ValueSet Expansion Should Preserve Order (#2724)
* Add test * FIxed * Add changelog * Add test * Intermittent test failure fix * Build fix * Build fix * Test fix * Test fixes * Fix checkstyle issue * Test fix * Add test logging
This commit is contained in:
James Agnew
GitHub
parent
6f680af3ce
commit
659efa786c
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@ -140,6 +140,25 @@
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</ignoredResourcePatterns>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-checkstyle-plugin</artifactId>
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<executions>
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<execution>
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<phase>process-sources</phase>
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<goals>
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<goal>checkstyle</goal>
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</goals>
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<configuration>
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<failsOnError>true</failsOnError>
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<enableRulesSummary>true</enableRulesSummary>
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<enableSeveritySummary>true</enableSeveritySummary>
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<consoleOutput>true</consoleOutput>
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<configLocation>${maven.multiModuleProjectDirectory}/src/checkstyle/checkstyle.xml</configLocation>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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@ -36,6 +36,7 @@ import org.fusesource.jansi.Ansi;
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import org.fusesource.jansi.AnsiConsole;
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import org.slf4j.LoggerFactory;
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import java.io.PrintStream;
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import java.io.PrintWriter;
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import java.lang.management.ManagementFactory;
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import java.util.ArrayList;
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@ -43,6 +44,7 @@ import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.fusesource.jansi.Ansi.ansi;
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@SuppressWarnings("WeakerAccess")
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@ -67,17 +69,27 @@ public abstract class BaseApp {
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private void logAppHeader() {
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System.out.flush();
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System.out.println("------------------------------------------------------------");
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String msg = "------------------------------------------------------------";
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printMessageToStdout(msg);
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logProductName();
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System.out.println("------------------------------------------------------------");
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System.out.println("Process ID : " + ManagementFactory.getRuntimeMXBean().getName());
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System.out.println("Max configured JVM memory (Xmx) : " + FileHelper.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
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System.out.println("Detected Java version : " + System.getProperty("java.version"));
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System.out.println("------------------------------------------------------------");
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printMessageToStdout("------------------------------------------------------------");
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printMessageToStdout("Process ID : " + ManagementFactory.getRuntimeMXBean().getName());
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printMessageToStdout("Max configured JVM memory (Xmx) : " + FileHelper.getFileSizeDisplay(Runtime.getRuntime().maxMemory(), 1));
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printMessageToStdout("Detected Java version : " + System.getProperty("java.version"));
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printMessageToStdout("------------------------------------------------------------");
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}
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private void printMessageToStdout(String theMsg) {
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PrintStream out = System.out;
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if (isNotBlank(theMsg)) {
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out.println(theMsg);
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} else {
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out.println();
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}
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}
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protected void logProductName() {
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System.out.println("\ud83d\udd25 " + ansi().bold() + " " + provideProductName() + ansi().boldOff() + " " + provideProductVersion() + " - Command Line Tool");
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printMessageToStdout("\ud83d\udd25 " + ansi().bold() + " " + provideProductName() + ansi().boldOff() + " " + provideProductVersion() + " - Command Line Tool");
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}
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private void logCommandUsage(BaseCommand theCommand) {
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@ -99,32 +111,32 @@ public abstract class BaseApp {
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}
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// Usage
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System.out.println("Usage:");
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System.out.println(" " + provideCommandName() + " " + theCommand.getCommandName() + " [options]");
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System.out.println();
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printMessageToStdout("Usage:");
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printMessageToStdout(" " + provideCommandName() + " " + theCommand.getCommandName() + " [options]");
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printMessageToStdout("");
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// Description
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String wrapped = WordUtils.wrap(theCommand.getCommandDescription(), columns);
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System.out.println(wrapped);
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System.out.println();
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printMessageToStdout(wrapped);
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printMessageToStdout("");
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// Usage Notes
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List<String> usageNotes = theCommand.provideUsageNotes();
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for (String next : usageNotes) {
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wrapped = WordUtils.wrap(next, columns);
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System.out.println(wrapped);
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System.out.println();
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printMessageToStdout(wrapped);
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printMessageToStdout("");
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}
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// Options
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System.out.println("Options:");
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printMessageToStdout("Options:");
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HelpFormatter fmt = new HelpFormatter();
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PrintWriter pw = new PrintWriter(System.out);
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fmt.printOptions(pw, columns, getOptions(theCommand), 2, 2);
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pw.flush();
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// That's it!
