diff --git a/compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportStudiesDialog.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportStudiesDialog.cy.tsx index 16a76640..607dfadf 100644 --- a/compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportStudiesDialog.cy.tsx +++ b/compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportStudiesDialog.cy.tsx @@ -198,14 +198,14 @@ describe('ImportStudiesDialog', () => { }); it('should set the source and show the input', () => { - cy.get('input[role="combobox"').click(); + cy.get('input[role="combobox"]').click(); cy.contains('li', 'Scopus').click(); cy.get('textarea').should('be.visible'); cy.contains(/Input is empty/).should('be.visible'); }); it('should set the sources and enable the next button', () => { - cy.get('input[role="combobox"').click(); + cy.get('input[role="combobox"]').click(); cy.contains('li', 'Scopus').click(); cy.get('textarea[placeholder="paste in valid endnote, bibtex, or RIS syntax"]') .click() @@ -220,7 +220,7 @@ describe('ImportStudiesDialog', () => { }); it('should show an error message', () => { - cy.get('input[role="combobox"').click(); + cy.get('input[role="combobox"]').click(); cy.contains('li', 'Scopus').click(); cy.get('textarea[placeholder="paste in valid endnote, bibtex, or RIS syntax"]').type( 'INVALID FORMAT' @@ -229,7 +229,7 @@ describe('ImportStudiesDialog', () => { }); it('should import studies', () => { - cy.get('input[role="combobox"').click(); + cy.get('input[role="combobox"]').click(); cy.contains('li', 'Scopus').click(); cy.get('textarea[placeholder="paste in valid endnote, bibtex, or RIS syntax"]') .click() @@ -249,7 +249,7 @@ describe('ImportStudiesDialog', () => { }); it('should upload a onenote (ENW) file', () => { - cy.get('input[role="combobox"').click(); + cy.get('input[role="combobox"]').click(); cy.contains('li', 'Scopus').click(); cy.get('label[role="button"]').selectFile( 'cypress/fixtures/standardFiles/onenoteStudies.txt' diff --git a/compose/neurosynth-frontend/cypress/e2e/workflows/Extraction/ExtractionTable.cy.tsx b/compose/neurosynth-frontend/cypress/e2e/workflows/Extraction/ExtractionTable.cy.tsx index 8dc4fda6..9a75dd51 100644 --- a/compose/neurosynth-frontend/cypress/e2e/workflows/Extraction/ExtractionTable.cy.tsx +++ b/compose/neurosynth-frontend/cypress/e2e/workflows/Extraction/ExtractionTable.cy.tsx @@ -1,16 +1,693 @@ /// +import { INeurosynthProjectReturn } from 'hooks/projects/useGetProjects'; +import { StudyReturn, StudysetReturn } from 'neurostore-typescript-sdk'; +import { IExtractionTableStudy } from 'pages/Extraction/components/ExtractionTable'; + describe('ExtractionTable', () => { beforeEach(() => { cy.clearLocalStorage(); cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture'); cy.intercept('GET', `**/api/projects/*`, { - fixture: 'projects/projectExtractionStep', + fixture: 'Extraction/project', }).as('projectFixture'); cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture'); + + cy.intercept('PUT', `**/api/projects/*`, { fixture: 'Extraction/project' }).as( + 'updateProjectFixture' + ); + + cy.intercept('GET', `**/api/studies/*`, { fixture: 'study' }).as('studyFixture'); + cy.intercept('GET', `**/api/annotations/*`, { fixture: 'annotation' }).as( + 'annotationsFixture' + ); + + cy.intercept('GET', `https://api.semanticscholar.org/**`, { + fixture: 'semanticScholar', + }).as('semanticScholarFixture'); + }); + + describe('Filtering', () => { + beforeEach(() => { + cy.login('mocked').visit(`/projects/abc123/extraction`); + }); + + it('should filter the table by year', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(0).click(); + cy.get(`input`) + .eq(0) + .type(studysetStudies[0].year?.toString() || ''); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should filter the table by name', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(1).click(); + cy.get(`input`) + .eq(1) + .type(studysetStudies[0].name || ''); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should filter the table by author', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(2).click(); + cy.get(`input`) + .eq(2) + .type(studysetStudies[0].authors || ''); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should show available journals as options', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + const uniqueJouranls = new Set(); + studysetStudies.forEach((study) => { + if (study.publication) uniqueJouranls.add(study.publication); + }); + cy.get('input').eq(3).click(); + cy.get('div[role="presentation"]').within(() => { + cy.get('li').should('have.length', uniqueJouranls.size); + }); + }); + }); + + it('should filter the table by journal', () => { + cy.get('input').eq(3).click(); + cy.get('div[role="presentation"]').within((menu) => { + cy.get('li').eq(0).click(); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should