@graphty/graph-io 0.3.48 → 0.3.50

package/dist/chunks/{generic-CP6YD34u.js → generic-Dc21MAdg.js}

@@ -1,6 +1,293 @@
-import { an as keptForStyles } from "./report-CgdsL9Hb.js";
-import { S as StyleBudget } from "./emit-CD8xnY8s.js";
-import { C as STYLE_PROPERTIES, I as interpolate, J as within, u as StyleNotes, t as toolDefaults, q as isStyleValue, K as describeFeature, a as STYLE_ISSUE, L as refSource, N as isShortPredicate, O as resolveRules, P as matches, Q as evalContinuous, R as numberOf, d as canonicalFor, s as styleFingerprint, v as parseStyleBlock, x as blockStyles, z as featuresOf, p as plainCell, S as STYLE_BLOCK_NAME, U as styleLengthUnit, g as canonColor, y as colorOpacity, l as canonEnum, o as canonText, m as canonBoolean, j as canonOpacity, h as canonNumber, H as DOT_POINTS_PER_INCH } from "./block-Cu22ewuS.js";
+import { an as keptForStyles } from "./report-CwMfYa9J.js";
+import { S as StyleBudget } from "./emit-7Jkpg0yd.js";
+import { w as STYLE_PROPERTIES, N as interpolate, O as within, h as StyleNotes, y as toolDefaults, l as isStyleValue, P as describeFeature, b as STYLE_ISSUE, Q as refSource, R as isShortPredicate, U as resolveRules, V as matches, W as evalContinuous, X as numberOf, C as canonicalFor, o as styleFingerprint, t as featuresOf, m as parseStyleBlock, q as blockStyles, Y as styleLengthUnit, p as plainCell, S as STYLE_BLOCK_NAME, d as canonColor, e as colorOpacity, a as canonEnum, f as canonText, k as canonBoolean, j as canonOpacity, g as canonSigned, c as canonNumber, H as DOT_POINTS_PER_INCH } from "./block-yl0f_qLO.js";
+const CYTOSCAPE_ANNOTATIONS_COLUMN = "__Annotations";
+const TYPE_PREFIX = "org.cytoscape.view.presentation.annotations.";
+const SHAPES = /* @__PURE__ */ new Map([
+  ["rectangle", "rectangle"],
+  ["roundedrectangle", "round-rectangle"],
+  ["rounded_rectangle", "round-rectangle"],
+  ["ellipse", "ellipse"],
+  ["triangle", "triangle"],
+  ["diamond", "diamond"],
+  ["pentagon", "pentagon"],
+  ["hexagon", "hexagon"],
+  ["octagon", "octagon"],
+  ["parallelogram", "parallelogram"],
+  ["star5", "star"],
+  ["star6", "star"],
+  ["v", "vee"]
+]);
+const ARROW_ORDER = [
+  "circle",
+  "triangle",
+  "vee",
+  "diamond",
+  "triangle-open",
+  "none",
+  "other:x",
+  "triangle",
+  "tee"
+];
+const ARROW_LENGTHS = [10, 17, 17, 17, 17, 0, 10, 5, 0];
+const ARROW_WIDTH = 10;
+const ARROW_NAMES = /* @__PURE__ */ new Map([
+  ["circle", "circle"],
+  ["closed arrow", "triangle"],
+  ["concave arrow", "vee"],
+  ["diamond", "diamond"],
+  ["open arrow", "triangle-open"],
+  ["no arrow", "none"],
+  ["pipe", "tee"],
+  ["triangle", "triangle"],
+  ["t", "tee"],
+  ["t-shape", "tee"],
+  ["triangular head", "triangle"],
+  ["x", "other:x"],
+  ["x arrow", "other:x"]
+]);
+function readAnnotations(snapshot) {
+  const { graph } = snapshot;
+  const cell = graph.has(CYTOSCAPE_ANNOTATIONS_COLUMN) ? graph.value(CYTOSCAPE_ANNOTATIONS_COLUMN, 0) : null;
+  const entries = cellStrings(cell);
+  const fields = entries.map(parseEntry);
+  const byId = new Map(fields.map((f, i) => [f.get("uuid") ?? String(i), f]));
+  const annotations = [];
+  const skipped = /* @__PURE__ */ new Set();
+  fields.forEach((f, i) => {
+    const read = readOne(f, String(i), byId);
