@vitessce/config 3.0.0 → 3.1.0

package/src/VitessceAutoConfig.test.js

@@ -1,9 +1,10 @@
-import { generateConfigs } from './VitessceAutoConfig.js';
+import { describe, it, expect } from 'vitest';
+import { generateConfig, getHintOptions } from './VitessceAutoConfig.js';
+import { HINT_TYPE_TO_FILE_TYPE_MAP } from './constants.js';
 
-describe('src/VitessceAutoConfig.js', () => {
+describe('generateConfig', () => {
   it('generates config for OME-TIFF file correctly', async () => {
     const urls = ['somefile.ome.tif'];
-    const expectedName = urls[0].split('/').at(-1);
     const expectedConfig = {
       version: '1.0.15',
       name: 'An automatically generated config. Adjust values and add layout components if needed.',
@@ -11,7 +12,7 @@ describe('src/VitessceAutoConfig.js', () => {
       datasets: [
         {
           uid: 'A',
-          name: expectedName,
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
           files: [
             {
               fileType: 'raster.json',
@@ -21,7 +22,7 @@ describe('src/VitessceAutoConfig.js', () => {
                     metadata: {
                       isBitmask: false,
                     },
-                    name: expectedName,
+                    name: 'somefile.ome.tif',
                     type: 'ome-tiff',
                     url: urls[0],
                   },
@@ -77,13 +78,12 @@ describe('src/VitessceAutoConfig.js', () => {
       initStrategy: 'auto',
     };
 
-    const config = await generateConfigs(urls);
+    const config = await generateConfig(urls);
     expect(config).toEqual(expectedConfig);
   });
 
   it('generates config for OME-ZARR file correctly', async () => {
     const urls = ['anotherfile.ome.zarr'];
-    const expectedName = urls[0].split('/').at(-1);
     const expectedConfig = {
       version: '1.0.15',
       name: 'An automatically generated config. Adjust values and add layout components if needed.',
@@ -91,7 +91,7 @@ describe('src/VitessceAutoConfig.js', () => {
       datasets: [
         {
           uid: 'A',
-          name: expectedName,
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
           files: [
             {
               url: urls[0],
@@ -135,28 +135,21 @@ describe('src/VitessceAutoConfig.js', () => {
           y: 6,
           w: 6,
           h: 6,
-        },
-        {
-          component: 'status',
-          coordinationScopes: {
-            dataset: 'A',
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
           },
-          x: 6,
-          y: 6,
-          w: 6,
-          h: 6,
         },
       ],
       initStrategy: 'auto',
     };
 
-    const config = await generateConfigs(urls);
+    const config = await generateConfig(urls);
     expect(config).toEqual(expectedConfig);
   });
 
   it('generates config for Anndata-ZARR file correctly', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/.anndata.zarr'];
-    const expectedName = urls[0].split('/').at(-1);
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
     const expectedConfig = {
       version: '1.0.15',
       name: 'An automatically generated config. Adjust values and add layout components if needed.',
@@ -164,7 +157,7 @@ describe('src/VitessceAutoConfig.js', () => {
       datasets: [
         {
           uid: 'A',
-          name: expectedName,
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
           files: [
             {
               url: urls[0],
@@ -219,7 +212,7 @@ describe('src/VitessceAutoConfig.js', () => {
           x: 0,
           y: 0,
           w: 6,
-          h: 6,
+          h: 4,
         },
         {
           component: 'scatterplot',
@@ -230,7 +223,27 @@ describe('src/VitessceAutoConfig.js', () => {
           x: 6,
           y: 0,
           w: 6,
-          h: 6,
+          h: 4,
+        },
+        {
+          component: 'obsSetSizes',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 4,
+          w: 6,
+          x: 0,
+          y: 4,
+        },
+        {
+          component: 'obsSetFeatureValueDistribution',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 4,
+          w: 6,
+          x: 6,
+          y: 4,
         },
         {
           component: 'heatmap',
@@ -238,9 +251,9 @@ describe('src/VitessceAutoConfig.js', () => {
             dataset: 'A',
           },
           x: 0,
-          y: 6,
+          y: 8,
           w: 6,
-          h: 6,
+          h: 4,
           props: {
             transpose: true,
           },
@@ -251,21 +264,20 @@ describe('src/VitessceAutoConfig.js', () => {
             dataset: 'A',
           },
           x: 6,
-          y: 6,
+          y: 8,
           w: 6,
-          h: 6,
+          h: 4,
         },
       ],
       initStrategy: 'auto',
     };
 
