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hapi-fhir
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Merge branch 'master' into 2732-bump-conceptmap-group-element-display-storage-size

This commit is contained in:
Josiah 2021-06-17 15:14:05 -04:00
parent 324201b105 5d246bcca8
commit 164e684d7c
196 changed files with 6398 additions and 1063 deletions
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29
hapi-deployable-pom/pom.xml
View File

@ -2,11 +2,11 @@
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>hapi-deployable-pom</artifactId>
<packaging>pom</packaging>
@ -140,6 +140,25 @@
</ignoredResourcePatterns>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<executions>
<execution>
<phase>process-sources</phase>
<goals>
<goal>checkstyle</goal>
</goals>
<configuration>
<failsOnError>true</failsOnError>
<enableRulesSummary>true</enableRulesSummary>
<enableSeveritySummary>true</enableSeveritySummary>
<consoleOutput>true</consoleOutput>
<configLocation>${maven.multiModuleProjectDirectory}/src/checkstyle/checkstyle.xml</configLocation>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

2
hapi-fhir-android/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

7
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -19,11 +19,14 @@
<dependencies>
<!-- JSON -->
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!-- XML -->
<dependency>
<groupId>com.fasterxml.woodstox</groupId>

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -225,6 +225,18 @@ public class FhirContext {
}
public static FhirContext forDstu3Cached() {
return forCached(FhirVersionEnum.DSTU3);
}
public static FhirContext forR4Cached() {
return forCached(FhirVersionEnum.R4);
}
public static FhirContext forR5Cached() {
return forCached(FhirVersionEnum.R5);
}
private String createUnknownResourceNameError(final String theResourceName, final FhirVersionEnum theVersion) {
return getLocalizer().getMessage(FhirContext.class, "unknownResourceName", theResourceName, theVersion);
}

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -1840,6 +1840,9 @@ public enum Pointcut implements IPointcut {
* pulled out of the servlet request. This parameter is identical to the RequestDetails parameter above but will
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* <li>
* ca.uhn.fhir.context.RuntimeResourceDefinition - the resource type being accessed
* </li>
* </ul>
* <p>
* Hooks must return void.
@ -1851,7 +1854,8 @@ public enum Pointcut implements IPointcut {
// Params
"ca.uhn.fhir.interceptor.model.RequestPartitionId",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"ca.uhn.fhir.context.RuntimeResourceDefinition"
),
/**

21
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/model/RequestPartitionId.java
View File

@ -20,6 +20,10 @@ package ca.uhn.fhir.interceptor.model;
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@ -41,12 +45,17 @@ import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
/**
* @since 5.0.0
*/
public class RequestPartitionId {
public class RequestPartitionId implements IModelJson {
private static final RequestPartitionId ALL_PARTITIONS = new RequestPartitionId();
private static final ObjectMapper ourObjectMapper = new ObjectMapper().registerModule(new com.fasterxml.jackson.datatype.jsr310.JavaTimeModule());
@JsonProperty("partitionDate")
private final LocalDate myPartitionDate;
@JsonProperty("allPartitions")
private final boolean myAllPartitions;
@JsonProperty("partitionIds")
private final List<Integer> myPartitionIds;
@JsonProperty("partitionNames")
private final List<String> myPartitionNames;
/**
@ -80,6 +89,10 @@ public class RequestPartitionId {
myAllPartitions = true;
}
public static RequestPartitionId fromJson(String theJson) throws JsonProcessingException {
return ourObjectMapper.readValue(theJson, RequestPartitionId.class);
}
public boolean isAllPartitions() {
return myAllPartitions;
}
@ -308,4 +321,8 @@ public class RequestPartitionId {
}
return retVal;
}
public String asJson() throws JsonProcessingException {
return ourObjectMapper.writeValueAsString(this);
}
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

@ -72,6 +72,7 @@ public enum VersionEnum {
V5_3_2,
V5_3_3,
V5_4_0,
V5_4_1,
V5_5_0,
;

31
hapi-fhir-base/src/test/java/ca/uhn/fhir/interceptor/model/RequestPartitionIdTest.java
View File

@ -1,16 +1,22 @@
package ca.uhn.fhir.interceptor.model;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.google.common.collect.Lists;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.time.LocalDate;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class RequestPartitionIdTest {
private static final Logger ourLog = LoggerFactory.getLogger(RequestPartitionIdTest.class);
@Test
public void testHashCode() {
@ -36,5 +42,30 @@ public class RequestPartitionIdTest {
assertFalse(RequestPartitionId.forPartitionIdsAndNames(null, Lists.newArrayList(1, 2), null).isDefaultPartition());
}
@Test
public void testSerDeserSer() throws JsonProcessingException {
{
RequestPartitionId start = RequestPartitionId.fromPartitionId(123, LocalDate.of(2020, 1, 1));
String json = assertSerDeserSer(start);
assertThat(json, containsString("\"partitionDate\":[2020,1,1]"));
assertThat(json, containsString("\"partitionIds\":[123]"));
}
{
RequestPartitionId start = RequestPartitionId.forPartitionIdsAndNames(Lists.newArrayList("Name1", "Name2"), null, null);
String json = assertSerDeserSer(start);
assertThat(json, containsString("partitionNames\":[\"Name1\",\"Name2\"]"));
}
assertSerDeserSer(RequestPartitionId.allPartitions());
assertSerDeserSer(RequestPartitionId.defaultPartition());
}
private String assertSerDeserSer(RequestPartitionId start) throws JsonProcessingException {
String json = start.asJson();
ourLog.info(json);
RequestPartitionId end = RequestPartitionId.fromJson(json);
assertEquals(start, end);
String json2 = end.asJson();
assertEquals(json, json2);
return json;
}
}

4
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

66
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java
View File

@ -36,6 +36,7 @@ import org.fusesource.jansi.Ansi;
import org.fusesource.jansi.AnsiConsole;
import org.slf4j.LoggerFactory;
import java.io.PrintStream;
import java.io.PrintWriter;
import java.lang.management.ManagementFactory;
import java.util.ArrayList;
@ -43,6 +44,7 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.fusesource.jansi.Ansi.ansi;
@SuppressWarnings("WeakerAccess")
@ -67,17 +69,27 @@ public abstract class BaseApp {
private void logAppHeader() {
System.out.flush();
System.out.println("------------------------------------------------------------");
String msg = "------------------------------------------------------------";
printMessageToStdout(msg);
logProductName();
System.out.println("------------------------------------------------------------");
System.out.println("Process ID : " + ManagementFactory.getRuntimeMXBean().getName());
System.out.println("Max configured JVM memory (Xmx) : " + FileHelper.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
System.out.println("Detected Java version : " + System.getProperty("java.version"));
System.out.println("------------------------------------------------------------");
printMessageToStdout("------------------------------------------------------------");
printMessageToStdout("Process ID : " + ManagementFactory.getRuntimeMXBean().getName());
printMessageToStdout("Max configured JVM memory (Xmx) : " + FileHelper.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
printMessageToStdout("Detected Java version : " + System.getProperty("java.version"));
printMessageToStdout("------------------------------------------------------------");
}
private void printMessageToStdout(String theMsg) {
PrintStream out = System.out;
if (isNotBlank(theMsg)) {
out.println(theMsg);
} else {
out.println();
}
}
protected void logProductName() {
System.out.println("\ud83d\udd25 " + ansi().bold() + " " + provideProductName() + ansi().boldOff() + " " + provideProductVersion() + " - Command Line Tool");
printMessageToStdout("\ud83d\udd25 " + ansi().bold() + " " + provideProductName() + ansi().boldOff() + " " + provideProductVersion() + " - Command Line Tool");
}
private void logCommandUsage(BaseCommand theCommand) {
@ -99,32 +111,32 @@ public abstract class BaseApp {
}
// Usage
System.out.println("Usage:");
System.out.println(" " + provideCommandName() + " " + theCommand.getCommandName() + " [options]");
System.out.println();
printMessageToStdout("Usage:");
printMessageToStdout(" " + provideCommandName() + " " + theCommand.getCommandName() + " [options]");
printMessageToStdout("");
// Description
String wrapped = WordUtils.wrap(theCommand.getCommandDescription(), columns);
System.out.println(wrapped);
System.out.println();
printMessageToStdout(wrapped);
printMessageToStdout("");
// Usage Notes
List<String> usageNotes = theCommand.provideUsageNotes();
for (String next : usageNotes) {
wrapped = WordUtils.wrap(next, columns);
System.out.println(wrapped);
System.out.println();
printMessageToStdout(wrapped);
printMessageToStdout("");
}
// Options
System.out.println("Options:");
printMessageToStdout("Options:");
HelpFormatter fmt = new HelpFormatter();
PrintWriter pw = new PrintWriter(System.out);
fmt.printOptions(pw, columns, getOptions(theCommand), 2, 2);
pw.flush();
// That's it!
System.out.println();
printMessageToStdout("");
}
private Options getOptions(BaseCommand theCommand) {
@ -135,10 +147,10 @@ public abstract class BaseApp {
private void logUsage() {
logAppHeader();
System.out.println("Usage:");
System.out.println(" " + provideCommandName() + " {command} [options]");
System.out.println();
System.out.println("Commands:");
printMessageToStdout("Usage:");
printMessageToStdout(" " + provideCommandName() + " {command} [options]");
printMessageToStdout("");
printMessageToStdout("Commands:");
int longestCommandLength = 0;
for (BaseCommand next : ourCommands) {
@ -151,12 +163,12 @@ public abstract class BaseApp {
for (int i = 1; i < rightParts.length; i++) {
rightParts[i] = StringUtils.leftPad("", left.length() + 3) + rightParts[i];
}
System.out.println(ansi().bold().fg(Ansi.Color.GREEN) + left + ansi().boldOff().fg(Ansi.Color.WHITE) + " - " + ansi().bold() + StringUtils.join(rightParts, LINESEP));
printMessageToStdout(ansi().bold().fg(Ansi.Color.GREEN) + left + ansi().boldOff().fg(Ansi.Color.WHITE) + " - " + ansi().bold() + StringUtils.join(rightParts, LINESEP));
}
System.out.println();
System.out.println(ansi().boldOff().fg(Ansi.Color.WHITE) + "See what options are available:");
System.out.println(" " + provideCommandName() + " help {command}");
System.out.println();
printMessageToStdout("");
printMessageToStdout(ansi().boldOff().fg(Ansi.Color.WHITE) + "See what options are available:");
printMessageToStdout(" " + provideCommandName() + " help {command}");
printMessageToStdout("");
}
protected abstract String provideCommandName();
@ -235,8 +247,8 @@ public abstract class BaseApp {
if (command == null) {
String message = "Unrecognized command: " + ansi().bold().fg(Ansi.Color.RED) + theArgs[0] + ansi().boldOff().fg(Ansi.Color.WHITE);
System.out.println(message);
System.out.println();
printMessageToStdout(message);
printMessageToStdout("");
logUsage();
exitDueToProblem(message);
return;

4
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -119,7 +119,7 @@
</execution>
</executions>
</plugin>
</plugins>
</plugins>
</build>
</project>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

9
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -141,6 +141,13 @@
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
<resources>
<resource>

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_1/version.yaml Normal file
View File

@ -0,0 +1,3 @@
---
release-date: "2021-06-15"
codename: "Pangolin"

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2509-fix-pagination-incorrect-offset-and-count-previous-link-of-last-page.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: add
issue: 2509
backport: 5.4.1
title: "Pagination returned incorrect offset and count in the previous link of the last page
when total element count was one more than multiple of page size. Problem is now fixed"

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2652-add-scheduled-task-enablement-settings.yaml
View File

@ -1,4 +1,5 @@
---
type: add
issue: 2652
backport: 5.4.1
title: "Settings have been added to the JPA Server DaoConfig to enable/disable various individual kinds of scheduled tasks."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2653-match-url-with-spaces.yaml
View File

@ -1,6 +1,7 @@
---
type: change
issue: 2653
backport: 5.4.1
title: "When performing a conditional create/update/delete on a JPA server, if the match URL
contained a plus character, this character was interpreted as a space (per legacy URL encoding
rules) even though this has proven to not be the intended behaviour in real life applications.

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2653-reject-conditonal-create-without-actual-match.yaml
View File

@ -1,6 +1,7 @@
---
type: add
issue: 2653
backport: 5.4.1
title: "When performing a conditional create operation on a JPA server, the system will now
verify that the conditional URL actually matches the data supplied in the resource body,
and aborts the conditional create if it does not."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2665-avoid-contained-resource-in-conditional-create.yaml
View File

@ -1,5 +1,6 @@
---
type: fix
issue: 2665
backport: 5.4.1
title: When performing a FHIR transaction containing a conditional create, references to that resource
were inadvertently replaced with contained references."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2672-fix-concurrency-error-under-load.yaml
View File

@ -1,5 +1,6 @@
---
type: fix
issue: 2672
backport: 5.4.1
title: "A concurrency error was fixed when using client assigned IDs on a highly concurrent server
with resource deletion disabled."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2672-support-include-restpe-star.yaml
View File

@ -1,5 +1,6 @@
---
type: add
issue: 2672
backport: 5.4.1
title: "Support has been added to the JPA server for `_include` and `_revinclude` where the
value is a qualified star, e.g. `_include=Observation:*`."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2674-fix-npe-on-display-population-interceptor.yaml
View File

@ -1,5 +1,6 @@
---
type: fix
issue: 2674
backport: 5.4.1
title: "A null-pointer exception was fixed when a ResponseTerminologyDisplayInterceptor is registered and a search
or read response returns a resource with code value that in turn returns a null code lookup."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2675-add-validation-suppression-interceptor.yaml
View File

@ -1,5 +1,6 @@
---
type: add
issue: 2675
backport: 5.4.1
title: "A new interceptor ValidationMessageSuppressingInterceptor has been added. This interceptor can be used
to selectively suppress specific vaLidation messages."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2676-add-legacy-date-search-mode.yaml
View File

@ -1,6 +1,7 @@
---
type: add
issue: 2676
backport: 5.4.1
title: "A new config option has been added to the DaoConfig that causes generated SQL statements to
account for potential null values in HAPI FHIR JPA date index rows. Nulls are no longer ever
used in this table after HAPI FHIR 5.3.0, but legacy data may still have nulls."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2676-add-max-includes-setting.yaml
View File

@ -1,5 +1,6 @@
---
type: add
issue: 2676
backport: 5.4.1
title: "A new setting has been added to the DaoConfig that allows the maximum number of
`_include` and `_revinclude` resources to be added to a single search page result."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2676-constrain-paging-in-synchronous-searches.yaml
View File

@ -1,5 +1,6 @@
---
type: add
issue: 2676
backport: 5.4.1
title: "When performing non-query cache JPA searches (i.e. searches with `Cache-Control: no-store`)
the loading of `_include` and `_revinclude` will now factor the maximum include count."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2676-dont-trigger-subscriptions-on-non-versioning-changes.yaml
View File

@ -1,6 +1,7 @@
---
type: fix
issue: 2676
backport: 5.4.1
title: "Subscription notifications will no longer be triggered by default in response to changes
that do not increment the resource version (e.g. `$meta-add` and `$meta-delete`). A new
DaoConfig setting has been added to make this configurable."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2677-fix-accurate-count-zero.yaml
View File

@ -1,5 +1,6 @@
---
type: fix
issue: 2674
backport: 5.4.1
title: "When myDaoConfig.setDefaultTotalMode(SearchTotalModeEnum.ACCURATE) and there are zero search results on an _id search,
An Index Out of Bounds error was thrown. This has been corrected."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2681-enable-mass-ingestion-mode.yaml
View File

@ -1,5 +1,6 @@
---
type: add
issue: 2681
backport: 5.4.1
title: "A new DaoConfig setting called Mass Ingestion Mode has been added. This mode enables rapid
data ingestion by skipping a number of unnecessary checks during backloading."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2682-fix-case-sensititivity-in-package-ids.yaml
View File

@ -1,4 +1,5 @@
---
type: fix
issue: 2682
backport: 5.4.1
title: "Fixes the problem that FHIR package IDs were incorrectly treated as case sensitive when being loaded, causing loads to fail when dependencies were declared with a different case than in the package itself."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2688-avoid-sql-dupe-check.yaml
View File

@ -1,5 +1,6 @@
---
type: perf
issue: 2688
backport: 5.4.1
title: "FHIR Transaction duplicate record checks are now performed without any database interactions or SQL statements,
reducing the processing load associated with FHIR transactions by at least a small amount."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2688-reduce-match-url-limit.yaml
View File

@ -1,5 +1,6 @@
---
type: perf
issue: 2688
backport: 5.4.1
title: "Conditional URL lookups in the JPA server will now explicitly specify a maximum fetch size of 2, avoiding
fetching more data that won't be used inadvertently in some situations."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2692-add-initiate-bulk-export-pointcut.yaml
View File

@ -1,4 +1,5 @@
---
type: add
issue: 2692
backport: 5.4.1
title: "A new Pointcut has been added that is invoked when a new Bulk Export is initiated."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2693-case-insensitive-retry-tables.yaml
View File

@ -1,6 +1,7 @@
---
type: fix
issue: 2693
backport: 5.4.1
title: "Constraint errors were not always auto-retried even when configured to do so on certain
platforms (particularly Postgresql) where constraint names are auto converted to lower case.
Thanks to Bruno Hedman for the pull request!"

