@platforma-open/milaboratories.redefine-clonotypes.model 1.0.1 → 1.0.3

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/redefine-clonotypes/redefine-clonotypes/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.redefine-clonotypes.model@1.0.1 build /home/runner/work/redefine-clonotypes/redefine-clonotypes/model
+> @platforma-open/milaboratories.redefine-clonotypes.model@1.0.3 build /home/runner/work/redefine-clonotypes/redefine-clonotypes/model
 > vite build && BUILD_UMD=true vite build && block-tools build-model
 
 vite v6.3.5 building SSR bundle for production...
@@ -9,23 +9,23 @@ transforming...
 rendering chunks...
 
 [vite:dts] Start generate declaration files...
-dist/index.js  2.47 kB │ map: 4.80 kB
+dist/index.js  2.19 kB │ map: 4.23 kB
 [vite:dts] Start rollup declaration files...
 Analysis will use the bundled TypeScript version 5.8.2
-[vite:dts] Declaration files built in 3283ms.
+[vite:dts] Declaration files built in 3591ms.
 
-dist/index.cjs  2.57 kB │ map: 4.82 kB
-✓ built in 3.38s
+dist/index.cjs  2.28 kB │ map: 4.25 kB
+✓ built in 3.66s
 vite v6.3.5 building for production...
 transforming...
-✓ 69 modules transformed.
+✓ 77 modules transformed.
 rendering chunks...
 
 [vite:dts] Start generate declaration files...
 computing gzip size...
 [vite:dts] Start rollup declaration files...
 Analysis will use the bundled TypeScript version 5.8.2
-dist/bundle.js  219.75 kB │ gzip: 39.07 kB │ map: 445.21 kB
-[vite:dts] Declaration files built in 3226ms.
+dist/bundle.js  225.02 kB │ gzip: 39.75 kB │ map: 454.84 kB
+[vite:dts] Declaration files built in 3345ms.
 
-✓ built in 3.88s
+✓ built in 4.00s

package/CHANGELOG.md

@@ -1,5 +1,20 @@
 # @platforma-open/milaboratories.redefine-clonotypes.model
 
+## 1.0.3
+
+### Patch Changes
+
+- 7359f01: Fix definition options
+
+## 1.0.2
+
+### Patch Changes
+
+- 53dc929: technical release
+- edeae1d: technical release
+- 9fc42b8: technical release
+- 5a7b685: technical release
+
 ## 1.0.1
 
