Merge branch 'main' into locality-search-filters

backend/src/api-tests/region/get.test.ts

@@ -2,7 +2,7 @@ import { beforeAll, afterAll, describe, it, expect, beforeEach } from '@jest/glo
 import { login, logout, resetDatabase, send, resetDatabaseTimeout } from '../utils'
 import { pool } from '../../utils/db'
 
-describe('Deleting a region works', () => {
+describe('Getting region data works', () => {
   beforeAll(async () => {
     await resetDatabase()
   }, resetDatabaseTimeout)

cypress/e2e/locality.cy.js

@@ -60,7 +60,7 @@ describe('Creating a new locality', () => {
     cy.get('[id=dms_lat-textfield]').should('have.value', '48 40 48 N')
     cy.contains('This field is required')
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('4 Invalid fields')
+    cy.contains('4 invalid fields')
   })
 
   it("and filling, then erasing needed data doesn't work", () => {
@@ -95,12 +95,12 @@ describe('Creating a new locality', () => {
     cy.get('[id=min_age-textfield]').type('{backspace}{backspace}{backspace}{backspace}{backspace}')
     cy.contains('This field is required')
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('1 Invalid fields')
+    cy.contains('1 invalid field')
 
     // make sure errors in other tabs disable the write button
     cy.get('[role=tablist]').contains('Locality').click()
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('1 Invalid fields')
+    cy.contains('1 invalid field')
   })
 
   it('write button is disabled if unvisited tab has validation errors', () => {
@@ -116,12 +116,12 @@ describe('Creating a new locality', () => {
 
     // Age tab has no errors, but Locality tab has unfilled mandatory fields
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('6 Invalid fields')
+    cy.contains('6 invalid fields')
     cy.get('[id=min_age-textfield-helper-text]').should('not.exist')
     cy.get('[id=max_age-textfield-helper-text]').should('not.exist')
     cy.get('[role=tablist]').contains('Locality').click()
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('6 Invalid fields')
+    cy.contains('6 invalid fields')
   })
 
   it('composite dating method works', () => {
@@ -233,7 +233,7 @@ describe('Editing a locality', () => {
     cy.get('[id=max_age-textfield]').type('{backspace}{backspace}{backspace}{backspace}{backspace}9')
     cy.contains('Min value cannot be higher than max')
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('4 Invalid fields')
+    cy.contains('4 invalid fields')
   })
 
