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6486 implement patient merge (#6568)
* begin with failing test * wpi merge operation provider * wip code resolve references and some refactoring * respect status code set in providers * more validation and code to update resources after refs are updated * added source-delete parameter and some validation tests on result-patient * update test * update test * return target patient as output parameter, do not add replacedby link to target if src is to be deleted * output definition * ignore identifiers in ref, more unit tests, return target in preview mode * output definition * return input parameters in the merge operation output * copy identifiers from source to target (no duplicate check) * add shared identifier * add shared identifier * moar asserts * moar asserts * fixing result patient * fixing result patient * fixing result patient * add duplicate check when copying source identifiers to target * copy result-patient before passing it to service * add preview to test * update preview asserts * move IReplaceReferencesSvc to storage-package, and call replaceReference in patient merge * moar tests * cleanup * add task test * add replace references test * kebab-case replace references * add sync -> async switch * test * test * start migrating to stream * validate result-patient does not have link to source if delete-source is true * add update count to msg in preview mode * spotless * change page size -> batch size and create new default max in storage settings * spotless * switched to patch transaction * switched to patch transaction * switched to patch transaction * switched to patch transaction * strip version from returned task * spotless * spotless * async replace references test passes * align tests * test small batch size * do src and target updates in trx, add validation src is not already replaced * start building batch 2 improve dao * start building batch 2 improve dao * start building batch 2 improve dao * move test setup out to helper * move replace references tests out * switch helper to use dao * incresed unit test coverage * build out batch * build out batch * update test to add link to result-patient only if the source is not to be deleted * batch passes test * batch passes test * batch passes test * made patient-merge return the Task returned from replace references * batch passes test * batch passes test * consolidate async and sync supporting methods into a single storage service * consolidate async and sync supporting methods into a single storage service * add merge batch job * add merge batch job * added FIXMES for ED * added FIXMES for ED * update test to not validate task in preview mode * mark identfier copied from source to target as old * copyright headers * runMaintenancePass before checking merge task status, and renamed test method for merge * fix test * fix test * default * invoke async merge job in merge service * starting work on new docs * starting work on new docs * document $replace-references * separate default from max * fixme * moar fixme * moar fixme * ken last fixme * return 202 status on async merge, update MergeBatchTest to do more validations * async success message, inject mergeservice, add async merge unit tests * make validatePatchResultBundle static again * added test for adding reference while merge in progress, and merge error handler * fixed * fixed * added error handler to replace references job * review * javadoc * organize imports * make ValidationResult immutable * make ValidationResult immutable * rename ReplaceReferencesRequest * rename ReplaceReferencesRequest * rename MergeResourceHelper * rename MergeResourceHelper * javadoc * split merge validation service out from merge service * split merge validation service out from merge service * split merge validation service out from merge service * review feedback * review feedback * rename param constants * rename param constants * remove IdentifierUtil for visibility * remove IdentifierUtil for visibility * final review of hapi side * review feedback * review feedback * fix checkstyle errors, rename MergeOperationInputParameters and add Msg.code * fix replace reference parameter type, and some copyright headers * review feedback * review feedback * review feedback * review feedback * review feedback * review feedback * review feedback * review feedback * move $merge into JPA R4 * move $merge into JPA R4 * still need to return 412 * still need to return 412 * return 412 * moar tests * moar tests * fix async batch size * fix async batch size * fix async batch size * exception code * exception code * fix bean wiring * fix bean wiring * fix test * fix test * fix test * fix test * fix test * bump pom versions --------- Co-authored-by: Ken Stevens <[email protected]>
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69 changes: 69 additions & 0 deletions
69
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/StopLimitAccumulator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| /*- | ||
| * #%L | ||
| * HAPI FHIR - Core Library | ||
| * %% | ||
| * Copyright (C) 2014 - 2024 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% | ||
| */ | ||
| package ca.uhn.fhir.util; | ||
|
|
||
| import jakarta.annotation.Nonnull; | ||
