@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

package/dist/view-config-upgraders.js

@@ -1,525 +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,
-    };
-}