@graphty/graph-io 0.3.19 → 0.3.21

package/dist/src/formats/cys/importer.js.map

@@ -0,0 +1 @@
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package/dist/src/formats/cys/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * The `@graphty/graph-io/cys` subpath: the Cytoscape session importer, its option type and its
+ * issue code table. Sessions are read-only: graph-io writes XGMML and CX2, which Cytoscape opens.
+ */
+export { CYS_ISSUE } from "./constants.js";
+export { cysImporter, type CysImportOptions } from "./importer.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/src/formats/cys/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/formats/cys/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAE,WAAW,EAAE,KAAK,gBAAgB,EAAE,MAAM,eAAe,CAAC"}

package/dist/src/formats/cys/index.js

@@ -0,0 +1,7 @@
+/**
+ * The `@graphty/graph-io/cys` subpath: the Cytoscape session importer, its option type and its
+ * issue code table. Sessions are read-only: graph-io writes XGMML and CX2, which Cytoscape opens.
+ */
+export { CYS_ISSUE } from "./constants.js";
+export { cysImporter } from "./importer.js";
+//# sourceMappingURL=index.js.map

package/dist/src/formats/cys/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/formats/cys/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAE,WAAW,EAAyB,MAAM,eAAe,CAAC"}

package/dist/src/formats/cys/session.d.ts

@@ -0,0 +1,132 @@
+/**
+ * The layout of a Cytoscape session archive (`research-session-and-style.md` sections 2.1 to 2.3;
+ * Cytoscape's `Cy3SessionReaderImpl`, `Cy2SessionReaderImpl` and `SessionUtil`): which entries
+ * are the version marker, the networks, views, tables, styles and the rest, read from the central
+ * directory alone. Entries are inflated one at a time, only when asked for, within the import's
+ * byte budget.
+ */
+import { type ResolvedImportOptions } from "../../common/options.js";
+import { ImportReportBuilder } from "../../common/report.js";
+import { type ZipEntry } from "../../common/zip.js";
+import { type ImportInput } from "../../types.js";
+/** An entry of the session, by its path under the session's root folder. */
+export interface SessionEntry {
+    /** The path under the root folder, as the archive spells it (URL-encoded parts). */
+    readonly path: string;
+    /** The full entry name, for messages. */
+    readonly name: string;
+    /** The zip entry. */
+    readonly zip: ZipEntry;
+}
+/** A 3.x network file: one root network (a collection). */
+export interface NetworkEntry extends SessionEntry {
+    /** The root network's saved SUID. */
+    readonly suid: string;
+    /** The file name's network name, decoded. */
+    readonly title: string;
+}
+/** A 3.x view file. */
+interface ViewEntry extends SessionEntry {
+    /** The SUID of the network the view shows. */
+    readonly network: string;
+    /** The view's SUID. */
+    readonly view: string;
+}
+/** A 3.x table file. */
+export interface TableEntry extends SessionEntry {
+    /** The path under `tables/` (what `cytables.xml` names). */
+    readonly tablePath: string;
+    /** The SUID of the network the table belongs to. */
+    readonly network: string;
+    /** The namespace: LOCAL_ATTRS, SHARED_ATTRS, HIDDEN or an app's. */
+    readonly namespace: string;
+    /** The element class: CyNode, CyEdge or CyNetwork. */
+    readonly element: "node" | "edge" | "network" | null;
+}
+/** What a session archive holds, by kind. */
+interface SessionLayout {
+    /** "3" for a 3.x session, "2" for a 2.x one. */
+    readonly era: "2" | "3";
+    /** The version marker as written (`3.0.0`), or the 2.x cysession.xml documentVersion. */
