Move CRMI operations to Visitors (#408)

* Start of visitors and adapters; release operation * merge master - further updates * WIP reorganizing adapters * WIP need to merge master * [APHL-551] $release, $draft, $package all working in r4 * [APHL-551] updated r4 draft tests * [APHL-551] Release operation tests * [APHL-551] $package tests updated * [APHL-551] package warning test * [APHL-551] fix style and API compatibility errors * [APHL-551] use existing packagehelper * [APHL-551] use existing searchhelper * [APHL-551] use existing searchhelper * [APHL-551] remove condition filter and remove duplication * [APHL-551] typo * [APHL-551] remove duplication * cleanup * cleanup * [APHL-551] cleanup * cleanup * merge conflict issues * cleanup * cleanup * cleanup * [APHL-551] remove vsm specific functionality * spotless * [APHL-551] update dependency tracing, add $approve support and make params in line with operation definitions * [APHL-551] fix VS dependency tracing * [APHL-551] cleanup * cleanup * [APHL-551] add coverage * [APHL-551] add coverage * [APHL-551] add coverage * [APHL-551] add coverage * [APHL-551] add coverage * [APHL-551] add coverage * fix pom * [APHL-551] add coverage * [APHL-551] spotless * [APHL-551] move transaction stub out of inMemoryFhirRepository * [APHL-551] make transaction stub generic * [APHL-551] spotless * [APHL-551] change to var * [APHL-551] line between methods * [APHL-551] line between methods * [APHL-551] propagate packagehelper changes to all versions * [APHL-551] fixed duplicate dependency * [APHL-551] DependencyInfo in the right folder * spotless * [APHL-551] DependencyInfo in the right folder * Apply suggestions from code review add missing Extension generic params per suggestion Co-authored-by: Brenin Rhodes <[email protected]> * [APHL-551] versionless interfaces * [APHL-551] Rename * spotless * consistent errors * [APHL-551] Rename * [APHL-551] update coverage * [APHL-551] update coverage * [APHL-551] better class check * spotless * [APHL-551] update coverage * [APHL-551] add support for dstu3 and r5 * [APHL-551] cleanup * [APHL-551] cleanup * [APHL-551] cleanup and test bugs * [APHL-551] cleanup * [APHL-551] cleanup * [APHL-551] cleanup * spotless * Add hasRelatedArtifact to KnowledgeArtifactAdapter and use adapter in version PackageHelpers --------- Co-authored-by: Adam Stevenson <[email protected]> Co-authored-by: [email protected] <[email protected]> Co-authored-by: Brenin Rhodes <[email protected]> Co-authored-by: Brenin Rhodes <[email protected]>
cqframework · Mar 19, 2024 · 0d344ed · 0d344ed
1 parent 42ec12b
commit 0d344ed
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Showing 123 changed files with 621,711 additions and 566 deletions.
diff --git a/...ir-cr/src/main/java/org/opencds/cqf/fhir/cr/plandefinition/packages/PackageProcessor.java b/...ir-cr/src/main/java/org/opencds/cqf/fhir/cr/plandefinition/packages/PackageProcessor.java
@@ -5,6 +5,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cr.common.IPackageProcessor;
+import org.opencds.cqf.fhir.utility.BundleHelper;
 
