Merge pull request #406 from icgc-argo/develop

Dictionary 1.17 merge to master
icgc-argo · May 10, 2023 · d586d5b · d586d5b
2 parents 7c3bc92 + a714723
commit d586d5b
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Showing 5 changed files with 55 additions and 13 deletions.
diff --git a/references/validationFunctions/primary_diagnosis/lymphNodesExaminedMethod.js b/references/validationFunctions/primary_diagnosis/lymphNodesExaminedMethod.js
@@ -30,21 +30,25 @@ const validation = () =>
       let result = {valid: true, message: "Ok"};
 
       const notExamined = ['cannot be determined', 'no', 'no lymph nodes found in resected specimen', 'not applicable'];
-      const lymphNodesExaminedStatus = $row.lymph_nodes_examined_status.trim().toLowerCase();
-
       /* checks for a string just consisting of whitespace */
       const checkforEmpty = (entry) => {return /^\s+$/g.test(decodeURI(entry).replace(/^"(.*)"$/, '$1'))};
 
-
-      if (!$field || $field === null || checkforEmpty($field)) {
-        if (lymphNodesExaminedStatus === 'yes') {
-          result = { valid: false, message: `The '${$name}' field must be submitted if the 'lymph_nodes_examined_status' field is 'Yes'`};
-        }
+      if (!$row.lymph_nodes_examined_status || $row.lymph_nodes_examined_status === null || checkforEmpty($row.lymph_nodes_examined_status)) {
+        result = {valid: false, message: `The 'lymph_nodes_examined_status' field must be submitted.`};
       }
       else {
-         if (notExamined.includes(lymphNodesExaminedStatus)) {
-           result = { valid: false, message: `The '${$name}' field should not be submitted if the 'lymph_nodes_examined_status' field is '${lymphNodesExaminedStatus}'`};
-         }
+        const lymphNodesExaminedStatus = $row.lymph_nodes_examined_status.trim().toLowerCase();
+
+        if (!$field || $field === null || checkforEmpty($field)) {
+          if (lymphNodesExaminedStatus === 'yes') {
+            result = { valid: false, message: `The '${$name}' field must be submitted if the 'lymph_nodes_examined_status' field is 'Yes'`};
+          }
+        }
+        else {
+          if (notExamined.includes(lymphNodesExaminedStatus)) {
+            result = { valid: false, message: `The '${$name}' field should not be submitted if the 'lymph_nodes_examined_status' field is '${lymphNodesExaminedStatus}'`};
+          }
+        }
       }
     return result;
 });

diff --git a/schemas/follow_up.json b/schemas/follow_up.json
@@ -208,9 +208,10 @@
       }
     },
     {
-      "description": "Indicate the ICD-O-3 topography code for the anatomic site where disease progression, relapse or recurrence occurred, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3). Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344.",
+      "description": "Indicate the ICD-O-3 topography code for the anatomic site(s) where disease progression, relapse or recurrence occurred, according to the International Classification of Diseases for Oncology, 3rd Edition (WHO ICD-O-3). Refer to the ICD-O-3 manual for guidelines at https://apps.who.int/iris/handle/10665/42344.",
       "name": "anatomic_site_progression_or_recurrence",
       "valueType": "string",
+      "isArray": true,
       "restrictions": {
         "script": "#/script/follow_up/anatomic_site_progression_or_recurrence",
         "regex": "^[C][0-9]{2}(.[0-9]{1})?$"
@@ -219,8 +220,8 @@
         "core": true,
         "dependsOn": "follow_up.disease_status_at_followup",
         "displayName": "Anatomic Site Progression or Recurrences",
-        "examples": "C50.1,C18",
-        "notes": "#/notes/disease_status_requirement"
+        "examples": "C50.1|C18",
+        "notes": "This field is required to be submitted if disease_status_at_followup indicates a state of progression, relapse, or recurrence.\nTo include multiple values, separate values with a pipe delimiter '|' within your file."
       }
     },
     {

diff --git a/schemas/sample_registration.json b/schemas/sample_registration.json
@@ -136,6 +136,7 @@
           "Primary tumour - adjacent to normal",
           "Primary tumour",
           "Recurrent tumour",
+          "Tumour - unknown if derived from primary or metastatic",
           "Xenograft - derived from primary tumour",
           "Xenograft - derived from tumour cell line"
         ],

diff --git a/schemas/specimen.json b/schemas/specimen.json
@@ -337,6 +337,24 @@
           }
       }
     },
+    {
+      "name": "percent_tumour_cells_measurement_method",
+      "description": "Indicate method used to measure percent_tumour_cells.",
+      "valueType": "string",
+      "meta": {
+        "core": true,
+        "dependsOn": "sample_registration.tumour_normal_designation",
+        "notes": "#/notes/if_tumour",
+        "displayName": "Percent Tumour Cells Measurement Method"
+      },
+      "restrictions": {
+        "codeList": [
+           "Genomics",
+           "Image analysis",
+           "Pathology estimate by percent nuclei"
+        ]
+      }
+    },
     {
       "name": "percent_proliferating_cells",
       "description": "Indicate a value, in decimals, that represents the count of proliferating cells determined during pathologic review of the specimen.",

diff --git a/tests/primary_diagnosis/lymphNodesExaminedMethod.test.js b/tests/primary_diagnosis/lymphNodesExaminedMethod.test.js
@@ -77,7 +77,25 @@ const myUnitTests = {
                     "lymph_nodes_examined_status": "Not applicable"
                 }
             )
+        ],
+        [
+            'lymph_nodes_examined_method is missing',
+            false,
+            loadObjects(primary_diagnosis,
+                {   
+                    "lymph_nodes_examined_method": null
+                }
+            )
+        ],
+        [
+            'lymph_nodes_examined_status is missing and lymph_nodes_examined_method not submitted',
+            false,
+            loadObjects(primary_diagnosis,
+                {   
+                }
+            )
         ]
+
     ]
 }