Copy identifiers to placeholder resources (#1675)
* Copy identifiers to placeholder resources * Add tests * Maven cleanup * Still messing around with azure * Adding to logging * More azure work * One more attempt * More messing around with azure * Test fix * Another caching attempt * More work on azure pipeline * Fix pipeline file * Keep working on pipeline * More work on azure * More azure * More azure work * More azure
This commit is contained in:
James Agnew
GitHub
parent
634458c447
commit
c0e929dacb
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@ -2,7 +2,9 @@
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variables:
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MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
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MAVEN_OPTS: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
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#MAVEN_CACHE_FOLDER: $(Agent.TempDirectory)/.m2/repository
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#MAVEN_OPTS: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
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MAVEN_OPTS: ''
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trigger:
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- master
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@ -15,17 +17,21 @@ jobs:
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timeoutInMinutes: 360
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container: maven:3-jdk-11
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steps:
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- task: CacheBeta@0
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- task: Cache@2
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inputs:
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key: maven
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key: 'maven | "$(Agent.OS)" | **/pom.xml'
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path: $(MAVEN_CACHE_FOLDER)
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- task: Bash@3
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inputs:
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targetType: 'inline'
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script: mkdir -p $(MAVEN_CACHE_FOLDER); pwd; ls -al $(MAVEN_CACHE_FOLDER)
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- task: Maven@3
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env:
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JAVA_HOME_11_X64: /usr/local/openjdk-11
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inputs:
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goals: 'clean dependency:resolve install'
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goals: 'clean install'
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# These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy
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options: '-P ALLMODULES,JACOCO,CI,ERRORPRONE -nsu'
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options: '-P ALLMODULES,JACOCO,CI,ERRORPRONE -nsu -e -B -Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
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# These are JVM options (and don't show up in the build logs)
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mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
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jdkVersionOption: 1.11
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@ -34,4 +34,9 @@ public interface IBaseReference extends ICompositeType {
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IBase setDisplay(String theValue);
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IPrimitiveType<String> getDisplayElement();
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default boolean hasIdentifier() {
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return false;
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}
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}
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@ -0,0 +1,5 @@
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---
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type: add
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title: "In the JPA server, a new setting called `setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean)` has
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been added to the DaoConfig. If this setting is enabled, when creating placeholder resources, the Reference.identifier
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value is copied to the target resource if possible."
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@ -53,6 +53,7 @@ import java.util.Set;
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import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR;
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import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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@ -95,7 +96,8 @@ public abstract class BaseStorageDao {
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if ("Bundle".equals(type)) {
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Set<String> allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage();
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String bundleType = BundleUtil.getBundleType(getContext(), (IBaseBundle) theResource);
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if (isBlank(bundleType) || !allowedBundleTypes.contains(bundleType)) {
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bundleType = defaultString(bundleType);
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if (!allowedBundleTypes.contains(bundleType)) {
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String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (isNotBlank(bundleType) ? bundleType : "(missing)");
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throw new UnprocessableEntityException(message);
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}
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@ -15,7 +15,12 @@ import org.hl7.fhir.r4.model.Bundle;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.*;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import java.util.Set;
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import java.util.TreeSet;
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/*
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* #%L
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@ -53,12 +58,6 @@ public class DaoConfig {
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* See {@link #setStatusBasedReindexingDisabled(boolean)}
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*/
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public static final String DISABLE_STATUS_BASED_REINDEX = "disable_status_based_reindex";
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/**
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* Default value for {@link #setMaximumSearchResultCountInTransaction(Integer)}
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*
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* @see #setMaximumSearchResultCountInTransaction(Integer)
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*/
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private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
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/**
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* Default {@link #setBundleTypesAllowedForStorage(Set)} value:
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* <ul>
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@ -73,12 +72,16 @@ public class DaoConfig {
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Bundle.BundleType.DOCUMENT.toCode(),
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Bundle.BundleType.MESSAGE.toCode()
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)));
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private static final Logger ourLog = LoggerFactory.getLogger(DaoConfig.class);
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private static final int DEFAULT_EXPUNGE_BATCH_SIZE = 800;
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// update setter javadoc if default changes
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public static final int DEFAULT_MAX_EXPANSION_SIZE = 1000;
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/**
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* Default value for {@link #setMaximumSearchResultCountInTransaction(Integer)}
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*
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* @see #setMaximumSearchResultCountInTransaction(Integer)
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*/
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private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
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private static final Logger ourLog = LoggerFactory.getLogger(DaoConfig.class);
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private static final int DEFAULT_EXPUNGE_BATCH_SIZE = 800;
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private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.DISABLED;
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/**
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@ -175,6 +178,11 @@ public class DaoConfig {
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*/
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private int myPreExpandValueSetsMaxCount = 1000;
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/**
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* @since 4.2.0
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*/
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private boolean myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets;
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/**
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* Constructor
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*/
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@ -570,7 +578,7 @@ public class DaoConfig {
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* the operation will be failed as too costly. Note that this setting applies only to
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* in-memory expansions and does not apply to expansions that are being pre-calculated.