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2695-make-bulk-import-job-local.yaml
View File

@ -1,5 +1,6 @@
---
type: change
issue: 2695
backport: 5.4.1
title: "Bulk import batch jobs are now activated in a local scheduled task, making bulk import
jobs better able to take advantage of large clusters."

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2697-delete-expunge-spring-batch.yaml Normal file
View File

@ -0,0 +1,8 @@
---
type: change
issue: 2697
title: "DELETE _expunge=true has been converted to use Spring Batch. It now simply returns the jobId of the Spring Batch
job while the job continues to run in the background. A new operation called $expunge-delete has been added to provide
more fine-grained control of the delete expunge operation. This operation accepts an ordered list of URLs to be delete
expunged and an optional batch-size parameter that will be used to perform the delete expunge. If no batch size is
specified in the operation, then the value of DaoConfig.getExpungeBatchSize() is used."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2702-add-icd10cm-support.yaml
View File

@ -1,5 +1,6 @@
---
type: add
issue: 2702
backport: 5.4.1
title: "The JPA server terminology uploader now supports uploading ICD-10-CM (US Edition) using the
native format for that vocabulary."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2705-search-by-source-incorrect-size.yaml
View File

@ -1,4 +1,5 @@
---
type: fix
issue: 2705
backport: 5.4.1
title: "When searching by source, if deleted resources are matched, the search returned an incorrect size. This has been corrected."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2706-filter-searchparam-capability-statement.yaml
View File

@ -1,5 +1,6 @@
---
type: fix
issue: 2695
backport: 5.4.1
title: "The _filter search parameter was incorrectly included in the server capability statement if it was disabled
on the server. This has been corrected."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2712-add-bulk-export-auth.yaml
View File

@ -1,4 +1,5 @@
---
type: add
issue: 2712
backport: 5.4.1
title: "AuthorizationInterceptor can now be used to authorize bulk export requests"

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2717-add-tag-versioning-mode.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 2717
title: "A new setting has been added to the DaoConfig called Tag Versioning Mode. This setting controls whether a single collection of
tags/profiles/security labels is maintained across all versions of a single resource, or whether each version of the
resource maintains its own independent collection. Previously each version always maintained an independent collection,
which is useful sometimes, but is often not useful and can affect performance."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2717-transaction-write-pre-caching.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: perf
issue: 2717
title: "FHIR transactions in the JPA server that perform writes will now aggressively pre-fetch as many entities
as possible at the very start of transaction processing. This can drastically reduce the number of
round-trips, especially as the number of resources in a transaction gets bigger."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2724-valueset-expansion-preserve-order.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 2624
title: "ValueSet expansion did not correctly preserve the order if multiple codes were included
in a single inclusion block."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/configuration.md
View File

@ -129,4 +129,7 @@ X-Retry-On-Version-Conflict: retry; max-retries=100
# Controlling Delete with Expunge size
During the delete with expunge operation there is an internal synchronous search which locates all the resources to be deleted. The default maximum size of this search is 10000. This can be configured via the [Internal Synchronous Search Size](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setInternalSynchronousSearchSize(java.lang.Integer)) property.
Delete with expunge submits a job to delete and expunge the requested resources. This is done in batches. If the DELETE
?_expunge=true syntax is used to trigger the delete expunge, then the batch size will be determined by the value
of [Expunge Batch Size](/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
property.

8
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -147,9 +147,9 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<executions>
<execution><id>validate</id><phase>none</phase></execution>
</executions>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-example/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-api/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

119
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
View File

@ -8,6 +8,7 @@ import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.util.HapiExtensions;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu2.model.Subscription;
@ -84,6 +85,10 @@ public class DaoConfig {
*/
public static final boolean DEFAULT_ENABLE_TASKS = true;
public static final int DEFAULT_MAXIMUM_INCLUDES_TO_LOAD_PER_PAGE = 1000;
/**
* @since 5.5.0
*/
public static final TagStorageModeEnum DEFAULT_TAG_STORAGE_MODE = TagStorageModeEnum.VERSIONED;
/**
* Default value for {@link #setMaximumSearchResultCountInTransaction(Integer)}
*
@ -129,6 +134,7 @@ public class DaoConfig {
private SearchTotalModeEnum myDefaultTotalMode = null;
private int myEverythingIncludesFetchPageSize = 50;
private int myBulkImportMaxRetryCount = 10;
private TagStorageModeEnum myTagStorageMode = DEFAULT_TAG_STORAGE_MODE;
/**
* update setter javadoc if default changes
*/
@ -215,11 +221,11 @@ public class DaoConfig {
* update setter javadoc if default changes
*/
@Nonnull
private Long myTranslationCachesExpireAfterWriteInMinutes = DEFAULT_TRANSLATION_CACHES_EXPIRE_AFTER_WRITE_IN_MINUTES;
private final Long myTranslationCachesExpireAfterWriteInMinutes = DEFAULT_TRANSLATION_CACHES_EXPIRE_AFTER_WRITE_IN_MINUTES;
/**
* @since 5.4.0
*/
private boolean myMatchUrlCache;
private boolean myMatchUrlCacheEnabled;
/**
* @since 5.5.0
*/
@ -266,6 +272,26 @@ public class DaoConfig {
}
}
/**
* Sets the tag storage mode for the server. Default is {@link TagStorageModeEnum#VERSIONED}.
*
* @since 5.5.0
*/
@Nonnull
public TagStorageModeEnum getTagStorageMode() {
return myTagStorageMode;
}
/**
* Sets the tag storage mode for the server. Default is {@link TagStorageModeEnum#VERSIONED}.
*
* @since 5.5.0
*/
public void setTagStorageMode(@Nonnull TagStorageModeEnum theTagStorageMode) {
Validate.notNull(theTagStorageMode, "theTagStorageMode must not be null");
myTagStorageMode = theTagStorageMode;
}
/**
* Specifies the maximum number of times that a chunk will be retried during bulk import
* processes before giving up.
@ -421,9 +447,11 @@ public class DaoConfig {
* Default is <code>false</code>
*
* @since 5.4.0
* @deprecated Deprecated in 5.5.0. Use {@link #isMatchUrlCacheEnabled()} instead (the name of this method is misleading)
*/
@Deprecated
public boolean getMatchUrlCache() {
return myMatchUrlCache;
return myMatchUrlCacheEnabled;
}
/**
@ -435,9 +463,39 @@ public class DaoConfig {
* Default is <code>false</code>
*
* @since 5.4.0
* @deprecated Deprecated in 5.5.0. Use {@link #setMatchUrlCacheEnabled(boolean)} instead (the name of this method is misleading)
*/
@Deprecated
public void setMatchUrlCache(boolean theMatchUrlCache) {
myMatchUrlCache = theMatchUrlCache;
myMatchUrlCacheEnabled = theMatchUrlCache;
}
/**
* If enabled, resolutions for match URLs (e.g. conditional create URLs, conditional update URLs, etc) will be
* cached in an in-memory cache. This cache can have a noticeable improvement on write performance on servers
* where conditional operations are frequently performed, but note that this cache will not be
* invalidated based on updates to resources so this may have detrimental effects.
* <p>
* Default is <code>false</code>
*
* @since 5.5.0
*/
public boolean isMatchUrlCacheEnabled() {
return getMatchUrlCache();
}
/**
* If enabled, resolutions for match URLs (e.g. conditional create URLs, conditional update URLs, etc) will be
* cached in an in-memory cache. This cache can have a noticeable improvement on write performance on servers
* where conditional operations are frequently performed, but note that this cache will not be
* invalidated based on updates to resources so this may have detrimental effects.
* <p>
* Default is <code>false</code>
*
* @since 5.5.0
*/
public void setMatchUrlCacheEnabled(boolean theMatchUrlCache) {
setMatchUrlCache(theMatchUrlCache);
}
/**
@ -1572,7 +1630,8 @@ public class DaoConfig {
/**
* The expunge batch size (default 800) determines the number of records deleted within a single transaction by the
* expunge operation.
* expunge operation. When expunging via DELETE ?_expunge=true, then this value determines the batch size for
* the number of resources deleted and expunged at a time.
*/
public int getExpungeBatchSize() {
return myExpungeBatchSize;
@ -1580,7 +1639,8 @@ public class DaoConfig {
/**
* The expunge batch size (default 800) determines the number of records deleted within a single transaction by the
* expunge operation.
* expunge operation. When expunging via DELETE ?_expunge=true, then this value determines the batch size for
* the number of resources deleted and expunged at a time.
*/
public void setExpungeBatchSize(int theExpungeBatchSize) {
myExpungeBatchSize = theExpungeBatchSize;
@ -2271,9 +2331,8 @@ public class DaoConfig {
/**
* <p>
* This determines the internal search size that is run synchronously during operations such as:
* 1. Delete with _expunge parameter.
* 2. Searching for Code System IDs by System and Code
* This determines the internal search size that is run synchronously during operations such as searching for
* Code System IDs by System and Code
* </p>
*
* @since 5.4.0
@ -2284,9 +2343,8 @@ public class DaoConfig {
/**
* <p>
* This determines the internal search size that is run synchronously during operations such as:
* 1. Delete with _expunge parameter.
* 2. Searching for Code System IDs by System and Code
* This determines the internal search size that is run synchronously during operations such as searching for
* Code System IDs by System and Code
* </p>
*
* @since 5.4.0
@ -2472,6 +2530,30 @@ public class DaoConfig {
myTriggerSubscriptionsForNonVersioningChanges = theTriggerSubscriptionsForNonVersioningChanges;
}
public boolean canDeleteExpunge() {
return isAllowMultipleDelete() && isExpungeEnabled() && isDeleteExpungeEnabled();
}
public String cannotDeleteExpungeReason() {
List<String> reasons = new ArrayList<>();
if (!isAllowMultipleDelete()) {
reasons.add("Multiple Delete");
}
if (!isExpungeEnabled()) {
reasons.add("Expunge");
}
if (!isDeleteExpungeEnabled()) {
reasons.add("Delete Expunge");
}
String retval = "Delete Expunge is not supported on this server. ";
if (reasons.size() == 1) {
retval += reasons.get(0) + " is disabled.";
} else {
retval += "The following configurations are disabled: " + StringUtils.join(reasons, ", ");
}
return retval;
}
public enum StoreMetaSourceInformationEnum {
NONE(false, false),
SOURCE_URI(true, false),
@ -2548,4 +2630,17 @@ public class DaoConfig {
ANY
}
public enum TagStorageModeEnum {
/**
* A separate set of tags is stored for each resource version
*/
VERSIONED,
/**
* A single set of tags is shared by all resource versions
*/
NON_VERSIONED
}
}

3
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoSubscription.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.api.dao;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -26,6 +27,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
public interface IFhirResourceDaoSubscription<T extends IBaseResource> extends IFhirResourceDao<T> {
Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest);
Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest, TransactionDetails theTransactionDetails);
}

21
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/DeleteMethodOutcome.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.api.model;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.MethodOutcome;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import java.util.List;
@ -32,31 +33,51 @@ import java.util.List;
public class DeleteMethodOutcome extends MethodOutcome {
private List<ResourceTable> myDeletedEntities;
@Deprecated
private long myExpungedResourcesCount;
@Deprecated
private long myExpungedEntitiesCount;
public DeleteMethodOutcome() {
}
public DeleteMethodOutcome(IBaseOperationOutcome theBaseOperationOutcome) {
super(theBaseOperationOutcome);
}
public List<ResourceTable> getDeletedEntities() {
return myDeletedEntities;
}
/**
* Use {@link ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter#ENTITY_TOTAL_UPDATED_OR_DELETED}
*/
@Deprecated
public DeleteMethodOutcome setDeletedEntities(List<ResourceTable> theDeletedEntities) {
myDeletedEntities = theDeletedEntities;
return this;
}
/**
* Use {@link ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener#RESOURCE_TOTAL_PROCESSED}
*/
@Deprecated
public long getExpungedResourcesCount() {
return myExpungedResourcesCount;
}
@Deprecated
public DeleteMethodOutcome setExpungedResourcesCount(long theExpungedResourcesCount) {
myExpungedResourcesCount = theExpungedResourcesCount;
return this;
}
@Deprecated
public long getExpungedEntitiesCount() {
return myExpungedEntitiesCount;
}
@Deprecated
public DeleteMethodOutcome setExpungedEntitiesCount(long theExpungedEntitiesCount) {
myExpungedEntitiesCount = theExpungedEntitiesCount;
return this;

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.5.0-PRE2-SNAPSHOT</version>
<version>5.5.0-PRE4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.batch;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.job.BulkImportJobConfig;
import ca.uhn.fhir.jpa.delete.job.DeleteExpungeJobConfig;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -32,9 +33,10 @@ import java.util.Set;
@Configuration
//When you define a new batch job, add it here.
@Import({
CommonBatchJobConfig.class,
BulkExportJobConfig.class,
BulkImportJobConfig.class
CommonBatchJobConfig.class,
BulkExportJobConfig.class,
BulkImportJobConfig.class,
DeleteExpungeJobConfig.class
})
public class BatchJobsConfig {
@ -73,4 +75,8 @@ public class BatchJobsConfig {
RECORD_PROCESSING_STEP_NAMES = Collections.unmodifiableSet(recordProcessingStepNames);
}
/**
* Delete Expunge
*/
public static final String DELETE_EXPUNGE_JOB_NAME = "deleteExpungeJob";
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/CommonBatchJobConfig.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.batch;
* #L%
*/
import ca.uhn.fhir.jpa.batch.processors.GoldenResourceAnnotatingProcessor;
import ca.uhn.fhir.jpa.batch.processors.PidToIBaseResourceProcessor;
import ca.uhn.fhir.jpa.batch.processor.GoldenResourceAnnotatingProcessor;
import ca.uhn.fhir.jpa.batch.processor.PidToIBaseResourceProcessor;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/listener/PidReaderCounterListener.java Normal file
View File

@ -0,0 +1,48 @@
package ca.uhn.fhir.jpa.batch.listener;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.annotation.AfterProcess;
import org.springframework.batch.core.annotation.BeforeStep;
import java.util.List;
/**
* Add the number of pids processed to the execution context so we can track progress of the job
*/
public class PidReaderCounterListener {
public static final String RESOURCE_TOTAL_PROCESSED = "resource.total.processed";
private StepExecution myStepExecution;
private Long myTotalPidsProcessed = 0L;
@BeforeStep
public void setStepExecution(StepExecution stepExecution) {
myStepExecution = stepExecution;
}
@AfterProcess
public void afterProcess(List<Long> thePids, List<String> theSqlList) {
myTotalPidsProcessed += thePids.size();
myStepExecution.getExecutionContext().putLong(RESOURCE_TOTAL_PROCESSED, myTotalPidsProcessed);
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/GoldenResourceAnnotatingProcessor.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processor/GoldenResourceAnnotatingProcessor.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.batch.processors;
package ca.uhn.fhir.jpa.batch.processor;
/*-
* #%L

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/PidToIBaseResourceProcessor.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processor/PidToIBaseResourceProcessor.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.batch.processors;
package ca.uhn.fhir.jpa.batch.processor;
/*-
* #%L

