@graphty/graph-io 0.3.25 → 0.3.27

package/dist/src/formats/xgmml/document.js

@@ -6,13 +6,13 @@
  * Cytoscape does, and the `.cys` importer reuses the same records for the network and view files
  * of a session.
  *
- * It recognises the five shapes of `research-xgmml.md` section 2: the 1.0 draft, the Cytoscape
+ * It recognizes the five shapes of `research-xgmml.md` section 2: the 1.0 draft, the Cytoscape
  * 2.x export and session, the 3.x export, the 3.x session network file (root `cy:registered="0"`)
  * and the 3.x session view file (root `cy:view="1"`).
  */
 import { escapeXmlAttribute, escapeXmlText } from "../../common/escape.js";
 import { isWhitespace, localName } from "../../common/xml.js";
-import { XGMML_ISSUE, XGMML_NAMESPACE } from "./constants.js";
+import { XGMML_ISSUE, XGMML_NAMESPACE, XLINK_NAMESPACE } from "./constants.js";
 /** The XML attributes the parser reads on `<node>`. */
 const NODE_READ = new Set(["id", "label", "name", "xlink:href", "cy:nodeId"]);
 /** The XML attributes the parser reads on `<edge>`. */
@@ -45,26 +45,35 @@ const TRUE_TEXT = /^(1|true|yes)$/i;
  * Whether a Cytoscape flag text is true.
  * @param text - the text, or undefined
  * @returns true for 1, true or yes in any case
+ * @category Plugin helpers
  */
 export function isCyTrue(text) {
     return text !== null && text !== undefined && TRUE_TEXT.test(text.trim());
 }
 /**
- * The name an XML attribute is known by, its `xlink` prefix normalised whatever prefix the file
- * binds XLink to (galFiltered.xgmml uses `ns1`).
+ * The name an XML attribute is known by, its `xlink` prefix normalized whatever prefix the file
+ * binds XLink to (galFiltered.xgmml uses `ns1`), on the element itself or on any ancestor; an
+ * unbound `xlink:` prefix is XLink too.
  * @param name - the attribute name as written
- * @param xlinkPrefixes - the prefixes bound to the XLink namespace
+ * @param scope - the namespace prefixes in scope (prefix to URI, "" for the default)
  * @returns the name with `xlink:` for XLink attributes
  */
-function normaliseName(name, xlinkPrefixes) {
+function normaliseName(name, scope) {
     const colon = name.indexOf(":");
-    if (colon > 0 && xlinkPrefixes.has(name.slice(0, colon))) {
+    if (colon <= 0) {
+        return name;
+    }
+    const prefix = name.slice(0, colon);
+    if (prefix === "xlink" || scope.get(prefix) === XLINK_NAMESPACE) {
         return `xlink:${name.slice(colon + 1)}`;
     }
     return name;
 }
+/** The namespaces in scope outside the root element. */
+const NO_SCOPE = new Map();
 /**
  * The tokenizer handler that builds an XgmmlDocument.
+ * @category Plugin helpers
  */
 export class XgmmlParser {
     /**
@@ -73,7 +82,8 @@ export class XgmmlParser {
      */
     constructor(report) {
         this.frames = [];
-        this.xlinkPrefixes = new Set(["xlink"]);
+        /** The namespace prefixes in scope at each open element (prefix to URI, "" for the default). */
+        this.scopes = [];
         this.rootGraph = null;
         this.nodes = [];
         this.edges = [];
@@ -84,6 +94,7 @@ export class XgmmlParser {
         this.rootPrefix = null;
         this.rdf = {};
         this.rdfXml = null;
+        this.doctypeText = null;
         /** The local name of the RDF element whose text is being read, or null. */
         this.rdfElement = null;
         this.report = report;
@@ -106,8 +117,16 @@ export class XgmmlParser {
             xgmmlNamespace: this.xgmmlNamespace,
             rdf: this.rdf,
             rdfXml: this.rdfXml,
+            doctype: this.doctypeText,
         };
     }
+    /**
+     * The DOCTYPE declaration.
+     * @param text - the declaration as written
+     */
+    doctype(text) {
+        this.doctypeText ?? (this.doctypeText = text);
+    }
     /**
      * An element starts.
