@platforma-open/milaboratories.immune-assay-data.model 1.0.1

package/dist/index.cjs

@@ -0,0 +1,100 @@
+'use strict';
+
+var model$1 = require('@platforma-sdk/model');
+
+// src/index.ts
+var model = model$1.BlockModel.create().withArgs({
+  settings: {
+    coverageMode: 2,
+    // default to coverage of clone,
+    coverageThreshold: 0.95
+    // default value matching MMseqs2 default
+  }
+}).withUiState({
+  title: "Immune Assay Data",
+  tableState: {
+    gridState: {}
+  }
+}).argsValid(
+  (ctx) => ctx.args.datasetRef !== void 0 && ctx.args.fileHandle !== void 0 && ctx.args.importColumns !== void 0 && ctx.args.sequenceColumnHeader !== void 0 && ctx.args.targetRef !== void 0 && ctx.uiState.fileImportError === void 0
+).output(
+  "datasetOptions",
+  (ctx) => ctx.resultPool.getOptions([{
+    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" }
+  }], { refsWithEnrichments: true })
+).output("targetOptions", (ctx) => {
+  const ref = ctx.args.datasetRef;
+  if (ref === void 0) return void 0;
+  const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === "pl7.app/vdj/scClonotypeKey";
+  const sequenceMatchers = [];
+  const allowedFeatures = [
+    "CDR1",
+    "CDR2",
+    "CDR3",
+    "FR1",
+    "FR2",
+    "FR3",
+    "FR4",
+    "VDJRegion"
+  ];
+  for (const feature of allowedFeatures) {
+    if (isSingleCell) {
+      sequenceMatchers.push({
+        axes: [{ anchor: "main", idx: 1 }],
+        name: "pl7.app/vdj/sequence",
+        domain: {
+          "pl7.app/vdj/feature": feature,
+          "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,
+      labelOps: {
+        includeNativeLabel: true
+      }
+    }
+  );
+}).output(
+  "dataImportHandle",
+  (ctx) => ctx.outputs?.resolve("dataImportHandle")?.getImportProgress(),
+  { isActive: true }
+).output("table", (ctx) => {
+  const cols = ctx.outputs?.resolve("table")?.getPColumns();
+  if (cols === void 0)
+    return void 0;
+  return model$1.createPlDataTableV2(
+    ctx,
+    cols,
+    (_) => true,
+    ctx.uiState.tableState
+  );
+}).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title((ctx) => ctx.uiState.title).sections((_ctx) => [
+  { type: "link", href: "/", label: "Main" }
+]).done();
+
+exports.model = model;
+//# sourceMappingURL=index.cjs.map
+//# sourceMappingURL=index.cjs.map

package/dist/index.cjs.map

@@ -0,0 +1 @@
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// fraction of aligned residues required\n  coverageMode: 0 | 1 | 2 | 3 | 4 | 5; // MMseqs2 coverage modes\n};\n\nexport type ImportColumnInfo = {\n  header: string;\n  type: 'Int' | 'Double' | 'String';\n  /** If this column is a sequence column, the type of the sequence */\n  sequenceType?: 'nucleotide' | 'aminoacid';\n};\n\nexport type BlockArgs = {\n  datasetRef?: PlRef;\n  targetRef?: SUniversalPColumnId;\n  fileHandle?: ImportFileHandle;\n  fileExtension?: string;\n  importColumns?: ImportColumnInfo[];\n  sequenceColumnHeader?: string;\n  settings: Settings;\n};\n\nexport type UiState = {\n  title: string;\n  fileImportError?: string;\n  tableState: PlDataTableState;\n};\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    settings: {\n      coverageMode: 2, // default to coverage of clone,\n      coverageThreshold: 0.95, // default value matching MMseqs2 default\n    },\n  })\n\n  .withUiState<UiState>({\n    title: 'Immune Assay Data',\n    tableState: {\n      gridState: {},\n    },\n  })\n\n  .argsValid((ctx) =>\n    ctx.args.datasetRef !== undefined\n    && ctx.args.fileHandle !== undefined\n    && ctx.args.importColumns !== undefined\n    && ctx.args.sequenceColumnHeader !== undefined\n    && ctx.args.targetRef !== undefined\n    && ctx.uiState.fileImportError === undefined,\n  )\n\n  .output('datasetOptions', (ctx) =>\n    ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/clonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }, {\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/scClonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }], { refsWithEnrichments: true }),\n  )\n\n  .output('targetOptions', (ctx) => {\n    const ref = ctx.args.datasetRef;\n    if (ref === undefined) return undefined;\n\n    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';\n    const sequenceMatchers = [];\n    const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',\n      'FR3', 'FR4', 'VDJRegion'];\n    for (const feature of allowedFeatures) {\n      if (isSingleCell) {\n        sequenceMatchers.push({\n          axes: [{ anchor: 'main', idx: 1 }],\n          name: 'pl7.app/vdj/sequence',\n          domain: {\n            'pl7.app/vdj/feature': feature,\n            'pl7.app/vdj/scClonotypeChain/index': 'primary',\n          },\n        });\n      } else {\n        sequenceMatchers.push({\n          axes: [{ anchor: 'main', idx: 1 }],\n          name: 'pl7.app/vdj/sequence',\n          domain: {\n            'pl7.app/vdj/feature': feature,\n          },\n        });\n      }\n    }\n\n    return ctx.resultPool.getCanonicalOptions(\n      { main: ref },\n      sequenceMatchers,\n      {\n        ignoreMissingDomains: true,\n        labelOps: {\n          includeNativeLabel: true,\n        },\n      });\n  })\n\n  .output(\n    'dataImportHandle',\n    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),\n    { isActive: true },\n  )\n\n  .output('table', (ctx) => {\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPlDataTableV2(\n      ctx,\n      cols,\n      (_) => true,\n      ctx.uiState.tableState,\n    );\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title((ctx) => ctx.uiState.title)\n\n  .sections((_ctx) => ([\n    { type: 'link', href: '/', label: 'Main' },\n  ]))\n\n  .done();\n\nexport type BlockOutputs = InferOutputsType<typeof model>;\n"]}

