@vitessce/vit-s 2.0.3-beta.0 → 3.0.0

package/src/view-config-utils.test.fixtures.js

@@ -0,0 +1,893 @@
+/* eslint-disable camelcase */
+export const legacyViewConfig0_1_0 = {
+  version: '0.1.0',
+  public: true,
+  name: 'My config name',
+  description: 'My config description',
+  layers: [{
+    name: 'cells',
+    type: 'CELLS',
+    fileType: 'cells.json',
+    url: 'https://example.com/cells.json',
+  }, {
+    name: 'cell-sets',
+    type: 'CELL-SETS',
+    fileType: 'cell-sets.json',
+    url: 'https://example.com/cell-sets.json',
+  }],
+  staticLayout: [{
+    component: 'description',
+    props: {
+      description: 'My component description',
+    },
+    x: 9,
+    y: 0,
+    w: 3,
+    h: 2,
+  }, {
+    component: 'scatterplot',
+    props: {
+      mapping: 't-SNE',
+      view: {
+        zoom: 3,
+        target: [0, 0, 0],
+      },
+    },
+    x: 0,
+    y: 2,
+    w: 5,
+    h: 4,
+  }, {
+    component: 'spatial',
+    props: {
+      cellRadius: 50,
+      view: {
+        zoom: -4.4,
+        target: [3800, -900, 0],
+      },
+    },
+    x: 5,
+    y: 0,
+    w: 4,
+    h: 4,
+  }],
+};
+
+export const upgradedLegacyViewConfig0_1_0 = {
+  version: '1.0.1',
+  public: true,
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    embeddingTargetX: {
+      A: 0,
+    },
+    embeddingTargetY: {
+      A: 0,
+    },
+    embeddingType: {
+      't-SNE': 't-SNE',
+    },
+    embeddingZoom: {
+      A: 3,
+    },
+    spatialTargetX: {
+      A: 3800,
+    },
+    spatialTargetY: {
+      A: -900,
+    },
+    spatialZoom: {
+      A: -4.4,
+    },
+  },
+  datasets: [
+    {
+      files: [
+        {
+          fileType: 'cells.json',
+          type: 'cells',
+          url: 'https://example.com/cells.json',
+        },
+        {
+          fileType: 'cell-sets.json',
+          type: 'cell-sets',
+          url: 'https://example.com/cell-sets.json',
+        },
+      ],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [
+    {
+      component: 'description',
+      coordinationScopes: {},
+      h: 2,
+      props: {
+        description: 'My component description',
+      },
+      w: 3,
+      x: 9,
+      y: 0,
+    },
+    {
+      component: 'scatterplot',
+      coordinationScopes: {
+        embeddingTargetX: 'A',
+        embeddingTargetY: 'A',
+        embeddingType: 't-SNE',
+        embeddingZoom: 'A',
+      },
+      h: 4,
+      props: {
+        mapping: 't-SNE',
+        view: {
+          target: [
+            0,
+            0,
+            0,
+          ],
+          zoom: 3,
+        },
+      },
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'spatial',
+      coordinationScopes: {
+        spatialTargetX: 'A',
+        spatialTargetY: 'A',
+        spatialZoom: 'A',
+      },
+      h: 4,
+      props: {
+        cellRadius: 50,
+        view: {
+          target: [
+            3800,
+            -900,
+            0,
+          ],
+          zoom: -4.4,
+        },
+      },
+      w: 4,
+      x: 5,
+      y: 0,
+    },
+  ],
+};
+
+export const legacyViewConfig1_0_0 = {
+  version: '1.0.0',
+  public: true,
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    dataset: {
+      A: 'A',
+    },
+    spatialLayers: {
+      A: [
+        { type: 'cells', radius: 10, visible: true },
+        { type: 'molecules', visible: false },
+        { type: 'raster', index: 2 },
+        { type: 'raster', index: 3 },
+      ],
+    },
+  },
+  datasets: [
+    {
+      files: [],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [
+    {
+      component: 'description',
+      coordinationScopes: {
+        dataset: 'A',
+        spatialLayers: 'A',
+      },
+      h: 2,
+      props: {
+        description: 'My component description',
+      },
+      w: 3,
+      x: 9,
+      y: 0,
+    },
+    {
+      component: 'spatial',
+      coordinationScopes: {
+        dataset: 'A',
+        spatialLayers: 'A',
+      },
+      h: 4,
+      props: {
+        cellRadius: 50,
+        view: {
+          target: [
+            3800,
+            -900,
+            0,
+          ],
+          zoom: -4.4,
+        },
+      },
+      w: 4,