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* <p>
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* The default value for this setting is 1000.
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* The default value for this setting is 1000.
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* </p>
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*/
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public void setMaximumExpansionSize(int theMaximumExpansionSize) {
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@ -993,6 +1001,108 @@ public class DaoConfig {
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myAutoCreatePlaceholderReferenceTargets = theAutoCreatePlaceholderReferenceTargets;
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}
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/**
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* When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this
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* setting is set to <code>true</code> (default is <code>false</code>) and the source
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* reference has an identifier populated, the identifier will be copied to the target
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* resource.
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* <p>
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* When enabled, if an Observation contains a reference like the one below,
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* and no existing resource was found that matches the given ID, a new
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* one will be created and its <code>Patient.identifier</code> value will be
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* populated using the value from <code>Observation.subject.identifier</code>.
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* </p>
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* <pre>
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* {
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* "resourceType": "Observation",
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* "subject": {
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* "reference": "Patient/ABC",
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* "identifier": {
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* "system": "http://foo",
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* "value": "123"
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* }
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* }
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* }
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* </pre>
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* <p>
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* This method is often combined with {@link #setAllowInlineMatchUrlReferences(boolean)}.
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* </p>
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* <p>
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* In other words if an Observation contains a reference like the one below,
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* and no existing resource was found that matches the given match URL, a new
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* one will be created and its <code>Patient.identifier</code> value will be
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* populated using the value from <code>Observation.subject.identifier</code>.
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* </p>
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* <pre>
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* {
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* "resourceType": "Observation",
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* "subject": {
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* "reference": "Patient?identifier=http://foo|123",
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* "identifier": {
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* "system": "http://foo",
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* "value": "123"
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* }
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* }
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* }
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* </pre>
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*
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* @since 4.2.0
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*/
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public boolean isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets() {
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return myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets;
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}
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/**
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* When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this
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* setting is set to <code>true</code> (default is <code>false</code>) and the source
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* reference has an identifier populated, the identifier will be copied to the target
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* resource.
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* <p>
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* When enabled, if an Observation contains a reference like the one below,
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* and no existing resource was found that matches the given ID, a new
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* one will be created and its <code>Patient.identifier</code> value will be
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* populated using the value from <code>Observation.subject.identifier</code>.
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* </p>
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* <pre>
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* {
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* "resourceType": "Observation",
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* "subject": {
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* "reference": "Patient/ABC",
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* "identifier": {
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* "system": "http://foo",
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* "value": "123"
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* }
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* }
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* }
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* </pre>
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* <p>
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* This method is often combined with {@link #setAllowInlineMatchUrlReferences(boolean)}.
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* </p>
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* <p>
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* In other words if an Observation contains a reference like the one below,
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* and no existing resource was found that matches the given match URL, a new
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* one will be created and its <code>Patient.identifier</code> value will be
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* populated using the value from <code>Observation.subject.identifier</code>.
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* </p>
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* <pre>
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* {
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* "resourceType": "Observation",
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* "subject": {
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* "reference": "Patient?identifier=http://foo|123",
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* "identifier": {
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* "system": "http://foo",
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* "value": "123"
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* }
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* }
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* }
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* </pre>
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*
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* @since 4.2.0
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*/
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public void setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean thePopulateIdentifierInAutoCreatedPlaceholderReferenceTargets) {
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myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets = thePopulateIdentifierInAutoCreatedPlaceholderReferenceTargets;
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}
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/**
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* If set to <code>false</code> (default is <code>true</code>) resources will be permitted to be
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* deleted even if other resources currently contain references to them.
