Feature/doi form

cypress/integration/doiForm.spec.js

@@ -0,0 +1,217 @@
+describe("DOI form", function () {
+  beforeEach(() => {
+    cy.login()
+
+    cy.get("button", { timeout: 10000 }).contains("Create Submission").click()
+
+    // Add folder name & description, navigate to submissions
+    cy.get("input[name='name']").type("Test name")
+    cy.get("textarea[name='description']").type("Test description")
+    cy.get("button[type=button]").contains("Next").click()
+
+    cy.wait(500)
+  })
+  it("should render DOI form correctly with formats' prefilled values and affiliation's autocomplete field", () => {
+    // Fill in Run form
+    cy.clickFillForm("Run")
+
+    const testRunData = {
+      title: "Test Run",
+      experimentRefLabel: "Test Experiment reference label",
+    }
+
+    cy.get("input[data-testid='title']").type(testRunData.title)
+    cy.get("h2[data-testid='experimentRef']").parents().children("button").click()
+    cy.get("[data-testid='experimentRef.0.label']").type(testRunData.experimentRefLabel)
+
+    const testRunFile = {
+      fileName: "Run file name",
+      fileType: "bam",
+      checksumMethod: "MD5",
+      checksum: "Run file check sum",
+    }
+    cy.get("h2[data-testid='files']").parents().children("button").click()
+    cy.get("input[name='files.0.filename']").type(testRunFile.fileName)
+    cy.get("select[name='files.0.filetype']").select(testRunFile.fileType)
+    cy.get("select[name='files.0.checksumMethod']").select(testRunFile.checksumMethod)
+    cy.get("input[name='files.0.checksum']").type(testRunFile.checksum)
+
+    // Submit form
+    cy.get("button[type=submit]").contains("Submit").click()
+
+    // Submitted objects list should have newly added item from Run form
+    cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
+
+    // Fill in Analysis form
+    cy.clickFillForm("Analysis")
+
+    const testAnalysisData = {
+      title1: "Test Analysis",
+      title2: "Test Analysis 2",
+      analysisType: "Reference Alignment",
+      refAlignmentAssembly: "Standard",
+      refAlignmentAssemblyId: "Standard Accession Id",
+    }
+
+    cy.get("input[name='title']").type(testAnalysisData.title1)
+    cy.get("select[name='analysisType']").select("Reference Alignment")
+    cy.get("select[name='analysisType.referenceAlignment.assembly']").select("Standard")
+    cy.get("input[name='analysisType.referenceAlignment.assembly.accessionId']").type("Standard Accession Id")
+
+    const testAnalysisFile = {
+      fileName: "Analysis file name",
+      fileType1: "cram",
+      fileType2: "bam",
+      checksumMethod: "SHA-256",
+      checksum: "Analysis file check sum",
+    }
+    // Select fileType
+    cy.get("h2[data-testid='files']").parents().children("button").click()
+    cy.get("input[name='files.0.filename']").type(testAnalysisFile.fileName)
+    cy.get("select[name='files.0.filetype']").select(testAnalysisFile.fileType1)
+    cy.get("select[name='files.0.checksumMethod']").select(testAnalysisFile.checksumMethod)
+    cy.get("input[name='files.0.checksum']").type(testAnalysisFile.checksum)
+
+    // Submit form
+    cy.get("button[type=submit]").contains("Submit").click()
+
+    // Submitted objects list should have newly added item from Run form
+    cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
+
+    // Fill another Analysis form with the same fileType as Run form: "bam"
+    cy.get("button").contains("New form").click()
+    cy.get("input[name='title']").type(testAnalysisData.title2)
+    cy.get("select[name='analysisType']").select("Reference Alignment")
+    cy.get("select[name='analysisType.referenceAlignment.assembly']").select("Standard")
+    cy.get("input[name='analysisType.referenceAlignment.assembly.accessionId']").type("Standard Accession Id")
+    // Select fileType
+    cy.get("input[name='files.0.filename']").type(testAnalysisFile.fileName)
+    cy.get("select[name='files.0.filetype']").select(testAnalysisFile.fileType2)
+    cy.get("select[name='files.0.checksumMethod']").select(testAnalysisFile.checksumMethod)
+    cy.get("input[name='files.0.checksum']").type(testAnalysisFile.checksum)
+
+    // Submit form
+    cy.get("button[type=submit]").contains("Submit").click()
+
+    // Submitted objects list should have newly added item from Run form
+    cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 2)
+
+    // Go to DOI form
+    cy.get("button[type=button]").contains("Next").click()
+    cy.get("button").contains("Add DOI information (optional)", { timeout: 10000 }).click()
+    cy.get("div[role='dialog']").should("be.visible")
+
+    // Check file types from submitted Run form and Analysis form are Uniquely pre-filled in DOI form
+    cy.get("input[data-testid='formats.0']", { timeout: 10000 }).should("have.value", "bam")
+    cy.get("input[data-testid='formats.1']", { timeout: 10000 }).should("have.value", "cram")
+
+    // Go to Creators section and Add new item
+    cy.get("h2[data-testid='creators']").parents().children("button").click()
+    cy.get("h3[data-testid='creators.0.affiliation']", { timeout: 10000 }).parent().children("button").click()
+    // Type search words in autocomplete field
+    cy.get("input[name='creators.0.affiliation.0.name']").type("csc")
+    // Select the first result