package/dist/index.d.cts

@@ -0,0 +1,97 @@
+import * as _platforma_sdk_model from '@platforma-sdk/model';
+import { PlRef, SUniversalPColumnId, ImportFileHandle, PlDataTableState, InferOutputsType } from '@platforma-sdk/model';
+
+type Settings = {
+    coverageThreshold: number;
+    coverageMode: 0 | 1 | 2 | 3 | 4 | 5;
+};
+type ImportColumnInfo = {
+    header: string;
+    type: 'Int' | 'Double' | 'String';
+    /** If this column is a sequence column, the type of the sequence */
+    sequenceType?: 'nucleotide' | 'aminoacid';
+};
+type BlockArgs = {
+    datasetRef?: PlRef;
+    targetRef?: SUniversalPColumnId;
+    fileHandle?: ImportFileHandle;
+    fileExtension?: string;
+    importColumns?: ImportColumnInfo[];
+    sequenceColumnHeader?: string;
+    settings: Settings;
+};
+type UiState = {
+    title: string;
+    fileImportError?: string;
+    tableState: PlDataTableState;
+};
+declare const model: _platforma_sdk_model.Platforma<BlockArgs, {
+    datasetOptions: _platforma_sdk_model.ValueOrErrors<{
+        readonly ref: {
+            readonly __isRef: true;
+            readonly blockId: string;
+            readonly name: string;
+            readonly requireEnrichments?: true | undefined;
+        };
+        readonly label: string;
+    }[]>;
+    targetOptions: _platforma_sdk_model.ValueOrErrors<{
+        label: string;
+        value: SUniversalPColumnId;
+    }[] | undefined>;
+    dataImportHandle: _platforma_sdk_model.ValueOrErrors<_platforma_sdk_model.ImportProgress | undefined>;
+    table: _platforma_sdk_model.ValueOrErrors<{
+        tableSpec: ({
+            type: "axis";
+            id: {
+                readonly type: _platforma_sdk_model.ValueType;
+                readonly name: string;
+                readonly domain?: {
+                    [x: string]: string;
+                } | undefined;
+            };
+            spec: {
+                readonly type: _platforma_sdk_model.ValueType;
+                readonly name: string;
+                readonly domain?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly annotations?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly parentAxes?: number[] | undefined;
+            };
+        } | {
+            type: "column";
+            id: _platforma_sdk_model.PObjectId;
+            spec: {
+                readonly valueType: _platforma_sdk_model.ValueType;
+                readonly kind: "PColumn";
+                readonly name: string;
+                readonly domain?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly annotations?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly parentAxes?: number[] | undefined;
+                readonly axesSpec: {
+                    readonly type: _platforma_sdk_model.ValueType;
+                    readonly name: string;
+                    readonly domain?: {
+                        [x: string]: string;
+                    } | undefined;
+                    readonly annotations?: {
+                        [x: string]: string;
+                    } | undefined;
+                    readonly parentAxes?: number[] | undefined;
+                }[];
+            };
+        })[];
+        tableHandle: _platforma_sdk_model.PTableHandle;
+    } | undefined>;
+    isRunning: _platforma_sdk_model.ValueOrErrors<boolean>;
+}, UiState, "/">;
+type BlockOutputs = InferOutputsType<typeof model>;
+
+export { type BlockArgs, type BlockOutputs, type ImportColumnInfo, type UiState, model };

