FOCUSED_ION':
+                if (!record.MS$FOCUSED_ION) {
+                    record.MS$FOCUSED_ION = [];
+                }
+                record.MS$FOCUSED_ION.push(value);
+                break;
+            case 'MS$DATA_PROCESSING':
+                if (!record.MS$DATA_PROCESSING) {
+                    record.MS$DATA_PROCESSING = [];
+                }
+                record.MS$DATA_PROCESSING.push(value);
+                break;
+            default:
+                break;
+        }
+    }
+}
+/**
+ * Peak (PK$) field parser (non-table fields)
+ */
+export class PeakFieldParser extends BaseFieldParser {
+    canParse(key) {
+        return (key.startsWith('PK$') && key !== 'PK$PEAK' && key !== 'PK$ANNOTATION');
+    }
+    parse(key, value, record) {
+        switch (key) {
+            case 'PK$SPLASH':
+                record.PK$SPLASH = value;
+                break;
+            case 'PK$NUM_PEAK': {
+                const numPeak = Number.parseInt(value, 10);
+                if (Number.isNaN(numPeak)) {
+                    throw new Error(`Invalid PK$NUM_PEAK value: ${value}`);
+                }
+                record.PK$NUM_PEAK = numPeak;
+                break;
+            }
+            default:
+                break;
+        }
+    }
+}
+/**
+ * Species (SP$) field parser
+ */
+export class SpeciesFieldParser extends BaseFieldParser {
+    canParse(key) {
+        return key.startsWith('SP$');
+    }
+    parse(key, value, record) {
+        switch (key) {
+            case 'SP$SCIENTIFIC_NAME':
+                record.SP$SCIENTIFIC_NAME = value;
+                break;
+            case 'SP$LINEAGE':
+                record.SP$LINEAGE = value;
+                break;
+            case 'SP$LINK':
+                if (!record.SP$LINK) {
+                    record.SP$LINK = [];
+                }
+                record.SP$LINK.push(value);
+                break;
+            case 'SP$SAMPLE':
+                record.SP$SAMPLE = value;
+                break;
+            default:
+                break;
+        }
+    }
+}
+//# sourceMappingURL=field-parsers.js.map

package/lib/parser/field-parsers.js.map

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package/lib/parser/index.d.ts

@@ -0,0 +1,5 @@
+export { RecordParser, createParser, parseRecord } from './record-parser.js';
+export { ParseException } from './exceptions.js';
+export type { IFieldParser, IRecordParser, ITableParser, } from './interfaces.js';
+export { PositionUtils } from './position-utils.js';
+//# sourceMappingURL=index.d.ts.map

package/lib/parser/index.d.ts.map

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package/lib/parser/index.js

@@ -0,0 +1,4 @@
+export { RecordParser, createParser, parseRecord } from './record-parser.js';
+export { ParseException } from './exceptions.js';
+export { PositionUtils } from './position-utils.js';
+//# sourceMappingURL=index.js.map

package/lib/parser/index.js.map

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package/lib/parser/interfaces.d.ts

@@ -0,0 +1,46 @@
+import type { Record } from '../record.js';
+/**
+ * Interface for parsing MassBank records
+ */
+export interface IRecordParser {
+    /**
+     * Parse a MassBank record string into a Record object
+     * @param text - The MassBank record text
+     * @returns The parsed Record object
+     * @throws {import('./exceptions.js').ParseException} if parsing fails
+     */
+    parse(text: string): Record;
+}
+/**
+ * Interface for parsing field values
+ */
+export interface IFieldParser {
+    /**
+     * Check if this parser can handle the given key
+     */
+    canParse(key: string): boolean;
+    /**
+     * Parse the field value
+     */
+    parse(key: string, value: string, record: Record): void;
+}
+/**
+ * Interface for parsing table data (peaks, annotations)
+ */
+export interface ITableParser {
+    /**
+     * Check if this parser can handle the given key
+     */
+    canParse(key: string): boolean;
+    /**
+     * Parse table data starting from the given line index
+     * @param key - The field key
+     * @param lines - All lines
+     * @param startIndex - Index of first data line (header is at startIndex - 1)
+     * @param record - Record to populate
+     * @param headerLine - The full header line (e.g., "PK$ANNOTATION: m/z ion")
+     * @returns The number of lines consumed
+     */
+    parse(key: string, lines: string[], startIndex: number, record: Record, headerLine?: string): number;
+}
+//# sourceMappingURL=interfaces.d.ts.map

package/lib/parser/interfaces.d.ts.map

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package/lib/parser/interfaces.js

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+export {};
+//# sourceMappingURL=interfaces.js.map

package/lib/parser/interfaces.js.map

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package/lib/parser/position-utils.d.ts

@@ -0,0 +1,39 @@
+import type { ParseError } from '../types.js';
+/**
+ * Utility functions for position calculations
+ * Handle position/line/column calculations
+ */
+export declare const PositionUtils: {
+    /**
+     * Get character position from line and column (both 1-based).
+     * Converts 1-based line/column to a 0-based character offset in the text.
+     * @param text - The full text being parsed (used to determine actual newline lengths)
+     * @param lineIndex - Line number (1-based)
+     * @param column - Column number (1-based)
+     * @returns 0-based character position in the original text
+     */
+    getPosition(text: string, lineIndex: number, column: number): number;
+    /**
+     * Create a ParseError from a 0-based character position.
+     * Converts the position to 1-based line and column numbers.
+     * Clamps position to valid range [0, text.length] to ensure correct line/column calculation.
+     * @param text - The full text being parsed
+     * @param position - 0-based character offset in the text
+     * @param message - Error message describing the problem
+     * @returns ParseError with 1-based line and column
+     */
+    createParseError(text: string, position: number, message: string): ParseError;
+    /**
+     * Get line and column from a 0-based character position.
+     * Converts the position to 1-based line and column numbers.
+     * Clamps position to valid range [0, text.length] and correctly handles the last line.
+     * @param text - The full text being parsed
+     * @param position - 0-based character offset in the text
+     * @returns Object with 1-based line and column
+     */
+    getLineColumn(text: string, position: number): {
+        line: number;
+        column: number;
+    };
+};
+//# sourceMappingURL=position-utils.d.ts.map

package/lib/parser/position-utils.d.ts.map

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