200
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/ReverseCronologicalBatchResourcePidReader.java Normal file
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@ -0,0 +1,200 @@
package ca.uhn.fhir.jpa.batch.reader;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.delete.model.PartitionedUrl;
import ca.uhn.fhir.jpa.delete.model.RequestListJson;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.DateRangeParam;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ExecutionContext;
import org.springframework.batch.item.ItemReader;
import org.springframework.batch.item.ItemStream;
import org.springframework.batch.item.ItemStreamException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
/**
* This Spring Batch reader takes 4 parameters:
* {@link #JOB_PARAM_REQUEST_LIST}: A list of URLs to search for along with the partitions those searches should be performed on
* {@link #JOB_PARAM_BATCH_SIZE}: The number of resources to return with each search. If ommitted, {@link DaoConfig#getExpungeBatchSize} will be used.
* {@link #JOB_PARAM_START_TIME}: The latest timestamp of resources to search for
* <p>
* The reader will return at most {@link #JOB_PARAM_BATCH_SIZE} pids every time it is called, or null
* once no more matching resources are available. It returns the resources in reverse chronological order
* and stores where it's at in the Spring Batch execution context with the key {@link #CURRENT_THRESHOLD_HIGH}
* appended with "." and the index number of the url list item it has gotten up to. This is to permit
* restarting jobs that use this reader so it can pick up where it left off.
*/
public class ReverseCronologicalBatchResourcePidReader implements ItemReader<List<Long>>, ItemStream {
public static final String JOB_PARAM_REQUEST_LIST = "url-list";
public static final String JOB_PARAM_BATCH_SIZE = "batch-size";
public static final String JOB_PARAM_START_TIME = "start-time";
public static final String CURRENT_URL_INDEX = "current.url-index";
public static final String CURRENT_THRESHOLD_HIGH = "current.threshold-high";
private static final Logger ourLog = LoggerFactory.getLogger(ReverseCronologicalBatchResourcePidReader.class);
@Autowired
private FhirContext myFhirContext;
@Autowired
private MatchUrlService myMatchUrlService;
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private DaoConfig myDaoConfig;
private List<PartitionedUrl> myPartitionedUrls;
private Integer myBatchSize;
private final Map<Integer, Date> myThresholdHighByUrlIndex = new HashMap<>();
private int myUrlIndex = 0;
private Date myStartTime;
@Autowired
public void setRequestListJson(@Value("#{jobParameters['" + JOB_PARAM_REQUEST_LIST + "']}") String theRequestListJson) {
RequestListJson requestListJson = RequestListJson.fromJson(theRequestListJson);
myPartitionedUrls = requestListJson.getPartitionedUrls();
}
@Autowired
public void setBatchSize(@Value("#{jobParameters['" + JOB_PARAM_BATCH_SIZE + "']}") Integer theBatchSize) {
myBatchSize = theBatchSize;
}
@Autowired
public void setStartTime(@Value("#{jobParameters['" + JOB_PARAM_START_TIME + "']}") Date theStartTime) {
myStartTime = theStartTime;
}
@Override
public List<Long> read() throws Exception {
while (myUrlIndex < myPartitionedUrls.size()) {
List<Long> nextBatch;
nextBatch = getNextBatch();
if (nextBatch.isEmpty()) {
++myUrlIndex;
continue;
}
return nextBatch;
}
return null;
}
private List<Long> getNextBatch() {
ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(myPartitionedUrls.get(myUrlIndex).getUrl());
SearchParameterMap map = buildSearchParameterMap(resourceSearch);
// Perform the search
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceSearch.getResourceName());
List<Long> retval = dao.searchForIds(map, buildSystemRequestDetails()).stream()
.map(ResourcePersistentId::getIdAsLong)
.collect(Collectors.toList());
if (ourLog.isDebugEnabled()) {
ourLog.debug("Search for {}{} returned {} results", resourceSearch.getResourceName(), map.toNormalizedQueryString(myFhirContext), retval.size());
ourLog.debug("Results: {}", retval);
}
if (!retval.isEmpty()) {
// Adjust the high threshold to be the earliest resource in the batch we found
Long pidOfOldestResourceInBatch = retval.get(retval.size() - 1);
IBaseResource earliestResource = dao.readByPid(new ResourcePersistentId(pidOfOldestResourceInBatch));
myThresholdHighByUrlIndex.put(myUrlIndex, earliestResource.getMeta().getLastUpdated());
}
return retval;
}
@NotNull
private SearchParameterMap buildSearchParameterMap(ResourceSearch resourceSearch) {
SearchParameterMap map = resourceSearch.getSearchParameterMap();
map.setLastUpdated(new DateRangeParam().setUpperBoundInclusive(myThresholdHighByUrlIndex.get(myUrlIndex)));
map.setLoadSynchronousUpTo(myBatchSize);
map.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.DESC));
return map;
}
@NotNull
private SystemRequestDetails buildSystemRequestDetails() {
SystemRequestDetails retval = new SystemRequestDetails();
retval.setRequestPartitionId(myPartitionedUrls.get(myUrlIndex).getRequestPartitionId());
return retval;
}
@Override
public void open(ExecutionContext executionContext) throws ItemStreamException {
if (myBatchSize == null) {
myBatchSize = myDaoConfig.getExpungeBatchSize();
}
if (executionContext.containsKey(CURRENT_URL_INDEX)) {
myUrlIndex = new Long(executionContext.getLong(CURRENT_URL_INDEX)).intValue();
}
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
String key = highKey(index);
if (executionContext.containsKey(key)) {
myThresholdHighByUrlIndex.put(index, new Date(executionContext.getLong(key)));
} else {
myThresholdHighByUrlIndex.put(index, myStartTime);
}
}
}
private static String highKey(int theIndex) {
return CURRENT_THRESHOLD_HIGH + "." + theIndex;
}
@Override
public void update(ExecutionContext executionContext) throws ItemStreamException {
executionContext.putLong(CURRENT_URL_INDEX, myUrlIndex);
for (int index = 0; index < myPartitionedUrls.size(); ++index) {
Date date = myThresholdHighByUrlIndex.get(index);
if (date != null) {
executionContext.putLong(highKey(index), date.getTime());
}
}
}
@Override
public void close() throws ItemStreamException {
}
}

67
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/writer/SqlExecutorWriter.java Normal file
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@ -0,0 +1,67 @@
package ca.uhn.fhir.jpa.batch.writer;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.annotation.BeforeStep;
import org.springframework.batch.item.ItemWriter;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.util.List;
/**
* This Spring Batch writer accepts a list of SQL commands and executes them.
* The total number of entities updated or deleted is stored in the execution context
* with the key {@link #ENTITY_TOTAL_UPDATED_OR_DELETED}. The entire list is committed within a
* single transaction (provided by Spring Batch).
*/
public class SqlExecutorWriter implements ItemWriter<List<String>> {
private static final Logger ourLog = LoggerFactory.getLogger(SqlExecutorWriter.class);
public static final String ENTITY_TOTAL_UPDATED_OR_DELETED = "entity.total.updated-or-deleted";
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
private Long totalUpdated = 0L;
private StepExecution myStepExecution;
@BeforeStep
public void setStepExecution(StepExecution stepExecution) {
myStepExecution = stepExecution;
}
@Override
public void write(List<? extends List<String>> theSqlLists) throws Exception {
for (List<String> sqlList : theSqlLists) {
ourLog.info("Executing {} sql commands", sqlList.size());
for (String sql : sqlList) {
ourLog.trace("Executing sql " + sql);
totalUpdated += myEntityManager.createNativeQuery(sql).executeUpdate();
myStepExecution.getExecutionContext().putLong(ENTITY_TOTAL_UPDATED_OR_DELETED, totalUpdated);
}
}
ourLog.debug("{} records updated", totalUpdated);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobConfig.java
View File

@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.bulk.export.job;
*/
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.processors.GoldenResourceAnnotatingProcessor;
import ca.uhn.fhir.jpa.batch.processors.PidToIBaseResourceProcessor;
import ca.uhn.fhir.jpa.batch.processor.GoldenResourceAnnotatingProcessor;
import ca.uhn.fhir.jpa.batch.processor.PidToIBaseResourceProcessor;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -61,6 +61,7 @@ import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderUri;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictFinderService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.delete.DeleteExpungeJobSubmitterImpl;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
@ -132,9 +133,11 @@ import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.validation.JpaResourceLoader;
import ca.uhn.fhir.jpa.validation.ValidationSettings;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -528,6 +531,18 @@ public abstract class BaseConfig {
return new BulkDataExportProvider();
}
@Bean
@Lazy
public IDeleteExpungeJobSubmitter myDeleteExpungeJobSubmitter() {
return new DeleteExpungeJobSubmitterImpl();
}
@Bean
@Lazy
public DeleteExpungeProvider deleteExpungeProvider(FhirContext theFhirContext, IDeleteExpungeJobSubmitter theDeleteExpungeJobSubmitter) {
return new DeleteExpungeProvider(theFhirContext, theDeleteExpungeJobSubmitter);
}
@Bean
@Lazy
public IBulkDataImportSvc bulkDataImportSvc() {

109
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -58,7 +58,6 @@ import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@ -84,6 +83,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.MetaUtil;
@ -137,6 +137,7 @@ import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@ -185,6 +186,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiFhirDao.class);
private static final Map<FhirVersionEnum, FhirContext> ourRetrievalContexts = new HashMap<>();
private static final String PROCESSING_SUB_REQUEST = "BaseHapiFhirDao.processingSubRequest";
private static final String TRANSACTION_DETAILS_CACHE_KEY_EXISTING_SEARCH_PARAMS = BaseHapiFhirDao.class.getName() + "_EXISTING_SEARCH_PARAMS";
private static boolean ourValidationDisabledForUnitTest;
private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
@ -394,6 +396,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
@Autowired
public void setContext(FhirContext theContext) {
super.myFhirContext = theContext;
myContext = theContext;
}
@ -604,10 +607,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
boolean skipUpdatingTags = false;
if (myConfig.isMassIngestionMode() && theEntity.isHasTags()) {
skipUpdatingTags = true;
}
boolean skipUpdatingTags = myConfig.isMassIngestionMode() && theEntity.isHasTags();
if (!skipUpdatingTags) {
Set<ResourceTag> allDefs = new HashSet<>();
@ -668,6 +668,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// Don't check existing - We'll rely on the SHA256 hash only
} else if (theEntity.getVersion() == 1L && theEntity.getCurrentVersionEntity() == null) {
// No previous version if this is the first version
} else {
ResourceHistoryTable currentHistoryVersion = theEntity.getCurrentVersionEntity();
if (currentHistoryVersion == null) {
@ -791,27 +795,23 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
res.getMeta().setLastUpdated(theEntity.getUpdatedDate());
IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
Collection<? extends BaseTag> tags = theTagList;
if (theEntity.isHasTags()) {
for (BaseTag next : tags) {
switch (next.getTag().getTagType()) {
case PROFILE:
res.getMeta().addProfile(next.getTag().getCode());
break;
case SECURITY_LABEL:
IBaseCoding sec = res.getMeta().addSecurity();
sec.setSystem(next.getTag().getSystem());
sec.setCode(next.getTag().getCode());
sec.setDisplay(next.getTag().getDisplay());
break;
case TAG:
IBaseCoding tag = res.getMeta().addTag();
tag.setSystem(next.getTag().getSystem());
tag.setCode(next.getTag().getCode());
tag.setDisplay(next.getTag().getDisplay());
break;
}
for (BaseTag next : theTagList) {
switch (next.getTag().getTagType()) {
case PROFILE:
res.getMeta().addProfile(next.getTag().getCode());
break;
case SECURITY_LABEL:
IBaseCoding sec = res.getMeta().addSecurity();
sec.setSystem(next.getTag().getSystem());
sec.setCode(next.getTag().getCode());
sec.setDisplay(next.getTag().getDisplay());
break;
case TAG:
IBaseCoding tag = res.getMeta().addTag();
tag.setSystem(next.getTag().getSystem());
tag.setCode(next.getTag().getCode());
tag.setDisplay(next.getTag().getDisplay());
break;
}
}
@ -912,7 +912,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// 1. get resource, it's encoding and the tags if any
byte[] resourceBytes;
ResourceEncodingEnum resourceEncoding;
Collection<? extends BaseTag> myTagList;
Collection<? extends BaseTag> tagList = Collections.emptyList();
long version;
String provenanceSourceUri = null;
String provenanceRequestId = null;
@ -921,10 +921,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
ResourceHistoryTable history = (ResourceHistoryTable) theEntity;
resourceBytes = history.getResource();
resourceEncoding = history.getEncoding();
if (history.isHasTags()) {
myTagList = history.getTags();
if (getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.VERSIONED) {
if (history.isHasTags()) {
tagList = history.getTags();
}
} else {
myTagList = Collections.emptyList();
if (history.getResourceTable().isHasTags()) {
tagList = history.getResourceTable().getTags();
}
}
version = history.getVersion();
if (history.getProvenance() != null) {
@ -948,9 +952,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
resourceBytes = history.getResource();
resourceEncoding = history.getEncoding();
if (resource.isHasTags()) {
myTagList = resource.getTags();
tagList = resource.getTags();
} else {
myTagList = Collections.emptyList();
tagList = Collections.emptyList();
}
version = history.getVersion();
if (history.getProvenance() != null) {
@ -966,9 +970,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
provenanceRequestId = view.getProvenanceRequestId();
provenanceSourceUri = view.getProvenanceSourceUri();
if (theTagList == null)
myTagList = new HashSet<>();
tagList = new HashSet<>();
else
myTagList = theTagList;
tagList = theTagList;
} else {
// something wrong
return null;
@ -980,7 +984,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// 3. Use the appropriate custom type if one is specified in the context
Class<R> resourceType = theResourceType;
if (myContext.hasDefaultTypeForProfile()) {
for (BaseTag nextTag : myTagList) {
for (BaseTag nextTag : tagList) {
if (nextTag.getTag().getTagType() == TagTypeEnum.PROFILE) {
String profile = nextTag.getTag().getCode();
if (isNotBlank(profile)) {
@ -1030,10 +1034,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// 5. fill MetaData
if (retVal instanceof IResource) {
IResource res = (IResource) retVal;
retVal = populateResourceMetadataHapi(resourceType, theEntity, myTagList, theForHistoryOperation, res, version);
retVal = populateResourceMetadataHapi(resourceType, theEntity, tagList, theForHistoryOperation, res, version);
} else {
IAnyResource res = (IAnyResource) retVal;
retVal = populateResourceMetadataRi(resourceType, theEntity, myTagList, theForHistoryOperation, res, version);
retVal = populateResourceMetadataRi(resourceType, theEntity, tagList, theForHistoryOperation, res, version);
}
// 6. Handle source (provenance)
@ -1152,14 +1156,22 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
} else {
// CREATE or UPDATE
existingParams = new ResourceIndexedSearchParams(entity);
IdentityHashMap<ResourceTable, ResourceIndexedSearchParams> existingSearchParams = theTransactionDetails.getOrCreateUserData(TRANSACTION_DETAILS_CACHE_KEY_EXISTING_SEARCH_PARAMS, () -> new IdentityHashMap<>());
existingParams = existingSearchParams.get(entity);
if (existingParams == null) {
existingParams = new ResourceIndexedSearchParams(entity);
existingSearchParams.put(entity, existingParams);
}
entity.setDeleted(null);
if (thePerformIndexing) {
// TODO: is this IF statement always true? Try removing it
if (thePerformIndexing || ((ResourceTable) theEntity).getVersion() == 1) {
newParams = new ResourceIndexedSearchParams();
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest);
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
@ -1175,7 +1187,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// to match a resource and then update it in a way that it no longer
// matches. We could certainly make this configurable though in the
// future.
if (entity.getVersion() <= 1L && entity.getCreatedByMatchUrl() != null) {
if (entity.getVersion() <= 1L && entity.getCreatedByMatchUrl() != null && thePerformIndexing) {
verifyMatchUrlForConditionalCreate(theResource, entity.getCreatedByMatchUrl(), entity, newParams);
}
@ -1205,7 +1217,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
if (thePerformIndexing && changed != null && !changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange()) {
if (thePerformIndexing && changed != null && !changed.isChanged() && !theForceUpdate && myConfig.isSuppressUpdatesWithNoChange() && (entity.getVersion() > 1 || theUpdateVersion)) {
ourLog.debug("Resource {} has not changed", entity.getIdDt().toUnqualified().getValue());
if (theResource != null) {
updateResourceMetadata(entity, theResource);
@ -1245,7 +1257,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
* Create history entry
*/
if (theCreateNewHistoryEntry) {
final ResourceHistoryTable historyEntry = entity.toHistory();
boolean versionedTags = getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.VERSIONED;
final ResourceHistoryTable historyEntry = entity.toHistory(versionedTags);
historyEntry.setEncoding(changed.getEncoding());
historyEntry.setResource(changed.getResource());
@ -1575,6 +1588,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// nothing yet
}
@VisibleForTesting
public void setDaoConfigForUnitTest(DaoConfig theDaoConfig) {
myConfig = theDaoConfig;
}
private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
private final TagDefinition myTagDefinition;
@ -1726,11 +1744,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
ourDisableIncrementOnUpdateForUnitTest = theDisableIncrementOnUpdateForUnitTest;
}
@VisibleForTesting
public void setDaoConfigForUnitTest(DaoConfig theDaoConfig) {
myConfig = theDaoConfig;
}
/**
* Do not call this method outside of unit tests
*/

