Aphl 969 refactor endpoint (#463)

* Refactor terminologyEndpoint param handling -Removed unneeded EndpointCredentials class, now using Extensions under Endpoint class * Refactor - throw specific errors for missing credentials and cast terminologyEndpoint * Add tests to validate credential handling
cqframework · May 24, 2024 · 59aecb6 · 59aecb6
1 parent e7e2d84
commit 59aecb6
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Showing 9 changed files with 219 additions and 112 deletions.
diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/Constants.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/Constants.java
@@ -136,4 +136,8 @@ private Constants() {}
  public static final String VSM_WORKFLOW_CODES_CODE_SYSTEM_URL =
  "http:https://aphl.org/fhir/vsm/CodeSystem/vsm-workflow-codes";
  public static final String VSM_VALUE_SET_TAG_VSM_AUTHORED_CODE = "vsm-authored";
+
+ public static final String VSAC_USERNAME = "vsacUsername";
+
+ public static final String APIKEY = "apiKey";
 }
diff --git a/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/EndpointCredentials.java b/cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/EndpointCredentials.java
diff --git a/...y/src/main/java/org/opencds/cqf/fhir/utility/visitor/KnowledgeArtifactPackageVisitor.java b/...y/src/main/java/org/opencds/cqf/fhir/utility/visitor/KnowledgeArtifactPackageVisitor.java
@@ -81,7 +81,7 @@ public IBaseResource visit(LibraryAdapter library, Repository repository, IBaseP
  && !endpointUri.get().isEmpty())
  || endpoint.isPresent()) {
  throw new NotImplementedOperationException(
- "This repository is not implementing custom Content and Terminology endpoints at this time");
+ "This repository is not implementing custom Content and endpoints at this time");
  }
  if (packageOnly.isPresent()) {
  throw new NotImplementedOperationException("This repository is not implementing packageOnly at this time");
@@ -134,7 +134,7 @@ protected void handleValueSetReferenceExtensions(
  (org.hl7.fhir.dstu3.model.MetadataResource) resource,
  ((org.hl7.fhir.dstu3.model.Bundle) packagedBundle).getEntry(),
  repository,
- terminologyEndpoint);
+ terminologyEndpoint.map(te -> (org.hl7.fhir.dstu3.model.Endpoint) te));
  break;
  case R4:
  org.opencds.cqf.fhir.utility.visitor.r4.KnowledgeArtifactPackageVisitor packageVisitorR4 =
@@ -143,7 +143,7 @@ protected void handleValueSetReferenceExtensions(
  (org.hl7.fhir.r4.model.MetadataResource) resource,
  ((org.hl7.fhir.r4.model.Bundle) packagedBundle).getEntry(),
  repository,
- terminologyEndpoint);
+ terminologyEndpoint.map(te -> (org.hl7.fhir.r4.model.Endpoint) te));
  break;
  case R5:
  org.opencds.cqf.fhir.utility.visitor.r5.KnowledgeArtifactPackageVisitor packageVisitorR5 =
@@ -152,7 +152,7 @@ protected void handleValueSetReferenceExtensions(
  (org.hl7.fhir.r5.model.MetadataResource) resource,
  ((org.hl7.fhir.r5.model.Bundle) packagedBundle).getEntry(),
  repository,
- terminologyEndpoint);
+ terminologyEndpoint.map(te -> (org.hl7.fhir.r5.model.Endpoint) te));
  break;
  default:
  throw new IllegalArgumentException(String.format(

diff --git a/...main/java/org/opencds/cqf/fhir/utility/visitor/dstu3/KnowledgeArtifactPackageVisitor.java b/...main/java/org/opencds/cqf/fhir/utility/visitor/dstu3/KnowledgeArtifactPackageVisitor.java
@@ -25,7 +25,6 @@
 import org.hl7.fhir.dstu3.model.RelatedArtifact;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.ResourceType;
-import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
 import org.hl7.fhir.dstu3.model.UsageContext;
 import org.hl7.fhir.dstu3.model.ValueSet;
@@ -214,7 +213,7 @@ public void handleValueSetReferenceExtensions(
  MetadataResource manifest,
  List<BundleEntryComponent> bundleEntries,
  Repository repository,
- Optional<IBaseResource> terminologyEndpoint)
+ Optional<Endpoint> terminologyEndpoint)
  throws UnprocessableEntityException, IllegalArgumentException {
  KnowledgeArtifactAdapter adapter = AdapterFactory.forFhirVersion(manifest.getStructureFhirVersionEnum())
  .createKnowledgeArtifactAdapter(manifest);
@@ -281,7 +280,7 @@ public void handleValueSetReferenceExtensions(
  }
 