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System.out.println();
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printMessageToStdout("");
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}
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private Options getOptions(BaseCommand theCommand) {
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@ -135,10 +147,10 @@ public abstract class BaseApp {
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private void logUsage() {
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logAppHeader();
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System.out.println("Usage:");
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System.out.println(" " + provideCommandName() + " {command} [options]");
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System.out.println();
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System.out.println("Commands:");
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printMessageToStdout("Usage:");
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printMessageToStdout(" " + provideCommandName() + " {command} [options]");
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printMessageToStdout("");
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printMessageToStdout("Commands:");
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int longestCommandLength = 0;
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for (BaseCommand next : ourCommands) {
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@ -151,12 +163,12 @@ public abstract class BaseApp {
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for (int i = 1; i < rightParts.length; i++) {
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rightParts[i] = StringUtils.leftPad("", left.length() + 3) + rightParts[i];
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}
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System.out.println(ansi().bold().fg(Ansi.Color.GREEN) + left + ansi().boldOff().fg(Ansi.Color.WHITE) + " - " + ansi().bold() + StringUtils.join(rightParts, LINESEP));
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printMessageToStdout(ansi().bold().fg(Ansi.Color.GREEN) + left + ansi().boldOff().fg(Ansi.Color.WHITE) + " - " + ansi().bold() + StringUtils.join(rightParts, LINESEP));
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}
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System.out.println();
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System.out.println(ansi().boldOff().fg(Ansi.Color.WHITE) + "See what options are available:");
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System.out.println(" " + provideCommandName() + " help {command}");
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System.out.println();
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printMessageToStdout("");
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printMessageToStdout(ansi().boldOff().fg(Ansi.Color.WHITE) + "See what options are available:");
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printMessageToStdout(" " + provideCommandName() + " help {command}");
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printMessageToStdout("");
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}
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protected abstract String provideCommandName();
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@ -235,8 +247,8 @@ public abstract class BaseApp {
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if (command == null) {
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String message = "Unrecognized command: " + ansi().bold().fg(Ansi.Color.RED) + theArgs[0] + ansi().boldOff().fg(Ansi.Color.WHITE);
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System.out.println(message);
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System.out.println();
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printMessageToStdout(message);
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printMessageToStdout("");
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logUsage();
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exitDueToProblem(message);
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return;
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@ -141,6 +141,13 @@
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<skip>true</skip>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-checkstyle-plugin</artifactId>
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<configuration>
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<skip>true</skip>
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</configuration>
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</plugin>
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</plugins>
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<resources>
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<resource>
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 2624
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title: "ValueSet expansion did not correctly preserve the order if multiple codes were included
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in a single inclusion block."
