Merge branch 'main' into data-dictionary-preview

.github/workflows/cd.yaml

@@ -14,7 +14,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up node env
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         node-version: 18
 
@@ -25,7 +25,7 @@ jobs:
       run: yarn generate
 
     - name: Deploy
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./dist

.github/workflows/handle_external_pr.yml

@@ -0,0 +1,20 @@
+name: Label pull requests from forks
+
+on:
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  handle_external_pr:
+    # Only run this entire workflow if the PR was opened from a forked repo
+    # The reasoning is that both bots and external contributors have to make
+    # a fork of the repo before they can open a PR because they don't have
+    # write access to the repo.
+    if: github.event.pull_request.head.repo.full_name != github.repository
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Label pull request with "_community"
+        run: gh pr edit ${{ github.event.pull_request.number }} -R ${{ github.repository }} --add-label "_community"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test_e2e.yml

@@ -10,7 +10,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up node env
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           node-version: 16
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Neurobagel Project, Oriagmi Lab, McGill University.
+Copyright (c) 2022 - Neurobagel Project, Origami Lab, McGill University.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

components/annot-explanation.vue

@@ -7,11 +7,13 @@
                 {{ uiText.cardTitle }}
             </b-card-header>
             <b-card-body>
-                <b-card-text><ul>
-                    <li v-for="(sentence, index) in explanationText.split('.')" :key="index">
+                <b-card-text>
+                    <ul>
+                        <li v-for="(sentence, index) in explanationText.split('.')" :key="index">
                             {{ sentence }}.
                         </li>
-                </ul></b-card-text>
+                    </ul>
+                </b-card-text>
             </b-card-body>
         </b-card>
 

components/tool-navbar.vue

@@ -13,7 +13,9 @@
                     alt="Neurobagel Logo"
                     class="nav-logo" />
                 <div class="nav-title-and-subtitle">
-                    {{ uiText.toolName }} <b-badge v-b-tooltip.hover.right="'This tool is under active development. Please report any requests or issues on GitHub.'" class="badge">beta</b-badge>
+                    {{ uiText.toolName }} <b-badge v-b-tooltip.hover.right="'This tool is under active development. Please report any requests or issues on GitHub.'" class="badge">
+                        beta
+                    </b-badge>
 
                     <br />
                     <p class="nav-subtitle">

cypress/component/home_page.cy.js

@@ -41,6 +41,17 @@ describe("The Home page", () => {
         cy.get("[data-cy='data-dictionary-selector']").should("be.visible").contains("Choose file");
     });
 
+    it("Shows a warning about not being able to reuse annotations in the data dictionary", () => {
+        cy.mount(homePage, {
+
+            mocks: { $store: store },
+            stubs: stubs,
+            plugins: ["bootstrap-vue"]
+        });
+
+        cy.get("[data-cy='cannot-reuse-annotations-button']").should('be.visible').contains("Cannot reuse annotations");
+    });
+
     it("Correctly displays previews of the loaded data", () => {
 
         // Act
@@ -136,4 +147,5 @@ describe("The Home page", () => {
         });
         cy.get("[data-cy='data-dictionary-selector']").contains("example_short.json");
     });
+
 });

cypress/e2e/page/index-pagetests.cy.js

@@ -92,6 +92,28 @@ describe("Tests on the index page via store interaction", () => {
                 // 3. Assert that categorization nav item and next button are *still* enabled
                 cy.assertNextPageAccess("categorization", true);
             });
+
+            it("A big red warning is shown next to the data dictionary button to say: can't use Annotations", () => {
+
+                // 1. Assert that categorization nav item and next button are disabled
+                cy.assertNextPageAccess("categorization", false);
+
+                // 2. Select data table file
+                cy.get("[data-cy='data-table-selector']")
+                    .contains("Choose file")
+                    .selectFile(dataFolder + p_dataset.data_table);
+
+                // 3. Assert that categorization nav item and next button are enabled
+                cy.assertNextPageAccess("categorization", true);
+
+                // 4. Select participants dictionary
+                cy.get("[data-cy='data-dictionary-selector']")
+                    .contains("Choose file")
+                    .selectFile(dataFolder + p_dataset.data_dictionary);
+
+                // 3. Assert that categorization nav item and next button are *still* enabled
+                cy.assertNextPageAccess("categorization", true);
+            });
         });
     });
 });

nuxt.config.js

@@ -22,6 +22,12 @@ export default {
 		script: [
 			{
 				src: 'https://w.appzi.io/w.js?token=YVTHd'
+			},
+			{
+				src: 'https://plausible.neurobagel.org/js/script.js',
+				'data-domain': 'annotate.neurobagel.org',
+				async: 'async',
+				defer: 'defer'
 			}
 		],
 		htmlAttrs: {