  protected void expandValueSet(
- ValueSet valueSet, Parameters expansionParameters, Optional<IBaseResource> terminologyEndpoint) {
+ ValueSet valueSet, Parameters expansionParameters, Optional<Endpoint> terminologyEndpoint) {
  // Gather the Terminology Service from the valueSet's authoritativeSourceUrl.
  Extension authoritativeSource = valueSet.getExtensionByUrl(Constants.AUTHORITATIVE_SOURCE_URL);
  String authoritativeSourceUrl = authoritativeSource != null && authoritativeSource.hasValue()
@@ -314,29 +313,27 @@ protected void expandValueSet(
  }
  valueSet.setExpansion(expansion);
  } else {
- Optional<StringType> username = Optional.empty();
- Optional<StringType> apiKey = Optional.empty();
+ String username;
+ String apiKey;
  if (terminologyEndpoint.isPresent()) {
- Endpoint endPnt = (Endpoint) terminologyEndpoint.get();
- username = endPnt.getHeader().stream()
- .filter(h -> h.getId().equals("username"))
- .findFirst();
- apiKey = endPnt.getHeader().stream()
- .filter(h -> h.getId().equals("apiKey"))
- .findFirst();
- }
-
- if (!username.isPresent() || !apiKey.isPresent()) {
+ username = terminologyEndpoint.get().getExtensionsByUrl(Constants.VSAC_USERNAME).stream()
+ .findFirst()
+ .map(ext -> ext.getValue().toString())
+ .orElseThrow(() -> new UnprocessableEntityException(
+ "Cannot expand ValueSet without VSAC Username: " + valueSet.getId()));
+ apiKey = terminologyEndpoint.get().getExtensionsByUrl(Constants.APIKEY).stream()
+ .findFirst()
+ .map(ext -> ext.getValue().toString())
+ .orElseThrow(() -> new UnprocessableEntityException(
+ "Cannot expand ValueSet without VSAC API Key: " + valueSet.getId()));
+ } else {
  throw new UnprocessableEntityException(
  "Cannot expand ValueSet without credentials: " + valueSet.getId());
  }
+
  try {
  expandedValueSet = terminologyServerClient.expand(
- valueSet,
- authoritativeSourceUrl,
- expansionParameters,
- username.get().getValue(),
- apiKey.get().getValue());
+ valueSet, authoritativeSourceUrl, expansionParameters, username, apiKey);
  valueSet.setExpansion(expandedValueSet.getExpansion());
  } catch (Exception ex) {
  System.out.println("Terminology Server expansion failed: {"

diff --git a/...rc/main/java/org/opencds/cqf/fhir/utility/visitor/r4/KnowledgeArtifactPackageVisitor.java b/...rc/main/java/org/opencds/cqf/fhir/utility/visitor/r4/KnowledgeArtifactPackageVisitor.java
@@ -17,6 +17,7 @@
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Endpoint;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.MetadataResource;
@@ -25,14 +26,12 @@
 import org.hl7.fhir.r4.model.RelatedArtifact;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ResourceType;
-import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.UsageContext;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.utility.Canonicals;
 import org.opencds.cqf.fhir.utility.Constants;
-import org.opencds.cqf.fhir.utility.EndpointCredentials;
 import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
 import org.opencds.cqf.fhir.utility.adapter.KnowledgeArtifactAdapter;
 import org.opencds.cqf.fhir.utility.client.TerminologyServerClient;
@@ -226,7 +225,7 @@ public void handleValueSetReferenceExtensions(
  MetadataResource manifest,
  List<BundleEntryComponent> bundleEntries,
  Repository repository,
- Optional<IBaseResource> terminologyEndpoint)
+ Optional<Endpoint> terminologyEndpoint)
  throws UnprocessableEntityException, IllegalArgumentException {
  KnowledgeArtifactAdapter adapter = AdapterFactory.forFhirVersion(manifest.getStructureFhirVersionEnum())
  .createKnowledgeArtifactAdapter(manifest);
@@ -293,7 +292,7 @@ public void handleValueSetReferenceExtensions(
  }
 
