diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java index 8aaffa92551..0dbc92416dd 100644 --- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java +++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java @@ -8,6 +8,7 @@ import ca.uhn.fhir.parser.DataFormatException; import ca.uhn.fhir.rest.api.QualifiedParamList; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.util.DateUtils; +import org.apache.commons.lang3.Validate; import org.hl7.fhir.instance.model.api.IPrimitiveType; import java.util.ArrayList; @@ -57,6 +58,17 @@ public class DateRangeParam implements IQueryParameterAnd { super(); } + /** + * Copy constructor. + */ + @SuppressWarnings("CopyConstructorMissesField") + public DateRangeParam(DateRangeParam theDateRangeParam) { + super(); + Validate.notNull(theDateRangeParam); + setLowerBound(theDateRangeParam.getLowerBound()); + setUpperBound(theDateRangeParam.getUpperBound()); + } + /** * Constructor which takes two Dates representing the lower and upper bounds of the range (inclusive on both ends) * @@ -235,7 +247,7 @@ public class DateRangeParam implements IQueryParameterAnd { * are the same value. As such, even though the prefixes for the lower and * upper bounds default to ge and le respectively, * the resulting prefix is effectively eq where only a single - * date is provided - as required by the FHIR specificiation (i.e. "If no + * date is provided - as required by the FHIR specification (i.e. "If no * prefix is present, the prefix eq is assumed"). *

*/ @@ -296,12 +308,12 @@ public class DateRangeParam implements IQueryParameterAnd { break; case EQUAL: case GREATERTHAN_OR_EQUALS: + case NOT_EQUAL: break; case LESSTHAN: case APPROXIMATE: case LESSTHAN_OR_EQUALS: case ENDS_BEFORE: - case NOT_EQUAL: throw new IllegalStateException(Msg.code(1926) + "Invalid lower bound comparator: " + myLowerBound.getPrefix()); } } @@ -326,11 +338,11 @@ public class DateRangeParam implements IQueryParameterAnd { break; case EQUAL: case LESSTHAN_OR_EQUALS: + case NOT_EQUAL: break; case GREATERTHAN_OR_EQUALS: case GREATERTHAN: case APPROXIMATE: - case NOT_EQUAL: case STARTS_AFTER: throw new IllegalStateException(Msg.code(1927) + "Invalid upper bound comparator: " + myUpperBound.getPrefix()); } @@ -355,13 +367,13 @@ public class DateRangeParam implements IQueryParameterAnd { retVal = myLowerBound.getPrecision().add(retVal, 1); break; case EQUAL: + case NOT_EQUAL: case GREATERTHAN_OR_EQUALS: break; case LESSTHAN: case APPROXIMATE: case LESSTHAN_OR_EQUALS: case ENDS_BEFORE: - case NOT_EQUAL: throw new IllegalStateException(Msg.code(1928) + "Invalid lower bound comparator: " + myLowerBound.getPrefix()); } } @@ -417,6 +429,7 @@ public class DateRangeParam implements IQueryParameterAnd { retVal = new Date(retVal.getTime() - 1L); break; case EQUAL: + case NOT_EQUAL: case LESSTHAN_OR_EQUALS: retVal = myUpperBound.getPrecision().add(retVal, 1); retVal = new Date(retVal.getTime() - 1L); @@ -424,7 +437,6 @@ public class DateRangeParam implements IQueryParameterAnd { case GREATERTHAN_OR_EQUALS: case GREATERTHAN: case APPROXIMATE: - case NOT_EQUAL: case STARTS_AFTER: throw new IllegalStateException(Msg.code(1929) + "Invalid upper bound comparator: " + myUpperBound.getPrefix()); } diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/HasAndListParam.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/HasAndListParam.java index 8b86be242c4..c4ddfc0c431 100644 --- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/HasAndListParam.java +++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/HasAndListParam.java @@ -23,7 +23,7 @@ import ca.uhn.fhir.util.CoverageIgnore; */ -public class HasAndListParam extends BaseAndListParam { +public class HasAndListParam extends BaseAndListParam { @Override HasOrListParam newInstance() { diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/DateRangeUtil.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/DateRangeUtil.java new file mode 100644 index 00000000000..55a56c68541 --- /dev/null +++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/DateRangeUtil.java @@ -0,0 +1,61 @@ +package ca.uhn.fhir.util; + +/*- + * #%L + * HAPI FHIR - Core Library + * %% + * Copyright (C) 2014 - 2022 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.rest.param.DateRangeParam; + +import javax.annotation.Nonnull; +import javax.annotation.Nullable; +import java.util.Date; + +public class DateRangeUtil { + + /** + * Narrow the DateRange to be within theStartInclusive, and theEndExclusive, if provided. + * @param theDateRangeParam the initial range, null for unconstrained + * @param theStartInclusive a lower bound to apply, or null for unchanged. + * @param theEndExclusive an upper bound to apply, or null for unchanged. + * @return a DateRange within the original range, and between theStartInclusive and theEnd + */ + @Nonnull + public static DateRangeParam narrowDateRange(@Nullable DateRangeParam theDateRangeParam, @Nullable Date theStartInclusive, @Nullable Date theEndExclusive) { + if (theStartInclusive == null && theEndExclusive == null) { + return theDateRangeParam; + } + DateRangeParam result = theDateRangeParam==null?new DateRangeParam():new DateRangeParam(theDateRangeParam); + + if (theStartInclusive != null) { + Date inputStart = result.getLowerBoundAsInstant(); + if (theDateRangeParam == null || inputStart == null || inputStart.before(theStartInclusive)) { + result.setLowerBoundInclusive(theStartInclusive); + } + } + if (theEndExclusive != null) { + Date inputEnd = result.getUpperBound() == null? null : result.getUpperBound().getValue(); + if (theDateRangeParam == null || inputEnd == null || inputEnd.after(theEndExclusive)) { + result.setUpperBoundExclusive(theEndExclusive); + } + } + + return result; + } + +} diff --git a/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java b/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java index 4d5a746fffb..af715ffe870 100644 --- a/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java +++ b/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java @@ -7,7 +7,9 @@ import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.mockito.Mockito; +import java.time.Instant; import java.util.ArrayList; +import java.util.Date; import java.util.List; import static org.junit.jupiter.api.Assertions.assertEquals; @@ -123,4 +125,18 @@ public class DateRangeParamTest { assertEquals(ParamPrefixEnum.NOT_EQUAL, dateRangeParam.getLowerBound().getPrefix()); assertEquals(ParamPrefixEnum.NOT_EQUAL, dateRangeParam.getUpperBound().getPrefix()); } + + @Test + public void testCopyConstructor() { + DateParam dateStart = new DateParam("gt2021-01-01"); + DateParam dateEnd = new DateParam("lt2021-02-01"); + DateRangeParam input = new DateRangeParam(dateStart, dateEnd); + + DateRangeParam copy = new DateRangeParam(input); + + assertEquals(dateStart, copy.getLowerBound()); + assertEquals(dateEnd, copy.getUpperBound()); + + } + } diff --git a/hapi-fhir-base/src/test/java/ca/uhn/fhir/util/DateRangeUtilTest.java b/hapi-fhir-base/src/test/java/ca/uhn/fhir/util/DateRangeUtilTest.java new file mode 100644 index 00000000000..b0d8d3499fc --- /dev/null +++ b/hapi-fhir-base/src/test/java/ca/uhn/fhir/util/DateRangeUtilTest.java @@ -0,0 +1,112 @@ +package ca.uhn.fhir.util; + +import ca.uhn.fhir.rest.param.DateParam; +import ca.uhn.fhir.rest.param.DateRangeParam; +import ca.uhn.fhir.rest.param.ParamPrefixEnum; +import org.apache.commons.lang3.builder.ToStringBuilder; +import org.apache.commons.lang3.builder.ToStringStyle; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.MethodSource; + +import java.time.Instant; +import java.util.Arrays; +import java.util.Date; +import java.util.List; + +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN_OR_EQUALS; +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.*; + +class DateRangeUtilTest { + + static Date dateOne = Date.from(Instant.parse("2021-01-01T01:00:00Z")); + static Date dateTwo = Date.from(Instant.parse("2021-01-01T02:00:00Z")); + static Date dateThree = Date.from(Instant.parse("2021-01-01T03:00:00Z")); + static Date dateFour = Date.from(Instant.parse("2021-01-01T04:00:00Z")); + static Date dateFive = Date.from(Instant.parse("2021-01-01T05:00:00Z")); + static Date dateSix = Date.from(Instant.parse("2021-01-01T06:00:00Z")); + + static class NarrowCase { + final String message; + final DateRangeParam range; + final Date narrowStart; + final Date narrowEnd; + final DateParam resultStart; + final DateParam resultEnd; + + public NarrowCase(String theMessage, DateRangeParam theRange, Date theNarrowStart, Date theNarrowEnd, DateParam theResultStart, DateParam theResultEnd) { + message = theMessage; + range = theRange; + narrowStart = theNarrowStart; + narrowEnd = theNarrowEnd; + resultStart = theResultStart; + resultEnd = theResultEnd; + } + + + static NarrowCase from(String theMessage, DateRangeParam theRange, Date theNarrowStart, Date theNarrowEnd, Date theResultStart, Date theResultEnd) { + return new NarrowCase(theMessage, theRange, theNarrowStart, theNarrowEnd, + theResultStart == null?null:new DateParam(GREATERTHAN_OR_EQUALS, theResultStart), + theResultEnd == null?null:new DateParam(LESSTHAN, theResultEnd)); + } + + static NarrowCase from(String theMessage, DateRangeParam theRange, Date theNarrowStart, Date theNarrowEnd, + ParamPrefixEnum theResultStartPrefix, Date theResultStart, ParamPrefixEnum theResultEndPrefix, Date theResultEnd) { + return new NarrowCase(theMessage, theRange, theNarrowStart, theNarrowEnd, + new DateParam(theResultStartPrefix, theResultStart), new DateParam(theResultEndPrefix, theResultEnd)); + } + + @Override + public String toString() { + return new ToStringBuilder(this, ToStringStyle.SIMPLE_STYLE) + .append(message) + .append("range", range) + .append("narrowStart", narrowStart) + .append("narrowEnd", narrowEnd) + .append("resultStart", resultStart) + .append("resultEnd", resultEnd) + .toString(); + } + } + + static public List narrowCases() { + + return Arrays.asList( + // null range cases + new NarrowCase("nulls on null yields null", null, null,null, null, null), + NarrowCase.from("start and end narrow null", null, dateTwo,dateThree, dateTwo, dateThree), + NarrowCase.from("start on null provides open range", null, dateTwo, null, dateTwo, null), + NarrowCase.from("end on null provides open range", null, null,dateThree, null, dateThree), + // middle range + // default range is inclusive at top + NarrowCase.from("start and end outside leaves range unchanged", new DateRangeParam(dateTwo, dateFive), dateOne, dateSix, GREATERTHAN_OR_EQUALS, dateTwo, LESSTHAN_OR_EQUALS ,dateFive), + NarrowCase.from("start inside narrows start", new DateRangeParam(dateTwo, dateFive), dateThree, dateSix, GREATERTHAN_OR_EQUALS, dateThree, LESSTHAN_OR_EQUALS ,dateFive), + + NarrowCase.from("end inside narrows end", new DateRangeParam(dateTwo, dateFive), dateOne, dateFour, dateTwo, dateFour), + // half-open cases + NarrowCase.from("end inside open end", new DateRangeParam(dateTwo, null), null, dateFour, dateTwo, dateFour), + NarrowCase.from("start inside open start", new DateRangeParam(null, dateFour), dateTwo, null, GREATERTHAN_OR_EQUALS, dateTwo, LESSTHAN_OR_EQUALS, dateFour), + NarrowCase.from("gt case preserved", new DateRangeParam(new DateParam(GREATERTHAN, dateTwo), null), null, dateFour, GREATERTHAN, dateTwo, LESSTHAN, dateFour) + + + ); + } + + @ParameterizedTest + @MethodSource("narrowCases") + public void testNarrowCase(NarrowCase c) { + DateRangeParam result = DateRangeUtil.narrowDateRange(c.range, c.narrowStart, c.narrowEnd); + + if (c.resultStart == null && c.resultEnd == null) { + assertThat(result, nullValue()); + } else { + assertThat(result, notNullValue()); + assertThat("range start", result.getLowerBound(), equalTo(c.resultStart)); + assertThat("range end", result.getUpperBound(), equalTo(c.resultEnd)); + } + } + +} diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java index ed98aff98da..81e35cc9b4d 100644 --- a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java @@ -22,9 +22,6 @@ package ca.uhn.fhir.cli; import ca.uhn.fhir.i18n.Msg; import ca.uhn.fhir.util.VersionUtil; -import ch.qos.logback.classic.LoggerContext; -import ch.qos.logback.classic.joran.JoranConfigurator; -import ch.qos.logback.core.joran.spi.JoranException; import com.helger.commons.io.file.FileHelper; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.DefaultParser; @@ -60,7 +57,7 @@ public abstract class BaseApp { static { System.setProperty(STACKFILTER_PATTERN_PROP, STACKFILTER_PATTERN); - loggingConfigOff(); + LogbackUtil.loggingConfigOff(); // We don't use qualified names for loggers in CLI ourLog = LoggerFactory.getLogger(App.class); @@ -198,7 +195,7 @@ public abstract class BaseApp { @SuppressWarnings("ResultOfMethodCallIgnored") public void run(String[] theArgs) { - loggingConfigOff(); + LogbackUtil.loggingConfigOff(); validateJavaVersion(); if (System.getProperty("unit_test") != null) { @@ -225,7 +222,7 @@ public abstract class BaseApp { } Optional commandOpt = parseCommand(theArgs); - if (! commandOpt.isPresent()) return; + if (commandOpt.isEmpty()) return; BaseCommand command = commandOpt.get(); @@ -238,7 +235,14 @@ public abstract class BaseApp { logAppHeader(); validateJavaVersion(); - loggingConfigOn(); + + if (System.console() == null) { + // Probably redirecting stdout to a file + LogbackUtil.loggingConfigOnWithoutColour(); + } else { + // Use colours if we're logging to a console + LogbackUtil.loggingConfigOnWithColour(); + } try { String[] args = Arrays.copyOfRange(theArgs, 1, theArgs.length); @@ -248,7 +252,7 @@ public abstract class BaseApp { } if (parsedOptions.hasOption("debug")) { - loggingConfigOnDebug(); + LogbackUtil.loggingConfigOnDebug(); ourDebugMode = true; } @@ -264,7 +268,7 @@ public abstract class BaseApp { } catch (ParseException e) { if (!"true".equals(System.getProperty("test"))) { - loggingConfigOff(); + LogbackUtil.loggingConfigOff(); } System.err.println("Invalid command options for command: " + command.getCommandName()); System.err.println(" " + ansi().fg(Ansi.Color.RED).bold() + e.getMessage()); @@ -287,7 +291,7 @@ public abstract class BaseApp { private Optional parseCommand(String[] theArgs) { Optional commandOpt = getNextCommand(theArgs, 0); - if (! commandOpt.isPresent()) { + if (commandOpt.isEmpty()) { String message = "Unrecognized command: " + ansi().bold().fg(Ansi.Color.RED) + theArgs[0] + ansi().boldOff().fg(Ansi.Color.WHITE); printMessageToStdout(message); printMessageToStdout(""); @@ -307,7 +311,7 @@ public abstract class BaseApp { return; } Optional commandOpt = getNextCommand(theArgs, 1); - if (! commandOpt.isPresent()) { + if (commandOpt.isEmpty()) { String message = "Unknown command: " + theArgs[1]; System.err.println(message); exitDueToProblem(message); @@ -339,7 +343,7 @@ public abstract class BaseApp { private void runCleanupHookAndUnregister() { if (myShutdownHookHasNotRun) { Runtime.getRuntime().removeShutdownHook(myShutdownHook); - myShutdownHook.run(); + myShutdownHook.start(); myShutdownHookHasNotRun = false; } } @@ -371,40 +375,4 @@ public abstract class BaseApp { public static boolean isDebugMode() { return ourDebugMode; } - - private static void loggingConfigOff() { - try { - JoranConfigurator configurator = new JoranConfigurator(); - configurator.setContext((LoggerContext) LoggerFactory.getILoggerFactory()); - configurator.doConfigure(App.class.getResourceAsStream("/logback-cli-off.xml")); - } catch (JoranException e) { - e.printStackTrace(); - } - } - - private static void loggingConfigOn() { - try { - JoranConfigurator configurator = new JoranConfigurator(); - configurator.setContext((LoggerContext) LoggerFactory.getILoggerFactory()); - ((LoggerContext) LoggerFactory.getILoggerFactory()).reset(); - configurator.doConfigure(App.class.getResourceAsStream("/logback-cli-on.xml")); - ourLog.info("Logging configuration set from file logback-cli-on.xml"); - } catch (JoranException e) { - e.printStackTrace(); - } - } - - private static void loggingConfigOnDebug() { - try { - JoranConfigurator configurator = new JoranConfigurator(); - configurator.setContext((LoggerContext) LoggerFactory.getILoggerFactory()); - ((LoggerContext) LoggerFactory.getILoggerFactory()).reset(); - configurator.doConfigure(App.class.getResourceAsStream("/logback-cli-on-debug.xml")); - ourLog.info("Logging configuration set from file logback-cli-on-debug.xml"); - } catch (JoranException e) { - e.printStackTrace(); - } - - ourLog.info("Debug logging is enabled"); - } } diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LogbackUtil.