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@ -1682,29 +1792,6 @@ public class DaoConfig {
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myStoreMetaSourceInformation = theStoreMetaSourceInformation;
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}
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public enum StoreMetaSourceInformationEnum {
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NONE(false, false),
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SOURCE_URI(true, false),
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REQUEST_ID(false, true),
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SOURCE_URI_AND_REQUEST_ID(true, true);
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private final boolean myStoreSourceUri;
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private final boolean myStoreRequestId;
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StoreMetaSourceInformationEnum(boolean theStoreSourceUri, boolean theStoreRequestId) {
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myStoreSourceUri = theStoreSourceUri;
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myStoreRequestId = theStoreRequestId;
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}
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public boolean isStoreSourceUri() {
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return myStoreSourceUri;
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}
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public boolean isStoreRequestId() {
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return myStoreRequestId;
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}
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}
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/**
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* <p>
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* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
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@ -1820,6 +1907,29 @@ public class DaoConfig {
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setPreExpandValueSetsDefaultCount(Math.min(getPreExpandValueSetsDefaultCount(), getPreExpandValueSetsMaxCount()));
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}
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public enum StoreMetaSourceInformationEnum {
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NONE(false, false),
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SOURCE_URI(true, false),
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REQUEST_ID(false, true),
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SOURCE_URI_AND_REQUEST_ID(true, true);
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private final boolean myStoreSourceUri;
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private final boolean myStoreRequestId;
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StoreMetaSourceInformationEnum(boolean theStoreSourceUri, boolean theStoreRequestId) {
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myStoreSourceUri = theStoreSourceUri;
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myStoreRequestId = theStoreRequestId;
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}
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public boolean isStoreSourceUri() {
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return myStoreSourceUri;
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}
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public boolean isStoreRequestId() {
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return myStoreRequestId;
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}
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}
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public enum IndexEnabledEnum {
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ENABLED,
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DISABLED
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@ -159,7 +159,7 @@ class ResourceExpungeService implements IResourceExpungeService {
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private void callHooks(RequestDetails theRequestDetails, AtomicInteger theRemainingCount, ResourceHistoryTable theVersion, IdDt theId) {
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final AtomicInteger counter = new AtomicInteger();
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if (JpaInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, myInterceptorBroadcaster, theRequestDetails)) {
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IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theId.getResourceType());
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IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(theId.getResourceType());
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IBaseResource resource = resourceDao.toResource(theVersion, false);
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HookParams params = new HookParams()
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.add(AtomicInteger.class, counter)
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@ -20,6 +20,9 @@ package ca.uhn.fhir.jpa.dao.index;
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* #L%
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*/
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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@ -33,19 +36,24 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseReference;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import javax.annotation.Nullable;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import java.util.Optional;
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@Service
