[MNT] Renamed examples files (#608)

* Renamed example files * Updated `validate-output-example_synthetic-e2etest` * Formatted example json files * Reformatted json example files
neurobagel · Nov 6, 2023 · 04583bc · 04583bc
1 parent b8e48bf
commit 04583bc
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Showing 4 changed files with 158 additions and 158 deletions.
diff --git a/cypress/e2e/app/validate-output-example-synthetic-e2etest.cy.js b/cypress/e2e/app/validate-output-example-synthetic-e2etest.cy.js
@@ -6,7 +6,7 @@ describe("to annotate an assessment ", () => {
 
         /* ==== Generated with Cypress Studio ==== */
         cy.get('[data-cy="data-dictionary-selector"] > .row > form > .file-selector-button').click();
-        cy.get('[data-cy="data-dictionary-selector"] > .row > form > .file-selector-button > input').selectFile('cypress/fixtures/examples/good/example_synthetic.json', { force: true });
+        cy.get('[data-cy="data-dictionary-selector"] > .row > form > .file-selector-button > input').selectFile('cypress/fixtures/examples/good/example_synthetic_participants.json', { force: true });
         /* ==== End Cypress Studio ==== */
         cy.get("[data-cy='button-nextpage']").click();
 
@@ -105,7 +105,7 @@ describe("to annotate an assessment ", () => {
         cy.task("downloads", "cypress/downloads").then(folderStateAfter => {
             cy.readFile('cypress/downloads/' + folderStateAfter[folderStateAfter.length - 1]).then((outputContent) => {
 
-                const expectedOutput = require('../../fixtures/examples/good/example_synthetic_expected_output.json');
+                const expectedOutput = require('../../fixtures/examples/good/example_synthetic.json');
                 expect(outputContent).to.deep.equal(expectedOutput);
               });
         });

diff --git a/cypress/fixtures/examples/good/example_synthetic.json b/cypress/fixtures/examples/good/example_synthetic.json
@@ -1,34 +1,131 @@
 {
-   "participant_id":{
-      "Description":"A participant ID"
+   "participant_id": {
+       "Description": "A participant ID",
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:ParticipantID",
+               "Label": "Subject Unique Identifier"
+           },
+           "Identifies": "participant"
+       }
    },
-   "session_id":{
-      "Description":"A session ID"
+   "session_id": {
+       "Description": "A session ID"
    },
-   "pheno_age":{
-      "Description":"Age of the participant"
+   "pheno_age": {
+       "Description": "Age of the participant",
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:Age",
+               "Label": "Age"
+           },
+           "Transformation": {
+               "TermURL": "nb:FromEuro",
+               "Label": "european decimal value"
+           },
+           "MissingValues": [
+               "NA"
+           ]
+       }
    },
-   "pheno_sex":{
-      "Description":"Sex variable",
-      "Levels":{
-         "M":"Male",
-         "F":"Female"
-      }
+   "pheno_sex": {
+       "Description": "Sex variable",
+       "Levels": {
+           "M": "Male",
+           "F": "Female"
+       },
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:Sex",
+               "Label": "Sex"
+           },
+           "Levels": {
+               "M": {
+                   "TermURL": "snomed:248153007",
+                   "Label": "Male"
+               },
+               "F": {
+                   "TermURL": "snomed:248152002",
+                   "Label": "Female"
+               }
+           },
+           "MissingValues": [
+               "missing"
+           ]
+       }
    },
-   "pheno_group":{
-      "Description":"Group variable",
-      "Levels":{
-         "PAT":"Patient",
-         "CTRL":"Control subject"
-      }
+   "pheno_group": {
+       "Description": "Group variable",
+       "Levels": {
+           "PAT": "Patient",
+           "CTRL": "Control subject"
+       },
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:Diagnosis",
+               "Label": "Diagnosis"
+           },
+           "Levels": {
+               "PAT": {
+                   "TermURL": "snomed:406506008",
+                   "Label": "Attention deficit hyperactivity disorder"
+               },
+               "CTRL": {
+                   "TermURL": "ncit:C94342",
+                   "Label": "Healthy Control"
+               }
+           },
+           "MissingValues": [
+               "NA"
+           ]
+       }
    },
-   "tool1_item1":{
-      "Description":"item 1 scores for tool1"
+   "tool1_item1": {
+       "Description": "item 1 scores for tool1",
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:Assessment",
+               "Label": "Assessment tool"
+           },
+           "IsPartOf": {
+               "TermURL": "cogatlas:trm_57964b8a66aed",
+               "Label": "Montreal Cognitive Assessment"
+           },
+           "MissingValues": [
+               "missing"
+           ]
+       }
    },
-   "tool1_item2":{
-      "Description":"item 2 scores for tool1"
+   "tool1_item2": {
+       "Description": "item 2 scores for tool1",
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:Assessment",
+               "Label": "Assessment tool"
+           },
+           "IsPartOf": {
+               "TermURL": "cogatlas:trm_57964b8a66aed",
+               "Label": "Montreal Cognitive Assessment"
+           },
+           "MissingValues": [
+               "missing"
+           ]
+       }
    },
-   "tool2_item1":{
-      "Description":"item 1 scores for tool2"
+   "tool2_item1": {
+       "Description": "item 1 scores for tool2",
+       "Annotations": {
+           "IsAbout": {
+               "TermURL": "nb:Assessment",
+               "Label": "Assessment tool"
+           },
+           "IsPartOf": {
+               "TermURL": "cogatlas:tsk_4a57abb949ece",
+               "Label": "Unified Parkinson's Disease Rating Scale"
+           },
+           "MissingValues": [
+               "not completed"
+           ]
+       }
    }
-}
+}
diff --git a/cypress/fixtures/examples/good/example_synthetic_expected_output.json b/cypress/fixtures/examples/good/example_synthetic_expected_output.json
diff --git a/cypress/fixtures/examples/good/example_synthetic_participants.json b/cypress/fixtures/examples/good/example_synthetic_participants.json
@@ -0,0 +1,34 @@
+{
+   "participant_id": {
+       "Description": "A participant ID"
+   },
+   "session_id": {
+       "Description": "A session ID"
+   },
+   "pheno_age": {
+       "Description": "Age of the participant"
+   },
+   "pheno_sex": {
+       "Description": "Sex variable",
+       "Levels": {
+           "M": "Male",
+           "F": "Female"
+       }
+   },
+   "pheno_group": {
+       "Description": "Group variable",
+       "Levels": {
+           "PAT": "Patient",
+           "CTRL": "Control subject"
+       }
+   },
+   "tool1_item1": {
+       "Description": "item 1 scores for tool1"
+   },
+   "tool1_item2": {
+       "Description": "item 2 scores for tool1"
+   },
+   "tool2_item1": {
+       "Description": "item 1 scores for tool2"
+   }
+}