      * @param rawName - the element name as written
@@ -115,6 +134,7 @@ export class XgmmlParser {
      * @param line - the line
      */
     start(rawName, rawAttrs, line) {
+        this.enterScope(rawAttrs);
         const top = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];
         if (top === null) {
             this.startRoot(rawName, rawAttrs, line);
@@ -128,8 +148,9 @@ export class XgmmlParser {
             this.capture(top, rawName, rawAttrs);
             return;
         }
-        const attrs = this.normalise(rawAttrs);
-        const name = localName(rawName);
+        const attrs = this.normalize(rawAttrs);
+        // an element of another namespace keeps its prefix, so no XGMML element name matches it
+        const name = this.isXgmmlName(rawName) ? localName(rawName) : rawName;
         switch (top.kind) {
             case "graph":
                 this.startInGraph(top.graph, rawName, name, attrs, line);
@@ -166,6 +187,7 @@ export class XgmmlParser {
      * @param _line - the line
      */
     end(name, _line) {
+        this.scopes.pop();
         const frame = this.frames.pop();
         const below = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];
         switch (frame?.kind) {
@@ -174,8 +196,11 @@ export class XgmmlParser {
                 frame.depth--;
                 if (frame.depth > 0) {
                     this.frames.push(frame);
+                    this.rdfElement = null;
+                    return;
                 }
-                else if (frame.att.name === "networkMetadata") {
+                frame.att.xml = bindPrefixes(frame.att.xml, frame.start, frame.scope);
+                if (frame.att.name === "networkMetadata") {
                     this.rdfXml = frame.att.xml;
                 }
                 this.rdfElement = null;
@@ -219,15 +244,40 @@ export class XgmmlParser {
             : "text where XGMML allows only elements was ignored", { line });
     }
     // ------------------------------------------------------------------ structure
+    /**
+     * Open the namespace scope of an element: its parent's, plus the prefixes it declares.
+     * @param attrs - the element's attributes as written
+     */
+    enterScope(attrs) {
+        const parent = this.scopes.at(-1) ?? NO_SCOPE;
+        let scope = parent;
+        for (const [key, value] of attrs) {
+            if (key === "xmlns" || key.startsWith("xmlns:")) {
+                if (scope === parent) {
+                    scope = new Map(parent);
+                }
+                scope.set(key === "xmlns" ? "" : key.slice(6), value);
+            }
+        }
+        this.scopes.push(scope);
+    }
+    /**
+     * The namespace prefixes in scope at the innermost open element.
+     * @returns prefix to URI
+     */
+    get scope() {
+        return this.scopes.at(-1) ?? NO_SCOPE;
+    }
     /**
      * The XML attribute map with every XLink prefix written `xlink:`.
      * @param attrs - the attributes as written
-     * @returns the normalised map
+     * @returns the normalized map
      */
-    normalise(attrs) {
+    normalize(attrs) {
         const out = new Map();
+        const { scope } = this;
         for (const [key, value] of attrs) {
-            out.set(normaliseName(key, this.xlinkPrefixes), value);
+            out.set(normaliseName(key, scope), value);
         }
         return out;
     }
@@ -240,10 +290,7 @@ export class XgmmlParser {
     startRoot(rawName, rawAttrs, line) {
         const local = localName(rawName);
         const prefix = rawName.includes(":") ? rawName.slice(0, rawName.indexOf(":")) : null;
-        for (const [key, value] of rawAttrs) {
-            if (key.startsWith("xmlns:") && value === "http://www.w3.org/1999/xlink") {
-                this.xlinkPrefixes.add(key.slice(6));
-            }
+        for (const key of rawAttrs.keys()) {
             if (key === "xmlns:cy" || key.startsWith("cy:")) {
                 this.cytoscape = true;
             }
@@ -254,7 +301,7 @@ export class XgmmlParser {
         if (local !== "graph") {
             this.report.fail(XGMML_ISSUE.NO_GRAPH, `the root element is <${rawName}>, not <graph>; an XGMML graph embedded in another document is not read`, { line });
         }
-        const graph = this.newGraph(this.normalise(rawAttrs), line, null, null);
+        const graph = this.newGraph(this.normalize(rawAttrs), line, null, null);
         this.rootGraph = graph;
         this.frames.push({ kind: "graph", graph });
     }
@@ -314,7 +361,7 @@ export class XgmmlParser {
                 return;
             }
             case "graphics":
-                this.beginGraphics(graph, attrs);
+                this.beginGraphics(graph, attrs, line);
                 return;
             default:
                 this.unknownElement(rawName, line);
@@ -337,7 +384,7 @@ export class XgmmlParser {
                 return;
             }
             case "graphics":
-                this.beginGraphics(element, attrs);
+                this.beginGraphics(element, attrs, line);
                 return;
             default:
                 this.unknownElement(rawName, line);
@@ -367,19 +414,30 @@ export class XgmmlParser {
         }
         // a second foreign element of the same att is appended to the first
         att.xml ?? (att.xml = "");
-        const capture = { kind: "capture", att, depth: 0 };
+        const capture = {
+            kind: "capture",
+            att,
+            depth: 0,
+            start: att.xml.length,
+            scope: this.scope,
+        };
         this.frames.push(capture);
         this.capture(capture, rawName, attrs);
     }
     /**
-     * Whether an element name inside an att is XGMML's own (unprefixed, or with the root's prefix,
-     * as in a document whose root is `<xgmml:graph>`) rather than foreign XML such as `rdf:RDF`.