 public class PackageProcessor implements IPackageProcessor {
  protected final Repository repository;
@@ -42,7 +43,8 @@ protected IBaseBundle packagePlanDefinition(IBaseResource planDefinition, boolea
  protected IBaseBundle packageDstu3(org.hl7.fhir.dstu3.model.PlanDefinition planDefinition, boolean isPut) {
  var packageBundle = new org.hl7.fhir.dstu3.model.Bundle();
  packageBundle.setType(org.hl7.fhir.dstu3.model.Bundle.BundleType.TRANSACTION);
- packageBundle.addEntry(org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(planDefinition, isPut));
+ BundleHelper.addEntry(
+ packageBundle, org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(planDefinition, isPut));
  // The CPG IG specifies a main cql library for a PlanDefinition
  var libraryCanonical = planDefinition.hasLibrary()
  ? new org.hl7.fhir.dstu3.model.StringType(
@@ -53,7 +55,8 @@ protected IBaseBundle packageDstu3(org.hl7.fhir.dstu3.model.PlanDefinition planD
  org.opencds.cqf.fhir.utility.dstu3.SearchHelper.searchRepositoryByCanonical(
  repository, libraryCanonical);
  if (library != null) {
- packageBundle.addEntry(org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(library, isPut));
+ BundleHelper.addEntry(
+ packageBundle, org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(library, isPut));
  if (library.hasRelatedArtifact()) {
  org.opencds.cqf.fhir.utility.dstu3.PackageHelper.addRelatedArtifacts(
  packageBundle, library.getRelatedArtifact(), repository, isPut);
@@ -71,7 +74,8 @@ protected IBaseBundle packageDstu3(org.hl7.fhir.dstu3.model.PlanDefinition planD
  protected IBaseBundle packageR4(org.hl7.fhir.r4.model.PlanDefinition planDefinition, boolean isPut) {
  var packageBundle = new org.hl7.fhir.r4.model.Bundle();
  packageBundle.setType(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION);
- packageBundle.addEntry(org.opencds.cqf.fhir.utility.r4.PackageHelper.createEntry(planDefinition, isPut));
+ packageBundle.addEntry((org.hl7.fhir.r4.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(planDefinition, isPut));
  // The CPG IG specifies a main cql library for a PlanDefinition
  var libraryCanonical =
  planDefinition.hasLibrary() ? planDefinition.getLibrary().get(0) : null;
@@ -80,7 +84,8 @@ protected IBaseBundle packageR4(org.hl7.fhir.r4.model.PlanDefinition planDefinit
  org.opencds.cqf.fhir.utility.r4.SearchHelper.searchRepositoryByCanonical(
  repository, libraryCanonical);
  if (library != null) {
- packageBundle.addEntry(org.opencds.cqf.fhir.utility.r4.PackageHelper.createEntry(library, isPut));
+ packageBundle.addEntry((org.hl7.fhir.r4.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(library, isPut));
  if (library.hasRelatedArtifact()) {
  org.opencds.cqf.fhir.utility.r4.PackageHelper.addRelatedArtifacts(
  packageBundle, library.getRelatedArtifact(), repository, isPut);
@@ -98,7 +103,8 @@ protected IBaseBundle packageR4(org.hl7.fhir.r4.model.PlanDefinition planDefinit
  protected IBaseBundle packageR5(org.hl7.fhir.r5.model.PlanDefinition planDefinition, boolean isPut) {
  var packageBundle = new org.hl7.fhir.r5.model.Bundle();
  packageBundle.setType(org.hl7.fhir.r5.model.Bundle.BundleType.TRANSACTION);
- packageBundle.addEntry(org.opencds.cqf.fhir.utility.r5.PackageHelper.createEntry(planDefinition, isPut));
+ packageBundle.addEntry((org.hl7.fhir.r5.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(planDefinition, isPut));
  // The CPG IG specifies a main cql library for a PlanDefinition
  var libraryCanonical =
  planDefinition.hasLibrary() ? planDefinition.getLibrary().get(0) : null;
@@ -107,7 +113,8 @@ protected IBaseBundle packageR5(org.hl7.fhir.r5.model.PlanDefinition planDefinit
  org.opencds.cqf.fhir.utility.r5.SearchHelper.searchRepositoryByCanonical(
  repository, libraryCanonical);
  if (library != null) {
- packageBundle.addEntry(org.opencds.cqf.fhir.utility.r5.PackageHelper.createEntry(library, isPut));
+ packageBundle.addEntry((org.hl7.fhir.r5.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(library, isPut));
  if (library.hasRelatedArtifact()) {
  org.opencds.cqf.fhir.utility.r5.PackageHelper.addRelatedArtifacts(
  packageBundle, library.getRelatedArtifact(), repository, isPut);

diff --git a/...hir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/packages/PackageProcessor.java b/...hir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/packages/PackageProcessor.java
@@ -5,6 +5,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cr.common.IPackageProcessor;
+import org.opencds.cqf.fhir.utility.BundleHelper;
 import org.opencds.cqf.fhir.utility.Constants;
 