package/dist/index.d.ts

@@ -0,0 +1,97 @@
+import * as _platforma_sdk_model from '@platforma-sdk/model';
+import { PlRef, SUniversalPColumnId, ImportFileHandle, PlDataTableState, InferOutputsType } from '@platforma-sdk/model';
+
+type Settings = {
+    coverageThreshold: number;
+    coverageMode: 0 | 1 | 2 | 3 | 4 | 5;
+};
+type ImportColumnInfo = {
+    header: string;
+    type: 'Int' | 'Double' | 'String';
+    /** If this column is a sequence column, the type of the sequence */
+    sequenceType?: 'nucleotide' | 'aminoacid';
+};
+type BlockArgs = {
+    datasetRef?: PlRef;
+    targetRef?: SUniversalPColumnId;
+    fileHandle?: ImportFileHandle;
+    fileExtension?: string;
+    importColumns?: ImportColumnInfo[];
+    sequenceColumnHeader?: string;
+    settings: Settings;
+};
+type UiState = {
+    title: string;
+    fileImportError?: string;
+    tableState: PlDataTableState;
+};
+declare const model: _platforma_sdk_model.Platforma<BlockArgs, {
+    datasetOptions: _platforma_sdk_model.ValueOrErrors<{
+        readonly ref: {
+            readonly __isRef: true;
+            readonly blockId: string;
+            readonly name: string;
+            readonly requireEnrichments?: true | undefined;
+        };
+        readonly label: string;
+    }[]>;
+    targetOptions: _platforma_sdk_model.ValueOrErrors<{
+        label: string;
+        value: SUniversalPColumnId;
+    }[] | undefined>;
+    dataImportHandle: _platforma_sdk_model.ValueOrErrors<_platforma_sdk_model.ImportProgress | undefined>;
+    table: _platforma_sdk_model.ValueOrErrors<{
+        tableSpec: ({
+            type: "axis";
+            id: {
+                readonly type: _platforma_sdk_model.ValueType;
+                readonly name: string;
+                readonly domain?: {
+                    [x: string]: string;
+                } | undefined;
+            };
+            spec: {
+                readonly type: _platforma_sdk_model.ValueType;
+                readonly name: string;
+                readonly domain?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly annotations?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly parentAxes?: number[] | undefined;
+            };
+        } | {
+            type: "column";
+            id: _platforma_sdk_model.PObjectId;
+            spec: {
+                readonly valueType: _platforma_sdk_model.ValueType;
+                readonly kind: "PColumn";
+                readonly name: string;
+                readonly domain?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly annotations?: {
+                    [x: string]: string;
+                } | undefined;
+                readonly parentAxes?: number[] | undefined;
+                readonly axesSpec: {
+                    readonly type: _platforma_sdk_model.ValueType;
+                    readonly name: string;
+                    readonly domain?: {
+                        [x: string]: string;
+                    } | undefined;
+                    readonly annotations?: {
+                        [x: string]: string;
+                    } | undefined;
+                    readonly parentAxes?: number[] | undefined;
+                }[];
+            };
+        })[];
+        tableHandle: _platforma_sdk_model.PTableHandle;
+    } | undefined>;
+    isRunning: _platforma_sdk_model.ValueOrErrors<boolean>;
+}, UiState, "/">;
+type BlockOutputs = InferOutputsType<typeof model>;
+
+export { type BlockArgs, type BlockOutputs, type ImportColumnInfo, type UiState, model };