+     * Whether an element name is XGMML's own (unprefixed, with the root's prefix as in a document
+     * whose root is `<xgmml:graph>`, or with any prefix bound to the XGMML namespace) rather than
+     * foreign XML such as `rdf:RDF` or `svg:node`.
      * @param rawName - the name as written
      * @returns true for an XGMML element name
      */
     isXgmmlName(rawName) {
         const colon = rawName.indexOf(":");
-        return colon < 0 || (this.rootPrefix !== null && rawName.slice(0, colon) === this.rootPrefix);
+        if (colon < 0) {
+            return true;
+        }
+        const prefix = rawName.slice(0, colon);
+        return prefix === this.rootPrefix || this.scope.get(prefix) === XGMML_NAMESPACE;
     }
     /**
      * A `<graph>` inside an `<att>`: a subnetwork of the root, a group or nested-network pointer
@@ -440,6 +498,9 @@ export class XgmmlParser {
         const labelAttr = attrs.get("label") ?? null;
         const nameAttr = attrs.get("name") ?? null;
         const label = labelAttr ?? nameAttr;
+        if (href !== null && id !== null) {
+            this.idAndHref("node", id, href, line);
+        }
         if (href === null && id === null) {
             if (label === null || label.length === 0) {
                 this.report.counts.skippedNodes++;
@@ -483,9 +544,13 @@ export class XgmmlParser {
      */
     beginEdge(graph, attrs, line) {
         const href = attrs.get("xlink:href") ?? null;
+        const id = attrs.get("id") ?? null;
+        if (href !== null && id !== null) {
+            this.idAndHref("edge", id, href, line);
+        }
         const edge = {
             kind: "edge",
-            id: href === null ? (attrs.get("id") ?? null) : null,
+            id: href === null ? id : null,
             href,
             source: attrs.get("source") ?? null,
             target: attrs.get("target") ?? null,
@@ -506,6 +571,16 @@ export class XgmmlParser {
         }
         this.frames.push({ kind: "edge", edge });
     }
+    /**
+     * W_XGMML_ID_AND_HREF: an element that both declares an id and references another element.
+     * @param kind - node or edge
+     * @param id - the id
+     * @param href - the reference
+     * @param line - the line
+     */
+    idAndHref(kind, id, href, line) {
+        this.report.warning("validation-error", XGMML_ISSUE.ID_AND_HREF, `<${kind}> has both id "${id}" and xlink:href "${href}"; it is read as a reference to ${href} and the id is not used`, { line, element: id });
+    }
     // ------------------------------------------------------------------ atts
     /**
      * An att record from its XML attributes.
@@ -559,7 +634,13 @@ export class XgmmlParser {
         frame.att.xml = `${frame.att.xml ?? ""}${tag}>`;
         frame.depth++;
         if (frame.att.name === "networkMetadata") {
-            this.rdfElement = localName(rawName);
+            const field = localName(rawName);
+            this.rdfElement = field;
+            if (this.rdf[field] !== undefined) {
+                // a second <dc:title>: the first is kept, the two are never joined
+                this.rdfElement = null;
+                this.report.warning("validation-error", XGMML_ISSUE.DUPLICATE_ATTRIBUTE, `the network metadata gives <${rawName}> twice; the first ("${this.rdf[field]}") is kept`, { line: frame.att.line, element: field });
+            }
         }
     }
     /**
@@ -577,14 +658,21 @@ export class XgmmlParser {
      * attribute is kept as written, merged key by key with an earlier `<graphics>`.