+    if (read === null) {
+      skipped.add((f.get("type") ?? "").replace(TYPE_PREFIX, ""));
+    } else {
+      annotations.push(...read);
+    }
+  });
+  return { annotations, skipped: [...skipped] };
+}
+function readImageAnnotations(snapshot) {
+  const { graph } = snapshot;
+  const cell = graph.has(CYTOSCAPE_ANNOTATIONS_COLUMN) ? graph.value(CYTOSCAPE_ANNOTATIONS_COLUMN, 0) : null;
+  return cellStrings(cell).flatMap((entry, i) => {
+    const f = parseEntry(entry);
+    const url = f.get("URL") ?? "";
+    if ((f.get("type") ?? "").replace(TYPE_PREFIX, "") !== "ImageAnnotation" || url === "") {
+      return [];
+    }
+    const zoom = positive(f.get("zoom")) ?? 1;
+    const x = num(f.get("x")) ?? 0;
+    const y = num(f.get("y")) ?? 0;
+    const width = (positive(f.get("width")) ?? 0) / zoom;
+    const height = (positive(f.get("height")) ?? 0) / zoom;
+    const border = javaColor(f.get("edgeColor")) ?? { color: "#000000", alpha: 1 };
+    const opacity = num(f.get("opacity"));
+    return [
+      {
+        id: f.get("uuid") ?? String(i),
+        layer: f.get("canvas") === "background" ? "background" : "foreground",
+        z: num(f.get("z")) ?? 0,
+        kind: "image",
+        rotation: num(f.get("rotation")) ?? 0,
+        center: { x: x + width / 2, y: -(y + height / 2) },
+        width,
+        height,
+        url,
+        opacity: opacity === null ? 1 : Math.min(1, Math.max(0, opacity)),
+        borderColor: border.color,
+        borderOpacity: border.alpha * percent(f.get("edgeOpacity")),
+        borderWidth: (num(f.get("edgeThickness")) ?? 0) / zoom
+      }
+    ];
+  });
+}
+function cellStrings(cell) {
+  if (typeof cell === "string") {
+    return cell.split(/[\r\n]+/).filter((s) => s !== "");
+  }
+  if (cell !== null && typeof cell === "object" && Symbol.iterator in cell) {
+    return Array.from(cell).filter((s) => typeof s === "string" && s !== "");
+  }
+  return [];
+}
+function parseEntry(entry) {
+  const out = /* @__PURE__ */ new Map();
+  for (const part of entry.split("|")) {
+    const eq = part.indexOf("=");
+    if (eq > 0) {
+      out.set(part.slice(0, eq), part.slice(eq + 1));
+    }
+  }
+  return out;
+}
+function readOne(f, index, byId) {
+  const type = (f.get("type") ?? "").replace(TYPE_PREFIX, "");
+  const zoom = positive(f.get("zoom")) ?? 1;
+  const base = {
+    id: f.get("uuid") ?? index,
+    layer: f.get("canvas") === "background" ? "background" : "foreground",
+    z: num(f.get("z")) ?? 0
+  };
+  switch (type) {
+    case "ShapeAnnotation":
+      return [shapeOf(f, base, zoom)];
+    case "TextAnnotation":
+      return [textOf(f, base, zoom, { x: num(f.get("x")) ?? 0, y: -(num(f.get("y")) ?? 0) }, "top-left")];
+    case "BoundedTextAnnotation": {
+      const shape = shapeOf(f, base, zoom);
+      return [shape, textOf(f, { ...base, id: `${base.id}:text` }, zoom, shape.center, "center")];
+    }
+    case "ArrowAnnotation":
+      return arrowOf(f, base, zoom, byId);
+    default:
+      return null;
+  }
+}
+function shapeOf(f, base, zoom) {
+  const x = num(f.get("x")) ?? 0;
+  const y = num(f.get("y")) ?? 0;
+  const width = (positive(f.get("width")) ?? 0) / zoom;
+  const height = (positive(f.get("height")) ?? 0) / zoom;