+    readonly version: string;
+    /** The root folder, with its trailing slash ("" when the entries have none). */
+    readonly root: string;
+    readonly networks: readonly NetworkEntry[];
+    readonly views: readonly ViewEntry[];
+    readonly tables: readonly TableEntry[];
+    /** `tables/cytables.xml`, if present. */
+    readonly cytables: SessionEntry | null;
+    /** `apps/org.cytoscape.swing-application/network_list.xml`, if present. */
+    readonly networkList: SessionEntry | null;
+    /** 2.x: `cysession.xml`. */
+    readonly cysession: SessionEntry | null;
+    /** 2.x: the network files by their path. */
+    readonly files: ReadonlyMap<string, SessionEntry>;
+    /** The style entries (`session_vizmap.xml`, `session_vizmap.props`). */
+    readonly styles: readonly SessionEntry[];
+    /** Every entry the importer does not read. */
+    readonly skipped: readonly string[];
+}
+/** An opened session: its bytes, its layout and an entry reader within the byte budget. */
+export interface Session {
+    readonly layout: SessionLayout;
+    /**
+     * Inflate one entry.
+     * @param entry - the entry
+     * @returns its bytes
+     */
+    read(entry: SessionEntry): Promise<Uint8Array>;
+}
+/**
+ * Java's `URLDecoder.decode` (UTF-8): `+` is a space, `%XX` a byte; a malformed escape leaves the
+ * text as it is.
+ * @param text - the encoded text
+ * @returns the decoded text
+ */
+export declare function urlDecode(text: string): string;
+/**
+ * Read the input as a zip and lay out its session entries. Fatal: text input or not a zip
+ * (E_CYS_NOT_ZIP), an empty input, a damaged archive (E_CYS_CORRUPT), a split archive
+ * (E_CYS_UNSUPPORTED), no session marker (E_CYS_NOT_SESSION), a version graph-io cannot read
+ * (E_CYS_VERSION).
+ * @param input - the input
+ * @param report - the report
+ * @param common - cancellation and progress
+ * @param maxBytes - the import's uncompressed byte budget
+ * @returns the session
+ */
+export declare function openSession(input: ImportInput, report: ImportReportBuilder, common: ResolvedImportOptions, maxBytes: number): Promise<Session>;
+/**
+ * A list of names for a message: the first ten, then a count.
+ * @param names - the names
+ * @returns the text
+ */
+export declare function listed(names: readonly string[]): string;
+/** One element of a small XML document, as a tree. */
+export interface XmlNode {
+    /** The local name. */
+    readonly name: string;
+    /** The attributes by name as written (prefix included). */
+    readonly attrs: ReadonlyMap<string, string>;
+    /** The child elements. */
+    readonly children: XmlNode[];
+}
+/**
+ * Read a small XML entry (`cytables.xml`, `network_list.xml`, `cysession.xml`) as a tree. A
+ * document that is not well-formed is E_CYS_CORRUPT naming the entry.
+ * @param bytes - the entry's bytes
+ * @param entry - the entry name
+ * @param report - the report
+ * @param common - cancellation
+ * @returns the root element
+ */
+export declare function readXmlTree(bytes: Uint8Array, entry: string, report: ImportReportBuilder, common: ResolvedImportOptions): Promise<XmlNode>;
+/**
+ * Every element of a tree with a local name, depth first.
+ * @param node - the tree
+ * @param name - the local name
+ * @returns the elements
+ */
+export declare function elementsNamed(node: XmlNode, name: string): XmlNode[];
+export {};
+//# sourceMappingURL=session.d.ts.map

package/dist/src/formats/cys/session.d.ts.map

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package/dist/src/formats/cys/session.js