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LogbackUtil.java new file mode 100644 index 00000000000..493551fd419 --- /dev/null +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LogbackUtil.java @@ -0,0 +1,66 @@ +package ca.uhn.fhir.cli; + +/*- + * #%L + * HAPI FHIR - Command Line Client - API + * %% + * Copyright (C) 2014 - 2022 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 ch.qos.logback.classic.LoggerContext; +import ch.qos.logback.classic.joran.JoranConfigurator; +import ch.qos.logback.core.joran.spi.JoranException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +class LogbackUtil { + private static final Logger ourLog = LoggerFactory.getLogger(LogbackUtil.class); + + static void loggingConfigOff() { + try { + JoranConfigurator configurator = new JoranConfigurator(); + configurator.setContext((LoggerContext) LoggerFactory.getILoggerFactory()); + configurator.doConfigure(App.class.getResourceAsStream("/logback-cli-off.xml")); + } catch (JoranException e) { + e.printStackTrace(); + } + } + + static void loggingConfigOnWithColour() { + setLogbackConfig("/logback-cli-on.xml"); + } + + static void loggingConfigOnWithoutColour() { + setLogbackConfig("/logback-cli-on-no-colour.xml"); + } + + static void loggingConfigOnDebug() { + setLogbackConfig("/logback-cli-on-debug.xml"); + ourLog.info("Debug logging is enabled"); + } + + static void setLogbackConfig(String logbackConfigFilename) { + try { + JoranConfigurator configurator = new JoranConfigurator(); + configurator.setContext((LoggerContext) LoggerFactory.getILoggerFactory()); + ((LoggerContext) LoggerFactory.getILoggerFactory()).reset(); + configurator.doConfigure(App.class.getResourceAsStream(logbackConfigFilename)); + ourLog.info("Logging configuration set from file " + logbackConfigFilename); + } catch (JoranException e) { + e.printStackTrace(); + } + } +} diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on-no-colour.xml b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on-no-colour.xml new file mode 100644 index 00000000000..be065ef56df --- /dev/null +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on-no-colour.xml @@ -0,0 +1,57 @@ + + + + + %d{yyyy-MM-dd} %d{HH:mm:ss.SS} [%thread] %-5level %logger{20} %msg%n + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml index c72b0a4ea05..100d8b27402 100644 --- a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml @@ -1,7 +1,7 @@ - true + true %green(%d{yyyy-MM-dd}) %boldGreen(%d{HH:mm:ss.SS}) %white([%thread]) %white(%-5level) %boldBlue(%logger{20}) %boldWhite(%msg%n) diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3608-documentation-on-offset-paging-with-_offset-doesnt-mention-possible-duplicate-entries-across-different-pages.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3608-documentation-on-offset-paging-with-_offset-doesnt-mention-possible-duplicate-entries-across-different-pages.yaml new file mode 100644 index 00000000000..ecddbf92711 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3608-documentation-on-offset-paging-with-_offset-doesnt-mention-possible-duplicate-entries-across-different-pages.yaml @@ -0,0 +1,5 @@ +--- +type: fix +issue: 3608 +title: "Documentation on offset paging with _offset doesn't mention possible duplicate entries across different pages. + The documentation has been updated, and a warning log is added to notify this behaviour as well." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3396-It-is-possible-to-write-to-a-resource-in-a-partition-the-user-is-not-authorized-to.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3396-It-is-possible-to-write-to-a-resource-in-a-partition-the-user-is-not-authorized-to.yaml new file mode 100644 index 00000000000..79c81664322 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3396-It-is-possible-to-write-to-a-resource-in-a-partition-the-user-is-not-authorized-to.yaml @@ -0,0 +1,4 @@ +--- +type: security +issue: 3396 +title: "Previously, it was possible to update a resource with wrong `tenantID`. This issue has been fixed." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3506-enhance-mdm-logging.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3506-enhance-mdm-logging.yaml new file mode 100644 index 00000000000..96d4c85dc0d --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3506-enhance-mdm-logging.yaml @@ -0,0 +1,4 @@ +--- +type: change +issue: 3506 +title: "Changing the MDM logging to contain scores for each applied matcher field. Deleting summary score when creating MDM link." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3579-fix-mdm-match.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3579-fix-mdm-match.yaml new file mode 100644 index 00000000000..018e362b9f8 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3579-fix-mdm-match.yaml @@ -0,0 +1,6 @@ +--- +type: fix +issue: 3579 +jira: SMILE-4167 +title: "Mdm was not excluding NO_MATCH from golden-resource candidates in eid mode. This caused mdm to produce an error +when a Patient eid is changed after that patient's link was updated to NO_MATCH. This has been corrected" diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3584-case-sensitive-elasticsearch.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3584-case-sensitive-elasticsearch.yaml new file mode 100644 index 00000000000..63e0a3b276b --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3584-case-sensitive-elasticsearch.yaml @@ -0,0 +1,5 @@ +--- +type: fix +issue: 3584 +title: "Unmodified string searches and string `:contains` search were incorrectly case-sensitive + when configured with recent versions of Lucene/Elasticsearch. This has been corrected." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3586-lastIndex-reindex-fix.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3586-lastIndex-reindex-fix.yaml new file mode 100644 index 00000000000..1dc2134d309 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3586-lastIndex-reindex-fix.yaml @@ -0,0 +1,6 @@ +--- +type: fix +issue: 3586 +jira: SMILE-3441 +title: "While converting the reindexing job to the new batch framework, a regression of [#3441](https://github.com/hapifhir/hapi-fhir/issues/3441) was introduced. Reindexing jobs were not respecting the passed in `_lastUpdated` parameter. + We now take date these date ranges into account when running re-indexing jobs." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3590-fix-ne-for-lastUpdated.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3590-fix-ne-for-lastUpdated.yaml new file mode 100644 index 00000000000..b28ce21b038 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3590-fix-ne-for-lastUpdated.yaml @@ -0,0 +1,4 @@ +--- +type: fix +issue: 3590 +title: "When searching with the `_lastUpdated` parameter and using the `ne` prefix, search would fail with HAPI-1928 error. This has been fixed." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3592-log-colours.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3592-log-colours.yaml new file mode 100644 index 00000000000..48814258af5 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3592-log-colours.yaml @@ -0,0 +1,6 @@ +--- +type: fix +issue: 3592 +jira: SMILE-691 +title: "Command-line log output now only sends colour commands if output is being printed to a console. Otherwise, + (e.g. if output is redirected to a file) the log output will not contain any special colour escape characters." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3602-batch2-jobs-stay-in-progress-after-cancelled.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3602-batch2-jobs-stay-in-progress-after-cancelled.yaml new file mode 100644 index 00000000000..cdb9e1bbcac --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3602-batch2-jobs-stay-in-progress-after-cancelled.yaml @@ -0,0 +1,5 @@ +--- +type: fix +issue: 3602 +title: "New batch job implementation (batch2) were staying on IN_PROGRESS status after being cancelled. + That is now fixed. After cancellation status is changed to CANCELLED." diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/version.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/version.yaml new file mode 100644 index 00000000000..94d2416d7b6 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/version.yaml @@ -0,0 +1,3 @@ +--- +release-date: "2022-05-18" +codename: "Tanuki" diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties index fcaf49fd2d0..537af8f530d 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties @@ -1,7 +1,8 @@ section.introduction.title=Welcome to HAPI FHIR page.introduction.table_of_contents=Table of Contents -page.introduction.changelog=Changelog: 2021 +page.introduction.changelog=Changelog: 2022 +page.introduction.changelog_2021=Changelog: 2021 page.introduction.changelog_2020=Changelog: 2020 page.introduction.changelog_2019=Changelog: 2019 page.introduction.changelog_2018=Changelog: 2018 @@ -53,6 +54,7 @@ section.server_jpa.title=JPA Server page.server_jpa.introduction=Introduction page.server_jpa.get_started=Get Started ⚡ page.server_jpa.architecture=Architecture +page.server_jpa.database_support=Database Support page.server_jpa.schema=Database Schema page.server_jpa.configuration=Configuration page.server_jpa.search=Search diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/empi-create-5.svg b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/empi-create-5.svg index 553c9fc3abb..90adf0cf699 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/empi-create-5.svg +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/empi-create-5.svg @@ -1 +1 @@ - \ No newline at end of file + \ No newline at end of file diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog.md index a094513e813..bab69254101 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog.md +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog.md @@ -1,4 +1,4 @@ -# Changelog: 2021 +# Changelog: 2022 - + diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog_2021.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog_2021.md new file mode 100644 index 00000000000..fe51dd8813a --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/changelog_2021.md @@ -0,0 +1,5 @@ + +# Changelog: 2021 + + + diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/database_support.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/database_support.md new file mode 100644 index 00000000000..5b5a473f744 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/database_support.md @@ -0,0 +1,29 @@ +# Database Support + +HAPI FHIR JPA Server maintains active support for several databases: + +- [MS SQL Server](https://www.microsoft.com/en-us/sql-server/sql-server-2019) +- [PostgreSQL](https://www.postgresql.org/) +- [Oracle](https://www.oracle.com/ca-en/database/12c-database/) + +Use of any of the above databases is fully supported by HAPI-FHIR, and code is actively written to work with them. + +# Experimental Support + +HAPI FHIR currently provides experimental for the following databases, but does not actively support them, or write code specifically to work with them: + +- [Cockroach DB](https://www.cockroachlabs.com/) + +HAPI FHIR uses the Hibernate ORM to provide database abstraction. This means that HAPI FHIR could theoretically also work on other databases supported by Hibernate. +For example, although we do not regularly test or validate on other platforms, community members have reported successfully running HAPI FHIR on: + +- DB2 +- Cache +- Firebird + +# Deprecated Support + +These databases were previously supported by HAPI FHIR JPA Server, but have since been deprecated, and should not be used. + +- [MySQL](https://www.mysql.com/) + diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md index cfca23c55d4..291ef86af96 100644 --- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md @@ -371,14 +371,19 @@ http://fhir.example.com/Patient?identifier=urn:foo|123&_count=10 ## Offset paging with `_offset` -HAPI FHIR supports also paging. Offset specification can be passed into handler methods with [@Offset](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/rest/annotation/Offset.html) annotation. -This annotation is *not* part of the FHIR standard. +**Warning:** Using `_offset` without sorting can result in duplicate entries to show up across the different pages when +following the next page link provided on each page. + +HAPI FHIR supports also paging. Offset specification can be passed into handler methods +with [@Offset](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/rest/annotation/Offset.html) annotation. +This annotation is *not* part of the FHIR standard. There are two possible ways to use paging. It is possible to define `_offset` parameter in the request which means that when combined with `_count` the paging is done on the database level. This type of paging benefits from not having to return so many items from the database when paging items. It's also possible to define default page size (i.e. default `_count` if not given) and maximum page size (i.e. maximum value -for the `_count` parameter). See [RestfulServer](/hapi-fhir/apidocs/hapi-fhir-server/ca/uhn/fhir/rest/server/RestfulServer.html) +for the `_count` parameter). +See [RestfulServer](/hapi-fhir/apidocs/hapi-fhir-server/ca/uhn/fhir/rest/server/RestfulServer.html) for more information. ```java diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java index 3a3302fa0da..06642b0b4f5 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java @@ -35,7 +35,6 @@ import org.springframework.data.domain.Sort; import javax.annotation.Nonnull; import javax.transaction.Transactional; -import java.util.Collection; import java.util.Date; import java.util.List; import java.util.Optional; @@ -120,7 +119,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence { } @Override - public Collection fetchRecentInstances(int thePageSize, int thePageIndex) { + public List fetchRecentInstances(int thePageSize, int thePageIndex) { PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.DESC, "myCreateTime"); return myJobInstanceRepository.findAll(pageRequest).stream().map(this::toInstance).collect(Collectors.toList()); } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java index 93c5773148c..ac2727561d5 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java @@ -163,6 +163,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.left; import static org.apache.commons.lang3.StringUtils.trim; +import static ca.uhn.fhir.jpa.model.util.JpaConstants.ALL_PARTITIONS_NAME; + /* * #%L * HAPI FHIR JPA Server @@ -1307,6 +1309,8 @@ public abstract class BaseHapiFhirDao extends BaseStora } else { requestPartitionId = RequestPartitionId.defaultPartition(); } + + failIfPartitionMismatch(theRequest, entity); mySearchParamWithInlineReferencesExtractor.populateFromResource(requestPartitionId, newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing); changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true); @@ -1474,6 +1478,24 @@ public abstract class BaseHapiFhirDao extends BaseStora return retval; } + /** + * TODO eventually consider refactoring this to be part of an interceptor. + * + * Throws an exception if the partition of the request, and the partition of the existing entity do not match. + * @param theRequest the request. + * @param entity the existing entity. + */ + private void failIfPartitionMismatch(RequestDetails theRequest, ResourceTable entity) { + if (myPartitionSettings.isPartitioningEnabled() && theRequest != null && theRequest.getTenantId() != null && entity.getPartitionId() != null && + theRequest.getTenantId() != ALL_PARTITIONS_NAME) { + PartitionEntity partitionEntity = myPartitionLookupSvc.getPartitionByName(theRequest.getTenantId()); + //partitionEntity should never be null + if (partitionEntity != null && !partitionEntity.getId().equals(entity.getPartitionId().getPartitionId())) { + throw new InvalidRequestException(Msg.code(2079) + "Resource " + entity.getResourceType() + "/" + entity.getId() + " is not known"); + } + } + } + private void createHistoryEntry(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, EncodedResource theChanged) { boolean versionedTags = getConfig().getTagStorageMode() == DaoConfig.TagStorageModeEnum.VERSIONED; final ResourceHistoryTable historyEntry = theEntity.toHistory(versionedTags); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneClauseBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneClauseBuilder.java index 07bf7575ffb..62eb83b70c4 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneClauseBuilder.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneClauseBuilder.java @@ -37,6 +37,7 @@ import ca.uhn.fhir.rest.param.StringParam; import ca.uhn.fhir.rest.param.TokenParam; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.util.DateUtils; +import ca.uhn.fhir.util.StringUtil; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.Pair; @@ -52,6 +53,7 @@ import java.time.Instant; import java.util.Arrays; import java.util.HashSet; import java.util.List; +import java.util.Locale; import java.util.Objects; import java.util.Optional; import java.util.Set; @@ -214,7 +216,7 @@ public class ExtendedLuceneClauseBuilder { for (List nextAnd : stringAndOrTerms) { Set terms = extractOrStringParams(nextAnd); ourLog.debug("addStringTextSearch {}, {}", theSearchParamName, terms); - if (terms.size() >= 1) { + if (!terms.isEmpty()) { String query = terms.stream() .map(s -> "( " + s + " )") .collect(Collectors.joining(" | ")); @@ -249,14 +251,29 @@ public class ExtendedLuceneClauseBuilder { Set terms = extractOrStringParams(nextAnd); ourLog.debug("addStringContainsSearch {} {}", theSearchParamName, terms); List orTerms = terms.stream() - .map(s -> - myPredicateFactory.wildcard().field(fieldPath).matching("*" + s + "*")) + // wildcard is a term-level query, so queries aren't analyzed. Do our own normalization first. + .map(s-> normalize(s)) + .map(s -> myPredicateFactory + .wildcard().field(fieldPath) + .matching("*" + s + "*")) .collect(Collectors.toList()); myRootClause.must(orPredicateOrSingle(orTerms)); } } + /** + * Normalize the string to match our standardAnalyzer. + * @see ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer#STANDARD_ANALYZER + * + * @param theString the raw string + * @return a case and accent normalized version of the input + */ + @Nonnull + private String normalize(String theString) { + return StringUtil.normalizeStringForSearchIndexing(theString).toLowerCase(Locale.ROOT); + } + public void addStringUnmodifiedSearch(String theSearchParamName, List> theStringAndOrTerms) { String fieldPath = SEARCH_PARAM_ROOT + "." + theSearchParamName + ".string." + IDX_STRING_NORMALIZED; for (List nextAnd : theStringAndOrTerms) { @@ -264,7 +281,10 @@ public class ExtendedLuceneClauseBuilder { ourLog.debug("addStringUnmodifiedSearch {} {}", theSearchParamName, terms); List orTerms = terms.stream() .map(s -> - myPredicateFactory.wildcard().field(fieldPath).matching(s + "*")) + myPredicateFactory.wildcard() + .field(fieldPath) + // wildcard is a term-level query, so it isn't analyzed. Do our own case-folding to match the normStringAnalyzer + .matching(normalize(s) + "*")) .collect(Collectors.toList()); myRootClause.must(orPredicateOrSingle(orTerms)); @@ -355,8 +375,8 @@ public class ExtendedLuceneClauseBuilder { * } * * - * @param theSearchParamName - * @param theDateAndOrTerms + * @param theSearchParamName e.g code + * @param theDateAndOrTerms The and/or list of DateParam values */ public void addDateUnmodifiedSearch(String theSearchParamName, List> theDateAndOrTerms) { for (List nextAnd : theDateAndOrTerms) { diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ResourceReindexSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ResourceReindexSvcImpl.java index f5fd577e02d..1a66403e1e7 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ResourceReindexSvcImpl.