ValueSet cleanup (#4227)

* POST release deferred cleanup * Fixes * One more test fix * Test fixes * Test fixes * Test cleanup * Test fixes * Fixes * ValueSet cleanup * Test fix * Test fixes * Fixes * Test fixes * Fixed * Test fixes * Test fixes * Test fixes * Test fixes * Test fixc * Build fix * Fix merge artifact * Build fix * Work on tests * Test fixes * Work * Fixes * Changelog fix * Add changelog * Test fix * Test fixes * Fixes * Test fixes * Test fixes * Test fixes * Test fix * Tests * Bumps * Fixes * Add errorprone * Drop bz2 bins * POM fix * Build fix * Update * Test fix Co-authored-by: James Agnew <[email protected]>
hapifhir · Nov 9, 2022 · b3ebbe7 · b3ebbe7
1 parent d3367cf
commit b3ebbe7
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Showing 323 changed files with 4,200 additions and 4,903 deletions.
diff --git a/.gitignore b/.gitignore
@@ -19,6 +19,9 @@ ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString/
 ca.uhn.fhir.jpa.entity.ResourceTable/
 ca.uhn.fhir.jpa.entity.TermConcept/
 
+# Ignore Java Heap Dumps
+java_pid*.*
+
 # Vagrant stuff.
 .vagrant
 /vagrant/build

diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../pom.xml</relativePath>
  </parent>
 
@@ -126,12 +126,11 @@
  <execution>
  <phase>process-sources</phase>
  <goals>
- <goal>checkstyle</goal>
+ <goal>check</goal>
  </goals>
  <configuration>
  <failsOnError>true</failsOnError>
- <enableRulesSummary>true</enableRulesSummary>
- <enableSeveritySummary>true</enableSeveritySummary>
+ <logViolationsToConsole>true</logViolationsToConsole>
  <consoleOutput>true</consoleOutput>
  <configLocation>${maven.multiModuleProjectDirectory}/src/checkstyle/checkstyle.xml</configLocation>
  </configuration>

diff --git a/hapi-fhir-android/pom.xml b/hapi-fhir-android/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
@@ -394,8 +394,9 @@ public INarrativeGenerator getNarrativeGenerator() {
  return myNarrativeGenerator;
  }
 
- public void setNarrativeGenerator(final INarrativeGenerator theNarrativeGenerator) {
+ public FhirContext setNarrativeGenerator(final INarrativeGenerator theNarrativeGenerator) {
  myNarrativeGenerator = theNarrativeGenerator;
+ return this;
  }
 
  /**

diff --git a/...-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupport.java b/...-fhir-base/src/main/java/ca/uhn/fhir/context/support/DefaultProfileValidationSupport.java
@@ -325,9 +325,9 @@ private void loadCodeSystems(Map<String, IBaseResource> theCodeSystems, Map<Stri
 
  private void loadStructureDefinitions(Map<String, IBaseResource> theCodeSystems, String theClasspath) {
  ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
- try (InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath)) {
- if (valuesetText != null) {
- try (InputStreamReader reader = new InputStreamReader(valuesetText, Constants.CHARSET_UTF8)) {
+ try (InputStream valueSetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath)) {
+ if (valueSetText != null) {
+ try (InputStreamReader reader = new InputStreamReader(valueSetText, Constants.CHARSET_UTF8)) {
 
  List<IBaseResource> resources = parseBundle(reader);
  for (IBaseResource next : resources) {

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/executor/BaseInterceptorService.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/executor/BaseInterceptorService.java
@@ -181,7 +181,11 @@ public void unregisterInterceptorsIf(Predicate<Object> theShouldUnregisterFuncti
 
  private void unregisterInterceptorsIf(Predicate<Object> theShouldUnregisterFunction, ListMultimap<POINTCUT, BaseInvoker> theGlobalInvokers) {
  synchronized (myRegistryMutex) {
- theGlobalInvokers.entries().removeIf(t -> theShouldUnregisterFunction.test(t.getValue().getInterceptor()));
+ for (Map.Entry<POINTCUT, BaseInvoker> nextInvoker : new ArrayList<>(theGlobalInvokers.entries())) {
+ if (theShouldUnregisterFunction.test(nextInvoker.getValue().getInterceptor())) {
+ unregisterInterceptor(nextInvoker.getValue().getInterceptor());
+ }
+ }
  }
  }
 

diff --git a/...pa/provider/JpaResourceProviderDstu2.java → ...il/BaseUnrecoverableRuntimeException.java b/...pa/provider/JpaResourceProviderDstu2.java → ...il/BaseUnrecoverableRuntimeException.java
@@ -1,8 +1,8 @@
-package ca.uhn.fhir.jpa.provider;
+package ca.uhn.fhir.util;
 
-/*
+/*-
  * #%L
- * HAPI FHIR JPA Server
+ * HAPI FHIR - Core Library
  * %%
  * Copyright (C) 2014 - 2022 Smile CDR, Inc.
  * %%
@@ -20,17 +20,15 @@
  * #L%
  */
 
