Rel 6 8 2 mb (#5299)
* version bump * Bump to core release 6.0.22 (#5028) * Bump to core release 6.0.16 * Bump to core version 6.0.20 * Fix errors thrown as a result of VersionSpecificWorkerContextWrapper * Bump to core 6.0.22 * Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127) * dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID * added changelog * changed to valid version number * changed to valid version number, need to be ordered by version number... * 5123 - Use DEFAULT partition for server-based requests if none specified (#5124) 5123 - Use DEFAULT partition for server-based requests if none specified * consent remove all suppresses next link in bundle (#5119) * added FIXME with source of issue * added FIXME with root cause * added FIXME with root cause * Providing solution to the issue and removing fixmes. * Providing changelog * auto-formatting. * Adding new test. * Adding a new test for standard paging * let's try this and see if it works...? * fix tests * cleanup to trigger a new run * fixing tests --------- Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> * 5117 MDM Score for No Match Fields Should Not Be Included in Total Score (#5118) * fix, test, changelog * fix, test, changelog --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * _source search parameter needs to support modifiers (#5095) _source search parameter needs to support modifiers - added support form :contains, :missing, :above modifiers * Fix HFQL docs (#5151) * Expunge operation on codesystem may throw 500 internal error with precondition fail message. (#5156) * Initial failing test. * Solution with changelog. * fixing format. * Addressing comment from code review. * fixing failing test. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * documentation update (#5154) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * Fix hsql jdbc driver deps (#5168) Avoid non-included classes in jdbc driver dependencies. * $delete-expunge over 10k resources will now delete all resources (#5144) * First commit with very rough fix and unit test. * Refinements to ResourceIdListStep and Batch2DaoSvcImpl. Make LoadIdsStepTest pass. Enhance Batch2DaoSvcImplTest. * Spotless * Fix checkstyle errors. * Fix test failures. * Minor refactoring. New unit test. Finalize changelist. * Spotless fix. * Delete now useless code from unit test. * Delete more useless code. * Test pre-commit hook * More spotless fixes. * Address most code review feedback. * Remove use of pageSize parameter and see if this breaks the pipeline. * Remove use of pageSize parameter and see if this breaks the pipeline. * Fix the noUrl case by passing an unlimited Pegeable instead. Effectively stop using page size for most databases. * Deprecate the old method and have it call the new one by default. * updating documentation (#5170) Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> * _source search parameter modifiers for Subscription matching (#5159) * _source search parameter modifiers for Subscription matching - test, implementation and changelog * Removal of meta tags during updates do not trigger subscription (#5181) * Initial failing test. * adding solution; fixing documentation; * spotless apply * adding changelog * modifying current test --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * Issue 5173 get gateway everything doesnt return all patients (#5174) * Failing test * Also set offset and count in base DAO override * Changelog * Fix for specific case where count has been set in parameters * spotless * Improve checks --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> * Do not 500 and continue IG ingestion when different IGs try to save different ValueSets with colliding FHIR IDs (#5175) * First commit with failing unit test and small tweaks. * Swallow resource version exceptions from colliding ValueSet OIDs and log a descriptive error instead. Add more detailed unit testing. * Tweaks to logic and update the changelog. Reverse all changes to TermReadSvcImpl. * Revert PackageResourceParsingSvc to release branch baseline. * Accept code reviewer suggestion to change changelog description. Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> --------- Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> * Fix link * Remove target slf4j version * dont use new API for a bit (#5191) * Return DropIdGeneratorTask from the Builder to permit clients to mutate the (#5193) DropIdGeneratorTask. * Dqm performance bug update and provider loader fix (#5180) * update tests, move properties, update operation loader * update wip * remove test * fixing tests, adding config * update config and provider loader * fix bundles * fix cache settings on tests * version bump and change log * version bump * fix formatting * CVE-2022-45868 * wip cve change * cve h2 add back in --------- Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> * bulkExportReuse with POST and GET (#5161) * string manipulation * Code to ensure bulkExportReuse works with POST and GET requests * Added formatting changes * Fixed tests that were not working * Formatting * Code clean up * fixing test failures * fixing test failures * Removed arrOfParams to now utilize ObjectMapper * Removing stack trace and adding an exception * Fixed test issue * formatting * formatting * Resolving code review comments * Reduce size of subscription max results (#5194) * Reduce MAX_SUBSCRIPTION_RESULTS to 10000 * Add changelog * 5037 goldenresource remains when target resource deleted (#5038) * draft test and fix * remove unused fields * remove unused fields * remove unused fields * draft test + solution for possible match case * combine sql statement + more error