-    const config = await generateConfigs(urls);
+    const config = await generateConfig(urls);
     expect(config).toEqual(expectedConfig);
   });
 
-  it('generates empty config for Anndata-ZARR file with empty .zmetadata', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/emptymeta.h5ad.zarr'];
-    const expectedName = urls[0].split('/').at(-1);
+  it('generates correct config for Anndata-ZARR file with empty .zmetadata', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/emptymeta.h5ad.zarr'];
     const expectedConfig = {
       version: '1.0.15',
       name: 'An automatically generated config. Adjust values and add layout components if needed.',
@@ -273,7 +285,7 @@ describe('src/VitessceAutoConfig.js', () => {
       datasets: [
         {
           uid: 'A',
-          name: expectedName,
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
           files: [
             {
               url: urls[0],
@@ -298,20 +310,43 @@ describe('src/VitessceAutoConfig.js', () => {
           A: 'A',
         },
       },
-      layout: [],
+      layout: [
+        {
+          component: 'obsSetSizes',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 6,
+          w: 12,
+          x: 0,
+          y: 0,
+        },
+        {
+          component: 'obsSetFeatureValueDistribution',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 6,
+          w: 12,
+          x: 0,
+          y: 6,
+        },
+      ],
       initStrategy: 'auto',
     };
 
-    const config = await generateConfigs(urls);
+    const config = await generateConfig(urls);
     expect(config).toEqual(expectedConfig);
   });
 
   it('raises an error for Anndata-ZARR file with misconfigured .zmetadata', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalidmeta.adata.zarr'];
-
-    await generateConfigs(urls).catch(
-      e => expect(e.message).toContain('Could not generate config: .zmetadata file is not valid.'),
-    );
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/invalidmeta.adata.zarr'];
+    // References:
+    // - https://vitest.dev/api/expect.html#tothrowerror
+    // - https://vitest.dev/api/expect.html#rejects
+    await expect(() => generateConfig(urls))
+      .rejects
+      .toThrowError('Could not generate config: .zmetadata file is not valid.');
   });
 