@@ -0,0 +1,315 @@
+/**
+ * The layout of a Cytoscape session archive (`research-session-and-style.md` sections 2.1 to 2.3;
+ * Cytoscape's `Cy3SessionReaderImpl`, `Cy2SessionReaderImpl` and `SessionUtil`): which entries
+ * are the version marker, the networks, views, tables, styles and the rest, read from the central
+ * directory alone. Entries are inflated one at a time, only when asked for, within the import's
+ * byte budget.
+ */
+import { readBytes, textChunks } from "../../common/input.js";
+import { ImportReportBuilder } from "../../common/report.js";
+import { tokenizeXml, xmlDeclaredEncoding, XmlSyntaxError } from "../../common/xml.js";
+import { readZipDirectory, readZipEntry, ZipError } from "../../common/zip.js";
+import { ImportError } from "../../types.js";
+import { CYS_ISSUE, FORMAT, MAX_RATIO } from "./constants.js";
+/**
+ * Java's `URLDecoder.decode` (UTF-8): `+` is a space, `%XX` a byte; a malformed escape leaves the
+ * text as it is.
+ * @param text - the encoded text
+ * @returns the decoded text
+ */
+export function urlDecode(text) {
+    const plus = text.replace(/\+/g, " ");
+    try {
+        return decodeURIComponent(plus);
+    }
+    catch {
+        return plus;
+    }
+}
+/**
+ * Read the input as a zip and lay out its session entries. Fatal: text input or not a zip
+ * (E_CYS_NOT_ZIP), an empty input, a damaged archive (E_CYS_CORRUPT), a split archive
+ * (E_CYS_UNSUPPORTED), no session marker (E_CYS_NOT_SESSION), a version graph-io cannot read
+ * (E_CYS_VERSION).
+ * @param input - the input
+ * @param report - the report
+ * @param common - cancellation and progress
+ * @param maxBytes - the import's uncompressed byte budget
+ * @returns the session
+ */
+export async function openSession(input, report, common, maxBytes) {
+    const bytes = await readBytes(input, common);
+    if (bytes === null) {
+        report.fail(CYS_ISSUE.NOT_ZIP, "a Cytoscape session is a zip archive; text input cannot hold one (pass the bytes)");
+    }
+    if (bytes.byteLength === 0) {
+        report.fail(CYS_ISSUE.EMPTY_INPUT, "the input is empty");
+    }
+    let zipEntries;
+    try {
+        zipEntries = readZipDirectory(bytes);
+    }
+    catch (err) {
+        return zipFailure(err, report);
+    }
+    const layout = layoutOf(zipEntries, report);
+    let budget = maxBytes;
+    let inflated = 0;
+    const total = zipEntries.reduce((sum, e) => sum + e.size, 0);
+    return {
+        layout,
+        read: async (entry) => {
+            const before = inflated;
+            try {
+                const data = await readZipEntry(bytes, entry.zip, {
+                    signal: common.signal,
+                    maxBytes: budget,
+                    maxRatio: MAX_RATIO,
+                    onBytes: (n) => common.onProgress?.(before + n, total),
+                });
+                budget -= data.byteLength;
+                inflated += data.byteLength;
+                return data;
+            }
+            catch (err) {
+                return zipFailure(err, report);
+            }
+        },
+    };
+}
+/**
+ * Fail the import with the fatal issue of a zip error (any other error is rethrown).
+ * @param err - the error
+ * @param report - the report
+ */
+function zipFailure(err, report) {
+    if (!(err instanceof ZipError)) {
+        throw err;
+    }
+    const code = {
+        "not-zip": CYS_ISSUE.NOT_ZIP,
+        corrupt: CYS_ISSUE.CORRUPT,
+        unsupported: CYS_ISSUE.UNSUPPORTED,
+        "too-large": CYS_ISSUE.TOO_LARGE,
+    }[err.kind];
+    if (err.kind === "too-large") {
+        // the size limits are not a parse error: graph-io records E_TOO_LARGE as unsupported
+        report.error("unsupported", code, err.message);
+        throw report.abort(err.message, { code });
+    }
