@vitessce/vit-s 2.0.3 → 3.0.0

package/src/view-config-upgraders.js

@@ -1,628 +0,0 @@
-/* eslint-disable camelcase */
-import uuidv4 from 'uuid/v4';
-import cloneDeep from 'lodash/cloneDeep';
-import { getNextScope, capitalize } from '@vitessce/utils';
-
-/**
- * A helper function for the `upgrade()` function,
- * which helps convert `props.view` (for scatterplot and spatial),
- * into new coordination scopes, setting their values
- * in the coordination space and returning the new scope mappings.
- * This function does mutate the `coordinationSpace` parameter.
- * @param {string} prefix The coordination type prefix,
- * either 'embedding' or 'spatial'.
- * @param {object} view The view prop object containing
- * the properties `.target` and `.zoom`.
- * @param {object} coordinationSpace The coordination space.
- * @returns {object} The new coordination scope names.
- */
-function upgradeReplaceViewProp(prefix, view, coordinationSpace) {
-  const prevZScopes = Object.keys(coordinationSpace[`${prefix}Zoom`]);
-  const prevTXScopes = Object.keys(coordinationSpace[`${prefix}TargetX`]);
-  const prevTYScopes = Object.keys(coordinationSpace[`${prefix}TargetY`]);
-
-  const nextZScope = getNextScope(prevZScopes);
-  const nextTXScope = getNextScope(prevTXScopes);
-  const nextTYScope = getNextScope(prevTYScopes);
-
-  const { zoom, target: [targetX, targetY] } = view;
-  // eslint-disable-next-line no-param-reassign
-  coordinationSpace[`${prefix}Zoom`][nextZScope] = zoom;
-  // eslint-disable-next-line no-param-reassign
-  coordinationSpace[`${prefix}TargetX`][nextTXScope] = targetX;
-  // eslint-disable-next-line no-param-reassign
-  coordinationSpace[`${prefix}TargetY`][nextTYScope] = targetY;
-  return {
-    [`${prefix}Zoom`]: nextZScope,
-    [`${prefix}TargetX`]: nextTXScope,
-    [`${prefix}TargetY`]: nextTYScope,
-  };
-}
-
-/**
- * Convert an older view config to a newer view config.
- * @param {object} config A v0.1.0 "legacy" view config.
- * @returns {object} A v1.0.0 "upgraded" view config.
- */
-export function upgradeFrom0_1_0(config, datasetUid = null) {
-  const coordinationSpace = {
-    embeddingType: {},
-    embeddingZoom: {},
-    embeddingTargetX: {},
-    embeddingTargetY: {},
-    spatialZoom: {},
-    spatialTargetX: {},
-    spatialTargetY: {},
-  };
-
-  const layout = [];
-  config.staticLayout.forEach((componentDef) => {
-    let newComponentDef = {
-      ...componentDef,
-      coordinationScopes: {},
-    };
-    if (componentDef.component === 'scatterplot') {
-      // Need to set up the coordinationSpace
-      // with embeddingType to replace scatterplot
-      // component prop "mapping".
-      if (componentDef.props.mapping) {
-        coordinationSpace.embeddingType[componentDef.props.mapping] = componentDef.props.mapping;
-        newComponentDef = {
-          ...newComponentDef,
-          coordinationScopes: {
-            ...newComponentDef.coordinationScopes,
-            embeddingType: componentDef.props.mapping,
-          },
-        };
-      }
-      // Need to set up the coordinationSpace
-      // with embeddingZoom / embeddingTargetX/Y to replace scatterplot
-      // component prop "view" ({ zoom, target }).
-      if (componentDef.props.view) {
-        // Note that the below function does mutate the coordinationSpace param.
-        const newScopeValues = upgradeReplaceViewProp(
-          'embedding', componentDef.props.view, coordinationSpace,
-        );
-        newComponentDef = {
-          ...newComponentDef,
-          coordinationScopes: {
-            ...newComponentDef.coordinationScopes,
-            ...newScopeValues,
-          },
-        };
-      }
-    }
-    if (componentDef.component === 'spatial') {
-      // Need to set up the coordinationSpace
-      // with spatialZoom / spatialTargetX/Y to replace spatial
-      // component prop "view" ({ zoom, target }).