checking * add test case for possible duplicate * add config for autodeleting grs * refactoring, adding support for mongo, docs * refactoring + fixing mongo queries * add changelogs * fix both way link removal * clean up test comments * rename method * remove unnecessary bean * merge master/resolve conflicts * mvn spotless * address comment * changes to avoid version bumping * spotless * change error code --------- Co-authored-by: justindar <justin.dar@smilecdr.com> * dont use new API for a bit (#5190) * licenses * Fixing terminology upload with large file. (#5204) * create initial test * adding fix; adding changelog; * fixing format. --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com> * up version to 6.8.0 from snapshot * fix up some duplicate deps for skipping * Force deployment of other projects * make dummy java class to pass sonatype checks * make dummy java class to pass sonatype checks * Cheeky test removal * Another test removal * Updating version to: 6.8.1 post release. * adding back in tests for release pipelines * Fix bad version insert * Bump to core library version 6.0.22.2 (#5261) * Bump to core library version 6.0.22.2 * Bump HAPI to 6.8.1-SNAPSHOT, core library version to 6.0.22.2 * up version to 6.8.1 * Prevent remote deployment * Updating version to: 6.8.2 post release. * Re-add deploy plugin skip * re-add version * Bump core library version to 6.0.22.2 * Bump HAPI to 6.8.2-SNAPSHOT * Fix up version enum * Version bump * Updating version to: 6.8.3 post release. * mvn spotless:apply --------- Co-authored-by: tadgh <garygrantgraham@gmail.com> Co-authored-by: dotasek <david.otasek@smilecdr.com> Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com> Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com> Co-authored-by: Ken Stevens <khstevens@gmail.com> Co-authored-by: Ken Stevens <ken@smilecdr.com> Co-authored-by: peartree <etienne.poirier@smilecdr.com> Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com> Co-authored-by: justindar <justin.dar@smilecdr.com> Co-authored-by: volodymyr-korzh <132366313+volodymyr-korzh@users.noreply.github.com> Co-authored-by: Nathan Doef <n.doef@protonmail.com> Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com> Co-authored-by: TipzCM <leif.stawnyczy@gmail.com> Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local> Co-authored-by: michaelabuckley <michaelabuckley@gmail.com> Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com> Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com> Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com> Co-authored-by: Justin McKelvy <60718638+Capt-Mac@users.noreply.github.com> Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com> Co-authored-by: LalithE <132382565+LalithE@users.noreply.github.com> Co-authored-by: Long Ma <long@smilecdr.com> Co-authored-by: markiantorno <markiantorno@gmail.com> Co-authored-by: volodymyr <volodymyr.korzh@smilecdr.com>
This commit is contained in:
longma1
GitHub
parent
7ecc0e66c8
commit
0c42229985
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@ -28,6 +28,7 @@ import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
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import ca.uhn.fhir.parser.json.JsonLikeStructure;
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import com.fasterxml.jackson.core.JsonGenerator;
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import com.fasterxml.jackson.core.JsonParser;
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import com.fasterxml.jackson.core.StreamReadConstraints;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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@ -388,6 +389,15 @@ public class JacksonStructure implements JsonLikeStructure {
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retVal = retVal.disable(JsonGenerator.Feature.AUTO_CLOSE_TARGET);
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retVal = retVal.disable(JsonParser.Feature.AUTO_CLOSE_SOURCE);
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retVal = retVal.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
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retVal.getFactory().setStreamReadConstraints(createStreamReadConstraints());
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return retVal;
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}
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private static StreamReadConstraints createStreamReadConstraints() {
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return StreamReadConstraints.builder()
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.maxStringLength(Integer.MAX_VALUE)
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.build();
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}
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}
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@ -119,7 +119,8 @@ public enum VersionEnum {
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V6_6_0,
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V6_7_0,
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V6_8_0,
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V6_8_1,
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V6_8_2,
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V6_9_0,
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V7_0_0;
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 5205
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title: "Previously, uploading a large vocabulary file (like Loinc) through the upload-external-code-system command would
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return an error. The issue has been fixed."
