adding additional data to (bulk data export) parameters (#5541)

* adding additional data to parameters * checkstyle * updated consent service * updating documentation * working * updating and cleaning * some review points * spotless * review fixes * bumping version * consent interceotpr fixes --------- Co-authored-by: leif stawnyczy <[email protected]> Co-authored-by: leif stawnyczy <[email protected]>
hapifhir · Jan 12, 2024 · d6128de · d6128de
1 parent 01c7481
commit d6128de
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diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseBatchJobParameters.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseBatchJobParameters.java
@@ -0,0 +1,51 @@
+package ca.uhn.fhir.model.api;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import org.apache.commons.lang3.Validate;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public abstract class BaseBatchJobParameters implements IModelJson {
+ /**
+ * A serializable map of key-value pairs that can be
+ * added to any extending job.
+ */
+ @JsonProperty("userData")
+ private Map<String, Object> myUserData;
+
+ public Map<String, Object> getUserData() {
+ if (myUserData == null) {
+ myUserData = new HashMap<>();
+ }
+ return myUserData;
+ }
+
+ public void setUserData(String theKey, Object theValue) {
+ Validate.isTrue(isNotBlank(theKey), "Invalid key; key must be non-empty, non-null.");
+ if (theValue == null) {
+ getUserData().remove(theKey);
+ } else {
+ Validate.isTrue(
+ validateValue(theValue),
+ String.format(
+ "Invalid data type provided %s", theValue.getClass().getName()));
+ getUserData().put(theKey, theValue);
+ }
+ }
+
+ private boolean validateValue(Object theValue) {
+ if (theValue instanceof Boolean) {
+ return true;
+ }
+ if (theValue instanceof Number) {
+ return true;
+ }
+ if (theValue instanceof String) {
+ return true;
+ }
+ return false;
+ }
+}
diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/system/HapiSystemProperties.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/system/HapiSystemProperties.java
@@ -105,7 +105,7 @@ public static boolean isTestModeEnabled() {
  }
 
  /**
- * This property is used to ensure unit test behaviour is deterministic. It is also used to add extra logging for unit tests.
+ * This property is used to ensure unit test behaviour is deterministic.
  */
  public static void enableUnitTestMode() {
  System.setProperty(UNIT_TEST_MODE, Boolean.TRUE.toString());

diff --git a/hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/BaseBatchJobParametersTest.java b/hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/BaseBatchJobParametersTest.java
@@ -0,0 +1,114 @@
+package ca.uhn.fhir.model.api;
+
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
+
+public class BaseBatchJobParametersTest {
+
+ private static class TestParameters extends BaseBatchJobParameters {
+
+ }
+
+ private static class TestParam {
+ private final Object myTestValue;
+ private final boolean myExpectedToWork;
+
+ public TestParam(Object theValue, boolean theExpected) {
+ myTestValue = theValue;
+ myExpectedToWork = theExpected;
+ }
+
+ public Object getTestValue() {
+ return myTestValue;
+ }
+
+ public boolean isExpectedToWork() {
+ return myExpectedToWork;
+ }
+ }
+
+ private static List<TestParam> parameters() {
+ List<TestParam> params = new ArrayList<>();
+
+ // should pass
+ params.add(new TestParam("string", true));
+ params.add(new TestParam(1, true));
+ params.add(new TestParam(1.1f, true));
+ params.add(new TestParam(1.1d, true));
+ params.add(new TestParam(true, true));
+ params.add(new TestParam(-1, true));
+
+ // should not pass
+ params.add(new TestParam(List.of("strings"), false));
+ params.add(new TestParam(new Object(), false));
+
+ return params;
+ }
+
+ @ParameterizedTest
+ @MethodSource("parameters")
+ public void setUserData_acceptsStringNumberAndBooleansOnly(TestParam theParams) {
+ // setup
+ String key = "key";
+ TestParameters parameters = new TestParameters();
+ Object testValue = theParams.getTestValue();
+
+ // test
+ if (theParams.isExpectedToWork()) {
+ parameters.setUserData(key, testValue);
+ assertFalse(parameters.getUserData().isEmpty());
+ assertEquals(testValue, parameters.getUserData().get(key));
+ } else {
+ try {
+ parameters.setUserData(key, testValue);
+ fail();
+ } catch (IllegalArgumentException ex) {
+ String dataType = testValue.getClass().getName();
+ assertTrue(ex.getMessage().contains("Invalid data type provided " + dataType),
+ ex.getMessage());
+ assertTrue(parameters.getUserData().isEmpty());
+ }
+ }
+ }
+
+ @Test
+ public void setUserData_invalidKey_throws() {
+ // setup
+ TestParameters parameters = new TestParameters();
+
+ // test
+ for (String key : new String[] { null, "" }) {
+ try {
+ parameters.setUserData(key, "test");
+ fail();
+ } catch (IllegalArgumentException ex) {
+ assertTrue(ex.getMessage().contains("Invalid key; key must be non-empty, non-null"),
+ ex.getMessage());
+ }
+ }
+ }
+
+ @Test
+ public void setUserData_nullValue_removes() {
+ // setup
+ TestParameters parameters = new TestParameters();
+ String key = "key";
+
+ // test
+ parameters.setUserData(key, "test");
+ assertTrue(parameters.getUserData().containsKey(key));
+
+ parameters.setUserData(key, null);
+ assertFalse(parameters.getUserData().containsKey(key));
+ }
+}
diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -4,15 +4,15 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-bom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../pom.xml</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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-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>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-docs/pom.xml b/hapi-fhir-docs/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...a/uhn/hapi/fhir/changelog/7_0_0/5527-added-additional-data-to-bulk-export-job-params.yaml b/...a/uhn/hapi/fhir/changelog/7_0_0/5527-added-additional-data-to-bulk-export-job-params.yaml
@@ -0,0 +1,10 @@
+---
+type: add
+issue: 5527
+title: "Added a map of `additionalData` to BulkExport job params.
+ This will allow consumers of BulkExport to add additional
+ data to be accessed at later steps by using various pointcuts
+ in the system.
+ Updated ConsentService so that BulkExport operations will
+ call the willSeeResource method for each exported resource.
+ "
diff --git a/hapi-fhir-jacoco/pom.xml b/hapi-fhir-jacoco/pom.xml
@@ -11,7 +11,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jaxrsserver-base/pom.xml b/hapi-fhir-jaxrsserver-base/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpa/pom.xml b/hapi-fhir-jpa/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...aserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java b/...aserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java
@@ -31,6 +31,7 @@
 import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
@@ -172,7 +173,7 @@ public <T extends IBaseResource> List<T> fetchAllStructureDefinitions() {
  }
  IBundleProvider search = myDaoRegistry
  .getResourceDao("StructureDefinition")
- .search(new SearchParameterMap().setLoadSynchronousUpTo(1000));
+ .search(new SearchParameterMap().setLoadSynchronousUpTo(1000), new SystemRequestDetails());
  return (List<T>) search.getResources(0, 1000);
  }
 

diff --git a/hapi-fhir-jpaserver-elastic-test-utilities/pom.xml b/hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-jpaserver-hfql/pom.xml b/hapi-fhir-jpaserver-hfql/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-jpaserver-ips/pom.xml b/hapi-fhir-jpaserver-ips/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.8-SNAPSHOT</version>
+ <version>6.11.9-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>