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feat: moved sleuth import functionality to import studies UI and added tests
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‎compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportFileFormat.cy.tsx‎

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/// <reference types="cypress" />
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describe('ImportFileFormatDialog', () => {
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beforeEach(() => {
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cy.clearLocalStorage();
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cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture');
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cy.intercept('GET', `**/api/projects/*`, {
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fixture: 'projects/projectExtractionStep',
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}).as('projectFixture');
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cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture');
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});
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describe('Import via File Format', () => {
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beforeEach(() => {
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cy.login('mocked').visit('/projects/abc123/curation').wait('@projectFixture').wait('@studysetFixture');
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cy.intercept('PUT', '**/api/projects/abc123').as('updateProjectFixture');
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cy.contains('button', 'import studies').click();
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cy.contains('Import via File Format').click();
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cy.contains('button', 'next').click();
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});
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it('should show the standard file import page', () => {
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cy.contains(/enter data source/).should('be.visible');
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});
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it('should disable the next button initially', () => {
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cy.contains('button', 'next').should('be.disabled');
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});
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it('should set the source and show the input', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('textarea').should('be.visible');
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cy.contains(/Input is empty/).should('be.visible');
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});
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it('should set the sources and enable the next button', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('textarea[placeholder="paste in valid endnote, bibtex, or RIS syntax"]')
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.click()
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.type(
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`%0 Journal Article\n%T Role of the anterior insula in task-level control and focal attention\n%A Nelson, Steven M\n%A Dosenbach, Nico UF\n%A Cohen, Alexander L\n%A Wheeler, Mark E\n%A Schlaggar, Bradley L\n%A Petersen, Steven E\n%J Brain structure and function\n%V 214\n%669-680\n%@ 1863-2653\n%D 2010\n%I Springer-Verlag\n`,
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{
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delay: 1,
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}
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);
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cy.contains('button', 'next').should('not.be.disabled');
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});
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it('should show an error message', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('textarea[placeholder="paste in valid endnote, bibtex, or RIS syntax"]').type('INVALID FORMAT');
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cy.contains(/Format is incorrect/).should('be.visible');
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});
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it('should import studies', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('textarea[placeholder="paste in valid endnote, bibtex, or RIS syntax"]')
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.click()
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.type(
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`%0 Journal Article\n%T Role of the anterior insula in task-level control and focal attention\n%A Nelson, Steven M\n%A Dosenbach, Nico UF\n%A Cohen, Alexander L\n%A Wheeler, Mark E\n%A Schlaggar, Bradley L\n%A Petersen, Steven E\n%J Brain structure and function\n%V 214\n%669-680\n%@ 1863-2653\n%D 2010\n%I Springer-Verlag\n`,
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{
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delay: 1,
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}
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);
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cy.contains('button', 'next').click();
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cy.get('input').type('my new import{enter}');
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cy.contains('button', 'next').click().url().should('include', '/projects/abc123/curation');
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});
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it('should upload a onenote (ENW) file', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('label[role="button"]').selectFile('cypress/fixtures/standardFiles/onenoteStudies.txt');
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cy.contains('button', 'next').should('be.visible');
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});
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it('should upload a .RIS file and import successfully', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('label[role="button"]').selectFile('cypress/fixtures/standardFiles/ris.ris');
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cy.contains('button', 'next').should('be.visible').and('not.be.disabled');
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cy.contains('button', 'next').click();
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});
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it('should handle the duplicates in an import file', () => {
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Scopus').click();
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cy.get('label[role="button"]').selectFile('cypress/fixtures/standardFiles/duplicates.ris');
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cy.contains('button', 'next').should('be.visible').and('not.be.disabled');
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cy.contains('button', 'next').click();
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cy.contains('Click to view 1 imported studies').click();
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cy.contains('(2023). Manifold Learning for fMRI time-varying FC').should(
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// doing this to enforce strict equals
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($el: JQuery<HTMLElement> | undefined) => {
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if (!$el) throw new Error('Could not find element');
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expect($el.text()).to.equal('(2023). Manifold Learning for fMRI time-varying FC');
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}
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);
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cy.contains(/^\bbioRxiv\b/).should('exist'); // \b is a word boundary which means there shouldnt be any other letters/words before and after
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});
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// TODO : create a test for importing bibtex file
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// it('should import studies via a file', () => {})
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});
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});

‎compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportManualCreate.cy.tsx‎

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/// <reference types="cypress" />
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describe('ImportManualCreateDialog', () => {
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beforeEach(() => {
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cy.clearLocalStorage();
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cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture');
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cy.intercept('GET', `**/api/projects/*`, {
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fixture: 'projects/projectExtractionStep',
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}).as('projectFixture');
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cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture');
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});
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describe('Manually create a new study', () => {
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beforeEach(() => {
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cy.login('mocked').visit('/projects/abc123/curation').wait('@projectFixture').wait('@studysetFixture');
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cy.intercept('PUT', '**/api/projects/abc123').as('updateProjectFixture');
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cy.contains('button', 'import studies').click();
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cy.contains('Manually create a new study').click();
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cy.contains('button', 'next').click();
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});
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it('should show the create new study page', () => {
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cy.contains('label', 'Study Name *').should('be.visible');
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cy.contains('label', 'Authors').should('be.visible');
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cy.contains('label', 'DOI').should('be.visible');
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cy.contains('label', 'Journal').should('be.visible');
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cy.contains('label', 'PubMed ID').should('be.visible');
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cy.contains('label', 'PubMed Central ID').should('be.visible');
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cy.contains('label', 'Article Year').should('be.visible');
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cy.contains('label', 'article link').should('be.visible');
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cy.contains('label', 'Keywords').should('be.visible');
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cy.contains('label', 'select study data source *').should('be.visible');
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});
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it('should be disabled initially', () => {
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cy.contains('button', 'next').should('be.disabled');
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});
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it('should be enabled when name and source are entered', () => {
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cy.get('input[placeholder="My study name"]').click().type('new study');
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Neurostore').click();
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cy.contains('button', 'next').should('not.be.disabled');
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});
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it('should import studies', () => {
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cy.get('input[placeholder="My study name"]').click().type('new study');
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cy.get('input[role="combobox"]').click();
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cy.contains('li', 'Neurostore').click();
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cy.contains('button', 'next').click();
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cy.get('input').type('my new import{enter}');
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cy.contains('button', 'next').click().url().should('include', '/projects/abc123/curation');
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});
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});
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});