+    report.fail(code, err.message);
+}
+/** A 3.x network entry name: `<SUID>[-<name>].xgmml`. */
+const NETWORK_FILE = /^networks\/(\d+)(?:-([^/]*))?\.xgmml$/;
+/** A 3.x view entry name: `<networkSUID>-<viewSUID>[-<title>].xgmml`. */
+const VIEW_FILE = /^views\/(\d+)-(\d+)(?:-[^/]*)?\.xgmml$/;
+/** A 3.x table: `tables/<networkSUID>[-<name>]/<namespace>-<class>-<title>.cytable`. */
+const TABLE_FILE = /^tables\/((\d+)(?:-[^/]*)?\/([^/-]+)-([^/-]+)-[^/]*\.cytable)$/;
+/** Entries of other tools that carry nothing: macOS resource forks and folder metadata. */
+const NOISE = /(^|\/)(__MACOSX\/|\.DS_Store$)/;
+/**
+ * Lay out the entries: drop directory entries and macOS noise, keep the first of a repeated name
+ * (W_CYS_DUPLICATE_ENTRY), find the session marker and its root folder, classify what is under
+ * it, and list what is not read.
+ * @param zipEntries - the central directory
+ * @param report - the report
+ * @returns the layout
+ */
+function layoutOf(zipEntries, report) {
+    const byName = new Map();
+    const repeated = [];
+    for (const entry of zipEntries) {
+        if (entry.directory || NOISE.test(entry.name)) {
+            continue;
+        }
+        if (byName.has(entry.name)) {
+            repeated.push(entry.name);
+            continue;
+        }
+        byName.set(entry.name, entry);
+    }
+    if (repeated.length > 0) {
+        report.warning("unsupported", CYS_ISSUE.DUPLICATE_ENTRY, `${repeated.length} entry name(s) appear more than once; the first of each is read: ${listed(repeated)}`);
+    }
+    const names = [...byName.keys()];
+    const marker = names.find((n) => /^([^/]*\/)?[^/]+\.version$/.test(n));
+    const cysession = names.find((n) => /^([^/]*\/)?cysession\.xml$/.test(n));
+    if (marker === undefined && cysession === undefined) {
+        report.fail(CYS_ISSUE.NOT_SESSION, "the zip holds neither a session version marker (<x.y.z>.version) nor cysession.xml: it is not a Cytoscape session");
+    }
+    const anchor = marker ?? cysession;
+    const root = anchor.slice(0, anchor.lastIndexOf("/") + 1);
+    let era = "2";
+    let version = "2.0.0";
+    if (marker !== undefined) {
+        version = marker.slice(root.length, -".version".length);
+        const major = Number(version.split(".")[0]);
+        if (!Number.isInteger(major) || major > 3) {
+            report.fail(CYS_ISSUE.VERSION, `the session version ${version} is newer than the Cytoscape 3 sessions graph-io reads`);
+        }
+        era = major === 3 ? "3" : "2";
+    }
+    const layout = {
+        era,
+        version,
+        root,
+        networks: [],
+        views: [],
+        tables: [],
+        cytables: null,
+        networkList: null,
+        cysession: null,
+        files: new Map(),
+        styles: [],
+        skipped: [],
+    };
+    for (const [name, zip] of byName) {
+        if (!name.startsWith(root) || name === marker) {
+            if (name !== marker) {
+                layout.skipped.push(name);
+            }
+            continue;
+        }
+        const path = name.slice(root.length);
+        const entry = { path, name, zip };
+        if (era === "3") {
+            classify3(entry, layout);
+        }
+        else {
+            classify2(entry, layout);
+        }
+    }
+    return layout;
+}
+/**
+ * Classify one entry of a 3.x session.
+ * @param entry - the entry
+ * @param layout - the layout being built
+ */
+function classify3(entry, layout) {
+    const { path } = entry;
+    const network = NETWORK_FILE.exec(path);
+    const view = VIEW_FILE.exec(path);
+    const table = TABLE_FILE.exec(path);
+    if (network !== null) {
+        layout.networks.push({ ...entry, suid: network[1], title: urlDecode(network[2] ?? "") });
+    }
+    else if (view !== null) {
