Use sequence field instead of sequence_checksum in payloads from Thoas (#537)

* ENSWBSITES-1160: update sequence payload from sequence_checksum to sequence.checksum
* make sequence type mandatory and updated test

src/ensembl/src/shared/components/instant-download/instant-download-fetch/fetchSequenceChecksums.ts

@@ -18,6 +18,8 @@ import { gql } from '@apollo/client';
 
 import { client } from 'src/gql-client';
 
+import { Sequence } from 'ensemblRoot/src/shared/types/thoas/sequence';
+
 export type TranscriptSequenceMetadata = {
   stable_id: string;
   unversioned_stable_id: string;
@@ -46,14 +48,14 @@ type TranscriptInResponse = {
   unversioned_stable_id: string;
   product_generating_contexts: Array<{
     cdna: {
-      sequence_checksum: string;
+      sequence: Sequence;
     };
     cds: {
-      sequence_checksum: string;
+      sequence: Sequence;
     };
     product: {
       stable_id: string;
-      sequence_checksum: string;
+      sequence: Sequence;
     };
   }>;
 };
@@ -87,14 +89,20 @@ const transcriptChecksumsQuery = gql`
       unversioned_stable_id
       product_generating_contexts {
         cds {
-          sequence_checksum
+          sequence {
+            checksum
+          }
         }
         cdna {
-          sequence_checksum
+          sequence {
+            checksum
+          }
         }
         product {
           stable_id
-          sequence_checksum
+          sequence {
+            checksum
+          }
         }
       }
     }
@@ -120,14 +128,20 @@ const geneChecksumsQuery = gql`
         unversioned_stable_id
         product_generating_contexts {
           cds {
-            sequence_checksum
+            sequence {
+              checksum
+            }
           }
           cdna {
-            sequence_checksum
+            sequence {
+              checksum
+            }
           }
           product {
             stable_id
-            sequence_checksum
+            sequence {
+              checksum
+            }
           }
         }
       }
@@ -151,15 +165,15 @@ const processTranscriptData = (transcript: TranscriptInResponse) => {
     stable_id,
     unversioned_stable_id,
     cdna: {
-      checksum: productGeneratingContext.cdna.sequence_checksum,
+      checksum: productGeneratingContext.cdna.sequence.checksum,
       label: `${stable_id} cdna`
     },
     cds: {
-      checksum: productGeneratingContext.cds.sequence_checksum,
+      checksum: productGeneratingContext.cds.sequence.checksum,
       label: `${stable_id} cds`
     },
     protein: {
-      checksum: productGeneratingContext.product.sequence_checksum,
+      checksum: productGeneratingContext.product.sequence.checksum,
       label: `${productGeneratingContext.product.stable_id} pep`
     }
   };

src/ensembl/src/shared/types/thoas/cdna.ts

@@ -14,9 +14,11 @@
  * limitations under the License.
  */
 
+import { Sequence } from './sequence';
+
 export type CDNA = {
   start: number;
   end: number;
   length: number;
-  sequence_checksum?: string;
+  sequence: Sequence;
 };

src/ensembl/src/shared/types/thoas/cds.ts

@@ -14,6 +14,8 @@
  * limitations under the License.
  */
 
+import { Sequence } from './sequence';
+
 export type FullCDS = {
   start: number;
   end: number;
@@ -21,5 +23,5 @@ export type FullCDS = {
   relative_end: number;
   protein_length: number;
   nucleotide_length: number;
-  sequence_checksum?: string;
+  sequence: Sequence;
 };

src/ensembl/src/shared/types/thoas/product.ts

@@ -16,6 +16,7 @@
 
 import { ExternalReference } from './externalReference';
 import { LocationWithinRegion } from './location';
+import { Sequence } from './sequence';
 
 export type ProteinDomainsResources = {
   [name_of_resource: string]: {
@@ -52,7 +53,7 @@ export type Product = {
   length: number;
   protein_domains: ProteinDomain[];
   external_references: ExternalReference[];
-  sequence_checksum?: string;
+  sequence: Sequence;
 };
 
 export type ProteinDomain = {

src/ensembl/src/shared/types/thoas/sequence.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.
+ */
+
+export type Sequence = {
+  checksum: string;
+};

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

@@ -40,6 +40,9 @@ export const createProduct = (fragment: Partial<Product> = {}): Product => {
     length: length,
     protein_domains: createProteinDomains(length),
     external_references: times(2, () => createExternalReference()),
+    sequence: {
+      checksum: faker.datatype.uuid()
+    },
     ...fragment
   };
 };

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

@@ -191,7 +191,10 @@ const createCDS = (transcriptSlice: Slice): FullCDS => {
     relative_start: 1,
     relative_end: nucleotideLength,
     nucleotide_length: nucleotideLength,
-    protein_length: proteinLength
+    protein_length: proteinLength,
+    sequence: {
+      checksum: faker.datatype.uuid()
+    }
   };
 };
 
@@ -201,7 +204,10 @@ const createCDNA = (transcriptSlice: Slice): CDNA => {
   return {
     start,
     end,
-    length: end - start + 1
+    length: end - start + 1,
+    sequence: {
+      checksum: faker.datatype.uuid()
+    }
   };
 };