APHL-1023-withdraw_draft_programs (#530)

* initial withdraw implementation * add test for non-draft library + only depends-on cascade delete * first check request resource id to work with * use specific withdraw resource file * return bundle and delete on ecr * fix in memory fhir repo * run code formatting * add InMemoryRepository tests * reformat code * add getEntryRequestId & isEntryRequestDelete tests * run code check * throw error if delete request entry is not present * artifacts that is owned and has composed-of relationship * run code check * update Exception thrown in in memory repo * run code check * add unsupported fhir version tests to bundle helper * rename getComponents method name * add approval removal on withdraw * add customSearchParams and fix runtime search param property --------- Co-authored-by: Ivan Baisi <[email protected]>
cqframework · Sep 24, 2024 · 3b34066 · 3b34066
1 parent 6100130
commit 3b34066
Show file tree

Hide file tree

Showing 17 changed files with 12,627 additions and 59 deletions.
diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/BundleHelper.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/BundleHelper.java
@@ -1,16 +1,23 @@
 package org.opencds.cqf.fhir.utility;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
+import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
+import java.util.stream.Collectors;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.SearchParameter;
+import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent;
+import org.hl7.fhir.r5.model.PrimitiveType;
 
 public class BundleHelper {
     private BundleHelper() {}
@@ -640,4 +647,57 @@ public static IBaseBackboneElement setEntryRequest(
                         String.format("Unsupported version of FHIR: %s", fhirVersion.getFhirVersionString()));
         }
     }
+
+    public static RuntimeSearchParam resourceToRuntimeSearchParam(IBaseResource resource) {
+        var fhirVersion = resource.getStructureFhirVersionEnum();
+        switch (fhirVersion) {
+            case DSTU3:
+                var res = (SearchParameter) resource;
+                return new RuntimeSearchParam(
+                        res.getIdElement(),
+                        res.getUrl(),
+                        res.getCode(),
+                        res.getDescription(),
+                        res.getExpression(),
+                        RestSearchParameterTypeEnum.REFERENCE,
+                        null,
+                        res.getTarget().stream().map(StringType::toString).collect(Collectors.toSet()),
+                        RuntimeSearchParamStatusEnum.ACTIVE,
+                        res.getBase().stream().map(StringType::toString).collect(Collectors.toList()));
+            case R4:
+                var resR4 = (org.hl7.fhir.r4.model.SearchParameter) resource;
+                return new RuntimeSearchParam(
+                        resR4.getIdElement(),
+                        resR4.getUrl(),
+                        resR4.getCode(),
+                        resR4.getDescription(),
+                        resR4.getExpression(),
+                        RestSearchParameterTypeEnum.REFERENCE,
+                        null,
+                        resR4.getTarget().stream()
+                                .map(org.hl7.fhir.r4.model.StringType::toString)
+                                .collect(Collectors.toSet()),
+                        RuntimeSearchParamStatusEnum.ACTIVE,
+                        resR4.getBase().stream()
+                                .map(org.hl7.fhir.r4.model.StringType::toString)
+                                .collect(Collectors.toList()));
+            case R5:
+                var resR5 = (org.hl7.fhir.r5.model.SearchParameter) resource;
+                return new RuntimeSearchParam(
+                        resR5.getIdElement(),
+                        resR5.getUrl(),
+                        resR5.getCode(),
+                        resR5.getDescription(),
+                        resR5.getExpression(),
+                        RestSearchParameterTypeEnum.REFERENCE,
+                        null,
+                        resR5.getTarget().stream().map(PrimitiveType::toString).collect(Collectors.toSet()),
+                        RuntimeSearchParamStatusEnum.ACTIVE,
+                        resR5.getBase().stream().map(PrimitiveType::toString).collect(Collectors.toList()));
+
+            default:
+                throw new IllegalArgumentException(
+                        String.format("Unsupported version of FHIR: %s", fhirVersion.getFhirVersionString()));
+        }
+    }
 }
diff --git a/...-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/KnowledgeArtifactAdapter.java b/...-utility/src/main/java/org/opencds/cqf/fhir/utility/adapter/KnowledgeArtifactAdapter.java
@@ -26,7 +26,7 @@
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.utility.BundleHelper;
-import org.opencds.cqf.fhir.utility.visitor.KnowledgeArtifactVisitor;
+import org.opencds.cqf.fhir.utility.visitor.IKnowledgeArtifactVisitor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -293,7 +293,8 @@ default List<IDependencyInfo> combineComponentsAndDependencies() {
                 .collect(Collectors.toList());
     }
 
