diff --git a/components/annot-explanation.vue b/components/annot-explanation.vue index abe54b41..36a2e384 100644 --- a/components/annot-explanation.vue +++ b/components/annot-explanation.vue @@ -7,11 +7,13 @@ {{ uiText.cardTitle }} - + diff --git a/components/tool-navbar.vue b/components/tool-navbar.vue index 11502d8e..fb0dc070 100644 --- a/components/tool-navbar.vue +++ b/components/tool-navbar.vue @@ -13,7 +13,9 @@ alt="Neurobagel Logo" class="nav-logo" />
- {{ uiText.toolName }} beta + {{ uiText.toolName }} + beta +

diff --git a/cypress/component/home_page.cy.js b/cypress/component/home_page.cy.js index 5fc0bc39..b56caa59 100644 --- a/cypress/component/home_page.cy.js +++ b/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"); }); + }); diff --git a/cypress/e2e/page/index-pagetests.cy.js b/cypress/e2e/page/index-pagetests.cy.js index bff5ebf5..27060253 100644 --- a/cypress/e2e/page/index-pagetests.cy.js +++ b/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); + }); }); }); }); \ No newline at end of file diff --git a/pages/home.vue b/pages/home.vue index 7ac98f4c..e8cec2ab 100644 --- a/pages/home.vue +++ b/pages/home.vue @@ -17,7 +17,9 @@ 🏗️ This tool (like all of neurobagel) is under active development and we welcome any feedback or suggestions. Feel free to use our feedback widget on the side of the page.

- Summary of annotation steps + + Summary of annotation steps +

@@ -27,14 +29,15 @@

  • Upload a TSV phenotypic file (see our docs for the TSV requirements)
  • Upload a BIDS-compatible JSON data dictionary (optional)
  • Annotate any or all COLUMNS in your data table by telling us what kind of subject information they are "about"
    • -
  • Annotate the unique VALUES in the columns you have annotated, by mapping them to controlled terms from +
  • + Annotate the unique VALUES in the columns you have annotated, by mapping them to controlled terms from existing vocabularies
  • Download your annotated JSON data dictionary
    • What next?

    - You can now use the new data dictionary to create a harmonized representation of your subject-level data (optional, uses other neurobagel tools).
    + You can now use the new data dictionary to create a harmonized representation of your subject-level data (optional, uses other neurobagel tools).
    To learn more about neurobagel, check out our website: neurobagel.org.

    @@ -71,6 +74,18 @@

    {{ uiText.dataDictionaryHeader }}

    + + Cannot reuse annotations + + +
    + At the moment, the annotation tool is not able to load previously created annotations. + This means that if you provide a data dictionary here that you created with Neurobagel, + any existing semantic annotations will be removed when the data dictionary is loaded. + + In practice this means that you cannot resume an aborted previous annotation. + This is a limitation we are going to address: #601. +     { + delete userDataDictionary[key].Annotations; + }); + + commit("setDataDictionary", { newDataDictionary: userDataDictionary, storeColumns: getters.getColumnNames }); commit("setDataDictionaryFilename", filename); },