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public class DaoResourceLinkResolver implements IResourceLinkResolver {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DaoResourceLinkResolver.class);
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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@Autowired
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private DaoConfig myDaoConfig;
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@Autowired
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@ -55,38 +63,37 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
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@Autowired
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private DaoRegistry myDaoRegistry;
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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@Override
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public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, String theId, RequestDetails theRequest) {
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public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest) {
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ResourceTable target;
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ResourcePersistentId valueOf;
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String idPart = theNextId.getIdPart();
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try {
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valueOf = myIdHelperService.translateForcedIdToPid(theTypeString, theId, theRequest);
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ourLog.trace("Translated {}/{} to resource PID {}", theType, theId, valueOf);
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valueOf = myIdHelperService.translateForcedIdToPid(theTypeString, idPart, theRequest);
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ourLog.trace("Translated {}/{} to resource PID {}", theType, idPart, valueOf);
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} catch (ResourceNotFoundException e) {
|
||||
if (myDaoConfig.isEnforceReferentialIntegrityOnWrite() == false) {
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return null;
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}
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RuntimeResourceDefinition missingResourceDef = myContext.getResourceDefinition(theType);
|
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String resName = missingResourceDef.getName();
|
||||
|
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if (myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) {
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IBaseResource newResource = missingResourceDef.newInstance();
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newResource.setId(resName + "/" + theId);
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IFhirResourceDao<IBaseResource> placeholderResourceDao = (IFhirResourceDao<IBaseResource>) myDaoRegistry.getResourceDao(newResource.getClass());
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ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
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valueOf = placeholderResourceDao.update(newResource).getEntity().getPersistentId();
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} else {
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throw new InvalidRequestException("Resource " + resName + "/" + theId + " not found, specified in path: " + theNextPathsUnsplit);
|
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Optional<ResourcePersistentId> pidOpt = createPlaceholderTargetIfConfiguredToDoSo(theType, theReference, idPart);
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if (!pidOpt.isPresent()) {
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|
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if (myDaoConfig.isEnforceReferentialIntegrityOnWrite() == false) {
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return null;
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||||
}
|
||||
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RuntimeResourceDefinition missingResourceDef = myContext.getResourceDefinition(theType);
|
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String resName = missingResourceDef.getName();
|
||||
throw new InvalidRequestException("Resource " + resName + "/" + idPart + " not found, specified in path: " + theNextPathsUnsplit);
|
||||
|
||||
}
|
||||
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valueOf = pidOpt.get();
|
||||
}
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||||
|
||||
target = myEntityManager.find(ResourceTable.class, valueOf.getIdAsLong());
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||||
RuntimeResourceDefinition targetResourceDef = myContext.getResourceDefinition(theType);
|
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if (target == null) {
|
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String resName = targetResourceDef.getName();
|
||||
throw new InvalidRequestException("Resource " + resName + "/" + theId + " not found, specified in path: " + theNextPathsUnsplit);
|
||||
throw new InvalidRequestException("Resource " + resName + "/" + idPart + " not found, specified in path: " + theNextPathsUnsplit);
|
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}
|
||||
|
||||
ourLog.trace("Resource PID {} is of type {}", valueOf, target.getResourceType());
|
||||
|
|
@ -98,7 +105,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
|
|||
|
||||
if (target.getDeleted() != null) {
|
||||
String resName = targetResourceDef.getName();
|
||||
