Merge branch 'master' into repo-sync/workflows/default

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = .git,*.pdf,*.svg,package-lock.json
+skip = .git,*.pdf,*.svg,package-lock.json,./static/toolTerms.json
 # 
 # ignore-words-list = 

.github/workflows/cd.yaml

@@ -16,7 +16,7 @@ jobs:
     - name: Set up node env
       uses: actions/[email protected]
       with:
-        node-version: 16
+        node-version: 18
 
     - name: Install dependencies
       run: yarn

components/annot-categorical.vue

@@ -40,6 +40,14 @@
                             {{ uiText.missingValueButton }}
                         </b-button>
                     </template>
+                    <template #cell(isControl)="row" v-if="activeCategory === 'Diagnosis'">
+                        <b-button
+                            :data-cy="'isControlButton_' + row.index"
+                            variant="info"
+                            @click="selectOptionAndUpdate('ncit:C94342', row.item['columnName'], row.item['rawValue'])">
+                            {{ uiText.isControlButton }}
+                        </b-button>
+                    </template>
 
                 </b-table>
 
@@ -85,7 +93,8 @@
 
                     instructions: "Annotate each unique value",
                     missingValueButton: "Mark as missing",
-                    saveButton: "Save Annotation"
+                    saveButton: "Save Annotation",
+                    isControlButton: "Mark as healthy control"
                 }
             };
 
@@ -125,6 +134,14 @@
             }
         },
 
+        mounted() {
+            if (this.activeCategory == 'Diagnosis') {
+                this.exampleFields.push("isControl");
+            }
+
+
+        },
+
         methods: {
 
             ...mapMutations([

components/annot-tool-groups.vue

@@ -12,7 +12,7 @@
                     :title="label">
                     <annot-single-tool
                         :name="identifier"
-                        :uniqueColumnValues="provideUniqueValues(identifier)"
+                        :unique-column-values="provideUniqueValues(identifier)"
                         @declareMissing="changeMissingStatus(Object.assign($event, {markAsMissing: true}))" />
                 </b-tab>
 

cypress/component/annot-categorical.cy.js

@@ -2,16 +2,16 @@ import annotCategorical from "~/components/annot-categorical.vue";
 
 
 let store;
-
-const props = {
-
-    activeCategory: "category1"
-};
+let props;
 
 
 describe("Categorical annotation", () => {
 
     beforeEach(() => {
+        props = {
+
+            activeCategory: "category1"
+        };
 
         store = {
 
@@ -175,4 +175,46 @@ describe("Categorical annotation", () => {
             propsData: props
         });
     });
+
+    it("Does not display the is healthy control button when the active category is not 'Diagnosis' ", () => {
+        cy.mount(annotCategorical, {
+            computed: store.getters,
+            mocks: {$store: store},
+            propsData: props
+        });
+        cy.get("[data-cy='isControlButton_0']").should("not.exist");
+        cy.get("[data-cy='categoricalTable']").should("not.contain", "Is Control");
+
+    });
+
+    it("Can find the is healthy control button", () => {
+        props.activeCategory = "Diagnosis";
+        cy.mount(annotCategorical, {
+            computed: store.getters,
+            mocks: {$store: store},
+            propsData: props
+        });
+        cy.get("[data-cy='isControlButton_0']").should("be.visible");
+    });
+
+    it("Fires the selectCategorialOption mutation with the correct payload if the is healthy control button is clicked", () => {
+
+        // Setup
+        props.activeCategory = "Diagnosis";
+
+        cy.spy(store, "commit").as("spy");
+
+        cy.mount(annotCategorical, {
+            computed: store.getters,
+            mocks: {$store: store},
+            propsData: props
+        });
+        cy.get("[data-cy='isControlButton_1']").click();
+        cy.get("@spy").should("have.been.calledWith", "selectCategoricalOption", {
+            optionValue: "ncit:C94342",
+            columnName: "column1",
+            rawValue: "HC"
+        });
+    });
+
 });

cypress/e2e/app/simple-e2etest.cy.js

@@ -33,7 +33,9 @@ describe("End to end test using a simple UI path through the app", () => {
                 categories: [
 
                     ["Subject ID", 1],
-                    ["Age", 1]
+                    ["Age", 1],
+                    ["Diagnosis", 1],
+                    ["Assessment Tool", 1]
                 ]
             };
 