+        layout.views.push({ ...entry, network: view[1], view: view[2] });
+    }
+    else if (path === "tables/cytables.xml") {
+        layout.cytables = entry;
+    }
+    else if (table !== null) {
+        const element = {
+            "org.cytoscape.model.CyNode": "node",
+            "org.cytoscape.model.CyEdge": "edge",
+            "org.cytoscape.model.CyNetwork": "network",
+        }[urlDecode(table[4])];
+        layout.tables.push({
+            ...entry,
+            tablePath: table[1],
+            network: table[2],
+            namespace: urlDecode(table[3]),
+            element: element ?? null,
+        });
+    }
+    else if (path === "apps/org.cytoscape.swing-application/network_list.xml") {
+        layout.networkList = entry;
+    }
+    else if (/(^|\/)session_vizmap\.(xml|props)$/.test(path)) {
+        layout.styles.push(entry);
+    }
+    else {
+        layout.skipped.push(entry.name);
+    }
+}
+/**
+ * Classify one entry of a 2.x session.
+ * @param entry - the entry
+ * @param layout - the layout being built
+ */
+function classify2(entry, layout) {
+    const { path } = entry;
+    if (path === "cysession.xml") {
+        layout.cysession = entry;
+    }
+    else if (/^[^/]+\.xgmml$/.test(path)) {
+        layout.files.set(path, entry);
+    }
+    else if (/^session_vizmap\.(props|xml)$/.test(path)) {
+        layout.styles.push(entry);
+    }
+    else {
+        layout.skipped.push(entry.name);
+    }
+}
+/**
+ * A list of names for a message: the first ten, then a count.
+ * @param names - the names
+ * @returns the text
+ */
+export function listed(names) {
+    const head = names.slice(0, 10).join(", ");
+    return names.length > 10 ? `${head} and ${names.length - 10} more` : head;
+}
+/**
+ * Read a small XML entry (`cytables.xml`, `network_list.xml`, `cysession.xml`) as a tree. A
+ * document that is not well-formed is E_CYS_CORRUPT naming the entry.
+ * @param bytes - the entry's bytes
+ * @param entry - the entry name
+ * @param report - the report
+ * @param common - cancellation
+ * @returns the root element
+ */
+export async function readXmlTree(bytes, entry, report, common) {
+    const scratch = new ImportReportBuilder(FORMAT, 0);
+    const stack = [{ name: "", attrs: new Map(), children: [] }];
+    try {
+        await tokenizeXml(textChunks(bytes, scratch, { signal: common.signal, declaredEncoding: xmlDeclaredEncoding }), {
+            start(name, attrs) {
+                const node = { name: name.slice(name.lastIndexOf(":") + 1), attrs, children: [] };
+                stack[stack.length - 1].children.push(node);
+                stack.push(node);
+            },
+            end() {
+                stack.pop();
+            },
+            text() {
+                // the session documents keep everything in attributes
+            },
+        });
+    }
+    catch (err) {
+        if (err instanceof XmlSyntaxError || err instanceof ImportError) {
+            report.fail(CYS_ISSUE.CORRUPT, `${entry}: ${err.message}`);
+        }
+        throw err;
+    }
+    const [root] = stack[0].children;
+    if (root === undefined) {
+        report.fail(CYS_ISSUE.CORRUPT, `${entry}: the document is empty`);
+    }
+    return root;
+}
+/**
+ * Every element of a tree with a local name, depth first.
+ * @param node - the tree
+ * @param name - the local name
+ * @returns the elements
+ */
+export function elementsNamed(node, name) {
+    const out = [];
+    const stack = [node];
+    while (stack.length > 0) {
+        const n = stack.pop();
+        if (n.name === name) {
+            out.push(n);
+        }
+        for (let i = n.children.length - 1; i >= 0; i--) {
+            stack.push(n.children[i]);
+        }
+    }
+    return out;
+}
+//# sourceMappingURL=session.js.map