      * @param target - the node, edge or graph
      * @param attrs - its attributes
+     * @param line - the line
      */
-    beginGraphics(target, attrs) {
+    beginGraphics(target, attrs, line) {
         const graphics = { ...(target.graphics ?? {}) };
         for (const [key, value] of attrs) {
             if ("x" in target && (key === "x" || key === "y" || key === "z")) {
+                if (target[key] !== null && target[key] !== undefined) {
+                    this.duplicateGraphics(key, line);
+                }
                 target[key] = value;
             }
             else if (key !== "xmlns" && !key.startsWith("xmlns:")) {
+                if (key in graphics) {
+                    this.duplicateGraphics(key, line);
+                }
                 graphics[key] = value;
             }
         }
@@ -636,14 +724,26 @@ export class XgmmlParser {
             this.report.warnOnce("validation-error", XGMML_ISSUE.BAD_ATT, "a graphics <att> without a name was skipped", { line: att.line }, `${XGMML_ISSUE.BAD_ATT}:graphics-name`);
             return;
         }
+        if (target.graphics !== null && att.name in target.graphics) {
+            this.duplicateGraphics(att.name, att.line);
+        }
         target.graphics = { ...(target.graphics ?? {}), [att.name]: attJson(att) };
     }
+    /**
+     * W_DUPLICATE_ATTRIBUTE for a graphics property given twice on one element (once per name).
+     * @param key - the property
+     * @param line - the line
+     */
+    duplicateGraphics(key, line) {
+        this.report.warnOnce("validation-error", XGMML_ISSUE.DUPLICATE_ATTRIBUTE, `the graphics property "${key}" is given twice on one element; the later value is kept`, { line, element: key }, `${XGMML_ISSUE.DUPLICATE_ATTRIBUTE}:graphics:${key}`);
+    }
 }
 /**
  * Whether an att's children are list items rather than named fields: they have no names, repeat
  * the parent's name (Cytoscape 3 lists), or are several that share one name (2.x bend handles).
  * @param att - the att
  * @returns true for a list
+ * @category Plugin helpers
  */
 export function isListLike(att) {
     const names = new Set(att.children.map((c) => c.name));
@@ -659,6 +759,7 @@ export function isListLike(att) {
  * else its other XML attributes (a 2.x bend handle's x and y), else null.
  * @param att - the att
  * @returns the value
+ * @category Plugin helpers
  */
 export function attJson(att) {
     if (att.children.length === 0) {
@@ -676,6 +777,34 @@ export function attJson(att) {
     }
     return out;
 }
+/**
+ * Declare on a captured element the namespace prefixes the captured XML uses but does not bind
+ * itself, so the stored XML is namespace-well-formed on its own.
+ * @param xml - the captured XML of the att
+ * @param start - where the captured element starts in it
+ * @param scope - the namespaces in scope at the captured element
+ * @returns the XML with the declarations added to the captured element's start tag
+ */
+function bindPrefixes(xml, start, scope) {
+    const segment = xml.slice(start);
+    const used = new Set();
+    for (const match of segment.matchAll(/<\/?([A-Za-z_][\w.-]*):|\s([A-Za-z_][\w.-]*):[\w.-]+="/g)) {
+        used.add(match[1] ?? match[2]);
+    }
+    let declarations = "";
+    for (const prefix of used) {
+        const uri = scope.get(prefix);
+        if (prefix !== "xmlns" && prefix !== "xml" && uri !== undefined && !segment.includes(` xmlns:${prefix}="`)) {
+            declarations += ` xmlns:${prefix}="${escapeXmlAttribute(uri)}"`;
+        }
+    }
+    if (declarations.length === 0) {
+        return xml;
+    }
+    const nameEnd = xml.slice(start).search(/[\s>]/);
+    const at = start + (nameEnd < 0 ? segment.length : nameEnd);
+    return `${xml.slice(0, at)}${declarations}${xml.slice(at)}`;
+}
 /**
  * The XML attributes of an element the parser does not read itself, without namespace
  * declarations.

package/dist/src/formats/xgmml/document.js.map

@@ -1 +1 @@
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package/dist/src/formats/xgmml/emit.d.ts

@@ -8,7 +8,10 @@ import { type ColumnDecl, type ColumnHandle, type GraphSink } from "@graphty/gra
 import { type ResolvedImportOptions } from "../../common/options.js";
 import { type ImportReportBuilder } from "../../common/report.js";
 import { type EdgeRec, type GraphRec, type NodeRec, type XgmmlDocument } from "./document.js";
-/** The XGMML-specific options, resolved. */
+/**
+ * The XGMML-specific options, resolved.
+ * @category Plugin helpers
+ */
 export interface XgmmlSettings {
     /** Resolve missing or unknown endpoints through `"a (pp) b"` edge labels. */
     readonly labelAliases: boolean;
@@ -17,7 +20,10 @@ export interface XgmmlSettings {
     /** Where Cytoscape's z goes. */
     readonly zAs: "column" | "position";
 }
-/** What a session adds to the document's own rules. */
+/**
+ * What a session adds to the document's own rules.