throw new InvalidRequestException("Resource " + resName + "/" + theId + " is deleted, specified in path: " + theNextPathsUnsplit);
|
||||
throw new InvalidRequestException("Resource " + resName + "/" + idPart + " is deleted, specified in path: " + theNextPathsUnsplit);
|
||||
}
|
||||
|
||||
if (!theNextSpDef.hasTargets() && theNextSpDef.getTargets().contains(theTypeString)) {
|
||||
|
|
@ -107,8 +114,60 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
|
|||
return target;
|
||||
}
|
||||
|
||||
/**
|
||||
* @param theIdToAssignToPlaceholder If specified, the placeholder resource created will be given a specific ID
|
||||
*/
|
||||
public <T extends IBaseResource> Optional<ResourcePersistentId> createPlaceholderTargetIfConfiguredToDoSo(Class<T> theType, IBaseReference theReference, @Nullable String theIdToAssignToPlaceholder) {
|
||||
ResourcePersistentId valueOf = null;
|
||||
|
||||
if (myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) {
|
||||
RuntimeResourceDefinition missingResourceDef = myContext.getResourceDefinition(theType);
|
||||
String resName = missingResourceDef.getName();
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
T newResource = (T) missingResourceDef.newInstance();
|
||||
|
||||
IFhirResourceDao<T> placeholderResourceDao = myDaoRegistry.getResourceDao(theType);
|
||||
ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
|
||||
|
||||
if (myDaoConfig.isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets()) {
|
||||
tryToCopyIdentifierFromReferenceToTargetResource(theReference, missingResourceDef, newResource);
|
||||
}
|
||||
|
||||
if (theIdToAssignToPlaceholder != null) {
|
||||
newResource.setId(resName + "/" + theIdToAssignToPlaceholder);
|
||||
valueOf = placeholderResourceDao.update(newResource).getEntity().getPersistentId();
|
||||
} else {
|
||||
valueOf = placeholderResourceDao.create(newResource).getEntity().getPersistentId();
|
||||
}
|
||||
}
|
||||
|
||||
return Optional.ofNullable(valueOf);
|
||||
}
|
||||
|
||||
private <T extends IBaseResource> void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
|
||||
boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
|
||||
if (referenceHasIdentifier) {
|
||||
BaseRuntimeChildDefinition targetIdentifier = theTargetResourceDef.getChildByName("identifier");
|
||||
if (targetIdentifier != null) {
|
||||
BaseRuntimeElementDefinition<?> identifierElement = targetIdentifier.getChildByName("identifier");
|
||||
String identifierElementName = identifierElement.getName();
|
||||
boolean targetHasIdentifierElement = identifierElementName.equals("Identifier");
|
||||
if (targetHasIdentifierElement) {
|
||||
|
||||
BaseRuntimeElementCompositeDefinition<?> referenceElement = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theSourceReference.getClass());
|
||||
BaseRuntimeChildDefinition referenceIdentifierChild = referenceElement.getChildByName("identifier");
|
||||
Optional<IBase> identifierOpt = referenceIdentifierChild.getAccessor().getFirstValueOrNull(theSourceReference);
|
||||
identifierOpt.ifPresent(theIBase -> targetIdentifier.getMutator().addValue(theTargetResource, theIBase));
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void validateTypeOrThrowException(Class<? extends IBaseResource> theType) {
|
||||
myDaoRegistry.getDaoOrThrowException(theType);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,8 +26,8 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
|
|||
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
|
||||
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
|
||||
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
|
||||
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
|
||||
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
|
||||
|
|
@ -61,6 +61,7 @@ import java.util.HashSet;
|
|||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
|
@ -81,17 +82,16 @@ public class SearchParamWithInlineReferencesExtractor {
|
|||
@Autowired
|
||||
private ISearchParamRegistry mySearchParamRegistry;
|
||||
@Autowired
|
||||
SearchParamExtractorService mySearchParamExtractorService;
|
||||
private SearchParamExtractorService mySearchParamExtractorService;
|
||||
@Autowired
|
||||
ResourceLinkExtractor myResourceLinkExtractor;
|
||||
private ResourceLinkExtractor myResourceLinkExtractor;
|
||||
@Autowired
|
||||
DaoResourceLinkResolver myDaoResourceLinkResolver;
|
||||
private DaoResourceLinkResolver myDaoResourceLinkResolver;
|
||||
@Autowired
|
||||
DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
|
||||
private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
|
||||
@Autowired
|
||||
private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
|
||||
|
||||
|
||||
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
|
||||
protected EntityManager myEntityManager;
|
||||
|
||||
|
|
@ -246,16 +246,25 @@ public class SearchParamWithInlineReferencesExtractor {
|
|||
}
|
||||
Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
|
||||
Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest);
|
||||
|
||||
ResourcePersistentId match;
|
||||
if (matches.isEmpty()) {
|
||||
String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
|
||||
throw new ResourceNotFoundException(msg);
|
||||
}
|
||||
if (matches.size() > 1) {
|
||||
|
||||
Optional<ResourcePersistentId> placeholderOpt = myDaoResourceLinkResolver.createPlaceholderTargetIfConfiguredToDoSo(matchResourceType, nextRef, null);
|
||||
if (placeholderOpt.isPresent()) {
|
||||
match = placeholderOpt.get();
|
||||
} else {
|
||||
String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
|
||||
throw new ResourceNotFoundException(msg);
|
||||
}
|
||||
} else if (matches.size() > 1) {
|
||||
String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlMultipleMatches", nextId.getValue());
|
||||
