@platforma-open/milaboratories.clonotype-clustering.model 2.5.1 → 2.6.1

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/clonotype-clustering/clonotype-clustering/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.clonotype-clustering.model@2.5.1 build /home/runner/work/clonotype-clustering/clonotype-clustering/model
+> @platforma-open/milaboratories.clonotype-clustering.model@2.6.1 build /home/runner/work/clonotype-clustering/clonotype-clustering/model
 > tsup && vite build && block-tools build-model
 
 CLI Building entry: src/index.ts
@@ -11,21 +11,21 @@
 CLI Cleaning output folder
 CJS Build start
 ESM Build start
-ESM dist/index.js     3.42 KB
-ESM dist/index.js.map 8.21 KB
-ESM ⚡️ Build success in 113ms
-CJS dist/index.cjs     3.42 KB
-CJS dist/index.cjs.map 8.27 KB
-CJS ⚡️ Build success in 114ms
+ESM dist/index.js     4.51 KB
+ESM dist/index.js.map 10.87 KB
+ESM ⚡️ Build success in 136ms
+CJS dist/index.cjs     4.52 KB
+CJS dist/index.cjs.map 10.94 KB
+CJS ⚡️ Build success in 137ms
 DTS Build start
-DTS ⚡️ Build success in 2251ms
-DTS dist/index.d.cts 4.12 KB
-DTS dist/index.d.ts  4.12 KB
+DTS ⚡️ Build success in 2361ms
+DTS dist/index.d.cts 5.17 KB
+DTS dist/index.d.ts  5.17 KB
 vite v6.3.5 building for production...
 transforming...
 ✓ 11 modules transformed.
 rendering chunks...
 computing gzip size...
-dist/bundle.js  191.12 kB │ gzip: 37.52 kB │ map: 406.27 kB
-dist/bundle.js  204.19 kB │ gzip: 38.19 kB │ map: 407.89 kB
-✓ built in 696ms
+dist/bundle.js  189.96 kB │ gzip: 37.07 kB │ map: 405.50 kB
+dist/bundle.js  202.95 kB │ gzip: 37.72 kB │ map: 407.12 kB
+✓ built in 732ms

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.clonotype-clustering.model
 
+## 2.6.1
+
+### Patch Changes
+
+- 15ffee5: SDK Upgrade, excessive CPU usage fix
+
+## 2.6.0
+
+### Minor Changes
+
+- d536272: MSA for clusters
+
 ## 2.5.1
 
 ### Patch Changes

package/dist/bundle.js

@@ -4007,7 +4007,7 @@
         }
       }
   }
-  function F(n2) {
+  function F$1(n2) {
     if (!n2 || typeof n2 != "object")
       return false;
     const e = n2;
@@ -4025,7 +4025,7 @@
     }
   }
   function gn(n2) {
-    return F(n2) ? n2.type === "JsonPartitioned" || n2.type === "BinaryPartitioned" : false;
+    return F$1(n2) ? n2.type === "JsonPartitioned" || n2.type === "BinaryPartitioned" : false;
   }
   function bn(n2) {
     switch (n2.type) {
@@ -4338,7 +4338,7 @@
       data: e(n2.data)
     };
   }
-  function Rn(n2) {
+  function Rn$1(n2) {
     const e = /* @__PURE__ */ new Map(), t = (r) => {
       switch (r.type) {
         case "column":
@@ -4531,14 +4531,14 @@
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-  var R = (t, e, n2) => Qe(t, typeof e != "symbol" ? e + "" : e, n2);
+  var F = (t, e, n2) => Qe(t, typeof e != "symbol" ? e + "" : e, n2);
   function re(t) {
     return { type: "Immediate", value: t };
   }
   function ht() {
     return typeof globalThis.getPlatforma < "u" || typeof globalThis.platforma < "u";
   }
-  function De(t) {
+  function Re(t) {
     if (t && typeof globalThis.getPlatforma == "function")
       return globalThis.getPlatforma(t);
     if (typeof globalThis.platforma < "u") return globalThis.platforma;
@@ -4566,8 +4566,8 @@
   }
   class I {
     constructor(e, n2 = (r) => r) {
-      R(this, "isResolved", false);
-      R(this, "resolvedValue");
+      F(this, "isResolved", false);
+      F(this, "resolvedValue");
       this.handle = e, this.postProcess = n2, mt(e, (r) => {
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     }
   }
-  const Fe = "staging", Ke = "main";
+  const De = "staging", Ke = "main";
   const bt = "pl7.app/label", wt = "pl7.app/trace", At = z$2.object({
     type: z$2.string(),
     importance: z$2.number().optional(),
@@ -4817,11 +4817,11 @@
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-      var S, D2;
