Merge branch 'develop' into gr-DUOS-2479

cypress/component/DataSubmission/README.md

@@ -0,0 +1,10 @@
+# Data Submission Schema Validation Tests
+
+Validation tests here rely on the fixture: `cypress/fixtures/dataset-registration-schema_v1.json` which is a copy of
+what is stored in Consent: https://consent.dsde-dev.broadinstitute.org/schemas/dataset-registration/v1
+If there are changes there, they need to be copied to this file for tests to reflect back end validation.
+
+From project root, run:
+```shell
+curl -s -S -X 'GET'  "https://consent.dsde-dev.broadinstitute.org/schemas/dataset-registration/v1"  -H 'accept: application/json' -o ./cypress/fixtures/dataset-registration-schema_v1.json
+```

cypress/component/DataSubmission/consent_group.spec.js

@@ -1,6 +1,6 @@
 /* eslint-disable no-undef */
 import React from 'react';
-import ConsentGroupForm from '../../../src/components/data_submission/consent_group/ConsentGroupForm';
+import ConsentGroupForm from '../../../src/pages/data_submission/consent_group/ConsentGroupForm';
 import { cloneDeep } from 'lodash/fp';
 import { mount } from 'cypress/react';
 

cypress/component/DataSubmission/data_access_governance.spec.js

@@ -1,7 +1,7 @@
 /* eslint-disable no-undef */
 import React from 'react';
-import { DAC, User, Institution, Schema, Study } from '../../../src/libs/ajax';
-import DataSubmissionForm from '../../../src/pages/DataSubmissionForm';
+import {DAC, User, Institution, Schema, Study, DataSet} from '../../../src/libs/ajax';
+import DataSubmissionForm from '../../../src/pages/data_submission/DataSubmissionForm';
 import { mount } from 'cypress/react';
 
 const dacs = [
@@ -23,6 +23,10 @@ beforeEach(() => {
   cy.stub(Institution, 'list').returns([{name: 'Test Institution'}]);
   cy.stub(Schema, 'datasetRegistrationV1').returns({});
   cy.stub(Study, 'getStudyNames').returns([]);
+  cy.stub(DataSet, 'getDatasetNames').returns([]);
+  cy.fixture('dataset-registration-schema_v1').then(function (data) {
+    cy.stub(DataSet, 'getRegistrationSchema').returns(data);
+  });
 });
 
 describe('Data Access Governance', function () {

cypress/component/DataSubmission/ds_nih_anvil_use.spec.js

@@ -2,7 +2,7 @@
 import React from 'react';
 import { mount } from 'cypress/react';
 import { cloneDeep } from 'lodash/fp';
-import  NihAnvilUse, { YES_NHGRI_YES_PHS_ID } from '../../../src/components/data_submission/NihAnvilUse';
+import  NihAnvilUse, { YES_NHGRI_YES_PHS_ID } from '../../../src/pages/data_submission/NihAnvilUse';
 
 let propCopy;
 

cypress/component/DataSubmission/ds_study_information.spec.js

@@ -3,7 +3,7 @@ import React from 'react';
 import { mount } from 'cypress/react';
 import { cloneDeep } from 'lodash/fp';
 import { User } from '../../../src/libs/ajax';
-import DataSubmissionStudyInformation from '../../../src/components/data_submission/ds_study_information';
+import DataSubmissionStudyInformation from '../../../src/pages/data_submission/ds_study_information';
 