   it('changing fractions and basis for age updates the age correctly', () => {

cypress/e2e/reference.cy.js

@@ -0,0 +1,175 @@
+before('Reset database', () => {
+  cy.request(Cypress.env('databaseResetUrl'))
+})
+
+describe('Creating a journal', () => {
+  beforeEach('Login as admin', () => {
+    cy.login('testSu')
+  })
+
+  it('with valid data works', () => {
+    cy.visit('/reference/new')
+    cy.contains('Journal')
+    cy.contains('7 invalid fields')
+
+    cy.get('[id=title_primary-textfield]').type('New test reference')
+
+    cy.get('[data-cy=Select\\ author-button]').click()
+    cy.get('[data-cy=detailview-button-1]').click()
+    cy.contains('Close').click()
+
+    cy.get('[id=date_primary-textfield]').type('2025')
+
+    cy.get('[data-cy=Select\\ Journal-button]').click()
+    cy.get('[data-cy=detailview-button-100]').click()
+    cy.contains('Close').click()
+
+    cy.get('[id=write-button]').click()
+    cy.contains('Saved reference successfully.')
+  })
+
+  it('with missing required fields does not work', () => {
+    cy.visit('/reference/new')
+    cy.contains('Journal')
+    cy.contains('7 invalid fields')
+
+    cy.get('[id=title_primary-textfield]').type('New test reference 2')
+    cy.contains('3 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[data-cy=Select\\ author-button]').click()
+    cy.get('[data-cy=detailview-button-1]').click()
+    cy.contains('Close').click()
+    cy.contains('2 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[id=date_primary-textfield]').type('2025')
+    cy.contains('1 invalid field')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[data-cy=Select\\ Journal-button]').click()
+    cy.get('[data-cy=detailview-button-100]').click()
+    cy.contains('Close').click()
+    cy.get('[id=write-button]').should('not.be.disabled')
+
+    cy.get('[data-testid=RemoveCircleOutlineIcon]').first().click() // removes the selected author
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.get('[data-cy=Select\\ author-button]').click()
+    cy.get('[data-cy=detailview-button-1]').click()
+    cy.contains('Close').click()
+    cy.get('[id=write-button]').should('not.be.disabled')
+  })
+
+  it('combined check with different types of titles and gen notes works', () => {
+    cy.visit('/reference/new')
+    cy.contains('Journal')
+    cy.contains('7 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[id=title_primary-textfield]').type('Title Primary')
+    cy.contains('3 invalid fields')
+    cy.get('[id=title_primary-textfield]').clear()
+    cy.contains('7 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[id=title_secondary-textfield]').type('Title Secondary')
+    cy.contains('3 invalid fields')
+    cy.get('[id=title_secondary-textfield]').clear()
+    cy.contains('7 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[id=title_series-textfield]').type('Title Series')
+    cy.contains('3 invalid fields')
+    cy.get('[id=title_series-textfield]').clear()
+    cy.contains('7 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+
+    cy.get('[id=gen_notes-textfield]').type('Gen Notes')
+    cy.contains('3 invalid fields')
+    cy.get('[id=gen_notes-textfield]').clear()
+    cy.contains('7 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+  })
+})
+
+// TODO: add more tests for different types of references
+
+describe('Editing a journal', () => {
+  beforeEach('Login as admin', () => {
+    cy.login('testSu')
+  })
+
+  it('with valid data works', () => {
+    cy.visit('reference/10039')
+    cy.contains('A new geomagnetic polarity time scale for the Late Cretaceous and Cenozoic.')
+    cy.get('[id=edit-button]').click()
+    cy.get('[id=title_primary-textfield]').clear()
+    cy.get('[id=title_primary-textfield]').type('New primary title.')
+
+    cy.get('[data-cy=Select\\ author-button]').click()
+    cy.get('[data-cy=detailview-button-2]').click()
+    cy.contains('Close').click()
+
+    cy.get('[id=write-button]').click()
+    cy.contains('Saved reference successfully.')
+    cy.contains('New primary title.')
+    cy.contains('Cande') // Author 1
+    cy.contains('Ciochon') // Author 2
+  })
+
+  it('with missing required fields does not work', () => {
+    cy.visit('reference/10039')
+    cy.contains('New primary title.')
+    cy.get('[id=edit-button]').click()
+    cy.get('[id=title_primary-textfield]').clear()
+    cy.contains('4 invalid fields')
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.get('[id=title_primary-textfield]').type('New primary title.')
+
+    cy.get('[data-testid=RemoveCircleOutlineIcon]').first().click()
+    cy.get('[data-testid=RemoveCircleOutlineIcon]').first().click() // removes the selected authors
+    cy.contains('1 invalid field')
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.get('[data-cy=Select\\ author-button]').click()
+    cy.get('[data-cy=detailview-button-1]').click()
+    cy.contains('Close').click()
+    cy.get('[id=write-button]').should('not.be.disabled')
+  })
+})
+
+// TODO: add more tests for different types of references
+
+describe('Deleting a reference', () => {
+  beforeEach('Login as admin', () => {
+    cy.login('testSu')
+  })
+
+  it('that is not linked to anything works and returns user to table view', () => {
+    cy.visit('/reference/25000')
+    cy.get('[id=delete-button]').should('exist').click()
+    cy.on('window:confirm', str => {
+      expect(str).to.eq('Are you sure you want to delete this item? This operation cannot be undone.')
+      // this automatically clicks the OK button and returns to table view
+    })
+    cy.contains('Deleted item successfully.')
+    cy.contains('Dated co-occurrence of Homo erectus and Gigantopithecus from Tham Khuyen Cave, Vietnam') // check that table view has been navigated to
+    cy.contains('A test reference that is not linked to any localities or species').should('not.exist')
+    cy.visit('/reference/25000')
+    cy.contains('Error loading data')
+  })
+
+  // Skipped because references that have linked localities or species cannot be deleted currently
+  it.skip('that is linked to a locality and a species works and returns user to table view', () => {
+    cy.visit('/reference/10039')
+    cy.get('[id=delete-button]').should('exist').click()
+    cy.on('window:confirm', str => {
+      expect(str).to.eq('Are you sure you want to delete this item? This operation cannot be undone.')
+      // this automatically clicks the OK button and returns to table view
+    })
+    cy.contains('Deleted item successfully.')
+    cy.contains('Dated co-occurrence of Homo erectus and Gigantopithecus from Tham Khuyen Cave, Vietnam') // check that table view has been navigated to
+    cy.contains('A new geomagnetic polarity time scale for the Late Cretaceous and Cenozoic').should('not.exist')
+    cy.visit('/reference/10039')
+    cy.contains('Error loading data')
+  })
+})