+  const fill = javaColor(f.get("fillColor"));
+  const border = javaColor(f.get("edgeColor")) ?? { color: "#000000", alpha: 1 };
+  return {
+    ...base,
+    kind: "shape",
+    rotation: num(f.get("rotation")) ?? 0,
+    center: { x: x + width / 2, y: -(y + height / 2) },
+    width,
+    height,
+    shape: SHAPES.get((f.get("shapeType") ?? "rectangle").toLowerCase()) ?? "rectangle",
+    fill: fill?.color ?? null,
+    fillOpacity: fill === null ? 0 : fill.alpha * percent(f.get("fillOpacity")),
+    borderColor: border.color,
+    borderOpacity: border.alpha * percent(f.get("edgeOpacity")),
+    borderWidth: (num(f.get("edgeThickness")) ?? 1) / zoom
+  };
+}
+function textOf(f, base, zoom, at, anchor) {
+  const style = num(f.get("fontStyle")) ?? 0;
+  const color = javaColor(f.get("color")) ?? { color: "#000000", alpha: 1 };
+  return {
+    ...base,
+    kind: "text",
+    rotation: num(f.get("rotation")) ?? 0,
+    text: f.get("text") ?? "",
+    at,
+    anchor,
+    fontSize: (positive(f.get("fontSize")) ?? 12) / zoom,
+    fontFamily: f.get("fontFamily") ?? "sans-serif",
+    bold: (style & 1) !== 0,
+    italic: (style & 2) !== 0,
+    color: color.color,
+    opacity: color.alpha
+  };
+}
+function arrowOf(f, base, zoom, byId) {
+  const sourceBox = boxOf(byId.get(f.get("sourceAnnotation") ?? ""), zoom);
+  const targetBox = boxOf(byId.get(f.get("targetAnnotation") ?? ""), zoom);
+  const toPoint = point(f.get("targetPoint")) ?? point(f.get("targetNode"));
+  const corner = { x: num(f.get("x")) ?? 0, y: num(f.get("y")) ?? 0 };
+  const sourceCenter = sourceBox === null ? corner : centerOfBox(sourceBox);
+  const aim = toPoint ?? (targetBox === null ? null : centerOfBox(targetBox));
+  if (aim === null) {
+    return null;
+  }
+  const from = sourceBox !== null && sourceBox.width > 0 && sourceBox.height > 0 ? facing(sourceBox, aim) : { x: aim.x > corner.x ? corner.x : sourceCenter.x, y: aim.y > corner.y ? corner.y : sourceCenter.y };
+  const to = toPoint ?? facing(targetBox ?? { x: aim.x, y: aim.y, width: 0, height: 0 }, sourceCenter);
+  const color = javaColor(f.get("lineColor")) ?? { color: "#000000", alpha: 1 };
+  const sourceColor = javaColor(f.get("sourceColor"))?.color ?? color.color;
+  const targetColor = javaColor(f.get("targetColor"))?.color ?? color.color;
+  return [
+    {
+      ...base,
+      kind: "arrow",
+      from: { x: from.x, y: -from.y },
+      to: { x: to.x, y: -to.y },
+      color: color.color,
+      opacity: color.alpha * percent(f.get("lineOpacity")),
+      width: Math.max(1, (positive(f.get("lineThickness")) ?? 1) / zoom / 2),
+      sourceArrow: arrowShape(f.get("sourceType")),
+      targetArrow: arrowShape(f.get("targetType")),
+      sourceSize: positive(f.get("sourceSize")) ?? 1,
+      targetSize: positive(f.get("targetSize")) ?? 1,
+      sourceColor,
+      targetColor,
+      ...heads("source", f.get("sourceType"), positive(f.get("sourceSize")) ?? 1),
+      ...heads("target", f.get("targetType"), positive(f.get("targetSize")) ?? 1)
+    }
+  ];
+}
+function heads(end, type, size) {
+  const shape = arrowShape(type);
+  if (shape === "none") {
+    return {};
+  }
+  const k = num(type) ?? ARROW_ORDER.indexOf(shape);