  protected void expandValueSet(
- ValueSet valueSet, Parameters expansionParameters, Optional<IBaseResource> terminologyEndpoint) {
+ ValueSet valueSet, Parameters expansionParameters, Optional<Endpoint> terminologyEndpoint) {
  // Gather the Terminology Service from the valueSet's authoritativeSourceUrl.
  Extension authoritativeSource = valueSet.getExtensionByUrl(Constants.AUTHORITATIVE_SOURCE_URL);
  String authoritativeSourceUrl = authoritativeSource != null && authoritativeSource.hasValue()
@@ -326,25 +325,27 @@ protected void expandValueSet(
  }
  valueSet.setExpansion(expansion);
  } else {
- Optional<StringType> username = Optional.empty();
- Optional<StringType> apiKey = Optional.empty();
+ String username;
+ String apiKey;
  if (terminologyEndpoint.isPresent()) {
- EndpointCredentials endPnt = (EndpointCredentials) terminologyEndpoint.get();
- username = Optional.of(endPnt.getVsacUsername());
- apiKey = Optional.of(endPnt.getApiKey());
- }
-
- if (!username.isPresent() || !apiKey.isPresent()) {
+ username = terminologyEndpoint.get().getExtensionsByUrl(Constants.VSAC_USERNAME).stream()
+ .findFirst()
+ .map(ext -> ext.getValue().toString())
+ .orElseThrow(() -> new UnprocessableEntityException(
+ "Cannot expand ValueSet without VSAC Username: " + valueSet.getId()));
+ apiKey = terminologyEndpoint.get().getExtensionsByUrl(Constants.APIKEY).stream()
+ .findFirst()
+ .map(ext -> ext.getValue().toString())
+ .orElseThrow(() -> new UnprocessableEntityException(
+ "Cannot expand ValueSet without VSAC API Key: " + valueSet.getId()));
+ } else {
  throw new UnprocessableEntityException(
  "Cannot expand ValueSet without credentials: " + valueSet.getId());
  }
+
  try {
  expandedValueSet = terminologyServerClient.expand(
- valueSet,
- authoritativeSourceUrl,
- expansionParameters,
- username.get().getValue(),
- apiKey.get().getValue());
+ valueSet, authoritativeSourceUrl, expansionParameters, username, apiKey);
  valueSet.setExpansion(expandedValueSet.getExpansion());
  } catch (Exception ex) {
  System.out.println("Terminology Server expansion failed: {"

diff --git a/...rc/main/java/org/opencds/cqf/fhir/utility/visitor/r5/KnowledgeArtifactPackageVisitor.java b/...rc/main/java/org/opencds/cqf/fhir/utility/visitor/r5/KnowledgeArtifactPackageVisitor.java
@@ -26,7 +26,6 @@
 import org.hl7.fhir.r5.model.RelatedArtifact;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.ResourceType;
-import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.UsageContext;
 import org.hl7.fhir.r5.model.ValueSet;
@@ -222,7 +221,7 @@ public void handleValueSetReferenceExtensions(
  MetadataResource manifest,
  List<Bundle.BundleEntryComponent> bundleEntries,
  Repository repository,
- Optional<IBaseResource> terminologyEndpoint)
+ Optional<Endpoint> terminologyEndpoint)
  throws UnprocessableEntityException, IllegalArgumentException {
  KnowledgeArtifactAdapter adapter = AdapterFactory.forFhirVersion(manifest.getStructureFhirVersionEnum())
  .createKnowledgeArtifactAdapter(manifest);
@@ -289,7 +288,7 @@ public void handleValueSetReferenceExtensions(
  }
 
  protected void expandValueSet(
- ValueSet valueSet, Parameters expansionParameters, Optional<IBaseResource> terminologyEndpoint) {
+ ValueSet valueSet, Parameters expansionParameters, Optional<Endpoint> terminologyEndpoint) {
  // Gather the Terminology Service from the valueSet's authoritativeSourceUrl.
  Extension authoritativeSource = valueSet.getExtensionByUrl(Constants.AUTHORITATIVE_SOURCE_URL);
  String authoritativeSourceUrl = authoritativeSource != null && authoritativeSource.hasValue()
@@ -322,29 +321,27 @@ protected void expandValueSet(
  }
  valueSet.setExpansion(expansion);
  } else {
- Optional<StringType> username = Optional.empty();
- Optional<StringType> apiKey = Optional.empty();
+ String username;
+ String apiKey;
  if (terminologyEndpoint.isPresent()) {
- Endpoint endPnt = (Endpoint) terminologyEndpoint.get();
- username = endPnt.getHeader().stream()
- .filter(h -> h.getId().equals("username"))
- .findFirst();
- apiKey = endPnt.getHeader().stream()
- .filter(h -> h.getId().equals("apiKey"))
- .findFirst();
- }
-
- if (!username.isPresent() || !apiKey.isPresent()) {
+ username = terminologyEndpoint.get().getExtensionsByUrl(Constants.VSAC_USERNAME).stream()
+ .findFirst()
+ .map(ext -> ext.getValue().toString())
+ .orElseThrow(() -> new UnprocessableEntityException(
+ "Cannot expand ValueSet without VSAC Username: " + valueSet.getId()));
+ apiKey = terminologyEndpoint.get().getExtensionsByUrl(Constants.APIKEY).stream()
+ .findFirst()
+ .map(ext -> ext.getValue().toString())
+ .orElseThrow(() -> new UnprocessableEntityException(
+ "Cannot expand ValueSet without VSAC API Key: " + valueSet.getId()));
+ } else {
  throw new UnprocessableEntityException(
  "Cannot expand ValueSet without credentials: " + valueSet.getId());
  }
+
  try {
  expandedValueSet = terminologyServerClient.expand(
- valueSet,
- authoritativeSourceUrl,
- expansionParameters,
- username.get().getValue(),
- apiKey.get().getValue());
+ valueSet, authoritativeSourceUrl, expansionParameters, username, apiKey);
  valueSet.setExpansion(expandedValueSet.getExpansion());
  } catch (Exception ex) {
  System.out.println("Terminology Server expansion failed: {"