Fix types (#454)

src/ensembl/src/content/app/browser/track-panel/track-panel-list/TrackPanelList.test.tsx

@@ -41,8 +41,7 @@ describe('<TrackPanelList />', () => {
     activeEnsObject: createEnsObject(),
     selectedTrackPanelTab: TrackSet.GENOMIC,
     genomeTrackCategories: createGenomeCategories(),
-    trackStates: createTrackStates(),
-    toggleDrawer: jest.fn()
+    trackStates: createTrackStates()
   };
 
   const mountTrackPanelList = (props?: Partial<TrackPanelListProps>) =>

src/ensembl/src/content/app/entity-viewer/gene-view/components/transcripts-filter/TranscriptsFilter.test.tsx

@@ -88,7 +88,7 @@ const wrapInRedux = (
   return mount(
     <Provider store={store}>
       <TranscriptsFilter
-        filterLabel={filterLabel}
+        label={filterLabel}
         transcripts={transcripts}
         toggleFilter={mockToggleFilter}
       />

src/ensembl/tests/fixtures/ens-object.ts

@@ -20,7 +20,7 @@ import {
   EnsObject,
   EnsObjectType
 } from 'src/shared/state/ens-object/ensObjectTypes';
-import { Strand } from 'src/content/app/entity-viewer/types/strand';
+import { Strand } from 'src/shared/types/thoas/strand';
 
 export const createEnsObject = (objectType?: EnsObjectType): EnsObject => {
   const genome_id = faker.lorem.word();
@@ -57,5 +57,6 @@ const createTrackInfo = () => ({
   object_id: faker.lorem.word(),
   support_level: null,
   track_id: faker.lorem.word(),
-  description: null
+  description: null,
+  stable_id: faker.lorem.words()
 });

src/ensembl/tests/fixtures/entity-viewer/gene.ts

@@ -21,7 +21,7 @@ import { scaleLinear } from 'd3';
 import { createSlice } from './slice';
 import { createTranscript } from './transcript';
 
-import { Gene } from 'src/content/app/entity-viewer/types/gene';
+import { Gene } from 'src/shared/types/thoas/gene';
 import { TicksAndScale } from 'src/content/app/entity-viewer/gene-view/components/base-pairs-ruler/BasePairsRuler';
 
 export const createGene = (fragment: Partial<Gene> = {}): Gene => {

src/ensembl/tests/fixtures/entity-viewer/product.ts

@@ -21,7 +21,7 @@ import {
   ProteinDomain,
   Product,
   ProductType
-} from 'src/content/app/entity-viewer/types/product';
+} from 'src/shared/types/thoas/product';
 
 export const createProduct = (fragment: Partial<Product> = {}): Product => {
   const length = fragment?.length || faker.random.number({ min: 10, max: 100 });

src/ensembl/tests/fixtures/entity-viewer/slice.ts

@@ -16,8 +16,8 @@
 
 import faker from 'faker';
 
-import { Slice } from 'src/content/app/entity-viewer/types/slice';
-import { Strand } from 'src/content/app/entity-viewer/types/strand';
+import { Slice } from 'src/shared/types/thoas/slice';
+import { Strand } from 'src/shared/types/thoas/strand';
 
 export const createSlice = (): Slice => {
   const start = faker.random.number({ min: 1, max: 1000000 });

src/ensembl/tests/fixtures/entity-viewer/transcript.ts

@@ -21,17 +21,14 @@ import { createSlice } from './slice';
 import { createProduct } from './product';
 import { getFeatureCoordinates } from 'src/content/app/entity-viewer/shared/helpers/entity-helpers';
 
-import { Transcript } from 'src/content/app/entity-viewer/types/transcript';
-import {
-  Exon,
-  SplicedExon,
-  PhasedExon
-} from 'src/content/app/entity-viewer/types/exon';
-import { Slice } from 'src/content/app/entity-viewer/types/slice';
-import { CDS } from 'src/content/app/entity-viewer/types/cds';
-import { CDNA } from 'src/content/app/entity-viewer/types/cdna';
-import { ProductGeneratingContext } from 'src/content/app/entity-viewer/types/productGeneratingContext';
-import { ProductType } from 'src/content/app/entity-viewer/types/product';
+import { Transcript } from 'src/shared/types/thoas/transcript';
+import { Exon, SplicedExon, PhasedExon } from 'src/shared/types/thoas/exon';
+import { Slice } from 'src/shared/types/thoas/slice';
+import { CDS } from 'src/shared/types/thoas/cds';
+import { CDNA } from 'src/shared/types/thoas/cdna';
+import { ProductGeneratingContext } from 'src/shared/types/thoas/productGeneratingContext';
+import { ProductType } from 'src/shared/types/thoas/product';
+import { ExternalReference } from 'src/shared/types/thoas/externalReference';
 
 export const createTranscript = (
   fragment: Partial<Transcript> = {}
@@ -51,6 +48,7 @@ export const createTranscript = (
     symbol: faker.lorem.word(),
     so_term: faker.lorem.word(),
     slice: transcriptSlice,
+    external_references: createExternalReferences(),
     relative_location: {
       start: 1,
       end: transcriptSlice.location.end,
@@ -64,6 +62,24 @@ export const createTranscript = (
   };
 };
 
+const createExternalReferences = (): ExternalReference[] => {
+  const numberOfExternalReferences = faker.random.number({ min: 1, max: 10 });
+
+  return times(numberOfExternalReferences, () => {
+    return {
+      accession_id: faker.random.uuid(),
+      name: faker.random.words(),
+      description: faker.random.words(),
+      url: faker.internet.url(),
+      source: {
+        name: faker.random.words(),
+        id: faker.random.uuid(),
+        url: faker.internet.url()
+      }
+    };
+  });
+};
+
 const createSplicedExons = (
   transcriptSlice: Slice,
   exons: Exon[]

src/ensembl/tests/fixtures/genomes.ts

+/**
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 import faker from 'faker';
 import times from 'lodash/times';
 
@@ -21,7 +37,8 @@ export const createGenomeCategories = (): GenomeTrackCategory[] => [
       {
         description: faker.lorem.words(),
         label: faker.lorem.words(),
-        track_id: faker.lorem.words()
+        track_id: faker.lorem.words(),
+        stable_id: faker.lorem.words()
       }
     ],
     types: [TrackSet.VARIATION]

src/ensembl/tests/fixtures/track-panel.ts

+/**
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 import faker from 'faker';
 
 import { Status } from 'src/shared/types/status';
@@ -17,7 +33,8 @@ export const createTrackInfo = (): EnsObjectTrack => ({
   additional_info: faker.lorem.words(),
   description: faker.lorem.words(),
   label: faker.lorem.words(),
-  track_id: 'gene-pc-fwd'
+  track_id: 'gene-pc-fwd',
+  stable_id: faker.lorem.words()
 });
 
 export const createMainTrackInfo = (): EnsObjectTrack => ({
@@ -29,11 +46,13 @@ export const createMainTrackInfo = (): EnsObjectTrack => ({
       description: faker.lorem.words(),
       label: faker.lorem.words(),
       support_level: faker.lorem.words(),
-      track_id: 'gene-feat-1'
+      track_id: 'gene-feat-1',
+      stable_id: faker.lorem.words()
     }
   ],
   description: faker.lorem.words(),
   ensembl_object_id: faker.lorem.words(),
   label: faker.lorem.words(),
-  track_id: 'gene-feat'
+  track_id: 'gene-feat',
+  stable_id: faker.lorem.words()
 });