@@ -75,8 +77,15 @@ describe("End to end test using a simple UI path through the app", () => {
                 // at least one other column must be categorized.
                 cy.assertNextPageAccess("annotation", false);
 
-                // D. Categorize "age" as "Age"
+                // D. Categorize "age" as "Age" and "group" as "Diagnosis"
                 cy.categorizeColumn("Age", p_dataset["category_columns"]["Age"][0]);
+                cy.categorizeColumn("Diagnosis", p_dataset["category_columns"]["Diagnosis"][0]);
+                cy.categorizeColumn("Assessment Tool", p_dataset["category_columns"]["Assessment Tool"][0]);
+
+                cy.get("[data-cy='toolgroup-select']").type("Wechsler Abbreviated Scale of Intelligence{enter}");
+                cy.get("[data-cy='assessment-tool-table']").contains("Wechsler Abbreviated Scale of Intelligence").click();
+                cy.get("[data-cy='assessment-column-table']").contains("iq").click();
+
 
                 // Since Age and subject ID have been categorized
                 // annotation page is no accessible.
@@ -104,6 +113,16 @@ describe("End to end test using a simple UI path through the app", () => {
                     cy.get("[data-cy='selectTransform_age']").click();
                     cy.get("[data-cy='selectTransform_age']").type("float{enter}");
 
+
+                    // B. Click on the 'Diagnosis' tab
+                    cy.get("[data-cy='annotation-category-tabs'] ul")
+                        .contains("li", "Diagnosis")
+                        .click();
+
+                    cy.get("[data-cy='categoricalSelector_0']").type("Acute{enter}");
+                    cy.get("[data-cy='isControlButton_1']").type("Acute{enter}");
+                    cy.get("[data-cy='categoricalSelector_2']").type("Hearing{enter}");
+
                     // D. Assert that next page nav and button are enabled for download page
                     cy.assertNextPageAccess("download", true);
 
@@ -118,6 +137,19 @@ describe("End to end test using a simple UI path through the app", () => {
 
                     // B. Assert that csv file has downloaded
                     // cy.verifyDownload(".json", { contains: true });
+
+                    // C. Check the contents of the output
+                    cy.task("downloads", "cypress/downloads").then(folderStateAfter => {
+                        cy.readFile('cypress/downloads/' + folderStateAfter[folderStateAfter.length - 1]).then((fileContent) => {
+                            expect(fileContent.group.Annotations.Levels.HC.Label).to.eq("Healthy Control");
+                            expect(fileContent.group.Annotations.Levels.HC.TermURL).to.eq("ncit:C94342");
+                            expect(fileContent.iq.Annotations.IsAbout.Label).to.eq("Assessment tool");
+                            expect(fileContent.iq.Annotations.IsAbout.TermURL).to.eq("nb:Assessment");
+                            expect(fileContent.iq.Annotations.IsPartOf.Label).to.eq("Wechsler Abbreviated Scale of Intelligence");
+                            expect(fileContent.iq.Annotations.IsPartOf.TermURL).to.eq("cogAtlas:trm_4b94affc43245");
+                          });
+                    });
+
                 }
             }
         });

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

@@ -78,6 +78,11 @@ describe("tests on download page ui via programmatic state loading and store int
 
                             expect(folderStateAfter[folderStateAfter.length - 1]).to.contain(dataDictionaryFilenameNoExt);
                         });
+                        // C. Check if the last file retrieved contains the Identifies property and its value under the participant_id key
+                        cy.readFile('cypress/downloads/' + folderStateAfter[folderStateAfter.length - 1]).then((fileContent) => {
+                            expect(fileContent.participant_id.Annotations).to.have.property("Identifies");
+                            expect(fileContent.participant_id.Annotations.Identifies).to.eq("participant");
+                          });
                     });
                 });
             });