   it('generates config for multiple files correctly', async () => {
@@ -325,7 +360,7 @@ describe('src/VitessceAutoConfig.js', () => {
       datasets: [
         {
           uid: 'A',
-          name: expectedNames[0],
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
           files: [
             {
               fileType: 'raster.json',
@@ -344,12 +379,6 @@ describe('src/VitessceAutoConfig.js', () => {
                 usePhysicalSizeScaling: false,
               },
             },
-          ],
-        },
-        {
-          uid: 'B',
-          name: expectedNames[1],
-          files: [
             {
               url: urls[1],
               fileType: 'raster.ome-zarr',
@@ -360,7 +389,6 @@ describe('src/VitessceAutoConfig.js', () => {
       coordinationSpace: {
         dataset: {
           A: 'A',
-          B: 'B',
         },
       },
       layout: [
@@ -371,7 +399,7 @@ describe('src/VitessceAutoConfig.js', () => {
           },
           x: 0,
           y: 0,
-          w: 4,
+          w: 6,
           h: 4,
         },
         {
@@ -379,9 +407,9 @@ describe('src/VitessceAutoConfig.js', () => {
           coordinationScopes: {
             dataset: 'A',
           },
-          x: 4,
+          x: 6,
           y: 0,
-          w: 4,
+          w: 6,
           h: 4,
         },
         {
@@ -389,9 +417,9 @@ describe('src/VitessceAutoConfig.js', () => {
           coordinationScopes: {
             dataset: 'A',
           },
-          x: 8,
-          y: 0,
-          w: 4,
+          x: 0,
+          y: 4,
+          w: 6,
           h: 4,
           props: {
             disable3d: [],
@@ -401,65 +429,587 @@ describe('src/VitessceAutoConfig.js', () => {
         {
           component: 'description',
           coordinationScopes: {
-            dataset: 'B',
+            dataset: 'A',
           },
-          x: 0,
+          x: 6,
           y: 4,
-          w: 4,
+          w: 6,
           h: 4,
         },
         {
           component: 'spatial',
           coordinationScopes: {
-            dataset: 'B',
+            dataset: 'A',
           },
-          x: 4,
-          y: 4,
-          w: 4,
+          x: 0,
+          y: 8,
+          w: 6,
           h: 4,
         },
         {
           component: 'layerController',
           coordinationScopes: {
-            dataset: 'B',
+            dataset: 'A',
           },
-          x: 8,
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
+          },
+          x: 6,
+          y: 8,
+          w: 6,
+          h: 4,
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const config = await generateConfig(urls);
+    expect(config).toEqual(expectedConfig);
+  });
+
+
+  it('Does the parsing when .zmetadata file not present in folder', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/anndata-0.8/anndata-csr.adata.zarr'];
+    const expectedConfig = {
+      version: '1.0.15',
+      name: 'An automatically generated config. Adjust values and add layout components if needed.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
+          files: [
+            {
+              url: urls[0],
+              fileType: 'anndata.zarr',
+              coordinationValues: {
+                obsType: 'cell',
+                featureType: 'gene',
+                featureValueType: 'expression',
+              },
+              options: {
+                obsEmbedding: [
+                  {
+                    path: 'obsm/X_umap',
+                    embeddingType: 'UMAP',
+                  },
+                ],
+                obsFeatureMatrix: {
+                  path: 'X',
+                },
+                obsSets: [
+                  {
+                    name: 'Cell Type',
+                    path: 'obs/leiden',
+                  },
+                ],
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+        embeddingType: {
+          A: 'UMAP',
+        },
+      },
+      layout: [
+        {
+          component: 'scatterplot',
+          coordinationScopes: {
+            dataset: 'A',
+            embeddingType: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 6,
+          h: 4,
+        },
+        {
+          component: 'obsSetSizes',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 4,
+          w: 6,
+          x: 6,
+          y: 0,
+        },
+        {
+          component: 'obsSetFeatureValueDistribution',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 4,
+          w: 6,
+          x: 0,
           y: 4,
-          w: 4,
+        },
+        {
+          component: 'heatmap',
+          coordinationScopes: {
+            dataset: 'A',
+          },
           h: 4,
+          props: {
+            transpose: true,
+          },
+          w: 6,
+          x: 6,
+          y: 4,
         },
         {
-          component: 'status',
+          component: 'featureList',
           coordinationScopes: {
-            dataset: 'B',
+            dataset: 'A',
           },
+          h: 4,
+          w: 6,
           x: 0,
           y: 8,
-          w: 4,
-          h: 4,
         },
       ],
       initStrategy: 'auto',
     };
 
-    const config = await generateConfigs(urls);
+    const config = await generateConfig(urls);
     expect(config).toEqual(expectedConfig);
   });
 
+  it('raises an error when URL with unsupported file format is passed', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/anndata-0.7/somefile.zarr'];
+
+    await generateConfig(urls, 'Transcriptomics / scRNA-seq (with heatmap)').catch(
+      e => expect(e.message).toContain('One or more of the URLs provided point to unsupported file types.'),
+    );
+  });
+
+  // ********** TESTS WITH HINTS **********
+
+  it('generates config with hints for OME-TIFF dataset types correctly', async () => {
+    const urls = ['somefile.ome.tif'];
+    const expectedConfig = {
+      version: '1.0.15',
+      name: 'An automatically generated config. Adjust values and add layout components if needed.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
+          files: [
+            {
+              fileType: 'raster.json',
+              options: {
+                images: [
+                  {
+                    metadata: {
+                      isBitmask: false,
+                    },
+                    name: 'somefile.ome.tif',
+                    type: 'ome-tiff',
+                    url: urls[0],
+                  },
+                ],
+                schemaVersion: '0.0.2',
+                usePhysicalSizeScaling: false,
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+      },
+      layout: [
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 8,
+          h: 12,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 8,
+          y: 0,
+          w: 4,
+          h: 7,
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
+          },
+        },
+        {
+          component: 'description',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 5,
+          w: 4,
+          x: 8,
+          y: 9,
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const viewConfig = await generateConfig(urls, 'Image');
+    expect(viewConfig).toEqual(expectedConfig);
+  });
+
+  it('generates config with hints for OME-ZARR dataset types correctly', async () => {
+    const urls = ['somefile.ome.zarr'];
 
