Add genomeSequences field to schema per spec

data-serving/data-service/schemas/cases.schema.json

@@ -73,6 +73,37 @@
           }
         }
       },
+      "genomeSequences": {
+        "bsonType": "array",
+        "uniqueItems": true,
+        "items": {
+          "bsonType": "object",
+          "additionalProperties": false,
+          "properties": {
+            "_id": {
+              "bsonType": "objectId"
+            },
+            "sampleCollectionDate": {
+              "bsonType": "date"
+            },
+            "repositoryUrl": {
+              "bsonType": "string"
+            },
+            "sequenceId": {
+              "bsonType": "string"
+            },
+            "sequenceName": {
+              "bsonType": "string"
+            },
+            "sequenceLength": {
+              "bsonType": "int"
+            },
+            "notes": {
+              "bsonType": "string"
+            }
+          }
+        }
+      },
       "location": {
         "bsonType": "object",
         "additionalProperties": false,

data-serving/data-service/src/model/case.ts

@@ -2,6 +2,10 @@ import { CaseReferenceDocument, caseReferenceSchema } from './case-reference';
 import { DemographicsDocument, demographicsSchema } from './demographics';
 import { DictionaryDocument, dictionarySchema } from './dictionary';
 import { EventDocument, eventSchema } from './event';
+import {
+    GenomeSequenceDocument,
+    genomeSequenceSchema,
+} from './genome-sequence';
 import { LocationDocument, locationSchema } from './location';
 import { PathogenDocument, pathogenSchema } from './pathogen';
 import {
@@ -27,6 +31,7 @@ const caseSchema = new mongoose.Schema(
                 message: 'Must include an event with name "confirmed"',
             },
         },
+        genomeSequences: [genomeSequenceSchema],
         importedCase: {},
         location: locationSchema,
         revisionMetadata: {
@@ -68,6 +73,7 @@ type CaseDocument = mongoose.Document & {
     caseReference: CaseReferenceDocument;
     demographics: DemographicsDocument;
     events: [EventDocument];
+    genomeSequences: [GenomeSequenceDocument];
     importedCase: {};
     location: LocationDocument;
     revisionMetadata: RevisionMetadataDocument;

data-serving/data-service/src/model/genome-sequence.ts

@@ -0,0 +1,21 @@
+import { dateFieldInfo } from './date';
+import mongoose from 'mongoose';
+import { positiveIntFieldInfo } from './positive-int';
+
+export const genomeSequenceSchema = new mongoose.Schema({
+    sampleCollectionDate: dateFieldInfo,
+    repositoryUrl: String,
+    sequenceId: String,
+    sequenceName: String,
+    sequenceLength: positiveIntFieldInfo,
+    notes: String,
+});
+
+export type GenomeSequenceDocument = mongoose.Document & {
+    sampleCollectionDate: Date;
+    repositoryUrl: string;
+    sequenceId: string;
+    sequenceName: string;
+    sequenceLength: number;
+    notes: string;
+};

data-serving/data-service/test/model/data/case.full.json

@@ -13,6 +13,16 @@
         "nationality": "Swedish",
         "ethnicity": "Other"
     },
+    "genomeSequences": [
+        {
+            "sampleCollectionDate": "2019-12-30",
+            "repositoryUrl": "https://www.ncbi.nlm.nih.gov/nuccore/NC_045512",
+            "sequenceId": "NC_045512.2",
+            "sequenceName": "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome",
+            "sequenceLength": 33000,
+            "notes": "The reference sequence is identical to MN908947."
+        }
+    ],
     "location": {
         "country": "France",
         "administrativeAreaLevel1": "Île-de-France",

data-serving/data-service/test/model/data/genome-sequence.full.json

@@ -0,0 +1,8 @@
+{
+        "sampleCollectionDate": "2019-12-30",
+        "repositoryUrl": "https://www.ncbi.nlm.nih.gov/nuccore/NC_045512",
+        "sequenceId": "NC_045512.2",
+        "sequenceName": "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome",
+        "sequenceLength": 33000,
+        "notes": "The reference sequence is identical to MN908947."
+}

data-serving/data-service/test/model/data/genome-sequence.minimal.json

@@ -0,0 +1 @@
+{}

data-serving/data-service/test/model/genome-sequence.test.ts

@@ -0,0 +1,42 @@
+import {
+    GenomeSequenceDocument,
+    genomeSequenceSchema,
+} from '../../src/model/genome-sequence';
+
+import { Error } from 'mongoose';
+import fullModel from './data/genome-sequence.full.json';
+import minimalModel from './data/genome-sequence.minimal.json';
+import mongoose from 'mongoose';
+
+const GenomeSequence = mongoose.model<GenomeSequenceDocument>(
+    'GenomeSequence',
+    genomeSequenceSchema,
+);
+
+describe('validate', () => {
+    it('genome sequence with non-conforming date is invalid', async () => {
+        return new GenomeSequence({
+            ...minimalModel,
+            ...{ sampleCollectionDate: Date.parse('2019-10-31') },
+        }).validate((e) => {
+            expect(e.name).toBe(Error.ValidationError.name);
+        });
+    });
+
+    it('genome sequence with non-integer length is invalid', async () => {
+        return new GenomeSequence({
+            ...minimalModel,
+            ...{ sequenceLength: 2.2 },
+        }).validate((e) => {
+            expect(e.name).toBe(Error.ValidationError.name);
+        });
+    });
+
+    it('minimal genome sequence model is valid', async () => {
+        return new GenomeSequence(minimalModel).validate();
+    });
+
+    it('fully specified genome sequence model is valid', async () => {
+        return new GenomeSequence(fullModel).validate();
+    });
+});

data-serving/samples/cases.json

@@ -12,6 +12,18 @@
             ],
             "ethnicity": "Other"
         },
+        "genomeSequences": [
+            {
+                "sampleCollectionDate": {
+                    "$date": "2019-12-30T00:00:00Z"
+                },
+                "repositoryUrl": "https://www.ncbi.nlm.nih.gov/nuccore/NC_045512",
+                "sequenceId": "NC_045512.2",
+                "sequenceName": "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome",
+                "sequenceLength": 33000,
+                "notes": "The reference sequence is identical to MN908947."
+            }
+        ],
         "location": {
             "country": "France",
             "administrativeAreaLevel1": "Île-de-France",