+      x: 5,
+      y: 0,
+    },
+  ],
+};
+
+export const upgradedLegacyViewConfig1_0_0 = {
+  version: '1.0.1',
+  public: true,
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    dataset: {
+      A: 'A',
+    },
+    spatialRasterLayers: {
+      A: [
+        { index: 2 },
+        { index: 3 },
+      ],
+    },
+    spatialCellsLayer: {
+      A: { radius: 10, visible: true },
+    },
+    spatialMoleculesLayer: {
+      A: { visible: false },
+    },
+    spatialNeighborhoodsLayer: {
+      A: null,
+    },
+  },
+  datasets: [
+    {
+      files: [],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [
+    {
+      component: 'description',
+      coordinationScopes: {
+        dataset: 'A',
+        spatialRasterLayers: 'A',
+      },
+      h: 2,
+      props: {
+        description: 'My component description',
+      },
+      w: 3,
+      x: 9,
+      y: 0,
+    },
+    {
+      component: 'spatial',
+      coordinationScopes: {
+        dataset: 'A',
+        spatialRasterLayers: 'A',
+        spatialCellsLayer: 'A',
+        spatialMoleculesLayer: 'A',
+        spatialNeighborhoodsLayer: 'A',
+      },
+      h: 4,
+      props: {
+        cellRadius: 50,
+        view: {
+          target: [
+            3800,
+            -900,
+            0,
+          ],
+          zoom: -4.4,
+        },
+      },
+      w: 4,
+      x: 5,
+      y: 0,
+    },
+  ],
+};
+
+
+export const missingViewUids = {
+  version: '1.0.9',
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    dataset: {
+      A: 'A',
+    },
+  },
+  datasets: [
+    {
+      files: [],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [
+    {
+      component: 'description',
+      coordinationScopes: {
+        dataset: 'A',
+      },
+      h: 2,
+      w: 3,
+      x: 9,
+      y: 0,
+    },
+    {
+      component: 'scatterplot',
+      uid: 'some-umap',
+      coordinationScopes: {
+        dataset: 'A',
+      },
+      h: 4,
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'scatterplot',
+      coordinationScopes: {
+        dataset: 'A',
+      },
+      h: 4,
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'spatial',
+      coordinationScopes: {
+        dataset: 'A',
+      },
+      h: 4,
+      w: 4,
+      x: 5,
+      y: 0,
+    },
+  ],
+};
+
+
+export const viewConfig1_0_10 = {
+  version: '1.0.10',
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    embeddingTargetX: {
+      A: 0,
+    },
+    embeddingTargetY: {
+      A: 0,
+    },
+    embeddingType: {
+      't-SNE': 't-SNE',
+    },
+    embeddingZoom: {
+      A: 3,
+    },
+    spatialTargetX: {
+      A: 3800,
+    },
+    spatialTargetY: {
+      A: -900,
+    },
+    spatialZoom: {
+      A: -4.4,
+    },
+  },
+  datasets: [
+    {
+      files: [
+        {
+          fileType: 'cells.json',
+          type: 'cells',
+          url: 'https://example.com/cells.json',
+        },
+        {
+          fileType: 'cell-sets.json',
+          type: 'cell-sets',
+          url: 'https://example.com/cell-sets.json',
+        },
+      ],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [
+    {
+      component: 'description',
+      coordinationScopes: {},
+      h: 2,
+      props: {
+        description: 'My component description',
+      },
+      w: 3,
+      x: 9,
+      y: 0,
+    },
+    {
+      component: 'scatterplot',
+      coordinationScopes: {
+        embeddingTargetX: 'A',
+        embeddingTargetY: 'A',
+        embeddingType: 't-SNE',
+        embeddingZoom: 'A',
+      },
+      h: 4,
+      props: {
+        mapping: 't-SNE',
+        view: {
+          target: [
+            0,
+            0,
+            0,
+          ],
+          zoom: 3,
+        },
+      },
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'spatial',
+      coordinationScopes: {
+        spatialTargetX: 'A',
+        spatialTargetY: 'A',
+        spatialZoom: 'A',
+      },
+      h: 4,
+      props: {
+        cellRadius: 50,
+        view: {
+          target: [
+            3800,
+            -900,
+            0,
+          ],
+          zoom: -4.4,
+        },
+      },
+      w: 4,
+      x: 5,