cypress/e2e/page/my_happy_annotation-page_tests.cy.js

@@ -35,17 +35,17 @@ describe("to annotate an assessment ", () => {
             cy.get("[data-cy='column-linking-table']").contains(desiredColumnMapping.column).click();
         });
         // Create two tools
-        cy.get("[data-cy='toolgroup-select']").type("MOCA{enter}");
-        cy.get("[data-cy='toolgroup-select']").type("UPDRS{enter}");
+        cy.get("[data-cy='toolgroup-select']").type("Wechsler Abbreviated Scale of Intelligence{enter}");
+        cy.get("[data-cy='toolgroup-select']").type("Unified Parkinson's Disease Rating Scale{enter}");
         // Map columns to tools
         const desiredColumnToolMappings = [
             {
                 "column": "iq",
-                "tool": "MOCA"
+                "tool": "Wechsler Abbreviated Scale of Intelligence"
             },
             {
                 "column": "stroop",
-                "tool": "UPDRS"
+                "tool": "Unified Parkinson's Disease Rating Scale"
             }
         ];
         desiredColumnToolMappings.forEach(desiredColumnToolMapping => {

cypress/unit/store-getter-getAssessmentToolJSONOutput.cy.js

@@ -0,0 +1,51 @@
+import { getters } from "~/store";
+
+let store = {
+
+    getters: getters,
+
+    state: {
+        dataDictionary:  {
+            annotated:  {
+                column1:  {
+                  Description: "Some cool description here.",
+                  missingValues: ["Missing"]
+                }
+            }
+        },
+        toolTerms: [
+            {
+                label: "MOCA",
+                identifier: "cogAtlas:MOCA",
+                selected: false
+            }
+        ],
+        columnToToolMap: {
+            column1: "cogAtlas:MOCA"
+        }
+
+    }
+};
+
+describe("getAssessmentToolJSONOutput", () => {
+
+    it("Make sure Assessment tool json output is schema compliant", () => {
+
+        const output = store.getters.getAssessmentToolJSONOutput(store.state)("column1");
+        expect(output).to.deep.equal(
+            {
+            Annotations: {
+                    IsAbout: {
+                        "TermURL": "nb:Assessment",
+                        "Label": "Assessment tool"
+                    },
+                    "IsPartOf": {
+                        "TermURL": "cogAtlas:MOCA",
+                        "Label": "MOCA"
+                    },
+                    MissingValues: ["Missing"]
+                },
+            Description: "Some cool description here."
+        });
+    });
+});

static/diagnosisTerms.json

@@ -0,0 +1,86 @@
+[
+    {
+       "label":"Acute depression",
+       "identifier":"snomed:712823008"
+    },
+    {
+       "label":"Anxiety",
+       "identifier":"snomed:48694002"
+    },
+    {
+       "label":"Anxiety disorder",
+       "identifier":"snomed:197480006"
+    },
+    {
+       "label":"Attention deficit hyperactivity disorder",
+       "identifier":"snomed:406506008"
+    },
+    {
+       "label":"Autism spectrum disorder",
+       "identifier":"snomed:35919005"
+    },
+    {
+       "label":"Borderline personality disorder",
+       "identifier":"snomed:20010003"
+    },
+    {
+       "label":"Concussion injury of brain",
+       "identifier":"snomed:110030002"
+    },
+    {
+       "label":"Disorder of cardiovascular system",
+       "identifier":"snomed:49601007"
+    },
+    {
+       "label":"Dyslexia",
+       "identifier":"snomed:59770006"
+    },
+    {
+       "label":"Fibromyalgia",
+       "identifier":"snomed:203082005"
+    },
+    {
+       "label":"Hearing problem",
+       "identifier":"snomed:300228004"
+    },
+    {
+       "label":"Mental disorder",
+       "identifier":"snomed:74732009"
+    },
+    {
+       "label":"Migraine",
+       "identifier":"snomed:37796009"
+    },
+    {
+       "label":"Schizophrenia",
+       "identifier":"snomed:58214004"
+    },
+    {
+       "label":"Separation anxiety",
+       "identifier":"snomed:126943008"
+    },
+    {
+       "label":"Smoker",
+       "identifier":"snomed:77176002"
+    },
+    {
+       "label":"Social phobia",
+       "identifier":"snomed:25501002"
+    },
+    {
+       "label":"Specific spelling disorder",
+       "identifier":"snomed:268738002"
+    },
+    {
+       "label":"Traumatic brain injury",
+       "identifier":"snomed:127295002"
+    },
+    {
+       "label":"Visual impairment",
+       "identifier":"snomed:397540003"
+    },
+    {
+       "label":"Healthy Control",
+       "identifier":"ncit:C94342"
+    }
+ ]