filter the table by doi', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(4).click(); + cy.get(`input`) + .eq(4) + .type(studysetStudies[0].doi || ''); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should filter the table by pmid', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(5).click(); + cy.get(`input`) + .eq(5) + .type(studysetStudies[0].pmid || ''); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should filter the table by status', () => { + cy.get('div[role="combobox"]').eq(0).click(); + cy.get('div[role="presentation"]').within(() => { + // set to completed + cy.get('li').eq(3).click(); + }); + + cy.get('tbody > tr').should('have.length', 1); + }); + + it('should show filtering chips at the bottom if one or more filters are applied', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(0).click(); + cy.get(`input`) + .eq(0) + .type(studysetStudies[0].year?.toString() || ''); + cy.get('input').eq(1).click(); + cy.get('input') + .eq(1) + .type(studysetStudies[0].name?.toString() || ''); + + cy.contains(`Filtering YEAR: ${studysetStudies[0].year?.toString()}`).should( + 'exist' + ); + cy.contains(`Filtering NAME: ${studysetStudies[0].name?.toString()}`).should( + 'exist' + ); + }); + }); + + it('should remove the filter if the delete button is clicked', () => { + // ARRANGE + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture?.response?.body as StudysetReturn; + const studysetStudies = studyset.studies as StudyReturn[]; + cy.get('input').eq(0).click(); + cy.get(`input`) + .eq(0) + .type(studysetStudies[0].year?.toString() || ''); + }); + cy.get('tbody > tr').should('have.length', 1); + cy.get('[data-testid="CancelIcon"]').should('exist'); + // ACT + cy.get('[data-testid="CancelIcon"]').click(); + + // ASSERT + cy.get('tbody > tr').should('have.length', 3); + cy.get(`[data-testid="CancelIcon"]`).should('not.exist'); + }); + }); + + describe('status', () => { + beforeEach(() => { + cy.login('mocked').visit(`/projects/abc123/extraction`); + }); + + it('should change the study status', () => { + // ARRANGE + cy.get('tbody > tr').eq(0).get('td').eq(6).as('getFirstRowStudyStatusCol'); + cy.get('@getFirstRowStudyStatusCol').within(() => { + cy.get('button').eq(0).should('have.class', 'MuiButton-contained'); + }); + + // ACT + cy.get('@getFirstRowStudyStatusCol').within(() => { + cy.get('button').eq(1).click(); + }); + + // ASSERT + cy.get('@getFirstRowStudyStatusCol').within(() => { + cy.get('button').eq(0).should('have.class', 'MuiButton-outlined'); + cy.get('button').eq(1).should('have.class', 'MuiButton-contained'); + }); + }); }); - it('should load the page', () => { - cy.login('mocked').visit(`/projects/abc123/`); + describe('sorting', () => { + beforeEach(() => { + cy.login('mocked').visit(`/projects/abc123/extraction`); + }); + + it('should sort by year desc', () => { + cy.contains('Year').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort( + (a, b) => (b.year as number) - (a.year as number) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td') + .eq(0) + .should('have.text', sortedStudies[index].year?.toString()); + }); + }); + }); + }); + + it('should sort by year asc', () => { + cy.contains('Year').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort( + (a, b) => (a.year as number) - (b.year as number) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td') + .eq(0) + .should('have.text', sortedStudies[index].year?.toString()); + }); + }); + }); + }); + + it('should sort by name asc', () => { + cy.contains('Name').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (b.name as string).localeCompare(a.name as string) + ); + + console.log(sortedStudies); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(1).should('have.text', sortedStudies[index].name); + }); + }); + }); + }); + + it('should sort by name desc', () => { + cy.contains('Name').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (a.name as string).localeCompare(b.name as string) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(1).should('have.text', sortedStudies[index].name); + }); + }); + }); + }); + + it('should sort by authors desc', () => { + cy.contains('Authors').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (b.authors as string).localeCompare(a.authors as string) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(2).should('have.text', sortedStudies[index].authors); + }); + }); + }); + }); + + it('should sort by authors asc', () => { + cy.contains('Authors').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (a.authors as string).localeCompare(b.authors as string) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(2).should('have.text', sortedStudies[index].authors); + }); + }); + }); + }); + + it('should sort by journal desc', () => { + cy.contains('Journal').