 ### Patch Changes

package/dist/bundle.js

@@ -3964,11 +3964,15 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     quotelessJson,
     ZodError
   });
+  z.object({
+    type: z.literal("plain"),
+    content: z.string()
+  });
   z.object({
     /** Included left border. */
-    from: z.number(),
+    from: z.number().min(0),
     /** Excluded right border. */
-    to: z.number()
+    to: z.number().min(1)
   });
   function assertNever(x) {
     throw new Error("Unexpected object: " + x);
@@ -4034,6 +4038,27 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       }
     }
   }
+  function visitDataInfo(dataInfo, cb) {
+    switch (dataInfo.type) {
+      case "Json":
+        break;
+      case "JsonPartitioned": {
+        Object.values(dataInfo.parts).forEach(cb);
+        break;
+      }
+      case "BinaryPartitioned": {
+        Object.values(dataInfo.parts).forEach((chunk) => {
+          cb(chunk.index);
+          cb(chunk.values);
+        });
+        break;
+      }
+      case "ParquetPartitioned": {
+        Object.values(dataInfo.parts).forEach(cb);
+        break;
+      }
+    }
+  }
   function isDataInfoEntries(value) {
     if (!value || typeof value !== "object") {
       return false;
@@ -4191,13 +4216,27 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   const Annotation = {
     DiscreteValues: "pl7.app/discreteValues",
     Graph: {
-      IsVirtual: "pl7.app/graph/isVirtual"
+      Axis: {
+        HighCardinality: "pl7.app/graph/axis/highCardinality",
+        LowerLimit: "pl7.app/graph/axis/lowerLimit",
+        SymmetricRange: "pl7.app/graph/axis/symmetricRange",
+        UpperLimit: "pl7.app/graph/axis/upperLimit"
+      },
+      IsDenseAxis: "pl7.app/graph/isDenseAxis",
+      IsVirtual: "pl7.app/graph/isVirtual",
+      Palette: "pl7.app/graph/palette",
+      Thresholds: "pl7.app/graph/thresholds",
+      TreatAbsentValuesAs: "pl7.app/graph/treatAbsentValuesAs"
     },
     HideDataFromUi: "pl7.app/hideDataFromUi",
+    HideDataFromGraphs: "pl7.app/hideDataFromGraphs",
+    IsDiscreteFilter: "pl7.app/isDiscreteFilter",
     IsLinkerColumn: "pl7.app/isLinkerColumn",
+    IsSubset: "pl7.app/isSubset",
     Label: "pl7.app/label",
     Max: "pl7.app/max",
     Min: "pl7.app/min",
+    MultipliesBy: "pl7.app/multipliesBy",
     Parents: "pl7.app/parents",
     Sequence: {
       Annotation: {
@@ -4210,13 +4249,29 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     },
     Trace: "pl7.app/trace"
   };
+  const ValueTypeSchema = z.enum(["Int", "Long", "Float", "Double", "String"]);
   ({
     [Annotation.DiscreteValues]: z.array(z.string()).or(z.array(z.number())),
+    [Annotation.Graph.Axis.HighCardinality]: z.boolean(),
+    [Annotation.Graph.Axis.LowerLimit]: z.number(),
+    [Annotation.Graph.Axis.UpperLimit]: z.number(),
+    [Annotation.Graph.Axis.SymmetricRange]: z.boolean(),
+    [Annotation.Graph.IsDenseAxis]: z.boolean(),
+    [Annotation.Graph.Palette]: z.object({ mapping: z.record(z.number()), name: z.string() }),
+    [Annotation.Graph.Thresholds]: z.array(z.object({
+      columnId: z.object({ valueType: ValueTypeSchema, name: z.string() }),
+      value: z.number()
+    })),
+    [Annotation.Graph.TreatAbsentValuesAs]: z.number(),
     [Annotation.Graph.IsVirtual]: z.boolean(),
     [Annotation.HideDataFromUi]: z.boolean(),
+    [Annotation.HideDataFromGraphs]: z.boolean(),
+    [Annotation.IsDiscreteFilter]: z.boolean(),
     [Annotation.IsLinkerColumn]: z.boolean(),
+    [Annotation.IsSubset]: z.boolean(),
     [Annotation.Max]: z.number(),
     [Annotation.Min]: z.number(),
+    [Annotation.MultipliesBy]: z.array(z.string()),
     [Annotation.Parents]: z.array(z.string()),
     [Annotation.Sequence.Annotation.Mapping]: z.record(z.string(), z.string()),
     [Annotation.Sequence.IsAnnotation]: z.boolean(),
@@ -4274,6 +4329,13 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
           newId: entry.newId,
           axisFilters: entry.axisFilters
         };
+      case "artificialColumn":
+        return {
+          type: "artificialColumn",
+          column: cb(entry.column),
+          newId: entry.newId,
+          axesIndices: entry.axesIndices
+        };
       case "inlineColumn":
         return entry;
       case "inner":
@@ -4510,6 +4572,9 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
         case "slicedColumn":
           columns.set(entry2.column.id, entry2.column);
           return;
+        case "artificialColumn":
+          columns.set(entry2.column.id, entry2.column);
+          return;
         case "inlineColumn":
           return;
         case "full":
@@ -4883,6 +4948,80 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   }
   const StagingAccessorName = "staging";
   const MainAccessorName = "main";
