@larsgw/formica 0.1.0

package/lib/catalog/tables/place.js

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+"use strict";
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Place = void 0;
+var value_1 = require("../value");
+var entity_1 = require("../entity");
+var Place = /** @class */ (function (_super) {
+    __extends(Place, _super);
+    function Place(values) {
+        return _super.call(this, values, {
+            name: { required: true, multiple: false },
+            qid: { required: false, multiple: false, format: value_1.FORMATS.QID },
+            display_name: { required: false, multiple: false }
+        }) || this;
+    }
+    return Place;
+}(entity_1.Entity));
+exports.Place = Place;

package/lib/catalog/tables/publisher.d.ts

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+import { Entity } from '../entity';
+export declare class Publisher extends Entity {
+    constructor(values: Record<string, string>);
+}

package/lib/catalog/tables/publisher.js

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+"use strict";
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Publisher = void 0;
+var value_1 = require("../value");
+var entity_1 = require("../entity");
+var Publisher = /** @class */ (function (_super) {
+    __extends(Publisher, _super);
+    function Publisher(values) {
+        return _super.call(this, values, {
+            name: { required: true, multiple: false },
+            qid: { required: false, multiple: false, format: value_1.FORMATS.QID },
+            full_name: { required: false, multiple: false },
+            long_name: { required: false, multiple: true }
+        }) || this;
+    }
+    return Publisher;
+}(entity_1.Entity));
+exports.Publisher = Publisher;

package/lib/catalog/tables/work.d.ts

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+import { Entity } from '../entity';
+export declare class Work extends Entity {
+    constructor(values: Record<string, string>);
+    deriveFields(): void;
+}

package/lib/catalog/tables/work.js

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+"use strict";
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Work = void 0;
+var value_1 = require("../value");
+var entity_1 = require("../entity");
+var Work = /** @class */ (function (_super) {
+    __extends(Work, _super);
+    function Work(values) {
+        return _super.call(this, values, {
+            id: { required: true, multiple: false, format: value_1.FORMATS.ID },
+            title: { required: true, multiple: value_1.CHECK.MULTILANG },
+            author: { required: false, multiple: true },
+            url: { required: false, multiple: true, format: value_1.FORMATS.URL },
+            fulltext_url: { required: false, multiple: true, format: value_1.FORMATS.URL },
+            archive_url: { required: false, multiple: true, format: value_1.FORMATS.URL },
+            entry_type: { required: true, multiple: false, format: value_1.FORMATS.ENTRY_TYPE },
+            date: { required: false, multiple: false, format: value_1.FORMATS.EDTF_0 },
+            publisher: { required: false, multiple: true },
+            series: { required: false, multiple: false },
+            ISSN: { required: false, multiple: false, format: value_1.FORMATS.ISSN_L },
+            ISBN: { required: false, multiple: value_1.CHECK.ISBN, format: value_1.FORMATS.ISBN },
+            DOI: { required: false, multiple: false, format: value_1.FORMATS.DOI },
+            QID: { required: false, multiple: false, format: value_1.FORMATS.QID },
+            volume: { required: false, multiple: false },
+            issue: { required: false, multiple: false },
+            pages: { required: false, multiple: false },
+            edition: { required: false, multiple: false },
+            language: { required: true, multiple: true, format: value_1.FORMATS.LANGUAGE },
+            license: { required: false, multiple: true, format: value_1.FORMATS.LICENSE },
+            key_type: { required: true, multiple: true, format: value_1.FORMATS.KEY_TYPE },
+            taxon: { required: true, multiple: true },
+            scope: { required: false, multiple: true },
+            region: { required: true, multiple: true },
+            complete: { required: false, multiple: false, format: value_1.FORMATS.COMPLETE },
+            target_taxa: { required: false, multiple: true },
+            listed_in: { required: false, multiple: true, format: value_1.FORMATS.ID },
+            part_of: { required: false, multiple: true, format: value_1.FORMATS.ID },
+            version_of: { required: false, multiple: true, format: value_1.FORMATS.ID }
+        }) || this;
+    }
+    Work.prototype.deriveFields = function () {
+        if (typeof this.fields.date === 'string') {
+            var year = parseInt(this.fields.date.split('-')[0]);
+            this.derivedFields.year = year.toString();
+            this.derivedFields.decade = (year - (year % 10)).toString();
+        }
+        if (typeof this.fields.license === 'string' && !this.fields.license.endsWith('?>')) {
+            this.derivedFields.access = 'Open license';
+        }
+        else {
+            var info = this.fields.url;
+            var content = this.fields.fulltext_url;
+            var archive = this.fields.archive_url;
+            if (typeof content === 'string') {
+                this.derivedFields.access = 'Full text available, no license';
+            }
+            else if (typeof archive === 'string' && (!(typeof info === 'string') || !archive.endsWith(info))) {
+                this.derivedFields.access = 'Archived full text available, no license';
+            }
+            else {
+                this.derivedFields.access = 'No full text available';
+            }
+        }
+    };
+    return Work;
+}(entity_1.Entity));
+exports.Work = Work;