 let propCopy;
 const user = {

cypress/component/DataSubmission/registration_validation.spec.js

@@ -0,0 +1,108 @@
+/* eslint-disable no-undef */
+import {compileSchema, validateForm} from '../../../src/pages/data_submission/RegistrationValidation.js';
+
+const formData = {
+  'studyType': 'Observational',
+  'studyName': 'name',
+  'studyDescription': 'description',
+  'dataTypes': ['types'],
+  'phenotypeIndication': 'phenotype',
+  'species': 'species',
+  'piName': 'PI Name',
+  'dataCustodianEmail': ['[email protected]'],
+  'publicVisibility': true,
+  'dataSubmitterUserId': 1,
+  'nihAnvilUse': 'I am not NHGRI funded and do not plan to store data in AnVIL',
+  'consentGroups': [{
+    'numberOfParticipants': 2,
+    'consentGroupName': 'name',
+    'generalResearchUse': true,
+    'dataAccessCommitteeId': 1,
+    'url': 'https://asdf.com'
+  }]
+};
+
+let schema = undefined;
+
+beforeEach(function () {
+  cy.fixture('dataset-registration-schema_v1').then(function (data) {
+    schema = data;
+  });
+});
+
+describe('Dataset Registration Schema Validator', () => {
+
+  it('Compiles schema and generates a validate function', () => {
+    const validateFunction = compileSchema(schema);
+    expect(validateFunction).to.not.be.null;
+  });
+
+  it('Validates a valid instance of a schema', () => {
+    const [valid, validation] = validateForm(schema, formData);
+    expect(valid).to.be.true;
+    expect(validation).to.be.empty;
+  });
+
+  it('Invalidates an invalid instance of a schema', () => {
+    const [valid, validation] = validateForm(schema, {});
+    expect(valid).to.be.false;
+    expect(validation).to.not.be.empty;
+  });
+
+  it('Validates a valid date field', () => {
+    const form = Object.assign({}, formData, {targetDeliveryDate: '2021-01-01', targetPublicReleaseDate: '2021-01-01'});
+    const [valid, validation] = validateForm(schema, form);
+    expect(valid).to.be.true;
+    expect(validation).to.be.empty;
+  });
+
+  it('Invalidates an invalid date field', () => {
+    const form = Object.assign({}, formData, {targetDeliveryDate: '20210101', targetPublicReleaseDate: '20210101'});
+    const [valid, validation] = validateForm(schema, form);
+    expect(valid).to.be.false;
+    expect(validation).to.not.be.empty;
+  });
+
+  it('Validates a valid email field', () => {
+    const form = Object.assign({}, formData, {dataCustodianEmail: ['[email protected]']});
+    const [valid, validation] = validateForm(schema, form);
+    expect(valid).to.be.true;
+    expect(validation).to.be.empty;
+  });
+
+  it('Invalidates an invalid email field', () => {
+    const form = Object.assign({}, formData, {dataCustodianEmail: ['user']});
+    const [valid, validation] = validateForm(schema, form);
+    expect(valid).to.be.false;
+    expect(validation).to.not.be.empty;
+  });
+
+  it('Validates a valid uri field', () => {
+    const consentGroup = {
+      'numberOfParticipants': 2,
+      'consentGroupName': 'name',
+      'generalResearchUse': true,
+      'dataAccessCommitteeId': 1,
+      'url': 'https://some.site.org'
+    };
+    const form = Object.assign({}, formData, {consentGroups: [consentGroup]});
+    const [valid, validation] = validateForm(schema, form);
+    expect(valid).to.be.true;
+    expect(validation).to.be.empty;
+  });
+
+  it('Invalidates an invalid uri field', () => {
+    const consentGroup = {
+      'numberOfParticipants': 2,
+      'consentGroupName': 'name',
+      'generalResearchUse': true,
+      'dataAccessCommitteeId': 1,
+      'url': 'some place . org'
+    };
+    const form = Object.assign({}, formData, {consentGroups: [consentGroup]});
+    const [valid, validation] = validateForm(schema, form);
+    expect(valid).to.be.false;
+    expect(validation).to.not.be.empty;
+  });
+
+});

src/assets/schemas/DataRegistrationV1.json → cypress/fixtures/dataset-registration-schema_v1.json

@@ -450,7 +450,6 @@
       "type": "object",
       "required": [
         "consentGroupName",
-        "fileTypes",
         "numberOfParticipants"
       ],
       "allOf": [
@@ -681,7 +680,6 @@
         },
         "fileTypes": {
           "type": "array",
-          "minItems": 1,
           "items": {
             "$ref": "#/$defs/fileTypeObject"
           },