v3.8.8 #259

.vscode/launch.json

@@ -85,6 +85,15 @@
       "vmArgs": "-Dspring.config.additional-location=file:../../matchbox-int-tests/src/test/resources/application-validate-r4-ch-epr-fhir.yaml",
       "cwd": "${workspaceFolder}/matchbox-server"
     },
+    {
+      "type": "java",
+      "name": "Launch Matchbox-Server (int-tests ch)",
+      "request": "launch",
+      "mainClass": "ca.uhn.fhir.jpa.starter.Application",
+      "projectName": "matchbox-server",
+      "vmArgs": "-Dspring.config.additional-location=file:../../matchbox-int-tests/src/test/resources/application-validate-r4-ch.yaml",
+      "cwd": "${workspaceFolder}/matchbox-server"
+    },
     {
       "type": "java",
       "name": "Launch Matchbox-Server (test)",

docs/changelog.md

@@ -1,3 +1,9 @@
+2024/06/25 Release 3.8.8
+
+- validation for 3 letter country codes [#259](https://github.com/ahdis/matchbox/issues/259)
+- making caching of txServer configurable
+- add support for dateTime [#243](https://github.com/ahdis/matchbox/issues/243)
+
 2024/06/24 Release 3.8.7
 
 - docker image for v3.8.6 not starting up [#258](https://github.com/ahdis/matchbox/issues/258)

matchbox-engine/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>3.8.7</version>
+        <version>3.8.8</version>
     </parent>
 
     <artifactId>matchbox-engine</artifactId>

matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/MatchboxEngine.java

@@ -832,8 +832,12 @@ public enum FilesystemPackageCacheMode {
 	 * @throws IOException
 	 */	
     public void initTxCache(String cacheDir) throws FileNotFoundException, FHIRException, IOException {
-		getContext().initTxCache(cacheDir);
-		getContext().setCachingAllowed(true);
+		if (cacheDir !=null) {
+			getContext().initTxCache(cacheDir);
+			getContext().setCachingAllowed(true);
+		} else {
+			getContext().setCachingAllowed(false);
+		}
 	}
 
 }

matchbox-frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matchbox",
-  "version": "3.8.7",
+  "version": "3.8.8",
   "license": "MIT",
   "scripts": {
     "ng": "ng",

matchbox-server/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>3.8.7</version>
+        <version>3.8.8</version>
     </parent>
 
     <artifactId>matchbox-server</artifactId>

matchbox-server/src/main/java/ch/ahdis/matchbox/CliContext.java

@@ -92,7 +92,11 @@ public CliContext setExtensions(List<String> extensions) {
   // @JsonProperty("htmlOutput")
   // private String htmlOutput = null;
   @JsonProperty("txServer")
-  private String txServer = "http://tx.fhir.org";
+  private String txServer = null;
+
+  @JsonProperty("txServerCache")
+  private boolean txServerCache = true;
+
   // @JsonProperty("sv")
   // private String sv = null;
   // @JsonProperty("txLog")
@@ -289,6 +293,16 @@ public void setTxServer(String txServer) {
     this.txServer = txServer;
   }
 