+  const length = ARROW_LENGTHS[k] ?? ARROW_LENGTHS[1];
+  return { [`${end}HeadLength`]: length * size, [`${end}HeadWidth`]: ARROW_WIDTH * size };
+}
+function boxOf(f, zoom) {
+  if (f === void 0) {
+    return null;
+  }
+  const x = num(f.get("x"));
+  const y = num(f.get("y"));
+  if (x === null || y === null) {
+    return null;
+  }
+  return { x, y, width: (positive(f.get("width")) ?? 0) / zoom, height: (positive(f.get("height")) ?? 0) / zoom };
+}
+function centerOfBox(b) {
+  return { x: b.x + b.width / 2, y: b.y + b.height / 2 };
+}
+function facing(b, p) {
+  const c = centerOfBox(b);
+  const dx = p.x - c.x;
+  const dy = p.y - c.y;
+  if (Math.abs(dx) * b.height >= Math.abs(dy) * b.width) {
+    return { x: c.x + Math.sign(dx) * (b.width / 2), y: c.y };
+  }
+  return { x: c.x, y: c.y + Math.sign(dy) * (b.height / 2) };
+}
+function arrowShape(raw) {
+  if (raw === void 0) {
+    return "none";
+  }
+  const n = num(raw);
+  if (n !== null) {
+    return ARROW_ORDER[n] ?? "triangle";
+  }
+  return ARROW_NAMES.get(raw.trim().toLowerCase()) ?? "triangle";
+}
+function point(raw) {
+  const [x, y] = (raw ?? "").split(",").map((s) => num(s));
+  return x === null || x === void 0 || y === null || y === void 0 ? null : { x, y };
+}
+function javaColor(raw) {
+  const n = num(raw);
+  if (n === null || !Number.isInteger(n)) {
+    return null;
+  }
+  const argb = n >>> 0;
+  return {
+    color: `#${(argb & 16777215).toString(16).padStart(6, "0")}`,
+    alpha: (argb >>> 24) / 255
+  };
+}
+function percent(raw) {
+  const n = num(raw);
+  return n === null ? 1 : Math.min(1, Math.max(0, n / 100));
+}
+function num(raw) {
+  if (raw === void 0 || raw.trim() === "") {
+    return null;
+  }
+  const n = Number(raw);
+  return Number.isFinite(n) ? n : null;
+}
+function positive(raw) {
+  const n = num(raw);
+  return n !== null && n > 0 ? n : null;
+}
 function valueKey(v) {
   return v === null || v === void 0 ? "\0null" : `${typeof v}:${String(v)}`;
 }
@@ -355,7 +642,19 @@ function rampOf(fam, values, ys0, tolerant, spend) {
 }
 const MAX_STYLE_RULES = 16;
 const MAX_FEATURES = 64;
-const LENGTHS = /* @__PURE__ */ new Set(["width", "height", "borderWidth", "labelSize"]);
+const LENGTHS = /* @__PURE__ */ new Set([
+  "width",
+  "height",
+  "borderWidth",
+  "labelSize",
+  "labelWrapWidth",
+  "labelPaddingX",
+  "labelPaddingY",
+  "labelOffsetX",
+  "labelOffsetY",
+  "fanSpacing",
+  "nodeGap"
+]);
 function planStyles(values, features, options = {}) {
   const notes = options.notes ?? new StyleNotes();
   const budget = options.budget ?? new StyleBudget();
@@ -386,7 +685,7 @@ function planStyles(values, features, options = {}) {
         out,
         allFeatures[target],
         new Set(options.rawColumns?.[target] ?? []),
-        toolSet,
+        { set: toolSet, derived: defaults?.derived ?? [] },
         options.signal
       )
     );
@@ -592,8 +891,9 @@ function passCandidate(plan, fam, truth, infos) {
   const raw = Array.from(cols.values()).some((f) => f.raw);
   return { type: "passdata", cols, raw, cost: raw ? 240 : 50 };
 }
-function planTarget(plan, out, features, rawNames, toolSet, signal) {
+function planTarget(plan, out, features, rawNames, tool, signal) {
   const { target, n } = plan;