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@ -147,9 +147,9 @@
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-checkstyle-plugin</artifactId>
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<executions>
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<execution><id>validate</id><phase>none</phase></execution>
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</executions>
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<configuration>
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<skip>true</skip>
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</configuration>
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</plugin>
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</plugins>
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</build>
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@ -26,6 +26,8 @@ import org.hibernate.search.mapper.pojo.bridge.PropertyBridge;
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import org.hibernate.search.mapper.pojo.bridge.binding.PropertyBindingContext;
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import org.hibernate.search.mapper.pojo.bridge.mapping.programmatic.PropertyBinder;
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import org.hibernate.search.mapper.pojo.bridge.runtime.PropertyBridgeWriteContext;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.Collection;
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@ -38,6 +40,7 @@ public class TermConceptPropertyBinder implements PropertyBinder {
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public static final String CONCEPT_FIELD_PROPERTY_PREFIX = "PROP";
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private static final Logger ourLog = LoggerFactory.getLogger(TermConceptPropertyBinder.class);
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@Override
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public void bind(PropertyBindingContext thePropertyBindingContext) {
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@ -65,10 +68,10 @@ public class TermConceptPropertyBinder implements PropertyBinder {
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if (properties != null) {
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for (TermConceptProperty next : properties) {
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theDocument.addValue(CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey(), next.getValue());
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System.out.println("Adding Prop: " + CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey() + " -- " + next.getValue());
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ourLog.trace("Adding Prop: {}{} -- {}", CONCEPT_FIELD_PROPERTY_PREFIX, next.getKey(), next.getValue());
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if (next.getType() == TermConceptPropertyTypeEnum.CODING && isNotBlank(next.getDisplay())) {
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theDocument.addValue(CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey(), next.getDisplay());
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System.out.println("Adding multivalue Prop: " + CONCEPT_FIELD_PROPERTY_PREFIX + next.getKey() + " -- " + next.getDisplay());
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ourLog.trace("Adding multivalue Prop: {}{} -- {}", CONCEPT_FIELD_PROPERTY_PREFIX, next.getKey(), next.getDisplay());
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}
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}
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}
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@ -132,6 +132,7 @@ import org.springframework.transaction.interceptor.NoRollbackRuleAttribute;
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import org.springframework.transaction.interceptor.RuleBasedTransactionAttribute;
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import org.springframework.transaction.support.TransactionSynchronizationManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import org.springframework.util.comparator.Comparators;
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import javax.annotation.Nonnull;
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import javax.annotation.Nullable;
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@ -938,7 +939,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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});
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PredicateFinalStep expansionStep = buildExpansionPredicate(theIncludeOrExclude, predicate);
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List<String> codes = theIncludeOrExclude
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.getConcept()
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.stream()
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.filter(Objects::nonNull)
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.map(ValueSet.ConceptReferenceComponent::getCode)
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.filter(StringUtils::isNotBlank)
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.collect(Collectors.toList());
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PredicateFinalStep expansionStep = buildExpansionPredicate(codes, predicate);
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final PredicateFinalStep finishedQuery;
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if (expansionStep == null) {
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finishedQuery = step;
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@ -973,9 +982,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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// jpaQuery.setMaxResults(maxResultsPerBatch);
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// jpaQuery.setFirstResult(theQueryIndex * maxResultsPerBatch);
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ourLog.debug("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
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StopWatch swForBatch = new StopWatch();
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@ -984,9 +990,22 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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SearchQuery<TermConcept> termConceptsQuery = searchSession.search(TermConcept.class)
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.where(f -> finishedQuery).toQuery();
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System.out.println("About to query:" + termConceptsQuery.queryString());
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ourLog.trace("About to query: {}", termConceptsQuery.queryString());
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List<TermConcept> termConcepts = termConceptsQuery.fetchHits(theQueryIndex * maxResultsPerBatch, maxResultsPerBatch);
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// If the include section had multiple codes, return the codes in the same order
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if (codes.size() > 1) {
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termConcepts = new ArrayList<>(termConcepts);
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Map<String, Integer> codeToIndex = new HashMap<>(codes.size());
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for (int i = 0; i < codes.size(); i++) {
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codeToIndex.put(codes.get(i), i);
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}
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termConcepts.sort(((o1, o2) -> {
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Integer idx1 = codeToIndex.get(o1.getCode());
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Integer idx2 = codeToIndex.get(o2.getCode());
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return Comparators.nullsHigh().compare(idx1, idx2);
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}));
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}
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int resultsInBatch = termConcepts.size();
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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.