+  function filterDataInfoEntries(dataInfoEntries, axisFilters) {
+    const sortedFilters = [...axisFilters].sort((a, b) => b[0] - a[0]);
+    const { type } = dataInfoEntries;
+    switch (type) {
+      case "Json": {
+        const { keyLength } = dataInfoEntries;
+        for (const [axisIdx] of axisFilters)
+          if (axisIdx >= keyLength)
+            throw new Error(`Can't filter on non-data axis ${axisIdx}. Must be >= ${keyLength}`);
+        break;
+      }
+      case "JsonPartitioned":
+      case "BinaryPartitioned":
+      case "ParquetPartitioned": {
+        const { partitionKeyLength } = dataInfoEntries;
+        for (const [axisIdx] of axisFilters)
+          if (axisIdx >= partitionKeyLength)
+            throw new Error(`Can't filter on non-partitioned axis ${axisIdx}. Must be >= ${partitionKeyLength}`);
+        break;
+      }
+      default:
+        throw new Error(`Unsupported data info type: ${type}`);
+    }
+    const keyMatchesFilters = (key) => {
+      for (const [axisIdx, axisValue] of sortedFilters)
+        if (key[axisIdx] !== axisValue)
+          return false;
+      return true;
+    };
+    const removeFilteredAxes = (key) => {
+      const newKey = [...key];
+      for (const [axisIdx] of sortedFilters)
+        newKey.splice(axisIdx, 1);
+      return newKey;
+    };
+    switch (dataInfoEntries.type) {
+      case "Json":
+        return {
+          type: "Json",
+          keyLength: dataInfoEntries.keyLength - axisFilters.length,
+          data: dataInfoEntries.data.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
+            key: removeFilteredAxes(entry.key),
+            value: entry.value
+          }))
+        };
+      case "JsonPartitioned":
+        return {
+          type: "JsonPartitioned",
+          partitionKeyLength: dataInfoEntries.partitionKeyLength - axisFilters.length,
+          parts: dataInfoEntries.parts.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
+            key: removeFilteredAxes(entry.key),
+            value: entry.value
+          }))
+        };
+      case "BinaryPartitioned":
+        return {
+          type: "BinaryPartitioned",
+          partitionKeyLength: dataInfoEntries.partitionKeyLength - axisFilters.length,
+          parts: dataInfoEntries.parts.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
+            key: removeFilteredAxes(entry.key),
+            value: entry.value
+          }))
+        };
+      case "ParquetPartitioned":
+        return {
+          type: "ParquetPartitioned",
+          partitionKeyLength: dataInfoEntries.partitionKeyLength - axisFilters.length,
+          parts: dataInfoEntries.parts.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
+            key: removeFilteredAxes(entry.key),
+            value: entry.value
+          }))
+        };
+    }
+  }
   const TraceEntry = z.object({
     type: z.string(),
     importance: z.number().optional(),
@@ -5008,9 +5147,11 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   const RT_RESOURCE_MAP_PARTITIONED = PCD_PREFIX + "Partitioned/ResourceMap";
   const RT_JSON_PARTITIONED = PCD_PREFIX + "JsonPartitioned";
   const RT_BINARY_PARTITIONED = PCD_PREFIX + "BinaryPartitioned";
+  const RT_PARQUET_PARTITIONED = PCD_PREFIX + "ParquetPartitioned";
   const PCD_SUP_PREFIX = PCD_PREFIX + "Partitioned/";
   const RT_JSON_SUPER_PARTITIONED = PCD_SUP_PREFIX + "JsonPartitioned";
   const RT_BINARY_SUPER_PARTITIONED = PCD_SUP_PREFIX + "BinaryPartitioned";
+  const RT_PARQUET_SUPER_PARTITIONED = PCD_SUP_PREFIX + "ParquetPartitioned";
   const removeIndexSuffix = (keyStr) => {
     if (keyStr.endsWith(".index")) {
       return { baseKey: keyStr.substring(0, keyStr.length - 6), type: "index" };
@@ -5036,10 +5177,12 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
         break;
       case RT_JSON_PARTITIONED:
       case RT_BINARY_PARTITIONED:
+      case RT_PARQUET_PARTITIONED:
         keyLength = meta["partitionKeyLength"];
         break;
       case RT_BINARY_SUPER_PARTITIONED:
       case RT_JSON_SUPER_PARTITIONED:
+      case RT_PARQUET_SUPER_PARTITIONED:
         keyLength = meta["superPartitionKeyLength"] + meta["partitionKeyLength"];
         break;
     }
@@ -5047,6 +5190,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       case RT_RESOURCE_MAP:
       case RT_JSON_PARTITIONED:
       case RT_BINARY_PARTITIONED:
+      case RT_PARQUET_PARTITIONED:
         for (let keyStr of acc.listInputFields()) {
           if (rt === RT_BINARY_PARTITIONED) {
             keyStr = removeIndexSuffix(keyStr).baseKey;
@@ -5058,6 +5202,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       case RT_RESOURCE_MAP_PARTITIONED:
       case RT_BINARY_SUPER_PARTITIONED:
       case RT_JSON_SUPER_PARTITIONED:
