Merge pull request #432 from CSCfi/develop

Release 0.11.0

.github/workflows/codestyle.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Setup node ${{ matrix.node }}
-        uses: actions/setup-node@v2.3.0
+        uses: actions/setup-node@v2.4.0
         with:
           node-version: ${{ matrix.node }}
       - name: Install dependencies

.github/workflows/e2etests.yml

@@ -13,7 +13,7 @@ jobs:
       - uses: actions/checkout@v2
       - name: Build Frontend
         run: |
-          sudo npm install -g npm@7.20.0
+          sudo npm install -g npm@7.21.0
           npx --quiet pinst --disable
           npm install --production
           npm run build --production

.github/workflows/formatstyle.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Setup node ${{ matrix.node }}
-        uses: actions/setup-node@v2.3.0
+        uses: actions/setup-node@v2.4.0
         with:
           node-version: ${{ matrix.node }}
       - name: Install dependencies

.github/workflows/typecheck.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Setup node ${{ matrix.node }}
-        uses: actions/setup-node@v2.3.0
+        uses: actions/setup-node@v2.4.0
         with:
           node-version: ${{ matrix.node }}
       - name: Install dependencies

.github/workflows/unittests.yml

@@ -3,7 +3,7 @@ name: Unit tests and coverage
 on: [push]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -12,18 +12,17 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Setup node ${{ matrix.node }}
-        uses: actions/setup-node@v2.3.0
+        uses: actions/setup-node@v2.4.0
         with:
           node-version: ${{ matrix.node-version }}
       - name: Install dependencies and coveralls
         run: |
           npm ci
           npm install coveralls
-      - name: Run unit tests with react-app-scripts and save coverage
+      - name: Run unit tests and save coverage
         run: CI=true npm test -- --coverage
-      - name: Report coverage to coveralls
-        env:
-          COVERALLS_REPO_TOKEN: "${{ secrets.COVERALLS_REPO_TOKEN }}"
-          COVERALLS_GIT_BRANCH: "${{ github.ref }}"
-        run: |
-          cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js
+      - name: Coveralls
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./coverage/lcov.info

.gitignore

@@ -8,6 +8,7 @@
 # testing
 /coverage
 debug.log
+cypress/videos
 
 # production
 /build

cypress.json

@@ -3,5 +3,10 @@
     "port": "3000",
     "mockAuthHost": "localhost",
     "mockAuthPort": "8000"
-  }
+  },
+  "retries": {
+    "runMode": 3,
+    "openMode": 0
+  },
+  "videoCompression": false
 }

cypress/integration/draft.spec.js

@@ -21,29 +21,34 @@ describe("Draft operations", function () {
     // Save a draft
     cy.get("button[type=button]").contains("Save as Draft").click()
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
-    cy.get("div[role=button]").contains("Choose from drafts").click()
-    cy.get("div[data-testid=Existing").find("li").should("have.length", 1)
+    cy.get("ul[data-testid='Draft-objects']").find("li").should("have.length", 1)
 
     // Save another draft
-    cy.get("div[role=button]").contains("Fill Form").click()
+    cy.get("button[type=button]").contains("New form").click()
     cy.get("input[name='descriptor.studyTitle']").type("Test title 2")
     cy.get("button[type=button]").contains("Save as Draft").click()
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
+    cy.get("ul[data-testid='Draft-objects']").find("li").should("have.length", 2)
 
     // Update draft, save from dialog
     cy.get("input[name='descriptor.studyTitle']").type(" second save")
-    cy.get("div[role=button]").contains("Choose from drafts").click()
+    cy.get("div[role=button]").contains("Fill Form").click()
     cy.get("h2").contains("Would you like to save draft version of this form")
     cy.get("div[role=dialog]").contains("Save").click()
-    cy.get("div[data-testid='Existing']").find("li").should("have.length", 2)
+    cy.get("ul[data-testid='Draft-objects']").find("li").should("have.length", 2)
 
     // Delete a draft
-    cy.get("button[aria-label='Delete draft']").first().click()
-    cy.get("div[data-testid='Existing']").find("li", { timeout: 60000 }).should("have.length", 1)
+    cy.get("ul[data-testid='Draft-objects']")
+      .find("li")
+      .first()
+      .within(() => {
+        cy.get("button[aria-label='Delete submission']").first().click()
+      })
+    cy.get("ul[data-testid='Draft-objects']").find("li", { timeout: 60000 }).should("have.length", 1)
 
     // Continue draft
     // Clear
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
     cy.get("input[name='descriptor.studyTitle']")
     cy.get("button[type=button]", { timeout: 10000 }).contains("Clear form").click()
 
@@ -52,6 +57,7 @@ describe("Draft operations", function () {
     cy.get("input[name='descriptor.studyTitle']").should("have.value", "New title")
     cy.get("select[name='descriptor.studyType']").select("Metagenomics")
     cy.get("button[type=button]").contains("Update draft").click()
+    cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft updated with")
 
