Add ClinicalTrialLocation

Author: mathieulemieux

src/definitions/ontology.ts

@@ -1,5 +1,5 @@
 import * as util from '../util';
-import { EXPOSE_READ, PERMISSIONS } from '../constants';
+import { EXPOSE_NONE, EXPOSE_READ, PERMISSIONS } from '../constants';
 import { BASE_PROPERTIES } from './util';
 import { PartialSchemaDefn } from '../types';
 
@@ -125,6 +125,38 @@ const models: PartialSchemaDefn = {
             },
         ],
     },
+    ClinicalTrialLocation: {
+        description: 'Location of a ClinicalTrial',
+        routes: EXPOSE_NONE,
+        embedded: true,
+        properties: [
+            {
+                name: 'city',
+                type: 'string',
+                nullable: true,
+                mandatory: false,
+            },
+            {
+                name: 'state',
+                type: 'string',
+                nullable: true,
+                mandatory: false,
+            },
+            {
+                name: 'country',
+                type: 'string',
+                nullable: true,
+                mandatory: false,
+            },
+            {
+                name: 'comment',
+                type: 'string',
+                nullable: true,
+                mandatory: false,
+            },
+        ],
+        isAbstract: true,
+    },
     ClinicalTrial: {
         inherits: ['Evidence', 'Ontology'],
         properties: [
@@ -136,8 +168,9 @@ const models: PartialSchemaDefn = {
             {
                 name: 'completionDate', type: 'string', format: 'date', pattern: '^\\d{4}(-\\d{2}(-\\d{2})?)?$',
             },
-            { name: 'country', type: 'string', description: 'The country the trial is held in' },
-            { name: 'city', type: 'string', description: 'The city the trial is held in' },
+            {
+                name: 'location', type: 'embeddedlist', linkedClass: 'ClinicalTrialLocation', description: 'The location the trial is held in',
+            },
             {
                 name: 'recruitmentStatus',
                 type: 'string',

src/definitions/user.ts

@@ -2,7 +2,7 @@ import isEmail from 'validator/lib/isEmail';
 
 import * as util from '../util';
 import { ValidationError } from '../error';
-import { EXPOSE_NONE, PERMISSIONS } from '../constants';
+import { PERMISSIONS } from '../constants';
 import { BASE_PROPERTIES, activeUUID } from './util';
 import { PartialSchemaDefn } from '../types';
 

src/types.ts

@@ -67,6 +67,7 @@ export type VertexName = (
 export type EmbeddedVertexName = (
     'Position'
     | 'CdsPosition'
+    | 'ClinicalTrialLocation'
     | 'CytobandPosition'
     | 'ExonicPosition'
     | 'GenomicPosition'

test/schema.test.ts

@@ -251,6 +251,7 @@ test('splitClassLevels', () => {
         ],
         [
             'Biomarker',
+            'ClinicalTrialLocation',
             'Evidence',
             'LicenseAgreement',
             'Permissions',
@@ -458,6 +459,7 @@ test.each([
     ['Permissions', { default: 0, readonly: 4 }],
     ['Ontology', { default: 4, readonly: 4 }],
     ['EvidenceLevel', { default: 15, readonly: 4 }],
+    ['ClinicalTrialLocation', { default: 0, readonly: 4 }],
     ['ClinicalTrial', { default: 15, readonly: 4 }],
     ['Abstract', { default: 15, readonly: 4 }],
     ['Publication', { default: 15, readonly: 4 }],