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@ -1027,17 +1046,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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/**
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* Helper method which builds a predicate for the expansion
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*/
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private PredicateFinalStep buildExpansionPredicate(ValueSet.ConceptSetComponent theTheIncludeOrExclude, SearchPredicateFactory thePredicate) {
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private PredicateFinalStep buildExpansionPredicate(List<String> theCodes, SearchPredicateFactory thePredicate) {
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PredicateFinalStep expansionStep;
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/*
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* Include/Exclude Concepts
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*/
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List<Term> codes = theTheIncludeOrExclude
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.getConcept()
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List<Term> codes = theCodes
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.stream()
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.filter(Objects::nonNull)
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.map(ValueSet.ConceptReferenceComponent::getCode)
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.filter(StringUtils::isNotBlank)
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.map(t -> new Term("myCode", t))
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.collect(Collectors.toList());
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@ -21,6 +21,7 @@ import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.exception.ExceptionUtils;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.DateTimeType;
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@ -55,6 +56,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.fail;
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public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
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@ -673,7 +675,8 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
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for (Future<Throwable> next : futures) {
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Throwable t = next.get();
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if (t != null) {
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throw t;
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String stackTrace = ExceptionUtils.getStackTrace(t);
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fail(t.toString() + "\n" + stackTrace);
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}
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}
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executor.shutdownNow();
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
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@ -13,6 +14,7 @@ import ca.uhn.fhir.jpa.dao.BaseJpaTest;
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import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
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import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.term.ValueSetExpansionR4Test;
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import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
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import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
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@ -32,6 +34,7 @@ import org.hl7.fhir.r4.model.AuditEvent;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.CarePlan;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeType;
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import org.hl7.fhir.r4.model.CompartmentDefinition;
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import org.hl7.fhir.r4.model.ConceptMap;
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import org.hl7.fhir.r4.model.Condition;
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@ -60,6 +63,9 @@ import java.io.InputStream;
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import java.nio.charset.StandardCharsets;
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import java.util.List;
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import static ca.uhn.fhir.util.HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.contains;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.fail;
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@ -263,6 +269,44 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
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}
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}
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@Test
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public void testExpandValueSetPreservesExplicitOrder() {
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CodeSystem cs = new CodeSystem();
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cs.setId("cs");
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cs.setUrl("http://cs");
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cs.addConcept().setCode("code1");
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cs.addConcept().setCode("code2");
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cs.addConcept().setCode("code3");
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cs.addConcept().setCode("code4");
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cs.addConcept().setCode("code5");
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myCodeSystemDao.update(cs);
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// Vs in reverse order
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ValueSet vs = new ValueSet();
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vs.setId("vs");
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vs.setUrl("http://vs");
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// Add some codes in separate compose sections, and some more codes in a single compose section.
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// Order should be preserved for all of them.