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/ResourceReindexSvcImpl.java @@ -35,6 +35,7 @@ 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 ca.uhn.fhir.util.DateRangeUtil; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.data.domain.Pageable; import org.springframework.data.domain.Slice; @@ -85,7 +86,8 @@ public class ResourceReindexSvcImpl implements IResourceReindexSvc { SearchParameterMap searchParamMap = myMatchUrlService.translateMatchUrl(theUrl, def); searchParamMap.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC)); - searchParamMap.setLastUpdated(new DateRangeParam(theStart, theEnd)); + DateRangeParam chunkDateRange = DateRangeUtil.narrowDateRange(searchParamMap.getLastUpdated(), theStart, theEnd); + searchParamMap.setLastUpdated(chunkDateRange); searchParamMap.setCount(thePageSize); IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceType); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java index be70b629ee5..36f1cdce6d9 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java @@ -47,7 +47,6 @@ import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc; import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc; import ca.uhn.fhir.jpa.search.cache.SearchCacheStatusEnum; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; -import ca.uhn.fhir.rest.server.interceptor.ServerInterceptorUtil; import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.model.api.Include; import ca.uhn.fhir.rest.api.CacheControlDirective; @@ -65,6 +64,7 @@ import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException; import ca.uhn.fhir.rest.server.exceptions.InternalErrorException; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException; +import ca.uhn.fhir.rest.server.interceptor.ServerInterceptorUtil; import ca.uhn.fhir.rest.server.method.PageMethodBinding; import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails; import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster; @@ -612,6 +612,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc { if (theParams.isOffsetQuery()) { bundleProvider.setCurrentPageOffset(theParams.getOffset()); bundleProvider.setCurrentPageSize(theParams.getCount()); + ourLog.warn("Query from search {} is using _offset, may result in duplicate entries across different pages.", theSearchUuid); } if (wantCount) { diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java index ab4bcc1f33a..e44556518be 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java @@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.search.builder; * #L% */ -import ca.uhn.fhir.i18n.Msg; import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.RuntimeSearchParam; +import ca.uhn.fhir.i18n.Msg; import ca.uhn.fhir.interceptor.model.RequestPartitionId; import ca.uhn.fhir.jpa.api.config.DaoConfig; import ca.uhn.fhir.jpa.dao.BaseStorageDao; @@ -329,10 +329,6 @@ public class QueryStack { return orCondidtion; } - private Condition createPredicateCompositePart(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theSpnamePrefix, RuntimeSearchParam theParam, IQueryParameterType theParamValue, RequestPartitionId theRequestPartitionId) { - return createPredicateCompositePart(theSourceJoinColumn, theResourceName, theSpnamePrefix, theParam, theParamValue, theRequestPartitionId, mySqlBuilder); - } - private Condition createPredicateCompositePart(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theSpnamePrefix, RuntimeSearchParam theParam, IQueryParameterType theParamValue, RequestPartitionId theRequestPartitionId, SearchQueryBuilder theSqlBuilder) { switch (theParam.getParamType()) { @@ -930,7 +926,7 @@ public class QueryStack { } public Condition createPredicateReferenceForContainedResource(@Nullable DbColumn theSourceJoinColumn, - String theResourceName, String theParamName, List theQualifiers, RuntimeSearchParam theSearchParam, + String theResourceName, RuntimeSearchParam theSearchParam, List theList, SearchFilterParser.CompareOperation theOperation, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) { // A bit of a hack, but we need to turn off cache reuse while in this method so that we don't try to reuse builders across different subselects @@ -1093,7 +1089,7 @@ public class QueryStack { } private Condition createIndexPredicate(DbColumn theSourceJoinColumn, String theResourceName, String theSpnamePrefix, String theParamName, RuntimeSearchParam theParamDefinition, ArrayList theOrValues, SearchFilterParser.CompareOperation theOperation, List theQualifiers, RequestDetails theRequest, RequestPartitionId theRequestPartitionId, SearchQueryBuilder theSqlBuilder) { - Condition containedCondition = null; + Condition containedCondition; switch (theParamDefinition.getParamType()) { case DATE: @@ -1312,7 +1308,7 @@ public class QueryStack { List tokens = new ArrayList<>(); boolean paramInverted = false; - TokenParamModifier modifier = null; + TokenParamModifier modifier; for (IQueryParameterType nextOr : theList) { if (nextOr instanceof TokenParam) { @@ -1337,7 +1333,7 @@ public class QueryStack { modifier = id.getModifier(); // for :not modifier, create a token and remove the :not modifier - if (modifier != null && modifier == TokenParamModifier.NOT) { + if (modifier == TokenParamModifier.NOT) { tokens.add(new TokenParam(((TokenParam) nextOr).getSystem(), ((TokenParam) nextOr).getValue())); paramInverted = true; } else { @@ -1434,7 +1430,7 @@ public class QueryStack { case Constants.PARAM_PROFILE: case Constants.PARAM_SECURITY: if (myDaoConfig.getTagStorageMode() == DaoConfig.TagStorageModeEnum.INLINE) { - return createPredicateSearchParameter(theSourceJoinColumn, theResourceName, theParamName, theAndOrParams, theRequest, theRequestPartitionId, theSearchContainedMode); + return createPredicateSearchParameter(theSourceJoinColumn, theResourceName, theParamName, theAndOrParams, theRequest, theRequestPartitionId); } else { return createPredicateTag(theSourceJoinColumn, theAndOrParams, theParamName, theRequestPartitionId); } @@ -1443,14 +1439,14 @@ public class QueryStack { return createPredicateSourceForAndList(theSourceJoinColumn, theAndOrParams); default: - return createPredicateSearchParameter(theSourceJoinColumn, theResourceName, theParamName, theAndOrParams, theRequest, theRequestPartitionId, theSearchContainedMode); + return createPredicateSearchParameter(theSourceJoinColumn, theResourceName, theParamName, theAndOrParams, theRequest, theRequestPartitionId); } } @Nullable - private Condition createPredicateSearchParameter(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theParamName, List> theAndOrParams, RequestDetails theRequest, RequestPartitionId theRequestPartitionId, SearchContainedModeEnum theSearchContainedMode) { + private Condition createPredicateSearchParameter(@Nullable DbColumn theSourceJoinColumn, String theResourceName, String theParamName, List> theAndOrParams, RequestDetails theRequest, RequestPartitionId theRequestPartitionId) { List andPredicates = new ArrayList<>(); RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName); if (nextParamDef != null) { @@ -1472,7 +1468,6 @@ public class QueryStack { operation = toOperation(param.getPrefix()); } andPredicates.add(createPredicateDate(theSourceJoinColumn, theResourceName, null, nextParamDef, nextAnd, operation, theRequestPartitionId)); - //andPredicates.add(createPredicateDate(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, null, theRequestPartitionId)); } break; case QUANTITY: @@ -1488,7 +1483,7 @@ public class QueryStack { case REFERENCE: for (List nextAnd : theAndOrParams) { if (isEligibleForContainedResourceSearch(nextAnd)) { - andPredicates.add(createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, new ArrayList<>(), nextParamDef, nextAnd, null, theRequest, theRequestPartitionId)); + andPredicates.add(createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId)); } else { andPredicates.add(createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, new ArrayList<>(), nextAnd, null, theRequest, theRequestPartitionId)); } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java index baf83e25b0a..01c44545b74 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java @@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.builder.sql; * #L% */ -import ca.uhn.fhir.i18n.Msg; import ca.uhn.fhir.context.FhirContext; +import ca.uhn.fhir.i18n.Msg; import ca.uhn.fhir.interceptor.model.RequestPartitionId; import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider; import ca.uhn.fhir.jpa.model.config.PartitionSettings; @@ -34,8 +34,8 @@ import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.ForcedIdPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.NumberPredicateBuilder; -import ca.uhn.fhir.jpa.search.builder.predicate.QuantityPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.QuantityNormalizedPredicateBuilder; +import ca.uhn.fhir.jpa.search.builder.predicate.QuantityPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.ResourceIdPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.ResourceTablePredicateBuilder; @@ -45,9 +45,10 @@ import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.TagPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder; import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder; +import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId; +import ca.uhn.fhir.rest.param.DateParam; import ca.uhn.fhir.rest.param.DateRangeParam; import ca.uhn.fhir.rest.param.ParamPrefixEnum; - import com.healthmarketscience.sqlbuilder.BinaryCondition; import com.healthmarketscience.sqlbuilder.ComboCondition; import com.healthmarketscience.sqlbuilder.Condition; @@ -69,17 +70,16 @@ import org.hibernate.engine.spi.RowSelection; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId; import javax.annotation.Nonnull; import javax.annotation.Nullable; import java.util.ArrayList; import java.util.Collection; import java.util.List; -import java.util.Locale; import java.util.Set; import java.util.UUID; import java.util.stream.Collectors; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.*; import static org.apache.commons.lang3.ObjectUtils.defaultIfNull; public class SearchQueryBuilder { @@ -556,21 +556,40 @@ public class SearchQueryBuilder { public ComboCondition addPredicateLastUpdated(DateRangeParam theDateRange) { ResourceTablePredicateBuilder resourceTableRoot = getOrCreateResourceTablePredicateBuilder(false); - List conditions = new ArrayList<>(2); + BinaryCondition condition; + + if (isNotEqualsComparator(theDateRange)) { + condition = createConditionForValueWithComparator(LESSTHAN, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getLowerBoundAsInstant()); + conditions.add(condition); + condition = createConditionForValueWithComparator(GREATERTHAN, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getUpperBoundAsInstant()); + conditions.add(condition); + return ComboCondition.or(conditions.toArray(new Condition[0])); + } + if (theDateRange.getLowerBoundAsInstant() != null) { - BinaryCondition condition = createConditionForValueWithComparator(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getLowerBoundAsInstant()); + condition = createConditionForValueWithComparator(GREATERTHAN_OR_EQUALS, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getLowerBoundAsInstant()); conditions.add(condition); } if (theDateRange.getUpperBoundAsInstant() != null) { - BinaryCondition condition = createConditionForValueWithComparator(ParamPrefixEnum.LESSTHAN_OR_EQUALS, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getUpperBoundAsInstant()); + condition = createConditionForValueWithComparator(LESSTHAN_OR_EQUALS, resourceTableRoot.getLastUpdatedColumn(), theDateRange.getUpperBoundAsInstant()); conditions.add(condition); } return ComboCondition.and(conditions.toArray(new Condition[0])); } + private boolean isNotEqualsComparator(DateRangeParam theDateRange) { + if (theDateRange != null) { + DateParam lb = theDateRange.getLowerBound(); + DateParam ub = theDateRange.getUpperBound(); + + return lb != null && ub != null && lb.getPrefix().equals(NOT_EQUAL) && ub.getPrefix().equals(NOT_EQUAL); + } + return false; + } + public void addResourceIdsPredicate(List thePidList) { DbColumn resourceIdColumn = getOrCreateFirstPredicateBuilder().getResourceIdColumn(); @@ -604,6 +623,8 @@ public class SearchQueryBuilder { return BinaryCondition.greaterThan(theColumn, generatePlaceholder(theValue)); case GREATERTHAN_OR_EQUALS: return BinaryCondition.greaterThanOrEq(theColumn, generatePlaceholder(theValue)); + case NOT_EQUAL: + return BinaryCondition.notEqualTo(theColumn, generatePlaceholder(theValue)); default: throw new IllegalArgumentException(Msg.code(1263)); } diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java index 1212bb4a7ba..705f4f71f67 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java @@ -40,10 +40,8 @@ import org.hl7.fhir.instance.model.api.IIdType; import org.slf4j.Logger; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.data.domain.Example; -import org.springframework.data.domain.Page; import org.springframework.data.domain.PageImpl; import org.springframework.data.domain.PageRequest; -import org.springframework.data.domain.Sort; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; @@ -100,7 +98,7 @@ public class MdmLinkDaoSvc { mdmLink.setPartitionId(new PartitionablePartitionId(partitionId.getFirstPartitionIdOrNull(), partitionId.getPartitionDate())); } - String message = String.format("Creating MdmLink from %s to %s -> %s", theGoldenResource.getIdElement().toUnqualifiedVersionless(), theSourceResource.getIdElement().toUnqualifiedVersionless(), theMatchOutcome); + String message = String.format("Creating MdmLink from %s to %s.", theGoldenResource.getIdElement().toUnqualifiedVersionless(), theSourceResource.getIdElement().toUnqualifiedVersionless()); theMdmTransactionContext.addTransactionLogMessage(message); ourLog.debug(message); save(mdmLink); @@ -279,11 +277,11 @@ public class MdmLinkDaoSvc { * Given a list of criteria, return all links from the database which fits the criteria provided * * @param theGoldenResourceId The resource ID of the golden resource being searched. - * @param theSourceId The resource ID of the source resource being searched. - * @param theMatchResult the {@link MdmMatchResultEnum} being searched. - * @param theLinkSource the {@link MdmLinkSourceEnum} being searched. - * @param thePageRequest the {@link MdmPageRequest} paging information - * @param thePartitionId List of partitions ID being searched, where the link's partition must be in the list. + * @param theSourceId The resource ID of the source resource being searched. + * @param theMatchResult the {@link MdmMatchResultEnum} being searched. + * @param theLinkSource the {@link MdmLinkSourceEnum} being searched. + * @param thePageRequest the {@link MdmPageRequest} paging information + * @param thePartitionId List of partitions ID being searched, where the link's partition must be in the list. * @return a list of {@link MdmLink} entities which match the example. */ public PageImpl executeTypedQuery(IIdType theGoldenResourceId, IIdType theSourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmPageRequest thePageRequest, List thePartitionId) { @@ -383,4 +381,13 @@ public class MdmLinkDaoSvc { } return retval; } + + public Optional getLinkByGoldenResourceAndSourceResource(@Nullable IAnyResource theGoldenResource, @Nullable IAnyResource theSourceResource) { + if (theGoldenResource == null || theSourceResource == null) { + return Optional.empty(); + } + return getLinkByGoldenResourcePidAndSourceResourcePid( + myJpaIdHelperService.getPidOrNull(theGoldenResource), + myJpaIdHelperService.getPidOrNull(theSourceResource)); + } } diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java index af74242e03a..79eee8cc7eb 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java @@ -40,6 +40,7 @@ import org.slf4j.Logger; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; +import javax.annotation.Nullable; import java.util.List; import java.util.Optional; @@ -182,6 +183,7 @@ public class MdmEidUpdateService { return myIncomingResourceHasAnEid; } + @Nullable public IAnyResource getExistingGoldenResource() { return myExistingGoldenResource; } diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java index cb1f4abe3e0..18d23ed820d 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java @@ -58,7 +58,7 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc { @Override @Transactional - public void updateLink(IAnyResource theGoldenResource, IAnyResource theSourceResource, MdmMatchOutcome theMatchOutcome, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmTransactionContext) { + public void updateLink(@Nonnull IAnyResource theGoldenResource, @Nonnull IAnyResource theSourceResource, MdmMatchOutcome theMatchOutcome, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmTransactionContext) { if (theMatchOutcome.isPossibleDuplicate() && goldenResourceLinkedAsNoMatch(theGoldenResource, theSourceResource)) { log(theMdmTransactionContext, theGoldenResource.getIdElement().toUnqualifiedVersionless() + " is linked as NO_MATCH with " + @@ -129,10 +129,7 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc { if (theGoldenResource.getIdElement().getIdPart() == null || theCandidate.getIdElement().getIdPart() == null) { return Optional.empty(); } else { - return myMdmLinkDaoSvc.getLinkByGoldenResourcePidAndSourceResourcePid( - myIdHelperService.getPidOrNull(theGoldenResource), - myIdHelperService.getPidOrNull(theCandidate) - ); + return myMdmLinkDaoSvc.getLinkByGoldenResourceAndSourceResource(theGoldenResource, theCandidate); } } diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchFinderSvcImpl.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchFinderSvcImpl.java index a224e14293c..fd117033c7e 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchFinderSvcImpl.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchFinderSvcImpl.java @@ -57,7 +57,7 @@ public class MdmMatchFinderSvcImpl implements IMdmMatchFinderSvc { .map(candidate -> new MatchedTarget(candidate, myMdmResourceMatcherSvc.getMatchResult(theResource, candidate))) .collect(Collectors.toList()); - ourLog.info("Found {} matched targets for {}", matches.size(), theResourceType); + ourLog.info("Found {} matched targets for {}.", matches.size(), theResourceType); return matches; } diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java index c73399f5804..08276d880b5 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java @@ -132,11 +132,11 @@ public class MdmMatchLinkSvc { // 1. Get the right helper // 2. Create source resource for the MDM source // 3. UPDATE MDM LINK TABLE + myMdmLinkSvc.updateLink(newGoldenResource, theResource, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, theMdmTransactionContext); } private void handleMdmCreate(IAnyResource theTargetResource, MatchedGoldenResourceCandidate theGoldenResourceCandidate, MdmTransactionContext theMdmTransactionContext) { - log(theMdmTransactionContext, "MDM has narrowed down to one candidate for matching."); IAnyResource goldenResource = myMdmGoldenResourceFindingSvc.getGoldenResourceFromMatchedGoldenResourceCandidate(theGoldenResourceCandidate, theMdmTransactionContext.getResourceType()); if (myGoldenResourceHelper.isPotentialDuplicate(goldenResource, theTargetResource)) { @@ -146,6 +146,8 @@ public class MdmMatchLinkSvc { myMdmLinkSvc.updateLink(newGoldenResource, theTargetResource, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, theMdmTransactionContext); myMdmLinkSvc.updateLink(newGoldenResource, goldenResource, MdmMatchOutcome.POSSIBLE_DUPLICATE, MdmLinkSourceEnum.AUTO, theMdmTransactionContext); } else { + log(theMdmTransactionContext, "MDM has narrowed down to one candidate for matching."); + if (theGoldenResourceCandidate.isMatch()) { myGoldenResourceHelper.handleExternalEidAddition(goldenResource, theTargetResource, theMdmTransactionContext); myEidUpdateService.applySurvivorshipRulesAndSaveGoldenResource(theTargetResource, goldenResource, theMdmTransactionContext); @@ -156,8 +158,8 @@ public class MdmMatchLinkSvc { } private void handleMdmWithSingleCandidate(IAnyResource theResource, MatchedGoldenResourceCandidate theGoldenResourceCandidate, MdmTransactionContext theMdmTransactionContext) { - log(theMdmTransactionContext, "MDM has narrowed down to one candidate for matching."); if (theMdmTransactionContext.getRestOperation().equals(MdmTransactionContext.OperationType.UPDATE_RESOURCE)) { + log(theMdmTransactionContext, "MDM has narrowed down to one candidate for matching."); myEidUpdateService.handleMdmUpdate(theResource, theGoldenResourceCandidate, theMdmTransactionContext); } else { handleMdmCreate(theResource, theGoldenResourceCandidate, theMdmTransactionContext); diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/CandidateList.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/CandidateList.java index 2a4b325b8d7..47b6aed2076 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/CandidateList.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/CandidateList.java @@ -67,4 +67,8 @@ public class CandidateList { public boolean isEidMatch() { return myStrategy.isEidMatch(); } + + public int size() { + return myList.size(); + } } diff --git a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByEidSvc.java b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByEidSvc.java index 9adf4e524c1..41875b15a7f 100644 --- a/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByEidSvc.java +++ b/hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByEidSvc.java @@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate; */ import ca.uhn.fhir.interceptor.model.RequestPartitionId; +import ca.uhn.fhir.jpa.entity.MdmLink; +import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc; import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc; import ca.uhn.fhir.mdm.api.MdmMatchOutcome; import ca.uhn.fhir.mdm.log.Logs; @@ -46,6 +48,8 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder { private EIDHelper myEIDHelper; @Autowired private MdmResourceDaoSvc myMdmResourceDaoSvc; + @Autowired + private MdmLinkDaoSvc myMdmLinkDaoSvc; @Override protected List findMatchGoldenResourceCandidates(IAnyResource theBaseResource) { @@ -57,6 +61,10 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder { Optional oFoundGoldenResource = myMdmResourceDaoSvc.searchGoldenResourceByEID(eid.getValue(), theBaseResource.getIdElement().getResourceType(), (RequestPartitionId) theBaseResource.getUserData(Constants.RESOURCE_PARTITION_ID)); if (oFoundGoldenResource.isPresent()) { IAnyResource foundGoldenResource = oFoundGoldenResource.get(); + // Exclude manually declared NO_MATCH links from candidates + if (isNoMatch(foundGoldenResource, theBaseResource)) { + continue; + } Long pidOrNull = myIdHelperService.getPidOrNull(foundGoldenResource); MatchedGoldenResourceCandidate mpc = new MatchedGoldenResourceCandidate(new ResourcePersistentId(pidOrNull), MdmMatchOutcome.EID_MATCH); ourLog.debug("Matched {} by EID {}", foundGoldenResource.getIdElement(), eid); @@ -67,6 +75,15 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder { return retval; } + private boolean isNoMatch(IAnyResource theGoldenResource, IAnyResource theSourceResource) { + Optional oLink = myMdmLinkDaoSvc.getLinkByGoldenResourceAndSourceResource(theGoldenResource, theSourceResource); + if (oLink.isEmpty()) { + return false; + } + MdmLink link = oLink.get(); + return link.isNoMatch(); + } + @Override protected CandidateStrategyEnum getStrategy() { return CandidateStrategyEnum.EID; diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java index 894359ca5a2..b66dd12c67a 100644 --- a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java +++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java @@ -88,11 +88,17 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test { protected static final String PAUL_ID = "ID.PAUL.456"; protected static final String FRANK_ID = "ID.FRANK.789"; protected static final String DUMMY_ORG_ID = "Organization/mfr"; + protected static final String EID_1 = "123"; + protected static final String EID_2 = "456"; + private static final Logger ourLog = getLogger(BaseMdmR4Test.class); private static final ContactPoint TEST_TELECOM = new ContactPoint() .setSystem(ContactPoint.ContactPointSystem.PHONE) .setValue("555-555-5555"); private static final String NAME_GIVEN_FRANK = "Frank"; + + + @Autowired protected IFhirResourceDao myPatientDao; @Autowired @@ -604,4 +610,12 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test { org.setId(DUMMY_ORG_ID); return myOrganizationDao.update(org); } + + @Nonnull + protected MdmTransactionContext buildUpdateLinkMdmTransactionContext() { + MdmTransactionContext retval = new MdmTransactionContext(); + retval.setResourceType("Patient"); + retval.setRestOperation(MdmTransactionContext.OperationType.UPDATE_LINK); + return retval; + } } diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImplTest.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImplTest.java new file mode 100644 index 00000000000..8be181e8262 --- /dev/null +++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImplTest.java @@ -0,0 +1,38 @@ +package ca.uhn.fhir.jpa.mdm.svc; + +import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test; +import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc; +import ca.uhn.fhir.mdm.model.MdmTransactionContext; +import org.hl7.fhir.r4.model.Patient; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; + +import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.MATCH; +import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.NO_MATCH; +import static org.junit.jupiter.api.Assertions.assertNotEquals; + +class MdmLinkUpdaterSvcImplTest extends BaseMdmR4Test { + @Autowired + private IMdmLinkUpdaterSvc myMdmLinkUpdaterSvc; + + @Test + public void testUpdateLinkNoMatch() { + // setup + + Patient jane = createPatientAndUpdateLinks(addExternalEID(buildJanePatient(), EID_1)); + Patient originalJaneGolden = getGoldenResourceFromTargetResource(jane); + + MdmTransactionContext mdmCtx = buildUpdateLinkMdmTransactionContext(); + + myMdmLinkUpdaterSvc.updateLink(originalJaneGolden, jane, NO_MATCH, mdmCtx); + Patient newJaneGolden = getGoldenResourceFromTargetResource(jane); + + assertNotEquals(newJaneGolden.getId(), originalJaneGolden.getId()); + + assertLinkCount(2); + + assertLinksMatchResult(NO_MATCH, MATCH); + assertLinksCreatedNewResource(true, true); + assertLinksMatchedByEid(false, false); + } +} diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java index b6d369f22c9..10eb292400f 100644 --- a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java +++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java @@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.entity.MdmLink; import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.mdm.api.IMdmLinkSvc; +import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc; import ca.uhn.fhir.mdm.api.MdmConstants; import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum; import ca.uhn.fhir.mdm.api.MdmMatchOutcome; @@ -15,13 +16,11 @@ import ca.uhn.fhir.mdm.util.MdmResourceUtil; import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.param.TokenParam; import org.hl7.fhir.instance.model.api.IAnyResource; -import org.hl7.fhir.r4.model.Enumerations; import org.hl7.fhir.r4.model.HumanName; import org.hl7.fhir.r4.model.Identifier; import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Practitioner; import org.junit.jupiter.api.Test; -import org.slf4j.Logger; import org.springframework.beans.factory.annotation.Autowired; import java.util.Date; @@ -35,22 +34,26 @@ import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.NO_MATCH; import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.POSSIBLE_DUPLICATE; import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.POSSIBLE_MATCH; import static org.hamcrest.MatcherAssert.assertThat; -import static org.hamcrest.Matchers.*; +import static org.hamcrest.Matchers.blankOrNullString; +import static org.hamcrest.Matchers.equalTo; +import static org.hamcrest.Matchers.equalToIgnoringCase; +import static org.hamcrest.Matchers.hasSize; +import static org.hamcrest.Matchers.in; +import static org.hamcrest.Matchers.is; +import static org.hamcrest.Matchers.not; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertFalse; import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.slf4j.LoggerFactory.getLogger; public class MdmMatchLinkSvcTest extends BaseMdmR4Test { - - private static final Logger ourLog = getLogger(MdmMatchLinkSvcTest.class); - @Autowired IMdmLinkSvc myMdmLinkSvc; @Autowired private EIDHelper myEidHelper; @Autowired private GoldenResourceHelper myGoldenResourceHelper; + @Autowired + private IMdmLinkUpdaterSvc myMdmLinkUpdaterSvc; @Test public void testAddPatientLinksToNewGoldenResourceIfNoneFound() { @@ -211,7 +214,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { //We want to make sure the patients were linked to the same Golden Resource. assertThat(patient, is(sameGoldenResourceAs(janePatient))); - Patient sourcePatient = (Patient) getGoldenResourceFromTargetResource(patient); + Patient sourcePatient = getGoldenResourceFromTargetResource(patient); List identifier = sourcePatient.getIdentifier(); @@ -397,11 +400,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { IBundleProvider bundle = myPatientDao.search(buildGoldenRecordSearchParameterMap()); assertEquals(1, bundle.size()); - Patient sourcePatient = (Patient) bundle.getResources(0, 1).get(0); - //assertEquals(Person.IdentityAssuranceLevel.LEVEL2, sourcePatient.getLink().get(0).getAssurance()); - //assertEquals(Person.IdentityAssuranceLevel.LEVEL1, sourcePatient.getLink().get(1).getAssurance()); - //assertEquals(Person.IdentityAssuranceLevel.LEVEL1, sourcePatient.getLink().get(2).getAssurance()); //TODO GGG MDM: Convert these asserts to checking the MPI_LINK table assertLinksMatchResult(MATCH, POSSIBLE_MATCH, POSSIBLE_MATCH); @@ -490,7 +489,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { @Test public void testPatientUpdateOverwritesGoldenResourceDataOnChanges() { Patient janePatient = createPatientAndUpdateLinks(buildJanePatient()); - Patient janeSourcePatient = (Patient) getGoldenResourceFromTargetResource(janePatient); + Patient janeSourcePatient = getGoldenResourceFromTargetResource(janePatient); //Change Jane's name to paul. Patient patient1 = buildPaulPatient(); @@ -500,7 +499,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { assertThat(janeSourcePatient, is(sameGoldenResourceAs(janePaulPatient))); //Ensure the related GoldenResource was updated with new info. - Patient sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(janePaulPatient); + Patient sourcePatientFromTarget = getGoldenResourceFromTargetResource(janePaulPatient); HumanName nameFirstRep = sourcePatientFromTarget.getNameFirstRep(); assertThat(nameFirstRep.getGivenAsSingleString(), is(equalToIgnoringCase("paul"))); @@ -514,7 +513,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { paul.getBirthDateElement().setValueAsString(incorrectBirthdate); paul = createPatientAndUpdateLinks(paul); - Patient sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(paul); + Patient sourcePatientFromTarget = getGoldenResourceFromTargetResource(paul); assertThat(sourcePatientFromTarget.getBirthDateElement().getValueAsString(), is(incorrectBirthdate)); String correctBirthdate = "1990-06-28"; @@ -522,7 +521,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { paul = updatePatientAndUpdateLinks(paul); - sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(paul); + sourcePatientFromTarget = getGoldenResourceFromTargetResource(paul); assertThat(sourcePatientFromTarget.getBirthDateElement().getValueAsString(), is(equalTo(correctBirthdate))); assertLinkCount(1); } @@ -530,33 +529,51 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { @Test // Test Case #3 public void testUpdatedEidThatWouldRelinkAlsoCausesPossibleDuplicate() { - String EID_1 = "123"; - String EID_2 = "456"; - Patient paul = createPatientAndUpdateLinks(addExternalEID(buildPaulPatient(), EID_1)); - Patient originalPaulPatient = (Patient) getGoldenResourceFromTargetResource(paul); + Patient originalPaulGolden = getGoldenResourceFromTargetResource(paul); Patient jane = createPatientAndUpdateLinks(addExternalEID(buildJanePatient(), EID_2)); - Patient originalJanePatient = (Patient) getGoldenResourceFromTargetResource(jane); + Patient originalJaneGolden = getGoldenResourceFromTargetResource(jane); clearExternalEIDs(paul); addExternalEID(paul, EID_2); updatePatientAndUpdateLinks(paul); - assertThat(originalJanePatient, is(possibleDuplicateOf(originalPaulPatient))); + assertThat(originalJaneGolden, is(possibleDuplicateOf(originalPaulGolden))); + assertThat(jane, is(sameGoldenResourceAs(paul))); + } + + @Test + // Test Case #3a + public void originalLinkIsNoMatch() { + // setup + Patient paul = createPatientAndUpdateLinks(addExternalEID(buildPaulPatient(), EID_1)); + Patient originalPaulGolden = getGoldenResourceFromTargetResource(paul); + + Patient jane = createPatientAndUpdateLinks(addExternalEID(buildJanePatient(), EID_2)); + Patient originalJaneGolden = getGoldenResourceFromTargetResource(jane); + + MdmTransactionContext mdmCtx = buildUpdateLinkMdmTransactionContext(); + myMdmLinkUpdaterSvc.updateLink(originalPaulGolden, paul, NO_MATCH, mdmCtx); + + clearExternalEIDs(paul); + addExternalEID(paul, EID_2); + + // execute + updatePatientAndUpdateLinks(paul); + + // verify + assertThat(originalJaneGolden, is(not(possibleDuplicateOf(originalPaulGolden)))); assertThat(jane, is(sameGoldenResourceAs(paul))); } @Test public void testSinglyLinkedGoldenResourceThatGetsAnUpdatedEidSimplyUpdatesEID() { //Use Case # 2 - String EID_1 = "123"; - String EID_2 = "456"; - Patient paul = createPatientAndUpdateLinks(addExternalEID(buildPaulPatient(), EID_1)); - Patient originalPaulPatient = (Patient) getGoldenResourceFromTargetResource(paul); + Patient originalPaulGolden = getGoldenResourceFromTargetResource(paul); - String oldEid = myEidHelper.getExternalEid(originalPaulPatient).get(0).getValue(); + String oldEid = myEidHelper.getExternalEid(originalPaulGolden).get(0).getValue(); assertThat(oldEid, is(equalTo(EID_1))); clearExternalEIDs(paul); @@ -565,8 +582,8 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test { paul = updatePatientAndUpdateLinks(paul); assertNoDuplicates(); - Patient newlyFoundPaulPatient = (Patient) getGoldenResourceFromTargetResource(paul); - assertThat(originalPaulPatient, is(sameGoldenResourceAs(newlyFoundPaulPatient))); + Patient newlyFoundPaulPatient = getGoldenResourceFromTargetResource(paul); + assertThat(originalPaulGolden, is(sameGoldenResourceAs(newlyFoundPaulPatient))); String newEid = myEidHelper.getExternalEid(newlyFoundPaulPatient).get(0).getValue(); assertThat(newEid, is(equalTo(EID_2))); } diff --git a/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvcTest.java b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvcTest.java new file mode 100644 index 00000000000..d83915aad80 --- /dev/null +++ b/hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvcTest.java @@ -0,0 +1,45 @@ +package ca.uhn.fhir.jpa.mdm.svc.candidate; + +import ca.uhn.fhir.jpa.entity.MdmLink; +import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test; +import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc; +import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum; +import ca.uhn.fhir.mdm.api.MdmMatchResultEnum; +import org.hl7.fhir.r4.model.Patient; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.junit.jupiter.MockitoExtension; +import org.springframework.beans.factory.annotation.Autowired; + +import java.util.List; + +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.hasSize; +import static org.junit.jupiter.api.Assertions.assertEquals; + +@ExtendWith(MockitoExtension.class) +class MdmGoldenResourceFindingSvcTest extends BaseMdmR4Test { + + @Autowired + MdmGoldenResourceFindingSvc myMdmGoldenResourceFindingSvc = new MdmGoldenResourceFindingSvc(); + @Autowired + MdmLinkDaoSvc myMdmLinkDaoSvc; + + @Test + public void testNoMatchCandidatesSkipped() { + // setup + Patient jane = createPatientAndUpdateLinks(addExternalEID(buildJanePatient(), EID_1)); + + // hack the link into a NO_MATCH + List links = myMdmLinkDaoSvc.findMdmLinksBySourceResource(jane); + assertThat(links, hasSize(1)); + MdmLink link = links.get(0); + link.setMatchResult(MdmMatchResultEnum.NO_MATCH); + link.setLinkSource(MdmLinkSourceEnum.MANUAL); + myMdmLinkDaoSvc.save(link); + + // the NO_MATCH golden resource should not be a candidate + CandidateList candidateList = myMdmGoldenResourceFindingSvc.findGoldenResourceCandidates(jane); + assertEquals(0, candidateList.size()); + } +} diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/HibernateSearchIndexWriter.