     // Create a new form and save as draft
     cy.get("button", { timeout: 10000 }).contains("New form").click({ force: true })
@@ -63,26 +69,24 @@ describe("Draft operations", function () {
 
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
 
-    // Check that there are 2 drafts saved in "Choose from drafts"
-    cy.get("div[role=button]").contains("Choose from drafts").click()
-    cy.get("div[data-testid='Existing']").find("li").should("have.length", 2)
+    // Check that there are 2 drafts saved in drafts list"
+    cy.get("ul[data-testid='Draft-objects']").find("li").should("have.length", 2)
 
     // Submit first form draft
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
     cy.get("button[type=submit]").contains("Submit").click()
-    cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
+    cy.get("div[role=alert]", { timeout: 10000 }).contains("Submitted with")
+    cy.get("ul[data-testid='Form-objects']").find("li").should("have.length", 1)
 
     // Submit second form draft
-    cy.get("div[role=button]").contains("Choose from drafts").click()
-    cy.get("div[data-testid='Existing']").find("li").should("have.length", 1)
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.get("ul[data-testid='Draft-objects']").find("li").should("have.length", 1)
+    cy.continueFirstDraft()
     cy.get("button[type=submit]").contains("Submit").click()
 
     // Check that there are 2 submitted objects
-    cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 2)
+    cy.get("ul[data-testid='Form-objects']", { timeout: 10000 }).find("li").should("have.length", 2)
 
-    // Drafts should be empty
-    cy.get("div[role=button]").contains("Choose from drafts").click()
-    cy.get("div").contains("No study drafts.")
+    // Drafts list should be unmounted
+    cy.get("ul[data-testid='Draft-objects']").should("not.exist")
   })
 })

cypress/integration/editForm.spec.js

@@ -114,8 +114,7 @@ describe("Populate form and render form elements by object data", function () {
     cy.get("button[type='button']").contains("Save as Draft").click()
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
 
-    cy.chooseFromDrafts()
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
 
     // Test that values exist
     cy.get("input[data-testid='title']").should("have.value", testData.title)
@@ -147,8 +146,7 @@ describe("Populate form and render form elements by object data", function () {
     cy.get("button[type='button']").contains("Update draft").click()
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft updated with")
 
-    cy.chooseFromDrafts()
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
 
     // Test that Prev Step Index is nulled
     cy.get("input[data-testid='processing[0].pipeline.pipeSection[0].prevStepIndex']").should("not.exist")
@@ -172,8 +170,7 @@ describe("Populate form and render form elements by object data", function () {
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
 
     // Select newly saved draft
-    cy.chooseFromDrafts()
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
 
     cy.get("select[name='runType.referenceAlignment.assembly']").should("have.value", testData.referenceAlignment)
     cy.get("input[data-testid='runType.referenceAlignment.assembly.accessionId']").should(
@@ -197,8 +194,7 @@ describe("Populate form and render form elements by object data", function () {
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
 
     // Select newly saved draft
-    cy.chooseFromDrafts()
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
 
     cy.get("[type='checkbox']").first().should("be.checked")
 

cypress/integration/emptyForm.spec.js

@@ -46,8 +46,7 @@ describe("empty form should not be alerted or saved", function () {
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
 
     // Select the Experiment draft
-    cy.chooseFromDrafts()
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
 
     cy.get("input[data-testid='title']").should("have.value", "Test experiment")
     cy.get("textarea[data-testid='description']").should("have.value", "Test experiment description")
@@ -58,8 +57,7 @@ describe("empty form should not be alerted or saved", function () {
     cy.get("textarea[data-testid='description']").should("have.value", "")
 
     // Select the Experiment draft again
-    cy.chooseFromDrafts()
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
 
     cy.get("input[data-testid='title']").should("have.value", "Test experiment")
     cy.get("textarea[data-testid='description']").should("have.value", "Test experiment description")

cypress/integration/home.spec.js

@@ -27,20 +27,74 @@ describe("Home e2e", function () {
     cy.get("input[name='descriptor.studyTitle']").type("Test title")
     cy.get("select[name='descriptor.studyType']").select("Resequencing")
 