116
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -34,7 +34,7 @@ import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.expunge.DeleteExpungeService;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
@ -55,9 +55,9 @@ import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.dstu2.resource.ListResource;
@ -77,6 +77,7 @@ import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.HasParam;
@ -91,6 +92,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.ReflectionUtil;
@ -111,9 +113,10 @@ import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Required;
import org.springframework.data.domain.SliceImpl;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.annotation.Propagation;
@ -131,6 +134,7 @@ import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
@ -168,7 +172,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Autowired
private MatchUrlService myMatchUrlService;
@Autowired
private DeleteExpungeService myDeleteExpungeService;
private IDeleteExpungeJobSubmitter myDeleteExpungeJobSubmitter;
private IInstanceValidatorModule myInstanceValidator;
private String myResourceName;
@ -257,9 +261,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
entity.setResourceType(toResourceName(theResource));
entity.setPartitionId(theRequestPartitionId);
entity.setCreatedByMatchUrl(theIfNoneExist);
entity.setVersion(1);
if (isNotBlank(theIfNoneExist)) {
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theRequest);
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theTransactionDetails, theRequest);
if (match.size() > 1) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
throw new PreconditionFailedException(msg);
@ -338,9 +343,17 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED, hookParams);
// Perform actual DB update
ResourceTable updatedEntity = updateEntity(theRequest, theResource, entity, null, thePerformIndexing, thePerformIndexing, theTransactionDetails, false, thePerformIndexing);
ResourceTable updatedEntity = updateEntity(theRequest, theResource, entity, null, thePerformIndexing, false, theTransactionDetails, false, thePerformIndexing);
IIdType id = myFhirContext.getVersion().newIdType().setValue(updatedEntity.getIdDt().toUnqualifiedVersionless().getValue());
ResourcePersistentId persistentId = new ResourcePersistentId(updatedEntity.getResourceId());
theTransactionDetails.addResolvedResourceId(id, persistentId);
if (entity.getForcedId() != null) {
myIdHelperService.addResolvedPidToForcedId(persistentId, theRequestPartitionId, updatedEntity.getResourceType(), updatedEntity.getForcedId().getForcedId());
}
theResource.setId(entity.getIdDt());
if (serverAssignedId) {
switch (getConfig().getResourceClientIdStrategy()) {
case NOT_ALLOWED:
@ -357,16 +370,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
if (theIfNoneExist != null) {
// Pre-cache the match URL
myMatchResourceUrlService.matchUrlResolved(theIfNoneExist, new ResourcePersistentId(entity.getResourceId()));
}
/*
* If we aren't indexing (meaning we're probably executing a sub-operation within a transaction),
* we'll manually increase the version. This is important because we want the updated version number
* to be reflected in the resource shared with interceptors
*/
if (!thePerformIndexing) {
incrementId(theResource, entity, theResource.getIdElement());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theIfNoneExist, new ResourcePersistentId(entity.getResourceId()));
}
// Update the version/last updated in the resource so that interceptors get
@ -399,9 +403,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
if (updatedEntity.getForcedId() != null) {
forcedId = updatedEntity.getForcedId().getForcedId();
}
if (myIdHelperService != null) {
myIdHelperService.addResolvedPidToForcedId(new ResourcePersistentId(updatedEntity.getResourceId()), theRequestPartitionId, getResourceName(), forcedId);
}
myIdHelperService.addResolvedPidToForcedId(persistentId, theRequestPartitionId, getResourceName(), forcedId);
ourLog.debug(msg);
return outcome;
@ -443,7 +445,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
validateIdPresentForDelete(theId);
validateDeleteEnabled();
final ResourceTable entity = readEntityLatestVersion(theId, theRequestDetails);
final ResourceTable entity = readEntityLatestVersion(theId, theRequestDetails, theTransactionDetails);
if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) {
throw new ResourceVersionConflictException("Trying to delete " + theId + " but this is not the current version");
}
@ -517,12 +519,17 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
public DeleteMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequestDetails) {
public DeleteMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequest) {
validateDeleteEnabled();
ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(theUrl);
return myTransactionService.execute(theRequestDetails, tx -> {
if (resourceSearch.isDeleteExpunge()) {
return deleteExpunge(theUrl, theRequest);
}
return myTransactionService.execute(theRequest, tx -> {
DeleteConflictList deleteConflicts = new DeleteConflictList();
DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequestDetails);
DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequest);
DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
return outcome;
});
@ -541,8 +548,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Nonnull
private DeleteMethodOutcome doDeleteByUrl(String theUrl, DeleteConflictList deleteConflicts, RequestDetails theRequest) {
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceType);
SearchParameterMap paramMap = myMatchUrlService.translateMatchUrl(theUrl, resourceDef);
ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(theUrl);
SearchParameterMap paramMap = resourceSearch.getSearchParameterMap();
paramMap.setLoadSynchronous(true);
Set<ResourcePersistentId> resourceIds = myMatchResourceUrlService.search(paramMap, myResourceType, theRequest);
@ -553,19 +560,21 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
if (paramMap.isDeleteExpunge()) {
return deleteExpunge(theUrl, theRequest, resourceIds);
} else {
return deletePidList(theUrl, resourceIds, deleteConflicts, theRequest);
}
return deletePidList(theUrl, resourceIds, deleteConflicts, theRequest);
}
private DeleteMethodOutcome deleteExpunge(String theUrl, RequestDetails theTheRequest, Set<ResourcePersistentId> theResourceIds) {
if (!getConfig().isExpungeEnabled() || !getConfig().isDeleteExpungeEnabled()) {
throw new MethodNotAllowedException("_expunge is not enabled on this server");
private DeleteMethodOutcome deleteExpunge(String theUrl, RequestDetails theRequest) {
if (!getConfig().canDeleteExpunge()) {
throw new MethodNotAllowedException("_expunge is not enabled on this server: " + getConfig().cannotDeleteExpungeReason());
}
return myDeleteExpungeService.expungeByResourcePids(theUrl, myResourceName, new SliceImpl<>(ResourcePersistentId.toLongList(theResourceIds)), theTheRequest);
List<String> urlsToDeleteExpunge = Collections.singletonList(theUrl);
try {
JobExecution jobExecution = myDeleteExpungeJobSubmitter.submitJob(getConfig().getExpungeBatchSize(), theRequest, urlsToDeleteExpunge);
return new DeleteMethodOutcome(createInfoOperationOutcome("Delete job submitted with id " + jobExecution.getId()));
} catch (JobParametersInvalidException e) {
throw new InvalidRequestException("Invalid Delete Expunge Request: " + e.getMessage(), e);
}
}
@Nonnull
@ -913,7 +922,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
throw new ResourceNotFoundException(theResourceId);
}
ResourceTable latestVersion = readEntityLatestVersion(theResourceId, theRequest);
ResourceTable latestVersion = readEntityLatestVersion(theResourceId, theRequest, transactionDetails);
if (latestVersion.getVersion() != entity.getVersion()) {
doMetaAdd(theMetaAdd, entity, theRequest, transactionDetails);
} else {
@ -948,7 +957,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
throw new ResourceNotFoundException(theResourceId);
}
ResourceTable latestVersion = readEntityLatestVersion(theResourceId, theRequest);
ResourceTable latestVersion = readEntityLatestVersion(theResourceId, theRequest, transactionDetails);
if (latestVersion.getVersion() != entity.getVersion()) {
doMetaDelete(theMetaDel, entity, theRequest, transactionDetails);
} else {
@ -1007,14 +1016,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public DaoMethodOutcome patch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest) {
return myTransactionService.execute(theRequest, tx -> doPatch(theId, theConditionalUrl, thePatchType, thePatchBody, theFhirPatchBody, theRequest));
return myTransactionService.execute(theRequest, tx -> doPatch(theId, theConditionalUrl, thePatchType, thePatchBody, theFhirPatchBody, theRequest, new TransactionDetails()));
}
private DaoMethodOutcome doPatch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest) {
private DaoMethodOutcome doPatch(IIdType theId, String theConditionalUrl, PatchTypeEnum thePatchType, String thePatchBody, IBaseParameters theFhirPatchBody, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
ResourceTable entityToUpdate;
if (isNotBlank(theConditionalUrl)) {
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theConditionalUrl, myResourceType, theRequest);
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theConditionalUrl, myResourceType, theTransactionDetails, theRequest);
if (match.size() > 1) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "PATCH", theConditionalUrl, match.size());
throw new PreconditionFailedException(msg);
@ -1027,7 +1036,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
} else {
entityToUpdate = readEntityLatestVersion(theId, theRequest);
entityToUpdate = readEntityLatestVersion(theId, theRequest, theTransactionDetails);
if (theId.hasVersionIdPart()) {
if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) {
throw new ResourceVersionConflictException("Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch");
@ -1064,7 +1073,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
public void start() {
assert getConfig() != null;
ourLog.debug("Starting resource DAO for type: {}", getResourceName());
myInstanceValidator = getApplicationContext().getBean(IInstanceValidatorModule.class);
myTxTemplate = new TransactionTemplate(myPlatformTransactionManager);
@ -1252,15 +1261,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Nonnull
protected ResourceTable readEntityLatestVersion(IIdType theId, RequestDetails theRequestDetails) {
protected ResourceTable readEntityLatestVersion(IIdType theId, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequest(theRequestDetails, getResourceName());
return readEntityLatestVersion(theId, requestPartitionId);
return readEntityLatestVersion(theId, requestPartitionId, theTransactionDetails);
}
@Nonnull
private ResourceTable readEntityLatestVersion(IIdType theId, @Nullable RequestPartitionId theRequestPartitionId) {
private ResourceTable readEntityLatestVersion(IIdType theId, @Nullable RequestPartitionId theRequestPartitionId, TransactionDetails theTransactionDetails) {
validateResourceTypeAndThrowInvalidRequestException(theId);
if (theTransactionDetails.isResolvedResourceIdEmpty(theId.toUnqualifiedVersionless())) {
throw new ResourceNotFoundException(theId);
}
ResourcePersistentId persistentId = myIdHelperService.resolveResourcePersistentIds(theRequestPartitionId, getResourceName(), theId.getIdPart());
ResourceTable entity = myEntityManager.find(ResourceTable.class, persistentId.getId());
if (entity == null) {
@ -1569,7 +1582,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
IIdType resourceId;
if (isNotBlank(theMatchUrl)) {
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theRequest);
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest);
if (match.size() > 1) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size());
throw new PreconditionFailedException(msg);
@ -1582,7 +1595,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
// Pre-cache the match URL
if (outcome.getPersistentId() != null) {
myMatchResourceUrlService.matchUrlResolved(theMatchUrl, outcome.getPersistentId());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, outcome.getPersistentId());
}
return outcome;
@ -1610,7 +1623,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
if (!create) {
try {
entity = readEntityLatestVersion(resourceId, requestPartitionId);
entity = readEntityLatestVersion(resourceId, requestPartitionId, theTransactionDetails);
} catch (ResourceNotFoundException e) {
create = true;
}
@ -1692,6 +1705,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
@Transactional(propagation = Propagation.SUPPORTS)
public MethodOutcome validate(T theResource, IIdType theId, String theRawResource, EncodingEnum theEncoding, ValidationModeEnum theMode, String theProfile, RequestDetails theRequest) {
TransactionDetails transactionDetails = new TransactionDetails();
if (theRequest != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequest, theResource, null, theId);
notifyInterceptors(RestOperationTypeEnum.VALIDATE, requestDetails);
@ -1701,7 +1716,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
if (theId == null || theId.hasIdPart() == false) {
throw new InvalidRequestException("No ID supplied. ID is required when validating with mode=DELETE");
}
final ResourceTable entity = readEntityLatestVersion(theId, theRequest);
final ResourceTable entity = readEntityLatestVersion(theId, theRequest, transactionDetails);
// Validate that there are no resources pointing to the candidate that
// would prevent deletion
@ -1799,6 +1814,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
@VisibleForTesting
public void setIdHelperSvcForUnitTest(IdHelperService theIdHelperService) {
myIdHelperService = theIdHelperService;
}
private static class IdChecker implements IValidatorModule {
private final ValidationModeEnum myMode;

36
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -145,6 +145,20 @@ public abstract class BaseTransactionProcessor {
@Autowired
private InMemoryResourceMatcher myInMemoryResourceMatcher;
@VisibleForTesting
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
}
public ITransactionProcessorVersionAdapter getVersionAdapter() {
return myVersionAdapter;
}
@VisibleForTesting
public void setVersionAdapter(ITransactionProcessorVersionAdapter theVersionAdapter) {
myVersionAdapter = theVersionAdapter;
}
@PostConstruct
public void start() {
ourLog.trace("Starting transaction processor");
@ -287,11 +301,6 @@ public abstract class BaseTransactionProcessor {
}
}
@VisibleForTesting
public void setVersionAdapter(ITransactionProcessorVersionAdapter theVersionAdapter) {
myVersionAdapter = theVersionAdapter;
}
@VisibleForTesting
public void setTxManager(PlatformTransactionManager theTxManager) {
myTxManager = theTxManager;
@ -582,8 +591,8 @@ public abstract class BaseTransactionProcessor {
myModelConfig = theModelConfig;
}
private Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
theTransactionDetails.beginAcceptingDeferredInterceptorBroadcasts(
Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED,
@ -1067,7 +1076,7 @@ public abstract class BaseTransactionProcessor {
if (!nextId.hasIdPart()) {
if (resourceReference.getResource() != null) {
IIdType targetId = resourceReference.getResource().getIdElement();
if (targetId.getValue() == null) {
if (targetId.getValue() == null || targetId.getValue().startsWith("#")) {
// This means it's a contained resource
continue;
} else if (theIdSubstitutions.containsValue(targetId)) {
@ -1136,10 +1145,7 @@ public abstract class BaseTransactionProcessor {
IBasePersistedResource updateOutcome = null;
if (updatedEntities.contains(nextOutcome.getEntity())) {
boolean forceUpdateVersion = false;
if (!theReferencesToAutoVersion.isEmpty()) {
forceUpdateVersion = true;
}
boolean forceUpdateVersion = !theReferencesToAutoVersion.isEmpty();
updateOutcome = jpaDao.updateInternal(theRequest, nextResource, true, forceUpdateVersion, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource(), theTransactionDetails);
} else if (!nonUpdatedEntities.contains(nextOutcome.getId())) {
@ -1258,7 +1264,6 @@ public abstract class BaseTransactionProcessor {
return dao;
}
private String toResourceName(Class<? extends IBaseResource> theResourceType) {
return myContext.getResourceType(theResourceType);
}
@ -1318,11 +1323,6 @@ public abstract class BaseTransactionProcessor {
return null;
}
@VisibleForTesting
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
}
public interface ITransactionProcessorVersionAdapter<BUNDLE extends IBaseBundle, BUNDLEENTRY extends IBase> {
void setResponseStatus(BUNDLEENTRY theBundleEntry, String theStatus);

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
View File

@ -25,9 +25,9 @@ import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.model.dstu2.resource.Subscription;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
@ -51,8 +51,8 @@ public class FhirResourceDaoSubscriptionDstu2 extends BaseHapiFhirResourceDao<Su
}
@Override
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest);
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest, theTransactionDetails);
SubscriptionTable table = mySubscriptionTableDao.findOneByResourcePid(entity.getId());
if (table == null) {
return null;

65
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/MatchResourceUrlService.java
View File

@ -31,19 +31,21 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nullable;
import java.util.Collections;
import java.util.Set;
@ -65,31 +67,63 @@ public class MatchResourceUrlService {
/**
* Note that this will only return a maximum of 2 results!!
*/
public <R extends IBaseResource> Set<ResourcePersistentId> processMatchUrl(String theMatchUrl, Class<R> theResourceType, RequestDetails theRequest) {
if (myDaoConfig.getMatchUrlCache()) {
ResourcePersistentId existing = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl);
if (existing != null) {
return Collections.singleton(existing);
public <R extends IBaseResource> Set<ResourcePersistentId> processMatchUrl(String theMatchUrl, Class<R> theResourceType, TransactionDetails theTransactionDetails, RequestDetails theRequest) {
String resourceType = myContext.getResourceType(theResourceType);
String matchUrl = massageForStorage(resourceType, theMatchUrl);
ResourcePersistentId resolvedInTransaction = theTransactionDetails.getResolvedMatchUrls().get(matchUrl);
if (resolvedInTransaction != null) {
if (resolvedInTransaction == TransactionDetails.NOT_FOUND) {
return Collections.emptySet();
} else {
return Collections.singleton(resolvedInTransaction);
}
}
ResourcePersistentId resolvedInCache = processMatchUrlUsingCacheOnly(resourceType, matchUrl);
if (resolvedInCache != null) {
return Collections.singleton(resolvedInCache);
}
RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(theResourceType);
SearchParameterMap paramMap = myMatchUrlService.translateMatchUrl(theMatchUrl, resourceDef);
SearchParameterMap paramMap = myMatchUrlService.translateMatchUrl(matchUrl, resourceDef);
if (paramMap.isEmpty() && paramMap.getLastUpdated() == null) {
throw new InvalidRequestException("Invalid match URL[" + theMatchUrl + "] - URL has no search parameters");
throw new InvalidRequestException("Invalid match URL[" + matchUrl + "] - URL has no search parameters");
}
paramMap.setLoadSynchronousUpTo(2);
Set<ResourcePersistentId> retVal = search(paramMap, theResourceType, theRequest);
if (myDaoConfig.getMatchUrlCache() && retVal.size() == 1) {
if (myDaoConfig.isMatchUrlCacheEnabled() && retVal.size() == 1) {
ResourcePersistentId pid = retVal.iterator().next();
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl, pid);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, matchUrl, pid);
}
return retVal;
}
private String massageForStorage(String theResourceType, String theMatchUrl) {
Validate.notBlank(theMatchUrl, "theMatchUrl must not be null or blank");
int questionMarkIdx = theMatchUrl.indexOf("?");
if (questionMarkIdx > 0) {
return theMatchUrl;
}
if (questionMarkIdx == 0) {
return theResourceType + theMatchUrl;
}
return theResourceType + "?" + theMatchUrl;
}
@Nullable
public ResourcePersistentId processMatchUrlUsingCacheOnly(String theResourceType, String theMatchUrl) {
ResourcePersistentId existing = null;
if (myDaoConfig.getMatchUrlCache()) {
String matchUrl = massageForStorage(theResourceType, theMatchUrl);
existing = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.MATCH_URL, matchUrl);
}
return existing;
}
public <R extends IBaseResource> Set<ResourcePersistentId> search(SearchParameterMap theParamMap, Class<R> theResourceType, RequestDetails theRequest) {
StopWatch sw = new StopWatch();
IFhirResourceDao<R> dao = myDaoRegistry.getResourceDao(theResourceType);
@ -102,7 +136,7 @@ public class MatchResourceUrlService {
// Interceptor broadcast: JPA_PERFTRACE_INFO
if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequest)) {
StorageProcessingMessage message = new StorageProcessingMessage();
message.setMessage("Processed conditional resource URL with " + retVal.size() + " result(s) in " + sw.toString());
message.setMessage("Processed conditional resource URL with " + retVal.size() + " result(s) in " + sw);
HookParams params = new HookParams()
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
@ -113,11 +147,14 @@ public class MatchResourceUrlService {
}
public void matchUrlResolved(String theMatchUrl, ResourcePersistentId theResourcePersistentId) {
public void matchUrlResolved(TransactionDetails theTransactionDetails, String theResourceType, String theMatchUrl, ResourcePersistentId theResourcePersistentId) {
Validate.notBlank(theMatchUrl);
Validate.notNull(theResourcePersistentId);
if (myDaoConfig.getMatchUrlCache()) {
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, theMatchUrl, theResourcePersistentId);
String matchUrl = massageForStorage(theResourceType, theMatchUrl);
theTransactionDetails.addResolvedMatchUrl(matchUrl, theResourcePersistentId);
if (myDaoConfig.isMatchUrlCacheEnabled()) {
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, matchUrl, theResourcePersistentId);
}
}
}