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/HibernateSearchIndexWriter.java index 1b134ea0946..b3b86e6b586 100644 --- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/HibernateSearchIndexWriter.java +++ b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/HibernateSearchIndexWriter.java @@ -74,6 +74,7 @@ public class HibernateSearchIndexWriter { public void writeStringIndex(String theSearchParam, String theValue) { DocumentElement stringIndexNode = getSearchParamIndexNode(theSearchParam, "string"); + // we are assuming that our analyzer matches StringUtil.normalizeStringForSearchIndexing(theValue).toLowerCase(Locale.ROOT)) stringIndexNode.addValue(IDX_STRING_NORMALIZED, theValue);// for default search stringIndexNode.addValue(IDX_STRING_EXACT, theValue); stringIndexNode.addValue(IDX_STRING_TEXT, theValue); diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java index 350018633ec..0f7c1c3bd7a 100644 --- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java +++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java @@ -38,6 +38,7 @@ import java.util.Map; import java.util.Set; import java.util.stream.Collectors; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.*; import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank; @@ -515,9 +516,14 @@ public class SearchParameterMap implements Serializable { if (getLastUpdated() != null) { DateParam lb = getLastUpdated().getLowerBound(); - addLastUpdateParam(b, ParamPrefixEnum.GREATERTHAN_OR_EQUALS, lb); DateParam ub = getLastUpdated().getUpperBound(); - addLastUpdateParam(b, ParamPrefixEnum.LESSTHAN_OR_EQUALS, ub); + + if (isNotEqualsComparator(lb, ub)) { + addLastUpdateParam(b, NOT_EQUAL, getLastUpdated().getLowerBound()); + } else { + addLastUpdateParam(b, GREATERTHAN_OR_EQUALS, lb); + addLastUpdateParam(b, LESSTHAN_OR_EQUALS, ub); + } } if (getCount() != null) { @@ -566,6 +572,10 @@ public class SearchParameterMap implements Serializable { return b.toString(); } + private boolean isNotEqualsComparator(DateParam theLowerBound, DateParam theUpperBound) { + return theLowerBound != null && theUpperBound != null && theLowerBound.getPrefix().equals(NOT_EQUAL) && theUpperBound.getPrefix().equals(NOT_EQUAL); + } + /** * @since 5.5.0 */ @@ -576,10 +586,10 @@ public class SearchParameterMap implements Serializable { @Override public String toString() { ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE); - if (isEmpty() == false) { + if (!isEmpty()) { b.append("params", mySearchParameterMap); } - if (getIncludes().isEmpty() == false) { + if (!getIncludes().isEmpty()) { b.append("includes", getIncludes()); } return b.toString(); @@ -668,7 +678,7 @@ public class SearchParameterMap implements Serializable { /** * Variant of removeByNameAndModifier for unmodified params. * - * @param theName + * @param theName the query parameter key * @return an And/Or List of Query Parameters matching the name with no modifier. */ public List> removeByNameUnmodified(String theName) { diff --git a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestElasticsearchContainerHelper.java b/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestElasticsearchContainerHelper.java index 80dfdf39c3d..0e0dbe3baa4 100644 --- a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestElasticsearchContainerHelper.java +++ b/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestElasticsearchContainerHelper.java @@ -29,7 +29,7 @@ import static java.time.temporal.ChronoUnit.SECONDS; public class TestElasticsearchContainerHelper { - public static final String ELASTICSEARCH_VERSION = "7.16.3"; + public static final String ELASTICSEARCH_VERSION = "7.17.3"; public static final String ELASTICSEARCH_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTICSEARCH_VERSION; public static ElasticsearchContainer getEmbeddedElasticSearch() { diff --git a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/TestDaoSearch.java b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/TestDaoSearch.java index 3203bfe3857..908751bf8b6 100644 --- a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/TestDaoSearch.java +++ b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/TestDaoSearch.java @@ -10,7 +10,10 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.rest.api.SortSpec; import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.server.method.SortParameter; +import org.hamcrest.Matcher; +import org.hamcrest.MatcherAssert; import org.hl7.fhir.instance.model.api.IBaseResource; +import org.hl7.fhir.instance.model.api.IIdType; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; @@ -21,10 +24,16 @@ import javax.annotation.Nonnull; import java.util.List; import java.util.stream.Collectors; +import static org.hamcrest.Matchers.everyItem; +import static org.hamcrest.Matchers.hasItems; +import static org.hamcrest.Matchers.in; +import static org.hamcrest.Matchers.not; + /** * Simplistic implementation of FHIR queries. */ public class TestDaoSearch { + @Configuration public static class Config { @Bean @@ -47,6 +56,55 @@ public class TestDaoSearch { myFhirCtx = theFhirCtx; } + /** + * Assert that the FHIR search has theIds in the search results. + * @param theReason junit reason message + * @param theQueryUrl FHIR query - e.g. /Patient?name=kelly + * @param theIds the resource ids to expect. + */ + public void assertSearchFinds(String theReason, String theQueryUrl, String ...theIds) { + assertSearchResultIds(theQueryUrl, theReason, hasItems(theIds)); + } + + /** + * Assert that the FHIR search has theIds in the search results. + * @param theReason junit reason message + * @param theQueryUrl FHIR query - e.g. /Patient?name=kelly + * @param theIds the id-part of the resource ids to expect. + */ + public void assertSearchFinds(String theReason, String theQueryUrl, IIdType...theIds) { + String[] bareIds = idTypeToIdParts(theIds); + + assertSearchResultIds(theQueryUrl, theReason, hasItems(bareIds)); + } + + public void assertSearchResultIds(String theQueryUrl, String theReason, Matcher> matcher) { + List ids = searchForIds(theQueryUrl); + + MatcherAssert.assertThat(theReason, ids, matcher); + } + + /** + * Assert that the FHIR search does not have theIds in the search results. + * @param theReason junit reason message + * @param theQueryUrl FHIR query - e.g. /Patient?name=kelly + * @param theIds the id-part of the resource ids to not-expect. + */ + public void assertSearchNotFound(String theReason, String theQueryUrl, IIdType ...theIds) { + List ids = searchForIds(theQueryUrl); + + MatcherAssert.assertThat(theReason, ids, everyItem(not(in(idTypeToIdParts(theIds))))); + } + + @Nonnull + private String[] idTypeToIdParts(IIdType[] theIds) { + String[] bareIds = new String[theIds.length]; + for (int i = 0; i < theIds.length; i++) { + bareIds[i] = theIds[i].getIdPart(); + } + return bareIds; + } + public List searchForResources(String theQueryUrl) { IBundleProvider result = searchForBundleProvider(theQueryUrl); return result.getAllResources(); diff --git a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java index d501118a756..ff0341dfe04 100644 --- a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java +++ b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java @@ -41,7 +41,6 @@ import ca.uhn.fhir.rest.param.HasAndListParam; import ca.uhn.fhir.rest.param.HasOrListParam; import ca.uhn.fhir.rest.param.HasParam; import ca.uhn.fhir.rest.param.NumberParam; -import ca.uhn.fhir.rest.param.ParamPrefixEnum; import ca.uhn.fhir.rest.param.QuantityParam; import ca.uhn.fhir.rest.param.ReferenceAndListParam; import ca.uhn.fhir.rest.param.ReferenceOrListParam; @@ -159,10 +158,18 @@ import java.util.Set; import java.util.TreeSet; import java.util.stream.Collectors; +import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS; +import static ca.uhn.fhir.rest.api.Constants.PARAM_ID; import static ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE; import static ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY; import static ca.uhn.fhir.rest.api.Constants.PARAM_TAG; import static ca.uhn.fhir.rest.api.Constants.PARAM_TYPE; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.EQUAL; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.GREATERTHAN_OR_EQUALS; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.LESSTHAN_OR_EQUALS; +import static ca.uhn.fhir.rest.param.ParamPrefixEnum.NOT_EQUAL; import static org.apache.commons.lang3.StringUtils.countMatches; import static org.apache.commons.lang3.StringUtils.leftPad; import static org.hamcrest.CoreMatchers.is; @@ -945,7 +952,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { HasAndListParam hasAnd = new HasAndListParam(); hasAnd.addValue(new HasOrListParam().add(new HasParam("Observation", "subject", "status", "final"))); hasAnd.addValue(new HasOrListParam().add(new HasParam("Observation", "subject", "date", "2001-01-01"))); - map.add("_has", hasAnd); + map.add(PARAM_HAS, hasAnd); List actual = toUnqualifiedVersionlessIdValues(myPatientDao.search(map)); assertThat(actual, containsInAnyOrder(p1id.getValue())); @@ -1025,7 +1032,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|FOO")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "identifier", "urn:system|FOO")); myCaptureQueriesListener.clear(); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(pid0.getValue())); myCaptureQueriesListener.logSelectQueriesForCurrentThread(0); @@ -1033,12 +1040,12 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { // No targets exist params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|UNKNOWN")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "identifier", "urn:system|UNKNOWN")); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), empty()); // Target exists but doesn't link to us params = new SearchParameterMap(); - params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|NOLINK")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "identifier", "urn:system|NOLINK")); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), empty()); } @@ -1081,7 +1088,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { // Double _has params = new SearchParameterMap(); - params.add("_has", new HasParam("Observation", "subject", "_has:DiagnosticReport:result:status", "final")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "_has:DiagnosticReport:result:status", "final")); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), containsInAnyOrder(pid0.getValue())); } @@ -1117,13 +1124,13 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { // No targets exist params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|UNKNOWN")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "identifier", "urn:system|UNKNOWN")); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), empty()); // Target exists but doesn't link to us params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation", "subject", "identifier", "urn:system|NOLINK")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "identifier", "urn:system|NOLINK")); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), empty()); } @@ -1131,7 +1138,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { public void testHasParameterInvalidResourceType() { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation__", "subject", "identifier", "urn:system|FOO")); + params.add(PARAM_HAS, new HasParam("Observation__", "subject", "identifier", "urn:system|FOO")); try { myPatientDao.search(params); fail(); @@ -1144,7 +1151,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { public void testHasParameterInvalidSearchParam() { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation", "subject", "IIIIDENFIEYR", "urn:system|FOO")); + params.add(PARAM_HAS, new HasParam("Observation", "subject", "IIIIDENFIEYR", "urn:system|FOO")); try { myPatientDao.search(params); fail(); @@ -1157,7 +1164,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { public void testHasParameterInvalidTargetPath() { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_has", new HasParam("Observation", "soooooobject", "identifier", "urn:system|FOO")); + params.add(PARAM_HAS, new HasParam("Observation", "soooooobject", "identifier", "urn:system|FOO")); try { myPatientDao.search(params); fail(); @@ -1199,7 +1206,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { mySystemDao.transaction(mySrd, input); SearchParameterMap params = new SearchParameterMap(); - params.add("_id", new TokenParam(null, "DR")); + params.add(PARAM_ID, new TokenParam(null, "DR")); params.addInclude(new Include("DiagnosticReport:subject").setRecurse(true)); params.addInclude(new Include("DiagnosticReport:result").setRecurse(true)); params.addInclude(Observation.INCLUDE_HAS_MEMBER.setRecurse(true)); @@ -1581,17 +1588,17 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1)); params = new SearchParameterMap(); - params.add("_id", new StringParam(id1)); + params.add(PARAM_ID, new StringParam(id1)); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1)); params = new SearchParameterMap(); - params.add("_id", new StringParam("9999999999999999")); + params.add(PARAM_ID, new StringParam("9999999999999999")); assertEquals(0, toList(myPatientDao.search(params)).size()); myCaptureQueriesListener.clear(); params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_id", new StringParam(id2)); + params.add(PARAM_ID, new StringParam(id2)); size = toList(myPatientDao.search(params)).size(); myCaptureQueriesListener.logAllQueries(); assertEquals(0, size); @@ -1653,12 +1660,12 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { // inverse params = SearchParameterMap.newSynchronous(); - params.add("_id", new TokenParam(id1).setModifier(TokenParamModifier.NOT)); + params.add(PARAM_ID, new TokenParam(id1).setModifier(TokenParamModifier.NOT)); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id2)); // Non-inverse params = SearchParameterMap.newSynchronous(); - params.add("_id", new TokenParam(id1)); + params.add(PARAM_ID, new TokenParam(id1)); assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(params)), contains(id1)); } @@ -1669,7 +1676,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_id", new StringParam("DiagnosticReport/123")); + params.add(PARAM_ID, new StringParam("DiagnosticReport/123")); myCaptureQueriesListener.clear(); myDiagnosticReportDao.search(params).size(); List selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread(); @@ -1686,7 +1693,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_id", new StringParam("DiagnosticReport/123")); + params.add(PARAM_ID, new StringParam("DiagnosticReport/123")); params.add("code", new TokenParam("foo", "bar")); myCaptureQueriesListener.clear(); myDiagnosticReportDao.search(params).size(); @@ -1707,8 +1714,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { public void testSearchByIdParamAndOtherSearchParam_QueryIsMinimal() { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_id", new StringParam("DiagnosticReport/123")); - params.add("_id", new StringParam("DiagnosticReport/123")); + params.add(PARAM_ID, new StringParam("DiagnosticReport/123")); + params.add(PARAM_ID, new StringParam("DiagnosticReport/123")); myCaptureQueriesListener.clear(); myDiagnosticReportDao.search(params).size(); List selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread(); @@ -1744,28 +1751,28 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { param = new StringAndListParam(); param.addAnd(new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); param.addAnd(new StringOrListParam().addOr(new StringParam(id1.getIdPart()))); - params.add("_id", param); + params.add(PARAM_ID, param); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1)); params = new SearchParameterMap(); param = new StringAndListParam(); param.addAnd(new StringOrListParam().addOr(new StringParam(id2.getIdPart()))); param.addAnd(new StringOrListParam().addOr(new StringParam(id1.getIdPart()))); - params.add("_id", param); + params.add(PARAM_ID, param); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty()); params = new SearchParameterMap(); param = new StringAndListParam(); param.addAnd(new StringOrListParam().addOr(new StringParam(id2.getIdPart()))); param.addAnd(new