+      var S, R;
       const w2 = e(f2);
       let c2, g, x2;
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+      const p2 = (S = c2.annotations) == null ? void 0 : S[bt], A2 = (R = c2.annotations) == null ? void 0 : R[wt], m2 = (A2 ? xt.safeParse(JSON.parse(A2)).data : void 0) ?? [], v = [
         ...g ?? [],
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         ...x2 ?? []
@@ -4963,7 +4963,7 @@
   }
   function It(t) {
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-    if (F(t))
+    if (F$1(t))
       return _t(t);
     const e = St(t);
     if (!e) return;
@@ -5078,7 +5078,7 @@
   }
   function Tt(t) {
     if (t !== void 0) {
-      if (F(t)) return t;
+      if (F$1(t)) return t;
       if (yn(t)) return bn(t);
       if (t instanceof O) return ye(t);
       throw new Error(`Unexpected input type: ${typeof t}`);
@@ -5166,7 +5166,7 @@
     if (t)
       return t.map((e) => [e.axisIdx, e.value]);
   }
-  function Rt(t, e) {
+  function Ft(t, e) {
     if (!e || e.length === 0) return t;
     const n2 = [...e].sort((r, i) => r[0] - i[0]);
     return ke({ id: t, axisFilters: n2 });
@@ -5176,7 +5176,7 @@
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     return !!e.domainAnchor || n2 || r;
   }
-  function Dt(t) {
+  function Rt(t) {
     if (typeof t != "object" || !("axes" in t) || t.axes === void 0)
       return [];
     const e = t.axes.map((n2, r) => typeof n2 == "object" && "split" in n2 && n2.split === true ? r : -1).filter((n2) => n2 !== -1);
@@ -5186,9 +5186,9 @@
   }
   class ve {
     constructor() {
-      R(this, "defaultProviderStore", []);
-      R(this, "providers", [new Et(this.defaultProviderStore)]);
-      R(this, "axisLabelProviders", []);
+      F(this, "defaultProviderStore", []);
+      F(this, "providers", [new Et(this.defaultProviderStore)]);
+      F(this, "axisLabelProviders", []);
     }
     addColumnProvider(e) {
       return this.providers.push(e), this;
@@ -5243,12 +5243,12 @@
             if (u2(S.spec)) continue;
             if (p2.has(S.id))
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-            const D2 = _n(S.spec);
-            b.has(D2) || (p2.add(S.id), b.add(D2), A2.push(S));
+            const R = _n(S.spec);
+            b.has(R) || (p2.add(S.id), b.add(R), A2.push(S));
           }
         }
         if (A2.length === 0) continue;
-        const m2 = Dt(c2), v = m2.length > 0;
+        const m2 = Rt(c2), v = m2.length > 0;
         for (const C2 of A2) {
           if (!f(C2.spec)) continue;
           const L = C2.spec;
@@ -5260,7 +5260,7 @@
             }
             if (!gn(S))
               throw new Error(`Splitting requires Partitioned DataInfoEntries, but parsing resulted in ${S.type} for column ${C2.id}`);
-            const D2 = It(S), k2 = m2[m2.length - 1];
+            const R = It(S), k2 = m2[m2.length - 1];
             if (k2 >= S.partitionKeyLength)
               throw new Error(`Not enough partition keys (${S.partitionKeyLength}) for requested split axes (max index ${k2}) in column ${L.name}`);
             const W = m2.map((_) => this.findLabels(p$1(L.axesSpec[_]))), V = [], N2 = (_, G2) => {
@@ -5270,9 +5270,9 @@
                 return;
               }
               const $ = m2[G2];
-              if ($ >= D2.length)
-                throw new Error(`Axis index ${$} out of bounds for unique keys array (length ${D2.length}) during split key generation for column ${C2.id}`);
-              const J = D2[$];
+              if ($ >= R.length)
+                throw new Error(`Axis index ${$} out of bounds for unique keys array (length ${R.length}) during split key generation for column ${C2.id}`);
+              const J = R[$];
               if (!J || J.length === 0) {
                 V.length = 0;
                 return;
@@ -5321,7 +5321,7 @@
