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Bug accelerator kit kalm62 (#502)
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* feature-acceleratorkit-hivcds-updates-david
Ongoing work : Fix branch build

* KALM [BUG] ASLPConcepts.cql acceleratorKit bugs #62
Fixed generation of ASLPConcepts.cql file as well as Added tests to verify it.

* KALM [BUG] ASLPConcepts.cql acceleratorKit bugs #62
Extra lines removed

* KALM [BUG] ASLPConcepts.cql acceleratorKit bugs #62
reverting to master processor

* KALM [BUG] ASLPConcepts.cql acceleratorKit bugs #62
Fixed CQL generation for Concepts.cql
Added scope based CodeSystem check
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@ddieppois
ddieppois authored Dec 8, 2023
1 parent 7d7b5d9 commit a324934
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53 changes: 39 additions & 14 deletions tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,9 @@ public class Processor extends Operation {
// TODO: These need to be per scope
private String dataElementIdentifierSystem = "http://fhir.org/guides/nachc/hiv-cds/Identifier/data-elements";
private String contentId;
private String activityCodeSystem = "http://fhir.org/guides/nachc/hiv-cds/CodeSystem/activity-codes";
private String activityCodeSystemUrl = "http://fhir.org/guides/nachc/hiv-cds/CodeSystem/activity-codes";

private String defaultCodeSystemUrl = "http://fhir.org/guides/nachc/hiv-cds/CodeSystem/";
private String projectCodeSystemBase;

private int questionnaireItemLinkIdCounter = 1;
Expand Down Expand Up @@ -327,9 +329,9 @@ private void processScope(Workbook workbook, String scope) {

if (scope != null && scope.length() > 0) {
contentId = getContentId(scope);
activityCodeSystem = getActivityCodeSystem(scope.toLowerCase());
defaultCodeSystemUrl = getScopeCodeSystemUrl(scope.toLowerCase());
setCanonicalBase(scopeCanonicalBaseMap.get(scope.toLowerCase()));
createActivityCodeSystem(activityCodeSystem);
createScopeCodeSystem(defaultCodeSystemUrl, scope);
}

// process workbook
Expand Down Expand Up @@ -561,21 +563,23 @@ private Coding getActivityCoding(String activityId) {
Coding activity = activityMap.get(activityCode);

if (activity == null) {
activity = new Coding().setCode(activityCode).setSystem(activityCodeSystem).setDisplay(activityDisplay);
activity = new Coding().setCode(activityCode).setSystem(activityCodeSystemUrl).setDisplay(activityDisplay);
activityMap.put(activityCode, activity);

CodeSystem cs = resolveCodeSystem(activityCodeSystem);
CodeSystem cs = resolveCodeSystem(activityCodeSystemUrl);
addCodeToSystem(cs, activity);
}

return activity;
}

private void addCodeToSystem(CodeSystem cs, Coding code) {
CodeSystem.ConceptDefinitionComponent concept = new CodeSystem.ConceptDefinitionComponent();
concept.setCode(code.getCode());
concept.setDisplay(code.getDisplay());
cs.addConcept(concept);
if(cs != null) {
CodeSystem.ConceptDefinitionComponent concept = new CodeSystem.ConceptDefinitionComponent();
concept.setCode(code.getCode());
concept.setDisplay(code.getDisplay());
cs.addConcept(concept);
}
}

private String getNextElementId(String activityCode) {
Expand Down Expand Up @@ -2695,6 +2699,7 @@ private CodeSystem createCodeSystem(String id, String name, String canonicalBase
codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
codeSystem.setCaseSensitive(true);

System.out.println(String.format("Creating CodeSystem: %s", codeSystem.getUrl()));
codeSystems.add(codeSystem);

return codeSystem;
Expand Down Expand Up @@ -3169,15 +3174,24 @@ private String getContentId(String scope) {
return "ANC";
}

private String getActivityCodeSystem(String scope) {
private String getActivityCodeSystemUrl(String scope) {
String canonicalBase = scopeCanonicalBaseMap.get(scope);
if (canonicalBase == null) {
return activityCodeSystem;
return activityCodeSystemUrl;
}

return canonicalBase + "/CodeSystem/activity-codes";
}

private String getScopeCodeSystemUrl(String scope) {
String canonicalBase = scopeCanonicalBaseMap.get(scope);
if (canonicalBase == null) {
canonicalBase = defaultCodeSystemUrl;
}

return canonicalBase + String.format("/CodeSystem/%s-codes",scope);
}

private CodeSystem createActivityCodeSystem(String system) {
CodeSystem codeSystem = resolveCodeSystem(system);