cypress/e2e/species.cy.js

@@ -1,3 +1,7 @@
+before('Reset database', () => {
+  cy.request(Cypress.env('databaseResetUrl'))
+})
+
 describe('Creating a species', () => {
   beforeEach('Login as admin', () => {
     cy.login('testSu')
@@ -24,7 +28,78 @@ describe('Creating a species', () => {
     cy.visit('/species/new')
     cy.contains('This field is required')
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('4 Invalid fields')
+    cy.contains('4 invalid fields')
+  })
+})
+
+describe('Editing a species', () => {
+  beforeEach('Login as admin', () => {
+    cy.login('testSu')
+  })
+
+  it('with valid data works', () => {
+    cy.visit('/species/21052/')
+    cy.contains('21052 Simplomys simplicidens')
+    cy.get('[id=edit-button]').click()
+
+    cy.get('[id=order_name-textfield]').clear()
+    cy.get('[id=order_name-textfield]').type('modifiedOrder')
+    cy.get('[id=family_name-textfield]').clear()
+    cy.get('[id=family_name-textfield]').type('modifiedFamily')
+    cy.get('[id=genus_name-textfield]').clear()
+    cy.get('[id=genus_name-textfield]').type('modifiedGenus')
+    cy.get('[id=species_name-textfield]').clear()
+    cy.get('[id=species_name-textfield]').type('modifiedSpecies')
+    cy.get('[id=subfamily_name-textfield]').type('heimo')
+
+    cy.get('[id=write-button]').should('not.be.disabled')
+    cy.get('[id=write-button]').click()
+    cy.contains('button', 'Add existing reference').click()
+    cy.get('button[data-cy^="detailview-button"]').first().click()
+    cy.contains('button', 'Close').click()
+    cy.get('[id=write-button]').should('not.be.disabled')
+    cy.get('[id=write-button]').click()
+    cy.contains('Saved species entry successfully.')
+    cy.contains('modifiedOrder')
+    cy.contains('Subfamily or Tribe heimo')
+  })
+
+  it('with missing required fields does not work', () => {
+    cy.visit('/species/21052/')
+    cy.contains('21052')
+    cy.get('[id=edit-button]').click()
+
+    cy.get('[id=order_name-textfield]').clear()
+    cy.contains('Order: This field is required')
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.contains('1 invalid field')
+
+    cy.get('[id=family_name-textfield]').clear()
+    cy.contains('Family: This field is required')
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.contains('2 invalid fields')
+
+    cy.get('[id=order_name-textfield]').type('newOrder')
+    cy.contains('Order: This field is required').should('not.exist')
+    cy.contains('Family: This field is required')
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.contains('1 invalid field')
+
+    cy.get('[id=family_name-textfield]').type('newFamily')
+    cy.contains('Family: This field is required').should('not.exist')
+    cy.get('[id=write-button]').click()
+
+    cy.contains('button', 'Add existing reference').click()
+    cy.get('button[data-cy^="detailview-button"]').first().click()
+    cy.contains('button', 'Close').click()
+    cy.get('[id=write-button]').should('not.be.disabled')
+    cy.get('[id=write-button]').click()
+
+    cy.contains('Saved species entry successfully.')
+    cy.contains('newOrder')
+    cy.contains('newFamily')
+    cy.contains('modifiedGenus')
+    cy.contains('Subfamily or Tribe heimo')
   })
 })
 

cypress/e2e/timeBound.cy.js

@@ -1,10 +1,35 @@
-describe('Editing time bound', () => {
+before('Reset database', () => {
+  cy.request(Cypress.env('databaseResetUrl'))
+})
+
+describe('Creating time bound', () => {
   beforeEach('Login as admin', () => {
     cy.login('testSu')
   })
 