       for (const { value: c2, label: g } of f$1) {
         const { originalColumn: x2, spec: p2 } = c2, A2 = c2.type === "split" ? c2.axisFilters : void 0, m2 = kt(A2);
         let v;
-        r ? v = r.deriveS(p2, m2) : v = Rt(x2.id, m2);
+        r ? v = r.deriveS(p2, m2) : v = Ft(x2.id, m2);
         let C2 = { ...c2.adjustedSpec };
         o && (C2 = {
           ...C2,
@@ -5371,9 +5371,9 @@
   function Ie(t) {
     return Kn(t, (e) => e instanceof O ? e.handle : yn(e) ? hn(e, (n2) => n2.handle) : e);
   }
-  class Ft {
+  class Dt {
     constructor() {
-      R(this, "ctx", h());
+      F(this, "ctx", h());
     }
     /**
      * @deprecated use getOptions()
@@ -5642,11 +5642,11 @@
   }
   class te {
     constructor() {
-      R(this, "ctx");
-      R(this, "args");
-      R(this, "uiState");
-      R(this, "_activeArgsCache");
-      R(this, "resultPool", new Ft());
+      F(this, "ctx");
+      F(this, "args");
+      F(this, "uiState");
+      F(this, "_activeArgsCache");
+      F(this, "resultPool", new Dt());
       this.ctx = h(), this.args = JSON.parse(this.ctx.args), this.uiState = this.ctx.uiState !== void 0 ? JSON.parse(this.ctx.uiState) : {};
     }
     /**
@@ -5669,7 +5669,7 @@
       );
     }
     get prerun() {
-      return this.getNamedAccessor(Fe);
+      return this.getNamedAccessor(De);
     }
     get outputs() {
       return this.getNamedAccessor(Ke);
@@ -5702,7 +5702,7 @@
         },
         filters: e.filters ?? [],
         sorting: e.sorting ?? []
-      } : n2 = e, this.verifyInlineAndExplicitColumnsSupport(Rn(n2.src)), this.ctx.createPTable(
+      } : n2 = e, this.verifyInlineAndExplicitColumnsSupport(Rn$1(n2.src)), this.ctx.createPTable(
         In(n2, (r) => Ie(r))
       );
     }
@@ -5723,7 +5723,7 @@
       this.ctx.logError(e);
     }
   }
-  const Y = "1.32.1";
+  const Y = "1.33.2";
   function Kt(t) {
     return t.__renderLambda === true;
   }
@@ -5929,31 +5929,12 @@
           Object.entries(this._outputs).map(([n2, r]) => [n2, de(r)])
         )
       };
-      return ht() ? De({ sdkVersion: Y }) : { config: e };
+      return ht() ? Re({ sdkVersion: Y }) : { config: e };
     }
   }
-  const jt = (t, e) => {
-    let n2 = t.toString();
-    return e == null || e.forEach((r) => {
-      if (r)
-        for (const [i, s2] of Object.entries(r))
-          n2 += i, n2 += s2;
-    }), n2;
-  };
-  function Vt(t) {
-    if (!t.length)
-      return [];
-    let e = [[]];
-    return t.forEach((n2) => {
-      const r = [];
-      n2.forEach((i) => {
-        r.push(...e.map((s2) => [...s2, i]));
-      }), e = r;
-    }), e;
-  }
   function $t(t) {
     var e;
-    return t.axesSpec.length === 2 && ((e = t.annotations) == null ? void 0 : e[Ut]) === "true";
+    return t.axesSpec.length === 2 && ((e = t.annotations) == null ? void 0 : e[Mt]) === "true";
   }
   function Nt(t) {
     var n2, r;
@@ -5982,74 +5963,12 @@
     }
     return false;
   }
-  function Jt(t, e, n2) {
-    const r = t.axesSpec.map(p$1), i = e.axesSpec.map(p$1);
-    return i.some((s2) => r.some((o) => X(o, s2) && X(s2, o))) || !!n2 && i.some((s2) => r.some((o) => Je(n2, o, s2)));
-  }
-  function Me(t, e, n2) {
+  function Ue(t, e, n2) {
     const r = t.axesSpec.map(p$1), i = e.axesSpec.map(p$1);
     return i.some((s2) => r.some((o) => X(o, s2))) || !!n2 && i.some((s2) => r.some((o) => Je(n2, o, s2)));
   }
-  const Mt = "pl7.app/graph/isVirtual", Te = "pl7.app/label", Ut = "pl7.app/isLinkerColumn";
-  function Le(t, e, n2) {
-    const r = t.spec.axesSpec.map(p$1), i = e.spec.axesSpec.map(p$1);
-    if (Jt(t.spec, e.spec, n2))
-      return [];
-    if (!Me(t.spec, e.spec, n2))
-      return [];
-    const a = i.map((b) => r.filter((f2) => X(f2, b))), l2 = Vt(a), u2 = /* @__PURE__ */ new Set(), d = /* @__PURE__ */ new Set(), y = l2.map((b) => {