StringOrListParam().addOr(new StringParam("9999999999999"))); - params.add("_id", param); + params.add(PARAM_ID, param); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty()); params = new SearchParameterMap(); param = new StringAndListParam(); param.addAnd(new StringOrListParam().addOr(new StringParam("9999999999999"))); param.addAnd(new StringOrListParam().addOr(new StringParam(id2.getIdPart()))); - params.add("_id", param); + params.add(PARAM_ID, param); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty()); } @@ -1791,21 +1798,21 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { } SearchParameterMap params = new SearchParameterMap(); - params.add("_id", new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); + params.add(PARAM_ID, new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1, id2)); params = new SearchParameterMap(); - params.add("_id", new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id1.getIdPart()))); + params.add(PARAM_ID, new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id1.getIdPart()))); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1)); params = new SearchParameterMap(); - params.add("_id", new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam("999999999999"))); + params.add(PARAM_ID, new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam("999999999999"))); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1)); // With lastupdated params = SearchParameterMap.newSynchronous(); - params.add("_id", new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); + params.add(PARAM_ID, new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); params.setLastUpdated(new DateRangeParam(new Date(betweenTime), null)); myCaptureQueriesListener.clear(); @@ -1831,7 +1838,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { } SearchParameterMap params = new SearchParameterMap(); - params.add("_id", new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); + params.add(PARAM_ID, new StringOrListParam().addOr(new StringParam(id1.getIdPart())).addOr(new StringParam(id2.getIdPart()))); assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(id1)); } @@ -2041,7 +2048,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { String param = Observation.SP_COMPONENT_VALUE_QUANTITY; { - QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1"); + QuantityParam v1 = new QuantityParam(GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1"); SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, v1); IBundleProvider result = myObservationDao.search(map); assertThat("Got: " + toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1.getValue())); @@ -2072,7 +2079,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { TokenParam v0 = new TokenParam("http://foo", "code1"); - QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1"); + QuantityParam v1 = new QuantityParam(GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1"); CompositeParam val = new CompositeParam<>(v0, v1); SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, val); myCaptureQueriesListener.clear(); @@ -2082,21 +2089,21 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { } { TokenParam v0 = new TokenParam("http://foo", "code1"); - QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 50, "http://bar", "code1"); + QuantityParam v1 = new QuantityParam(GREATERTHAN_OR_EQUALS, 50, "http://bar", "code1"); CompositeParam val = new CompositeParam<>(v0, v1); IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val)); assertThat(toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1.getValue(), id2.getValue())); } { TokenParam v0 = new TokenParam("http://foo", "code4"); - QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 50, "http://bar", "code1"); + QuantityParam v1 = new QuantityParam(GREATERTHAN_OR_EQUALS, 50, "http://bar", "code1"); CompositeParam val = new CompositeParam<>(v0, v1); IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val)); assertThat(toUnqualifiedVersionlessIdValues(result), empty()); } { TokenParam v0 = new TokenParam("http://foo", "code1"); - QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 50, "http://bar", "code4"); + QuantityParam v1 = new QuantityParam(GREATERTHAN_OR_EQUALS, 50, "http://bar", "code4"); CompositeParam val = new CompositeParam<>(v0, v1); IBundleProvider result = myObservationDao.search(new SearchParameterMap().setLoadSynchronous(true).add(param, val)); assertThat(toUnqualifiedVersionlessIdValues(result), empty()); @@ -2487,7 +2494,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { // Don't load synchronous SearchParameterMap map = new SearchParameterMap(); - map.setLastUpdated(new DateRangeParam().setUpperBound(new DateParam(ParamPrefixEnum.LESSTHAN, "2042-01-01"))); + map.setLastUpdated(new DateRangeParam().setUpperBound(new DateParam(LESSTHAN, "2042-01-01"))); IBundleProvider found = myPatientDao.search(map); Set dates = new HashSet<>(); String searchId = found.getUuid(); @@ -2534,11 +2541,10 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { } SearchParameterMap params; - List result; params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_id", new StringParam("TEST")); + params.add(PARAM_ID, new StringParam("TEST")); assertEquals(1, toList(myPatientDao.search(params)).size()); params = new SearchParameterMap(); @@ -2555,7 +2561,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add("_id", new StringParam("TEST")); + params.add(PARAM_ID, new StringParam("TEST")); assertEquals(0, toList(myPatientDao.search(params)).size()); params = new SearchParameterMap(); @@ -2574,7 +2580,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { public void testSearchForUnknownAlphanumericId() { { SearchParameterMap map = new SearchParameterMap(); - map.add("_id", new StringParam("testSearchForUnknownAlphanumericId")); + map.add(PARAM_ID, new StringParam("testSearchForUnknownAlphanumericId")); IBundleProvider retrieved = myPatientDao.search(map); assertEquals(0, retrieved.size().intValue()); } @@ -2614,55 +2620,37 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless(); } + List result; + { SearchParameterMap params = new SearchParameterMap(); List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); assertThat(patients, hasItems(id1a, id1b, id2)); } - { - SearchParameterMap params = new SearchParameterMap(); - params.setLastUpdated(new DateRangeParam(beforeAny, null)); - List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); - assertThat(patients, hasItems(id1a, id1b, id2)); - } - { - SearchParameterMap params = new SearchParameterMap(); - params.setLastUpdated(new DateRangeParam(beforeR2, null)); - List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); - assertThat(patients, hasItems(id2)); - assertThat(patients, not(hasItems(id1a, id1b))); - } - { - SearchParameterMap params = new SearchParameterMap(); - params.setLastUpdated(new DateRangeParam(beforeAny, beforeR2)); - List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); - assertThat(patients.toString(), patients, not(hasItems(id2))); - assertThat(patients.toString(), patients, (hasItems(id1a, id1b))); - } - { - SearchParameterMap params = new SearchParameterMap(); - params.setLastUpdated(new DateRangeParam(null, beforeR2)); - List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); - assertThat(patients, (hasItems(id1a, id1b))); - assertThat(patients, not(hasItems(id2))); - } + + result = performSearchLastUpdatedAndReturnIds(new DateRangeParam(beforeAny, null)); + assertThat(result, hasItems(id1a, id1b, id2)); + + result = performSearchLastUpdatedAndReturnIds(new DateRangeParam(beforeR2, null)); + assertThat(result, hasItems(id2)); + assertThat(result, not(hasItems(id1a, id1b))); - { - SearchParameterMap params = new SearchParameterMap(); - params.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, beforeR2))); - List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); - assertThat(patients, not(hasItems(id1a, id1b))); - assertThat(patients, (hasItems(id2))); - } - { - SearchParameterMap params = new SearchParameterMap(); - params.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, beforeR2))); - List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); - assertThat(patients, (hasItems(id1a, id1b))); - assertThat(patients, not(hasItems(id2))); - } + result = performSearchLastUpdatedAndReturnIds(new DateRangeParam(beforeAny, beforeR2)); + assertThat(result.toString(), result, not(hasItems(id2))); + assertThat(result.toString(), result, (hasItems(id1a, id1b))); + result = performSearchLastUpdatedAndReturnIds(new DateRangeParam(null, beforeR2)); + assertThat(result, (hasItems(id1a, id1b))); + assertThat(result, not(hasItems(id2))); + + result = performSearchLastUpdatedAndReturnIds(new DateRangeParam(new DateParam(GREATERTHAN_OR_EQUALS, beforeR2))); + assertThat(result, not(hasItems(id1a, id1b))); + assertThat(result, (hasItems(id2))); + + result = performSearchLastUpdatedAndReturnIds(new DateRangeParam(new DateParam(LESSTHAN_OR_EQUALS, beforeR2))); + assertThat(result, (hasItems(id1a, id1b))); + assertThat(result, not(hasItems(id2))); } @Test @@ -2696,40 +2684,66 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { id1b = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless(); } - ourLog.info("Res 1: {}", myPatientDao.read(id0, mySrd).getMeta().getLastUpdatedElement().getValueAsString()); - ourLog.info("Res 2: {}", myPatientDao.read(id1a, mySrd).getMeta().getLastUpdatedElement().getValueAsString()); - ourLog.info("Res 3: {}", myPatientDao.read(id1b, mySrd).getMeta().getLastUpdatedElement().getValueAsString()); + InstantType p0LastUpdated = myPatientDao.read(id0, mySrd).getMeta().getLastUpdatedElement(); + InstantType p1aLastUpdated = myPatientDao.read(id1a, mySrd).getMeta().getLastUpdatedElement(); + InstantType p1bLastUpdated = myPatientDao.read(id1b, mySrd).getMeta().getLastUpdatedElement(); + + ourLog.info("Res 1: {}", p0LastUpdated.getValueAsString()); + ourLog.info("Res 2: {}", p1aLastUpdated.getValueAsString()); + ourLog.info("Res 3: {}", p1bLastUpdated.getValueAsString()); TestUtil.sleepOneClick(); long end = System.currentTimeMillis(); - SearchParameterMap map; + List result; + DateRangeParam dateRange; Date startDate = new Date(start); Date endDate = new Date(end); DateTimeType startDateTime = new DateTimeType(startDate, TemporalPrecisionEnum.MILLI); DateTimeType endDateTime = new DateTimeType(endDate, TemporalPrecisionEnum.MILLI); - map = new SearchParameterMap(); - map.setLastUpdated(new DateRangeParam(startDateTime, endDateTime)); - ourLog.info("Searching: {}", map.getLastUpdated()); - assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a, id1b)); + dateRange = new DateRangeParam(startDateTime, endDateTime); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id1a, id1b)); - map = new SearchParameterMap(); - map.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, startDateTime), new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, endDateTime))); - ourLog.info("Searching: {}", map.getLastUpdated()); - assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a, id1b)); + dateRange = new DateRangeParam(new DateParam(GREATERTHAN_OR_EQUALS, startDateTime), new DateParam(LESSTHAN_OR_EQUALS, endDateTime)); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id1a, id1b)); - map = new SearchParameterMap(); - map.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.GREATERTHAN, startDateTime), new DateParam(ParamPrefixEnum.LESSTHAN, endDateTime))); - ourLog.info("Searching: {}", map.getLastUpdated()); - assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a, id1b)); + dateRange = new DateRangeParam(new DateParam(GREATERTHAN, startDateTime), new DateParam(LESSTHAN, endDateTime)); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id1a, id1b)); - map = new SearchParameterMap(); - map.setLastUpdated(new DateRangeParam(new DateParam(ParamPrefixEnum.GREATERTHAN, startDateTime.getValue()), - new DateParam(ParamPrefixEnum.LESSTHAN, TestUtil.getTimestamp(myPatientDao.read(id1b, mySrd))))); + dateRange = new DateRangeParam(new DateParam(GREATERTHAN, startDateTime.getValue()), new DateParam(LESSTHAN, TestUtil.getTimestamp(myPatientDao.read(id1b, mySrd)))); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id1a)); + + dateRange = new DateRangeParam(new DateParam(EQUAL, p0LastUpdated), new DateParam(EQUAL, p0LastUpdated)); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id0)); + assertThat(result, not(containsInAnyOrder(id1a, id1b))); + + DateTimeType p0LastUpdatedDay = new DateTimeType(p0LastUpdated.getValue(), TemporalPrecisionEnum.DAY); + dateRange = new DateRangeParam(new DateParam(EQUAL, p0LastUpdatedDay), new DateParam(EQUAL, p0LastUpdatedDay)); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id0, id1a, id1b)); + + dateRange = new DateRangeParam(new DateParam(NOT_EQUAL, p0LastUpdated), new DateParam(NOT_EQUAL, p0LastUpdated)); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertThat(result, containsInAnyOrder(id1a, id1b)); + assertThat(result, not(containsInAnyOrder(id0))); + + dateRange = new DateRangeParam(new DateParam(NOT_EQUAL, p0LastUpdatedDay), new DateParam(NOT_EQUAL, p0LastUpdatedDay)); + result = performSearchLastUpdatedAndReturnIds(dateRange); + assertEquals(0, result.size()); + } + + private List performSearchLastUpdatedAndReturnIds(DateRangeParam theDateRange) { + SearchParameterMap map = new SearchParameterMap(); + map.setLastUpdated(theDateRange); ourLog.info("Searching: {}", map.getLastUpdated()); - assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), containsInAnyOrder(id1a)); + return toUnqualifiedVersionlessIds(myPatientDao.search(map)); } @Test @@ -3704,7 +3718,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { sp.setLastUpdated(new DateRangeParam() .setUpperBound(new DateParam("le2019-02-22T17:50:00")) .setLowerBound(new DateParam("ge2019-02-22T13:50:00"))); - IBundleProvider retrieved = myMedicationRequestDao.search(sp); + myMedicationRequestDao.search(sp); myCaptureQueriesListener.logSelectQueriesForCurrentThread(); List queries = myCaptureQueriesListener @@ -3731,7 +3745,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { myCaptureQueriesListener.clear(); sp.setLoadSynchronous(true); - IBundleProvider retrieved = myProcedureDao.search(sp); + myProcedureDao.search(sp); myCaptureQueriesListener.logSelectQueriesForCurrentThread(); // List queries = myCaptureQueriesListener @@ -4126,7 +4140,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { map = new SearchParameterMap(); map.setLoadSynchronous(true); - param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null); + param = new QuantityParam(GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, null); map.add(Observation.SP_VALUE_QUANTITY, param); myCaptureQueriesListener.clear(); found = myObservationDao.search(map); @@ -4141,28 +4155,28 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { map = new SearchParameterMap(); map.setLoadSynchronous(true); - param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, methodName + "units"); + param = new QuantityParam(GREATERTHAN_OR_EQUALS, new BigDecimal("10"), null, methodName + "units"); map.add(Observation.SP_VALUE_QUANTITY, param); found = myObservationDao.search(map); assertThat(toUnqualifiedVersionlessIdValues(found), contains(id1)); map = new SearchParameterMap(); map.setLoadSynchronous(true); - param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, null); + param = new QuantityParam(GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, null); map.add(Observation.SP_VALUE_QUANTITY, param); found = myObservationDao.search(map); assertThat(toUnqualifiedVersionlessIdValues(found), contains(id1)); map = new SearchParameterMap(); map.setLoadSynchronous(true); - param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, methodName + "units"); + param = new QuantityParam(GREATERTHAN_OR_EQUALS, new BigDecimal("10"), "urn:bar:" + methodName, methodName + "units"); map.add(Observation.SP_VALUE_QUANTITY, param); found = myObservationDao.search(map); assertThat(toUnqualifiedVersionlessIdValues(found), contains(id1)); map = new SearchParameterMap(); map.setLoadSynchronous(true); - param = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, new BigDecimal("1000"), "urn:bar:" + methodName, methodName + "units"); + param = new QuantityParam(GREATERTHAN_OR_EQUALS, new BigDecimal("1000"), "urn:bar:" + methodName, methodName + "units"); map.add(Observation.SP_VALUE_QUANTITY, param); found = myObservationDao.search(map); assertThat(toUnqualifiedVersionlessIdValues(found), empty()); @@ -4312,14 +4326,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add(Patient.SP_BIRTHDATE, new DateParam("2011-01-03").setPrefix(ParamPrefixEnum.LESSTHAN)); + params.add(Patient.SP_BIRTHDATE, new DateParam("2011-01-03").setPrefix(LESSTHAN)); List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); assertThat(patients, contains(id2)); } { SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add(Patient.SP_BIRTHDATE, new DateParam("2010-01-01").setPrefix(ParamPrefixEnum.LESSTHAN)); + params.add(Patient.SP_BIRTHDATE, new DateParam("2010-01-01").setPrefix(LESSTHAN)); List patients = toUnqualifiedVersionlessIds(myPatientDao.search(params)); assertThat(patients, empty()); } @@ -4474,7 +4488,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { map.setLoadSynchronous(true); myCaptureQueriesListener.clear(); IBundleProvider values = myPatientDao.search(map); - assertEquals(null, values.size()); + assertNull(values.size()); assertEquals(5, values.getResources(0, 1000).size()); String sql = myCaptureQueriesListener.logSelectQueriesForCurrentThread(0); @@ -4870,13 +4884,13 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { } { SearchParameterMap params = new SearchParameterMap(); - params.add("_security", new TokenParam("urn:taglist", methodName + "1a")); + params.add(PARAM_SECURITY, new TokenParam("urn:taglist", methodName + "1a")); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag1id)); } { SearchParameterMap params = new SearchParameterMap(); - params.add("_profile", new UriParam("http://" + methodName)); + params.add(PARAM_PROFILE, new UriParam("http://" + methodName)); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag2id)); } @@ -4911,14 +4925,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { // One tag SearchParameterMap params = new SearchParameterMap(); - params.add("_tag", new TokenParam("urn:taglist", methodName + "1a")); + params.add(PARAM_TAG, new TokenParam("urn:taglist", methodName + "1a")); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag1id)); } { // Code only SearchParameterMap params = new SearchParameterMap(); - params.add("_tag", new TokenParam(null, methodName + "1a")); + params.add(PARAM_TAG, new TokenParam(null, methodName + "1a")); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag1id)); } @@ -4928,7 +4942,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { TokenOrListParam orListParam = new TokenOrListParam(); orListParam.add(new TokenParam("urn:taglist", methodName + "1a")); orListParam.add(new TokenParam("urn:taglist", methodName + "2a")); - params.add("_tag", orListParam); + params.add(PARAM_TAG, orListParam); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag1id, tag2id)); } @@ -4938,7 +4952,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { TokenOrListParam orListParam = new TokenOrListParam(); orListParam.add(new TokenParam("urn:taglist", methodName + "1a")); orListParam.add(new TokenParam("urn:taglist", methodName + "2a")); - params.add("_tag", orListParam); + params.add(PARAM_TAG, orListParam); params.setLastUpdated(new DateRangeParam(betweenDate, null)); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag2id)); @@ -4951,7 +4965,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { TokenAndListParam andListParam = new TokenAndListParam(); andListParam.addValue(new TokenOrListParam("urn:taglist", methodName + "1a")); andListParam.addValue(new TokenOrListParam("urn:taglist", methodName + "2a")); - params.add("_tag", andListParam); + params.add(PARAM_TAG, andListParam); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertEquals(0, patients.size()); } @@ -4962,7 +4976,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { TokenAndListParam andListParam = new TokenAndListParam(); andListParam.addValue(new TokenOrListParam("urn:taglist", methodName + "1a")); andListParam.addValue(new TokenOrListParam("urn:taglist", methodName + "1b")); - params.add("_tag", andListParam); + params.add(PARAM_TAG, andListParam); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag1id)); } @@ -4993,7 +5007,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { // One tag SearchParameterMap params = SearchParameterMap.newSynchronous(); - params.add("_tag", new TokenParam("urn:taglist", methodName + "1a").setModifier(TokenParamModifier.NOT)); + params.add(PARAM_TAG, new TokenParam("urn:taglist", methodName + "1a").setModifier(TokenParamModifier.NOT)); myCaptureQueriesListener.clear(); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); myCaptureQueriesListener.logSelectQueriesForCurrentThread(0); @@ -5003,14 +5017,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { { // Non existant tag SearchParameterMap params = new SearchParameterMap(); - params.add("_tag", new TokenParam("urn:taglist", methodName + "FOO").setModifier(TokenParamModifier.NOT)); + params.add(PARAM_TAG, new TokenParam("urn:taglist", methodName + "FOO").setModifier(TokenParamModifier.NOT)); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, containsInAnyOrder(tag1id, tag2id)); } { // Common tag SearchParameterMap params = new SearchParameterMap(); - params.add("_tag", new TokenParam("urn:taglist", methodName + "1b").setModifier(TokenParamModifier.NOT)); + params.add(PARAM_TAG, new TokenParam("urn:taglist", methodName + "1b").setModifier(TokenParamModifier.NOT)); List patients = toUnqualifiedVersionlessIds(myOrganizationDao.search(params)); assertThat(patients, empty()); } @@ -5489,7 +5503,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test { myCaptureQueriesListener.clear(); SearchParameterMap params = new SearchParameterMap(); params.setLoadSynchronous(true); - params.add(CommunicationRequest.SP_OCCURRENCE, new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, "2015-08-10T11:33:00-04:00")); + params.add(CommunicationRequest.SP_OCCURRENCE, new DateParam(GREATERTHAN_OR_EQUALS, "2015-08-10T11:33:00-04:00")); IBundleProvider outcome = myCommunicationRequestDao.search(params); myCaptureQueriesListener.logSelectQueriesForCurrentThread(); assertThat(toUnqualifiedVersionlessIdValues(outcome), contains(crId)); diff --git a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java index 2c361d9123e..17e3629b76e 100644 --- a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java +++ b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java @@ -68,6 +68,7 @@ import org.hl7.fhir.r4.model.Reference; import org.hl7.fhir.r4.model.StringType; import org.hl7.fhir.r4.model.ValueSet; import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Nested; @@ -89,14 +90,14 @@ import org.springframework.transaction.PlatformTransactionManager; import javax.persistence.EntityManager; import java.io.IOException; -import java.time.Month; +import java.net.URLEncoder; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; import java.util.function.Consumer; import java.util.stream.Collectors; import static ca.uhn.fhir.jpa.model.util.UcumServiceUtil.UCUM_CODESYSTEM_URL; +import static ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8; import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.Matchers.contains; import static org.hamcrest.Matchers.containsInAnyOrder; @@ -105,6 +106,7 @@ import static org.hamcrest.Matchers.equalTo; import static org.hamcrest.Matchers.hasItem; import static org.hamcrest.Matchers.hasSize; import static org.hamcrest.Matchers.not; +import static org.hamcrest.Matchers.notNullValue; import static org.hamcrest.Matchers.stringContainsInOrder; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; @@ -588,7 +590,50 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest { } } + /** + * Verify unmodified, :contains, and :text searches are case-insensitive and normalized; + * :exact is still sensitive + * https://github.com/hapifhir/hapi-fhir/issues/3584 + */ + @Test + void testStringCaseFolding() { + IIdType kelly = myTestDataBuilder.createPatient(myTestDataBuilder.withGiven("Kelly")); + IIdType keely = myTestDataBuilder.createPatient(myTestDataBuilder.withGiven("Kélly")); + // un-modified, :contains, and :text are all ascii normalized, and case-folded + myTestDaoSearch.assertSearchFinds("lowercase matches capitalized", "/Patient?name=kelly", kelly, keely); + myTestDaoSearch.assertSearchFinds("uppercase matches capitalized", "/Patient?name=KELLY", kelly, keely); + myTestDaoSearch.assertSearchFinds("unmodified is accent insensitive", "/Patient?name=" + urlencode("Kélly"), kelly, keely); + + myTestDaoSearch.assertSearchFinds("contains case-insensitive", "/Patient?name:contains=elly", kelly, keely); + myTestDaoSearch.assertSearchFinds("contains case-insensitive", "/Patient?name:contains=ELLY", kelly, keely); + myTestDaoSearch.assertSearchFinds("contains accent-insensitive", "/Patient?name:contains=ELLY", kelly, keely); + myTestDaoSearch.assertSearchFinds("contains accent-insensitive", "/Patient?name:contains=" + urlencode("éLLY"), kelly, keely); + + myTestDaoSearch.assertSearchFinds("text also accent and case-insensitive", "/Patient?name:text=kelly", kelly, keely); + myTestDaoSearch.assertSearchFinds("text also accent and case-insensitive", "/Patient?name:text=KELLY", kelly, keely); + myTestDaoSearch.assertSearchFinds("text also accent and case-insensitive", "/Patient?name:text=" + urlencode("KÉLLY"), kelly, keely); + + myTestDaoSearch.assertSearchFinds("exact case and accent sensitive", "/Patient?name:exact=Kelly", kelly); + // ugh. Our url parser won't handle raw utf8 urls. It requires everything to be single-byte encoded. + myTestDaoSearch.assertSearchFinds("exact case and accent sensitive", "/Patient?name:exact=" + urlencode("Kélly"), keely); + myTestDaoSearch.assertSearchNotFound("exact case and accent sensitive", "/Patient?name:exact=KELLY,kelly", kelly); + myTestDaoSearch.assertSearchNotFound("exact case and accent sensitive", + "/Patient?name:exact=" + urlencode("KÉLLY,kélly"), + keely); + + myTestDaoSearch.assertSearchFinds("exact accent sensitive", "/Patient?name:exact=Kelly", kelly); + myTestDaoSearch.assertSearchFinds("exact accent sensitive", "/Patient?name:exact=" + urlencode("Kélly"), keely); + myTestDaoSearch.assertSearchNotFound("exact accent sensitive", "/Patient?name:exact=Kelly", keely); + myTestDaoSearch.assertSearchNotFound("exact accent sensitive", "/Patient?name:exact=" + + urlencode("kélly"), kelly); + + } + + /** Our url parser requires all chars to be single-byte, and in utf8, that means ascii. */ + private String urlencode(String theParam) { + return URLEncoder.encode(theParam, CHARSET_UTF8); + } private void assertObservationSearchMatchesNothing(String message, SearchParameterMap map) { assertObservationSearchMatches(message, map); @@ -637,14 +682,13 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest { "}"; Observation o = myFhirCtx.newJsonParser().parseResource(Observation.class, json); - myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless(); + IIdType id = myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless(); // no error. + assertThat(id, notNullValue()); } } - - @Test public void testExpandWithIsAInExternalValueSet() { createExternalCsAndLocalVs(); @@ -1570,7 +1614,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest { } - @Disabled // keeping to check search scrolling + @Disabled("keeping to debug search scrolling") @Test public void withoutCount() { createObservations(600); diff --git a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLR4Test.java b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLR4Test.java index 361eb1dd92b..4e730953429 100644 --- a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLR4Test.java +++ b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLR4Test.java @@ -10,7 +10,9 @@ import org.apache.http.client.methods.HttpPost; import org.apache.http.entity.ContentType; import org.apache.http.entity.StringEntity; import org.hl7.fhir.instance.model.api.IIdType; +import org.hl7.fhir.r4.model.DateType; import org.hl7.fhir.r4.model.Patient; +import org.intellij.lang.annotations.Language; import org.junit.jupiter.api.MethodOrderer; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.TestMethodOrder; @@ -43,14 +45,37 @@ public class GraphQLR4Test extends BaseResourceProviderR4Test { try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) { String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8); ourLog.info(resp); - assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" + - " \"name\":[{\n" + - " \"family\":\"FAM\",\n" + - " \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" + - " },{\n" + - " \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" + - " }]\n" + - "}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp)); + @Language("json") + String expected = """ + { + "name":[{ + "family":"FAM", + "given":["GIVEN1","GIVEN2"] + },{ + "given":["GivenOnly1","GivenOnly2"] + }] + }"""; + assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + expected + DATA_SUFFIX), TestUtil.stripWhitespace(resp)); + } + + } + + @Test + public void testInstance_Patient_Birthdate() throws IOException { + initTestPatients(); + + String query = "{birthDate}"; + HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query)); + + try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) { + String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8); + ourLog.info(resp); + @Language("json") + String expected = """ + { + "birthDate": "1965-08-09" + }"""; + assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + expected + DATA_SUFFIX), TestUtil.stripWhitespace(resp)); } } @@ -113,13 +138,13 @@ public class GraphQLR4Test extends BaseResourceProviderR4Test { initTestPatients(); String uri = ourServerBase + "/$graphql"; - HttpPost httpGet = new HttpPost(uri); - httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON)); + HttpPost httpPost = new HttpPost(uri); + httpPost.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON)); // Repeat a couple of times to make sure it doesn't fail after the first one. At one point // the generator polluted the structure userdata and failed the second time for (int i = 0; i < 3; i++) { - try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) { + try (CloseableHttpResponse response = ourHttpClient.execute(httpPost)) { String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8); ourLog.info("Response has size: {}", FileUtil.formatFileSize(resp.length())); assertEquals(200, response.getStatusLine().getStatusCode()); @@ -144,24 +169,27 @@ public class GraphQLR4Test extends BaseResourceProviderR4Test { try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) { String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8); ourLog.info(resp); + + @Language("json") + String expected = """ + { + "Patient":{ + "name":[{ + "family":"FAM", + "given":["GIVEN1","GIVEN2"] + },{ + "given":["GivenOnly1","GivenOnly2"] + }] + } + }"""; assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + - "{\n" + - "\"Patient\":{\n" + - "\"name\":[{\n" + - "\"family\":\"FAM\",\n" + - "\"given\":[\"GIVEN1\",\"GIVEN2\"]\n" + - "},{\n" + - "\"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" + - "}]\n" + - "}\n" + - "}" + + expected + DATA_SUFFIX), TestUtil.stripWhitespace(resp)); } } - @Test public void testRoot_Search_Patient() throws IOException { initTestPatients(); @@ -172,20 +200,23 @@ public class GraphQLR4Test extends BaseResourceProviderR4Test { try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) { String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8); ourLog.info(resp); - assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" + - " \"PatientList\":[{\n" + - " \"name\":[{\n" + - " \"family\":\"FAM\",\n" + - " \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" + - " },{\n" + - " \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" + - " }]\n" + - " },{\n" + - " \"name\":[{\n" + - " \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" + - " }]\n" + - " }]\n" + - "}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp)); + @Language("json") + String expected = """ + { + "PatientList":[{ + "name":[{ + "family":"FAM", + "given":["GIVEN1","GIVEN2"] + },{ + "given":["GivenOnly1","GivenOnly2"] + }] + },{ + "name":[{ + "given":["GivenOnlyB1","GivenOnlyB2"] + }] + }] + }"""; + assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + expected + DATA_SUFFIX), TestUtil.stripWhitespace(resp)); } } @@ -214,6 +245,7 @@ public class GraphQLR4Test extends BaseResourceProviderR4Test { p.addName() .addGiven("GivenOnly1") .addGiven("GivenOnly2"); + p.setBirthDateElement(new DateType("1965-08-09")); myPatientId0 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless(); p = new Patient(); diff --git a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantServerR4Test.java b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantServerR4Test.java index bccb0389c88..7cb1a865d68 100644 --- a/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantServerR4Test.java +++ b/hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantServerR4Test.java @@ -14,6 +14,7 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants; import ca.uhn.fhir.jpa.partition.