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@ -0,0 +1 @@
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Note: this release has been decommissioned, and you should not be using it. Please upgrade to a newer version.
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@ -0,0 +1,3 @@
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---
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release-date: "2023-08-31"
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codename: "Yucatán"
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@ -0,0 +1 @@
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Note: this release has been decommissioned, and you should not be using it. Please upgrade to a newer version.
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@ -0,0 +1,3 @@
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---
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release-date: "2023-09-05"
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codename: "Yucatán"
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@ -10,9 +10,13 @@ import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
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import ca.uhn.fhir.parser.json.JsonLikeStructure;
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import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
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import ca.uhn.fhir.parser.view.ExtPatient;
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import ca.uhn.fhir.util.AttachmentUtil;
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import ca.uhn.fhir.util.ParametersUtil;
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import ca.uhn.fhir.util.TestUtil;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.ICompositeType;
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import org.hl7.fhir.r4.model.Extension;
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import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.Patient;
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@ -21,6 +25,7 @@ import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.Reader;
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import java.io.StringReader;
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import java.io.Writer;
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@ -63,6 +68,22 @@ public class JsonLikeParserTest {
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assertEquals(parsed.getClass().getName(), resource.getClass().getName(), "reparsed resource classes not equal");
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}
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@Test
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public void testJacksonStructureCanLoadLoincTerminogy() throws IOException {
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// given
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IBaseParameters inputParametersForLoinc = getUploadTerminologyCommandInputParametersForLoinc();
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String s = ourCtx.newJsonParser().encodeResourceToString(inputParametersForLoinc);
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StringReader stringReader = new StringReader(s);
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// when
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JsonLikeStructure jsonLikeStructure = new JacksonStructure();
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jsonLikeStructure.load(stringReader);
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// then
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assertNotNull(jsonLikeStructure.getRootObject());
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}
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/**
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* Test JSON-Like writer using custom stream writer
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*
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@ -151,14 +172,34 @@ public class JsonLikeParserTest {
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assertEquals(0, va.getExtension().size());
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}
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private IBaseParameters getUploadTerminologyCommandInputParametersForLoinc() throws IOException {
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IBaseParameters inputParameters = ParametersUtil.newInstance(ourCtx);
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ParametersUtil.addParameterToParametersUri(
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ourCtx, inputParameters, "system", "http://loinc.org");
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try(InputStream inputStream = JsonLikeParserTest.class.getResourceAsStream("/Loinc_2.72.zip")) {
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ICompositeType attachment = AttachmentUtil.newInstance(ourCtx);
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AttachmentUtil.setContentType(ourCtx, attachment, "application/zip");
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AttachmentUtil.setUrl(ourCtx, attachment, "Loinc_2.72.zip");
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AttachmentUtil.setData(ourCtx, attachment, IOUtils.toByteArray(inputStream));
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ParametersUtil.addParameterToParameters(
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ourCtx, inputParameters, "file", attachment);
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}
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return inputParameters;
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}
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@AfterAll
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public static void afterClassClearContext() {
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TestUtil.randomizeLocaleAndTimezone();
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}
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public static class JsonLikeMapWriter extends BaseJsonLikeWriter {
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private Map<String,Object> target;
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2
pom.xml
2
pom.xml
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@ -897,7 +897,7 @@
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</licenses>
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<properties>
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<fhir_core_version>6.0.22</fhir_core_version>
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<fhir_core_version>6.0.22.2</fhir_core_version>
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<spotless_version>2.37.0</spotless_version>
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<ucum_version>1.0.3</ucum_version>
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<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
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@ -0,0 +1,4 @@
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/**
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* This class exists to satisfy Sonatype.
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*/
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public class Sample {}
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