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vs.getCompose().addInclude().setSystem("http://cs")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code5")));
|
||||
vs.getCompose().addInclude().setSystem("http://cs")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code4")));
|
||||
vs.getCompose().addInclude().setSystem("http://cs")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code3")))
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code2")))
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code1")));
|
||||
myValueSetDao.update(vs);
|
||||
|
||||
// Non Pre-Expanded
|
||||
ValueSet outcome = myValueSetDao.expand(vs, new ValueSetExpansionOptions());
|
||||
assertEquals("ValueSet \"ValueSet.url[http://vs]\" has not yet been pre-expanded. Performing in-memory expansion without parameters. Current status: NOT_EXPANDED | The ValueSet is waiting to be picked up and pre-expanded by a scheduled task.", outcome.getMeta().getExtensionString(EXT_VALUESET_EXPANSION_MESSAGE));
|
||||
assertThat(ValueSetExpansionR4Test.toCodes(outcome).toString(), ValueSetExpansionR4Test.toCodes(outcome), contains(
|
||||
"code5", "code4", "code3", "code2", "code1"
|
||||
));
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchByCodeIn() {
|
||||
CodeSystem cs = new CodeSystem();
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import java.util.ArrayList;
|
|||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
|
|
@ -136,13 +137,7 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
|
|||
assertEquals(response0.getId(), response1.getId());
|
||||
|
||||
// Pretend the search was errored out
|
||||
runInTransaction(() -> {
|
||||
assertEquals(1L, mySearchEntityDao.count());
|
||||
Search search = mySearchEntityDao.findAll().iterator().next();
|
||||
search.setStatus(SearchStatusEnum.FAILED);
|
||||
search.setFailureMessage("Some Failure Message");
|
||||
search.setFailureCode(501);
|
||||
});
|
||||
markSearchErrored();
|
||||
|
||||
// Perform the search again (shouldn't return the errored out search)
|
||||
Bundle response3 = myClient.search()
|
||||
|
|
@ -155,6 +150,25 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
|
|||
|
||||
}
|
||||
|
||||
private void markSearchErrored() {
|
||||
while (true) {
|
||||
try {
|
||||
runInTransaction(() -> {
|
||||
assertEquals(1L, mySearchEntityDao.count());
|
||||
Search search = mySearchEntityDao.findAll().iterator().next();
|
||||
search.setStatus(SearchStatusEnum.FAILED);
|
||||
search.setFailureMessage("Some Failure Message");
|
||||
search.setFailureCode(501);
|
||||
mySearchEntityDao.save(search);
|
||||
});
|
||||
break;
|
||||
} catch (ResourceVersionConflictException e) {
|
||||
ourLog.warn("Conflict while updating search: " + e);
|
||||
continue;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testErroredSearchReturnsAppropriateResponse() {
|
||||
Patient pt1 = new Patient();
|
||||
|
|
@ -174,14 +188,11 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
|
|||
.execute();
|
||||
assertEquals(1, response0.getEntry().size());
|
||||
|
||||
// Make sure it works for now
|
||||
myClient.loadPage().next(response0).execute();
|
||||
|
||||
// Pretend the search was errored out
|
||||
runInTransaction(() -> {
|
||||
assertEquals(1L, mySearchEntityDao.count());
|
||||
Search search = mySearchEntityDao.findAll().iterator().next();
|
||||
search.setStatus(SearchStatusEnum.FAILED);
|
||||
search.setFailureMessage("Some Failure Message");
|
||||
search.setFailureCode(501);
|
||||
});
|
||||
markSearchErrored();
|
||||
|
||||
// Request the second page
|
||||
try {
|
||||
|
|
|
|||
|
|
@ -19,6 +19,7 @@ import ca.uhn.fhir.util.HapiExtensions;
|
|||
import com.google.common.collect.Lists;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.Extension;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
|
||||
|
|
@ -38,6 +39,7 @@ import java.util.List;
|
|||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static ca.uhn.fhir.util.HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE;
|
||||
import static org.hamcrest.CoreMatchers.containsString;
|
||||
import static org.hamcrest.CoreMatchers.equalTo;
|
||||
import static org.hamcrest.CoreMatchers.is;
|
||||
|
|
@ -444,11 +446,6 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
|
|||
assertThat(lastSelectQuery, containsString(" like '%display value 9%'"));
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
public List<String> toCodes(ValueSet theExpandedValueSet) {
|
||||
return theExpandedValueSet.getExpansion().getContains().stream().map(t -> t.getCode()).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@SuppressWarnings("SpellCheckingInspection")
|
||||
@Test
|
||||
public void testExpandTermValueSetAndChildren() throws Exception {
|
||||
|
|
@ -514,7 +511,6 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
|
|||
assertEquals(3, expandedValueSet.getExpansion().getContains().size());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testExpandExistingValueSetNotPreExpanded() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
|
||||
|
|
@ -870,7 +866,6 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
|
|||
assertEquals("Unknown CodeSystem URI \"http://unknown-system\" referenced from ValueSet", extensionByUrl.getValueAsPrimitive().getValueAsString());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testExpandTermValueSetAndChildrenWithOffsetAndCountWithClientAssignedId() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSets(true);
|
||||
|
|
@ -955,6 +950,54 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
|
|||
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection(), nullable(Long.class), nullable(String.class));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandValueSetPreservesExplicitOrder() {
|
||||
CodeSystem cs = new CodeSystem();
|
||||
cs.setId("cs");
|
||||
cs.setUrl("http://cs");
|
||||
cs.addConcept().setCode("code1");
|
||||
cs.addConcept().setCode("code2");
|
||||
cs.addConcept().setCode("code3");
|
||||
cs.addConcept().setCode("code4");
|
||||
cs.addConcept().setCode("code5");
|
||||
myCodeSystemDao.update(cs);
|
||||
|
||||
// Vs in reverse order
|
||||
ValueSet vs = new ValueSet();
|
||||
vs.setId("vs");
|
||||
vs.setUrl("http://vs");
|
||||
// Add some codes in separate compose sections, and some more codes in a single compose section.
|
||||
// Order should be preserved for all of them.
