Merge pull request #382 from icgc-argo/375_radiation_boost

375 radiation boost

references/validationFunctions/radiation/radiationBoost.js

@@ -0,0 +1,47 @@
+/*
+ * Copyright (c) 2022 The Ontario Institute for Cancer Research. All rights reserved
+ *
+ * This program and the accompanying materials are made available under the terms of the GNU Affero General Public License v3.0.
+ * You should have received a copy of the GNU Affero General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *  
+ *
+ */
+
+/**
+ * If a radiation boost was given, then the 'reference_radiation_treatment_id' must be submitted.
+ */
+const validation = () => 
+    (function validate(inputs) {
+        const {$row, $name, $field} = inputs;
+        let result = {valid: true, message: "Ok"};
+        const currField = typeof($field) === 'string' ? $field.trim().toLowerCase() : $field;
+
+        if ($row.radiation_boost != null) {
+           const radiationBoost = $row.radiation_boost.trim().toLowerCase();
+
+           if (!currField && radiationBoost === "yes") {
+              result = {valid: false, message: `${$name} must be provided when if a radiation boost was given.`}
+           }
+           else if (currField && radiationBoost != "yes"){
+              result = {valid: false, message: `${$name} cannot be provided if the 'radiation_boost' field is '${radiationBoost}'.`}
+           }
+        }
+        else if ((!$row.radiation_boost) && (currField)) {
+           result = {valid: false, message: `'${$name}' requires the 'radiation_boost' field.` }
+        }
+        return result;
+    });
+
+
+module.exports = validation;

schemas/radiation.json

@@ -135,6 +135,28 @@
         "core": true,
         "displayName": "Anatomical Site Irradiated"
       }
+    },
+    {
+      "name": "radiation_boost",
+      "description": "A radiation boost is an extra radiation treatment targeted at the tumor bed, given after the regular sessions of radiation is complete (Reference NCIt: C137812). Indicate if this radiation treatment was a radiation boost.",
+      "valueType": "string",
+      "restrictions": {
+        "codeList": "#/list/yes_no_na"
+      },
+      "meta": {
+        "displayName": "Radiation Boost"
+      }
+    },
+    {
+      "name": "reference_radiation_treatment_id",
+      "description": "If a radiation boost was given, indicate the 'submitter_treatment_id' of the primary radiation treatment the radiation boost treatment is linked to.",
+      "valueType": "string",
+      "restrictions": {
+        "script": "#/script/radiation/radiationBoost"
+      },
+      "meta": {
+        "displayName": "Reference Radiation Treatment for Boost"
+      }
     }
   ]
 }

tests/radiation/radiationBoost.test.js

@@ -0,0 +1,121 @@
+/*
+ * Copyright (c) 2022 The Ontario Institute for Cancer Research. All rights reserved
+ *
+ * This program and the accompanying materials are made available under the terms of the GNU Affero General Public License v3.0.
+ * You should have received a copy of the GNU Affero General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *  
+ *
+ */
+
+const validation = require('./../../references/validationFunctions/radiation/radiationBoost.js');
+const universalTest = require('../universal');
+const loadObjects = require('../loadObjects');
+
+// load in all fields with entries prepopulated to null
+const radiation = require('../constructDummyData').getSchemaDummy('radiation');
+
+const myUnitTests = {
+    "reference_radiation_treatment_id": [
+        [
+            'reference_radiation_treatment_id submitted when radiation boost was given.',
+            true,
+            loadObjects(radiation,
+                {   
+                    "radiation_boost": "yes",
+                    "reference_radiation_treatment_id": "tr2"
+                }
+            )
+        ],
+        [
+            'reference_radiation_treatment_id is empty when radiation boost was given.',
+            false,
+            loadObjects(radiation,
+                {   
+                    "radiation_boost": "yes",
+                    "reference_radiation_treatment_id": ""
+                }
+            )
+        ],
+        [
+            'reference_radiation_treatment_id is not submitted when radiation boost was given.',
+            false,
+            loadObjects(radiation,
+                {   
+                    "radiation_boost": "yes",
+                }
+            )
+        ],
+        [
+            'reference_radiation_treatment_id is submitted when radiation boost was not given.',
+            false,
+            loadObjects(radiation,
+                {   
+                    "radiation_boost": "no",
+                    "reference_radiation_treatment_id": "tr40"
+                }
+            )
+        ],
+        [
+            'reference_radiation_treatment_id is submitted when radiation boost was unknown.',
+            false,
+            loadObjects(radiation,
+                {   
+                    "radiation_boost": "unknown",
+                    "reference_radiation_treatment_id": "tr25"
+                }
+            )
+        ],
+        [
+            'reference_radiation_treatment_id is submitted when radiation boost is missing.',
+            false,
+            loadObjects(radiation,
+                {   
+                    "reference_radiation_treatment_id": "tr3"
+                }
+            )
+        ],
+        [
+            'Both radiation_boost and reference_radiation_treatment_id are missing',
+            true,
+            loadObjects(radiation, {})
+        ]
+    ]
+};
+
+describe("Common Tests",()=>{
+    Object.entries(myUnitTests).forEach(field =>{
+        const name = field[0];
+        const unitTests = field[1];
+        unitTests.forEach(test=>{
+            const testIndex = 2;
+            const testInputs = test[testIndex];
+            universalTest(validation()({ $row: testInputs, $name: name, $field: testInputs[name]}));
+        })
+    })
+
+})
+
+describe("Unit Tests for Radiation Boost",()=>{
+    Object.entries(myUnitTests).forEach(field => {
+        const name = field[0];
+        const unitTests = field[1];
+        describe(`Tests for the ${name} field.`,() => {
+            test.each(unitTests)('\n Test %# : %s \nExpecting result.valid to be: %s',(description,target,inputs) =>{
+                const scriptOutput = validation()({ $row: inputs, $field: inputs[name], $name: name});
+                expect(scriptOutput.valid).toBe(target);
+            })
+        })
+    })
+})
+