support for bundle option #348

ahdis · Feb 18, 2025 · 0476e04 · 0476e04
1 parent 26d6235
commit 0476e04
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Showing 5 changed files with 86 additions and 8 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -4,6 +4,7 @@
   // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
   "version": "0.2.0",
   "configurations": [
+
 
 
 
@@ -86,6 +87,15 @@
       "vmArgs": "-Dspring.config.additional-location=file:with-elm/application.yaml",
       "cwd": "${workspaceFolder}/matchbox-server"
     },
+    {
+      "type": "java",
+      "name": "Launch Matchbox-Server (ips)",
+      "request": "launch",
+      "mainClass": "ca.uhn.fhir.jpa.starter.Application",
+      "projectName": "matchbox-server",
+      "vmArgs": "-Dspring.config.additional-location=file:with-ips/application.yaml",
+      "cwd": "${workspaceFolder}/matchbox-server"
+    },
     {
       "type": "java",
       "name": "Launch Matchbox-Server (ch)",

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,6 +1,7 @@
-Unreleased
+2025/03/xx Release 3.9.13
 
 - No more GUI version mismatch [#346](https://github.com/ahdis/matchbox/issues/346)
+- Support for bundle option to validate directly a resource within the bundle [#348](https://github.com/ahdis/matchbox/issues/348)
 
 2025/02/05 Release 3.9.12
 

diff --git a/matchbox-server/src/main/java/ch/ahdis/matchbox/CliContext.java b/matchbox-server/src/main/java/ch/ahdis/matchbox/CliContext.java
@@ -169,12 +169,16 @@ public CliContext setExtensions(List<String> extensions) {
   // @JsonProperty("outputStyle")
   // private String outputStyle = null;
 
-  // TODO: Mark what goes here?
-  // private List<BundleValidationRule> bundleValidationRules = new ArrayList<>();
-
   @JsonProperty("jurisdiction")
   private String jurisdiction = JurisdictionUtilities.getJurisdictionFromLocale(Locale.getDefault().getCountry());
 
+  @JsonProperty("check-ips-codes")
+  private boolean checkIpsCodes = false;
+
+  @JsonProperty("bundle")
+  private String bundle = null;
+
+
   private String igsPreloaded[];
 
   public String[] getIgsPreloaded() {
@@ -686,6 +690,23 @@ public void setDisableDefaultResourceFetcher(boolean disableDefaultResourceFetch
     this.disableDefaultResourceFetcher = disableDefaultResourceFetcher;
   }
 
+  public boolean isCheckIpsCodes() {
+    return this.checkIpsCodes;
+  }
+
+  @JsonProperty("check-ips-codes")
+  public void setCheckIpsCodes(boolean checkIpsCodes) {
+    this.checkIpsCodes = checkIpsCodes;
+  }
+
+  public String getBundle() {
+    return this.bundle;
+  }
+
+  @JsonProperty("bundle")
+  public void setBundle(String bundle) {
+    this.bundle = bundle;
+  }
 
   @Override
   public boolean equals(final Object o) {
@@ -735,7 +756,9 @@ public boolean equals(final Object o) {
         && Arrays.equals(igsPreloaded, that.igsPreloaded)
         && checkReferences == that.checkReferences
         && Objects.equals(resolutionContext, that.resolutionContext)
-        && disableDefaultResourceFetcher == that.disableDefaultResourceFetcher;
+        && disableDefaultResourceFetcher == that.disableDefaultResourceFetcher
+        && checkIpsCodes == that.checkIpsCodes
+        && bundle == that.bundle;
   }
 