package/dist/src/formats/cys/session.js.map

@@ -0,0 +1 @@
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package/dist/src/formats/cys/tables.d.ts

@@ -0,0 +1,90 @@
+/**
+ * The tables of a Cytoscape 3 session: the CyCSV `.cytable` files (`research-session-and-style.md`
+ * section 2.4; Cytoscape's `CSVCyReader`) and the virtual columns `tables/cytables.xml` joins into
+ * them. Cells become XGMML att records, typed by the column's Java class, so the XGMML emitter
+ * applies the same column rules (types, widening, equations, hidden columns, renames) to a
+ * session's tables as to an XGMML file's atts.
+ */
+import { type ResolvedImportOptions } from "../../common/options.js";
+import { ImportReportBuilder } from "../../common/report.js";
+import { type AttRec } from "../xgmml/document.js";
+/** One column of a table. */
+interface CyColumn {
+    /** The name. */
+    readonly name: string;
+    /** The Cytoscape type of a scalar column, or of a list's items. */
+    readonly type: string;
+    /** A list column. */
+    readonly list: boolean;
+}
+/** One table, read. */
+export interface CyTable {
+    /** The table's path under `tables/` as the archive spells it (what cytables.xml names). */
+    readonly path: string;
+    /** The entry name, for messages. */
+    readonly entry: string;
+    /** The columns; the first is the primary key. */
+    readonly columns: readonly CyColumn[];
+    /** The rows by key text, in file order (the first row of a repeated key). */
+    readonly rows: ReadonlyMap<string, readonly string[]>;
+    /** The line each row starts on, by key. */
+    readonly lines: ReadonlyMap<string, number>;
+}
+/**
+ * Read one CyCSV table. A table that cannot be read at all (an unknown CyCSV version or column
+ * class, a malformed header, broken CSV) is recorded as E_CYS_TABLE and skipped (null); rows with
+ * the wrong number of cells or a repeated key are counted in one W_CYS_TABLE_ROW.
+ * @param bytes - the entry's bytes
+ * @param path - the table's path under `tables/`
+ * @param entry - the entry name, for messages
+ * @param report - the import's report
+ * @param common - cancellation
+ * @returns the table, or null
+ */
+export declare function readCyTable(bytes: Uint8Array, path: string, entry: string, report: ImportReportBuilder, common: ResolvedImportOptions): Promise<CyTable | null>;
+/**
+ * The att record of one cell, or null for an unset cell. CyCSV's rules: an empty cell is unset
+ * except in a String column, where it is the empty string; a list cell holds its items separated
+ * by newlines (Java's `split`, so trailing empty items vanish; an empty String-list cell is one
+ * empty item, any other empty list cell unset); a cell starting with `=` is an equation.
+ * @param column - the column
+ * @param text - the cell text
+ * @param line - the row's line
+ * @param namespace - the table namespace the column belongs to (null for the network's own table)
+ * @param hidden - whether the column is hidden (HIDDEN and app tables)
+ * @returns the att, or null
+ */
+export declare function cellAtt(column: CyColumn, text: string, line: number, namespace: string | null, hidden: boolean): AttRec | null;
+/** One virtual column of `tables/cytables.xml`. */
+export interface VirtualColumn {
+    /** The column name in the target table. */
+    readonly name: string;
+    /** The target table's path under `tables/`. */
+    readonly targetTable: string;
+    /** The source table's path. */
+    readonly sourceTable: string;
+    /** The source column's name. */
+    readonly sourceColumn: string;
+    /** The join column of the source (normally SUID). */
+    readonly sourceJoinKey: string;
+    /** The join column of the target (normally SUID). */
+    readonly targetJoinKey: string;
+}
+/** A resolved virtual column: its type and its value per target row key. */
+interface VirtualValues {
+    readonly column: CyColumn;
+    readonly values: ReadonlyMap<string, string>;
+}
+/**
+ * Resolve the virtual columns of one table: each one's values joined from its source table,
+ * following a source that is itself a virtual column. A column whose source table or column is
+ * missing, or whose sources form a cycle, is E_CYS_TABLE and skipped.
+ * @param target - the table
+ * @param virtuals - every virtual column of the session
+ * @param tableOf - reads (and caches) a table by path, null when it cannot be read or is absent
+ * @param report - the report
+ * @returns the virtual columns of the table, in cytables.xml order
+ */
+export declare function virtualColumnsOf(target: CyTable, virtuals: readonly VirtualColumn[], tableOf: (path: string) => Promise<CyTable | null>, report: ImportReportBuilder): Promise<VirtualValues[]>;
+export {};
+//# sourceMappingURL=tables.d.ts.map