@vitessce/config 2.0.3-beta.0 → 3.0.0

package/src/VitessceAutoConfig.test.js

@@ -0,0 +1,465 @@
+import { generateConfigs } from './VitessceAutoConfig.js';
+
+describe('src/VitessceAutoConfig.js', () => {
+  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.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: expectedName,
+          files: [
+            {
+              fileType: 'raster.json',
+              options: {
+                images: [
+                  {
+                    metadata: {
+                      isBitmask: false,
+                    },
+                    name: expectedName,
+                    type: 'ome-tiff',
+                    url: urls[0],
+                  },
+                ],
+                schemaVersion: '0.0.2',
+                usePhysicalSizeScaling: false,
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+      },
+      layout: [
+        {
+          component: 'description',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 6,
+          y: 0,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 6,
+          w: 6,
+          h: 6,
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
+          },
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const config = await generateConfigs(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.',
+      description: 'Populate with text relevant to this visualisation.',
+      datasets: [
+        {
+          uid: 'A',
+          name: expectedName,
+          files: [
+            {
+              url: urls[0],
+              fileType: 'raster.ome-zarr',
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+      },
+      layout: [
+        {
+          component: 'description',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 6,
+          y: 0,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 6,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'status',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 6,
+          y: 6,
+          w: 6,
+          h: 6,
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const config = await generateConfigs(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 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: expectedName,
+          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/cell_type',
+                      'obs/disease',
+                      'obs/leiden',
+                      'obs/organism',
+                      'obs/self_reported_ethnicity',
+                      'obs/sex',
+                      'obs/tissue'],
+                  },
+                ],
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+        embeddingType: {
+          A: 'UMAP',
+        },
+      },
+      layout: [
+        {
+          component: 'obsSets',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'scatterplot',
+          coordinationScopes: {
+            dataset: 'A',
+            embeddingType: 'A',
+          },
+          x: 6,
+          y: 0,
+          w: 6,
+          h: 6,
+        },
+        {
+          component: 'heatmap',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 6,
+          w: 6,
+          h: 6,
+          props: {
+            transpose: true,
+          },
+        },
+        {
+          component: 'featureList',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 6,
+          y: 6,
+          w: 6,
+          h: 6,
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const config = await generateConfigs(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);
+    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: expectedName,
+          files: [
+            {
+              url: urls[0],
+              fileType: 'anndata.zarr',
+              coordinationValues: {
+                obsType: 'cell',
+                featureType: 'gene',
+                featureValueType: 'expression',
+              },
+              options: {
+                obsEmbedding: [],
+                obsFeatureMatrix: {
+                  path: 'X',
+                },
+              },
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+        },
+      },
+      layout: [],
+      initStrategy: 'auto',
+    };
+
+    const config = await generateConfigs(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.'),
+    );
+  });
+
+  it('generates config for multiple files correctly', async () => {
+    const urls = ['somefile.ome.tif', 'anoterfile.ome.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: expectedNames[0],
+          files: [
+            {
+              fileType: 'raster.json',
+              options: {
+                images: [
+                  {
+                    metadata: {
+                      isBitmask: false,
+                    },
+                    name: expectedNames[0],
+                    type: 'ome-tiff',
+                    url: urls[0],
+                  },
+                ],
+                schemaVersion: '0.0.2',
+                usePhysicalSizeScaling: false,
+              },
+            },
+          ],
+        },
+        {
+          uid: 'B',
+          name: expectedNames[1],
+          files: [
+            {
+              url: urls[1],
+              fileType: 'raster.ome-zarr',
+            },
+          ],
+        },
+      ],
+      coordinationSpace: {
+        dataset: {
+          A: 'A',
+          B: 'B',
+        },
+      },
+      layout: [
+        {
+          component: 'description',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 0,
+          y: 0,
+          w: 4,
+          h: 4,
+        },
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 4,
+          y: 0,
+          w: 4,
+          h: 4,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+          },
+          x: 8,
+          y: 0,
+          w: 4,
+          h: 4,
+          props: {
+            disable3d: [],
+            disableChannelsIfRgbDetected: true,
+          },
+        },
+        {
+          component: 'description',
+          coordinationScopes: {
+            dataset: 'B',
+          },
+          x: 0,
+          y: 4,
+          w: 4,
+          h: 4,
+        },
+        {
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'B',
+          },
+          x: 4,
+          y: 4,
+          w: 4,
+          h: 4,
+        },
+        {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'B',
+          },
+          x: 8,
+          y: 4,
+          w: 4,
+          h: 4,
+        },
+        {
+          component: 'status',
+          coordinationScopes: {
+            dataset: 'B',
+          },
+          x: 0,
+          y: 8,
+          w: 4,
+          h: 4,
+        },
+      ],
+      initStrategy: 'auto',
+    };
+
+    const config = await generateConfigs(urls);
+    expect(config).toEqual(expectedConfig);
+  });
+
+
+  it('raises an Error when .zmetadata file not present in folder', async () => {
+    const urls = ['http://localhost:51204/@fixtures/zarr/partials/invalid.adata.zarr'];
+
+    await generateConfigs(urls).catch(
+      e => expect(e.message).toContain('Could not generate config. File .zmetadata not found in supplied file URL'),
+    );
+  });
+
+  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'];
+
+    await generateConfigs(urls).catch(
+      e => expect(e.message).toContain('This file type is not supported.'),
+    );
+  });
+});