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions; +import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.test.utilities.ITestDataBuilder; @@ -270,6 +271,20 @@ public class MultitenantServerR4Test extends BaseMultitenantResourceProviderR4Te } + @Test + public void testPartitionInRequestDetails_UpdateWithWrongTenantId() { + IIdType idA = createPatient(withTenant(TENANT_A), withActiveTrue()).toVersionless(); + IBaseResource patientA = buildPatient(withId(idA), withActiveTrue()); + RequestDetails requestDetails = new SystemRequestDetails(); + requestDetails.setTenantId(TENANT_B); + try { + myPatientDao.update((Patient) patientA, requestDetails); + fail(); + } catch (InvalidRequestException e) { + assertEquals(Msg.code(2079) + "Resource " + ((Patient) patientA).getResourceType() + "/" + ((Patient) patientA).getIdElement().getIdPart() + " is not known", e.getMessage()); + } + } + @Test public void testDirectDaoAccess_PartitionInRequestDetails_Update() { diff --git a/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/json/MdmRulesJson.java b/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/json/MdmRulesJson.java index 0d49c25c0d6..8e89d243a16 100644 --- a/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/json/MdmRulesJson.java +++ b/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/json/MdmRulesJson.java @@ -204,7 +204,7 @@ public class MdmRulesJson implements IModelJson { return myVectorMatchResultMap.getFieldMatchNames(theVector); } - public String getDetailedFieldMatchResultForUnmatchedVector(long theVector) { + public String getDetailedFieldMatchResultWithSuccessInformation(long theVector) { List fieldMatchResult = new ArrayList<>(); for (int i = 0; i < myMatchFieldJsonList.size(); ++i) { if ((theVector & (1 << i)) == 0) { diff --git a/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvc.java b/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvc.java index d87abec7c3d..2c1618783e2 100644 --- a/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvc.java +++ b/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvc.java @@ -92,10 +92,9 @@ public class MdmResourceMatcherSvc { MdmMatchResultEnum matchResultEnum = myMdmRulesJson.getMatchResult(matchResult.vector); matchResult.setMatchResultEnum(matchResultEnum); if (ourLog.isDebugEnabled()) { - if (matchResult.isMatch() || matchResult.isPossibleMatch()) { - ourLog.debug("{} {} with field matchers {}", matchResult, theRightResource.getIdElement().toUnqualifiedVersionless(), myMdmRulesJson.getFieldMatchNamesForVector(matchResult.vector)); - } else if (ourLog.isTraceEnabled()) { - ourLog.trace("{} {}. Field matcher results: {}", matchResult, theRightResource.getIdElement().toUnqualifiedVersionless(), myMdmRulesJson.getDetailedFieldMatchResultForUnmatchedVector(matchResult.vector)); + ourLog.debug("{} {}: {}", matchResult.getMatchResultEnum(), theRightResource.getIdElement().toUnqualifiedVersionless(), matchResult); + if (ourLog.isTraceEnabled()) { + ourLog.trace("Field matcher results:\n{}", myMdmRulesJson.getDetailedFieldMatchResultWithSuccessInformation(matchResult.vector)); } } return matchResult; @@ -135,6 +134,9 @@ public class MdmResourceMatcherSvc { MdmMatchEvaluation matchEvaluation = fieldComparator.match(theLeftResource, theRightResource); if (matchEvaluation.match) { vector |= (1 << i); + ourLog.trace("Match: Successfully matched matcher {} with score {}.", fieldComparator.getName(), matchEvaluation.score); + } else { + ourLog.trace("No match: Matcher {} did not match (score: {}).", fieldComparator.getName(), matchEvaluation.score); } score += matchEvaluation.score; appliedRuleCount += 1; diff --git a/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java b/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java index 2fdd66a58f2..d4671ce180a 100644 --- a/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java +++ b/hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java @@ -42,6 +42,7 @@ import org.slf4j.Logger; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; +import javax.annotation.Nonnull; import java.util.ArrayList; import java.util.List; import java.util.Objects; @@ -80,6 +81,7 @@ public class GoldenResourceHelper { * @param theIncomingResource The resource that will be used as the starting point for the MDM linking. * @param theMdmTransactionContext */ + @Nonnull public T createGoldenResourceFromMdmSourceResource(T theIncomingResource, MdmTransactionContext theMdmTransactionContext) { validateContextSupported(); diff --git a/hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvcLoggingTest.java b/hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvcLoggingTest.java new file mode 100644 index 00000000000..7ee69ea4d22 --- /dev/null +++ b/hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvcLoggingTest.java @@ -0,0 +1,107 @@ +package ca.uhn.fhir.mdm.rules.svc; + +import ca.uhn.fhir.context.RuntimeSearchParam; +import ca.uhn.fhir.mdm.api.MdmMatchOutcome; +import ca.uhn.fhir.mdm.log.Logs; +import ch.qos.logback.classic.Level; +import ch.qos.logback.classic.Logger; +import ch.qos.logback.classic.spi.ILoggingEvent; +import ch.qos.logback.core.read.ListAppender; +import org.hl7.fhir.r4.model.Patient; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.mock; +import static org.mockito.Mockito.when; + +public class MdmResourceMatcherSvcLoggingTest extends BaseMdmRulesR4Test { + private MdmResourceMatcherSvc myMdmResourceMatcherSvc; + private Patient myJohn; + private Patient myJohny; + + @Override + @BeforeEach + public void before() { + super.before(); + + when(mySearchParamRetriever.getActiveSearchParam("Patient", "birthdate")).thenReturn(mock(RuntimeSearchParam.class)); + when(mySearchParamRetriever.getActiveSearchParam("Patient", "identifier")).thenReturn(mock(RuntimeSearchParam.class)); + when(mySearchParamRetriever.getActiveSearchParam("Practitioner", "identifier")).thenReturn(mock(RuntimeSearchParam.class)); + when(mySearchParamRetriever.getActiveSearchParam("Medication", "identifier")).thenReturn(mock(RuntimeSearchParam.class)); + when(mySearchParamRetriever.getActiveSearchParam("Patient", "active")).thenReturn(mock(RuntimeSearchParam.class)); + + myMdmResourceMatcherSvc = buildMatcher(buildActiveBirthdateIdRules()); + + myJohn = buildJohn(); + myJohny = buildJohny(); + + myJohn.addName().setFamily("LastName"); + myJohny.addName().setFamily("DifferentLastName"); + + } + + @Test + public void testMatchWillProvideLogsAboutSuccessOnTraceLevel() { + Logger logger = (Logger) Logs.getMdmTroubleshootingLog(); + logger.setLevel(Level.TRACE); + + MemoryAppender memoryAppender = createAndAssignMemoryAppender(logger); + + MdmMatchOutcome result = myMdmResourceMatcherSvc.match(myJohn, myJohny); + assertNotNull(result); + + //this test assumes, that the defined algorithm for calculating scores doesn't change + assertTrue(memoryAppender.contains("No match: Matcher patient-last did not match (score: 0.4", Level.TRACE)); + assertTrue(memoryAppender.contains("Match: Successfully matched matcher patient-given with score 0.8", Level.TRACE)); + } + + @Test + public void testMatchWillProvideSummaryOnMatchingSuccessForEachField() { + Patient someoneElse = buildSomeoneElse(); + Logger logger = (Logger) Logs.getMdmTroubleshootingLog(); + logger.setLevel(Level.TRACE); + + MemoryAppender memoryAppender = createAndAssignMemoryAppender(logger); + + MdmMatchOutcome result = myMdmResourceMatcherSvc.match(myJohn, someoneElse); + assertNotNull(result); + + assertTrue(memoryAppender.contains("NO_MATCH Patient/", Level.DEBUG)); + assertTrue(memoryAppender.contains("Field matcher results:\npatient-given: NO\npatient-last: YES", Level.TRACE)); + } + + protected Patient buildSomeoneElse() { + Patient patient = new Patient(); + patient.addName().addGiven("SomeOneElse"); + patient.addName().setFamily("LastName"); + patient.setId("Patient/3"); + return patient; + } + + + protected MemoryAppender createAndAssignMemoryAppender(Logger theLogger) { + + MemoryAppender memoryAppender = new MemoryAppender(); + memoryAppender.setContext(theLogger.getLoggerContext()); + theLogger.addAppender(memoryAppender); + memoryAppender.start(); + + return memoryAppender; + } + + public static class MemoryAppender extends ListAppender { + public void reset() { + this.list.clear(); + } + + public boolean contains(String string, Level level) { + return this.list.stream() + .anyMatch(event -> event.toString().contains(string) + && event.getLevel().equals(level)); + } + + } + +} diff --git a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobCoordinator.java b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobCoordinator.java index db52e78e0c2..74dbd33ddcd 100644 --- a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobCoordinator.java +++ b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobCoordinator.java @@ -52,7 +52,10 @@ public interface IJobCoordinator { */ List getInstances(int thePageSize, int thePageIndex); - List getRecentInstances(int thePageSize, int thePageIndex); + /** + * Fetch job instances + */ + List getRecentInstances(int theCount, int theStart); void cancelInstance(String theInstanceId) throws ResourceNotFoundException; diff --git a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java index 601cadab264..9f65ad2db23 100644 --- a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java +++ b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java @@ -24,7 +24,6 @@ import ca.uhn.fhir.batch2.impl.BatchWorkChunk; import ca.uhn.fhir.batch2.model.JobInstance; import ca.uhn.fhir.batch2.model.WorkChunk; -import java.util.Collection; import java.util.List; import java.util.Optional; @@ -70,9 +69,9 @@ public interface IJobPersistence { List fetchInstances(int thePageSize, int thePageIndex); /** - * Fetch instance in 'myCreateTime' descending order + * Fetch instances ordered by myCreateTime DESC */ - Collection fetchRecentInstances(int thePageSize, int thePageIndex); + List fetchRecentInstances(int thePageSize, int thePageIndex); /** * Fetch a given instance and update the stored status diff --git a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobCoordinatorImpl.java b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobCoordinatorImpl.java index b0b694f9e99..dc67190ee88 100644 --- a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobCoordinatorImpl.java +++ b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobCoordinatorImpl.java @@ -162,9 +162,9 @@ public class JobCoordinatorImpl extends BaseJobService implements IJobCoordinato } @Override - public List getRecentInstances(int thePageSize, int thePageIndex) { - return myJobPersistence.fetchRecentInstances(thePageSize, thePageIndex).stream() - .map(this::massageInstanceForUserAccess).collect(Collectors.toList()); + public List getRecentInstances(int theCount, int theStart) { + return myJobPersistence.fetchRecentInstances(theCount, theStart) + .stream().map(this::massageInstanceForUserAccess).collect(Collectors.toList()); } @Override diff --git a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImpl.java b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImpl.java index c8f89dd692e..14596bfb733 100644 --- a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImpl.java +++ b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImpl.java @@ -71,6 +71,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank; *
  • For instances that are COMPLETE, purges chunk data
    • *
  • For instances that are IN_PROGRESS where at least one chunk is FAILED, marks instance as FAILED and propagates the error message to the instance, and purges chunk data
    • *
  • For instances that are IN_PROGRESS with an error message set where no chunks are ERRORED or FAILED, clears the error message in the instance (meaning presumably there was an error but it cleared)
    • + *
  • For instances that are IN_PROGRESS and isCancelled flag is set marks them as ERRORED and indicating the current running step if any
    • *
  • For instances that are COMPLETE or FAILED and are old, delete them entirely
    • * *

    @@ -125,6 +126,7 @@ public class JobMaintenanceServiceImpl extends BaseJobService implements IJobMai for (JobInstance instance : instances) { if (processedInstanceIds.add(instance.getInstanceId())) { + handleCancellation(instance); cleanupInstance(instance, progressAccumulator); triggerGatedExecutions(instance, progressAccumulator); } @@ -136,6 +138,21 @@ public class JobMaintenanceServiceImpl extends BaseJobService implements IJobMai } } + private void handleCancellation(JobInstance theInstance) { + if (! theInstance.isCancelled()) { return; } + + if (theInstance.getStatus() == StatusEnum.QUEUED || theInstance.getStatus() == StatusEnum.IN_PROGRESS) { + String msg = "Job instance cancelled"; + if (theInstance.getCurrentGatedStepId() != null) { + msg += " while running step " + theInstance.getCurrentGatedStepId(); + } + theInstance.setErrorMessage(msg); + theInstance.setStatus(StatusEnum.CANCELLED); + myJobPersistence.updateInstance(theInstance); + } + + } + private void cleanupInstance(JobInstance theInstance, JobChunkProgressAccumulator theProgressAccumulator) { switch (theInstance.getStatus()) { case QUEUED: @@ -146,6 +163,7 @@ public class JobMaintenanceServiceImpl extends BaseJobService implements IJobMai break; case COMPLETED: case FAILED: + case CANCELLED: if (theInstance.getEndTime() != null) { long cutoff = System.currentTimeMillis() - PURGE_THRESHOLD; if (theInstance.getEndTime().getTime() < cutoff) { @@ -157,7 +175,8 @@ public class JobMaintenanceServiceImpl extends BaseJobService implements IJobMai break; } - if ((theInstance.getStatus() == StatusEnum.COMPLETED || theInstance.getStatus() == StatusEnum.FAILED) && !theInstance.isWorkChunksPurged()) { + if ((theInstance.getStatus() == StatusEnum.COMPLETED || theInstance.getStatus() == StatusEnum.FAILED + || theInstance.getStatus() == StatusEnum.CANCELLED) && !theInstance.isWorkChunksPurged()) { theInstance.setWorkChunksPurged(true); myJobPersistence.deleteChunks(theInstance.getInstanceId()); myJobPersistence.updateInstance(theInstance); @@ -214,6 +233,8 @@ public class JobMaintenanceServiceImpl extends BaseJobService implements IJobMai failedChunkCount++; errorMessage = chunk.getErrorMessage(); break; + case CANCELLED: + break; } } diff --git a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/SynchronizedJobPersistenceWrapper.java b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/SynchronizedJobPersistenceWrapper.java index 56c52361ae6..99cc71af692 100644 --- a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/SynchronizedJobPersistenceWrapper.java +++ b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/SynchronizedJobPersistenceWrapper.java @@ -24,7 +24,6 @@ import ca.uhn.fhir.batch2.api.IJobPersistence; import ca.uhn.fhir.batch2.model.JobInstance; import ca.uhn.fhir.batch2.model.WorkChunk; -import java.util.Collection; import java.util.List; import java.util.Optional; @@ -65,7 +64,7 @@ public class SynchronizedJobPersistenceWrapper implements IJobPersistence { } @Override - public Collection fetchRecentInstances(int thePageSize, int thePageIndex) { + public List fetchRecentInstances(int thePageSize, int thePageIndex) { return myWrap.fetchRecentInstances(thePageSize, thePageIndex); } diff --git a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/StatusEnum.java b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/StatusEnum.java index e645f12bb45..06dab306d4c 100644 --- a/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/StatusEnum.java +++ b/hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/StatusEnum.java @@ -51,7 +51,12 @@ public enum StatusEnum { * Task has failed and is known to be unrecoverable. There is no reason to believe that retrying will * result in a different outcome. */ - FAILED(true); + FAILED(true), + + /** + * Task has been cancelled. + */ + CANCELLED(true); private final boolean myIncomplete; private static Set ourIncompleteStatuses; diff --git a/hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImplTest.java b/hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImplTest.java index 6f5ad680fdc..b5f75ada647 100644 --- a/hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImplTest.java +++ b/hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/impl/JobMaintenanceServiceImplTest.java @@ -3,6 +3,7 @@ package ca.uhn.fhir.batch2.impl; import ca.uhn.fhir.batch2.api.IJobCompletionHandler; import ca.uhn.fhir.batch2.api.IJobPersistence; import ca.uhn.fhir.batch2.api.JobCompletionDetails; +import ca.uhn.fhir.batch2.model.JobDefinition; import ca.uhn.fhir.batch2.model.JobInstance; import ca.uhn.fhir.batch2.model.JobWorkNotification; import ca.uhn.fhir.batch2.model.StatusEnum; @@ -11,6 +12,7 @@ import ca.uhn.fhir.jpa.subscription.channel.api.IChannelProducer; import com.google.common.collect.Lists; import org.hl7.fhir.r4.model.DateTimeType; import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.ArgumentCaptor; @@ -28,6 +30,7 @@ import static ca.uhn.fhir.batch2.impl.JobCoordinatorImplTest.createWorkChunkStep import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNull; +import static org.junit.jupiter.api.Assertions.assertTrue; import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.anyInt; import static org.mockito.ArgumentMatchers.eq; @@ -244,6 +247,62 @@ public class JobMaintenanceServiceImplTest extends BaseBatch2Test { verifyNoMoreInteractions(myJobPersistence); } + + @Nested + public class CancellationTests { + + @Test + public void afterFirstMaintenancePass() { + // Setup + myJobDefinitionRegistry.addJobDefinition(createJobDefinition(JobDefinition.Builder::gatedExecution)); + when(myJobPersistence.fetchWorkChunksWithoutData(eq(INSTANCE_ID), eq(100), eq(0))).thenReturn(Lists.newArrayList( + createWorkChunkStep2().setStatus(StatusEnum.QUEUED).setId(CHUNK_ID), + createWorkChunkStep2().setStatus(StatusEnum.QUEUED).setId(CHUNK_ID_2) + )); + JobInstance instance1 = createInstance(); + instance1.setCurrentGatedStepId(STEP_1); + when(myJobPersistence.fetchInstances(anyInt(), eq(0))).thenReturn(Lists.newArrayList(instance1)); + + mySvc.runMaintenancePass(); + + // Execute + instance1.setCancelled(true); + + mySvc.runMaintenancePass(); + + // Verify + assertEquals(StatusEnum.CANCELLED, instance1.getStatus()); + assertTrue(instance1.getErrorMessage().startsWith("Job instance cancelled")); + } + + @Test + public void afterSecondMaintenancePass() { + // Setup + myJobDefinitionRegistry.addJobDefinition(createJobDefinition(JobDefinition.Builder::gatedExecution)); + when(myJobPersistence.fetchWorkChunksWithoutData(eq(INSTANCE_ID), eq(100), eq(0))).thenReturn(Lists.newArrayList( + createWorkChunkStep2().setStatus(StatusEnum.QUEUED).setId(CHUNK_ID), + createWorkChunkStep2().setStatus(StatusEnum.QUEUED).setId(CHUNK_ID_2) + )); + JobInstance instance1 = createInstance(); + instance1.setCurrentGatedStepId(STEP_1); + when(myJobPersistence.fetchInstances(anyInt(), eq(0))).thenReturn(Lists.newArrayList(instance1)); + + mySvc.runMaintenancePass(); + mySvc.runMaintenancePass(); + + // Execute + instance1.setCancelled(true); + + mySvc.runMaintenancePass(); + + // Verify + assertEquals(StatusEnum.CANCELLED, instance1.getStatus()); + assertTrue(instance1.getErrorMessage().startsWith("Job instance cancelled")); + } + + } + + private static Date parseTime(String theDate) { return new DateTimeType(theDate).getValue(); } diff --git a/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java b/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java index 4d8d8cfe58e..2f1185d2dc9 100644 --- a/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java +++ b/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java @@ -74,6 +74,13 @@ public interface ITestDataBuilder { }; } + + /** Patient.name.given */ + default Consumer withGiven(String theName) { + return withPrimitiveAttribute("name.given", theName); + } + + /** * Set Patient.birthdate */ @@ -293,5 +300,4 @@ public interface ITestDataBuilder { booleanType.setValueAsString(theValue); activeChild.getMutator().addValue(theTarget, booleanType); } - }