throw new PreconditionFailedException(msg);
|
||||
} else {
|
||||
match = matches.iterator().next();
|
||||
}
|
||||
ResourcePersistentId next = matches.iterator().next();
|
||||
String newId = myIdHelperService.translatePidIdToForcedId(resourceTypeString, next);
|
||||
|
||||
String newId = myIdHelperService.translatePidIdToForcedId(resourceTypeString, match);
|
||||
ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
|
||||
nextRef.setReference(newId);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -8,10 +8,14 @@ import ca.uhn.fhir.rest.param.TokenParam;
|
|||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import com.google.common.collect.Sets;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.AuditEvent;
|
||||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.hl7.fhir.r4.model.Observation;
|
||||
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.hl7.fhir.r4.model.Reference;
|
||||
import org.hl7.fhir.r4.model.Task;
|
||||
import org.junit.After;
|
||||
import org.junit.AfterClass;
|
||||
|
|
@ -21,9 +25,12 @@ import java.util.List;
|
|||
|
||||
import static org.hamcrest.CoreMatchers.startsWith;
|
||||
import static org.hamcrest.Matchers.contains;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertFalse;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.fail;
|
||||
|
||||
@SuppressWarnings({"unchecked", "deprecation"})
|
||||
@SuppressWarnings({"ConstantConditions"})
|
||||
public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCreatePlaceholdersR4Test.class);
|
||||
|
|
@ -32,6 +39,9 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
|
|||
public final void afterResetDao() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(new DaoConfig().isAutoCreatePlaceholderReferenceTargets());
|
||||
myDaoConfig.setResourceClientIdStrategy(new DaoConfig().getResourceClientIdStrategy());
|
||||
myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(new DaoConfig().isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets());
|
||||
myDaoConfig.setBundleTypesAllowedForStorage(new DaoConfig().getBundleTypesAllowedForStorage());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -163,6 +173,90 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Patient/999999999999999", outcome.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless().getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedByDefault() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(true);
|
||||
|
||||
Observation obsToCreate = new Observation();
|
||||
obsToCreate.setStatus(ObservationStatus.FINAL);
|
||||
obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123");
|
||||
obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123");
|
||||
IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
|
||||
|
||||
Observation createdObs = myObservationDao.read(id);
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
|
||||
|
||||
Patient patient = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
|
||||
assertEquals(0, patient.getIdentifier().size());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testCreatePlaceholderWithMatchUrl_IdentifierCopied_NotPreExisting() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(true);
|
||||
myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
|
||||
|
||||
Observation obsToCreate = new Observation();
|
||||
obsToCreate.setStatus(ObservationStatus.FINAL);
|
||||
obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123");
|
||||
obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123");
|
||||
IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
|
||||
|
||||
Observation createdObs = myObservationDao.read(id);
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
|
||||
|
||||
Patient patient = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
|
||||
assertEquals(1, patient.getIdentifier().size());
|
||||
assertEquals("http://foo", patient.getIdentifier().get(0).getSystem());
|
||||
assertEquals("123", patient.getIdentifier().get(0).getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedBecauseNoFieldMatches() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(true);
|
||||
myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setBundleTypesAllowedForStorage(Sets.newHashSet(""));
|
||||
|
||||
AuditEvent eventToCreate = new AuditEvent();
|
||||
Reference what = eventToCreate.addEntity().getWhat();
|
||||
what.setReference("Bundle/ABC");
|
||||
what.getIdentifier().setSystem("http://foo");
|
||||
what.getIdentifier().setValue("123");
|
||||
IIdType id = myAuditEventDao.create(eventToCreate, mySrd).getId();
|
||||
|
||||
AuditEvent createdEvent = myAuditEventDao.read(id);
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEvent));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreatePlaceholderWithMatchUrl_PreExisting() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(true);
|
||||
myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("ABC");
|
||||
patient.addIdentifier().setSystem("http://foo").setValue("123");
|
||||
myPatientDao.update(patient);
|
||||
|
||||
Observation obsToCreate = new Observation();
|
||||
obsToCreate.setStatus(ObservationStatus.FINAL);
|
||||
obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123");
|
||||
obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123");
|
||||
IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
|
||||
|
||||
Observation createdObs = myObservationDao.read(id);
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
|
||||
assertEquals("Patient/ABC", obsToCreate.getSubject().getReference());
|
||||
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
|
|
|
|||
|
|
@ -23,11 +23,12 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
|
|||
