chore: appzi changes and merged in master

neurostuff · Oct 22, 2024 · 161d5fd · 161d5fd
2 parents 0c27a34 + f8591a5
commit 161d5fd
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Showing 71 changed files with 2,873 additions and 779 deletions.
diff --git a/compose/neurosynth-frontend/cypress/e2e/pages/BaseStudyPage.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/pages/BaseStudyPage.cy.tsx
@@ -22,7 +22,6 @@ describe(PAGE_NAME, () => {
         cy.intercept('GET', `**/api/base-studies/**`, {
             fixture: 'study',
         }).as('studyFixture');
-        cy.visit(PATH).wait('@semanticScholarFixture').wait('@studyFixture');
         // .get('tr')
         // .eq(2)
         // .click()

diff --git a/compose/neurosynth-frontend/cypress/e2e/pages/EditStudyPage.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/pages/EditStudyPage.cy.tsx
@@ -36,7 +36,6 @@ describe(PAGE_NAME, () => {
             .wait('@studyFixture')
             .wait('@projectFixture')
             .wait('@annotationFixture')
-            .wait('@semanticScholarFixture')
             .wait('@studysetFixture');
     });
 
@@ -48,15 +47,14 @@ describe(PAGE_NAME, () => {
             .wait('@studyFixture')
             .wait('@projectFixture')
             .wait('@annotationFixture')
-            .wait('@semanticScholarFixture')
             .wait('@studysetFixture');
 
         // ACT
         cy.get('div').contains('(name, authors, description, doi, pmid, etc)').click();
         cy.contains('label', 'doi').next().clear();
         cy.contains('label', 'pmid').next().clear();
         cy.contains('label', 'pmcid').next().clear();
-        cy.contains('button', 'save').click();
+        cy.get('[data-testid="SaveIcon"]').click();
 
         // ASSERT
         cy.get('@editStudy').its('request.body').should('not.have.a.property', 'doi');

diff --git a/compose/neurosynth-frontend/cypress/e2e/pages/PublicStudiesPage.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/pages/PublicStudiesPage.cy.tsx
@@ -7,7 +7,7 @@ export {};
 const PATH = '/base-studies';
 const PAGE_NAME = 'StudiesPage';
 
-describe.skip(PAGE_NAME, () => {
+describe(PAGE_NAME, () => {
     beforeEach(() => {
         cy.clearLocalStorage();
         cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture');
@@ -16,7 +16,7 @@ describe.skip(PAGE_NAME, () => {
     it('should load successfully', () => {
         cy.intercept('GET', `**/api/projects*`).as('realProjectsRequest');
         cy.intercept('GET', `**/api/base-studies/**`).as('realStudiesRequest');
-        cy.visit(PATH).wait('@realStudiesRequest');
+        cy.visit(PATH);
     });
 
     // describe('Search', () => {

diff --git a/compose/neurosynth-frontend/cypress/e2e/workflows/Extraction/ExtractionTable.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/workflows/Extraction/ExtractionTable.cy.tsx
@@ -3,6 +3,7 @@
 import { INeurosynthProjectReturn } from 'hooks/projects/useGetProjects';
 import { StudyReturn, StudysetReturn } from 'neurostore-typescript-sdk';
 import { IExtractionTableStudy } from 'pages/Extraction/components/ExtractionTable';
+import { getAuthorShortName } from 'pages/Extraction/components/ExtractionTable.helpers';
 
 describe('ExtractionTable', () => {
     beforeEach(() => {
@@ -303,7 +304,12 @@ describe('ExtractionTable', () => {
 
                 cy.get('tbody > tr').each((tr, index) => {
                     cy.wrap(tr).within(() => {
-                        cy.get('td').eq(2).should('have.text', sortedStudies[index].authors);
+                        cy.get('td')
+                            .eq(2)
+                            .should(
+                                'have.text',
+                                getAuthorShortName(sortedStudies?.[index]?.authors || '')
+                            );
                     });
                 });
             });
@@ -324,7 +330,12 @@ describe('ExtractionTable', () => {
 