-    default IBase accept(KnowledgeArtifactVisitor visitor, Repository repository, IBaseParameters operationParameters) {
+    default IBase accept(
+            IKnowledgeArtifactVisitor visitor, Repository repository, IBaseParameters operationParameters) {
         return visitor.visit(this, repository, operationParameters);
     }
 

diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/matcher/ResourceMatcher.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/matcher/ResourceMatcher.java
@@ -1,6 +1,7 @@
 package org.opencds.cqf.fhir.utility.matcher;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.fhirpath.IFhirPath;
 import ca.uhn.fhir.fhirpath.IFhirPath.IParsedExpression;
 import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -12,6 +13,7 @@
 import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.param.UriParam;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import org.apache.commons.lang3.NotImplementedException;
@@ -69,12 +71,25 @@ public boolean equals(Object obj) {
 
     public Map<SPPathKey, IParsedExpression> getPathCache();
 
+    public Map<String, RuntimeSearchParam> customSearchParams = new HashMap<>();
+
+    default void addCustomParameter(RuntimeSearchParam searchParam) {
+        this.customSearchParams.put(searchParam.getName(), searchParam);
+    }
+
+    default Map<String, RuntimeSearchParam> getCustomParameters() {
+        return this.customSearchParams;
+    }
+
     // The list here is an OR list. Meaning, if any element matches it's a match
     default boolean matches(String name, List<IQueryParameterType> params, IBaseResource resource) {
         boolean match = true;
 
         var context = getContext();
         var s = context.getResourceDefinition(resource).getSearchParam(name);
+        if (s == null) {
+            s = this.getCustomParameters().get(name);
+        }
         if (s == null) {
             throw new RuntimeException(String.format(
                     "The SearchParameter %s for Resource %s is not supported.", name, resource.fhirType()));

diff --git a/...utility/src/main/java/org/opencds/cqf/fhir/utility/repository/InMemoryFhirRepository.java b/...utility/src/main/java/org/opencds/cqf/fhir/utility/repository/InMemoryFhirRepository.java
@@ -107,7 +107,12 @@ public <T extends IBaseResource> MethodOutcome update(T resource, Map<String, St
         if (!resources.containsKey(theId)) {
             outcome.setCreated(true);
         }
+        if (resource.fhirType().equals("SearchParameter")) {
+            var resourceMatcher = Repositories.getResourceMatcher(this.context);
+            resourceMatcher.addCustomParameter(BundleHelper.resourceToRuntimeSearchParam(resource));
+        }
         resources.put(theId, resource);
+
         return outcome;
     }
 