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-      return b.map((w2, c2) => {
-        const g = e.spec.axesSpec[c2].domain, x2 = w2.domain;
-        return Object.entries(x2 ?? {}).forEach(([p2, A2]) => {
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-            const m2 = JSON.stringify([p2, A2]);
-            f2.add(m2), u2.add(m2);
-          }
-        }), {
-          ...w2,
-          annotations: e.spec.axesSpec[c2].annotations
-        };
-      }), f2;
-    });
-    return [...u2].forEach((b) => {
-      y.some((f2) => !f2.has(b)) && d.add(b);
-    }), l2.map((b, f2) => {
-      var p2;
-      const w2 = jt(e.id, b.map((A2) => A2.domain)), c2 = ((p2 = e.spec.annotations) == null ? void 0 : p2[Te]) ?? "", g = [...y[f2]].filter((A2) => d.has(A2)).sort().map((A2) => {
-        var m2;
-        return (m2 = JSON.parse(A2)) == null ? void 0 : m2[1];
-      }).join(" / "), x2 = {
-        ...e.spec.annotations,
-        [Mt]: "true"
-      };
-      return (c2 || g) && (x2[Te] = c2 && g ? c2 + " / " + g : c2 + g), {
-        id: w2,
-        spec: {
-          ...e.spec,
-          axesSpec: b.map((A2, m2) => ({
-            ...A2,
-            annotations: e.spec.axesSpec[m2].annotations
-          })),
-          annotations: x2
-        },
-        data: e.data
-      };
-    });
-  }
-  function Bt(t, e = /* @__PURE__ */ new Map()) {
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-    for (let r = 0; r < t.length; r++)
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-        n2.push(
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-          ...Le(o, s2, e)
-        );
-      }
-    return n2;
-  }
-  function Wt(t, e, n2 = [], r = /* @__PURE__ */ new Map()) {
+  const Mt = "pl7.app/isLinkerColumn";
+  function Bt(t, e, n2 = [], r = /* @__PURE__ */ new Map()) {
     const i = /* @__PURE__ */ new Set(), s2 = /* @__PURE__ */ new Map();
     t.forEach((a) => {
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@@ -6060,7 +5979,7 @@
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       if (!s2.has(l2)) {
         for (const u2 of s2.values())
-          if (Me(u2.spec, a.spec, r)) {
+          if (Ue(u2.spec, a.spec, r)) {
             o.set(l2, a);
             break;
           }
@@ -6073,18 +5992,18 @@
     }
     return [...s2.values(), ...o.values()];
   }
-  function Dn(t, e) {
+  function Rn(t, e) {
     if (!e) return;
-    const n2 = t.resultPool.getData().entries.map((l2) => l2.obj).filter(Z$1), i = [...e, ...n2].filter((l2) => $t(l2.spec)), s2 = Nt(i), o = Wt(e, n2, i, s2), a = [...o, ...Bt(o, s2)];
+    const n2 = t.resultPool.getData().entries.map((l2) => l2.obj).filter(Z$1), i = [...e, ...n2].filter((l2) => $t(l2.spec)), s2 = Nt(i), a = [...Bt(e, n2, i, s2)];
     if (!a.some(
       (l2) => l2.data instanceof O && !l2.data.getIsReadyOrError()
     ))
       return t.createPFrame(a);
   }
-  function Gt(t) {
+  function Wt(t) {
     return t.axesSpec.length === 1 && t.name === "pl7.app/label";
   }
-  function Ue(t) {
+  function Me(t) {
     return new ve().addAxisLabelProvider(t).addColumnProvider(t).getColumns({
       name: "pl7.app/label",
       axes: [{}]
@@ -6094,7 +6013,7 @@
   function Be(t, e) {
     const n2 = [], r = [];
     for (const a of t)
-      Gt(a.spec) ? n2.push(a) : r.push(a);
+      Wt(a.spec) ? n2.push(a) : r.push(a);
     const i = [];
     for (const a of r)
       for (const l2 of a.spec.axesSpec) {
@@ -6164,24 +6083,24 @@
       sorting: i
     };
   }
-  function Ht(t) {
+  function Gt(t) {
     var e;
     return ((e = t.annotations) == null ? void 0 : e["pl7.app/table/visibility"]) === "hidden";
   }
-  function qt(t) {
+  function Ht(t) {
     var e;
     return ((e = t.annotations) == null ? void 0 : e["pl7.app/table/visibility"]) === "optional";
   }
