Review Notes column updated: SpreadsheetValidateVSandCS output adjusted; (#538)

* beginning

* temp stopping place

* getting vs from server

* valueset functionality mostly there.

* Functionality mostly finished

* clean up code

* more code clean up

* yet more code cleanup

* added missed functionality for compare codesystem concepts

* refactoring of reporting

* refactoring ; adding funcitonality and fixing reporting

* full functionality

* break out classes for reuse; Added explanations

* changes on <Needed> column and update to validationReport to include whole url

* removed println and added missing stuff from merge

* added spreadsheet updates; naming of output to spreadsheet title

---------

Co-authored-by: Bryn Rhodes <brynrhodes@users.noreply.github.com>
Co-authored-by: c-schuler <hoofschu@gmail.com>

Author: 3 people

tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java

@@ -1,5 +1,10 @@
 package org.opencds.cqf.tooling.cli;
 
+//import org.opencds.cqf.tooling.jsonschema.SchemaGenerator;
+import org.opencds.cqf.tooling.casereporting.transformer.ErsdTransformer;
+import org.opencds.cqf.tooling.dateroller.DataDateRollerOperation;
+import org.opencds.cqf.tooling.terminology.*;
+import org.opencds.cqf.tooling.terminology.templateToValueSetGenerator.TemplateToValueSetGenerator;
 import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
 import java.util.HashMap;
@@ -216,8 +221,10 @@ static Operation createOperation(String operationName) {
                 return new QICoreElementsToSpreadsheet();
             case "StripGeneratedContent":
                 return new StripGeneratedContentOperation();
+            case "SpreadsheetValidateVSandCS":
+                return new SpreadsheetValidateVSandCS();
             default:
                 throw new IllegalArgumentException("Invalid operation: " + operationName);
         }
     }
-}
+}

tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/StructureDefinitionBindingObject.java

@@ -6,6 +6,8 @@ public class StructureDefinitionBindingObject extends StructureDefinitionBaseObj
     String bindingValueSetURL;
     String bindingValueSetVersion;
     String bindingValueSetName;
+    String bindingObjectExtension;
+    int cardinalityMin;
 
     public String getBindingStrength() {return bindingStrength;}
     public void setBindingStrength(String bindingStrength) {this.bindingStrength = bindingStrength;}
@@ -17,4 +19,8 @@ public class StructureDefinitionBindingObject extends StructureDefinitionBaseObj
     public void setBindingValueSetName(String bindingValueSetName) {this.bindingValueSetName = bindingValueSetName;}
     public String getCodeSystemsURLs() {return codeSystemsURLs;}
     public void setCodeSystemsURLs(String codeSystemsURLs) {this.codeSystemsURLs = codeSystemsURLs;}
+    public String getBindingObjectExtension() {return bindingObjectExtension;}
+    public void setBindingObjectExtension(String bindingObjectExtension) {this.bindingObjectExtension = bindingObjectExtension;}
+    public int getCardinalityMin(){return cardinalityMin;};
+    public void setCardinalityMin(int cardinalityMin){this.cardinalityMin = cardinalityMin;}
 }

tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/StructureDefinitionElementBindingVisitor.java

@@ -2,10 +2,7 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
-import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.ElementDefinition;
-import org.hl7.fhir.r4.model.StructureDefinition;
-import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.*;
 
 import java.util.*;
 import java.util.concurrent.atomic.AtomicReference;
@@ -75,6 +72,10 @@ private void getBindings(String sdName, List<ElementDefinition> eds, String sdUR
                 if (ed.hasMin() && ed.hasMax()) {
                     String edCardinality = ed.getMin() + "..." + ed.getMax();
                     sdbo.setCardinality(edCardinality);
+                    if(ed.getMin() > 0){sdbo.setCardinalityMin(ed.getMin());}
+                }
+                if(getBindingObjectExtension(ed).equalsIgnoreCase("qicore-keyelement")){
+                    sdbo.setBindingObjectExtension("qicore-keyelement");
                 }
                 String bindingValueSet = ed.getBinding().getValueSet();
                 String pipeVersion = "";
@@ -129,6 +130,17 @@ else if (ed.hasExtension()) {
         }
     }
 
+    private String getBindingObjectExtension(ElementDefinition ed) {
+        for (Extension ext : ed.getExtension()) {
+            if (!ext.getUrl().isEmpty()) {
+                if (ext.getUrl().contains("qicore-keyelement")) {
+                    return "qicore-keyelement";
+                }
+            }
+        }
+        return "";
+    }
+
     private void visitExtensions(ElementDefinition ed, Map<String, StructureDefinitionBindingObject> bindingObjects, String sdName, String sdURL, String sdVersion) {
         StructureDefinitionBindingObject sdbo = new StructureDefinitionBindingObject();
         sdbo.setSdName(sdName);

tooling/src/main/java/org/opencds/cqf/tooling/operation/ProfilesToSpreadsheet.java

@@ -94,7 +94,7 @@ private void createOutput(List<StructureDefinitionBindingObject> bindingObjects)
 
     private List<String> createHeaderNameList() {
         List<String> headerNameList = new ArrayList<String>() {{
-            add("QI Core Profile");
+            add(modelName + " Profile");
             add("Id");
             add("Conformance");
             add("ValueSet");
@@ -155,7 +155,10 @@ private void addBindingObjectRowDataToCurrentSheet(XSSFSheet currentSheet, int r
 
         currentCell = currentRow.createCell(cellCount++);
         if ((null != bo.getBindingStrength() && bo.getBindingStrength().equalsIgnoreCase("required")) ||
-                null != bo.getMustSupport() && bo.getMustSupport().equalsIgnoreCase("Y")) {
+                null != bo.getMustSupport() && bo.getMustSupport().equalsIgnoreCase("Y") ||
+                null != bo.getBindingObjectExtension() && bo.getBindingObjectExtension().equalsIgnoreCase("qicore-keyElement") ||
+                bo.getCardinalityMin() > 0
+        ) {
             currentCell.setCellValue("Needed");
         }
     }