package/lib/catalog/value.d.ts

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+export declare const FORMATS: {
+    ENTRY_TYPE: string[];
+    KEY_TYPE: string[];
+    COMPLETE: string[];
+    ID: RegExp;
+    EDTF_0: RegExp;
+    ISSN_L: RegExp;
+    ISBN: RegExp;
+    DOI: RegExp;
+    QID: RegExp;
+    URL: RegExp;
+    LICENSE(value: SingleValue): true;
+    LANGUAGE(value: SingleValue): any;
+};
+export declare const CHECK: {
+    MULTILANG(entry: Record<string, Value>): boolean;
+    ISBN(entry: Record<string, Value>): boolean;
+};
+export declare function parseValue(value: string, multiple: boolean): Value | null;

package/lib/catalog/value.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseValue = exports.CHECK = exports.FORMATS = void 0;
+var spdxLicenseList = require("spdx-license-list");
+// eslint-disable-next-line @typescript-eslint/ban-ts-comment
+// @ts-ignore
+var ietfTagListFactory = require("ietf-language-tag-regex");
+var ietfTagList = ietfTagListFactory();
+exports.FORMATS = {
+    ENTRY_TYPE: ['print', 'online', 'cd'],
+    KEY_TYPE: ['key', 'matrix', 'reference', 'gallery', 'checklist', 'supplement', 'collection'],
+    COMPLETE: ['TRUE', 'FALSE'],
+    ID: /^B\d+$/,
+    EDTF_0: /^(\d{4}(-\d{2}(-\d{2}(T\d{2}:\d{2}:\d{2}(Z|[-+]\d{2}(:\d{2})?))?)?)?|\d{4}(-\d{2}(-\d{2})?)?\/(\d{4}(-\d{2}(-\d{2})?)?|\.\.))$/,
+    ISSN_L: /^[0-9]{4}-[0-9]{3}[0-9X]$/,
+    ISBN: /^(\d{13}|\d{9}[0-9X])$/,
+    DOI: /^10\./,
+    QID: /^Q[1-9][0-9]*$/,
+    URL: /^(ftp|http|https):\/\/((?:[a-z0-9][a-z0-9-_]*?[a-z0-9]?\.)+(?:xn--)?[a-z0-9]+)(:\d*)?((?:\/(?:%\d\d|[!$&'()*+,\-.0-9";=@A-Z_a-z~])*)*)(\?(?:%\d\d|[!$&'()*+,\-./0-9:;=?@A-Z_a-z~])*)?(#(?:%\d\d|[!$&'()*+,\-./0-9:;=?@A-Z_a-z~])*)?/i,
+    LICENSE: function (value) { return /^<(public domain|.+\?)>$/.test(value) || !!spdxLicenseList[value]; },
+    LANGUAGE: function (value) { return ietfTagList.test(value); }
+};
+exports.CHECK = {
+    MULTILANG: function (entry) {
+        return entry.language.length > 1;
+    },
+    ISBN: function (entry) {
+        if (entry.ISBN.length < 2) {
+            return false;
+        }
+        var a = entry.ISBN[0].length === 10;
+        var b = entry.ISBN[0].length === 13;
+        var c = entry.ISBN[1].length === 10;
+        var d = entry.ISBN[1].length === 13;
+        return (a && d) || (b && c);
+    }
+};
+function parseValue(value, multiple) {
+    if (value === '') {
+        return null;
+    }
+    else if (multiple) {
+        return value.split('; ');
+    }
+    else {
+        return value;
+    }
+}
+exports.parseValue = parseValue;