Expand All @@ -3189,10 +3203,21 @@ private CodeSystem createActivityCodeSystem(String system) {
return codeSystem;
}

private CodeSystem resolveCodeSystem(String system) {
private CodeSystem createScopeCodeSystem(String systemUrl, String scope) {
CodeSystem codeSystem = resolveCodeSystem(systemUrl);

if (codeSystem == null) {
codeSystem = createCodeSystem(scope + "-codes", String.format("%sCodes", contentId), projectCodeSystemBase, String.format("%s Codes", contentId),
"Set of codes representing all code systems used in the implementation guide");
}

return codeSystem;
}

private CodeSystem resolveCodeSystem(String systemUrl) {
CodeSystem codeSystem = null;
for (CodeSystem cs : codeSystems) {
if (cs.getUrl().equals(system)) {
if (cs.getUrl().equals(systemUrl)) {
codeSystem = cs;
}
}
Expand All @@ -3203,7 +3228,7 @@ private CodeSystem resolveCodeSystem(String system) {
private Coding getActivityCoding(CodeableConcept concept) {
if (concept.hasCoding()) {
for (Coding c : concept.getCoding()) {
if (activityCodeSystem.equals(c.getSystem())) {
if (activityCodeSystemUrl.equals(c.getSystem())) {
return c;
}
}
Expand Down
4 changes: 2 additions & 2 deletions tooling/src/test/java/org/opencds/cqf/tooling/acceleratorkit/ANCMiniContentTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,8 @@ public void validateCQLContent() throws IOException {
public void validateCodeSystem() {
var codeSystem = resourceAtPath(
CodeSystem.class,
vocabularyPath().resolve("codesystem/codesystem-activity-codes.json"));
assertEquals(codeSystem.getTitle(), "ANCM Activity Codes");
vocabularyPath().resolve("codesystem/codesystem-ancm-codes.json"));
assertEquals(codeSystem.getTitle(), "ANCM Codes");
}

@Test
Expand Down
50 changes: 46 additions & 4 deletions tooling/src/test/java/org/opencds/cqf/tooling/acceleratorkit/DTRContentTest.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,15 @@
package org.opencds.cqf.tooling.acceleratorkit;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;

import org.hl7.fhir.r4.model.CodeSystem;
import org.testng.annotations.Ignore;
import org.testng.annotations.Test;

import java.io.IOException;
import java.nio.file.Files;

import static org.testng.Assert.*;
import static org.testng.Assert.assertTrue;

public class DTRContentTest extends BaseContentTest {

public DTRContentTest() {
Expand All @@ -15,15 +20,52 @@ public DTRContentTest() {
}

@Test
@Ignore
public void validateContentCount() {
assertEquals(cqlPath().toFile().listFiles().length, 4);
assertEquals(examplesPath().toFile().listFiles().length, 8);
assertFalse(extensionsPath().toFile().exists());
assertEquals(profilesPath().toFile().listFiles().length, 8);
assertEquals(resourcesPath().toFile().listFiles().length, 1);
assertFalse(testsPath().toFile().exists());
assertEquals(vocabularyPath().resolve("codesystem").toFile().listFiles().length, 2);
assertEquals(vocabularyPath().resolve("conceptmap").toFile().listFiles().length, 2);
assertEquals(vocabularyPath().resolve("valueset").toFile().listFiles().length, 4);
}

@Test
public void validateCQLContent() throws IOException {

assertTrue(cqlPath().resolve("ASLPContactDataElements.cql").toFile().exists());
assertTrue(cqlPath().resolve("ASLPDataElements.cql").toFile().exists());

var cqlLines = Files.readAllLines(cqlPath().resolve("ASLPConcepts.cql"));
assertEquals(cqlLines.get(0), "library ASLPConcepts");
}

@Test
public void validateConceptsCqlContentIssueKALM62() throws IOException {
assertTrue(cqlPath().resolve("ASLPConcepts.cql").toFile().exists());
var cqlLines = Files.readAllLines(cqlPath().resolve("ASLPConcepts.cql"));
assertEquals(cqlLines.get(0), "library ASLPConcepts");
assertEquals(cqlLines.get(2), "// Code Systems");
assertEquals(cqlLines.get(15), "codesystem \"ASLP Codes\": 'http://example.org/sdh/dtr/aslp/CodeSystem/aslp-codes'");
assertEquals(cqlLines.get(16), "");
assertEquals(cqlLines.get(17), "// Value Sets");
assertEquals(cqlLines.get(23), "// Codes");
assertEquals(cqlLines.get(26), "code \"Neck Circumference\": 'ASLP.A1.DE20' from \"ASLP Codes\" display 'Neck Circumference'");
assertEquals(cqlLines.get(27), "code \"Height\": 'ASLP.A1.DE20' from \"ASLP Codes\" display 'Height'");
}

@Test
@Ignore
public void validateCodeSystem() {
var codeSystemActivity = resourceAtPath(
CodeSystem.class,
vocabularyPath().resolve("codesystem/codesystem-activity-codes.json"));
assertEquals(codeSystemActivity.getTitle(), "ASLP Activity Codes");
var codeSystemConcept = resourceAtPath(
CodeSystem.class,
vocabularyPath().resolve("codesystem/codesystem-concept-codes.json"));
assertEquals(codeSystemConcept.getTitle(), "ASLP Concept Codes");
}
}

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