                 cy.get('tbody > tr').each((tr, index) => {
                     cy.wrap(tr).within(() => {
-                        cy.get('td').eq(2).should('have.text', sortedStudies[index].authors);
+                        cy.get('td')
+                            .eq(2)
+                            .should(
+                                'have.text',
+                                getAuthorShortName(sortedStudies?.[index]?.authors || '')
+                            );
                     });
                 });
             });

diff --git a/...e/neurosynth-frontend/cypress/e2e/workflows/MetaAnalyses/CreateSpecificationDialog.cy.tsx b/...e/neurosynth-frontend/cypress/e2e/workflows/MetaAnalyses/CreateSpecificationDialog.cy.tsx
@@ -14,6 +14,9 @@ describe('CreateSpecificationDialog', () => {
             fixture: 'projects/projectCanCreateSpecification',
         }).as('projectFixture');
         cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture');
+        cy.intercept('GET', '**/api/annotations/*', { fixture: 'annotation' }).as(
+            'annotationFixture'
+        );
     });
 
     it('should show the dialog', () => {
@@ -23,5 +26,51 @@ describe('CreateSpecificationDialog', () => {
         cy.contains('button', 'Meta-Analyses').click();
         cy.contains('button', 'Meta-Analysis Specification').click();
         cy.get('.MuiDialog-container').should('be.visible');
+        cy.contains('button', 'Back').should('be.disabled');
+    });
+
+    it('should set the default specification values', () => {
+        cy.login('mocked', { sub: 'github|26612023' })
+            .visit('/projects/abc123')
+            .wait('@projectFixture');
+        cy.contains('button', 'Meta-Analyses').click();
+        cy.contains('button', 'Meta-Analysis Specification').click();
+        cy.get('.MuiDialog-container').should('be.visible');
+        cy.contains('MKDADensity').should('exist');
+        cy.contains('FDRCorrector').should('exist');
+    });
+
+    it('should step through the wizard', () => {
+        cy.intercept('POST', '**/api/specifications', {
+            id: 'mockedSpecificationId',
+        }).as('createSpecificationFixture');
+        cy.intercept('POST', '**/api/studysets', {
+            id: 'mockedStudySetId',
+        });
+        cy.intercept('POST', '**/api/annotations', {
+            id: 'mockedAnnotationId',
+        });
+        cy.intercept('POST', '**/api/meta-analyses', {
+            id: 'mockedMetaAnalysisId',
+            specification: {},
+        });
+        cy.intercept('GET', '**/api/specifications/*', {
+            fixture: 'specification',
+        });
+
+        cy.intercept('GET', '**/api/meta-analyses/mockedMetaAnalysisId*', {
+            fixture: 'metaAnalysis',
+        }).as('metaAnalysesFixture');
+
+        cy.login('mocked', { sub: 'github|26612023' })
+            .visit('/projects/abc123')
+            .wait('@projectFixture');
+        cy.contains('button', 'Meta-Analyses').click();
+        cy.contains('button', 'Meta-Analysis Specification').click();
+        cy.contains('Next').click();
+        cy.contains('included').should('exist');
+        cy.contains('button', 'Next').click();
+        cy.contains('button', 'Next').click();
+        cy.contains('button', 'Create Meta-Analysis Specification').click();
     });
 });
diff --git a/compose/neurosynth-frontend/cypress/e2e/workflows/SleuthImport/DoSleuthImport.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/workflows/SleuthImport/DoSleuthImport.cy.tsx
@@ -433,7 +433,7 @@ describe('DoSleuthImport', () => {
     });
 
     describe('edge cases', () => {
-        it.only('should apply the pubmed details to the study if a matching pubmed study is found', () => {
+        it('should apply the pubmed details to the study if a matching pubmed study is found', () => {
             // this stuff exists just to make sure cypress doesnt send any real requests. They are not under test
             // synth API responses
             cy.intercept('POST', `${neurostoreAPIBaseURL}/analyses/**`, {