package/lib/csv.d.ts

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+export declare function parseCsv(file: string): string[][];
+export declare function formatCsv(table: string[][], delimiter?: string): string;

package/lib/csv.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.formatCsv = exports.parseCsv = void 0;
+function parseCsv(file) {
+    var values = file
+        .trim()
+        .match(/("([^"]|"")*?"|[^,\n]+|(?!$))(,|\n|$)/g);
+    if (values === null) {
+        throw new TypeError('Failed to parse csv');
+    }
+    return values.reduce(function (rows, value) {
+        var last = rows[rows.length - 1];
+        if (value.endsWith('\n')) {
+            rows.push([]);
+        }
+        value = value.replace(/[,\n]$/, '');
+        last.push(value.startsWith('"') ? value.replace(/""/g, '"').slice(1, -1) : value);
+        return rows;
+    }, [[]]);
+}
+exports.parseCsv = parseCsv;
+function formatCsv(table, delimiter) {
+    if (delimiter === void 0) { delimiter = ','; }
+    return table
+        .map(function (row) {
+        return row.map(function (value) {
+            if (/["\n]/.test(value) || value.includes(delimiter)) {
+                return "\"".concat(value.replace(/"/, '"""'), "\"");
+            }
+            else {
+                return value;
+            }
+        }).join(delimiter);
+    })
+        .join('\n') + '\n';
+}
+exports.formatCsv = formatCsv;

package/lib/index.d.ts

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+export * as catalog from './catalog/index';
+export * as resources from './resources/index';
+export * as csv from './csv';

package/lib/index.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.csv = exports.resources = exports.catalog = void 0;
+exports.catalog = require("./catalog/index");
+exports.resources = require("./resources/index");
+exports.csv = require("./csv");

package/lib/resources/diff-resource.d.ts

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+export declare enum ResourceDiffType {
+    Added = "+",
+    Deleted = "-",
+    Modified = "~",
+    Unchanged = "="
+}
+export declare function createDiff(a: string, b: string, tokenize?: ResourceDiffTokenizer): ResourceDiffPart[];