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
-import ca.uhn.fhir.model.api.IResource;
-
-public class JpaResourceProviderDstu2<T extends IResource> extends BaseJpaResourceProvider<T> {
-
- public JpaResourceProviderDstu2() {
- // nothing
+/**
+ * Exception superclass for an exception representing an unrecoverable failure
+ */
+public abstract class BaseUnrecoverableRuntimeException extends RuntimeException {
+ public BaseUnrecoverableRuntimeException(String theMessage) {
+ super(theMessage);
  }
 
- public JpaResourceProviderDstu2(IFhirResourceDao<T> theDao) {
- super(theDao);
+ public BaseUnrecoverableRuntimeException(String theMessage, Throwable theCause) {
+ super(theMessage, theCause);
  }
-
 }
diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/DatatypeUtil.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/DatatypeUtil.java
@@ -61,4 +61,12 @@ public static String joinStringsSpaceSeparated(List<? extends IPrimitiveType<Str
  return b.toString();
  }
 
+ /**
+ * Returns {@link IPrimitiveType#getValueAsString()} if <code>thePrimitiveType</code> is
+ * not null, else returns null.
+ */
+ public static String toStringValue(IPrimitiveType<?> thePrimitiveType) {
+ return thePrimitiveType != null ? thePrimitiveType.getValueAsString() : null;
+ }
+
 }
diff --git a/hapi-fhir-batch/pom.xml b/hapi-fhir-batch/pom.xml
diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -3,14 +3,14 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-bom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-checkstyle/pom.xml b/hapi-fhir-checkstyle/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../pom.xml</relativePath>
  </parent>
 
@@ -18,8 +18,6 @@
  <dependency>
  <groupId>com.puppycrawl.tools</groupId>
  <artifactId>checkstyle</artifactId>
- <!-- FIXME move version up -->
- <version>8.43</version>
  </dependency>
  <dependency>
  <groupId>commons-io</groupId>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 
@@ -78,10 +78,6 @@
  <groupId>ch.qos.logback</groupId>
  <artifactId>logback-classic</artifactId>
  </dependency>
- <dependency>
- <groupId>javax.servlet</groupId>
- <artifactId>javax.servlet-api</artifactId>
- </dependency>
 
  <dependency>
  <groupId>commons-cli</groupId>
@@ -177,11 +173,15 @@
  </dependency>
  <dependency>
  <groupId>org.eclipse.jetty.websocket</groupId>
- <artifactId>websocket-api</artifactId>
+ <artifactId>websocket-jetty-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.eclipse.jetty.websocket</groupId>
+ <artifactId>websocket-core-client</artifactId>
  </dependency>
  <dependency>
  <groupId>org.eclipse.jetty.websocket</groupId>
- <artifactId>websocket-client</artifactId>
+ <artifactId>websocket-jetty-client</artifactId>
  </dependency>
  <dependency>
  <groupId>org.slf4j</groupId>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/WebsocketSubscribeCommand.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/WebsocketSubscribeCommand.java
@@ -25,9 +25,14 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
+import org.eclipse.jetty.websocket.api.Frame;
 import org.eclipse.jetty.websocket.api.Session;
-import org.eclipse.jetty.websocket.api.annotations.*;
-import org.eclipse.jetty.websocket.api.extensions.Frame;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketClose;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketConnect;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketError;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketFrame;
+import org.eclipse.jetty.websocket.api.annotations.OnWebSocketMessage;
+import org.eclipse.jetty.websocket.api.annotations.WebSocket;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
 

diff --git a/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-cli</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../../hapi-deployable-pom</relativePath>
  </parent>
 

diff --git a/hapi-fhir-cli/pom.xml b/hapi-fhir-cli/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-client-okhttp/pom.xml b/hapi-fhir-client-okhttp/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-client-okhttp/src/test/java/ca/uhn/fhir/okhttp/GenericOkHttpClientDstu2Test.java b/hapi-fhir-client-okhttp/src/test/java/ca/uhn/fhir/okhttp/GenericOkHttpClientDstu2Test.java
@@ -1818,7 +1818,7 @@ public static void beforeClass() throws Exception {
  @Override
  public void handle(String theArg0, Request theRequest, HttpServletRequest theServletRequest, HttpServletResponse theResp) throws IOException, ServletException {
  theRequest.setHandled(true);
- ourRequestUri = "http:" + theRequest.getHttpURI().toString();
+ ourRequestUri = theRequest.getHttpURI().toString();
  ourRequestUriAll.add(ourRequestUri);
  ourRequestMethod = theRequest.getMethod();
  ourRequestContentType = theServletRequest.getContentType();

diff --git a/hapi-fhir-client/pom.xml b/hapi-fhir-client/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-converter/pom.xml b/hapi-fhir-converter/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.3.0-PRE3-SNAPSHOT</version>
+ <version>6.3.0-PRE4-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>