diff --git a/.../src/main/java/org/opencds/cqf/fhir/utility/visitor/AbstractKnowledgeArtifactVisitor.java b/.../src/main/java/org/opencds/cqf/fhir/utility/visitor/AbstractKnowledgeArtifactVisitor.java
@@ -0,0 +1,35 @@
+package org.opencds.cqf.fhir.utility.visitor;
+
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import java.util.List;
+import java.util.stream.Collectors;
+import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.fhir.api.Repository;
+
+public abstract class AbstractKnowledgeArtifactVisitor implements IKnowledgeArtifactVisitor {
+    protected List<IBaseBackboneElement> findArtifactCommentsToUpdate(
+            IBaseResource artifact, String releaseVersion, Repository repository) {
+        if (artifact instanceof org.hl7.fhir.dstu3.model.MetadataResource) {
+            return org.opencds.cqf.fhir.utility.visitor.dstu3.ReleaseVisitor.findArtifactCommentsToUpdate(
+                            (org.hl7.fhir.dstu3.model.MetadataResource) artifact, releaseVersion, repository)
+                    .stream()
+                    .map(r -> (IBaseBackboneElement) r)
+                    .collect(Collectors.toList());
+        } else if (artifact instanceof org.hl7.fhir.r4.model.MetadataResource) {
+            return org.opencds.cqf.fhir.utility.visitor.r4.ReleaseVisitor.findArtifactCommentsToUpdate(
+                            (org.hl7.fhir.r4.model.MetadataResource) artifact, releaseVersion, repository)
+                    .stream()
+                    .map(r -> (IBaseBackboneElement) r)
+                    .collect(Collectors.toList());
+        } else if (artifact instanceof org.hl7.fhir.r5.model.MetadataResource) {
+            return org.opencds.cqf.fhir.utility.visitor.r5.ReleaseVisitor.findArtifactCommentsToUpdate(
+                            (org.hl7.fhir.r5.model.MetadataResource) artifact, releaseVersion, repository)
+                    .stream()
+                    .map(r -> (IBaseBackboneElement) r)
+                    .collect(Collectors.toList());
+        } else {
+            throw new UnprocessableEntityException("Version not supported");
+        }
+    }
+}
diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/ApproveVisitor.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/ApproveVisitor.java
@@ -17,7 +17,7 @@
 import org.opencds.cqf.fhir.utility.PackageHelper;
 import org.opencds.cqf.fhir.utility.adapter.KnowledgeArtifactAdapter;
 
-public class ApproveVisitor implements KnowledgeArtifactVisitor {
+public class ApproveVisitor implements IKnowledgeArtifactVisitor {
     @Override
     public IBase visit(KnowledgeArtifactAdapter adapter, Repository repository, IBaseParameters approveParameters) {
         Date currentDate = new Date();

diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/DraftVisitor.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/DraftVisitor.java
@@ -25,7 +25,7 @@
 import org.opencds.cqf.fhir.utility.adapter.KnowledgeArtifactAdapter;
 import org.opencds.cqf.fhir.utility.r4.PackageHelper;
 
-public class DraftVisitor implements KnowledgeArtifactVisitor {
+public class DraftVisitor implements IKnowledgeArtifactVisitor {
     @Override
     public IBase visit(KnowledgeArtifactAdapter adapter, Repository repository, IBaseParameters draftParameters) {
         var fhirVersion = adapter.get().getStructureFhirVersionEnum();

diff --git a/...ity/visitor/KnowledgeArtifactVisitor.java → ...ty/visitor/IKnowledgeArtifactVisitor.java b/...ity/visitor/KnowledgeArtifactVisitor.java → ...ty/visitor/IKnowledgeArtifactVisitor.java
@@ -5,6 +5,6 @@
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.utility.adapter.KnowledgeArtifactAdapter;
 
-public interface KnowledgeArtifactVisitor {
+public interface IKnowledgeArtifactVisitor {
     IBase visit(KnowledgeArtifactAdapter knowledgeArtifact, Repository repository, IBaseParameters draftParameters);
 }
diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/PackageVisitor.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/PackageVisitor.java
@@ -42,7 +42,7 @@
 import org.opencds.cqf.fhir.utility.adapter.ValueSetAdapter;
 import org.opencds.cqf.fhir.utility.client.TerminologyServerClient;
 