|
||||
vs.getCompose().addInclude().setSystem("http://cs")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code5")));
|
||||
vs.getCompose().addInclude().setSystem("http://cs")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code4")));
|
||||
vs.getCompose().addInclude().setSystem("http://cs")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code3")))
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code2")))
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code1")));
|
||||
myValueSetDao.update(vs);
|
||||
|
||||
// Non Pre-Expanded
|
||||
ValueSet outcome = myValueSetDao.expand(vs, new ValueSetExpansionOptions());
|
||||
assertEquals("ValueSet \"ValueSet.url[http://vs]\" has not yet been pre-expanded. Performing in-memory expansion without parameters. Current status: NOT_EXPANDED | The ValueSet is waiting to be picked up and pre-expanded by a scheduled task.", outcome.getMeta().getExtensionString(EXT_VALUESET_EXPANSION_MESSAGE));
|
||||
assertThat(toCodes(outcome).toString(), toCodes(outcome), contains(
|
||||
"code5", "code4", "code3", "code2", "code1"
|
||||
));
|
||||
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
// Pre-Expanded
|
||||
myCaptureQueriesListener.clear();
|
||||
outcome = myValueSetDao.expand(vs, new ValueSetExpansionOptions());
|
||||
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
|
||||
assertEquals("ValueSet was expanded using a pre-calculated expansion", outcome.getMeta().getExtensionString(EXT_VALUESET_EXPANSION_MESSAGE));
|
||||
assertThat(toCodes(outcome).toString(), toCodes(outcome), contains(
|
||||
"code5", "code4", "code3", "code2", "code1"
|
||||
));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testStoreTermCodeSystemAndChildren() throws Exception {
|
||||
loadAndPersistCodeSystemWithDesignations(HttpVerb.POST);
|
||||
|
|
@ -1431,5 +1474,10 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
public static List<String> toCodes(ValueSet theExpandedValueSet) {
|
||||
return theExpandedValueSet.getExpansion().getContains().stream().map(t -> t.getCode()).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
7
pom.xml
7
pom.xml
|
|
@ -2233,12 +2233,9 @@
|
|||
<dependency>
|
||||
<groupId>com.puppycrawl.tools</groupId>
|
||||
<artifactId>checkstyle</artifactId>
|
||||
<version>8.42</version>
|
||||
<version>8.43</version>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<configuration>
|
||||
<configLocation>${project.basedir}/src/checkstyle/checkstyle.xml</configLocation>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
|
|
@ -2818,7 +2815,7 @@
|
|||
<id>validate</id>
|
||||
<phase>generate-sources</phase>
|
||||
<configuration>
|
||||
<configLocation>src/checkstyle/checkstyle_config_nofixmes.xml</configLocation>
|
||||
<configLocation>${maven.multiModuleProjectDirectory}/src/checkstyle/checkstyle_config_nofixmes.xml</configLocation>
|
||||
<encoding>UTF-8</encoding>
|
||||
<consoleOutput>true</consoleOutput>
|
||||
<failOnViolation>true</failOnViolation>
|
||||
|
|
|
|||
|
|
@ -5,11 +5,16 @@
|
|||
|
||||
<module name="Checker">
|
||||
<property name="charset" value="UTF-8"/>
|
||||
<property name="cacheFile" value="target/cache_non_main_files"/>
|
||||
|
||||
<property name="severity" value="warning"/>
|
||||
|
||||
<!--<property name="fileExtensions" value="java, properties, xml"/> -->
|
||||
<module name="TreeWalker">
|
||||
<module name="RegexpSinglelineJava">
|
||||
<property name="format" value="System\.out\.println"/>
|
||||
<property name="ignoreComments" value="true"/>
|
||||
</module>
|
||||
</module>
|
||||
|
||||
<!--
|
||||
<module name="TreeWalker">
|
||||
<property name="tabWidth" value="3"/>
|
||||
<module name="OuterTypeFilename"/>
|
||||
|
|
@ -40,7 +45,7 @@
