Merge pull request #411 from icgc-argo/develop

Develop
icgc-argo · Aug 25, 2023 · 05e1adf · 05e1adf
2 parents d586d5b + 742f767
commit 05e1adf
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Showing 7 changed files with 100 additions and 7 deletions.
diff --git a/references/validationFunctions/chemotherapy/drugDose.js b/references/validationFunctions/chemotherapy/drugDose.js
@@ -33,12 +33,23 @@ const validation = () =>
 
       // 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)) && (!($row[checkField]) || $row[checkField] === null || checkforEmpty(!($row[checkField])))) {
-        result = {
-          valid: false,
-          message: `Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' fields must be submitted.`
-        };
+
+      // Check for when chemotherapy dose has a clinical exception value of 'not applicable'
+      if ($row.chemotherapy_drug_dose_units && $row.chemotherapy_drug_dose_units != null && !(checkforEmpty($row.chemotherapy_drug_dose_units)) && $row.chemotherapy_drug_dose_units.trim().toLowerCase() === 'not applicable') {
+        if ($field && $field != null && !(checkforEmpty($field))) {
+          result = {
+            valid: false,
+            message: `The '${$name}' field cannot be submitted when 'chemotherapy_drug_dose_units' = 'Not applicable'`
+          };
+        }
+      }
+      else {
+        if ( (!$field || $field === null || checkforEmpty($field)) && (!($row[checkField]) || $row[checkField] === null || checkforEmpty(!($row[checkField])))) {
+          result = {
+            valid: false,
+            message: `Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' fields must be submitted.`
+          };
+        }
       }
       return result;
   });

diff --git a/references/validationFunctions/primary_diagnosis/lymphNodesExaminedMethod.js b/references/validationFunctions/primary_diagnosis/lymphNodesExaminedMethod.js
@@ -29,7 +29,7 @@ const validation = () =>
       const {$row, $name, $field} = inputs;
       let result = {valid: true, message: "Ok"};
 
-      const notExamined = ['cannot be determined', 'no', 'no lymph nodes found in resected specimen', 'not applicable'];
+      const notExamined = ['cannot be determined', 'no', 'no lymph nodes found in resected specimen', 'not applicable', 'unknown'];
       /* checks for a string just consisting of whitespace */
       const checkforEmpty = (entry) => {return /^\s+$/g.test(decodeURI(entry).replace(/^"(.*)"$/, '$1'))};
 

diff --git a/references/validationFunctions/specimen/tumourGrade.js b/references/validationFunctions/specimen/tumourGrade.js
@@ -95,6 +95,12 @@ const validation = () =>
         case 'nuclear grading system for dcis':
           codeList = tieredGradingList;
           break;
+        case 'unknown':
+          codeList = ['unknown'];
+          break;
+        case 'not applicable':
+          codeList = ['not applicable'];
+          break;
       }
 
       if (!codeList.includes($field.trim().toLowerCase())) {

diff --git a/schemas/chemotherapy.json b/schemas/chemotherapy.json
@@ -103,6 +103,7 @@
       "meta": {
         "core": true,
         "displayName": "Prescribed Cumulative Drug Dose",
+        "validationDependency": true,
         "dependsOn": "chemotherapy.actual_cumulative_drug_dose",
         "notes": "Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted."
       }
@@ -120,6 +121,7 @@
       "meta": {
         "core": true,
         "displayName": "Actual Cumulative Drug Dose",
+        "validationDependency": true,
         "dependsOn": "chemotherapy.prescribed_cumulative_drug_dose",
         "notes": "Either the 'actual_cumulative_drug_dose' or the 'prescribed_cumulative_drug_dose' field must be submitted."
       }

diff --git a/tests/chemotherapy/drugDose.test.js b/tests/chemotherapy/drugDose.test.js
@@ -57,6 +57,25 @@ const myUnitTests = {
                     "prescribed_cumulative_drug_dose": 350
                 }
             )
+        ],
+        [
+            'chemotherapy_drug_dose_units is not applicable and actual_cumulative_drug_dose is submitted',
+            false,
+            loadObjects(chemotherapy,
+                {   
+                    "chemotherapy_drug_dose_units": 'not applicable',
+                    "actual_cumulative_drug_dose": 300,
+                }
+            )
+        ],
+        [
+            'chemotherapy_drug_dose_units is not applicable and actual_cumulative_drug_dose is not submitted',
+            true,
+            loadObjects(chemotherapy,
+                {   
+                    "chemotherapy_drug_dose_units": 'not applicable'
+                }
+            )
         ]
     ],
     'prescribed_cumulative_drug_dose': [
@@ -88,6 +107,25 @@ const myUnitTests = {
                 }
             )
         ],
+        [
+            'chemotherapy_drug_dose_units is not applicable and prescribed_cumulative_drug_dose is submitted',
+            false,
+            loadObjects(chemotherapy,
+                {   
+                    "chemotherapy_drug_dose_units": 'not applicable',
+                    "prescribed_cumulative_drug_dose": 350
+                }
+            )
+        ],
+        [
+            'chemotherapy_drug_dose_units is not applicable and prescribed_cumulative_drug_dose is not submitted',
+            true,
+            loadObjects(chemotherapy,
+                {   
+                    "chemotherapy_drug_dose_units": 'not applicable'
+                }
+            )
+        ],
         [
             'Both cumulative_drug_dose and prescribed_cumulative_drug_dose are missing',
             false,

diff --git a/tests/primary_diagnosis/lymphNodesExaminedMethod.test.js b/tests/primary_diagnosis/lymphNodesExaminedMethod.test.js
@@ -60,6 +60,26 @@ const myUnitTests = {
                 }
             )
         ],
+        [
+            'lymph nodes examined status is unknown and lymph_nodes_examined_method is left blank',
+            true,
+            loadObjects(primary_diagnosis,
+                {   
+                    "lymph_nodes_examined_status": "Unknown",
+                    "lymph_nodes_examined_method": ""
+                }
+            )
+        ],
+        [
+            'lymph nodes examined status is unknown and lymph_nodes_examined_method is submitted',
+            false,
+            loadObjects(primary_diagnosis,
+                {   
+                    "lymph_nodes_examined_status": "Unknown",
+                    "lymph_nodes_examined_method": "Imaging"
+                }
+            )
+        ],
         [
             'lymph nodes were examined and lymph_nodes_examined_method not submitted',
             false,

diff --git a/tests/specimen/tumourGrade.test.js b/tests/specimen/tumourGrade.test.js
@@ -203,6 +203,22 @@ const unitTests = [
       tumour_grade: 'g4'
     }),
   ],
+  [
+    'tumour_grading_system has an exception value of "not applicable", while tumour_grade is submitted as "G3"',
+    false,
+    loadObjects(specimen, {
+      tumour_grading_system: 'Not applicable',
+      tumour_grade: 'G3',
+    }),
+  ],
+  [
+    'tumour_grading_system has an exception value of "unknown", while tumour_grade is submitted as "G2"',
+    false,
+    loadObjects(specimen, {
+      tumour_grading_system: 'unknown',
+      tumour_grade: 'G2',
+    }),
+  ],
  // [
  //   'both grade system and grade are undefined',
  //   false,