package/lib/resources/diff-resource.js

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+"use strict";
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createDiff = exports.ResourceDiffType = void 0;
+var ResourceDiffType;
+(function (ResourceDiffType) {
+    ResourceDiffType["Added"] = "+";
+    ResourceDiffType["Deleted"] = "-";
+    ResourceDiffType["Modified"] = "~";
+    ResourceDiffType["Unchanged"] = "=";
+})(ResourceDiffType = exports.ResourceDiffType || (exports.ResourceDiffType = {}));
+function LCS(X, Y) {
+    var m = X.length;
+    var n = Y.length;
+    // Build matrix
+    var C = Array(m + 1).fill(0).map(function () { return Array(n + 1).fill(0); });
+    for (var i_1 = 0; i_1 < m; i_1++) {
+        for (var j_1 = 0; j_1 < n; j_1++) {
+            if (X[i_1] === Y[j_1]) {
+                C[i_1 + 1][j_1 + 1] = C[i_1][j_1] + 1;
+            }
+            else {
+                C[i_1 + 1][j_1 + 1] = Math.max(C[i_1][j_1 + 1], C[i_1 + 1][j_1]);
+            }
+        }
+    }
+    // Backtrace
+    var diff = [];
+    var i = m;
+    var j = n;
+    while (i + j !== 0) {
+        if (X[i - 1] === Y[j - 1]) {
+            diff.unshift({
+                text: X[i - 1],
+                type: ResourceDiffType.Unchanged
+            });
+            i--, j--;
+        }
+        else if (i !== 0 && (j === 0 || C[i - 1][j] > C[i][j - 1])) {
+            diff.unshift({
+                text: X[i - 1],
+                type: ResourceDiffType.Added
+            });
+            i--;
+        }
+        else {
+            diff.unshift({
+                text: Y[j - 1],
+                type: ResourceDiffType.Deleted
+            });
+            j--;
+        }
+    }
+    return diff;
+}
+function gitTokenize(text) {
+    if (text.length === 0) {
+        return [];
+    }
+    return text.match(/\S+|\n|[\r\t\f\v \u00a0\u1680\u2000-\u200a\u2028\u2029\u202f\u205f\u3000\ufeff]+/g);
+}
+function createDiff(a, b, tokenize) {
+    if (tokenize === void 0) { tokenize = gitTokenize; }
+    var X = tokenize(a.trimEnd());
+    var Y = tokenize(b.trimEnd());
+    // Remove common prefix
+    var prefix = [];
+    while (X.length && X[0] === Y[0]) {
+        prefix.push({
+            text: X[0],
+            type: ResourceDiffType.Unchanged
+        });
+        X.shift();
+        Y.shift();
+    }
+    // Remove common suffix
+    var suffix = [];
+    while (X.length && X[X.length - 1] === Y[Y.length - 1]) {
+        suffix.unshift({
+            text: X[X.length - 1],
+            type: ResourceDiffType.Unchanged
+        });
+        X.pop();
+        Y.pop();
+    }
+    // Generate word from remains, combine with prefix and suffix, add trailing
+    // newline
+    var changes = __spreadArray(__spreadArray(__spreadArray(__spreadArray([], prefix, true), LCS(X, Y), true), suffix, true), [
+        { text: '\n', type: ResourceDiffType.Unchanged }
+    ], false);
+    // Convert word diff to line diff
+    var lines = [];
+    var line = null;
+    var deletedNewlines = 0;
+    var nextLineNew = false;
+    for (var _i = 0, changes_1 = changes; _i < changes_1.length; _i++) {
+        var change = changes_1[_i];
+        // Start of line
+        if (line === null) {
+            deletedNewlines = 0;
+            line = { text: '', type: change.type };
+        }
+        // End of line (could be same token)
+        if (change.text === '\n') {
+            if (change.type === ResourceDiffType.Deleted) {
+                // Keep track of deleted newlines. These indicate the merging of
+                // lines. To keep the taxon identifiers consistent, it is
+                // important that deleted taxa are tracked.
+                deletedNewlines++;
+                continue;
+            }
+            // If there is a new newline, there is a new... line. If the current
+            // line is not seen as new, the next one should be marked as new.
+            if (nextLineNew) {
+                line.type = ResourceDiffType.Added;
+                nextLineNew = false;
+            }
+            if (change.type === ResourceDiffType.Added && line.type !== ResourceDiffType.Added) {
+                nextLineNew = true;
+            }
+            // Line ended
+            lines.push(line);
+            line = null;
+            // Add placeholders for deleted lines
+            while (deletedNewlines--) {
+                lines.push({
+                    text: '',
+                    type: ResourceDiffType.Deleted
+                });
+            }
+            continue;
+        }
+        // Added/Deleted/Unchanged on the same line -> line is modified but did
+        // already exist.
+        if (change.type !== line.type) {
+            line.type = ResourceDiffType.Modified;
+        }
+        if (change.type !== ResourceDiffType.Deleted) {
+            line.text += change.text;
+        }
+    }
+    return lines;
+}
+exports.createDiff = createDiff;

package/lib/resources/index.d.ts

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+export { parseFile as parseTextFile, parseFileHeader as parseTextFileHeader } from './parse-text';

package/lib/resources/index.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseTextFileHeader = exports.parseTextFile = void 0;
+var parse_text_1 = require("./parse-text");
+Object.defineProperty(exports, "parseTextFile", { enumerable: true, get: function () { return parse_text_1.parseFile; } });
+Object.defineProperty(exports, "parseTextFileHeader", { enumerable: true, get: function () { return parse_text_1.parseFileHeader; } });

package/lib/resources/parse-text.d.ts

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+export declare function parseFile(file: string, id: WorkId, old?: ResourceHistory): Resource[];
+export declare function parseFileHeader(file: string): ResourceMetadata[];