-public class PackageVisitor implements KnowledgeArtifactVisitor {
+public class PackageVisitor implements IKnowledgeArtifactVisitor {
     protected final FhirContext fhirContext;
     protected final TerminologyServerClient terminologyServerClient;
     protected final ExpandHelper expandHelper;

diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/ReleaseVisitor.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/ReleaseVisitor.java
@@ -16,7 +16,6 @@
 import java.util.stream.Collectors;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -35,7 +34,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class ReleaseVisitor implements KnowledgeArtifactVisitor {
+public class ReleaseVisitor extends AbstractKnowledgeArtifactVisitor {
     private Logger log = LoggerFactory.getLogger(ReleaseVisitor.class);
 
     @Override
@@ -527,31 +526,6 @@ private void checkReleasePreconditions(KnowledgeArtifactAdapter artifact, Date a
         }
     }
 
-    private List<IBaseBackboneElement> findArtifactCommentsToUpdate(
-            IBaseResource artifact, String releaseVersion, Repository repository) {
-        if (artifact instanceof org.hl7.fhir.dstu3.model.MetadataResource) {
-            return org.opencds.cqf.fhir.utility.visitor.dstu3.ReleaseVisitor.findArtifactCommentsToUpdate(
-                            (org.hl7.fhir.dstu3.model.MetadataResource) artifact, releaseVersion, repository)
-                    .stream()
-                    .map(r -> (IBaseBackboneElement) r)
-                    .collect(Collectors.toList());
-        } else if (artifact instanceof org.hl7.fhir.r4.model.MetadataResource) {
-            return org.opencds.cqf.fhir.utility.visitor.r4.ReleaseVisitor.findArtifactCommentsToUpdate(
-                            (org.hl7.fhir.r4.model.MetadataResource) artifact, releaseVersion, repository)
-                    .stream()
-                    .map(r -> (IBaseBackboneElement) r)
-                    .collect(Collectors.toList());
-        } else if (artifact instanceof org.hl7.fhir.r5.model.MetadataResource) {
-            return org.opencds.cqf.fhir.utility.visitor.r5.ReleaseVisitor.findArtifactCommentsToUpdate(
-                            (org.hl7.fhir.r5.model.MetadataResource) artifact, releaseVersion, repository)
-                    .stream()
-                    .map(r -> (IBaseBackboneElement) r)
-                    .collect(Collectors.toList());
-        } else {
-            throw new UnprocessableEntityException("Version not supported");
-        }
-    }
-
     private void checkReleaseVersion(String version, Optional<String> versionBehavior)
             throws UnprocessableEntityException {
         if (!versionBehavior.isPresent()) {

diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/WithdrawVisitor.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/WithdrawVisitor.java
@@ -15,7 +15,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class WithdrawVisitor implements KnowledgeArtifactVisitor {
+public class WithdrawVisitor extends AbstractKnowledgeArtifactVisitor {
     private Logger log = LoggerFactory.getLogger(WithdrawVisitor.class);
     String isOwnedUrl = "http://hl7.org/fhir/StructureDefinition/crmi-isOwned";
 
@@ -25,14 +25,21 @@ public IBase visit(
         if (!rootAdapter.getStatus().equals("draft")) {
             throw new PreconditionFailedException("Cannot withdraw an artifact that is not in draft status");
         }
+        var fhirVersion = rootAdapter.get().getStructureFhirVersionEnum();
+        var transactionBundle = BundleHelper.newBundle(fhirVersion, null, "transaction");
+
         var resToUpdate = new ArrayList<IDomainResource>();
         resToUpdate.add(rootAdapter.get());
 
-        var resourcesToUpdate = getComponents(rootAdapter, repository, resToUpdate);
+        findArtifactCommentsToUpdate(rootAdapter.get(), fhirVersion.getFhirVersionString(), repository)
+                .forEach(artifact -> {
+                    var resource = BundleHelper.getEntryResource(fhirVersion, artifact);
+                    var entry = PackageHelper.deleteEntry(resource);
+                    BundleHelper.addEntry(transactionBundle, entry);
+                });
 
-        var fhirVersion = rootAdapter.get().getStructureFhirVersionEnum();
+        var resourcesToUpdate = getComponents(rootAdapter, repository, resToUpdate);
 