-  it('raises an Error when .zmetadata file not present in folder', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalid.adata.zarr'];
+    const expectedConfig = {
+      version: '1.0.15',
+      name: 'An automatically generated config. Adjust values and add layout components if needed.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
+          files: [
+            {
+              fileType: 'raster.ome-zarr',
+              url: 'somefile.ome.zarr',
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+      },
+      layout: [
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 8,
+          h: 12,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 8,
+          y: 0,
+          w: 4,
+          h: 7,
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
+          },
+        },
+        {
+          component: 'description',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 5,
+          w: 4,
+          x: 8,
+          y: 9,
+        },
+      ],
+      initStrategy: 'auto',
+    };
 
-    await generateConfigs(urls).catch(
-      e => expect(e.message).toContain('Could not generate config. File .zmetadata not found in supplied file URL'),
+    const viewConfig = await generateConfig(urls, 'Image');
+    expect(viewConfig).toEqual(expectedConfig);
+  });
+
+  it('generates config hints for Anndata-Zarr, OME-TIFF dataset types correctly', async () => {
+    const urls = ['somefile.ome.tif', 'http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
+    const expectedNames = [urls[0].split('/').at(-1), urls[1].split('/').at(-1)];
+
+    const expectedConfig = {
+      version: '1.0.15',
+      name: 'An automatically generated config. Adjust values and add layout components if needed.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: 'An automatically generated view config for dataset. Adjust values and add layout components if needed.',
+          files: [
+            {
+              fileType: 'raster.json',
+              options: {
+                images: [
+                  {
+                    metadata: {
+                      isBitmask: false,
+                    },
+                    name: expectedNames[0],
+                    type: 'ome-tiff',
+                    url: urls[0],
+                  },
+                ],
+                schemaVersion: '0.0.2',
+                usePhysicalSizeScaling: false,
+              },
+            },
+            {
+              url: urls[1],
+              coordinationValues: {
+                featureType: 'gene',
+                featureValueType: 'expression',
+                obsType: 'cell',
+              },
+              fileType: 'anndata.zarr',
+              options: {
+                obsFeatureMatrix: {
+                  path: 'X',
+                },
+                obsEmbedding: [
+                  {
+                    embeddingType: 'UMAP',
+                    path: 'obsm/X_umap',
+                  },
+                ],
+                obsSets: [
+                  {
+                    name: 'Cell Type',
+                    path: [
+                      'obs/cell_type',
+                      'obs/disease',
+                      'obs/leiden',
+                      'obs/organism',
+                      'obs/self_reported_ethnicity',
+                      'obs/sex',
+                      'obs/tissue',
+                    ],
+                  },
+                ],
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+        spatialSegmentationLayer: {
+          A: {
+            radius: 65,
+            stroked: true,
+            visible: true,
+            opacity: 1,
+          },
+        },
+        spatialImageLayer: {
+          A: [
+            {
+              type: 'raster',
+              index: 0,
+              colormap: null,
+              transparentColor: null,
+              opacity: 1,
+              domainType: 'Min/Max',
+              channels: [
+                {
+                  selection: {
+                    c: 0,
+                  },
+                  color: [
+                    255,
+                    0,
+                    0,
+                  ],
+                  visible: true,
+                  slider: [
+                    0,
+                    255,
+                  ],
+                },
+                {
+                  selection: {
+                    c: 1,
+                  },
+                  color: [
+                    0,
+                    255,
+                    0,
+                  ],
+                  visible: true,
+                  slider: [
+                    0,
+                    255,
+                  ],
+                },
+                {
+                  selection: {
+                    c: 2,
+                  },
+                  color: [
+                    0,
+                    0,
+                    255,
+                  ],
+                  visible: true,
+                  slider: [
+                    0,
+                    255,
+                  ],
+                },
+              ],
+            },
+          ],
+        },
+        spatialZoom: {
+          A: null,
+        },
+        spatialTargetX: {
+          A: null,
+        },
+        spatialTargetY: {
+          A: null,
+        },
+      },
+      layout: [
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+            spatialImageLayer: 'A',
+            spatialSegmentationLayer: 'A',
+            spatialTargetX: 'A',
+            spatialTargetY: 'A',
+            spatialZoom: 'A',
+          },
+          h: 6,
+          w: 6,
+          x: 0,
+          y: 0,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+            spatialImageLayer: 'A',
+            spatialSegmentationLayer: 'A',
+            spatialTargetX: 'A',
+            spatialTargetY: 'A',
+            spatialZoom: 'A',
+          },
+          h: 6,
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
+          },
+          w: 4,
+          x: 8,
+          y: 6,
+        },
+        {
+          component: 'heatmap',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 6,
+          w: 8,
+          h: 6,
+          props: {
+            transpose: true,
+          },
+        },
+        {
+          component: 'obsSets',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 9,
+          y: 0,
+          w: 3,
+          h: 6,
+        },
+        {
+          component: 'featureList',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          h: 6,
+          w: 3,
+          x: 6,
+          y: 0,
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const viewConfig = await generateConfig(
+      urls,
+      'Spatial transcriptomics (with histology image and polygon cell segmentations)',
+    );
+
+    expect(viewConfig).toEqual(expectedConfig);
+  });
+
+  it('raises an error if the supplied dataset URLs and hint do not have any compatible views', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
+    const hint = 'Image';
+
+    await generateConfig(urls, hint).catch(
+      e => expect(e.message).toContain('No views found that are compatible with the supplied dataset URLs and hint.'),
     );
   });
 