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (b.publication as string).localeCompare(a.publication as string) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(3).should('have.text', sortedStudies[index].publication); + }); + }); + }); + }); + + it('should sort by journal desc', () => { + cy.contains('Journal').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (a.publication as string).localeCompare(b.publication as string) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(3).should('have.text', sortedStudies[index].publication); + }); + }); + }); + }); + + it('should sort by doi desc', () => { + cy.contains('DOI').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (b.doi as string).localeCompare(a.doi as string) + ); + + console.log(sortedStudies); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(4).should('have.text', sortedStudies[index].doi); + }); + }); + }); + }); + it('should sort by doi asc', () => { + cy.contains('DOI').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (a.doi as string).localeCompare(b.doi as string) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td').eq(4).should('have.text', sortedStudies[index].doi); + }); + }); + }); + }); + + it('should sort by pmid desc', () => { + cy.contains('PMID').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (b?.pmid || '').localeCompare(a?.pmid || '', undefined, { + numeric: true, + }) + ); + + console.log(sortedStudies); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td') + .eq(5) + .should('have.text', sortedStudies[index].pmid ?? ''); + }); + }); + }); + }); + + it('should sort by pmid asc', () => { + cy.contains('PMID').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies = studies.sort((a, b) => + (a?.pmid || '').localeCompare(b?.pmid || '', undefined, { + numeric: true, + }) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td') + .eq(5) + .should('have.text', sortedStudies[index].pmid ?? ''); + }); + }); + }); + }); + + it('should sort by status desc', () => { + cy.contains('Status').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').should('exist'); + + cy.wait('@projectFixture').then((projectFixture) => { + const project = projectFixture?.response?.body as INeurosynthProjectReturn; + const studyStatusList = project.provenance.extractionMetadata.studyStatusList; + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies: IExtractionTableStudy[] = studies + .map((study) => ({ + ...study, + status: studyStatusList.find((status) => status.id === study.id) + ?.status, + })) + .sort((a, b) => + (a?.status || '').localeCompare(b?.status || '', undefined, { + numeric: true, + }) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td') + .eq(6) + .within(() => { + const studyStatus = sortedStudies[index].status; + const buttonIndex = + studyStatus === 'completed' + ? 2 + : studyStatus === 'savedforlater' + ? 1 + : 0; + + cy.get('button').each((button, index) => { + if (index === buttonIndex) { + cy.wrap(button).should( + 'have.class', + 'MuiButton-contained' + ); + } else { + cy.wrap(button).should( + 'have.class', + 'MuiButton-outlined' + ); + } + }); + }); + }); + }); + }); + }); + }); + + it('should sort by status asc', () => { + cy.contains('Status').click(); + cy.get('[data-testid="ArrowDownwardIcon"]').click(); + cy.get('[data-testid="ArrowUpwardIcon"]').should('exist'); + + cy.wait('@projectFixture').then((projectFixture) => { + const project = projectFixture?.response?.body as INeurosynthProjectReturn; + const studyStatusList = project.provenance.extractionMetadata.studyStatusList; + + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + const studies = [...(studyset.studies || [])] as StudyReturn[]; + + const sortedStudies: IExtractionTableStudy[] = studies + .map((study) => ({ + ...study, + status: studyStatusList.find((status) => status.id === study.id) + ?.status, + })) + .sort((a, b) => + (b?.status || '').localeCompare(a?.status || '', undefined, { + numeric: true, + }) + ); + + cy.get('tbody > tr').each((tr, index) => { + cy.wrap(tr).within(() => { + cy.get('td') + .eq(6) + .within(() => { + const studyStatus = sortedStudies[index].status; + const buttonIndex = + studyStatus === 'completed' + ? 2 + : studyStatus === 'savedforlater' + ? 1 + : 0; + + cy.get('button').each((button, index) => { + if (index === buttonIndex) { + cy.wrap(button).should( + 'have.class', + 'MuiButton-contained' + ); + } else { + cy.wrap(button).should( + 'have.class', + 'MuiButton-outlined' + ); + } + }); + }); + }); + }); + }); + }); + }); + }); + + describe.only('pagination', () => { + beforeEach(() => { + cy.fixture('studyset').then((studyset) => { + // as we are artificially creating new studies below, the out of sync popup wil appear. That's expected and + // we can just ignore it during out test + console.log(studyset); + const studies = []; + for (let i = 0; i < 100; i++) { + studies.push(...