-  beforeEach('Reset database', () => {
-    cy.request(Cypress.env('databaseResetUrl'))
+  it('with correct values works', () => {
+    cy.visit(`/time-bound/new/`)
+    cy.contains('Creating new time-bound')
+    cy.contains('Name: This field is required')
+    cy.contains('Age (Ma): This field is required')
+    cy.get('[id=b_name-textfield]').first().type('test bound')
+    cy.contains('Name: This field is required').should('not.exist')
+    cy.get('[id=write-button]').should('be.disabled')
+    cy.get('[id=age-textfield]').first().type('20')
+    cy.contains('Age (Ma): This field is required').should('not.exist')
+    cy.get('[id=write-button]').click()
+    cy.contains('button', 'Add existing reference').click()
+    cy.get('button[data-cy^="detailview-button"]').first().click()
+    cy.contains('button', 'Close').click()
+    cy.get('[id=write-button]').should('not.be.disabled')
+    cy.get('[id=write-button]').click()
+    cy.contains('Edited item successfully.')
+  })
+})
+
+describe('Editing time bound', () => {
+  beforeEach('Login as admin', () => {
+    cy.login('testSu')
   })
 
   it('with correct values works', () => {
@@ -20,6 +45,7 @@ describe('Editing time bound', () => {
     cy.contains('button', 'Close').click()
     cy.get('[id=write-button]').should('not.be.disabled')
     cy.get('[id=write-button]').click()
+    cy.contains('Edited item successfully.')
     cy.contains('1.5')
   })
 
@@ -30,7 +56,7 @@ describe('Editing time bound', () => {
     cy.get('[id=age-textfield]').first().type('{backspace}{backspace}{backspace}{backspace}{backspace}')
     cy.contains('This field is required')
     cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('1 Invalid fields')
+    cy.contains('1 invalid field')
   })
 })
 

frontend/src/components/DetailView/common/SelectingTable.tsx

@@ -67,7 +67,7 @@ export const SelectingTable = <T extends MRT_RowData, ParentType extends object>
   if (isError) return <Box>Error fetching data for the selecting table.</Box>
   if (!data) return <CircularProgress />
   return (
-    <EditingModal buttonText={buttonText}>
+    <EditingModal dataCy={`${buttonText}-button`} buttonText={buttonText}>
       {data ? (
         <TableView<T>
           data={filteredData}

frontend/src/components/DetailView/components.tsx

@@ -113,6 +113,8 @@ export const ErrorBox = <T,>() => {
   const { fieldsWithErrors } = useDetailContext<T>()
   const fields = Object.keys(fieldsWithErrors)
 
+  const title = fields.length > 1 ? `${fields.length} invalid fields` : '1 invalid field'
+
   return (
     <Box
       sx={{
@@ -126,7 +128,7 @@ export const ErrorBox = <T,>() => {
       }}
     >
       <Typography color="text.secondary" gutterBottom>
-        {`${fields.length} Invalid fields`}
+        {title}
       </Typography>
       <List sx={{ maxHeight: '5em', maxWidth: '30em', padding: '0em 0.8em 0em 0.8em', overflow: 'auto' }}>
         {fields.map(field => (

test_data/sqlfiles/now_test.sql

@@ -1709,7 +1709,8 @@ INSERT INTO `ref_authors` VALUES
 (21368,2,1,'Ciochon','Russell'),
 (24151,2,1,'Ogg','J.G.'),
 (24187,2,1,'Kaakinen','A.'),
-(24188,2,1,'Wang','X.');
+(24188,2,1,'Wang','X.'),
+(25000,2,1,'Doe','D.');
 /*!40000 ALTER TABLE `ref_authors` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -2198,7 +2199,8 @@ INSERT INTO `ref_ref` VALUES
 (21368,1,100,'Dated co-occurrence of Homo erectus and Gigantopithecus from Tham Khuyen Cave, Vietnam',1996,'93',NULL,3016,3020,NULL,NULL,NULL,NULL,NULL,NULL,'abstract','http://www.pnas.org/cgi/reprint/93/7/3016',NULL,NULL,NULL,'English',NULL,NULL,1,NULL),
 (24151,2,NULL,'A Concise Geologic Time Scale: 2016',2016,NULL,NULL,NULL,240,'Elsevier',NULL,NULL,NULL,NULL,'9780444594686',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,1,0),
 (24187,13,NULL,'Helsinki Asian time update',2020,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2020-01-29',NULL,1,NULL),
-(24188,2,NULL,'Fossil Mammals of Asia',2013,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL);
+(24188,2,NULL,'Fossil Mammals of Asia',2013,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL),
+(25000,1,100,'A test reference that is not linked to any localities or species',2025,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
 /*!40000 ALTER TABLE `ref_ref` ENABLE KEYS */;
 UNLOCK TABLES;