+      y: 0,
+    },
+  ],
+};
+
+export const initializedViewConfig = {
+  version: '1.0.10',
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    obsType: {
+      A: 'cell',
+    },
+    featureType: {
+      A: 'gene',
+    },
+    featureValueType: {
+      A: 'expression',
+    },
+    obsColorEncoding: {
+      A: 'cellSetSelection',
+    },
+    obsFilter: {
+      A: null,
+    },
+    obsHighlight: {
+      A: null,
+    },
+    obsSetHighlight: {
+      A: null,
+    },
+    obsSetSelection: {
+      A: null,
+    },
+    dataset: {
+      A: 'A',
+    },
+    embeddingObsOpacity: {
+      A: 1,
+    },
+    embeddingObsOpacityMode: {
+      A: 'auto',
+    },
+    embeddingObsRadius: {
+      A: 1,
+    },
+    embeddingObsRadiusMode: {
+      A: 'auto',
+    },
+    embeddingRotation: {
+      A: 0,
+    },
+    embeddingTargetX: {
+      A: 0,
+    },
+    embeddingTargetY: {
+      A: 0,
+    },
+    embeddingTargetZ: {
+      A: 0,
+    },
+    embeddingType: {
+      't-SNE': 't-SNE',
+    },
+    embeddingZoom: {
+      A: 3,
+    },
+    embeddingObsSetLabelSize: {
+      A: 14,
+    },
+    embeddingObsSetLabelsVisible: {
+      A: false,
+    },
+    embeddingObsSetPolygonsVisible: {
+      A: false,
+    },
+    featureValueColormap: {
+      A: 'plasma',
+    },
+    featureValueColormapRange: {
+      A: [
+        0,
+        1,
+      ],
+    },
+    featureHighlight: {
+      A: null,
+    },
+    featureSelection: {
+      A: null,
+    },
+    spatialImageLayer: {
+      A: null,
+    },
+    spatialSegmentationLayer: {
+      A: null,
+    },
+    spatialPointLayer: {
+      A: null,
+    },
+    spatialNeighborhoodLayer: {
+      A: null,
+    },
+    spatialRotation: {
+      A: 0,
+    },
+    spatialRotationOrbit: {
+      A: 0,
+    },
+    spatialOrbitAxis: {
+      A: 'Y',
+    },
+    spatialRotationX: {
+      A: null,
+    },
+    spatialRotationY: {
+      A: null,
+    },
+    spatialRotationZ: {
+      A: null,
+    },
+    spatialTargetX: {
+      A: 3800,
+    },
+    spatialTargetY: {
+      A: -900,
+    },
+    spatialTargetZ: {
+      A: null,
+    },
+    spatialZoom: {
+      A: -4.4,
+    },
+    spatialAxisFixed: {
+      A: false,
+    },
+    additionalObsSets: {
+      A: null,
+    },
+    obsSetColor: {
+      A: null,
+    },
+    obsLabelsType: {
+      A: null,
+    },
+    moleculeHighlight: {
+      A: null,
+    },
+  },
+  datasets: [
+    {
+      files: [
+        {
+          fileType: 'obsSegmentations.cells.json',
+          url: 'https://example.com/cells.json',
+          coordinationValues: {
+            obsType: 'cell',
+          },
+        },
+        {
+          fileType: 'obsLocations.cells.json',
+          url: 'https://example.com/cells.json',
+          coordinationValues: {
+            obsType: 'cell',
+          },
+        },
+        {
+          fileType: 'obsSets.cell-sets.json',
+          url: 'https://example.com/cell-sets.json',
+          coordinationValues: {
+            obsType: 'cell',
+          },
+        },
+      ],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [
+    {
+      component: 'description',
+      coordinationScopes: {
+        dataset: 'A',
+        spatialImageLayer: 'A',
+      },
+      h: 2,
+      props: {
+        description: 'My component description',
+      },
+      uid: 'A',
+      w: 3,
+      x: 9,
+      y: 0,
+    },
+    {
+      component: 'scatterplot',
+      coordinationScopes: {
+        obsType: 'A',
+        obsLabelsType: 'A',
+        featureType: 'A',
+        featureValueType: 'A',
+        obsColorEncoding: 'A',
+        obsFilter: 'A',
+        obsHighlight: 'A',
+        obsSetHighlight: 'A',
+        obsSetSelection: 'A',
+        obsSetColor: 'A',
+        dataset: 'A',
+        embeddingObsOpacity: 'A',
+        embeddingObsOpacityMode: 'A',
+        embeddingObsRadius: 'A',
+        embeddingObsRadiusMode: 'A',
+        embeddingRotation: 'A',
+        embeddingTargetX: 'A',
+        embeddingTargetY: 'A',
+        embeddingTargetZ: 'A',
+        embeddingType: 't-SNE',
+        embeddingZoom: 'A',
+        embeddingObsSetLabelSize: 'A',