295
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View File

@ -20,12 +20,31 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -35,17 +54,48 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.PersistenceException;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.dao.index.IdHelperService.EMPTY_PREDICATE_ARRAY;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class TransactionProcessor extends BaseTransactionProcessor {
public static final Pattern SINGLE_PARAMETER_MATCH_URL_PATTERN = Pattern.compile("^[^?]+[?][a-z0-9-]+=[^&,]+$");
private static final Logger ourLog = LoggerFactory.getLogger(TransactionProcessor.class);
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
@Autowired(required = false)
private HapiFhirHibernateJpaDialect myHapiFhirHibernateJpaDialect;
@Autowired
private IdHelperService myIdHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private FhirContext myFhirContext;
@Autowired
private MatchResourceUrlService myMatchResourceUrlService;
@Autowired
private MatchUrlService myMatchUrlService;
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionSvc;
public void setEntityManagerForUnitTest(EntityManager theEntityManager) {
myEntityManager = theEntityManager;
@ -58,6 +108,225 @@ public class TransactionProcessor extends BaseTransactionProcessor {
Validate.notNull(myEntityManager);
}
@VisibleForTesting
public void setFhirContextForUnitTest(FhirContext theFhirContext) {
myFhirContext = theFhirContext;
}
@Override
protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
ITransactionProcessorVersionAdapter versionAdapter = getVersionAdapter();
RequestPartitionId requestPartitionId = null;
if (!myPartitionSettings.isPartitioningEnabled()) {
requestPartitionId = RequestPartitionId.allPartitions();
} else {
// If all entries in the transaction point to the exact same partition, we'll try and do a pre-fetch
Set<RequestPartitionId> requestPartitionIdsForAllEntries = new HashSet<>();
for (IBase nextEntry : theEntries) {
IBaseResource resource = versionAdapter.getResource(nextEntry);
if (resource != null) {
RequestPartitionId requestPartition = myRequestPartitionSvc.determineReadPartitionForRequest(theRequest, myFhirContext.getResourceType(resource));
requestPartitionIdsForAllEntries.add(requestPartition);
}
}
if (requestPartitionIdsForAllEntries.size() == 1) {
requestPartitionId = requestPartitionIdsForAllEntries.iterator().next();
}
}
if (requestPartitionId != null) {
Set<String> foundIds = new HashSet<>();
List<Long> idsToPreFetch = new ArrayList<>();
/*
* Pre-Fetch any resources that are referred to normally by ID, e.g.
* regular FHIR updates within the transaction.
*/
List<IIdType> idsToPreResolve = new ArrayList<>();
for (IBase nextEntry : theEntries) {
IBaseResource resource = versionAdapter.getResource(nextEntry);
if (resource != null) {
String fullUrl = versionAdapter.getFullUrl(nextEntry);
boolean isPlaceholder = defaultString(fullUrl).startsWith("urn:");
if (!isPlaceholder) {
if (resource.getIdElement().hasIdPart() && resource.getIdElement().hasResourceType()) {
idsToPreResolve.add(resource.getIdElement());
}
}
}
}
List<ResourcePersistentId> outcome = myIdHelperService.resolveResourcePersistentIdsWithCache(requestPartitionId, idsToPreResolve);
for (ResourcePersistentId next : outcome) {
foundIds.add(next.getAssociatedResourceId().toUnqualifiedVersionless().getValue());
theTransactionDetails.addResolvedResourceId(next.getAssociatedResourceId(), next);
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY || !next.getAssociatedResourceId().isIdPartValidLong()) {
idsToPreFetch.add(next.getIdAsLong());
}
}
for (IIdType next : idsToPreResolve) {
if (!foundIds.contains(next.toUnqualifiedVersionless().getValue())) {
theTransactionDetails.addResolvedResourceId(next.toUnqualifiedVersionless(), null);
}
}
/*
* Pre-resolve any conditional URLs we can
*/
List<MatchUrlToResolve> searchParameterMapsToResolve = new ArrayList<>();
for (IBase nextEntry : theEntries) {
IBaseResource resource = versionAdapter.getResource(nextEntry);
if (resource != null) {
String verb = versionAdapter.getEntryRequestVerb(myFhirContext, nextEntry);
String requestUrl = versionAdapter.getEntryRequestUrl(nextEntry);
String requestIfNoneExist = versionAdapter.getEntryIfNoneExist(nextEntry);
String resourceType = myFhirContext.getResourceType(resource);
if ("PUT".equals(verb) && requestUrl != null && requestUrl.contains("?")) {
ResourcePersistentId cachedId = myMatchResourceUrlService.processMatchUrlUsingCacheOnly(resourceType, requestUrl);
if (cachedId != null) {
idsToPreFetch.add(cachedId.getIdAsLong());
} else if (SINGLE_PARAMETER_MATCH_URL_PATTERN.matcher(requestUrl).matches()) {
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(resource);
SearchParameterMap matchUrlSearchMap = myMatchUrlService.translateMatchUrl(requestUrl, resourceDefinition);
searchParameterMapsToResolve.add(new MatchUrlToResolve(requestUrl, matchUrlSearchMap, resourceDefinition));
}
} else if ("POST".equals(verb) && requestIfNoneExist != null && requestIfNoneExist.contains("?")) {
ResourcePersistentId cachedId = myMatchResourceUrlService.processMatchUrlUsingCacheOnly(resourceType, requestIfNoneExist);
if (cachedId != null) {
idsToPreFetch.add(cachedId.getIdAsLong());
} else if (SINGLE_PARAMETER_MATCH_URL_PATTERN.matcher(requestIfNoneExist).matches()) {
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(resource);
SearchParameterMap matchUrlSearchMap = myMatchUrlService.translateMatchUrl(requestIfNoneExist, resourceDefinition);
searchParameterMapsToResolve.add(new MatchUrlToResolve(requestIfNoneExist, matchUrlSearchMap, resourceDefinition));
}
}
}
}
if (searchParameterMapsToResolve.size() > 0) {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceIndexedSearchParamToken> cq = cb.createQuery(ResourceIndexedSearchParamToken.class);
Root<ResourceIndexedSearchParamToken> from = cq.from(ResourceIndexedSearchParamToken.class);
List<Predicate> orPredicates = new ArrayList<>();
for (MatchUrlToResolve next : searchParameterMapsToResolve) {
Collection<List<List<IQueryParameterType>>> values = next.myMatchUrlSearchMap.values();
if (values.size() == 1) {
List<List<IQueryParameterType>> andList = values.iterator().next();
IQueryParameterType param = andList.get(0).get(0);
if (param instanceof TokenParam) {
TokenParam tokenParam = (TokenParam) param;
Predicate hashPredicate = null;
if (isNotBlank(tokenParam.getValue()) && isNotBlank(tokenParam.getSystem())) {
next.myHashSystemAndValue = ResourceIndexedSearchParamToken.calculateHashSystemAndValue(myPartitionSettings, requestPartitionId, next.myResourceDefinition.getName(), next.myMatchUrlSearchMap.keySet().iterator().next(), tokenParam.getSystem(), tokenParam.getValue());
hashPredicate = cb.equal(from.get("myHashSystemAndValue").as(Long.class), next.myHashSystemAndValue);
} else if (isNotBlank(tokenParam.getValue())) {
next.myHashValue = ResourceIndexedSearchParamToken.calculateHashValue(myPartitionSettings, requestPartitionId, next.myResourceDefinition.getName(), next.myMatchUrlSearchMap.keySet().iterator().next(), tokenParam.getValue());
hashPredicate = cb.equal(from.get("myHashValue").as(Long.class), next.myHashValue);
}
if (hashPredicate != null) {
if (myPartitionSettings.isPartitioningEnabled() && !myPartitionSettings.isIncludePartitionInSearchHashes()) {
if (requestPartitionId.isDefaultPartition()) {
Predicate partitionIdCriteria = cb.isNull(from.get("myPartitionIdValue").as(Integer.class));
hashPredicate = cb.and(hashPredicate, partitionIdCriteria);
} else if (!requestPartitionId.isAllPartitions()) {
Predicate partitionIdCriteria = from.get("myPartitionIdValue").as(Integer.class).in(requestPartitionId.getPartitionIds());
hashPredicate = cb.and(hashPredicate, partitionIdCriteria);
}
}
orPredicates.add(hashPredicate);
}
}
}
}
if (orPredicates.size() > 1) {
cq.where(cb.or(orPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
TypedQuery<ResourceIndexedSearchParamToken> query = myEntityManager.createQuery(cq);
List<ResourceIndexedSearchParamToken> results = query.getResultList();
for (ResourceIndexedSearchParamToken nextResult : results) {
for (MatchUrlToResolve nextSearchParameterMap : searchParameterMapsToResolve) {
if (nextSearchParameterMap.myHashSystemAndValue != null && nextSearchParameterMap.myHashSystemAndValue.equals(nextResult.getHashSystemAndValue())) {
idsToPreFetch.add(nextResult.getResourcePid());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
nextSearchParameterMap.myResolved = true;
}
if (nextSearchParameterMap.myHashValue != null && nextSearchParameterMap.myHashValue.equals(nextResult.getHashValue())) {
idsToPreFetch.add(nextResult.getResourcePid());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
nextSearchParameterMap.myResolved = true;
}
}
}
for (MatchUrlToResolve nextSearchParameterMap : searchParameterMapsToResolve) {
// No matches
if (!nextSearchParameterMap.myResolved) {
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, TransactionDetails.NOT_FOUND);
}
}
}
}
/*
* Pre-fetch the resources we're touching in this transaction in mass - this reduced the
* number of database round trips.
*
* The thresholds below are kind of arbitrary. It's not
* actually guaranteed that this pre-fetching will help (e.g. if a Bundle contains
* a bundle of NOP conditional creates for example, the pre-fetching is actually loading
* more data than would otherwise be loaded).
*
* However, for realistic average workloads, this should reduce the number of round trips.
*/
if (idsToPreFetch.size() > 2) {
List<ResourceTable> loadedResourceTableEntries = preFetchIndexes(idsToPreFetch, "forcedId", "myForcedId");
if (loadedResourceTableEntries.stream().filter(t -> t.isParamsStringPopulated()).count() > 1) {
preFetchIndexes(idsToPreFetch, "string", "myParamsString");
}
if (loadedResourceTableEntries.stream().filter(t -> t.isParamsTokenPopulated()).count() > 1) {
preFetchIndexes(idsToPreFetch, "token", "myParamsToken");
}
if (loadedResourceTableEntries.stream().filter(t -> t.isParamsDatePopulated()).count() > 1) {
preFetchIndexes(idsToPreFetch, "date", "myParamsDate");
}
if (loadedResourceTableEntries.stream().filter(t -> t.isParamsDatePopulated()).count() > 1) {
preFetchIndexes(idsToPreFetch, "quantity", "myParamsQuantity");
}
if (loadedResourceTableEntries.stream().filter(t -> t.isHasLinks()).count() > 1) {
preFetchIndexes(idsToPreFetch, "resourceLinks", "myResourceLinks");
}
}
}
return super.doTransactionWriteOperations(theRequest, theActionName, theTransactionDetails, theAllIds, theIdSubstitutions, theIdToPersistedOutcome, theResponse, theOriginalRequestOrder, theEntries, theTransactionStopWatch);
}
private List<ResourceTable> preFetchIndexes(List<Long> ids, String typeDesc, String fieldName) {
TypedQuery<ResourceTable> query = myEntityManager.createQuery("FROM ResourceTable r LEFT JOIN FETCH r." + fieldName + " WHERE r.myId IN ( :IDS )", ResourceTable.class);
query.setParameter("IDS", ids);
List<ResourceTable> indexFetchOutcome = query.getResultList();
ourLog.debug("Pre-fetched {} {}} indexes", indexFetchOutcome.size(), typeDesc);
return indexFetchOutcome;
}
@Override
protected void flushSession(Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome) {
@ -86,5 +355,29 @@ public class TransactionProcessor extends BaseTransactionProcessor {
}
}
@VisibleForTesting
public void setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings) {
myPartitionSettings = thePartitionSettings;
}
@VisibleForTesting
public void setIdHelperServiceForUnitTest(IdHelperService theIdHelperService) {
myIdHelperService = theIdHelperService;
}
private static class MatchUrlToResolve {
private final String myRequestUrl;
private final SearchParameterMap myMatchUrlSearchMap;
private final RuntimeResourceDefinition myResourceDefinition;
public boolean myResolved;
private Long myHashValue;
private Long myHashSystemAndValue;
public MatchUrlToResolve(String theRequestUrl, SearchParameterMap theMatchUrlSearchMap, RuntimeResourceDefinition theResourceDefinition) {
myRequestUrl = theRequestUrl;
myMatchUrlSearchMap = theMatchUrlSearchMap;
myResourceDefinition = theResourceDefinition;
}
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java
View File

@ -26,8 +26,8 @@ import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.dstu3.model.Subscription;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -48,8 +48,8 @@ public class FhirResourceDaoSubscriptionDstu3 extends BaseHapiFhirResourceDao<Su
}
@Override
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest);
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest, theTransactionDetails);
SubscriptionTable table = mySubscriptionTableDao.findOneByResourcePid(entity.getId());
if (table == null) {
return null;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeService.java
View File

@ -30,10 +30,10 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.StopWatch;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
@ -55,6 +55,10 @@ import java.util.concurrent.atomic.AtomicLong;
import java.util.stream.Collectors;
@Service
/**
* DeleteExpunge is now performed using the {@link ca.uhn.fhir.jpa.delete.DeleteExpungeJobSubmitterImpl} Spring Batch job.
*/
@Deprecated
public class DeleteExpungeService {
private static final Logger ourLog = LoggerFactory.getLogger(DeleteExpungeService.class);