+  const toolSet = tool.set;
   for (const [k, v] of out?.columns ?? []) {
     plan.columns.set(k, v);
   }
@@ -608,6 +908,7 @@ function planTarget(plan, out, features, rawNames, toolSet, signal) {
       set: toolSet
     }
   ];
+  toolRule.push(...derivedRules(plan, tool.derived, features, out?.rules ?? [], truth));
   const declared = prepareDeclared(plan, out?.rules ?? [], features);
   const declaredProps = new Set(declared.flatMap(writes));
   const { defaults, rest } = splitDefaults(n, truth, declaredProps);
@@ -694,6 +995,31 @@ function planTarget(plan, out, features, rawNames, toolSet, signal) {
   }
   return drafts.map(finish);
 }
+function derivedRules(plan, derived, features, given, truth) {
+  const stated = /* @__PURE__ */ new Set([...given.filter((r) => r.origin === "tool").flatMap(writes), ...truth.keys()]);
+  const out = [];
+  for (const d of derived) {
+    if (plan.target !== "node" || d.kind !== "labelFromColumn" || stated.has("label")) {
+      continue;
+    }
+    const { column } = d;
+    const feature = features.find((f) => "data" in f.ref && f.ref.data === column);
+    if (feature?.values.some((v) => v !== null && v !== "") !== true) {
+      continue;
+    }
+    stated.add("label");
+    out.push({
+      id: uniqueId(plan, "node.tool.label"),
+      target: "node",
+      role: "passthrough",
+      origin: "tool",
+      where: { has: { data: column } },
+      map: { label: { kind: "passthrough", by: { data: column } } },
+      facts: { reason: "NODE_NAME" }
+    });
+  }
+  return out;
+}
 function splitDefaults(n, truth, declaredProps) {
   const defaults = {};
   const rest = [];
@@ -903,10 +1229,11 @@ function enforceCap(plan, drafts, truth, src) {
     if (cands.length === 0) {
       break;
     }
+    const everyone = (r) => r.origin === "tool" && "all" in r.where ? 1 : 0;
     cands.sort((a, b) => {
       const pa = a.role === "passthrough" ? 1 : 0;
       const pb = b.role === "passthrough" ? 1 : 0;
-      return pa - pb || (FOLD_ORDER[a.origin] ?? 1) - (FOLD_ORDER[b.origin] ?? 1) || ruleSize(b) - ruleSize(a) || drafts.indexOf(b) - drafts.indexOf(a);
+      return pa - pb || (FOLD_ORDER[a.origin] ?? 1) - (FOLD_ORDER[b.origin] ?? 1) || everyone(a) - everyone(b) || ruleSize(b) - ruleSize(a) || drafts.indexOf(b) - drafts.indexOf(a);
     });
     const victim = cands[0];
     const before = drafts.map(finish);
@@ -980,34 +1307,32 @@ function replay(plan, drafts, truth, toolSet, tolerated, src) {
   };
 }
 const TARGETS = ["node", "edge"];
-const ENUM_KINDS = /* @__PURE__ */ new Set(["shape", "borderStyle", "lineStyle", "arrow", "weight", "position"]);
+const ENUM_KINDS = /* @__PURE__ */ new Set([
+  "shape",
+  "borderStyle",
+  "lineStyle",
+  "arrow",
+  "arrowSide",
+  "weight",
+  "position",
+  "labelFit",
+  "borderPosition"
+]);
 function extractStyles(importer, snapshot, report, options = {}) {
   const signal = options.signal ?? void 0;
   const notes = new StyleNotes();
   const budget = options.budget ?? new StyleBudget();
+  const pictures = readImageAnnotations(snapshot).length > 0;
+  for (const kind of readAnnotations(snapshot).skipped) {
+    if (!(pictures && kind === "ImageAnnotation")) {