-    // Submit form
+    // Save draft
+    cy.get("button[type=button]").contains("Save as Draft").click()
+    cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
+
+    // Save another draft for later use
+    cy.get("button").contains("New form").click()
+    cy.get("input[name='descriptor.studyTitle']").type("Second test title")
+    cy.get("button[type=button]").contains("Save as Draft").click()
+    cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
+
+    // Save folder and navigate to Home page
+    cy.get("button[type=button]").contains("Save and Exit").click()
+    cy.get('button[aria-label="Save a new folder and move to frontpage"]').contains("Return to homepage").click()
+    cy.get("div", { timeout: 10000 }).contains("Logged in as:")
+
+    cy.get("button[data-testid='ViewAll-draft']", { timeout: 10000 }).click()
+
+    // Navigate to home & find folder
+    cy.findDraftFolder("Test unpublished folder")
+
+    cy.get('button[aria-label="Publish current folder"]').should("be.disabled")
+    cy.get('button[aria-label="Edit current folder"]').contains("Edit").click()
+    cy.get("input[name='name']").clear().type("Edited unpublished folder")
+    cy.get("button[type=button]").contains("Next").click()
+
+    // Navigate to home and delete object
+    cy.findDraftFolder("Edited unpublished folder")
+
+    cy.get("tr[data-testid='Test title']").within(() => cy.get('button[aria-label="Delete this object"]').click())
+    cy.get("tr[data-testid='Test title']").should("not.exist")
+
+    // Edit remaining object
+    cy.get("tr[data-testid='Second test title']").within(() => cy.get('button[aria-label="Edit this object"]').click())
+    cy.get("select[name='descriptor.studyType']").select("Metagenomics")
     cy.get("button[type=submit]").contains("Submit").click()
-    cy.get(".MuiListItem-container", { timeout: 10000 }).should("have.length", 1)
+    cy.get(".MuiListItem-container", { timeout: 30000 }).should("have.length", 2)
 
     // Navigate to summary
-    cy.get("button[type=button]").contains("Next").click()
+    cy.get("button[type=button]").contains("Next", { timeout: 10000 }).click()
 
     // Check the amount of submitted objects in Study
     cy.get("h6").contains("Study").parent("div").children().eq(1).should("have.text", 1)
 
-    // Save folder and navigate to Home page
-    cy.get("button[type=button]").contains("Save and Exit").click()
-    cy.get('button[aria-label="Save a new folder and move to frontpage"]').contains("Return to homepage").click()
-    cy.get("div", { timeout: 10000 }).contains("Logged in as:")
+    // Navigate to home & edit submitted object
+    cy.findDraftFolder("Edited unpublished folder")
+    cy.get('button[aria-label="Edit this object"]').click()
+    cy.get("input[name='descriptor.studyTitle']").type(" edited")
+    cy.get("button[type=button]").contains("Update").click()
+    cy.get("div[role=alert]").contains("Object updated")
+
+    //  Publish test folder from draft folders list
+    cy.findDraftFolder("Edited unpublished folder")
+    cy.get('button[aria-label="Publish current folder"]').click()
+    cy.get('button[aria-label="Publish folder contents and move to frontpage"]').click()
+
+    // Find published folder in corresponding list
+    cy.get("button[data-testid='ViewAll-published']", { timeout: 10000 }).click()
+    cy.get("body").then($body => {
+      if ($body.find("div[aria-haspopup='listbox']").length > 0) {
+        cy.get("div[aria-haspopup='listbox']", { timeout: 10000 }).contains(10).click()
+        cy.get("ul").children().last().contains("All").click()
+        cy.wait(500)
+      }
+    })
+
+    cy.get("ul[data-testId='published-submissions']").within(() => {
+      cy.get("div[role=button]").contains("Edited unpublished folder")
+    })
   })
 
   it("create a published folder, navigate to see folder details, delete object inside folder, navigate back to Overview submissions", () => {

cypress/integration/objectTitles.spec.js

@@ -16,7 +16,7 @@ describe("draft and submitted objects' titles", function () {
     cy.get("div[role=button]").contains("Fill Form").click()
 
     // Variables
-    cy.get("input[name='descriptor.studyTitle']").as("studyTitle")
+    cy.get("[data-testid='descriptor.studyTitle']").as("studyTitle")
 
     // Fill a Study form and submit object
     cy.get("@studyTitle").type("Test title")
@@ -62,21 +62,21 @@ describe("draft and submitted objects' titles", function () {
     // Save a draft
     cy.get("button[type=button]").contains("Save as Draft").click()
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft saved with")
-    cy.get("div[role=button]").contains("Choose from drafts").click()
-    cy.get("div[data-testid=Existing").find("li").should("have.length", 1)
+    cy.get("ul[data-testid='Draft-objects']").find("li").should("have.length", 1)
 
     // Check the draft object has correct displayTitle
     cy.get("div[data-schema='draft-study']", { timeout: 10000 }).should("contain.text", "Draft title")
 
     // Edit draft object's title
-    cy.get("button[aria-label='Continue draft']").first().click()
+    cy.continueFirstDraft()
     cy.get("input[name='descriptor.studyTitle']").type(" 2")
     cy.get("input[name='descriptor.studyTitle']").should("have.value", "Draft title 2")
     cy.get("button[type=button]").contains("Update draft").click()
 
     // Check the draft object has correctly updated displayTitle
     cy.get("div[role=alert]", { timeout: 10000 }).contains("Draft updated")
-    cy.get("div[role=button]").contains("Choose from drafts").click()
-    cy.get("div[data-schema='draft-study']", { timeout: 10000 }).should("contain.text", "Draft title 2")
+    cy.get("ul[data-testid='Draft-objects']").within(() => {
+      cy.get("div[data-schema='draft-study']", { timeout: 10000 }).should("contain.text", "Draft title 2")
+    })
   })
 })