@platforma-open/milaboratories.clonotype-clustering.model 2.0.1 → 2.2.0

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@2.0.1 build /home/runner/work/clonotype-clustering/clonotype-clustering/model
+> @platforma-open/milaboratories.clonotype-clustering.model@2.2.0 build /home/runner/work/clonotype-clustering/clonotype-clustering/model
 > tsup && vite build && block-tools build-model
 
 CLI Building entry: src/index.ts
@@ -11,14 +11,14 @@
 CLI Cleaning output folder
 CJS Build start
 ESM Build start
-CJS dist/index.cjs     2.67 KB
-CJS dist/index.cjs.map 6.50 KB
-CJS ⚡️ Build success in 121ms
-ESM dist/index.js     2.67 KB
-ESM dist/index.js.map 6.42 KB
-ESM ⚡️ Build success in 121ms
+CJS dist/index.cjs     3.27 KB
+CJS dist/index.cjs.map 7.58 KB
+CJS ⚡️ Build success in 97ms
+ESM dist/index.js     3.27 KB
+ESM dist/index.js.map 7.51 KB
+ESM ⚡️ Build success in 97ms
 DTS Build start
-DTS ⚡️ Build success in 2189ms
+DTS ⚡️ Build success in 2159ms
 DTS dist/index.d.cts 3.98 KB
 DTS dist/index.d.ts  3.98 KB
 vite v6.2.3 building for production...
@@ -26,6 +26,6 @@ transforming...
 ✓ 11 modules transformed.
 rendering chunks...
 computing gzip size...
-dist/bundle.js  187.82 kB │ gzip: 36.72 kB │ map: 397.50 kB
-dist/bundle.js  200.68 kB │ gzip: 37.35 kB │ map: 399.09 kB
-✓ built in 758ms
+dist/bundle.js  188.26 kB │ gzip: 36.79 kB │ map: 398.50 kB
+dist/bundle.js  201.18 kB │ gzip: 37.42 kB │ map: 400.10 kB
+✓ built in 725ms

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.clonotype-clustering.model
 
+## 2.2.0
+
+### Minor Changes
+
+- 9a8e64d: Fix for bulk data
+
+## 2.1.0
+
+### Minor Changes
+
+- fb91da8: Calculate abundance automatically; Add ability to specify sequence/
+
 ## 2.0.1
 
 ### Patch Changes

package/dist/bundle.js

@@ -6154,31 +6154,66 @@
         }
       }
     }
-  }).argsValid((ctx) => ctx.args.aaSeqCDR3Ref !== void 0 && ctx.args.abundanceRef !== void 0).output(
-    "cdr3Options",
+  }).argsValid((ctx) => ctx.args.datasetRef !== void 0 && ctx.args.sequenceRef !== void 0).output(
+    "datasetOptions",
     (ctx) => ctx.resultPool.getOptions(
-      (c2) => {
-        var _a, _b, _c, _d, _e, _f;
-        return f(c2) && c2.valueType === "String" && c2.name === "pl7.app/vdj/sequence" && ((_a = c2.domain) == null ? void 0 : _a["pl7.app/vdj/feature"]) === "CDR3" && ((_b = c2.domain) == null ? void 0 : _b["pl7.app/alphabet"]) === "aminoacid" && (!((_c = c2.domain) == null ? void 0 : _c["pl7.app/vdj/scClonotypeChain"]) || ((_d = c2.domain) == null ? void 0 : _d["pl7.app/vdj/scClonotypeChain"]) === "A") && (!((_e = c2.domain) == null ? void 0 : _e["pl7.app/vdj/scClonotypeChain/index"]) || ((_f = c2.domain) == null ? void 0 : _f["pl7.app/vdj/scClonotypeChain/index"]) === "primary");
+      [{
+        axes: [
+          { name: "pl7.app/sampleId" },
+          { name: "pl7.app/vdj/clonotypeKey" }
+        ],
+        annotations: { "pl7.app/isAnchor": "true" }
+      }, {
+        axes: [
+          { name: "pl7.app/sampleId" },
+          { name: "pl7.app/vdj/scClonotypeKey" }
+        ],
+        annotations: { "pl7.app/isAnchor": "true" }
+      }],
+      {
+        // suppress native label of the column (e.g. "Number of Reads") to show only the dataset label
+        label: { includeNativeLabel: false }
       }
     )
-  ).output("abundanceOptions", (ctx) => {
-    const aaSeqCDR3Ref = ctx.args.aaSeqCDR3Ref;
-    if (aaSeqCDR3Ref === void 0) return void 0;
-    return ctx.resultPool.getCanonicalOptions({ main: aaSeqCDR3Ref }, {
-      axes: [{ name: "pl7.app/sampleId" }, { anchor: "main", idx: 0 }],
-      annotations: {
-        "pl7.app/isAbundance": "true",
-        "pl7.app/abundance/normalized": "true"
-      }
-    }, { ignoreMissingDomains: true });
+  ).output("sequenceOptions", (ctx) => {
+    var _a;
+    const ref = ctx.args.datasetRef;
+    if (ref === void 0) return void 0;
+    const isSingleCell = ((_a = ctx.resultPool.getPColumnSpecByRef(ref)) == null ? void 0 : _a.axesSpec[1].name) === "pl7.app/vdj/scClonotypeKey";
+    const sequenceMatchers = [];
+    for (const feature of ["CDR3", "VDJRegion"]) {
+      if (isSingleCell) {
+        sequenceMatchers.push({
+          axes: [{ anchor: "main", idx: 1 }],
+          name: "pl7.app/vdj/sequence",
+          domain: {
+            "pl7.app/vdj/feature": feature,
+            "pl7.app/vdj/scClonotypeChain": "A",
+            "pl7.app/vdj/scClonotypeChain/index": "primary"
+          }
+        });
+      } else {
+        sequenceMatchers.push({
+          axes: [{ anchor: "main", idx: 1 }],
+          name: "pl7.app/vdj/sequence",
+          domain: {
+            "pl7.app/vdj/feature": feature
+          }
+        });
+      }
+    }
+    return ctx.resultPool.getCanonicalOptions(
+      { main: ref },
+      sequenceMatchers,
+      { ignoreMissingDomains: true }
+    );
   }).output("isSingleCell", (ctx) => {
-    if (ctx.args.aaSeqCDR3Ref === void 0) return void 0;
-    const spec = ctx.resultPool.getPColumnSpecByRef(ctx.args.aaSeqCDR3Ref);
+    if (ctx.args.datasetRef === void 0) return void 0;
+    const spec = ctx.resultPool.getPColumnSpecByRef(ctx.args.datasetRef);
     if (spec === void 0) {
       return void 0;
     }
-    return spec.axesSpec[0].name === "pl7.app/vdj/scClonotypeKey";
+    return spec.axesSpec[1].name === "pl7.app/vdj/scClonotypeKey";
   }).output("clustersTable", (ctx) => {
     var _a, _b, _c;
     const pCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve("clustersPf")) == null ? void 0 : _b.getPColumns();