 public class PackageProcessor implements IPackageProcessor {
@@ -43,8 +44,10 @@ protected IBaseBundle packageQuestionnaire(IBaseResource questionnaire, boolean
  protected IBaseBundle packageDstu3(IBaseResource questionnaire, Boolean isPut) {
  var bundle = new org.hl7.fhir.dstu3.model.Bundle();
  bundle.setType(org.hl7.fhir.dstu3.model.Bundle.BundleType.TRANSACTION);
- bundle.addEntry(org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(
- (org.hl7.fhir.dstu3.model.Resource) questionnaire, isPut));
+ BundleHelper.addEntry(
+ bundle,
+ org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(
+ (org.hl7.fhir.dstu3.model.Resource) questionnaire, isPut));
  var libraryExtension =
  ((org.hl7.fhir.dstu3.model.Questionnaire) questionnaire).getExtensionByUrl(Constants.CQF_LIBRARY);
  if (libraryExtension != null) {
@@ -53,7 +56,8 @@ protected IBaseBundle packageDstu3(IBaseResource questionnaire, Boolean isPut) {
  org.opencds.cqf.fhir.utility.dstu3.SearchHelper.searchRepositoryByCanonical(
  repository, libraryCanonical);
  if (library != null) {
- bundle.addEntry(org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(library, isPut));
+ BundleHelper.addEntry(
+ bundle, org.opencds.cqf.fhir.utility.dstu3.PackageHelper.createEntry(library, isPut));
  if (library.hasRelatedArtifact()) {
  org.opencds.cqf.fhir.utility.dstu3.PackageHelper.addRelatedArtifacts(
  bundle, library.getRelatedArtifact(), repository, isPut);
@@ -66,8 +70,9 @@ protected IBaseBundle packageDstu3(IBaseResource questionnaire, Boolean isPut) {
  protected IBaseBundle packageR4(IBaseResource questionnaire, Boolean isPut) {
  var bundle = new org.hl7.fhir.r4.model.Bundle();
  bundle.setType(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION);
- bundle.addEntry(org.opencds.cqf.fhir.utility.r4.PackageHelper.createEntry(
- (org.hl7.fhir.r4.model.Resource) questionnaire, isPut));
+ bundle.addEntry((org.hl7.fhir.r4.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(
+ (org.hl7.fhir.r4.model.Resource) questionnaire, isPut));
  var libraryExtension =
  ((org.hl7.fhir.r4.model.Questionnaire) questionnaire).getExtensionByUrl(Constants.CQF_LIBRARY);
  if (libraryExtension != null) {
@@ -76,7 +81,8 @@ protected IBaseBundle packageR4(IBaseResource questionnaire, Boolean isPut) {
  org.opencds.cqf.fhir.utility.r4.SearchHelper.searchRepositoryByCanonical(
  repository, libraryCanonical);
  if (library != null) {
- bundle.addEntry(org.opencds.cqf.fhir.utility.r4.PackageHelper.createEntry(library, isPut));
+ bundle.addEntry((org.hl7.fhir.r4.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(library, isPut));
  if (library.hasRelatedArtifact()) {
  org.opencds.cqf.fhir.utility.r4.PackageHelper.addRelatedArtifacts(
  bundle, library.getRelatedArtifact(), repository, isPut);
@@ -89,8 +95,9 @@ protected IBaseBundle packageR4(IBaseResource questionnaire, Boolean isPut) {
  protected IBaseBundle packageR5(IBaseResource questionnaire, Boolean isPut) {
  var bundle = new org.hl7.fhir.r5.model.Bundle();
  bundle.setType(org.hl7.fhir.r5.model.Bundle.BundleType.TRANSACTION);
- bundle.addEntry(org.opencds.cqf.fhir.utility.r5.PackageHelper.createEntry(
- (org.hl7.fhir.r5.model.Resource) questionnaire, isPut));
+ bundle.addEntry((org.hl7.fhir.r5.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(
+ (org.hl7.fhir.r5.model.Resource) questionnaire, isPut));
  var libraryExtension =
  ((org.hl7.fhir.r5.model.Questionnaire) questionnaire).getExtensionByUrl(Constants.CQF_LIBRARY);
  if (libraryExtension != null) {
@@ -99,7 +106,8 @@ protected IBaseBundle packageR5(IBaseResource questionnaire, Boolean isPut) {
  org.opencds.cqf.fhir.utility.r5.SearchHelper.searchRepositoryByCanonical(
  repository, libraryCanonical);
  if (library != null) {
- bundle.addEntry(org.opencds.cqf.fhir.utility.r5.PackageHelper.createEntry(library, isPut));
+ bundle.addEntry((org.hl7.fhir.r5.model.Bundle.BundleEntryComponent)
+ org.opencds.cqf.fhir.utility.PackageHelper.createEntry(library, isPut));
  if (library.hasRelatedArtifact()) {
  org.opencds.cqf.fhir.utility.r5.PackageHelper.addRelatedArtifacts(
  bundle, library.getRelatedArtifact(), repository, isPut);

diff --git a/cqf-fhir-utility/pom.xml b/cqf-fhir-utility/pom.xml
@@ -21,6 +21,12 @@
  <artifactId>cqf-fhir-api</artifactId>
  <version>3.2.0-SNAPSHOT</version>
  </dependency>
+ <dependency>
+ <groupId>org.opencds.cqf.fhir</groupId>
+ <artifactId>cqf-fhir-test</artifactId>
+ <version>3.2.0-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
  <dependency>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-base</artifactId>
@@ -66,10 +72,8 @@
  <artifactId>hapi-fhir-validation-resources-r5</artifactId>
  </dependency>
  <dependency>
- <groupId>org.opencds.cqf.fhir</groupId>
- <artifactId>cqf-fhir-test</artifactId>
- <version>3.2.0-SNAPSHOT</version>
- <scope>test</scope>
- </dependency>
+ <groupId>ch.qos.logback</groupId>
+ <artifactId>logback-classic</artifactId>
+ </dependency>
  </dependencies>
 </project>