+        embeddingObsSetLabelsVisible: 'A',
+        embeddingObsSetPolygonsVisible: 'A',
+        featureValueColormap: 'A',
+        featureValueColormapRange: 'A',
+        featureHighlight: 'A',
+        featureSelection: 'A',
+        additionalObsSets: 'A',
+      },
+      h: 4,
+      props: {
+        mapping: 't-SNE',
+        view: {
+          target: [
+            0,
+            0,
+            0,
+          ],
+          zoom: 3,
+        },
+      },
+      uid: 'B',
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'spatial',
+      coordinationScopes: {
+        obsType: 'A',
+        obsLabelsType: 'A',
+        obsColorEncoding: 'A',
+        obsFilter: 'A',
+        obsHighlight: 'A',
+        obsSetHighlight: 'A',
+        obsSetSelection: 'A',
+        obsSetColor: 'A',
+        dataset: 'A',
+        featureValueColormap: 'A',
+        featureValueColormapRange: 'A',
+        featureValueType: 'A',
+        featureHighlight: 'A',
+        featureSelection: 'A',
+        featureType: 'A',
+        spatialImageLayer: 'A',
+        spatialSegmentationLayer: 'A',
+        spatialPointLayer: 'A',
+        spatialNeighborhoodLayer: 'A',
+        spatialRotation: 'A',
+        spatialRotationOrbit: 'A',
+        spatialOrbitAxis: 'A',
+        spatialRotationX: 'A',
+        spatialRotationY: 'A',
+        spatialRotationZ: 'A',
+        spatialTargetX: 'A',
+        spatialTargetY: 'A',
+        spatialTargetZ: 'A',
+        spatialAxisFixed: 'A',
+        spatialZoom: 'A',
+        additionalObsSets: 'A',
+        moleculeHighlight: 'A',
+      },
+      h: 4,
+      props: {
+        cellRadius: 50,
+        view: {
+          target: [
+            3800,
+            -900,
+            0,
+          ],
+          zoom: -4.4,
+        },
+      },
+      uid: 'C',
+      w: 4,
+      x: 5,
+      y: 0,
+    },
+  ],
+};
+
+export const implicitPerDatasetCoordinations = {
+  version: '1.0.9',
+  name: 'Per-dataset coordinations',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    dataset: {
+      A: 'first',
+      B: 'second',
+    },
+    embeddingCellRadius: {
+      small: 2,
+      big: 20,
+    },
+    embeddingCellRadiusMode: {
+      all: 'manual',
+    },
+  },
+  datasets: [
+    {
+      files: [],
+      name: 'First dataset',
+      uid: 'first',
+    },
+    {
+      files: [],
+      name: 'Second dataset',
+      uid: 'second',
+    },
+  ],
+  layout: [
+    {
+      component: 'somePluginView',
+      coordinationScopes: {
+        dataset: ['A', 'B'],
+        embeddingCellRadius: { A: 'small', B: 'big' },
+        embeddingCellRadiusMode: 'all',
+      },
+      h: 4,
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'scatterplot',
+      coordinationScopes: {
+        dataset: 'A',
+        embeddingCellRadius: 'small',
+        embeddingCellRadiusMode: 'all',
+      },
+      h: 4,
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+  ],
+};
+
+export const explicitPerDatasetCoordinations = {
+  version: '1.0.16',
+  name: 'Per-dataset coordinations',
+  description: 'My config description',
+  initStrategy: 'auto',
+  coordinationSpace: {
+    dataset: {
+      A: 'first',
+      B: 'second',
+    },
+    embeddingCellRadius: {
+      small: 2,
+      big: 20,
+    },
+    embeddingCellRadiusMode: {
+      all: 'manual',
+    },
+  },
+  datasets: [
+    {
+      files: [],
+      name: 'First dataset',
+      uid: 'first',
+    },
+    {
+      files: [],
+      name: 'Second dataset',
+      uid: 'second',
+    },
+  ],
+  layout: [
+    {
+      component: 'somePluginView',
+      coordinationScopes: {
+        dataset: ['A', 'B'],
+        embeddingCellRadiusMode: 'all',
+      },
+      coordinationScopesBy: {
+        dataset: {
+          embeddingCellRadius: { A: 'small', B: 'big' },
+        },
+      },
+      h: 4,
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+    {
+      component: 'scatterplot',
+      coordinationScopes: {
+        dataset: 'A',
+        embeddingCellRadius: 'small',
+        embeddingCellRadiusMode: 'all',
+      },
+      h: 4,
+      w: 5,
+      x: 0,
+      y: 2,
+    },
+  ],
+};