   @Override
@@ -781,7 +804,9 @@ public int hashCode() {
         xVersion,
         checkReferences,
         resolutionContext,
-        disableDefaultResourceFetcher);
+        disableDefaultResourceFetcher,
+        checkIpsCodes,
+        bundle);
     result = 31 * result + Arrays.hashCode(igsPreloaded);
     return result;
   }
@@ -832,6 +857,8 @@ public String toString() {
         ", checkReferences=" + checkReferences +
         ", resolutionContext=" + resolutionContext +
         ", disableDefaultResourceFetcher=" + disableDefaultResourceFetcher +
+        ", checkIpsCodes=" + checkIpsCodes +
+        ", bundle=" + bundle +
         '}';
   }
 
@@ -887,6 +914,8 @@ public void addContextToExtension(final Extension ext) {
 	addExtension(ext, "check-references", new BooleanType(this.checkReferences));
 	addExtension(ext, "resolution-context", new StringType(this.resolutionContext));
 	addExtension(ext, "disableDefaultResourceFetcher", new BooleanType(this.disableDefaultResourceFetcher));
+	addExtension(ext, "check-ips-codes", new BooleanType(this.checkIpsCodes));
+	addExtension(ext, "bundle", new StringType(this.bundle));
   for( var extension : this.extensions) {
     addExtension(ext, "extensions", new StringType(extension));
   }

diff --git a/matchbox-server/src/main/java/ch/ahdis/matchbox/util/MatchboxEngineSupport.java b/matchbox-server/src/main/java/ch/ahdis/matchbox/util/MatchboxEngineSupport.java
@@ -548,7 +548,18 @@ private void configureValidationEngine(final MatchboxEngine validator,
 		validator.setForPublication(cli.isForPublication());
 		validator.setShowTimes(true);
 		validator.setAllowExampleUrls(cli.isAllowExampleUrls());
-
+		validator.setCheckIPSCodes(cli.isCheckIpsCodes());
+		if (cli.getBundle() != null) {
+			validator.setQuestionnaireMode(cli.getQuestionnaireMode());
+			String[] bundle = cli.getBundle().split(" ");
+			if (bundle.length != 2) {
+				log.error("Bundle parameter must have two values, the rule and the profile, ignoring the bundle parameter");
+			} else {
+				String rule = bundle[0];
+				String profile = bundle[1];
+				validator.getBundleValidationRules().add(new org.hl7.fhir.r5.utils.validation.BundleValidationRule().setRule(rule).setProfile(profile));
+			}
+		}
 		if (!cli.isDisableDefaultResourceFetcher()) {
 			StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(validator.getPcm(), validator.getContext(),
 					validator);
@@ -568,7 +579,6 @@ private void configureValidationEngine(final MatchboxEngine validator,
 			// validator.setPolicyAdvisor(fetcher);
 			// refpol = ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS;
 		}
-		// validator.getBundleValidationRules().addAll(cliContext.getBundleValidationRules());
 		validator.setJurisdiction(CodeSystemUtilities.readCoding(cli.getJurisdiction()));
 		// TerminologyCache.setNoCaching(cliContext.isNoInternalCaching());
 

diff --git a/matchbox-server/with-ips/application.yaml b/matchbox-server/with-ips/application.yaml
@@ -0,0 +1,28 @@
+server:
+  port: 8080
+  servlet:
+    context-path: /matchboxv3
+hapi:
+  fhir:
+    server_address: http://localhost:8080/matchboxv3/fhir
+    implementationguides:
+      fhir_r4_core:
+        name: hl7.fhir.r4.core
+        version: 4.0.1
+        url: classpath:/hl7.fhir.r4.core.tgz
+      fhir_terminology:
+        name: hl7.terminology.r4
+        version: 6.2.0
+        url: classpath:/hl7.terminology.r4#6.2.0.tgz
+      fhir_extensions:
+        name: hl7.fhir.uv.extensions.r4
+        version: 1.0.0
+        url: classpath:/hl7.fhir.uv.extensions.r4#1.0.0.tgz
+      ch-ips:
+        name: hl7.fhir.uv.ips
+        version: 1.1.0
+matchbox:
+  fhir:
+    context:
+      fhirVersion: 4.0.1
+      txServer: http://tx.fhir.org