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+    const s2 = "full", o = [...[], ...((g = r == null ? void 0 : r.pTableParams) == null ? void 0 : g.filters) ?? []], a = ((x2 = r == null ? void 0 : r.pTableParams) == null ? void 0 : x2.sorting) ?? [], l2 = e.filter((p2) => !Gt(p2.spec)), u2 = l2.find((p2) => n2(p2.spec));
     if (!u2) return;
-    const d = Ue(t.resultPool);
+    const d = Me(t.resultPool);
     if (!d) return;
     const y = new Set((() => {
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       const p2 = (m2 = (A2 = r == null ? void 0 : r.gridState.columnVisibility) == null ? void 0 : A2.hiddenColIds) == null ? void 0 : m2.map(ne).filter((v) => v.type === "column").map((v) => v.id);
-      return p2 || l2.filter((v) => qt(v.spec)).map((v) => v.id);
+      return p2 || l2.filter((v) => Ht(v.spec)).map((v) => v.id);
     })());
     y.delete(u2.id), [...o.map((p2) => p2.column), ...a.map((p2) => p2.column)].filter((p2) => p2.type === "column").map((p2) => y.delete(p2.id));
     const b = l2.filter((p2) => !y.has(p2.id)), f2 = Be(b.map(On), d), w2 = [
@@ -6228,7 +6147,8 @@
           normalizationDirection: null
         }
       }
-    }
+    },
+    alignmentModel: {}
   }).argsValid((ctx) => ctx.args.datasetRef !== void 0 && ctx.args.sequencesRef.length > 0).output(
     "datasetOptions",
     (ctx) => ctx.resultPool.getOptions(
@@ -6279,7 +6199,12 @@
     return ctx.resultPool.getCanonicalOptions(
       { main: ref },
       sequenceMatchers,
-      { ignoreMissingDomains: true }
+      {
+        ignoreMissingDomains: true,
+        labelOps: {
+          includeNativeLabel: true
+        }
+      }
     );
   }).output("isSingleCell", (ctx) => {
     if (ctx.args.datasetRef === void 0) return void 0;
@@ -6300,18 +6225,51 @@
       (_) => true,
       (_c = ctx.uiState) == null ? void 0 : _c.tableState
     );
+  }).output("msaPf", (ctx) => {
+    var _a, _b;
+    const msaCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve("msaPf")) == null ? void 0 : _b.getPColumns();
+    if (!msaCols) return void 0;
+    const datasetRef = ctx.args.datasetRef;
+    if (datasetRef === void 0)
+      return void 0;
+    const sequencesRef = ctx.args.sequencesRef;
+    if (sequencesRef.length === 0)
+      return void 0;
+    const seqCols = ctx.resultPool.getAnchoredPColumns(
+      { main: datasetRef },
+      sequencesRef.map((s2) => JSON.parse(s2))
+    );
+    if (seqCols === void 0)
+      return void 0;
+    return Rn(ctx, [...msaCols, ...seqCols]);
+  }).output("linkerColumnId", (ctx) => {
+    var _a, _b, _c;
+    const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve("msaPf")) == null ? void 0 : _b.getPColumns();
+    if (!pCols) return void 0;
+    return (_c = pCols.find((p2) => {
+      var _a2;
+      return ((_a2 = p2.spec.annotations) == null ? void 0 : _a2["pl7.app/isLinkerColumn"]) === "true";
+    })) == null ? void 0 : _c.id;
   }).output("clusterAbundanceSpec", (ctx) => {
     var _a, _b;
     const spec = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve("clusterAbundanceSpec")) == null ? void 0 : _b.getDataAsJson();
     if (spec === void 0) return void 0;
     return spec;
+  }).output("inputSpec", (ctx) => {
+    const anchor = ctx.args.datasetRef;
+    if (anchor === void 0)
+      return void 0;
+    const anchorSpec = ctx.resultPool.getPColumnSpecByRef(anchor);
+    if (anchorSpec === void 0)
+      return void 0;
+    return anchorSpec;
   }).output("clustersPf", (ctx) => {
     var _a, _b;
     const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve("pf")) == null ? void 0 : _b.getPColumns();
     if (pCols === void 0) {
       return void 0;
     }
-    return Dn(ctx, pCols);
+    return Rn(ctx, pCols);
   }).output("isRunning", (ctx) => {
     var _a;
     return ((_a = ctx.outputs) == null ? void 0 : _a.getIsReadyOrError()) === false;