-      if (componentDef?.props?.view) {
-        // Note that the below function does mutate the coordinationSpace param.
-        const newScopeValues = upgradeReplaceViewProp(
-          'spatial', componentDef.props.view, coordinationSpace,
-        );
-        newComponentDef = {
-          ...newComponentDef,
-          coordinationScopes: {
-            ...newComponentDef.coordinationScopes,
-            ...newScopeValues,
-          },
-        };
-      }
-    }
-    layout.push(newComponentDef);
-  });
-
-  const lcDef = layout.find(c => c.component === 'layerController');
-  const spatialDef = layout.find(c => c.component === 'spatial');
-  if (lcDef && spatialDef.coordinationScopes) {
-    lcDef.coordinationScopes = spatialDef.coordinationScopes;
-  }
-
-  // Use a random dataset ID when initializing automatically,
-  // so that it changes with each new v0.1.0 view config.
-  // However, check if the `datasetUid` parameter was passed,
-  // which allows for unit testing.
-  const newDatasetUid = datasetUid || uuidv4();
-
-  return {
-    version: '1.0.1',
-    name: config.name,
-    description: config.description,
-    public: config.public,
-    datasets: [
-      {
-        uid: newDatasetUid,
-        name: newDatasetUid,
-        files: config.layers.map(layer => ({
-          type: layer.type.toLowerCase(),
-          fileType: layer.fileType,
-          url: layer.url,
-        })),
-      },
-    ],
-    initStrategy: 'auto',
-    coordinationSpace,
-    layout,
-  };
-}
-
-export function upgradeFrom1_0_0(config) {
-  const newConfig = cloneDeep(config);
-  const { coordinationSpace } = newConfig;
-
-  function replaceLayerType(layerType) {
-    // Layer type could be one of a few things, bitmask or raster at the moment.
-    const isRaster = layerType === 'raster';
-    coordinationSpace[`spatial${capitalize(layerType)}Layer${isRaster ? 's' : ''}`] = {};
-    Object.entries(coordinationSpace.spatialLayers).forEach(([scope, layers]) => {
-      if (Array.isArray(layers) && layers.find(layer => layer.type === layerType)) {
-        const typedLayers = layers
-          .filter(layer => layer.type === layerType)
-          .map((layer) => {
-            const newLayer = { ...layer };
-            delete newLayer.type;
-            return newLayer;
-          });
-        coordinationSpace[`spatial${capitalize(layerType)}Layer${isRaster ? 's' : ''}`][scope] = isRaster ? typedLayers : typedLayers[0];
-      } else {
-        coordinationSpace[`spatial${capitalize(layerType)}Layer${isRaster ? 's' : ''}`][scope] = null;
-      }
-    });
-  }
-
-  if (coordinationSpace.spatialLayers) {
-    replaceLayerType('raster');
-    replaceLayerType('cells');
-    replaceLayerType('molecules');
-    replaceLayerType('neighborhoods');
-    delete coordinationSpace.spatialLayers;
-  }
-
-  const layout = newConfig.layout.map((component) => {
-    const newComponent = { ...component };
-
-    function replaceCoordinationScope(layerType) {
-      const isRaster = layerType === 'raster';
-      if (
-        ['spatial', 'layerController'].includes(newComponent.component)
-        || (newComponent.component === 'description' && isRaster)
-      ) {
-        newComponent.coordinationScopes[`spatial${capitalize(layerType)}Layer${isRaster ? 's' : ''}`] = newComponent
-          .coordinationScopes.spatialLayers;
-      }
-    }
-
-    if (newComponent.coordinationScopes && newComponent.coordinationScopes.spatialLayers) {
-      replaceCoordinationScope('raster');
-      replaceCoordinationScope('cells');
-      replaceCoordinationScope('molecules');
-      replaceCoordinationScope('neighborhoods');
-      delete newComponent.coordinationScopes.spatialLayers;
-    }
-    return newComponent;
-  });
-
-  return {
-    ...newConfig,
-    coordinationSpace,
-    layout,
-    version: '1.0.1',
-  };
-}
-
-
-export function upgradeFrom1_0_1(config) {
-  // Need to add the globalDisable3d prop to any layer controller views,
-  // to match the previous lack of 3D auto-detection behavior.