‎compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportNeurostore.cy.tsx‎

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/// <reference types="cypress" />
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describe('ImportStudiesDialog', () => {
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beforeEach(() => {
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cy.clearLocalStorage();
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cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture');
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cy.intercept('GET', `**/api/projects/*`, {
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fixture: 'projects/projectExtractionStep',
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}).as('projectFixture');
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cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture');
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});
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describe('Search Neurostore', () => {
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beforeEach(() => {
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cy.login('mocked').visit('/projects/abc123/curation');
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cy.intercept('GET', '**/api/base-studies/**', {
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fixture: 'baseStudies/baseStudiesWithResults',
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}).as('baseStudiesFixture');
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cy.intercept('PUT', '**/api/projects/abc123').as('updateProjectFixture');
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cy.visit('/projects/abc123/curation').wait('@projectFixture').wait('@studysetFixture');
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cy.contains('button', 'import studies').click();
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cy.contains('button', 'next').click();
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});
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it('should show the neurostore search page', () => {
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// we can target the table as the neurostore search is the only table HTML that appears in this workflow
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cy.get('.MuiTableContainer-root').should('be.visible');
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});
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it('should be disabled initially', () => {
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cy.wait('@baseStudiesFixture').then((baseStudiesResponse) => {
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cy.contains(
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'button',
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`Import ${baseStudiesResponse.response?.body?.results?.length} studies from neurostore`
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).should('be.disabled');
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});
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});
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it('should import studies', () => {
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cy.get('input[type="text"]').type('neuron');
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cy.get('button').contains('Search').click();
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cy.wait('@baseStudiesFixture').then((baseStudiesResponse) => {
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cy.contains(
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'button',
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`Import ${baseStudiesResponse.response?.body?.results?.length} studies from neurostore`
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).click();
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});
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cy.get('input').type('my new import{enter}');
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cy.contains('button', 'next').click().url().should('include', '/projects/abc123/curation');
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});
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});
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});

‎compose/neurosynth-frontend/cypress/e2e/workflows/Curation/ImportPubmed.cy.tsx‎

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/// <reference types="cypress" />
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describe('ImportPubmedDialog', () => {
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beforeEach(() => {
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cy.clearLocalStorage();
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cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture');
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cy.intercept('GET', `**/api/projects/*`, {
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fixture: 'projects/projectExtractionStep',
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}).as('projectFixture');
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cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture');
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});
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describe('Import via Pubmed IDs', () => {
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beforeEach(() => {
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cy.login('mocked').visit('/projects/abc123/curation').wait('@projectFixture').wait('@studysetFixture');
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cy.intercept('PUT', '**/api/projects/abc123').as('updateProjectFixture');
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// not going to mock this for now as cypress does not seem to support XML fixtures
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// cy.intercept('POST', 'https://eutils.ncbi.nlm.nih.gov/**', {
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// fixture: 'NIHPMIDResponse',
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// }).as('NIHPMIDFixture.xml');
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cy.contains('button', 'import studies').click();
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cy.contains(/PMID/).click();
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cy.contains('button', 'next').click();
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});
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it('should show the pmid input page', () => {
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cy.get('textarea[placeholder="Enter list of pubmed IDs separated by a newline"]').should('be.visible');
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});
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it('should be disabled initially', () => {
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cy.contains('button', 'next').should('be.disabled');
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});
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it('should be enabled when an input is entered', () => {
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cy.get('textarea[placeholder="Enter list of pubmed IDs separated by a newline"]')
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.click()
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.type('123{enter}456{enter}789');
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cy.contains('button', 'next').should('not.be.disabled');
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});
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it('should show invalid for invalid input', () => {
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cy.get('textarea[placeholder="Enter list of pubmed IDs separated by a newline"]')
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.click()
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.type('123{enter}456{enter}789A');
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cy.contains(/format is incorrect/);
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cy.contains('button', 'next').should('be.disabled');
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});
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it('should import studies', () => {
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cy.get('textarea[placeholder="Enter list of pubmed IDs separated by a newline"]')
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.click()
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.type('123{enter}456{enter}789');
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cy.contains('button', 'next').click();
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cy.get('input').type('my new import{enter}');
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cy.contains('button', 'next').click().url().should('include', '/projects/abc123/curation');
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});
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it('should import studies via a file', () => {
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cy.get('label[role="button"]').selectFile('cypress/fixtures/pmids.txt');
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cy.contains('button', 'next').should('not.be.disabled');
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});
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});
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});

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