123
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -50,11 +50,20 @@ import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
@ -62,7 +71,6 @@ import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
@ -86,6 +94,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class IdHelperService {
private static final String RESOURCE_PID = "RESOURCE_PID";
private static final Logger ourLog = LoggerFactory.getLogger(IdHelperService.class);
public static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[0];
@Autowired
protected IForcedIdDao myForcedIdDao;
@Autowired
@ -167,6 +176,9 @@ public class IdHelperService {
return RequestPartitionId.stringifyForKey(theRequestPartitionId) + "/" + theResourceType + "/" + theId;
}
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
/**
* Given a collection of resource IDs (resource type + id), resolves the internal persistent IDs.
* <p>
@ -181,71 +193,80 @@ public class IdHelperService {
return Collections.emptyList();
}
List<ResourcePersistentId> retVal = new ArrayList<>();
List<ResourcePersistentId> retVal = new ArrayList<>(theIds.size());
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) {
theIds
.stream()
.filter(IdHelperService::isValidPid)
.map(IIdType::getIdPartAsLong)
.map(ResourcePersistentId::new)
.forEach(retVal::add);
Set<IIdType> idsToCheck = new HashSet<>(theIds.size());
for (IIdType nextId : theIds) {
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) {
if (nextId.isIdPartValidLong()) {
retVal.add(new ResourcePersistentId(nextId.getIdPartAsLong()).setAssociatedResourceId(nextId));
continue;
}
}
String key = toForcedIdToPidKey(theRequestPartitionId, nextId.getResourceType(), nextId.getIdPart());
ResourcePersistentId cachedId = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key);
if (cachedId != null) {
retVal.add(cachedId);
continue;
}
idsToCheck.add(nextId);
}
ListMultimap<String, String> typeToIds = organizeIdsByResourceType(theIds);
if (idsToCheck.size() > 0) {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ForcedId> criteriaQuery = cb.createQuery(ForcedId.class);
Root<ForcedId> from = criteriaQuery.from(ForcedId.class);
for (Map.Entry<String, Collection<String>> nextEntry : typeToIds.asMap().entrySet()) {
String nextResourceType = nextEntry.getKey();
Collection<String> nextIds = nextEntry.getValue();
if (isBlank(nextResourceType)) {
List<Predicate> predicates = new ArrayList<>(idsToCheck.size());
for (IIdType next : idsToCheck) {
List<Long> views = myForcedIdDao.findByForcedId(nextIds);
views.forEach(t -> retVal.add(new ResourcePersistentId(t)));
List<Predicate> andPredicates = new ArrayList<>(3);
} else {
// String partitionIdStringForKey = RequestPartitionId.stringifyForKey(theRequestPartitionId);
for (Iterator<String> idIterator = nextIds.iterator(); idIterator.hasNext(); ) {
String nextId = idIterator.next();
String key = toForcedIdToPidKey(theRequestPartitionId, nextResourceType, nextId);
ResourcePersistentId nextCachedPid = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key);
if (nextCachedPid != null) {
idIterator.remove();
retVal.add(nextCachedPid);
}
if (isNotBlank(next.getResourceType())) {
Predicate typeCriteria = cb.equal(from.get("myResourceType").as(String.class), next.getResourceType());
andPredicates.add(typeCriteria);
}
if (nextIds.size() > 0) {
Predicate idCriteria = cb.equal(from.get("myForcedId").as(String.class), next.getIdPart());
andPredicates.add(idCriteria);
Collection<Object[]> views;
if (theRequestPartitionId.isAllPartitions()) {
views = myForcedIdDao.findByTypeAndForcedId(nextResourceType, nextIds);
} else {
if (theRequestPartitionId.isDefaultPartition()) {
views = myForcedIdDao.findByTypeAndForcedIdInPartitionNull(nextResourceType, nextIds);
} else if (theRequestPartitionId.hasDefaultPartitionId()) {
views = myForcedIdDao.findByTypeAndForcedIdInPartitionIdsOrNullPartition(nextResourceType, nextIds, theRequestPartitionId.getPartitionIds());
} else {
views = myForcedIdDao.findByTypeAndForcedIdInPartitionIds(nextResourceType, nextIds, theRequestPartitionId.getPartitionIds());
}
}
for (Object[] nextView : views) {
String forcedId = (String) nextView[0];
Long pid = (Long) nextView[1];
ResourcePersistentId persistentId = new ResourcePersistentId(pid);
retVal.add(persistentId);
String key = toForcedIdToPidKey(theRequestPartitionId, nextResourceType, forcedId);
myMemoryCacheService.put(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, persistentId);
}
if (theRequestPartitionId.isDefaultPartition()) {
Predicate partitionIdCriteria = cb.isNull(from.get("myPartitionIdValue").as(Integer.class));
andPredicates.add(partitionIdCriteria);
} else if (!theRequestPartitionId.isAllPartitions()) {
Predicate partitionIdCriteria = from.get("myPartitionIdValue").as(Integer.class).in(theRequestPartitionId.getPartitionIds());
andPredicates.add(partitionIdCriteria);
}
predicates.add(cb.and(andPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
}
criteriaQuery.where(cb.or(predicates.toArray(EMPTY_PREDICATE_ARRAY)));
TypedQuery<ForcedId> query = myEntityManager.createQuery(criteriaQuery);
List<ForcedId> results = query.getResultList();
for (ForcedId nextId : results) {
ResourcePersistentId persistentId = new ResourcePersistentId(nextId.getResourceId());
populateAssociatedResourceId(nextId.getResourceType(), nextId.getForcedId(), persistentId);
retVal.add(persistentId);
String key = toForcedIdToPidKey(theRequestPartitionId, nextId.getResourceType(), nextId.getForcedId());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, persistentId);
}
}
return retVal;
}
private void populateAssociatedResourceId(String nextResourceType, String forcedId, ResourcePersistentId persistentId) {
IIdType resourceId = myFhirCtx.getVersion().newIdType();
resourceId.setValue(nextResourceType + "/" + forcedId);
persistentId.setAssociatedResourceId(resourceId);
}
/**
* Given a persistent ID, returns the associated resource ID
*/
@ -501,6 +522,10 @@ public class IdHelperService {
*/
public void addResolvedPidToForcedId(ResourcePersistentId theResourcePersistentId, @Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, @Nullable String theForcedId) {
if (theForcedId != null) {
if (theResourcePersistentId.getAssociatedResourceId() == null) {
populateAssociatedResourceId(theResourceType, theForcedId, theResourcePersistentId);
}
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theResourcePersistentId.getIdAsLong(), Optional.of(theForcedId));
String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theForcedId);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theResourcePersistentId);

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
View File

@ -111,8 +111,8 @@ public class SearchParamWithInlineReferencesExtractor {
mySearchParamRegistry = theSearchParamRegistry;
}
public void populateFromResource(ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest) {
extractInlineReferences(theResource, theRequest);
public void populateFromResource(ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest, boolean theFailOnInvalidReference) {
extractInlineReferences(theResource, theTransactionDetails, theRequest);
RequestPartitionId partitionId;
if (myPartitionSettings.isPartitioningEnabled()) {
@ -121,7 +121,7 @@ public class SearchParamWithInlineReferencesExtractor {
partitionId = RequestPartitionId.allPartitions();
}
mySearchParamExtractorService.extractFromResource(partitionId, theRequest, theParams, theEntity, theResource, theTransactionDetails, true);
mySearchParamExtractorService.extractFromResource(partitionId, theRequest, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference);
Set<Map.Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
@ -245,7 +245,7 @@ public class SearchParamWithInlineReferencesExtractor {
* Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
* matching resource.
*/
public void extractInlineReferences(IBaseResource theResource, RequestDetails theRequest) {
public void extractInlineReferences(IBaseResource theResource, TransactionDetails theTransactionDetails, RequestDetails theRequest) {
if (!myDaoConfig.isAllowInlineMatchUrlReferences()) {
return;
}
@ -277,7 +277,7 @@ public class SearchParamWithInlineReferencesExtractor {
}
Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
//Attempt to find the target reference before creating a placeholder
Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest);
Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theTransactionDetails, theRequest);
ResourcePersistentId match;
if (matches.isEmpty()) {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSubscriptionR4.java
View File

@ -26,8 +26,8 @@ import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Subscription;
@ -48,8 +48,8 @@ public class FhirResourceDaoSubscriptionR4 extends BaseHapiFhirResourceDao<Subsc
}
@Override
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest);
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest, theTransactionDetails);
SubscriptionTable table = mySubscriptionTableDao.findOneByResourcePid(entity.getId());
if (table == null) {
return null;
@ -72,7 +72,7 @@ public class FhirResourceDaoSubscriptionR4 extends BaseHapiFhirResourceDao<Subsc
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (theDeletedTimestampOrNull != null) {
Long subscriptionId = getSubscriptionTablePidForSubscriptionResource(theEntity.getIdDt(), theRequest);
Long subscriptionId = getSubscriptionTablePidForSubscriptionResource(theEntity.getIdDt(), theRequest, theTransactionDetails);
if (subscriptionId != null) {
mySubscriptionTableDao.deleteAllForSubscription(retVal);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSubscriptionR5.java
View File

@ -26,8 +26,8 @@ import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.Subscription;
@ -48,8 +48,8 @@ public class FhirResourceDaoSubscriptionR5 extends BaseHapiFhirResourceDao<Subsc
}
@Override
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest);
public Long getSubscriptionTablePidForSubscriptionResource(IIdType theId, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
ResourceTable entity = readEntityLatestVersion(theId, theRequest, theTransactionDetails);
SubscriptionTable table = mySubscriptionTableDao.findOneByResourcePid(entity.getId());
if (table == null) {
return null;
@ -72,7 +72,7 @@ public class FhirResourceDaoSubscriptionR5 extends BaseHapiFhirResourceDao<Subsc
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (theDeletedTimestampOrNull != null) {
Long subscriptionId = getSubscriptionTablePidForSubscriptionResource(theEntity.getIdDt(), theRequest);
Long subscriptionId = getSubscriptionTablePidForSubscriptionResource(theEntity.getIdDt(), theRequest, theTransactionDetails);
if (subscriptionId != null) {
mySubscriptionTableDao.deleteAllForSubscription(retVal);
}

100
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteExpungeJobSubmitterImpl.java Normal file
View File

@ -0,0 +1,100 @@
package ca.uhn.fhir.jpa.delete;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.delete.job.DeleteExpungeJobConfig;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import javax.transaction.Transactional;
import java.util.ArrayList;
import java.util.List;
public class DeleteExpungeJobSubmitterImpl implements IDeleteExpungeJobSubmitter {
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
@Qualifier(BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME)
private Job myDeleteExpungeJob;
@Autowired
FhirContext myFhirContext;
@Autowired
MatchUrlService myMatchUrlService;
@Autowired
IRequestPartitionHelperSvc myRequestPartitionHelperSvc;
@Autowired
DaoConfig myDaoConfig;
@Autowired
IInterceptorBroadcaster myInterceptorBroadcaster;
@Override
@Transactional(Transactional.TxType.NEVER)
public JobExecution submitJob(Integer theBatchSize, RequestDetails theRequest, List<String> theUrlsToDeleteExpunge) throws JobParametersInvalidException {
List<RequestPartitionId> requestPartitionIds = requestPartitionIdsFromRequestAndUrls(theRequest, theUrlsToDeleteExpunge);
if (!myDaoConfig.canDeleteExpunge()) {
throw new ForbiddenOperationException("Delete Expunge not allowed: " + myDaoConfig.cannotDeleteExpungeReason());
}
for (String url : theUrlsToDeleteExpunge) {
HookParams params = new HookParams()
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(String.class, url);
CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PRE_DELETE_EXPUNGE, params);
}
JobParameters jobParameters = DeleteExpungeJobConfig.buildJobParameters(theBatchSize, theUrlsToDeleteExpunge, requestPartitionIds);
return myBatchJobSubmitter.runJob(myDeleteExpungeJob, jobParameters);
}
/**
* This method will throw an exception if the user is not allowed to add the requested resource type on the partition determined by the request
*/
private List<RequestPartitionId> requestPartitionIdsFromRequestAndUrls(RequestDetails theRequest, List<String> theUrlsToDeleteExpunge) {
List<RequestPartitionId> retval = new ArrayList<>();
for (String url : theUrlsToDeleteExpunge) {
ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(url);
RequestPartitionId requestPartitionId = myRequestPartitionHelperSvc.determineReadPartitionForRequest(theRequest, resourceSearch.getResourceName());
retval.add(requestPartitionId);
}
return retval;
}
}

139
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobConfig.java Normal file
View File

@ -0,0 +1,139 @@
package ca.uhn.fhir.jpa.delete.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.batch.listener.PidReaderCounterListener;
import ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader;
import ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter;
import ca.uhn.fhir.jpa.delete.model.RequestListJson;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobParameter;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersValidator;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.batch.core.listener.ExecutionContextPromotionListener;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import javax.annotation.Nonnull;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME;
/**
* Spring batch Job configuration file. Contains all necessary plumbing to run a
* Delete Expunge job.
*/
@Configuration
public class DeleteExpungeJobConfig {
public static final String DELETE_EXPUNGE_URL_LIST_STEP_NAME = "delete-expunge-url-list-step";
private static final int MINUTES_IN_FUTURE_TO_DELETE_FROM = 1;
@Autowired
private StepBuilderFactory myStepBuilderFactory;
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Bean(name = DELETE_EXPUNGE_JOB_NAME)
@Lazy
public Job deleteExpungeJob(FhirContext theFhirContext, MatchUrlService theMatchUrlService, DaoRegistry theDaoRegistry) throws Exception {
return myJobBuilderFactory.get(DELETE_EXPUNGE_JOB_NAME)
.validator(deleteExpungeJobParameterValidator(theFhirContext, theMatchUrlService, theDaoRegistry))
.start(deleteExpungeUrlListStep())
.build();
}
@Nonnull
public static JobParameters buildJobParameters(Integer theBatchSize, List<String> theUrlList, List<RequestPartitionId> theRequestPartitionIds) {
Map<String, JobParameter> map = new HashMap<>();
RequestListJson requestListJson = RequestListJson.fromUrlStringsAndRequestPartitionIds(theUrlList, theRequestPartitionIds);
map.put(ReverseCronologicalBatchResourcePidReader.JOB_PARAM_REQUEST_LIST, new JobParameter(requestListJson.toString()));
map.put(ReverseCronologicalBatchResourcePidReader.JOB_PARAM_START_TIME, new JobParameter(DateUtils.addMinutes(new Date(), MINUTES_IN_FUTURE_TO_DELETE_FROM)));
if (theBatchSize != null) {
map.put(ReverseCronologicalBatchResourcePidReader.JOB_PARAM_BATCH_SIZE, new JobParameter(theBatchSize.longValue()));
}
JobParameters parameters = new JobParameters(map);
return parameters;
}
@Bean
public Step deleteExpungeUrlListStep() {
return myStepBuilderFactory.get(DELETE_EXPUNGE_URL_LIST_STEP_NAME)
.<List<Long>, List<String>>chunk(1)
.reader(reverseCronologicalBatchResourcePidReader())
.processor(deleteExpungeProcessor())
.writer(sqlExecutorWriter())
.listener(pidCountRecorderListener())
.listener(promotionListener())
.build();
}
@Bean
@StepScope
public PidReaderCounterListener pidCountRecorderListener() {
return new PidReaderCounterListener();
}
@Bean
@StepScope
public ReverseCronologicalBatchResourcePidReader reverseCronologicalBatchResourcePidReader() {
return new ReverseCronologicalBatchResourcePidReader();
}
@Bean
@StepScope
public DeleteExpungeProcessor deleteExpungeProcessor() {
return new DeleteExpungeProcessor();
}
@Bean
@StepScope
public SqlExecutorWriter sqlExecutorWriter() {
return new SqlExecutorWriter();
}
@Bean
public JobParametersValidator deleteExpungeJobParameterValidator(FhirContext theFhirContext, MatchUrlService theMatchUrlService, DaoRegistry theDaoRegistry) {
return new DeleteExpungeJobParameterValidator(theMatchUrlService, theDaoRegistry);
}
@Bean
public ExecutionContextPromotionListener promotionListener() {
ExecutionContextPromotionListener listener = new ExecutionContextPromotionListener();
listener.setKeys(new String[]{SqlExecutorWriter.ENTITY_TOTAL_UPDATED_OR_DELETED, PidReaderCounterListener.RESOURCE_TOTAL_PROCESSED});
return listener;
}
}

67
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeJobParameterValidator.java Normal file
View File

@ -0,0 +1,67 @@
package ca.uhn.fhir.jpa.delete.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.delete.model.PartitionedUrl;
import ca.uhn.fhir.jpa.delete.model.RequestListJson;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.JobParametersValidator;
import static ca.uhn.fhir.jpa.batch.reader.ReverseCronologicalBatchResourcePidReader.JOB_PARAM_REQUEST_LIST;
/**
* This class will prevent a job from running any of the provided URLs are not valid on this server.
*/
public class DeleteExpungeJobParameterValidator implements JobParametersValidator {
private final MatchUrlService myMatchUrlService;
private final DaoRegistry myDaoRegistry;
public DeleteExpungeJobParameterValidator(MatchUrlService theMatchUrlService, DaoRegistry theDaoRegistry) {
myMatchUrlService = theMatchUrlService;
myDaoRegistry = theDaoRegistry;
}
@Override
public void validate(JobParameters theJobParameters) throws JobParametersInvalidException {
if (theJobParameters == null) {
throw new JobParametersInvalidException("This job requires Parameters: [urlList]");
}
RequestListJson requestListJson = RequestListJson.fromJson(theJobParameters.getString(JOB_PARAM_REQUEST_LIST));
for (PartitionedUrl partitionedUrl : requestListJson.getPartitionedUrls()) {
String url = partitionedUrl.getUrl();
try {
ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(url);
String resourceName = resourceSearch.getResourceName();
if (!myDaoRegistry.isResourceTypeSupported(resourceName)) {
throw new JobParametersInvalidException("The resource type " + resourceName + " is not supported on this server.");
}
} catch (UnsupportedOperationException e) {
throw new JobParametersInvalidException("Failed to parse " + ProviderConstants.OPERATION_DELETE_EXPUNGE + " " + JOB_PARAM_REQUEST_LIST + " item " + url + ": " + e.getMessage());
}
}
}
}

123
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeProcessor.java Normal file
View File