+      case RT_PARQUET_SUPER_PARTITIONED:
         for (const supKeyStr of acc.listInputFields()) {
           const keyPrefix = [...JSON.parse(supKeyStr)];
           const value = acc.resolve({ field: supKeyStr, assertFieldType: "Input" });
@@ -5076,7 +5221,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     return { data, keyLength };
   }
   function getUniquePartitionKeysForDataEntries(list) {
-    if (list.type !== "JsonPartitioned" && list.type !== "BinaryPartitioned")
+    if (list.type !== "JsonPartitioned" && list.type !== "BinaryPartitioned" && list.type !== "ParquetPartitioned")
       throw new Error(`Splitting requires Partitioned DataInfoEntries, got ${list.type}`);
     const { parts, partitionKeyLength } = list;
     const result = [];
@@ -5124,7 +5269,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       return void 0;
     const resourceType = acc.resourceType.name;
     const meta = acc.getDataAsJson();
-    if (keyPrefix.length > 0 && (resourceType === RT_JSON_SUPER_PARTITIONED || resourceType === RT_BINARY_SUPER_PARTITIONED)) {
+    if (keyPrefix.length > 0 && (resourceType === RT_JSON_SUPER_PARTITIONED || resourceType === RT_BINARY_SUPER_PARTITIONED || resourceType === RT_PARQUET_SUPER_PARTITIONED)) {
       throw new Error(`Unexpected nested super-partitioned resource: ${resourceType}`);
     }
     switch (resourceType) {
@@ -5189,6 +5334,24 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
           parts
         };
       }
+      case RT_PARQUET_PARTITIONED: {
+        if (typeof (meta == null ? void 0 : meta.partitionKeyLength) !== "number") {
+          throw new Error(`Missing partitionKeyLength in metadata for ${resourceType}`);
+        }
+        const parts = [];
+        for (const keyStr of acc.listInputFields()) {
+          const value = acc.resolve({ field: keyStr, assertFieldType: "Input" });
+          if (value === void 0)
+            return void 0;
+          const key = [...keyPrefix, ...JSON.parse(keyStr)];
+          parts.push({ key, value });
+        }
+        return {
+          type: "ParquetPartitioned",
+          partitionKeyLength: meta.partitionKeyLength,
+          parts
+        };
+      }
       case RT_JSON_SUPER_PARTITIONED: {
         if (typeof (meta == null ? void 0 : meta.superPartitionKeyLength) !== "number" || typeof (meta == null ? void 0 : meta.partitionKeyLength) !== "number") {
           throw new Error(`Missing superPartitionKeyLength or partitionKeyLength in metadata for ${resourceType}`);
@@ -5241,6 +5404,32 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
           parts
         };
       }
+      case RT_PARQUET_SUPER_PARTITIONED: {
+        if (typeof (meta == null ? void 0 : meta.superPartitionKeyLength) !== "number" || typeof (meta == null ? void 0 : meta.partitionKeyLength) !== "number") {
+          throw new Error(`Missing superPartitionKeyLength or partitionKeyLength in metadata for ${resourceType}`);
+        }
+        const totalKeyLength = meta.superPartitionKeyLength + meta.partitionKeyLength;
+        const parts = [];
+        for (const supKeyStr of acc.listInputFields()) {
+          const superPartition = acc.resolve({ field: supKeyStr, assertFieldType: "Input" });
+          if (superPartition === void 0)
+            return void 0;
+          if (superPartition.resourceType.name !== RT_PARQUET_PARTITIONED) {
+            throw new Error(`Expected ${RT_PARQUET_PARTITIONED} inside ${resourceType}, but got ${superPartition.resourceType.name}`);
+          }
+          const innerResult = parsePColumnData(superPartition, JSON.parse(supKeyStr));
+          if (innerResult === void 0)
+            return void 0;
+          if (innerResult.type !== "ParquetPartitioned")
+            throw new Error(`Unexpected inner result type for ${resourceType}: ${innerResult.type}`);
+          parts.push(...innerResult.parts);
+        }
+        return {
+          type: "ParquetPartitioned",
+          partitionKeyLength: totalKeyLength,
+          parts
+        };
+      }
       default:
         throw new Error(`Unknown resource type: ${resourceType}`);
     }
@@ -5256,79 +5445,21 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       return parsePColumnData(acc);
     throw new Error(`Unexpected input type: ${typeof acc}`);
   }
-  function filterDataInfoEntries(dataInfoEntries, axisFilters) {
-    const sortedFilters = [...axisFilters].sort((a, b) => b[0] - a[0]);
-    const { type } = dataInfoEntries;
-    switch (type) {
-      case "Json": {
-        const { keyLength } = dataInfoEntries;
-        for (const [axisIdx] of axisFilters)
-          if (axisIdx >= keyLength)
-            throw new Error(`Can't filter on non-data axis ${axisIdx}. Must be >= ${keyLength}`);
-        break;
-      }