+  @JsonProperty("txServerCache")
+  public boolean getTxServerCache() {
+    return txServerCache;
+  }
+
+  @JsonProperty("txServerCache")
+  public void setTxServerCache(boolean txServerCache) {
+    this.txServerCache = txServerCache;
+  }
+
   @JsonProperty("doNative")
   public boolean isDoNative() {
     return doNative;
@@ -597,6 +611,7 @@ public boolean equals(final Object o) {
         && htmlInMarkdownCheck == that.htmlInMarkdownCheck
         && Objects.equals(extensions, that.extensions)
         && Objects.equals(txServer, that.txServer)
+        && txServerCache == that.txServerCache
         && Objects.equals(lang, that.lang)
         && Objects.equals(snomedCT, that.snomedCT)
         && Objects.equals(fhirVersion, that.fhirVersion)
@@ -633,6 +648,7 @@ public int hashCode() {
         allowExampleUrls,
         htmlInMarkdownCheck,
         txServer,
+        txServerCache,
         lang,
         snomedCT,
         fhirVersion,
@@ -666,6 +682,7 @@ public String toString() {
         ", doImplicitFHIRPathStringConversion=" + doImplicitFHIRPathStringConversion +
         ", htmlInMarkdownCheck=" + htmlInMarkdownCheck +
         ", txServer='" + txServer + '\'' +
+        ", txServerCache='" + txServerCache + '\'' +
         ", lang='" + lang + '\'' +
         ", snomedCT='" + snomedCT + '\'' +
         ", fhirVersion='" + fhirVersion + '\'' +
@@ -717,6 +734,7 @@ public void addContextToExtension(final Extension ext) {
 	addExtension(ext, "httpReadOnly", new BooleanType(this.httpReadOnly));
 	addExtension(ext, "allowExampleUrls", new BooleanType(this.allowExampleUrls));
 	addExtension(ext, "txServer", new UriType(this.txServer));
+	addExtension(ext, "txServerCache", new BooleanType(this.txServerCache));
 	addExtension(ext, "lang", new StringType(this.lang));
 	addExtension(ext, "snomedCT", new StringType(this.snomedCT));
 	addExtension(ext, "fhirVersion", new StringType(this.fhirVersion));

matchbox-server/src/main/java/ch/ahdis/matchbox/MatchboxEngineSupport.java

@@ -461,6 +461,9 @@ private String getTxCachePath(String txServer) {
 	private void configureValidationEngine(final MatchboxEngine validator,
 														final CliContext cli) throws MatchboxEngineCreationException {
 		log.info("Terminology server {}", cli.getTxServer());
+		if (cli.getTxServer() == null) {
+			throw new MatchboxEngineCreationException("Terminology server is not set, you need to set it in the configuration file.");
+		}
 		if ("n/a".equals(cli.getTxServer())) {
 			validator.getContext().setCanRunWithoutTerminology(true);
 			validator.getContext().setNoTerminologyServer(true);
@@ -470,13 +473,14 @@ private void configureValidationEngine(final MatchboxEngine validator,
 			validator.getContext().setNoTerminologyServer(false);
 
 			try {
+				// set "txLog" for second parameter to activate
 				final String txver = validator.setTerminologyServer(cli.getTxServer(), null, FhirPublication.R4, true);
 				log.debug("Version of the terminology server: {}", txver);
 			} catch (final Exception e) {
 				throw new TerminologyServerException("Error while setting the terminology server: " + e.getMessage(), e);
 			}
 			try {
-				validator.initTxCache(getTxCachePath(cli.getTxServer()));
+				validator.initTxCache(cli.getTxServerCache() ? getTxCachePath(cli.getTxServer()) : null);
 			} catch (final Exception e) {
 				throw new TerminologyServerException("Error while setting the terminology server cache: " + getTxCachePath(cli.getTxServer()), e);
 			}

matchbox-server/src/main/java/ch/ahdis/matchbox/terminology/ValueSetCodeValidationProvider.java

@@ -235,7 +235,7 @@ private CodeMembership evaluateCodeInComposition(final Coding coding,
 
 			for (final var filter : include.getFilter()) {
 				if ("regex".equals(filter.getOp().toCode())) {
-					final var pattern = Pattern.compile(filter.getOp().toCode());
+					final var pattern = Pattern.compile(filter.getValue());
 					// Try to match the full code with the regex
 					if (!pattern.matcher(coding.getCode()).matches()) {
 						return CodeMembership.EXCLUDED;