-  it('raises an error when URL with unsupported file format is passed', async () => {
-    const urls = ['http://localhost:51204/@fixtures/zarr/anndata-0.7/somefile.zarr'];
+  it('raises an error if no views are found for the supplied hint string', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
+    const hint = 'I do not exist';
 
-    await generateConfigs(urls).catch(
-      e => expect(e.message).toContain('This file type is not supported.'),
+    await generateConfig(urls, hint).catch(
+      e => expect(e.message).toContain('Hints config not found for the supplied hint: I do not exist'),
     );
   });
+
+  // ********** TESTS OF GET HINTS OPTIONS **********
+
+  it('returns a list of hints options for the supplied dataset URLs', async () => {
+    const urls = ['http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr'];
+    const actualHintOptions = getHintOptions(urls);
+
+    expect(actualHintOptions).toEqual(HINT_TYPE_TO_FILE_TYPE_MAP['AnnData-Zarr']);
+  });
+
+  it('returns a list of hints options for the supplied dataset URLs', async () => {
+    const urls = [
+      'http://localhost:4204/@fixtures/zarr/partials/.anndata.zarr',
+      'somefile.ome.zarr',
+      'http://localhost:4204/@fixtures/zarr/partials/.adata.zarr',
+      'somefile.ome.tiff',
+    ];
+    const actualHintOptions = getHintOptions(urls);
+
+    expect(actualHintOptions).toEqual(HINT_TYPE_TO_FILE_TYPE_MAP['AnnData-Zarr,OME-TIFF']);
+  });
+
+  it('raises an error if no hints options are found for the supplied dataset URLs', async () => {
+    const urls = ['unsupportedfiletype.txt', 'unsupportedfiletype2.ome.tiff'];
+
+    try {
+      getHintOptions(urls);
+    } catch (e) {
+      expect(e.message).toContain('One or more of the URLs provided point to unsupported file types.');
+    }
+  });
 });