-
-  const layout = config.layout.map((component) => {
-    const newComponent = { ...component };
-    if (newComponent.component === 'layerController') {
-      newComponent.props = {
-        ...newComponent.props,
-        globalDisable3d: true,
-      };
-    }
-    return newComponent;
-  });
-
-  // Enforce bitmask or raster as spatial raster layer type, defaulting
-  // to raster layer if it is not one of bitmask or raster from the old config.
-
-  const newConfig = cloneDeep(config);
-  Object.keys((newConfig?.coordinationSpace?.spatialRasterLayers || {})).forEach((key) => {
-    if (newConfig.coordinationSpace.spatialRasterLayers[key]) {
-      newConfig.coordinationSpace.spatialRasterLayers[key].forEach((layer, index) => {
-        newConfig.coordinationSpace.spatialRasterLayers[key][index].type = ['bitmask', 'raster'].includes(layer.type) ? layer.type : 'raster';
-      });
-    }
-  });
-
-  return {
-    ...newConfig,
-    layout,
-    version: '1.0.2',
-  };
-}
-
-export function upgradeFrom1_0_2(config) {
-  // Need to add the globalDisable3d prop to any layer controller views,
-  // to match the previous lack of 3D auto-detection behavior.
-
-  const layout = config.layout.map((component) => {
-    const newComponent = { ...component };
-    if (newComponent.component === 'layerController') {
-      newComponent.props = {
-        ...newComponent.props,
-        disableChannelsIfRgbDetected: true,
-      };
-    }
-    return newComponent;
-  });
-
-  // Enforce bitmask or raster as spatial raster layer type, defaulting
-  // to raster layer if it is not one of bitmask or raster from the old config.
-
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    layout,
-    version: '1.0.3',
-  };
-}
-
-export function upgradeFrom1_0_3(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.4',
-  };
-}
-
-// Added in version 1.0.5:
-// - Support for an array of strings in the setName property within options array items
-//   for the anndata-cell-sets.zarr file type.
-export function upgradeFrom1_0_4(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.5',
-  };
-}
-
-
-// Added in version 1.0.6:
-// - Support for the scoreName property within options array items
-//   for the anndata-cell-sets.zarr file type.
-export function upgradeFrom1_0_5(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.6',
-  };
-}
-
-// Added in version 1.0.7:
-// - Support for aliasing the gene identifiers using a different var dataframe column
-// via a new `geneAlias` option for the `anndata-expression-matrix.zarr` fileType.
-export function upgradeFrom1_0_6(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.7',
-  };
-}
-
-// Added in version 1.0.8:
-// - Support for multiple `dataset` coordination scopes and
-// dataset-specific coordination scope mappings for all
-// other coordination types.
-export function upgradeFrom1_0_7(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.8',
-  };
-}
-
-// Added in version 1.0.9:
-// - Support for plugin coordination types.
-export function upgradeFrom1_0_8(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.9',
-  };
-}
-
-// Added in version 1.0.10:
-// - Support for the optional 'uid' property for views.
-export function upgradeFrom1_0_9(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.10',
-  };
-}
-
-// Added in version 1.0.11:
-// - Changes to spatial layer coordination type names.
-// - Cell -> Obs, Gene -> Feature in coordination type names.