+    cy.get(".MuiAutocomplete-option")
+      .should("be.visible")
+      .then($el => $el.first().click())
+    // Check the rest 3 fields are auto-filled and disabled
+    cy.get("input[data-testid='creators.0.affiliation.0.schemeUri']").should("have.value", "https://ror.org")
+    cy.get("input[data-testid='creators.0.affiliation.0.schemeUri']").should("be.disabled")
+
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifier").should(
+      "have.value",
+      "https://ror.org/04m8m1253"
+    )
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifier").should("be.disabled")
+
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifierScheme']").should("have.value", "ROR")
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifierScheme']").should("be.disabled")
+
+    // Remove Creators > Affiliations field and add a new field again
+    cy.get("div[data-testid='creators.0.affiliation']").children("button").click()
+    cy.get("h3[data-testid='creators.0.affiliation']").parent().children("button").click()
+
+    // Repeat search words in autocomplete field
+    cy.get("input[name='creators.0.affiliation.0.name']").type("csc")
+    // Select the first result
+    cy.get(".MuiAutocomplete-option")
+      .should("be.visible")
+      .then($el => $el.first().click())
+
+    // Check the rest 3 fields are auto-filled and disabled as they should be
+    cy.get("input[data-testid='creators.0.affiliation.0.schemeUri']").should("have.value", "https://ror.org")
+    cy.get("input[data-testid='creators.0.affiliation.0.schemeUri']").should("be.disabled")
+
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifier").should(
+      "have.value",
+      "https://ror.org/04m8m1253"
+    )
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifier").should("be.disabled")
+
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifierScheme']").should("have.value", "ROR")
+    cy.get("input[data-testid='creators.0.affiliation.0.affiliationIdentifierScheme']").should("be.disabled")
+
+    // Go to Contributors and Add new item
+    cy.get("h2[data-testid='contributors']").parents().children("button").click()
+    cy.get("h3[data-testid='contributors.0.affiliation']", { timeout: 10000 }).parent().children("button").click()
+    // Type search words in autocomplete field
+    cy.get("input[name='contributors.0.affiliation.0.name']").type("demos")
+    // Select the first result
+    cy.get(".MuiAutocomplete-option")
+      .should("be.visible")
+      .then($el => $el.first().click())
+    // Check the rest 3 fields are auto-filled and disabled
+    cy.get("input[data-testid='contributors.0.affiliation.0.schemeUri").should("have.value", "https://ror.org")
+    cy.get("input[data-testid='contributors.0.affiliation.0.schemeUri").should("be.disabled")
+
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifier").should(
+      "have.value",
+      "https://ror.org/032bmj362"
+    )
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifier").should("be.disabled")
+
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifierScheme']").should("have.value", "ROR")
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifierScheme']").should("be.disabled")
+
+    // Delete the autocompleteField value and check the field <affiliationIdentifier> also removed
+    cy.get("input[name='contributors.0.affiliation.0.name']")
+      .parent()
+      .children("div[class='MuiAutocomplete-endAdornment']")
+      .click()
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifier']").should("have.value", "")
+
+    // Type new search words
+    cy.get("input[name='contributors.0.affiliation.0.name']").type("test")
+    // Select the first result and check the <affiliationIdentifier> field is filled and disabled
+    cy.get(".MuiAutocomplete-option")
+      .should("be.visible")
+      .then($el => $el.first().click())
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifier").should(
+      "have.value",
+      "https://ror.org/03fknzz27"
+    )
+    cy.get("input[data-testid='contributors.0.affiliation.0.affiliationIdentifier").should("be.disabled")
+  }),
+    it("should fill the required fields and save DOI form successfully", () => {
+      // Go to DOI form
+      cy.get("button[type=button]").contains("Next").click()
+      cy.get("button").contains("Add DOI information (optional)", { timeout: 10000 }).click()
+      cy.get("div[role='dialog']").should("be.visible")
+
+      // Fill in required Creators field
+      cy.get("h2[data-testid='creators']").parent().children("button").click()
+      cy.get("input[data-testid='creators.0.givenName']").type("John Smith")
+
+      // Fill in required Subjects field
+      cy.get("h2[data-testid='subjects']").parent().children("button").click()
+      cy.get("select[name='subjects.0.subject']").select("FOS: Mathematics")
+
+      cy.get("button[type='submit']").click()
+      cy.contains(".MuiAlert-message", "DOI form has been saved successfully")
+
+      // Open the DOI form again and check the fields render correctly
+      cy.get("button").contains("Add DOI information (optional)", { timeout: 10000 }).click()
+      cy.get("input[data-testid='creators.0.givenName']").should("have.value", "John Smith")
+      cy.get("select[name='subjects.0.subject']").should("have.value", "FOS: Mathematics")
+    })
+})