-      case "JsonPartitioned":
-      case "BinaryPartitioned":
-      case "ParquetPartitioned": {
-        const { partitionKeyLength } = dataInfoEntries;
-        for (const [axisIdx] of axisFilters)
-          if (axisIdx >= partitionKeyLength)
-            throw new Error(`Can't filter on non-partitioned axis ${axisIdx}. Must be >= ${partitionKeyLength}`);
-        break;
-      }
-      default:
-        throw new Error(`Unsupported data info type: ${type}`);
-    }
-    const keyMatchesFilters = (key) => {
-      for (const [axisIdx, axisValue] of sortedFilters)
-        if (key[axisIdx] !== axisValue)
-          return false;
-      return true;
-    };
-    const removeFilteredAxes = (key) => {
-      const newKey = [...key];
-      for (const [axisIdx] of sortedFilters)
-        newKey.splice(axisIdx, 1);
-      return newKey;
-    };
-    switch (dataInfoEntries.type) {
-      case "Json":
-        return {
-          type: "Json",
-          keyLength: dataInfoEntries.keyLength - axisFilters.length,
-          data: dataInfoEntries.data.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
-            key: removeFilteredAxes(entry.key),
-            value: entry.value
-          }))
-        };
-      case "JsonPartitioned":
-        return {
-          type: "JsonPartitioned",
-          partitionKeyLength: dataInfoEntries.partitionKeyLength - axisFilters.length,
-          parts: dataInfoEntries.parts.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
-            key: removeFilteredAxes(entry.key),
-            value: entry.value
-          }))
-        };
-      case "BinaryPartitioned":
-        return {
-          type: "BinaryPartitioned",
-          partitionKeyLength: dataInfoEntries.partitionKeyLength - axisFilters.length,
-          parts: dataInfoEntries.parts.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
-            key: removeFilteredAxes(entry.key),
-            value: entry.value
-          }))
-        };
-      case "ParquetPartitioned":
-        return {
-          type: "ParquetPartitioned",
-          partitionKeyLength: dataInfoEntries.partitionKeyLength - axisFilters.length,
-          parts: dataInfoEntries.parts.filter((entry) => keyMatchesFilters(entry.key)).map((entry) => ({
-            key: removeFilteredAxes(entry.key),
-            value: entry.value
-          }))
-        };
-    }
+  function isPColumnReady(c) {
+    const isValues = (d) => Array.isArray(d);
+    const isAccessor = (d) => d instanceof TreeNodeAccessor;
+    let ready = true;
+    if (isAccessor(c.data)) {
+      ready && (ready = c.data.getIsReadyOrError());
+    } else if (isDataInfo(c.data)) {
+      visitDataInfo(c.data, (v) => ready && (ready = v.getIsReadyOrError()));
+    } else if (!isValues(c.data)) {
+      throw Error(`unsupported column data type: ${c.data}`);
+    }
+    return ready;
+  }
+  function allPColumnsReady(columns) {
+    return columns.every(isPColumnReady);
   }
   function isPColumnValues(value) {
     if (!Array.isArray(value))
@@ -6080,6 +6211,8 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     // TODO remove all non-PColumn fields
     createPFrame(def) {
       this.verifyInlineAndExplicitColumnsSupport(def);
+      if (!allPColumnsReady(def))
+        return void 0;
       return this.ctx.createPFrame(def.map((c) => transformPColumnData(c)));
     }
     createPTable(def) {
@@ -6097,7 +6230,10 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       } else {
         rawDef = this.patchPTableDef(def);
       }
-      this.verifyInlineAndExplicitColumnsSupport(extractAllColumns(rawDef.src));
+      const columns = extractAllColumns(rawDef.src);
+      this.verifyInlineAndExplicitColumnsSupport(columns);
+      if (!allPColumnsReady(columns))
+        return void 0;
       return this.ctx.createPTable(mapPTableDef(rawDef, (po) => transformPColumnData(po)));
     }
     /** @deprecated scheduled for removal from SDK */
@@ -6117,7 +6253,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       this.ctx.logError(msg);
     }
   }
-  var version = "1.42.36";
+  var version = "1.45.30";
   const PlatformaSDKVersion = version;
   function isConfigLambda(cfgOrFh) {
     return cfgOrFh.__renderLambda === true;
@@ -6376,19 +6512,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
         },
         {
           axes: [{ anchor: "main", idx: 1 }],
-          name: "pl7.app/vdj/vGene"
-        },
-        {
-          axes: [{ anchor: "main", idx: 1 }],
-          name: "pl7.app/vdj/dGene"
-        },
-        {
-          axes: [{ anchor: "main", idx: 1 }],
-          name: "pl7.app/vdj/jGene"
-        },
-        {
-          axes: [{ anchor: "main", idx: 1 }],
-          name: "pl7.app/vdj/cGene"
+          name: "pl7.app/vdj/geneHit"
         }
       ]
     );