-        var transactionBundle = BundleHelper.newBundle(fhirVersion, null, "transaction");
         for (var artifact : resourcesToUpdate) {
             var entry = PackageHelper.deleteEntry(artifact);
             BundleHelper.addEntry(transactionBundle, entry);

diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/r4/ReleaseVisitor.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/visitor/r4/ReleaseVisitor.java
@@ -91,7 +91,7 @@ public static void updateReleaseLabel(MetadataResource artifact, String releaseL
     public static Bundle searchArtifactAssessmentForArtifact(IIdType reference, Repository repository) {
         Map<String, List<IQueryParameterType>> searchParams = new HashMap<>();
         List<IQueryParameterType> urlList = new ArrayList<>();
-        urlList.add(new ReferenceParam(reference));
+        urlList.add(new ReferenceParam(reference.getResourceType() + "/" + reference.getIdPart()));
         searchParams.put("artifact", urlList);
         Bundle searchResultsBundle = repository.search(Bundle.class, Basic.class, searchParams);
         return searchResultsBundle;

diff --git a/...r-utility/src/test/java/org/opencds/cqf/fhir/utility/visitor/dstu3/DraftVisitorTests.java b/...r-utility/src/test/java/org/opencds/cqf/fhir/utility/visitor/dstu3/DraftVisitorTests.java
@@ -42,7 +42,7 @@
 import org.opencds.cqf.fhir.utility.dstu3.MetadataResourceHelper;
 import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository;
 import org.opencds.cqf.fhir.utility.visitor.DraftVisitor;
-import org.opencds.cqf.fhir.utility.visitor.KnowledgeArtifactVisitor;
+import org.opencds.cqf.fhir.utility.visitor.IKnowledgeArtifactVisitor;
 
 class DraftVisitorTests {
     private final FhirContext fhirContext = FhirContext.forDstu3Cached();
@@ -86,7 +86,7 @@ void library_draft_test() {
         Bundle bundle = (Bundle)
                 jsonParser.parseResource(DraftVisitorTests.class.getResourceAsStream("Bundle-ersd-example.json"));
         spyRepository.transaction(bundle);
-        KnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
+        IKnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
         Library library = spyRepository
                 .read(Library.class, new IdType("Library/SpecificationLibrary"))
                 .copy();
@@ -149,7 +149,7 @@ void draftOperation_no_effectivePeriod_test() {
                 .copy();
         assertTrue(baseLib.hasEffectivePeriod());
         LibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(baseLib);
-        KnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
+        IKnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
         PlanDefinition planDef = spyRepository
                 .read(PlanDefinition.class, new IdType("PlanDefinition/plandefinition-ersd-instance-example"))
                 .copy();
@@ -182,7 +182,7 @@ void draftOperation_version_conflict_test() {
                 .read(Library.class, new IdType(specificationLibReference))
                 .copy();
         LibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(baseLib);
-        KnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
+        IKnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
 
         try {
             libraryAdapter.accept(draftVisitor, spyRepository, params);
@@ -205,7 +205,7 @@ void draftOperation_cannot_create_draft_of_draft_test() {
                 .read(Library.class, new IdType("Library/SpecificationLibraryDraftVersion-1-0-0"))
                 .copy();
         LibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(baseLib);
-        KnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
+        IKnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
         try {
             libraryAdapter.accept(draftVisitor, spyRepository, params);
         } catch (PreconditionFailedException e) {
@@ -224,7 +224,7 @@ void draftOperation_version_format_test() {
                 .read(Library.class, new IdType("Library/SpecificationLibraryDraftVersion-1-0-0"))
                 .copy();
         LibraryAdapter libraryAdapter = new AdapterFactory().createLibrary(baseLib);
-        KnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
+        IKnowledgeArtifactVisitor draftVisitor = new DraftVisitor();
 
         for (String version : badVersionList) {
             UnprocessableEntityException maybeException = null;