matchbox-server/validation-ch-samples.http

@@ -434,4 +434,35 @@ GET {{host}}/ImplementationGuide
 
 ###
 GET  {{host}}/ImplementationGuide/ch.fhir.ig.ch-vacd-3.0.0  HTTP/1.1
-Accept: application/gzip
+Accept: application/gzip
+
+### CH-Core Franz Muster )
+POST {{host}}/$validate?profile=http://fhir.ch/ig/ch-core/StructureDefinition/ch-core-patient HTTP/1.1
+Content-Type: application/fhir+xml; charset=UTF-8
+
+<Patient xmlns="http://hl7.org/fhir">
+  <id value="Pat-LillyLiechtenstein"/>
+  <identifier>
+    <system value="urn:oid:2.16.438.10.20.10.10.1.2.1"/>
+    <value value="1234567890123"/>
+  </identifier>
+  <name>
+    <family value="Liechtenstein"/>
+    <given value="Lilly"/>
+  </name>
+  <gender value="female"/>
+  <birthDate value="2000-09-14"/>
+  <address>
+    <use value="home"/>
+    <state value="FL"/>
+    <country value="LI">
+      <extension
+                 url="http://hl7.org/fhir/StructureDefinition/iso21090-SC-coding">
+        <valueCoding>
+          <system value="urn:iso:std:iso:3166"/>
+          <code value="LIE"/>
+        </valueCoding>
+      </extension>
+    </country>
+  </address>
+</Patient>

matchbox-server/with-ch/application.yaml

@@ -20,26 +20,38 @@ hapi:
       ch-emed:
         name: ch.fhir.ig.ch-emed
         version: 5.0.0-ballot 
-        url: https://fhir.ch/ig/ch-emed/package.tgz
       ch-ips:
         name: ch.fhir.ig.ch-ips
         version: 1.0.0-ballot 
-        url: https://fhir.ch/ig/ch-ips/package.tgz
       ch-vacd:
         name: ch.fhir.ig.ch-vacd
         version: 5.0.0-ballot 
-        url: https://fhir.ch/ig/ch-vacd/package.tgz
       ch-allergyintolerance:
         name: ch.fhir.ig.ch-allergyintolerance
         version: 3.0.0-ballot 
-        url: https://fhir.ch/ig/ch-allergyintolerance/package.tgz
       ch-lab-report:
         name: ch.fhir.ig.ch-lab-report
-        version: 1.0.0-ballot 
-        url: https://fhir.ch/ig/ch-lab-report/package.tgz
-    staticLocation: file:/apps/
+        version: 1.0.0-ballot
+      ch-lab-order:
+        name: ch.fhir.ig.ch-lab-order
+        version: 2.0.0
+      ch-rad-order:
+        name: ch.fhir.ig.ch-rad-order
+        version: 2.0.0-ballot
+      ch-etoc:
+        name: ch.fhir.ig.ch-etoc
+        version: 3.0.0-ballot
+      ch-epr-fhir:
+        name: ch.fhir.ig.ch-epr-fhir
+        version: 4.0.1-ballot 
+      ch-atc:
+        name: ch.fhir.ig.ch-atc
+        version: 3.3.0-ballot
 matchbox:
   fhir:
     context:
       fhirVersion: 4.0.1
-      txServer: http://tx.fhir.org
+      txServer: http://tx.fhir.org
+      suppressWarnInfo:
+        hl7.fhir.r4.core#4.0.1:
+          - "Constraint failed: dom-6:"

matchbox-server/with-elm/application.yaml

@@ -28,7 +28,6 @@ matchbox:
     context:
       fhirVersion: 4.0.1
       txServer: http://localhost:${server.port}/matchboxv3/fhir
-#      txServer: http://tx.fhir.org
       suppressWarnInfo:
         hl7.fhir.r4.core#4.0.1:
           - "Constraint failed: dom-6:"

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>health.matchbox</groupId>
     <artifactId>matchbox</artifactId>
-    <version>3.8.7</version>
+    <version>3.8.8</version>
     <packaging>pom</packaging>
     <name>matchbox</name>
     <description>An open-source implementation to support testing and implementation of FHIR based solutions and map or