|
|
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| import java.util.ArrayList; | ||
| import java.util.Collections; | ||
| import java.util.List; | ||
| import java.util.concurrent.atomic.AtomicBoolean; | ||
| import java.util.stream.Stream; | ||
|
|
||
| /** | ||
| * This class collects items from a stream to a given limit and know whether there are | ||
| * still more items beyond that limit. | ||
| * | ||
| * @param <T> the type of object being streamed | ||
| */ | ||
| public class StopLimitAccumulator<T> { | ||
| private final boolean isTruncated; | ||
| private final List<T> myList; | ||
|
|
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| private StopLimitAccumulator(List<T> theList, boolean theIsTruncated) { | ||
| myList = Collections.unmodifiableList(theList); | ||
| isTruncated = theIsTruncated; | ||
| } | ||
|
|
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| public static <T> StopLimitAccumulator<T> fromStreamAndLimit(@Nonnull Stream<T> theItemStream, long theLimit) { | ||
| assert theLimit > 0; | ||
| AtomicBoolean isBeyondLimit = new AtomicBoolean(false); | ||
| List<T> accumulator = new ArrayList<>(); | ||
|
|
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| theItemStream | ||
| .limit(theLimit + 1) // Fetch one extra item to see if there are any more items past our limit | ||
| .forEach(item -> { | ||
| if (accumulator.size() < theLimit) { | ||
| accumulator.add(item); | ||
| } else { | ||
| isBeyondLimit.set(true); | ||
| } | ||
| }); | ||
| return new StopLimitAccumulator<>(accumulator, isBeyondLimit.get()); | ||
| } | ||
|
|
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| public boolean isTruncated() { | ||
| return isTruncated; | ||
| } | ||
|
|
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| public List<T> getItemList() { | ||
| return myList; | ||
| } | ||
| } |
69 changes: 69 additions & 0 deletions
69
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/StopLimitAccumulatorTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| package ca.uhn.fhir.util; | ||
|
|
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| import org.junit.jupiter.api.Test; | ||
|
|
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| import java.util.List; | ||
| import java.util.stream.Stream; | ||
|
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| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertFalse; | ||
| import static org.junit.jupiter.api.Assertions.assertThrows; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
|
|
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| class StopLimitAccumulatorTest { | ||
|
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| @Test | ||
| void testFromStreamAndLimit_withNoTruncation() { | ||
| // setup | ||
| Stream<Integer> stream = Stream.of(1, 2, 3, 4, 5); | ||
| int limit = 5; | ||
|
|
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| // execute | ||
| StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit); | ||
|
|
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| // verify | ||
| assertFalse(accumulator.isTruncated(), "The result should not be truncated"); | ||
| assertEquals(List.of(1, 2, 3, 4, 5), accumulator.getItemList(), "The list should contain all items within the limit"); | ||
| } | ||
|
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| @Test | ||
| void testFromStreamAndLimit_withTruncation() { | ||
| // setup | ||
| Stream<Integer> stream = Stream.of(1, 2, 3, 4, 5, 6, 7); | ||
| int limit = 5; | ||
|
|
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| // execute | ||
| StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit); | ||
|
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| // verify | ||
| assertTrue(accumulator.isTruncated(), "The result should be truncated"); | ||
| assertEquals(List.of(1, 2, 3, 4, 5), accumulator.getItemList(), "The list should contain only the items within the limit"); | ||
| } | ||
|
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| @Test | ||
| void testFromStreamAndLimit_withEmptyStream() { | ||
| // setup | ||
| Stream<Integer> stream = Stream.empty(); | ||
| int limit = 5; | ||
|
|
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| // execute | ||
| StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit); | ||
|
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| // verify | ||
| assertFalse(accumulator.isTruncated(), "The result should not be truncated for an empty stream"); | ||
| assertTrue(accumulator.getItemList().isEmpty(), "The list should be empty"); | ||
| } | ||
|
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| @Test | ||
| void testImmutabilityOfItemList() { | ||
| // setup | ||
| Stream<Integer> stream = Stream.of(1, 2, 3); | ||
| int limit = 3; | ||
|
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| StopLimitAccumulator<Integer> accumulator = StopLimitAccumulator.fromStreamAndLimit(stream, limit); | ||
|
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| // execute and Assert | ||
| List<Integer> itemList = accumulator.getItemList(); | ||
| assertThrows(UnsupportedOperationException.class, () -> itemList.add(4), "The list should be immutable"); | ||
| } | ||
| } |
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