package/dist/index.js

@@ -0,0 +1,98 @@
+import { BlockModel, createPlDataTableV2 } from '@platforma-sdk/model';
+
+// src/index.ts
+var model = BlockModel.create().withArgs({
+  settings: {
+    coverageMode: 2,
+    // default to coverage of clone,
+    coverageThreshold: 0.95
+    // default value matching MMseqs2 default
+  }
+}).withUiState({
+  title: "Immune Assay Data",
+  tableState: {
+    gridState: {}
+  }
+}).argsValid(
+  (ctx) => ctx.args.datasetRef !== void 0 && ctx.args.fileHandle !== void 0 && ctx.args.importColumns !== void 0 && ctx.args.sequenceColumnHeader !== void 0 && ctx.args.targetRef !== void 0 && ctx.uiState.fileImportError === void 0
+).output(
+  "datasetOptions",
+  (ctx) => ctx.resultPool.getOptions([{
+    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" }
+  }], { refsWithEnrichments: true })
+).output("targetOptions", (ctx) => {
+  const ref = ctx.args.datasetRef;
+  if (ref === void 0) return void 0;
+  const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === "pl7.app/vdj/scClonotypeKey";
+  const sequenceMatchers = [];
+  const allowedFeatures = [
+    "CDR1",
+    "CDR2",
+    "CDR3",
+    "FR1",
+    "FR2",
+    "FR3",
+    "FR4",
+    "VDJRegion"
+  ];
+  for (const feature of allowedFeatures) {
+    if (isSingleCell) {
+      sequenceMatchers.push({
+        axes: [{ anchor: "main", idx: 1 }],
+        name: "pl7.app/vdj/sequence",
+        domain: {
+          "pl7.app/vdj/feature": feature,
+          "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,
+      labelOps: {
+        includeNativeLabel: true
+      }
+    }
+  );
+}).output(
+  "dataImportHandle",
+  (ctx) => ctx.outputs?.resolve("dataImportHandle")?.getImportProgress(),
+  { isActive: true }
+).output("table", (ctx) => {
+  const cols = ctx.outputs?.resolve("table")?.getPColumns();
+  if (cols === void 0)
+    return void 0;
+  return createPlDataTableV2(
+    ctx,
+    cols,
+    (_) => true,
+    ctx.uiState.tableState
+  );
+}).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title((ctx) => ctx.uiState.title).sections((_ctx) => [
+  { type: "link", href: "/", label: "Main" }
+]).done();
+
+export { model };
+//# sourceMappingURL=index.js.map
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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// fraction of aligned residues required\n  coverageMode: 0 | 1 | 2 | 3 | 4 | 5; // MMseqs2 coverage modes\n};\n\nexport type ImportColumnInfo = {\n  header: string;\n  type: 'Int' | 'Double' | 'String';\n  /** If this column is a sequence column, the type of the sequence */\n  sequenceType?: 'nucleotide' | 'aminoacid';\n};\n\nexport type BlockArgs = {\n  datasetRef?: PlRef;\n  targetRef?: SUniversalPColumnId;\n  fileHandle?: ImportFileHandle;\n  fileExtension?: string;\n  importColumns?: ImportColumnInfo[];\n  sequenceColumnHeader?: string;\n  settings: Settings;\n};\n\nexport type UiState = {\n  title: string;\n  fileImportError?: string;\n  tableState: PlDataTableState;\n};\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    settings: {\n      coverageMode: 2, // default to coverage of clone,\n      coverageThreshold: 0.95, // default value matching MMseqs2 default\n    },\n  })\n\n  .withUiState<UiState>({\n    title: 'Immune Assay Data',\n    tableState: {\n      gridState: {},\n    },\n  })\n\n  .argsValid((ctx) =>\n    ctx.args.datasetRef !== undefined\n    && ctx.args.fileHandle !== undefined\n    && ctx.args.importColumns !== undefined\n    && ctx.args.sequenceColumnHeader !== undefined\n    && ctx.args.targetRef !== undefined\n    && ctx.uiState.fileImportError === undefined,\n  )\n\n  .output('datasetOptions', (ctx) =>\n    ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/clonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }, {\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/scClonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }], { refsWithEnrichments: true }),\n  )\n\n  .output('targetOptions', (ctx) => {\n    const ref = ctx.args.datasetRef;\n    if (ref === undefined) return undefined;\n\n    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';\n    const sequenceMatchers = [];\n    const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',\n      'FR3', 'FR4', 'VDJRegion'];\n    for (const feature of allowedFeatures) {\n      if (isSingleCell) {\n        sequenceMatchers.push({\n          axes: [{ anchor: 'main', idx: 1 }],\n          name: 'pl7.app/vdj/sequence',\n          domain: {\n            'pl7.app/vdj/feature': feature,\n            'pl7.app/vdj/scClonotypeChain/index': 'primary',\n          },\n        });\n      } else {\n        sequenceMatchers.push({\n          axes: [{ anchor: 'main', idx: 1 }],\n          name: 'pl7.app/vdj/sequence',\n          domain: {\n            'pl7.app/vdj/feature': feature,\n          },\n        });\n      }\n    }\n\n    return ctx.resultPool.getCanonicalOptions(\n      { main: ref },\n      sequenceMatchers,\n      {\n        ignoreMissingDomains: true,\n        labelOps: {\n          includeNativeLabel: true,\n        },\n      });\n  })\n\n  .output(\n    'dataImportHandle',\n    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),\n    { isActive: true },\n  )\n\n  .output('table', (ctx) => {\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPlDataTableV2(\n      ctx,\n      cols,\n      (_) => true,\n      ctx.uiState.tableState,\n    );\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title((ctx) => ctx.uiState.title)\n\n  .sections((_ctx) => ([\n    { type: 'link', href: '/', label: 'Main' },\n  ]))\n\n  .done();\n\nexport type BlockOutputs = InferOutputsType<typeof model>;\n"]}