(studyset?.studies as StudyReturn[])); + } + studyset.studies = studies; + console.log(studyset); + cy.intercept('GET', `**/api/studysets/*`, studyset).as('studysetFixture'); + }); + }); + + beforeEach(() => { + cy.login('mocked').visit(`/projects/abc123/extraction`); + }); + + it('should give the correct number of studies', () => { + cy.wait('@studysetFixture').then((studysetFixture) => { + const studyset = studysetFixture.response?.body as StudysetReturn; + cy.contains(`Total: ${studyset.studies?.length} studies`).should('exist'); + }); + }); + + it('should change the number of rows per page', () => { + cy.get('[role="combobox"]').eq(2).click(); + cy.get('div[role="presentation"]').within(() => { + cy.contains('10').click(); + }); + cy.get('tbody > tr').should('have.length', 10); + cy.get('.MuiPaginationItem-root').contains('30'); + + cy.get('[role="combobox"]').eq(2).click(); + cy.get('div[role="presentation"]').within(() => { + cy.contains('25').click(); + }); + cy.get('tbody > tr').should('have.length', 25); + cy.get('.MuiPaginationItem-root').contains('12'); + + cy.get('[role="combobox"]').eq(2).click(); + cy.get('div[role="presentation"]').within(() => { + cy.contains('50').click(); + }); + cy.get('tbody > tr').should('have.length', 50); + + cy.get('[role="combobox"]').eq(2).click(); + cy.get('div[role="presentation"]').within(() => { + cy.contains('100').click(); + }); + cy.get('tbody > tr').should('have.length', 100); + cy.get('.MuiPaginationItem-root').contains('3'); + }); + }); + + describe('navigation', () => { + beforeEach(() => { + cy.login('mocked').visit(`/projects/abc123/extraction`); + }); + + it('should navigate to the selected study with the saved table state', () => { + cy.get('tbody > tr').eq(0).click(); + cy.url().should('include', `/projects/abc123/extraction/studies/3Jvrv4Pct3hb/edit`); + + cy.window().then((window) => { + const item = window.sessionStorage.getItem(`abc123-extraction-table`); + cy.wrap(item).should('exist'); + }); + }); + + it('should keep the table state', () => { + cy.get('tbody > tr').eq(0).click(); + cy.url().should('include', `/projects/abc123/extraction/studies/3Jvrv4Pct3hb/edit`); + + cy.visit(`/projects/abc123/extraction`); + + cy.window().then((window) => { + const item = window.sessionStorage.getItem(`abc123-extraction-table`); + cy.wrap(item).should('exist'); + }); + }); + + it('should save the filter and sorting to the table state', () => { + cy.contains('Year').click(); + cy.get('input').eq(1).click(); + cy.get(`input`).eq(1).type('Activation'); + + // we wait because of the debounce + // eslint-disable-next-line cypress/no-unnecessary-waiting + cy.wait(800); + + cy.get('tbody > tr').eq(0).click(); + + cy.window().then((window) => { + const state = window.sessionStorage.getItem(`abc123-extraction-table`); + const parsedState = JSON.parse(state || '{}'); + console.log(parsedState); + cy.wrap(parsedState).should('deep.equal', { + columnFilters: [{ id: 'name', value: 'Activation' }], + sorting: [{ id: 'year', desc: true }], + studies: ['3zutS8kyg2sy'], + }); + }); + }); }); }); diff --git a/compose/neurosynth-frontend/cypress/fixtures/Extraction/project.json b/compose/neurosynth-frontend/cypress/fixtures/Extraction/project.json new file mode 100644 index 00000000..c7d4209e --- /dev/null +++ b/compose/neurosynth-frontend/cypress/fixtures/Extraction/project.json @@ -0,0 +1,184 @@ +{ + "created_at": "2023-11-02T15:48:04.630172+00:00", + "description": "this is a bulk import test", + "id": "abc123", + "meta_analyses": ["3xHJJQWFURob"], + "name": "Bulk import test", + "neurostore_study": { + "created_at": "2023-11-02T15:48:04.640598+00:00", + "exception": null, + "neurostore_id": "7BrAuwJ2tjPW", + "status": "PENDING", + "traceback": null, + "updated_at": "2023-11-02T15:48:04.653465+00:00" + }, + "neurostore_url": "https://neurostore.org/api/studies/7BrAuwJ2tjPW", + "provenance": { + "curationMetadata": { + "columns": [ + { + "id": "370ba40c-91e8-47e7-9b4d-926bc8f31d10", + "name": "not included", + "stubStudies": [] + }, + { + "id": "1f15d9a7-968e-44a6-8574-caa3794e050e", + "name": "included", + "stubStudies": [ + { + "abstractText": "", + "articleLink": "https://pubmed.ncbi.nlm.nih.gov/9808463", + "articleYear": "1998", + "authors": "Corbetta M, Akbudak E, Conturo TE, Snyder AZ, Ollinger JM, Drury HA, Linenweber MR, Petersen SE, Raichle ME, Van Essen DC, Shulman GL", + "doi": "10.1016/S0896-6273(00)80593-0", + "exclusionTag": null, + "id": "1", + "identificationSource": { + "id": "neurosynth_neurostore_id_source", + "label": "Neurostore" + }, + "journal": "Neuron", + "keywords": "", + "neurostoreId": "3Jvrv4Pct3hb", + "pmcid": "", + "pmid": "9808463", + "searchTerm": "?genericSearchStr=psychosis&dataType=all&source=all&sortBy=relevance&descOrder=true", + "tags": [], + "title": "A common network of functional areas for attention and eye movements." + }, + { + "abstractText": "Important decisions are often made under stressful\r\ncircumstances thatmight compromise self-regulatory\r\nbehavior. Yet the neural mechanisms by which\r\nstress influences self-control choices are unclear.