Configurable DAK processor (#493)

* Fixed observation-style data elements Enhanced questionnaire support Streamlined concept/valueset creation and usage Expanded support for base profiles used in context and selector logic * Added configuration support to the data dictionary * Fixed concept maps not being generated in some cases * Code system generation fixes * Fixed DTProcessor write issue * #469: Added a libraryPath parameter to support specifying expected lo… 26701a1 …cation for library resources * Updated translator to 3.3.2 Added skip-packages option to refresh ig operation Removed operation processing for narrative refresh operations and drools operation NOTE: This is known not to compile at this point, I've removed all the code related to the narrative refresh and drools operations locally, and have published a release based on that local code. This is in anticipation of a reorganization of the tooling that moves different operations into different packages, so I'm committing the changes here that are released as 2.6.0 from my local compile. * Test Cases for DAK (#496) * Unit test cases for WHO content. * Fixed platform specific differences causing test failures * Added separator to avoid windows discrapencies. * simplify the tests, going to start with counts and drill down * WIP Who tests --------- Co-authored-by: Chalma Maadaadi <[email protected]> Co-authored-by: Bryn Rhodes <[email protected]> --------- Co-authored-by: Bryn Rhodes <[email protected]> Co-authored-by: Chalma Maadaadi <[email protected]>
cqframework · Nov 30, 2023 · 8c4092a · 8c4092a
1 parent 3b42f54
commit 8c4092a
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Showing 19 changed files with 851 additions and 297 deletions.
diff --git a/tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java b/tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java
@@ -228,4 +228,4 @@ static Operation createOperation(String operationName) {
                 throw new IllegalArgumentException("Invalid operation: " + operationName);
         }
     }
-}
+}
diff --git a/tooling/pom.xml b/tooling/pom.xml
@@ -217,7 +217,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.module</groupId>
             <artifactId>jackson-module-jaxb-annotations</artifactId>
-            <version>2.13.2</version>
+            <version>2.14.2</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
@@ -304,7 +304,6 @@
             <artifactId>model-jackson</artifactId>
             <scope>test</scope>
         </dependency>
-
         <dependency>
             <groupId>info.cqframework</groupId>
             <artifactId>engine</artifactId>

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/DTProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/DTProcessor.java
@@ -34,11 +34,11 @@
 import org.opencds.cqf.tooling.Operation;
 import org.opencds.cqf.tooling.terminology.SpreadsheetHelper;
 import org.opencds.cqf.tooling.utilities.IOUtils;
-
-import ca.uhn.fhir.context.FhirContext;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import ca.uhn.fhir.context.FhirContext;
+
 public class DTProcessor extends Operation {
 
     private static final Logger logger = LoggerFactory.getLogger(DTProcessor.class);
@@ -362,7 +362,7 @@ private void mergeActions(PlanDefinition.PlanDefinitionActionComponent currentAc
             currentAction.getCondition().add(newCondition);
         }
         else if (newCondition != null) {
-            currentCondition.getExpression().setDescription(String.format("(%s)\n  OR (%s)", currentCondition.getExpression().getDescription(), newCondition.getExpression().getDescription()));
+            currentCondition.getExpression().setDescription(String.format("(%s)%n  OR (%s)", currentCondition.getExpression().getDescription(), newCondition.getExpression().getDescription()));
         }
     }
 
@@ -473,7 +473,7 @@ private PlanDefinition.PlanDefinitionActionComponent processAction(Iterator<Row>
             else {
                 for (String conditionValue : conditionValues) {
                     if (applicabilityCondition.length() > 0) {
-                        applicabilityCondition.append(String.format("\n  AND "));
+                        applicabilityCondition.append(String.format("%n  AND "));
                     }
                     applicabilityCondition.append("(");
                     applicabilityCondition.append(conditionValue);
@@ -690,11 +690,11 @@ private String buildPlanDefinitionIndex() {
     }
 
     public void writePlanDefinitionIndex(String outputPath) {
-        String outputFilePath = IOUtils.concatFilePath(outputPath,
-                "input", "pagecontent", "PlanDefinitionIndex.md");
+        String outputFilePath = outputPath + File.separator + "input" + File.separator + "pagecontent";
         ensurePath(outputFilePath);
 
-        try (FileOutputStream writer = new FileOutputStream(outputFilePath)) {
+        String outputFile = outputFilePath + File.separator + "PlanDefinitionIndex.md";
+        try (FileOutputStream writer = new FileOutputStream(outputFile)) {
             writer.write(buildPlanDefinitionIndex().getBytes());
             writer.flush();
         }

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/ExampleBuilder.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/ExampleBuilder.java
@@ -685,15 +685,17 @@ else if (value instanceof Extension) {
             if (ed.getType("Extension") != null && ed.getType("Extension").getProfile() != null && atlas != null && atlas.getValueSets() != null && atlas.getExtensions() != null) {
                 StructureDefinition sdExtension = atlas.getExtensions().getByCanonicalUrlWithVersion(ed.getType("Extension").getProfile().get(0).getValue());
                 ElementDefinition extensionElement = sdExtension.getDifferential().getElement().stream()
-                    .filter(x -> x.hasBinding() && x.getBinding().hasValueSetElement()).findFirst().get();
+                    .filter(x -> x.hasBinding() && x.getBinding().hasValueSetElement()).findFirst().orElse(null);
 
-                Type extensionValue = null;
-                if (extensionElement.getType("CodeableConcept") != null) {
-                    extensionValue = new CodeableConcept();
-                }
+                if (extensionElement != null) {
+                    Type extensionValue = null;
+                    if (extensionElement.getType("CodeableConcept") != null) {
+                        extensionValue = new CodeableConcept();
+                    }
 
-                generateValue(sdExtension, extensionElement, extensionValue, givenValue);
-                value.addExtension(new Extension().setUrl(extensionElement.getShort()).setValue(extensionValue));
+                    generateValue(sdExtension, extensionElement, extensionValue, givenValue);
+                    value.addExtension(new Extension().setUrl(extensionElement.getShort()).setValue(extensionValue));
+                }
             }
         }
     }
-Original file line number
+Diff line change
@@ Expand Up / @@ -228,4 +228,4 @@ static Operation createOperation(String operationName) { @@
                     throw new IllegalArgumentException("Invalid operation: " + operationName);
             }
         }
-    }
+    }