[ENH] Added Assessment Tool annoatatoins to the JSON output file (#588

) * Implemented `getAssessmentToolJSONOutput` getter * Implemented unit test for `getAssessmentToolJSONOutput` getter * Added `Assessment Tool` annotations to the JSON output * Addressed comments from PR review
neurobagel · Oct 26, 2023 · 9536598 · 9536598
1 parent b7455ab
commit 9536598
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Showing 4 changed files with 107 additions and 4 deletions.
diff --git a/components/annot-tool-groups.vue b/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>
 

diff --git a/cypress/e2e/app/simple-e2etest.cy.js b/cypress/e2e/app/simple-e2etest.cy.js
@@ -34,7 +34,8 @@ describe("End to end test using a simple UI path through the app", () => {
 
                     ["Subject ID", 1],
                     ["Age", 1],
-                    ["Diagnosis", 1]
+                    ["Diagnosis", 1],
+                    ["Assessment Tool", 1]
                 ]
             };
 
@@ -79,6 +80,12 @@ describe("End to end test using a simple UI path through the app", () => {
                 // 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("MOCA{enter}");
+                cy.get("[data-cy='assessment-tool-table']").contains("MOCA").click();
+                cy.get("[data-cy='assessment-column-table']").contains("iq").click();
+
 
                 // Since Age and subject ID have been categorized
                 // annotation page is no accessible.
@@ -116,8 +123,6 @@ describe("End to end test using a simple UI path through the app", () => {
                     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);
 
@@ -138,6 +143,10 @@ describe("End to end test using a simple UI path through the app", () => {
                         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("MOCA");
+                            expect(fileContent.iq.Annotations.IsPartOf.TermURL).to.eq("cogAtlas:MOCA");
                           });
                     });
 

diff --git a/cypress/unit/store-getter-getAssessmentToolJSONOutput.cy.js b/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."
+        });
+    });
+});
diff --git a/store/index.js b/store/index.js
@@ -216,6 +216,44 @@ export const getters = {
         return p_state.categories[p_category].componentName;
     },
 
+    getAssessmentToolJSONOutput: (p_state) => (p_columnName) => {
+        const annotatedDictColumn = p_state.dataDictionary.annotated[p_columnName];
+        const formattedOutput = {
+            Annotations: {
+                IsAbout: {
+                    TermURL: "nb:Assessment",
+                    Label: "Assessment tool"
+                },
+                IsPartOf: {
+                    TermURL: "",
+                    Label: ""
+                },
+                MissingValues: []
+            }
+        };
+        const tool = p_state.columnToToolMap[p_columnName];
+
+        p_state.toolTerms.forEach(term => {
+            if ( term.identifier === tool ) {
+                formattedOutput.Annotations.IsPartOf.Label = term.label;
+                formattedOutput.Annotations.IsPartOf.TermURL = term.identifier;
+            }
+        });
+
+        // Add existing keys from user provided dictionary
+        Object.keys(annotatedDictColumn).forEach(columnEntry => {
+
+            if ( "missingValues" !== columnEntry && "valueMap" !== columnEntry ) {
+
+                formattedOutput[columnEntry] = annotatedDictColumn[columnEntry];
+            }
+        });
+
+        formattedOutput.Annotations.MissingValues = annotatedDictColumn.missingValues;
+
+        return formattedOutput;
+    },
+
     getCategoricalJsonOutput: (p_state) => (p_columnName) => {
 
         // 0. Initialize output object
@@ -456,6 +494,11 @@ export const getters = {
                                 Identifies: "participant"
                             }
                         };
+                        break;
+
+                    case "annot-tool-groups":
+                        columnOutput = p_getters.getAssessmentToolJSONOutput(columnName);
+                        break;
                 }
 
             }