\r\nWe investigated these mechanisms in human participants\r\nwho faced self-control dilemmas over food\r\nreward while undergoing fMRI following stress.\r\nWe found that stress increased the influence of\r\nimmediately rewarding taste attributes on choice\r\nand reduced self-control. This choice pattern was\r\naccompanied by increased functional connectivity\r\nbetween ventromedial prefrontal cortex (vmPFC)\r\nand amygdala and striatal regions encoding tastiness.\r\nFurthermore, stress was associated with\r\nreduced connectivity between the vmPFC and\r\ndorsolateral prefrontal cortex regions linked to selfcontrol\r\nsuccess. Notably, alterations in connectivity\r\npathways could be dissociated by their differential\r\nrelationships with cortisol and perceived stress.\r\nOur results indicate that stress may compromise\r\nself-control decisions by both enhancing the impact\r\nof immediately rewarding attributes and reducing the\r\nefficacy of regions promoting behaviors that are\r\nconsistent with long-term goals.\r\n\r\nThis collection contains second level correlations of stress induced differences in the influence of taste based decisions on vStr,Amyg and vmPFC and their connectivity.\r\n\r\nKey words: food choice, decision making, self-regulation", + "articleLink": "", + "articleYear": "", + "authors": "Silvia U. Maier, Aidan B. Makwana and Todd A. Hare", + "doi": "10.1016/j.neuron.2015.07.005", + "exclusionTag": null, + "id": "2", + "identificationSource": { + "id": "neurosynth_neurostore_id_source", + "label": "Neurostore" + }, + "journal": "Neuron", + "keywords": "", + "neurostoreId": "36nHEsLLPwBB", + "pmcid": "", + "pmid": "26247866", + "searchTerm": "?genericSearchStr=psychosis&dataType=all&source=all&sortBy=relevance&descOrder=true", + "tags": [], + "title": "Acute Stress Impairs Self-Control in Goal-Directed Choice by Altering Multiple Functional Connections within the Brain’s Decision Circuits" + }, + { + "abstractText": "", + "articleLink": "", + "articleYear": "", + "authors": "Ethan M. McCormick, Yang Qu and Eva H. Telzer", + "doi": "10.3389/fnhum.2017.00141", + "exclusionTag": null, + "id": "3", + "identificationSource": { + "id": "neurosynth_neurostore_id_source", + "label": "Neurostore" + }, + "journal": "Frontiers in Human Neuroscience", + "keywords": "", + "neurostoreId": "3zutS8kyg2sy", + "pmcid": "", + "pmid": "", + "searchTerm": "?genericSearchStr=psychosis&dataType=all&source=all&sortBy=relevance&descOrder=true", + "tags": [], + "title": "Activation in Context: Differential Conclusions Drawn from Cross-Sectional and Longitudinal Analyses of Adolescents’ Cognitive Control-Related Neural Activity" + } + ] + } + ], + "exclusionTags": [ + { + "id": "neurosynth_exclude_exclusion", + "isAssignable": true, + "isExclusionTag": true, + "label": "Exclude" + }, + { + "id": "neurosynth_duplicate_exclusion", + "isAssignable": true, + "isExclusionTag": true, + "label": "Duplicate" + } + ], + "identificationSources": [ + { + "id": "neurosynth_neurostore_id_source", + "label": "Neurostore" + }, + { + "id": "neurosynth_pubmed_id_source", + "label": "PubMed" + }, + { + "id": "neurosynth_scopus_id_source", + "label": "Scopus" + }, + { + "id": "neurosynth_web_of_science_id_source", + "label": "Web of Science" + }, + { + "id": "neurosynth_psycinfo_id_source", + "label": "PsycInfo" + } + ], + "infoTags": [ + { + "id": "neurosynth_untagged_tag", + "isAssignable": false, + "isExclusionTag": false, + "label": "Untagged studies" + }, + { + "id": "neurosynth_uncategorized_tag", + "isAssignable": false, + "isExclusionTag": false, + "label": "Uncategorized Studies" + }, + { + "id": "neurosynth_needs_review_tag", + "isAssignable": false, + "isExclusionTag": false, + "label": "Needs Review" + }, + { + "id": "6f299c47-766c-48bd-a56b-9c77019ea9de", + "isAssignable": true, + "isExclusionTag": false, + "label": "marijuana" + } + ], + "prismaConfig": { + "eligibility": { + "exclusionTags": [] + }, + "identification": { + "exclusionTags": [] + }, + "isPrisma": false, + "screening": { + "exclusionTags": [] + } + } + }, + "extractionMetadata": { + "annotationId": "5LSBDTGqA6RF", + "studyStatusList": [ + { "id": "3zutS8kyg2sy", "status": "completed" } + ], + "studysetId": "73HRs8HaJbR8" + }, + "metaAnalysisMetadata": { + "canEditMetaAnalyses": false + } + }, + "public": false, + "updated_at": "2023-11-02T19:42:04.265234+00:00", + "user": "auth0|62e0e6c9dd47048572613b4d", + "username": "Test User" +} diff --git a/compose/neurosynth-frontend/cypress/fixtures/studyset.json b/compose/neurosynth-frontend/cypress/fixtures/studyset.json index 0335eaf3..5f75b2f6 100644 --- a/compose/neurosynth-frontend/cypress/fixtures/studyset.json +++ b/compose/neurosynth-frontend/cypress/fixtures/studyset.json @@ -1,660 +1,606 @@ { - "id":"5ATjENA3VVyE", - "name":"a test studyset", - "user":"auth0|62de78bc11222b208cd022c8", - "description":"some new studyset", - "publication":null, - "doi":null, - "pmid":null, - "created_at":"2022-07-25T11:08:25.999097+00:00", - "updated_at":null, - "studies":[ + "id": "5ATjENA3VVyE", + "name": "a test studyset", + "user": "auth0|62de78bc11222b208cd022c8", + "description": "some new studyset", + "publication": null, + "doi": null, + "pmid": null, + "created_at": "2022-07-25T11:08:25.999097+00:00", + "updated_at": null, + "studies": [ { - "id":"3Jvrv4Pct3hb", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "user":null, - "name":"A common network of functional areas for attention and eye movements.", - "description":null, - "publication":"Neuron", - "doi":"10.1016/S0896-6273(00)80593-0", - "pmid":"9808463", - "authors":"Corbetta M, Akbudak E, Conturo TE, Snyder AZ, Ollinger JM, Drury HA, Linenweber MR, Petersen SE, Raichle ME, Van Essen DC, Shulman GL", - "year":1998, - "metadata":null, - "source":"neurosynth", - "source_id":"9808463", - "source_updated_at":null, - "analyses":[ + "id": "3Jvrv4Pct3hb", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "user": null, + "name": "A common network of functional areas for attention and eye movements.", + "description": null, + "publication": "Neuron", + "doi": "10.1016/S0896-6273(00)80593-0", + "pmid": "9808463", + "authors": "Corbetta M, Akbudak E, Conturo TE, Snyder AZ, Ollinger JM, Drury HA, Linenweber MR, Petersen SE, Raichle ME, Van Essen DC, Shulman GL", + "year": 1998, + "metadata": null, + "source": "neurosynth", + "source_id": "9808463", + "source_updated_at": null, + "analyses": [ { - "id":"6h7WzZ7sXd7S", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "user":null, - "study":"3Jvrv4Pct3hb", - "name":"35975", - "description":null, - "conditions":[ - - ], - "weights":[ - - ], - "points":[ + "id": "6h7WzZ7sXd7S", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "user": null, + "study": "3Jvrv4Pct3hb", + "name": "35975", + "description": null, + "conditions": [], + "weights": [], + "points": [ { - "id":"7bUZdF3z59wk", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "user":null, - "coordinates":[ - 6.0, - -49.0, - 10.0 - ], - "analysis":"6h7WzZ7sXd7S", - "kind":"unknown", - "space":"TAL", - "image":null, - "label_id":null, - "entities":[ + "id": "7bUZdF3z59wk", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "user": null, + "coordinates": [6.0, -49.0, 10.0], + "analysis": "6h7WzZ7sXd7S", + "kind": "unknown", + "space": "TAL", + "image": null, + "label_id": null, + "entities": [ { - "id":"4BPFBTeFwqWj", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "level":"group", - "label":"35975", - "analysis":"6h7WzZ7sXd7S" + "id": "4BPFBTeFwqWj", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "level": "group", + "label": "35975", + "analysis": "6h7WzZ7sXd7S" } ], - "values":[ - - ] + "values": [] }, { - "id":"4GbFME36aBgD", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "user":null, - "coordinates":[ - 6.0, - -67.0, - 8.0 - ], - "analysis":"6h7WzZ7sXd7S", - "kind":"unknown", - "space":"TAL", - "image":null, - "label_id":null, - "entities":[ + "id": "4GbFME36aBgD", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "user": null, + "coordinates": [6.0, -67.0, 8.0], + "analysis": "6h7WzZ7sXd7S", + "kind": "unknown", + "space": "TAL", + "image": null, + "label_id": null, + "entities": [ { - "id":"6tmukHRo3zZB", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "level":"group", - "label":"35975", - "analysis":"6h7WzZ7sXd7S" + "id": "6tmukHRo3zZB", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "level": "group", + "label": "35975", + "analysis": "6h7WzZ7sXd7S" } ], - "values":[ - - ] + "values": [] }, { - "id":"6RZfQRn4KBa9", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "user":null, - "coordinates":[ - 6.0, - -67.0, - 8.0 - ], - "analysis":"6h7WzZ7sXd7S", - "kind":"unknown", - "space":"TAL", - "image":null, - "label_id":null, - "entities":[ + "id": "6RZfQRn4KBa9", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "user": null, + "coordinates": [6.0, -67.0, 8.0], + "analysis": "6h7WzZ7sXd7S", + "kind": "unknown", + "space": "TAL", + "image": null, + "label_id": null, + "entities": [ { - "id":"3ko2zEd4Adjf", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "level":"group", - "label":"35975", - "analysis":"6h7WzZ7sXd7S" + "id": "3ko2zEd4Adjf", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "level": "group", + "label": "35975", + "analysis": "6h7WzZ7sXd7S" } ], - "values":[ - - ] + "values": [] }, { - "id":"849pEYuZMgtH", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "user":null, - "coordinates":[ - -37.0, - -7.0, - 46.0 - ], - "analysis":"6h7WzZ7sXd7S", - "kind":"unknown", - "space":"TAL", - "image":null, - "label_id":null, - "entities":[ + "id": "849pEYuZMgtH", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "user": null, + "coordinates": [-37.0, -7.0, 46.0], + "analysis": "6h7WzZ7sXd7S", + "kind": "unknown", + "space": "TAL", + "image": null, + "label_id": null, + "entities": [ { - "id":"PmrzkXkgkLn7", - "created_at":"2022-07-22T08:26:40.465069+00:00", - "updated_at":null, - "level":"group", - "label":"35975", - "analysis":"6h7WzZ7sXd7S" + "id": "PmrzkXkgkLn7", + "created_at": "2022-07-22T08:26:40.465069+00:00", + "updated_at": null, + "level": "group", + "label": "35975", + "analysis": "6h7WzZ7sXd7S" } ], - "values":[ - - ] + "values": [] } ], - "images":[ - - ] + "images": [] } ] }, { - "id":"36nHEsLLPwBB", - "created_at":"2022-07-22T08:29:51.625947+00:00", - "updated_at":null, - "user":null, - "name":"Acute Stress Impairs Self-Control in Goal-Directed Choice by Altering Multiple Functional Connections within the Brain’s Decision Circuits", - "description":"Important decisions are often made under stressful\r\ncircumstances thatmight compromise self-regulatory\r\nbehavior. Yet the neural mechanisms by which\r\nstress influences self-control choices are unclear.\r\nWe investigated these mechanisms in human participants\r\nwho faced self-control dilemmas over food\r\nreward while undergoing fMRI following stress.\r\nWe found that stress increased the influence of\r\nimmediately rewarding taste attributes on choice\r\nand reduced self-control. This choice pattern was\r\naccompanied by increased functional connectivity\r\nbetween ventromedial prefrontal cortex (vmPFC)\r\nand amygdala and striatal regions encoding tastiness.\r\nFurthermore, stress was associated with\r\nreduced connectivity between the vmPFC and\r\ndorsolateral prefrontal cortex regions linked to selfcontrol\r\nsuccess. Notably, alterations in connectivity\r\npathways could be dissociated by their differential\r\nrelationships with cortisol and perceived stress.\r\nOur results indicate that stress may compromise\r\nself-control decisions by both enhancing the impact\r\nof immediately rewarding attributes and reducing the\r\nefficacy of regions promoting behaviors that are\r\nconsistent with long-term goals.\r\n\r\nThis collection contains second level correlations of stress induced differences in the influence of taste based decisions on vStr,Amyg and vmPFC and their connectivity.\r\n\r\nKey words: food choice, decision making, self-regulation", - "publication":"Neuron", - "doi":"10.1016/j.neuron.2015.07.005", - "pmid":null, - "authors":"Silvia U. Maier, Aidan B. Makwana and Todd A. Hare", - "year":null, - "metadata":{ - "url":"https://neurovault.org/collections/3259/", - "download_url":"https://neurovault.org/collections/3259/download", - "owner":1349, - "contributors":"HareLab", - "owner_name":"silvia.maier", - "number_of_images":4, - "paper_url":"https://linkinghub.elsevier.com/retrieve/pii/S0896627315006273", - "full_dataset_url":"", - "private":false, - "add_date":"2017-12-12T13:45:50.068678Z", - "modify_date":"2018-11-05T08:22:52.152005Z", - "doi_add_date":"2017-12-12T13:45:50.068157Z", - "type_of_design":"eventrelated", - "number_of_imaging_runs":3, - "number_of_experimental_units":70, - "length_of_runs":null, - "length_of_blocks":null, - "length_of_trials":"variable", - "optimization":true, - "optimization_method":"", - "subject_age_mean":21.15, - "subject_age_min":18.0, - "subject_age_max":27.0, - "handedness":"right", - "proportion_male_subjects":1.0, - "inclusion_exclusion_criteria":"normal or corrected-to-normal vision, non-smokers and refrained from taking any medication for 3 days prior to their scanning session,no history of eating disorders or food allergies and intolerances", - "number_of_rejected_subjects":3, - "group_comparison":true, - "group_description":"stress induction via socially evaluated cold pressor test vs control group (warm water condition)", - "scanner_make":"Phillips", - "scanner_model":"Philips Achieva 3 T whole-body scanner", - "field_strength":3.0, - "pulse_sequence":"T2* EPI ", - "parallel_imaging":"SENSE factor 2", - "field_of_view":null, - "matrix_size":null, - "slice_thickness":3.1, - "skip_distance":0.6, - "acquisition_orientation":"axial at +15 degree tilt to