Merge pull request #383 from icgc-argo/358_ltf

Added optional field in Donor schema for lost to follow up

references/validationFunctions/donor/lost_to_followup.js

@@ -0,0 +1,44 @@
+/*
+ * Copyright (c) 2023 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.
+ *  
+ *
+ */
+
+/**
+ * The lost_to_followup_after_clinical_event_id field should only be submitted if vital_status is Alive. It should not be allowed to be submitted if vital_status is Deceased.
+ */
+const validation = () => 
+    (function validate(inputs) {
+        const {$row, $name, $field} = inputs;
+        let result = {valid: true, message: "Ok"};
+        const currField = typeof($field) === 'string' ? $field.trim().toLowerCase() : $field;
+
+        /* checks for a string just consisting of whitespace */
+        const checkforEmpty = (entry) => {return /^\s+$/g.test(decodeURI(entry).replace(/^"(.*)"$/, '$1'))};
+
+        if (currField != null && !(checkforEmpty(currField))) {
+           const vitalStatus = $row.vital_status.trim().toLowerCase();
+
+           if (vitalStatus === "deceased") {
+              result = {valid: false, message: `${$name} cannot be submitted if the donor's vital_status is deceased.`}
+           }
+        }
+        return result;
+    });
+
+
+module.exports = validation;

schemas/donor.json

@@ -267,6 +267,19 @@
         "units": "months",
         "dependsOn": "donor.contraception_type"
       }
+    },
+    {
+      "description": "If the donor became lost to follow up, indicate the identifier of the clinical event (eg. submitter_primary_diagnosis_id, submitter_treatment_id or submitter_follow_up_id) after which the donor became lost to follow up.",
+      "name": "lost_to_followup_after_clinical_event_id",
+      "valueType": "string",
+      "restrictions": {
+        "script": "#/script/donor/lost_to_followup"
+      },
+      "meta": { 
+        "displayName": "Lost To Follow Up After Clinical Event",
+        "foreignKey": "primary_diagnosis.submitter_primary_diagnosis_id",
+        "validationDependency": true
+      }
     }
   ]
 }

tests/donor/lost_to_followup.test.js

@@ -0,0 +1,79 @@
+/*
+ * Copyright (c) 2020 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/donor/lost_to_followup.js');
+const universalTest = require('../universal');
+const loadObjects = require('../loadObjects');
+
+// load in all fields with entries prepopulated to null
+const donor = require('../constructDummyData').getSchemaDummy('donor');
+
+const myUnitTests = {
+    "lost_to_followup_after_clinical_event_id": [
+        [
+            'Alive donor with lost to follow up indicated.',
+            true,
+            loadObjects(donor,
+                {   
+                    "vital_status": "alive",
+                    "lost_to_followup_after_clinical_event_id": "PD1"
+                }
+            )
+        ],
+        [
+            'Lost to follow up indicated when donor is known to be deceased.',
+            false,
+            loadObjects(donor,
+                {   
+                    "vital_status": "deceased",
+                    "lost_to_followup_after_clinical_event_id" : "Tr-1"
+                }
+            )
+
+        ]
+    ]
+};
+
+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 Lost to follow up",()=>{
+    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);
+            })
+        })
+    })
+})
+