-export function upgradeFrom1_0_10(config) {
-  const coordinationSpace = { ...config.coordinationSpace };
-
-  const scopeAnalogies = {
-    // Spatial layer types
-    spatialRasterLayers: 'spatialImageLayer',
-    spatialCellsLayer: 'spatialSegmentationLayer',
-    spatialMoleculesLayer: 'spatialPointLayer',
-    spatialNeighborhoodsLayer: 'spatialNeighborhoodLayer',
-    // Other types
-    cellFilter: 'obsFilter',
-    cellHighlight: 'obsHighlight',
-    cellSelection: 'obsSelection',
-    cellSetSelection: 'obsSetSelection',
-    cellSetHighlight: 'obsSetHighlight',
-    cellSetColor: 'obsSetColor',
-    geneFilter: 'featureFilter',
-    geneHighlight: 'featureHighlight',
-    geneSelection: 'featureSelection',
-    geneExpressionColormap: 'featureValueColormap',
-    geneExpressionColormapRange: 'featureValueColormapRange',
-    cellColorEncoding: 'obsColorEncoding',
-    additionalCellSets: 'additionalObsSets',
-    embeddingCellSetPolygonsVisible: 'embeddingObsSetPolygonsVisible',
-    embeddingCellSetLabelsVisible: 'embeddingObsSetLabelsVisible',
-    embeddingCellSetLabelSize: 'embeddingObsSetLabelSize',
-    embeddingCellRadius: 'embeddingObsRadius',
-    embeddingCellRadiusMode: 'embeddingObsRadiusMode',
-    embeddingCellOpacity: 'embeddingObsOpacity',
-    embeddingCellOpacityMode: 'embeddingObsOpacityMode',
-  };
-
-  Object.entries(scopeAnalogies).forEach(([oldKey, newKey]) => {
-    if (coordinationSpace[oldKey]) {
-      coordinationSpace[newKey] = coordinationSpace[oldKey];
-      delete coordinationSpace[oldKey];
-    }
-  });
-
-  const layout = config.layout.map((component) => {
-    const newComponent = { ...component };
-    const { coordinationScopes = {} } = newComponent;
-
-    Object.entries(scopeAnalogies).forEach(([oldKey, newKey]) => {
-      if (coordinationScopes[oldKey]) {
-        coordinationScopes[newKey] = coordinationScopes[oldKey];
-        delete coordinationScopes[oldKey];
-      }
-    });
-
-    return {
-      ...newComponent,
-      coordinationScopes,
-    };
-  });
-
-  return {
-    ...config,
-    coordinationSpace,
-    layout,
-    version: '1.0.11',
-  };
-}
-
-// Added in version 1.0.12:
-// - Added a fileType-to-dataType mapping
-// so that datasets[].files[].type is no longer required.
-export function upgradeFrom1_0_11(config) {
-  const newConfig = cloneDeep(config);
-
-  const {
-    datasets,
-    coordinationSpace,
-  } = newConfig;
-
-  if (coordinationSpace.embeddingType) {
-    // This array may contain more embedding types than
-    // the cells.json file actually contains, but the tradeoff is that
-    // we do not have to load the cells.json file to double check what
-    // embedding types are actually present. CellsJsonAsObsEmbedding
-    // will just load the embedding as null if it is not present.
-    const embeddingTypes = Object.values(coordinationSpace.embeddingType);
-    datasets.forEach((dataset, i) => {
-      const { files } = dataset;
-      files.forEach((fileDef, j) => {
-        const { fileType } = fileDef;
-        if (fileType === 'cells.json') {
-          datasets[i].files[j].options = {
-            embeddingTypes,
-          };
-        }
-      });
-    });
-  }
-
-  return {
-    ...newConfig,
-    datasets,
-    version: '1.0.12',
-  };
-}
-
-// Added in version 1.0.13:
-// - Adds the property `coordinationValues` for
-// view config file definitions but is not yet
-// used to do file matching/lookups.
-export function upgradeFrom1_0_12(config) {
-  const newConfig = cloneDeep(config);
-
-  // Set up coordination scopes for anndata-cells.zarr's options.factors
-  // in the coordination space, and create a new coordinationScopes.obsLabelsType array
-  // for each component in the layout.
-  const { datasets, coordinationSpace, layout } = newConfig;
-  const datasetUidToObsLabelsTypeScopes = {};
-  datasets.forEach((dataset) => {
-    const { files, uid } = dataset;
-    files.forEach((fileDef) => {
-      const { fileType, options = {} } = fileDef;
-      if (fileType === 'anndata-cells.zarr') {
-        const { factors } = options;
-        if (factors) {
-          const obsLabelsTypeScopes = [];
-          factors.forEach((olt) => {
-            const nextScope = getNextScope(Object.keys(coordinationSpace?.obsLabelsType || {}));
-            coordinationSpace.obsLabelsType = {
-              ...coordinationSpace.obsLabelsType,
-              // Need to remove the obs/ prefix.