ACPC", - "order_of_acquisition":"ascending", - "repetition_time":2460.0, - "echo_time":30.0, - "flip_angle":77.0, - "software_package":"", - "software_version":"", - "order_of_preprocessing_operations":"", - "quality_control":"", - "used_b0_unwarping":null, - "b0_unwarping_software":"", - "used_slice_timing_correction":null, - "slice_timing_correction_software":"", - "used_motion_correction":null, - "motion_correction_software":"", - "motion_correction_reference":"", - "motion_correction_metric":"", - "motion_correction_interpolation":"", - "used_motion_susceptibiity_correction":null, - "used_intersubject_registration":null, - "intersubject_registration_software":"", - "intersubject_transformation_type":null, - "nonlinear_transform_type":"", - "transform_similarity_metric":"", - "interpolation_method":"", - "object_image_type":"", - "functional_coregistered_to_structural":null, - "functional_coregistration_method":"", - "coordinate_space":null, - "target_template_image":"", - "target_resolution":null, - "used_smoothing":null, - "smoothing_type":"", - "smoothing_fwhm":null, - "resampled_voxel_size":null, - "intrasubject_model_type":"", - "intrasubject_estimation_type":"", - "intrasubject_modeling_software":"", - "hemodynamic_response_function":"", - "used_temporal_derivatives":null, - "used_dispersion_derivatives":null, - "used_motion_regressors":null, - "used_reaction_time_regressor":null, - "used_orthogonalization":null, - "orthogonalization_description":"", - "used_high_pass_filter":null, - "high_pass_filter_method":"", - "autocorrelation_model":"", - "group_model_type":"", - "group_estimation_type":"", - "group_modeling_software":"", - "group_inference_type":null, - "group_model_multilevel":"", - "group_repeated_measures":null, - "group_repeated_measures_method":"", - "nutbrain_hunger_state":"II", - "nutbrain_food_viewing_conditions":"palatable-healthy, unpalatable-healthy, palatable-unhealthy, unpalatable-unhealthy", - "nutbrain_food_choice_type":"two-alternative forced choice, all combinations of the above foods / image categories possible", - "nutbrain_taste_conditions":"none", - "nutbrain_odor_conditions":"none", - "communities":[ - 2 - ] + "id": "36nHEsLLPwBB", + "created_at": "2022-07-22T08:29:51.625947+00:00", + "updated_at": null, + "user": null, + "name": "Acute Stress Impairs Self-Control in Goal-Directed Choice by Altering Multiple Functional Connections within the Brain’s Decision Circuits", + "description": "Important decisions are often made under stressful\r\ncircumstances thatmight compromise self-regulatory\r\nbehavior. Yet the neural mechanisms by which\r\nstress influences self-control choices are unclear.\r\nWe investigated these mechanisms in human participants\r\nwho faced self-control dilemmas over food\r\nreward while undergoing fMRI following stress.\r\nWe found that stress increased the influence of\r\nimmediately rewarding taste attributes on choice\r\nand reduced self-control. This choice pattern was\r\naccompanied by increased functional connectivity\r\nbetween ventromedial prefrontal cortex (vmPFC)\r\nand amygdala and striatal regions encoding tastiness.\r\nFurthermore, stress was associated with\r\nreduced connectivity between the vmPFC and\r\ndorsolateral prefrontal cortex regions linked to selfcontrol\r\nsuccess. Notably, alterations in connectivity\r\npathways could be dissociated by their differential\r\nrelationships with cortisol and perceived stress.\r\nOur results indicate that stress may compromise\r\nself-control decisions by both enhancing the impact\r\nof immediately rewarding attributes and reducing the\r\nefficacy of regions promoting behaviors that are\r\nconsistent with long-term goals.\r\n\r\nThis collection contains second level correlations of stress induced differences in the influence of taste based decisions on vStr,Amyg and vmPFC and their connectivity.\r\n\r\nKey words: food choice, decision making, self-regulation", + "publication": "Neuron", + "doi": "10.1016/j.neuron.2015.07.005", + "pmid": null, + "authors": "Silvia U. Maier, Aidan B. Makwana and Todd A. 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+
{table.getHeaderGroups().map((headerGroup) => ( @@ -371,7 +375,7 @@ const ExtractionTable: React.FC = () => { sx={{ maxWidth: '40vw', display: 'flex', - justifyContent: 'flex-start', + justifyContent: 'flex-end', flexWrap: 'wrap', marginRight: '1rem', }} @@ -412,7 +416,7 @@ const ExtractionTable: React.FC = () => { ))} - + Viewing {table.getFilteredRowModel().rows.length} / {data.length} diff --git a/compose/neurosynth-frontend/tsconfig.json b/compose/neurosynth-frontend/tsconfig.json index b81f5299..46916174 100644 --- a/compose/neurosynth-frontend/tsconfig.json +++ b/compose/neurosynth-frontend/tsconfig.json @@ -18,5 +18,5 @@ "jsx": "react-jsx", "types": ["cypress", "node", "jest"] }, - "include": ["src"] + "include": ["src", "cypress"] }