|
|||
<property name="format" value="org.jetbrains.annotations.Nullable"/>
|
||||
<property name="message" value="Incorrect Nullable annotation used: The "javax.annotation.Nullable" annotation should be used for nullable things"/>
|
||||
</module>
|
||||
<!--<module name="AvoidStarImport"/> -->
|
||||
|
||||
<module name="OneTopLevelClass"/>
|
||||
<module name="NoLineWrap"/>
|
||||
<module name="EmptyBlock">
|
||||
|
|
@ -49,28 +54,15 @@
|
|||
value="LITERAL_TRY, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE, LITERAL_SWITCH"/>
|
||||
</module>
|
||||
<module name="NeedBraces"/>
|
||||
<!--
|
||||
<module name="LeftCurly">
|
||||
<property name="maxLineLength" value="300"/>
|
||||
</module>
|
||||
-->
|
||||
<module name="RightCurly"/>
|
||||
<module name="RightCurly">
|
||||
<property name="option" value="alone"/>
|
||||
<property name="tokens"
|
||||
value="CLASS_DEF, METHOD_DEF, CTOR_DEF, LITERAL_FOR, LITERAL_WHILE, LITERAL_DO, STATIC_INIT, INSTANCE_INIT"/>
|
||||
</module>
|
||||
<!-- <module name="WhitespaceAround"> <property name="allowEmptyConstructors"
|
||||
value="true"/> <property name="allowEmptyMethods" value="true"/> <property
|
||||
name="allowEmptyTypes" value="true"/> <property name="allowEmptyLoops" value="true"/>
|
||||
<message key="ws.notFollowed" value="WhitespaceAround: ''{0}'' is not followed
|
||||
by whitespace. Empty blocks may only be represented as '{}' when not part
|
||||
of a multi-block statement (4.1.3)"/> <message key="ws.notPreceded" value="WhitespaceAround:
|
||||
''{0}'' is not preceded with whitespace."/> </module> -->
|
||||
<module name="OneStatementPerLine"/>
|
||||
<module name="MultipleVariableDeclarations"/>
|
||||
<module name="ArrayTypeStyle"/>
|
||||
<!-- <module name="MissingSwitchDefault"/> -->
|
||||
<module name="FallThrough"/>
|
||||
<module name="UpperEll"/>
|
||||
<module name="ModifierOrder"/>
|
||||
|
|
@ -145,10 +137,6 @@
|
|||
</module>
|
||||
<module name="OverloadMethodsDeclarationOrder"/>
|
||||
<module name="VariableDeclarationUsageDistance"/>
|
||||
<!-- <module name="CustomImportOrder"> <property name="specialImportsRegExp"
|
||||
value="com.google"/> <property name="sortImportsInGroupAlphabetically" value="true"/>
|
||||
<property name="customImportOrderRules" value="STATIC###SPECIAL_IMPORTS###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
|
||||
</module> -->
|
||||
<module name="MethodParamPad"/>
|
||||
<module name="OperatorWrap">
|
||||
<property name="option" value="NL"/>
|
||||
|
|
@ -174,21 +162,13 @@
|
|||
<property name="target"
|
||||
value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>
|
||||
</module>
|
||||
<!-- <module name="JavadocMethod"> <module name="JavadocParagraph"/> <property
|
||||
name="scope" value="public"/> <property name="allowMissingParamTags" value="true"/>
|
||||
<property name="allowMissingThrowsTags" value="true"/> <property name="allowMissingReturnTag"
|
||||
value="true"/> <property name="minLineCount" value="2"/> <property name="allowedAnnotations"
|
||||
value="Override, Test"/> <property name="allowThrowsTagsForSubclasses" value="true"/>
|
||||
</module> -->
|
||||
<module name="MethodName">
|
||||
<property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9_]*$"/>
|
||||
<message key="name.invalidPattern"
|
||||
value="Method name ''{0}'' must match pattern ''{1}''."/>
|
||||
</module>
|
||||
<module name="SingleLineJavadoc"/>
|
||||
<!--<property name="ignoreInlineTags" value="false"/> -->
|
||||
<!--<module name="EmptyCatchBlock"> <property name="exceptionVariableName"
|
||||
value="expected"/> </module> -->
|
||||
</module>
|
||||
-->
|
||||
</module>
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue