TmMolStar/src/reader/cif/text/parser.ts

/**
 * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */

/**
 * mmCIF parser.
 *
 * Trying to be as close to the specification http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax
 *
 * Differences I'm aware of:
 * - Except keywords (data_, loop_, save_) everything is case sensitive.
 * - The tokens . and ? are treated the same as the values '.' and '?'.
 * - Ignores \ in the multiline values:
 *     ;abc\
 *     efg
 *     ;
 *   should have the value 'abcefg' but will have the value 'abc\\nefg' instead.
 *   Post processing of this is left to the consumer of the data.
 * - Similarly, things like punctuation (\', ..) are left to be processed by the user if needed.
 *
 */

import * as Data from '../data-model'
import Field from './field'
import { Tokens, TokenBuilder } from '../../common/text/tokenizer'
import Result from '../../result'
import Computation from '../../../utils/computation'

/**
 * Types of supported mmCIF tokens.
 */
const enum CifTokenType {
    Data = 0,
    Save = 1,
    Loop = 2,
    Value = 3,
    ColumnName = 4,
    Comment = 5,
    End = 6
}

interface TokenizerState {
    data: string;

    position: number;
    length: number;
    isEscaped: boolean;

    lineNumber: number;
    tokenType: CifTokenType;
    tokenStart: number;
    tokenEnd: number;

    chunker: Computation.Chunker
}

/**
 * Eat everything until a whitespace/newline occurs.
 */
function eatValue(state: TokenizerState) {
    while (state.position < state.length) {
        switch (state.data.charCodeAt(state.position)) {
            case 9:  // \t
            case 10: // \n
            case 13: // \r
            case 32: // ' '
                state.tokenEnd = state.position;
                return;
            default:
                ++state.position;
                break;
        }
    }
    state.tokenEnd = state.position;
}

/**
 * Eats an escaped values. Handles the "degenerate" cases as well.
 *
 * "Degenerate" cases:
 * - 'xx'x' => xx'x
 * - 'xxxNEWLINE => 'xxx
 *
 */
function eatEscaped(state: TokenizerState, esc: number) {
    let next: number, c: number;

    ++state.position;
    while (state.position < state.length) {
        c = state.data.charCodeAt(state.position);

        if (c === esc) {
            next = state.data.charCodeAt(state.position + 1);
            switch (next) {
                case 9:  // \t
                case 10: // \n
                case 13: // \r
                case 32: // ' '
                    // get rid of the quotes.
                    state.tokenStart++;
                    state.tokenEnd = state.position;
                    state.isEscaped = true;
                    ++state.position;
                    return;
                default:
                    if (next === void 0) { // = "end of stream"
                        // get rid of the quotes.
                        state.tokenStart++;
                        state.tokenEnd = state.position;
                        state.isEscaped = true;
                        ++state.position;
                        return;
                    }
                    ++state.position;
                    break;
            }
        } else {
            // handle 'xxxNEWLINE => 'xxx
            if (c === 10 || c === 13) {
                state.tokenEnd = state.position;
                return;
            }
            ++state.position;
        }
    }

    state.tokenEnd = state.position;
}

/**
 * Eats a multiline token of the form NL;....NL;
 */
function eatMultiline(state: TokenizerState) {
    let prev = 59, pos = state.position + 1, c: number;
    while (pos < state.length) {
        c = state.data.charCodeAt(pos);
        if (c === 59 && (prev === 10 || prev === 13)) { // ;, \n \r
            state.position = pos + 1;
            // get rid of the ;
            state.tokenStart++;

            // remove trailing newlines
            pos--;
            c = state.data.charCodeAt(pos);
            while (c === 10 || c === 13) {
                pos--;
                c = state.data.charCodeAt(pos);
            }
            state.tokenEnd = pos + 1;

            state.isEscaped = true;
            return;
        } else {
            // handle line numbers
            if (c === 13) { // \r
                state.lineNumber++;
            } else if (c === 10 && prev !== 13) { // \r\n
                state.lineNumber++;
            }

            prev = c;
            ++pos;
        }
    }

    state.position = pos;
    return prev;
}

/**
 * Skips until \n or \r occurs -- therefore the newlines get handled by the "skipWhitespace" function.
 */
function skipCommentLine(state: TokenizerState) {
    while (state.position < state.length) {
        let c = state.data.charCodeAt(state.position);
        if (c === 10 || c === 13) {
            return;
        }
        ++state.position;
    }
}

/**
 * Skips all the whitespace - space, tab, newline, CR
 * Handles incrementing line count.
 */
function skipWhitespace(state: TokenizerState): number {
    let prev = 10;
    while (state.position < state.length) {
        let c = state.data.charCodeAt(state.position);
        switch (c) {
            case 9: // '\t'
            case 32: // ' '
                prev = c;
                ++state.position;
                break;
            case 10: // \n
                // handle \r\n
                if (prev !== 13) {
                    ++state.lineNumber;
                }
                prev = c;
                ++state.position;
                break;
            case 13: // \r
                prev = c;
                ++state.position;
                ++state.lineNumber;
                break;
            default:
                return prev;
        }
    }
    return prev;
}

function isData(state: TokenizerState): boolean {
    // here we already assume the 5th char is _ and that the length >= 5

    // d/D
    let c = state.data.charCodeAt(state.tokenStart);
    if (c !== 68 && c !== 100) return false;
    // a/A
    c = state.data.charCodeAt(state.tokenStart + 1);
    if (c !== 65 && c !== 97) return false;
    // t/t
    c = state.data.charCodeAt(state.tokenStart + 2);
    if (c !== 84 && c !== 116) return false;
    // a/A
    c = state.data.charCodeAt(state.tokenStart + 3);
    if (c !== 65 && c !== 97) return false;

    return true;
}

function isSave(state: TokenizerState): boolean {
    // here we already assume the 5th char is _ and that the length >= 5

    // s/S
    let c = state.data.charCodeAt(state.tokenStart);
    if (c !== 83 && c !== 115) return false;
    // a/A
    c = state.data.charCodeAt(state.tokenStart + 1);
    if (c !== 65 && c !== 97) return false;
    // v/V
    c = state.data.charCodeAt(state.tokenStart + 2);
    if (c !== 86 && c !== 118) return false;
    // e/E
    c = state.data.charCodeAt(state.tokenStart + 3);
    if (c !== 69 && c !== 101) return false;

    return true;
}

function isLoop(state: TokenizerState): boolean {
    // here we already assume the 5th char is _ and that the length >= 5

    if (state.tokenEnd - state.tokenStart !== 5) return false;

    // l/L
    let c = state.data.charCodeAt(state.tokenStart);
    if (c !== 76 && c !== 108) return false;
    // o/O
    c = state.data.charCodeAt(state.tokenStart + 1);
    if (c !== 79 && c !== 111) return false;
    // o/O
    c = state.data.charCodeAt(state.tokenStart + 2);
    if (c !== 79 && c !== 111) return false;
    // p/P
    c = state.data.charCodeAt(state.tokenStart + 3);
    if (c !== 80 && c !== 112) return false;

    return true;
}

/**
 * Checks if the current token shares the namespace with string at <start,end).
 */
function isNamespace(state: TokenizerState, start: number, end: number): boolean {
    let i: number,
        nsLen = end - start,
        offset = state.tokenStart - start,
        tokenLen = state.tokenEnd - state.tokenStart;

    if (tokenLen < nsLen) return false;

    for (i = start; i < end; ++i) {
        if (state.data.charCodeAt(i) !== state.data.charCodeAt(i + offset)) return false;
    }

    if (nsLen === tokenLen) return true;
    if (state.data.charCodeAt(i + offset) === 46) { // .
        return true;
    }

    return false;
}

/**
 * Returns the index of '.' in the current token. If no '.' is present, returns currentTokenEnd.
 */
function getNamespaceEnd(state: TokenizerState): number {
    let i: number;
    for (i = state.tokenStart; i < state.tokenEnd; ++i) {
        if (state.data.charCodeAt(i) === 46) return i;
    }
    return i;
}

/**
 * Get the namespace string. endIndex is obtained by the getNamespaceEnd() function.
 */
function getNamespace(state: TokenizerState, endIndex: number) {
    return state.data.substring(state.tokenStart, endIndex);
}

/**
 * String representation of the current token.
 */
function getTokenString(state: TokenizerState) {
    return state.data.substring(state.tokenStart, state.tokenEnd);
}

/**
 * Move to the next token.
 */
function moveNextInternal(state: TokenizerState) {
    let prev = skipWhitespace(state);

    if (state.position >= state.length) {
        state.tokenType = CifTokenType.End;
        return;
    }

    state.tokenStart = state.position;
    state.tokenEnd = state.position;
    state.isEscaped = false;
    let c = state.data.charCodeAt(state.position);
    switch (c) {
        case 35: // #, comment
            skipCommentLine(state);
            state.tokenType = CifTokenType.Comment;
            break;
        case 34: // ", escaped value
        case 39: // ', escaped value
            eatEscaped(state, c);
            state.tokenType = CifTokenType.Value;
            break;
        case 59: // ;, possible multiline value
            // multiline value must start at the beginning of the line.
            if (prev === 10 || prev === 13) { // /n or /r
                eatMultiline(state);
            } else {
                eatValue(state);
            }
            state.tokenType = CifTokenType.Value;
            break;
        default:
            eatValue(state);
            // escaped is always Value
            if (state.isEscaped) {
                state.tokenType = CifTokenType.Value;
                // _ always means column name
            } else if (state.data.charCodeAt(state.tokenStart) === 95) { // _
                state.tokenType = CifTokenType.ColumnName;
                // 5th char needs to be _ for data_ or loop_
            } else if (state.tokenEnd - state.tokenStart >= 5 && state.data.charCodeAt(state.tokenStart + 4) === 95) {
                if (isData(state)) state.tokenType = CifTokenType.Data;
                else if (isSave(state)) state.tokenType = CifTokenType.Save;
                else if (isLoop(state)) state.tokenType = CifTokenType.Loop;
                else state.tokenType = CifTokenType.Value;
                // all other tests failed, we are at Value token.
            } else {
                state.tokenType = CifTokenType.Value;
            }
            break;
    }
}

/**
 * Moves to the next non-comment token.
 */
function moveNext(state: TokenizerState) {
    moveNextInternal(state);
    while (state.tokenType === CifTokenType.Comment) moveNextInternal(state);
}

function createTokenizer(data: string, ctx: Computation.Context): TokenizerState {
    return {
        data,
        length: data.length,
        position: 0,
        tokenStart: 0,
        tokenEnd: 0,
        tokenType: CifTokenType.End,
        lineNumber: 1,
        isEscaped: false,

        chunker: Computation.chunker(ctx, 1000000)
    };
}

/**
 * Helper shape of the category result.
 */
interface CifCategoryResult {
    hasError: boolean;
    errorLine: number;
    errorMessage: string;
}

/**
 * Reads a category containing a single row.
 */
function handleSingle(tokenizer: TokenizerState, categories: { [name: string]: Data.Category }): CifCategoryResult {
    const nsStart = tokenizer.tokenStart, nsEnd = getNamespaceEnd(tokenizer);
    const name = getNamespace(tokenizer, nsEnd);
    const fields = Object.create(null);

    let readingNames = true;
    while (readingNames) {
        if (tokenizer.tokenType !== CifTokenType.ColumnName || !isNamespace(tokenizer, nsStart, nsEnd)) {
            readingNames = false;
            break;
        }

        const fieldName = getTokenString(tokenizer).substring(name.length + 1);
        moveNext(tokenizer);
        if (tokenizer.tokenType as any !== CifTokenType.Value) {
            return {
                hasError: true,
                errorLine: tokenizer.lineNumber,
                errorMessage: 'Expected value.'
            }
        }
        fields[fieldName] = Field({ data: tokenizer.data, indices: [tokenizer.tokenStart, tokenizer.tokenEnd], count: 1 }, 1);
        moveNext(tokenizer);
    }

    categories[name] = Data.Category(1, fields);

    return {
        hasError: false,
        errorLine: 0,
        errorMessage: ''
    };
}

interface LoopReadState {
    tokenizer: TokenizerState,
    tokens: Tokens[],
    fieldCount: number,
    tokenCount: number
}

function readLoopChunk(state: LoopReadState, chunkSize: number) {
    const { tokenizer, tokens, fieldCount } = state;
    let tokenCount = state.tokenCount;
    let counter = 0;
    while (tokenizer.tokenType === CifTokenType.Value && counter < chunkSize) {
        TokenBuilder.add(tokens[(tokenCount++) % fieldCount], tokenizer.tokenStart, tokenizer.tokenEnd);
        moveNext(tokenizer);
        counter++;
    }
    state.tokenCount = tokenCount;
    return counter;
}

function readLoopChunks(state: LoopReadState) {
    return state.tokenizer.chunker.process(
        chunkSize => readLoopChunk(state, chunkSize),
        update => update({ message: 'Parsing...', current: state.tokenizer.position, max: state.tokenizer.data.length }));
}