@ -0,0 +1,123 @@
package ca.uhn.fhir.jpa.delete.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.expunge.PartitionRunner;
import ca.uhn.fhir.jpa.dao.expunge.ResourceForeignKey;
import ca.uhn.fhir.jpa.dao.expunge.ResourceTableFKProvider;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Slice;
import org.springframework.data.domain.SliceImpl;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
/**
* Input: list of pids of resources to be deleted and expunged
* Output: list of sql statements to be executed
*/
public class DeleteExpungeProcessor implements ItemProcessor<List<Long>, List<String>> {
private static final Logger ourLog = LoggerFactory.getLogger(DeleteExpungeProcessor.class);
@Autowired
ResourceTableFKProvider myResourceTableFKProvider;
@Autowired
DaoConfig myDaoConfig;
@Autowired
IdHelperService myIdHelper;
@Autowired
IResourceLinkDao myResourceLinkDao;
@Autowired
PartitionRunner myPartitionRunner;
@Override
public List<String> process(List<Long> thePids) throws Exception {
validateOkToDeleteAndExpunge(new SliceImpl<>(thePids));
List<String> retval = new ArrayList<>();
String pidListString = thePids.toString().replace("[", "(").replace("]", ")");
List<ResourceForeignKey> resourceForeignKeys = myResourceTableFKProvider.getResourceForeignKeys();
for (ResourceForeignKey resourceForeignKey : resourceForeignKeys) {
retval.add(deleteRecordsByColumnSql(pidListString, resourceForeignKey));
}
// Lastly we need to delete records from the resource table all of these other tables link to:
ResourceForeignKey resourceTablePk = new ResourceForeignKey("HFJ_RESOURCE", "RES_ID");
retval.add(deleteRecordsByColumnSql(pidListString, resourceTablePk));
return retval;
}
public void validateOkToDeleteAndExpunge(Slice<Long> thePids) {
if (!myDaoConfig.isEnforceReferentialIntegrityOnDelete()) {
ourLog.info("Referential integrity on delete disabled. Skipping referential integrity check.");
return;
}
List<ResourceLink> conflictResourceLinks = Collections.synchronizedList(new ArrayList<>());
myPartitionRunner.runInPartitionedThreads(thePids, someTargetPids -> findResourceLinksWithTargetPidIn(thePids.getContent(), someTargetPids, conflictResourceLinks));
if (conflictResourceLinks.isEmpty()) {
return;
}
ResourceLink firstConflict = conflictResourceLinks.get(0);
//NB-GGG: We previously instantiated these ID values from firstConflict.getSourceResource().getIdDt(), but in a situation where we
//actually had to run delete conflict checks in multiple partitions, the executor service starts its own sessions on a per thread basis, and by the time
//we arrive here, those sessions are closed. So instead, we resolve them from PIDs, which are eagerly loaded.
String sourceResourceId = myIdHelper.resourceIdFromPidOrThrowException(firstConflict.getSourceResourcePid()).toVersionless().getValue();
String targetResourceId = myIdHelper.resourceIdFromPidOrThrowException(firstConflict.getTargetResourcePid()).toVersionless().getValue();
throw new InvalidRequestException("DELETE with _expunge=true failed. Unable to delete " +
targetResourceId + " because " + sourceResourceId + " refers to it via the path " + firstConflict.getSourcePath());
}
public void findResourceLinksWithTargetPidIn(List<Long> theAllTargetPids, List<Long> theSomeTargetPids, List<ResourceLink> theConflictResourceLinks) {
// We only need to find one conflict, so if we found one already in an earlier partition run, we can skip the rest of the searches
if (theConflictResourceLinks.isEmpty()) {
List<ResourceLink> conflictResourceLinks = myResourceLinkDao.findWithTargetPidIn(theSomeTargetPids).stream()
// Filter out resource links for which we are planning to delete the source.
// theAllTargetPids contains a list of all the pids we are planning to delete. So we only want
// to consider a link to be a conflict if the source of that link is not in theAllTargetPids.
.filter(link -> !theAllTargetPids.contains(link.getSourceResourcePid()))
.collect(Collectors.toList());
// We do this in two steps to avoid lock contention on this synchronized list
theConflictResourceLinks.addAll(conflictResourceLinks);
}
}
private String deleteRecordsByColumnSql(String thePidListString, ResourceForeignKey theResourceForeignKey) {
return "DELETE FROM " + theResourceForeignKey.table + " WHERE " + theResourceForeignKey.key + " IN " + thePidListString;
}
}

57
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/model/PartitionedUrl.java Normal file
View File

@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.delete.model;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
public class PartitionedUrl implements IModelJson {
@JsonProperty("url")
private String myUrl;
@JsonProperty("requestPartitionId")
private RequestPartitionId myRequestPartitionId;
public PartitionedUrl() {
}
public PartitionedUrl(String theUrl, RequestPartitionId theRequestPartitionId) {
myUrl = theUrl;
myRequestPartitionId = theRequestPartitionId;
}
public String getUrl() {
return myUrl;
}
public void setUrl(String theUrl) {
myUrl = theUrl;
}
public RequestPartitionId getRequestPartitionId() {
return myRequestPartitionId;
}
public void setRequestPartitionId(RequestPartitionId theRequestPartitionId) {
myRequestPartitionId = theRequestPartitionId;
}
}

79
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/model/RequestListJson.java Normal file
View File

@ -0,0 +1,79 @@
package ca.uhn.fhir.jpa.delete.model;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.model.api.IModelJson;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.util.ArrayList;
import java.util.List;
/**
* Serialize a list of URLs and partition ids so Spring Batch can store it as a String
*/
public class RequestListJson implements IModelJson {
static final ObjectMapper ourObjectMapper = new ObjectMapper();
@JsonProperty("partitionedUrls")
private List<PartitionedUrl> myPartitionedUrls;
public static RequestListJson fromUrlStringsAndRequestPartitionIds(List<String> theUrls, List<RequestPartitionId> theRequestPartitionIds) {
assert theUrls.size() == theRequestPartitionIds.size();
RequestListJson retval = new RequestListJson();
List<PartitionedUrl> partitionedUrls = new ArrayList<>();
for (int i = 0; i < theUrls.size(); ++i) {
partitionedUrls.add(new PartitionedUrl(theUrls.get(i), theRequestPartitionIds.get(i)));
}
retval.setPartitionedUrls(partitionedUrls);
return retval;
}
public static RequestListJson fromJson(String theJson) {
try {
return ourObjectMapper.readValue(theJson, RequestListJson.class);
} catch (JsonProcessingException e) {
throw new InternalErrorException("Failed to decode " + RequestListJson.class);
}
}
@Override
public String toString() {
try {
return ourObjectMapper.writeValueAsString(this);
} catch (JsonProcessingException e) {
throw new InvalidRequestException("Failed to encode " + RequestListJson.class, e);
}
}
public List<PartitionedUrl> getPartitionedUrls() {
return myPartitionedUrls;
}
public void setPartitionedUrls(List<PartitionedUrl> thePartitionedUrls) {
myPartitionedUrls = thePartitionedUrls;
}
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptPropertyBinder.java
View File

@ -26,6 +26,8 @@ import org.hibernate.search.mapper.pojo.bridge.PropertyBridge;
import org.hibernate.search.mapper.pojo.bridge.binding.PropertyBindingContext;
import org.hibernate.search.mapper.pojo.bridge.mapping.programmatic.PropertyBinder;
import org.hibernate.search.mapper.pojo.bridge.runtime.PropertyBridgeWriteContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Collection;
@ -38,6 +40,7 @@ public class TermConceptPropertyBinder implements PropertyBinder {
public static final String CONCEPT_FIELD_PROPERTY_PREFIX = "PROP";
private static final Logger ourLog = LoggerFactory.getLogger(TermConceptPropertyBinder.class);
@Override
public void bind(PropertyBindingContext thePropertyBindingContext) {
@ -65,10 +68,10 @@ public class TermConceptPropertyBinder implements PropertyBinder {
if (properties != null) {
for (TermConceptProperty next : properties) {
theDocument.addValue(CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey(), next.getValue());
System.out.println("Adding Prop: " + CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey() + " -- " + next.getValue());
ourLog.trace("Adding Prop: {}{} -- {}", CONCEPT_FIELD_PROPERTY_PREFIX, next.getKey(), next.getValue());
if (next.getType() == TermConceptPropertyTypeEnum.CODING && isNotBlank(next.getDisplay())) {
theDocument.addValue(CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey(), next.getDisplay());
System.out.println("Adding multivalue Prop: " + CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey() + " -- " + next.getDisplay());
theDocument.addValue(CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey(), next.getDisplay());
ourLog.trace("Adding multivalue Prop: {}{} -- {}", CONCEPT_FIELD_PROPERTY_PREFIX, next.getKey(), next.getDisplay());
}
}
}

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.partition;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -109,7 +110,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
}
if (theRequest instanceof SystemRequestDetails) {
requestPartitionId = getSystemRequestPartitionId(theRequest, nonPartitionableResource);
requestPartitionId = getSystemRequestPartitionId((SystemRequestDetails) theRequest, nonPartitionableResource);
// Interceptor call: STORAGE_PARTITION_IDENTIFY_READ
} else if (hasHooks(Pointcut.STORAGE_PARTITION_IDENTIFY_READ, myInterceptorBroadcaster, theRequest)) {
HookParams params = new HookParams()
@ -122,22 +123,18 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
validateRequestPartitionNotNull(requestPartitionId, Pointcut.STORAGE_PARTITION_IDENTIFY_READ);
return validateNormalizeAndNotifyHooksForRead(requestPartitionId, theRequest);
return validateNormalizeAndNotifyHooksForRead(requestPartitionId, theRequest, theResourceType);
}
return RequestPartitionId.allPartitions();
}
/**
*
* For system requests, read partition from tenant ID if present, otherwise set to DEFAULT. If the resource they are attempting to partition
* is non-partitionable scream in the logs and set the partition to DEFAULT.
*
* @param theRequest
* @param theNonPartitionableResource
* @return
*/
private RequestPartitionId getSystemRequestPartitionId(RequestDetails theRequest, boolean theNonPartitionableResource) {
private RequestPartitionId getSystemRequestPartitionId(SystemRequestDetails theRequest, boolean theNonPartitionableResource) {
RequestPartitionId requestPartitionId;
requestPartitionId = getSystemRequestPartitionId(theRequest);
if (theNonPartitionableResource && !requestPartitionId.isDefaultPartition()) {
@ -148,7 +145,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
/**
* Determine the partition for a System Call (defined by the fact that the request is of type SystemRequestDetails)
*
* <p>
* 1. If the tenant ID is set to the constant for all partitions, return all partitions
* 2. If there is a tenant ID set in the request, use it.
* 3. Otherwise, return the Default Partition.
@ -157,7 +154,10 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
* @return the {@link RequestPartitionId} to be used for this request.
*/
@Nonnull
private RequestPartitionId getSystemRequestPartitionId(@Nonnull RequestDetails theRequest) {
private RequestPartitionId getSystemRequestPartitionId(@Nonnull SystemRequestDetails theRequest) {
if (theRequest.getRequestPartitionId() != null) {
return theRequest.getRequestPartitionId();
}
if (theRequest.getTenantId() != null) {
if (theRequest.getTenantId().equals(ALL_PARTITIONS_NAME)) {
return RequestPartitionId.allPartitions();
@ -186,7 +186,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
}
if (theRequest instanceof SystemRequestDetails) {
requestPartitionId = getSystemRequestPartitionId(theRequest, nonPartitionableResource);
requestPartitionId = getSystemRequestPartitionId((SystemRequestDetails) theRequest, nonPartitionableResource);
} else {
//This is an external Request (e.g. ServletRequestDetails) so we want to figure out the partition via interceptor.
HookParams params = new HookParams()// Interceptor call: STORAGE_PARTITION_IDENTIFY_CREATE
@ -204,7 +204,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
String resourceName = myFhirContext.getResourceType(theResource);
validateSinglePartitionForCreate(requestPartitionId, resourceName, Pointcut.STORAGE_PARTITION_IDENTIFY_CREATE);
return validateNormalizeAndNotifyHooksForRead(requestPartitionId, theRequest);
return validateNormalizeAndNotifyHooksForRead(requestPartitionId, theRequest, theResourceType);
}
return RequestPartitionId.allPartitions();
@ -218,7 +218,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
* If the partition has both, they are validated to ensure that they correspond.
*/
@Nonnull
private RequestPartitionId validateNormalizeAndNotifyHooksForRead(@Nonnull RequestPartitionId theRequestPartitionId, RequestDetails theRequest) {
private RequestPartitionId validateNormalizeAndNotifyHooksForRead(@Nonnull RequestPartitionId theRequestPartitionId, RequestDetails theRequest, String theResourceType) {
RequestPartitionId retVal = theRequestPartitionId;
if (retVal.getPartitionNames() != null) {
@ -229,11 +229,15 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
// Note: It's still possible that the partition only has a date but no name/id
HookParams params = new HookParams()
.add(RequestPartitionId.class, retVal)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest);
doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PARTITION_SELECTED, params);
if (myInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_PARTITION_SELECTED)) {
RuntimeResourceDefinition runtimeResourceDefinition = myFhirContext.getResourceDefinition(theResourceType);
HookParams params = new HookParams()
.add(RequestPartitionId.class, retVal)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(RuntimeResourceDefinition.class, runtimeResourceDefinition);
doCallHooks(myInterceptorBroadcaster, theRequest, Pointcut.STORAGE_PARTITION_SELECTED, params);
}
return retVal;

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/SystemRequestDetails.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
@ -58,10 +59,23 @@ public class SystemRequestDetails extends RequestDetails {
private ListMultimap<String, String> myHeaders;
/**
* If a SystemRequestDetails has a RequestPartitionId, it will take precedence over the tenantId
*/
private RequestPartitionId myRequestPartitionId;
public SystemRequestDetails(IInterceptorBroadcaster theInterceptorBroadcaster) {
super(theInterceptorBroadcaster);
}
public RequestPartitionId getRequestPartitionId() {
return myRequestPartitionId;
}
public void setRequestPartitionId(RequestPartitionId theRequestPartitionId) {
myRequestPartitionId = theRequestPartitionId;
}
@Override
protected byte[] getByteStreamRequestContents() {
return new byte[0];

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProvider.java
View File

@ -49,6 +49,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.IBaseMetaType;
@ -61,9 +62,9 @@ import org.springframework.beans.factory.annotation.Required;
import javax.servlet.http.HttpServletRequest;
import java.util.Date;
import static ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_META;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_ADD;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_DELETE;
import static ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_META;
public abstract class BaseJpaResourceProvider<T extends IBaseResource> extends BaseJpaProvider implements IResourceProvider {
@ -188,25 +189,25 @@ public abstract class BaseJpaResourceProvider<T extends IBaseResource> extends B
}
}
@Operation(name = JpaConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@Operation(name = ProviderConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_OUT_PARAM_EXPUNGE_COUNT, typeName = "integer")
})
public IBaseParameters expunge(
@IdParam IIdType theIdParam,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_LIMIT, typeName = "integer") IPrimitiveType<Integer> theLimit,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES, typeName = "boolean") IPrimitiveType<Boolean> theExpungeDeletedResources,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS, typeName = "boolean") IPrimitiveType<Boolean> theExpungeOldVersions,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_LIMIT, typeName = "integer") IPrimitiveType<Integer> theLimit,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES, typeName = "boolean") IPrimitiveType<Boolean> theExpungeDeletedResources,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS, typeName = "boolean") IPrimitiveType<Boolean> theExpungeOldVersions,
RequestDetails theRequest) {
return doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
}
@Operation(name = JpaConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@Operation(name = ProviderConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_OUT_PARAM_EXPUNGE_COUNT, typeName = "integer")
})
public IBaseParameters expunge(
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_LIMIT, typeName = "integer") IPrimitiveType<Integer> theLimit,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES, typeName = "boolean") IPrimitiveType<Boolean> theExpungeDeletedResources,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS, typeName = "boolean") IPrimitiveType<Boolean> theExpungeOldVersions,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_LIMIT, typeName = "integer") IPrimitiveType<Integer> theLimit,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES, typeName = "boolean") IPrimitiveType<Boolean> theExpungeDeletedResources,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS, typeName = "boolean") IPrimitiveType<Boolean> theExpungeOldVersions,
RequestDetails theRequest) {
return doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.rest.annotation.Since;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
@ -58,14 +59,14 @@ public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider implements IJp
return myResourceReindexingSvc;
}
@Operation(name = JpaConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@Operation(name = ProviderConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_OUT_PARAM_EXPUNGE_COUNT, typeName = "integer")
})
public IBaseParameters expunge(
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_LIMIT, typeName = "integer") IPrimitiveType<Integer> theLimit,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES, typeName = "boolean") IPrimitiveType<Boolean> theExpungeDeletedResources,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS, typeName = "boolean") IPrimitiveType<Boolean> theExpungeOldVersions,
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_EVERYTHING, typeName = "boolean") IPrimitiveType<Boolean> theExpungeEverything,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_LIMIT, typeName = "integer") IPrimitiveType<Integer> theLimit,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES, typeName = "boolean") IPrimitiveType<Boolean> theExpungeDeletedResources,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS, typeName = "boolean") IPrimitiveType<Boolean> theExpungeOldVersions,
@OperationParam(name = ProviderConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_EVERYTHING, typeName = "boolean") IPrimitiveType<Boolean> theExpungeEverything,
RequestDetails theRequestDetails
) {
ExpungeOptions options = createExpungeOptions(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -796,7 +796,7 @@ public class SearchBuilder implements ISearchBuilder {
// Account for _include=[resourceType]:*
String wantResourceType = null;
if (!matchAll) {
if (nextInclude.getParamName().equals("*")) {
if ("*".equals(nextInclude.getParamName())) {
wantResourceType = nextInclude.getParamType();
matchAll = true;
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java
View File