+ * @category Plugin helpers
+ */
 export interface EmitExtras {
     /** Ids of nodes the session's group bookkeeping lists as groups. */
     readonly groupNodes?: ReadonlySet<string> | undefined;
@@ -38,8 +44,19 @@ export interface EmitExtras {
      * session): the session records it instead of E_UNKNOWN_PARENT.
      */
     readonly onMissingMember?: ((group: string, member: string) => void) | undefined;
+    /**
+     * A 3.x session: the label of a node or edge is its table's `name` (what Cytoscape shows), in
+     * a label column named `name`; the XGMML `label` attribute is read only when no element of
+     * the table has a `name`.
+     */
+    readonly labelFromName?: boolean | undefined;
+    /** Node ids to read in place of the written ones (ids an exporter mangled, by written id). */
+    readonly restoredIds?: ReadonlyMap<string, string> | undefined;
 }
-/** The dialect facts the rules depend on. */
+/**
+ * The dialect facts the rules depend on.
+ * @category Plugin helpers
+ */
 export interface Dialect {
     /** The documentVersion as written, or null. */
     readonly versionText: string | null;
@@ -59,6 +76,7 @@ export interface Dialect {
  * @param doc - the document
  * @param report - the report the unparseable-version warning goes to
  * @returns the dialect
+ * @category Plugin helpers
  */
 export declare function dialectOf(doc: XgmmlDocument, report: ImportReportBuilder): Dialect;
 /**
@@ -67,13 +85,23 @@ export declare function dialectOf(doc: XgmmlDocument, report: ImportReportBuilde
  * @param doc - the document
  * @param dialect - its dialect
  * @returns the graphs, in document order
+ * @category Plugin helpers
  */
 export declare function graphsOf(doc: XgmmlDocument, dialect: Dialect): GraphRec[];
+/**
+ * A graphics coordinate as Java's `Double.parseDouble` reads Cytoscape's (no hex, no `_`), and
+ * finite.
+ * @param text - the text
+ * @returns the number, or null when it does not parse or is not finite
+ * @category Plugin helpers
+ */
+export declare function parseCoordinate(text: string): number | null;
 /**
  * The nodes and edges a graph holds: its direct members, references resolved.
  * @param doc - the document
  * @param graph - the graph (a registered subnetwork), or null for the whole document
  * @returns the declared node and edge records it holds, references resolved, in order
+ * @category Plugin helpers
  */
 export declare function membersOf(doc: XgmmlDocument, graph: GraphRec | null): {
     readonly nodes: NodeRec[];
@@ -89,6 +117,7 @@ interface NodeRow {
 }
 /**
  * Pushes one graph of a document into a sink.
+ * @category Plugin helpers
  */
 export declare class XgmmlEmitter {
     private readonly doc;
@@ -191,6 +220,14 @@ export declare class XgmmlEmitter {
      * @returns whether the edge is directed
      */
     private edgeDirection;
+    /**
+     * The default direction of the edges of a graph: the `directed` attribute of the graph or of
+     * the nearest graph it is nested in that has one, else the header.
+     * @param graph - the graph that holds the edge
+     * @param header - the header direction
+     * @returns whether the graph's edges are directed by default
+     */
+    private graphDirected;
     /**
      * The direction the sink starts with: the one every edge has when they all agree (a
      * Cytoscape file writes cy:directed on every edge and may omit the root attribute), else the
@@ -214,6 +251,26 @@ export declare class XgmmlEmitter {
      * @param records - the node records
      */
     private addNodes;
+    /**
+     * The sink id of a node's written id: the restored original, else the written id, coerced.
+     * @param text - the written id
+     * @returns the id
+     */
+    private idOf;
+    /** Per table: the label is the `name` att (labelFromName and some element has one). */
+    private readonly nameLabel;
+    /**
+     * Decide whether a table's label comes from its `name` atts.
+     * @param domain - node or edge
+     * @param records - the table's records
+     */
+    private decideNameLabel;
+    /**
+     * The label of a record: its `name` att, or its XGMML label.
+     * @param record - the node or edge
+     * @returns the label, or undefined
+     */
+    private labelOf;
     /**
      * The coerced id of a node text.
      * @param text - the id text
@@ -335,6 +392,7 @@ export declare class XgmmlEmitter {
  * The three parts of a Cytoscape edge label (`source (interaction) target`).
  * @param label - the label, or null
  * @returns source alias, interaction, target alias; null when the label has another shape
+ * @category Plugin helpers
  */
 export declare function aliasesOf(label: string | null): [string, string, string] | null;
 export {};

package/dist/src/formats/xgmml/emit.d.ts.map

@@ -1 +1 @@
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