+      notes.add(STYLE_ISSUE.ANNOTATION_SKIPPED, "graph", "annotations", { sample: kind });
+    }
+  }
   const canonical = readStyleValues(importer, snapshot, report, { notes, budget, signal });
   const fingerprint = styleFingerprint(snapshot);
-  const blockText = canonical?.block ?? graphValue(snapshot, STYLE_BLOCK_NAME);
-  if (blockText !== void 0) {
-    const parsed = parseStyleBlock(blockText, fingerprint);
-    if (parsed.ok) {
-      const truth = canonical === null ? {} : { node: canonical.node.values, edge: canonical.edge.values };
-      const fromBlock = blockStyles(
-        parsed.block,
-        snapshot,
-        importer.format,
-        truth,
-        canonical?.notes ?? [],
-        canonical?.tool ?? null,
-        canonical?.opacityInColor === true
-      );
-      if (fromBlock !== null) {
-        return fromBlock;
-      }
-      notes.add(STYLE_ISSUE.BLOCK_IGNORED, null, null, { sample: "INVALID" });
-    } else {
-      notes.add(STYLE_ISSUE.BLOCK_IGNORED, null, null, { sample: parsed.reason });
-    }
+  const fromBlock = stylesFromBlock(importer, snapshot, canonical, notes, fingerprint);
+  if (fromBlock !== null) {
+    return fromBlock;
   }
   if (canonical === null) {
     const list = notes.list();
@@ -1043,6 +1368,33 @@ function extractStyles(importer, snapshot, report, options = {}) {
   }
   return { ...planned, styles: { ...planned.styles, notes: [...canonical.notes, ...planned.styles.notes] } };
 }
+function stylesFromBlock(importer, snapshot, canonical, notes, fingerprint) {
+  const blockText = canonical?.block ?? graphValue(snapshot, STYLE_BLOCK_NAME);
+  if (blockText === void 0) {
+    return null;
+  }
+  const parsed = parseStyleBlock(blockText, fingerprint);
+  if (!parsed.ok) {
+    notes.add(STYLE_ISSUE.BLOCK_IGNORED, null, null, { sample: parsed.reason });
+    return null;
+  }
+  const truth = canonical === null ? {} : { node: canonical.node.values, edge: canonical.edge.values };
+  const fromBlock = blockStyles(
+    parsed.block,
+    snapshot,
+    importer.format,
+    truth,
+    canonical?.notes ?? [],
+    canonical?.tool ?? null,
+    canonical?.opacityInColor === true
+  );
+  if (fromBlock === null) {
+    notes.add(STYLE_ISSUE.BLOCK_IGNORED, null, null, { sample: "INVALID" });
+    return null;
+  }
+  const skipped = notes.list();
+  return skipped.length === 0 ? fromBlock : { ...fromBlock, styles: { ...fromBlock.styles, notes: [...fromBlock.styles.notes, ...skipped] } };
+}
 function readStyleValues(importer, snapshot, report, context) {
   const { notes, budget, signal } = context;
   signal?.throwIfAborted();
@@ -1257,6 +1609,8 @@ function canonValue(kind, property, raw, dialect, site) {
         site,
         dialect === "graphviz" && (property === "width" || property === "height") ? DOT_POINTS_PER_INCH : 1
       );
+    case "signed":
+      return canonSigned(raw, site);
     case "opacity":
       return canonOpacity(raw, dialect, site);
     case "boolean":
@@ -1341,7 +1695,9 @@ function channelsColor(v, dtype) {
 }
 export {
   MAX_STYLE_RULES as M,
+  readImageAnnotations as a,
   extractStyles as e,
-  planStyles as p
+  planStyles as p,
+  readAnnotations as r
 };
-//# sourceMappingURL=generic-CP6YD34u.js.map
+//# sourceMappingURL=generic-Dc21MAdg.js.map