import ca.uhn.fhir.context.RuntimeSearchParam;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.hl7.fhir.instance.model.api.IBaseReference;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
|
||||
public interface IResourceLinkResolver {
|
||||
ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, String theId, RequestDetails theRequest);
|
||||
ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest);
|
||||
|
||||
void validateTypeOrThrowException(Class<? extends IBaseResource> theType);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -39,7 +39,6 @@ import org.springframework.beans.factory.annotation.Autowired;
|
|||
import org.springframework.stereotype.Service;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.Map;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
|
@ -73,8 +72,8 @@ public class ResourceLinkExtractor {
|
|||
}
|
||||
|
||||
private void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest) {
|
||||
IBaseReference nextObject = thePathAndRef.getRef();
|
||||
IIdType nextId = nextObject.getReferenceElement();
|
||||
IBaseReference nextReference = thePathAndRef.getRef();
|
||||
IIdType nextId = nextReference.getReferenceElement();
|
||||
String path = thePathAndRef.getPath();
|
||||
|
||||
/*
|
||||
|
|
@ -82,8 +81,8 @@ public class ResourceLinkExtractor {
|
|||
* programmatically with a Bundle (not through the FHIR REST API)
|
||||
* but Smile does this
|
||||
*/
|
||||
if (nextId.isEmpty() && nextObject.getResource() != null) {
|
||||
nextId = nextObject.getResource().getIdElement();
|
||||
if (nextId.isEmpty() && nextReference.getResource() != null) {
|
||||
nextId = nextReference.getResource().getIdElement();
|
||||
}
|
||||
|
||||
theParams.myPopulatedResourceLinkParameters.add(thePathAndRef.getSearchParamName());
|
||||
|
|
@ -152,15 +151,15 @@ public class ResourceLinkExtractor {
|
|||
}
|
||||
|
||||
theResourceLinkResolver.validateTypeOrThrowException(type);
|
||||
ResourceLink resourceLink = createResourceLink(theEntity, theUpdateTime, theResourceLinkResolver, theRuntimeSearchParam, path, thePathAndRef, nextId, typeString, type, id, theRequest);
|
||||
ResourceLink resourceLink = createResourceLink(theEntity, theUpdateTime, theResourceLinkResolver, theRuntimeSearchParam, path, thePathAndRef, nextId, typeString, type, nextReference, theRequest);
|
||||
if (resourceLink == null) {
|
||||
return;
|
||||
}
|
||||
theParams.myLinks.add(resourceLink);
|
||||
}
|
||||
|
||||
private ResourceLink createResourceLink(ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, String theId, RequestDetails theRequest) {
|
||||
ResourceTable targetResource = theResourceLinkResolver.findTargetResource(nextSpDef, theNextPathsUnsplit, theNextId, theTypeString, theType, theId, theRequest);
|
||||
private ResourceLink createResourceLink(ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest) {
|
||||
ResourceTable targetResource = theResourceLinkResolver.findTargetResource(nextSpDef, theNextPathsUnsplit, theNextId, theTypeString, theType, theReference, theRequest);
|
||||
|
||||
if (targetResource == null) {
|
||||
return null;
|
||||
|
|
@ -169,7 +168,4 @@ public class ResourceLinkExtractor {
|
|||
return new ResourceLink(nextPathAndRef.getPath(), theEntity, targetResource, theUpdateTime);
|
||||
}
|
||||
|
||||
private String toResourceName(Class<? extends IBaseResource> theResourceType) {
|
||||
return myContext.getResourceDefinition(theResourceType).getName();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.model.entity.ForcedId;
|
|||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.hl7.fhir.instance.model.api.IBaseReference;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.springframework.stereotype.Service;
|
||||
|
|
@ -33,7 +34,7 @@ import org.springframework.stereotype.Service;
|
|||
public class InlineResourceLinkResolver implements IResourceLinkResolver {
|
||||
|
||||
@Override
|
||||
public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, String theId, RequestDetails theRequest) {
|
||||
public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest) {
|
||||
ResourceTable target;
|
||||
target = new ResourceTable();
|
||||
target.setResourceType(theTypeString);
|
||||
|
|
@ -41,7 +42,7 @@ public class InlineResourceLinkResolver implements IResourceLinkResolver {
|
|||
target.setId(theNextId.getIdPartAsLong());
|
||||
} else {
|
||||
ForcedId forcedId = new ForcedId();
|
||||
forcedId.setForcedId(theId);
|
||||
forcedId.setForcedId(theNextId.getIdPart());
|
||||
target.setForcedId(forcedId);
|
||||
}
|
||||
return target;
|
||||
|
|
|
|||
|
|
@ -265,7 +265,7 @@ public class ClientServerValidationDstu2Test {
|
|||
|
||||
@Test
|
||||
public void testServerReturnsWrongVersionForDstu2() throws Exception {
|
||||
String wrongFhirVersion = "3.0.1";
|
||||
String wrongFhirVersion = FhirVersionEnum.DSTU3.getFhirVersionString();
|
||||
assertThat(wrongFhirVersion, is(FhirVersionEnum.DSTU3.getFhirVersionString())); // asserting that what we assume to be the DSTU3 FHIR version is still correct
|
||||
Conformance conf = new Conformance();
|
||||
conf.setFhirVersion(wrongFhirVersion);
|
||||
|
|
@ -285,7 +285,7 @@ public class ClientServerValidationDstu2Test {
|
|||
fail();
|
||||
} catch (FhirClientInappropriateForServerException e) {
|
||||
String out = e.toString();
|
||||
String want = "The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"3.0.1\" which corresponds to DSTU3, but this client is configured to use DSTU2 (via the FhirContext)";
|
||||
String want = "The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"" + wrongFhirVersion + "\" which corresponds to DSTU3, but this client is configured to use DSTU2 (via the FhirContext)";
|
||||
ourLog.info(out);
|
||||
ourLog.info(want);
|
||||
assertThat(out, containsString(want));
|
||||
|
|
|
|||
Loading…
Reference in New Issue