cypress/integration/objectLinksAttributes.spec.js

@@ -81,5 +81,12 @@ describe("render objects' links and attributes ", function () {
 
     cy.get("input[name='studyAttributes.0.tag']").should("have.value", "Test Attributes Tag")
     cy.get("textarea[name='studyAttributes.0.value']").should("have.value", "Test Attributes Value")
+
+    // Remove URL Link and check that the rest of the Study Links render correctly
+    cy.get("div[data-testid='studyLinks[1]']").children("button").click()
+    cy.get("div[class='arrayRow']", { timeout: 10000 }).should("have.length", 2)
+
+    cy.get("select[name='studyLinks.0']").should("have.value", "XRef Link")
+    cy.get("select[name='studyLinks.1']").should("have.value", "Entrez Link")
   })
 })

src/App.js

@@ -90,7 +90,10 @@ const App = (): React$Element<typeof React.Fragment> => {
       if (isMounted) {
         if (response.ok) {
           const schemas = response.data
-            .filter(schema => schema.title !== "Project" && schema.title !== "Submission")
+            .filter(
+              schema =>
+                schema.title !== "Project" && schema.title !== "Submission" && schema.title !== "Datacite DOI schema"
+            )
             .map(schema => schema.title.toLowerCase())
           dispatch(setObjectTypesArray(schemas))
         } else {

src/__tests__/FormAutocompleteField.test.js

@@ -2,7 +2,7 @@ import React from "react"
 
 import "@testing-library/jest-dom/extend-expect"
 import { ThemeProvider } from "@material-ui/core/styles"
-import { render, screen, waitFor, within } from "@testing-library/react"
+import { render, screen, waitFor, within, act } from "@testing-library/react"
 import userEvent from "@testing-library/user-event"
 import { rest } from "msw"
 import { setupServer } from "msw/node"
@@ -81,11 +81,12 @@ describe("Test autocomplete on organisation field", () => {
 
     const autocomplete = await waitFor(() => screen.getByTestId("organisation"))
     const input = await waitFor(() => within(autocomplete).getByRole("textbox"))
-
     autocomplete.focus()
 
-    // Assign value to input field
-    userEvent.type(input, "test")
+    act(() => {
+      // Assign value to input field
+      userEvent.type(input, "test")
+    })
 
     // Find loading indicator
     await waitFor(() => screen.getByRole("progressbar"))

src/components/Home/UserDraftTemplateActions.js

@@ -38,7 +38,7 @@ const UserDraftTemplateActions = (props: { item: { schema: string, accessionId:
         updateStatus({
           status: ResponseStatus.error,
           response: response,
-          errorPrefix: "Unable to delete template",
+          helperText: "Unable to delete template",
         })
       )
     }

src/components/NewDraftWizard/WizardComponents/WizardFooter.js

@@ -11,6 +11,7 @@ import WizardAlert from "./WizardAlert"
 
 import saveDraftsAsTemplates from "components/NewDraftWizard/WizardHooks/WizardSaveTemplatesHook"
 import { ResponseStatus } from "constants/responseStatus"
+import { resetFileTypes } from "features/fileTypesSlice"
 import { updateStatus } from "features/statusMessageSlice"
 import { resetObjectType } from "features/wizardObjectTypeSlice"
 import { publishFolderContent, deleteFolderAndContent, resetFolder } from "features/wizardSubmissionFolderSlice"
@@ -98,6 +99,7 @@ const WizardFooter = (): React$Element<any> => {
             })
           )
         })
+      dispatch(resetFileTypes())
     } else {
       setDialogOpen(false)
     }

src/components/NewDraftWizard/WizardComponents/WizardSavedObjectActions.js

@@ -8,7 +8,8 @@ import { useDispatch, useSelector } from "react-redux"
 import { useHistory } from "react-router-dom"
 
 import { ResponseStatus } from "constants/responseStatus"
-import { ObjectSubmissionTypes, ObjectStatus } from "constants/wizardObject"
+import { ObjectSubmissionTypes, ObjectStatus, ObjectTypes } from "constants/wizardObject"
+import { deleteFileType } from "features/fileTypesSlice"
 import { updateStatus } from "features/statusMessageSlice"
 import { setCurrentObject, resetCurrentObject } from "features/wizardCurrentObjectSlice"
 import { setObjectType } from "features/wizardObjectTypeSlice"
@@ -40,6 +41,7 @@ const WizardSavedObjectActions = (props: WizardSavedObjectActionsProps): React$E
   const classes = useStyles()
   const dispatch = useDispatch()
   const currentObject = useSelector(state => state.currentObject)
+
   const history = useHistory()
 
   const handleObjectEdit = async () => {
@@ -114,6 +116,11 @@ const WizardSavedObjectActions = (props: WizardSavedObjectActionsProps): React$E
     }
 
     if (currentObject.accessionId === props.objectId) dispatch(resetCurrentObject())
+
+    // Delete fileType that is equivalent to deleted object
+    if (props.objectType === ObjectTypes.analysis || props.objectType === ObjectTypes.run) {
+      dispatch(deleteFileType(props.objectId))
+    }
   }
 
   const renderEditLabel = submissionType => {