/**
 * Reads a loop.
 */
async function handleLoop(tokenizer: TokenizerState, categories: { [name: string]: Data.Category }): Promise<CifCategoryResult> {
    const loopLine = tokenizer.lineNumber;

    moveNext(tokenizer);
    const name = getNamespace(tokenizer, getNamespaceEnd(tokenizer));
    const fieldNames: string[] = [];

    while (tokenizer.tokenType === CifTokenType.ColumnName) {
        fieldNames[fieldNames.length] = getTokenString(tokenizer).substring(name.length + 1);
        moveNext(tokenizer);
    }

    const rowCountEstimate = name === '_atom_site' ? (tokenizer.data.length / 100) | 0 : 32;
    const tokens: Tokens[] = [];
    const fieldCount = fieldNames.length;
    for (let i = 0; i < fieldCount; i++) tokens[i] = TokenBuilder.create(tokenizer, rowCountEstimate);

    const state: LoopReadState = {
        fieldCount,
        tokenCount: 0,
        tokenizer,
        tokens
    };

    await readLoopChunks(state);

    if (state.tokenCount % fieldCount !== 0) {
        return {
            hasError: true,
            errorLine: tokenizer.lineNumber,
            errorMessage: 'The number of values for loop starting at line ' + loopLine + ' is not a multiple of the number of columns.'
        };
    }

    const rowCount = (state.tokenCount / fieldCount) | 0;
    const fields = Object.create(null);
    for (let i = 0; i < fieldCount; i++) {
        fields[fieldNames[i]] = Field(tokens[i], rowCount);
    }

    categories[name] = Data.Category(rowCount, fields);

    return {
        hasError: false,
        errorLine: 0,
        errorMessage: ''
    };
}

/**
 * Creates an error result.
 */
function error(line: number, message: string) {
    return Result.error<Data.File>(message, line);
}

/**
 * Creates a data result.
 */
function result(data: Data.File) {
    return Result.success(data);
}

/**
 * Parses an mmCIF file.
 *
 * @returns CifParserResult wrapper of the result.
 */
async function parseInternal(data: string, ctx: Computation.Context) {
    const dataBlocks: Data.Block[] = [];
    const tokenizer = createTokenizer(data, ctx);
    let blockHeader: string = '';
    let blockCategories = Object.create(null);

    let inSaveFrame = false

    // the next three initial values are never used in valid files
    let saveFrames: Data.SafeFrame[] = [];
    let saveCategories = Object.create(null);
    let saveFrame: Data.SafeFrame = Data.SafeFrame(saveCategories, '');

    ctx.update({ message: 'Parsing...', current: 0, max: data.length });

    moveNext(tokenizer);
    while (tokenizer.tokenType !== CifTokenType.End) {
        let token = tokenizer.tokenType;

        // Data block
        if (token === CifTokenType.Data) {
            if (inSaveFrame) {
                return error(tokenizer.lineNumber, "Unexpected data block inside a save frame.");
            }
            if (Object.keys(blockCategories).length > 0) {
                dataBlocks.push(Data.Block(blockCategories, blockHeader, saveFrames));
            }
            blockHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
            blockCategories = Object.create(null);
            saveFrames = []
            moveNext(tokenizer);
        // Save frame
        } else if (token === CifTokenType.Save) {
            const saveHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
            if (saveHeader.length === 0) {
                if (Object.keys(saveCategories).length > 0) {
                    saveFrames[saveFrames.length] = saveFrame
                }
                inSaveFrame = false;
            } else {
                if (inSaveFrame) {
                    return error(tokenizer.lineNumber, "Save frames cannot be nested.");
                }
                inSaveFrame = true;
                saveCategories = Object.create(null);
                saveFrame = Data.SafeFrame(saveCategories, saveHeader);
            }
            moveNext(tokenizer);
        // Loop
        } else if (token === CifTokenType.Loop) {
            const cat = await handleLoop(tokenizer, inSaveFrame ? saveCategories : blockCategories);
            if (cat.hasError) {
                return error(cat.errorLine, cat.errorMessage);
            }
        // Single row
        } else if (token === CifTokenType.ColumnName) {
            const cat = handleSingle(tokenizer, inSaveFrame ? saveCategories : blockCategories);
            if (cat.hasError) {
                return error(cat.errorLine, cat.errorMessage);
            }
        // Out of options
        } else {
            return error(tokenizer.lineNumber, 'Unexpected token. Expected data_, loop_, or data name.');
        }
    }

    // Check if the latest save frame was closed.
    if (inSaveFrame) {
        return error(tokenizer.lineNumber, "Unfinished save frame (`" + saveFrame.header + "`).");
    }

    if (Object.keys(blockCategories).length > 0) {
        dataBlocks.push(Data.Block(blockCategories, blockHeader, saveFrames));
    }

    return result(Data.File(dataBlocks));
}

export default function parse(data: string) {
    return Computation.create<Result<Data.File>>(async ctx => {
        return await parseInternal(data, ctx);
    });
}