-              [nextScope]: olt.split('/').at(-1),
-            };
-            obsLabelsTypeScopes.push(nextScope);
-          });
-          datasetUidToObsLabelsTypeScopes[uid] = obsLabelsTypeScopes;
-        }
-      }
-    });
-  });
-  function getDatasetUidForView(viewDef) {
-    if (viewDef.coordinationScopes?.dataset) {
-      return coordinationSpace.dataset[viewDef.coordinationScopes.dataset];
-    }
-    if (datasets.length > 0) {
-      return datasets[0].uid;
-    }
-    return null;
-  }
-  const newLayout = layout.map((viewDef) => {
-    const viewDatasetUid = getDatasetUidForView(datasets, coordinationSpace, viewDef);
-    const datasetObsLabelsTypeScopes = datasetUidToObsLabelsTypeScopes[viewDatasetUid];
-    if (datasetObsLabelsTypeScopes) {
-      return {
-        ...viewDef,
-        coordinationScopes: {
-          ...viewDef.coordinationScopes,
-          obsLabelsType: datasetObsLabelsTypeScopes,
-        },
-      };
-    }
-    return viewDef;
-  });
-
-  return {
-    ...newConfig,
-    coordinationSpace,
-    layout: newLayout,
-    version: '1.0.13',
-  };
-}
-
-// Added in version 1.0.14:
-// - Adds the coordination types
-// gatingFeatureSelectionX,
-// gatingFeatureSelectionY,
-// featureValueTransformCoefficient.
-export function upgradeFrom1_0_13(config) {
-  const newConfig = cloneDeep(config);
-
-  return {
-    ...newConfig,
-    version: '1.0.14',
-  };
-}
-
-// Added in version 1.0.15:
-// - Changes the following view names:
-//   - genes -> featureList
-//   - cellSets -> obsSets
-//   - cellSetSizes -> obsSetSizes
-//   - cellSetExpression -> obsSetFeatureValueDistribution
-//   - expressionHistogram -> featureValueHistogram
-// - Deprecates the props:
-//   - variablesLabelOverride
-//   - observationsLabelOverride
-export function upgradeFrom1_0_14(config) {
-  const newConfig = cloneDeep(config);
-  const { layout } = newConfig;
-
-  const viewTypeAnalogies = {
-    genes: 'featureList',
-    cellSets: 'obsSets',
-    cellSetSizes: 'obsSetSizes',
-    cellSetExpression: 'obsSetFeatureValueDistribution',
-    expressionHistogram: 'featureValueHistogram',
-  };
-  // Handle the view type renaming.
-  const newLayout = layout.map((viewDef) => {
-    // Replace the old component name with the new one.
-    if (viewTypeAnalogies[viewDef.component]) {
-      return {
-        ...viewDef,
-        component: viewTypeAnalogies[viewDef.component],
-      };
-    }
-    return viewDef;
-  });
-  const propAnalogies = {
-    variablesLabelOverride: 'featureType',
-    observationsLabelOverride: 'obsType',
-  };
-  // Warn about the prop usage.
-  newLayout.forEach((viewDef) => {
-    // Iterate over each old prop key.
-    Object.entries(propAnalogies).forEach(([oldProp, newType]) => {
-      if (viewDef.props?.[oldProp]) {
-        console.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
-      }
-    });
-  });
-  return {
-    ...newConfig,
-    version: '1.0.15',
-    layout: newLayout,
-  };
-}
-
-// Added in version 1.0.16:
-// - Explict coordinationScopesBy property for view definitions,
-// to replace the previous implicit mapping of per-dataset coordination
-// scopes.
-export function upgradeFrom1_0_15(config) {
-  const newConfig = cloneDeep(config);
-
-  const { layout } = newConfig;
-  const newLayout = layout.map((view) => {
-    const { coordinationScopes = {} } = view;
-    if (coordinationScopes.dataset && Array.isArray(coordinationScopes.dataset)) {
-      const coordinationScopesBy = {
-        dataset: {},
-      };
-      Object.entries(coordinationScopes).forEach(([coordinationType, coordinationScope]) => {
-        if (coordinationType !== 'dataset' && !Array.isArray(coordinationScope) && typeof coordinationScope === 'object') {
-          coordinationScopesBy.dataset[coordinationType] = coordinationScope;
-          delete coordinationScopes[coordinationType];
-        }
-      });
-      return {
-        ...view,
-        coordinationScopes,
-        coordinationScopesBy,
-      };
-    }
-    return view;
-  });
-
-  return {
-    ...newConfig,
-    layout: newLayout,
-    version: '1.0.16',
-  };
-}