@ -54,7 +54,8 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
}
@Override
public AddRemoveCount updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
public AddRemoveCount
updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
AddRemoveCount retVal = new AddRemoveCount();
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
return retVal;

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -132,6 +132,7 @@ import org.springframework.transaction.interceptor.NoRollbackRuleAttribute;
import org.springframework.transaction.interceptor.RuleBasedTransactionAttribute;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import org.springframework.util.comparator.Comparators;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
@ -938,7 +939,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
});
PredicateFinalStep expansionStep = buildExpansionPredicate(theIncludeOrExclude, predicate);
List<String> codes = theIncludeOrExclude
.getConcept()
.stream()
.filter(Objects::nonNull)
.map(ValueSet.ConceptReferenceComponent::getCode)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());
PredicateFinalStep expansionStep = buildExpansionPredicate(codes, predicate);
final PredicateFinalStep finishedQuery;
if (expansionStep == null) {
finishedQuery = step;
@ -973,9 +982,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
}
// jpaQuery.setMaxResults(maxResultsPerBatch);
// jpaQuery.setFirstResult(theQueryIndex * maxResultsPerBatch);
ourLog.debug("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
StopWatch swForBatch = new StopWatch();
@ -984,9 +990,22 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
SearchQuery<TermConcept> termConceptsQuery = searchSession.search(TermConcept.class)
.where(f -> finishedQuery).toQuery();
System.out.println("About to query:" + termConceptsQuery.queryString());
ourLog.trace("About to query: {}", termConceptsQuery.queryString());
List<TermConcept> termConcepts = termConceptsQuery.fetchHits(theQueryIndex * maxResultsPerBatch, maxResultsPerBatch);
// If the include section had multiple codes, return the codes in the same order
if (codes.size() > 1) {
termConcepts = new ArrayList<>(termConcepts);
Map<String, Integer> codeToIndex = new HashMap<>(codes.size());
for (int i = 0; i < codes.size(); i++) {
codeToIndex.put(codes.get(i), i);
}
termConcepts.sort(((o1, o2) -> {
Integer idx1 = codeToIndex.get(o1.getCode());
Integer idx2 = codeToIndex.get(o2.getCode());
return Comparators.nullsHigh().compare(idx1, idx2);
}));
}
int resultsInBatch = termConcepts.size();
int firstResult = theQueryIndex * maxResultsPerBatch;// TODO GGG HS we lose the ability to check the index of the first result, so just best-guessing it here.
@ -1027,17 +1046,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
/**
* Helper method which builds a predicate for the expansion
*/
private PredicateFinalStep buildExpansionPredicate(ValueSet.ConceptSetComponent theTheIncludeOrExclude, SearchPredicateFactory thePredicate) {
private PredicateFinalStep buildExpansionPredicate(List<String> theCodes, SearchPredicateFactory thePredicate) {
PredicateFinalStep expansionStep;
/*
* Include/Exclude Concepts
*/
List<Term> codes = theTheIncludeOrExclude
.getConcept()
List<Term> codes = theCodes
.stream()
.filter(Objects::nonNull)
.map(ValueSet.ConceptReferenceComponent::getCode)
.filter(StringUtils::isNotBlank)
.map(t -> new Term("myCode", t))
.collect(Collectors.toList());

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/CircularQueueCaptureQueriesListener.java
View File

@ -378,6 +378,9 @@ public class CircularQueueCaptureQueriesListener extends BaseCaptureQueriesListe
b.append(new InstantType(new Date(theQuery.getQueryTimestamp())).getValueAsString());
b.append(" took ").append(StopWatch.formatMillis(theQuery.getElapsedTime()));
b.append(" on Thread: ").append(theQuery.getThreadName());
if (theQuery.getSize() > 1) {
b.append("\nExecution Count: ").append(theQuery.getSize()).append(" (parameters shown are for first execution)");
}
b.append("\nSQL:\n").append(formattedSql);
if (theQuery.getStackTrace() != null) {
b.append("\nStack:\n ");

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SqlQuery.java
View File

@ -26,7 +26,6 @@ import org.hibernate.engine.jdbc.internal.BasicFormatterImpl;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.regex.Pattern;
import static org.apache.commons.lang3.StringUtils.trim;
@ -93,11 +92,7 @@ public class SqlQuery {
}
}
if (mySize > 1) {
retVal += "\nsize: " + mySize + "\n";
}
return trim(retVal);
}
public StackTraceElement[] getStackTrace() {

145
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/batch/reader/ReverseCronologicalBatchResourcePidReaderTest.java Normal file
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@ -0,0 +1,145 @@
package ca.uhn.fhir.jpa.batch.reader;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.delete.model.PartitionedUrl;
import ca.uhn.fhir.jpa.delete.model.RequestListJson;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.jsonldjava.shaded.com.google.common.collect.Lists;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collections;
import java.util.GregorianCalendar;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
class ReverseCronologicalBatchResourcePidReaderTest {
static FhirContext ourFhirContext = FhirContext.forR4Cached();
static String URL_A = "a";
static String URL_B = "b";
static String URL_C = "c";
static Set<ResourcePersistentId> emptySet = Collections.emptySet();
static RequestPartitionId partId = RequestPartitionId.defaultPartition();
Patient myPatient;
@Mock
MatchUrlService myMatchUrlService;
@Mock
DaoRegistry myDaoRegistry;
@Mock
IFhirResourceDao<Patient> myPatientDao;
@InjectMocks
ReverseCronologicalBatchResourcePidReader myReader = new ReverseCronologicalBatchResourcePidReader();
@BeforeEach
public void before() throws JsonProcessingException {
RequestListJson requestListJson = new RequestListJson();
requestListJson.setPartitionedUrls(Lists.newArrayList(new PartitionedUrl(URL_A, partId), new PartitionedUrl(URL_B, partId), new PartitionedUrl(URL_C, partId)));
ObjectMapper mapper = new ObjectMapper();
String requestListJsonString = mapper.writeValueAsString(requestListJson);
myReader.setRequestListJson(requestListJsonString);
SearchParameterMap map = new SearchParameterMap();
RuntimeResourceDefinition patientResDef = ourFhirContext.getResourceDefinition("Patient");
when(myMatchUrlService.getResourceSearch(URL_A)).thenReturn(new ResourceSearch(patientResDef, map));
when(myMatchUrlService.getResourceSearch(URL_B)).thenReturn(new ResourceSearch(patientResDef, map));
when(myMatchUrlService.getResourceSearch(URL_C)).thenReturn(new ResourceSearch(patientResDef, map));
when(myDaoRegistry.getResourceDao("Patient")).thenReturn(myPatientDao);
myPatient = new Patient();
when(myPatientDao.readByPid(any())).thenReturn(myPatient);
Calendar cal = new GregorianCalendar(2021, 1, 1);
myPatient.getMeta().setLastUpdated(cal.getTime());
}
private Set<ResourcePersistentId> buildPidSet(Integer... thePids) {
return Arrays.stream(thePids)
.map(Long::new)
.map(ResourcePersistentId::new)
.collect(Collectors.toSet());
}
@Test
public void test3x1() throws Exception {
when(myPatientDao.searchForIds(any(), any()))
.thenReturn(buildPidSet(1, 2, 3))
.thenReturn(emptySet)
.thenReturn(buildPidSet(4, 5, 6))
.thenReturn(emptySet)
.thenReturn(buildPidSet(7, 8))
.thenReturn(emptySet);
assertListEquals(myReader.read(), 1, 2, 3);
assertListEquals(myReader.read(), 4, 5, 6);
assertListEquals(myReader.read(), 7, 8);
assertNull(myReader.read());
}
@Test
public void test1x3start() throws Exception {
when(myPatientDao.searchForIds(any(), any()))
.thenReturn(buildPidSet(1, 2, 3))
.thenReturn(buildPidSet(4, 5, 6))
.thenReturn(buildPidSet(7, 8))
.thenReturn(emptySet)
.thenReturn(emptySet)
.thenReturn(emptySet);
assertListEquals(myReader.read(), 1, 2, 3);
assertListEquals(myReader.read(), 4, 5, 6);
assertListEquals(myReader.read(), 7, 8);
assertNull(myReader.read());
}
@Test
public void test1x3end() throws Exception {
when(myPatientDao.searchForIds(any(), any()))
.thenReturn(emptySet)
.thenReturn(emptySet)
.thenReturn(buildPidSet(1, 2, 3))
.thenReturn(buildPidSet(4, 5, 6))
.thenReturn(buildPidSet(7, 8))
.thenReturn(emptySet);
assertListEquals(myReader.read(), 1, 2, 3);
assertListEquals(myReader.read(), 4, 5, 6);
assertListEquals(myReader.read(), 7, 8);
assertNull(myReader.read());
}
private void assertListEquals(List<Long> theList, Integer... theValues) {
assertThat(theList, hasSize(theValues.length));
for (int i = 0; i < theList.size(); ++i) {
assertEquals(theList.get(i), Long.valueOf(theValues[i]));
}
}
}

75
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BaseBatchJobR4Test.java
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@ -1,75 +0,0 @@
package ca.uhn.fhir.jpa.bulk;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import org.junit.jupiter.api.AfterEach;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.BatchStatus;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobInstance;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.repository.dao.JobExecutionDao;
import org.springframework.batch.core.repository.dao.JobInstanceDao;
import org.springframework.batch.core.repository.dao.MapJobExecutionDao;
import org.springframework.batch.core.repository.dao.MapJobInstanceDao;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.fail;
public class BaseBatchJobR4Test extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(BaseBatchJobR4Test.class);
@Autowired
private JobExplorer myJobExplorer;
// @Autowired
// private JobExecutionDao myMapJobExecutionDao;
// @Autowired
// private JobInstanceDao myMapJobInstanceDao;
//
// @AfterEach
// public void after() {
// ((MapJobExecutionDao)myMapJobExecutionDao).clear();
// ((MapJobInstanceDao)myMapJobInstanceDao).clear();
// }
protected List<JobExecution> awaitAllBulkJobCompletions(String... theJobNames) {
assert theJobNames.length > 0;
List<JobInstance> bulkExport = new ArrayList<>();
for (String nextName : theJobNames) {
bulkExport.addAll(myJobExplorer.findJobInstancesByJobName(nextName, 0, 100));
}
if (bulkExport.isEmpty()) {
List<String> wantNames = Arrays.asList(theJobNames);
List<String> haveNames = myJobExplorer.getJobNames();
fail("There are no jobs running - Want names " + wantNames + " and have names " + haveNames);
}
List<JobExecution> bulkExportExecutions = bulkExport.stream().flatMap(jobInstance -> myJobExplorer.getJobExecutions(jobInstance).stream()).collect(Collectors.toList());
awaitJobCompletions(bulkExportExecutions);
// Return the final state
bulkExportExecutions = bulkExport.stream().flatMap(jobInstance -> myJobExplorer.getJobExecutions(jobInstance).stream()).collect(Collectors.toList());
return bulkExportExecutions;
}
protected void awaitJobCompletions(Collection<JobExecution> theJobs) {
theJobs.forEach(jobExecution -> awaitJobCompletion(jobExecution));
}
protected void awaitJobCompletion(JobExecution theJobExecution) {
await().atMost(120, TimeUnit.SECONDS).until(() -> {
JobExecution jobExecution = myJobExplorer.getJobExecution(theJobExecution.getId());
ourLog.info("JobExecution {} currently has status: {}- Failures if any: {}", theJobExecution.getId(), jobExecution.getStatus(), jobExecution.getFailureExceptions());
return jobExecution.getStatus() == BatchStatus.COMPLETED || jobExecution.getStatus() == BatchStatus.FAILED;
});
}
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
View File

@ -15,6 +15,7 @@ import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
@ -26,6 +27,7 @@ import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
@ -80,7 +82,7 @@ import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
public static final String TEST_FILTER = "Patient?gender=female";
private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportSvcImplR4Test.class);
@ -94,6 +96,8 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
private IBulkDataExportSvc myBulkDataExportSvc;
@Autowired
private IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
private BatchJobHelper myBatchJobHelper;
@Autowired
@Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
@ -321,10 +325,11 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
}
private void awaitAllBulkJobCompletions() {
awaitAllBulkJobCompletions(
myBatchJobHelper.awaitAllBulkJobCompletions(
BatchJobsConfig.BULK_EXPORT_JOB_NAME,
BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME,
BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME
BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME,
BatchJobsConfig.DELETE_EXPUNGE_JOB_NAME
);
}
@ -589,7 +594,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
JobExecution jobExecution = myBatchJobSubmitter.runJob(myBulkJob, paramBuilder.toJobParameters());
awaitJobCompletion(jobExecution);
myBatchJobHelper.awaitJobCompletion(jobExecution);
String jobUUID = (String) jobExecution.getExecutionContext().get("jobUUID");
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobUUID);
@ -615,7 +620,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
JobExecution jobExecution = myBatchJobSubmitter.runJob(myBulkJob, paramBuilder.toJobParameters());
awaitJobCompletion(jobExecution);
myBatchJobHelper.awaitJobCompletion(jobExecution);
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
assertThat(jobInfo.getStatus(), equalTo(BulkExportJobStatusEnum.COMPLETE));
@ -733,7 +738,7 @@ public class BulkDataExportSvcImplR4Test extends BaseBatchJobR4Test {
JobExecution jobExecution = myBatchJobSubmitter.runJob(myPatientBulkJob, paramBuilder.toJobParameters());
awaitJobCompletion(jobExecution);
myBatchJobHelper.awaitJobCompletion(jobExecution);
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
assertThat(jobInfo.getStatus(), equalTo(BulkExportJobStatusEnum.COMPLETE));

18
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java
View File

@ -5,7 +5,7 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.bulk.BaseBatchJobR4Test;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
@ -13,12 +13,14 @@ import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobDao;
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobFileDao;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
import ca.uhn.fhir.jpa.entity.BulkImportJobFileEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
import ca.uhn.fhir.util.BundleBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -54,7 +56,7 @@ import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
public class BulkDataImportR4Test extends BaseBatchJobR4Test implements ITestDataBuilder {
public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuilder {
private static final Logger ourLog = LoggerFactory.getLogger(BulkDataImportR4Test.class);
@Autowired
@ -67,6 +69,8 @@ public class BulkDataImportR4Test extends BaseBatchJobR4Test implements ITestDat
private JobExplorer myJobExplorer;
@Autowired
private JobRegistry myJobRegistry;
@Autowired
private BatchJobHelper myBatchJobHelper;
@AfterEach
public void after() {
@ -90,7 +94,7 @@ public class BulkDataImportR4Test extends BaseBatchJobR4Test implements ITestDat
boolean activateJobOutcome = mySvc.activateNextReadyJob();
assertTrue(activateJobOutcome);
List<JobExecution> executions = awaitAllBulkJobCompletions();
List<JobExecution> executions = awaitAllBulkImportJobCompletion();
assertEquals("testFlow_TransactionRows", executions.get(0).getJobParameters().getString(BulkExportJobConfig.JOB_DESCRIPTION));
runInTransaction(() -> {
@ -127,7 +131,7 @@ public class BulkDataImportR4Test extends BaseBatchJobR4Test implements ITestDat
boolean activateJobOutcome = mySvc.activateNextReadyJob();
assertTrue(activateJobOutcome);
awaitAllBulkJobCompletions();
awaitAllBulkImportJobCompletion();
ArgumentCaptor<HookParams> paramsCaptor = ArgumentCaptor.forClass(HookParams.class);
verify(interceptor, times(50)).invoke(any(), paramsCaptor.capture());
@ -207,8 +211,8 @@ public class BulkDataImportR4Test extends BaseBatchJobR4Test implements ITestDat
assertEquals(true, job.isRestartable());
}
protected List<JobExecution> awaitAllBulkJobCompletions() {
return awaitAllBulkJobCompletions(BULK_IMPORT_JOB_NAME);
protected List<JobExecution> awaitAllBulkImportJobCompletion() {
return myBatchJobHelper.awaitAllBulkJobCompletions(BatchJobsConfig.BULK_IMPORT_JOB_NAME);
}
@Interceptor
@ -223,7 +227,5 @@ public class BulkDataImportR4Test extends BaseBatchJobR4Test implements ITestDat
throw new InternalErrorException(ERROR_MESSAGE);
}
}
}
}

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java
View File

@ -8,6 +8,8 @@ import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -62,4 +64,9 @@ public class TestJPAConfig {
public SubscriptionDeliveringRestHookSubscriber stoppableSubscriptionDeliveringRestHookSubscriber() {
return new StoppableSubscriptionDeliveringRestHookSubscriber();
}
@Bean
public BatchJobHelper batchJobHelper(JobExplorer theJobExplorer) {
return new BatchJobHelper(theJobExplorer);
}
}

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