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tadghdotasekTynerGjssteve-corbett-smilecdrfil512
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GM1 Mergeback (#5203)
* 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 <[email protected]> Co-authored-by: peartree <[email protected]> * 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 <[email protected]> * Rename file to force IT mode * _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 <[email protected]> * documentation update (#5154) Co-authored-by: leif stawnyczy <[email protected]> * 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 <[email protected]> * _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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: michaelabuckley <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * dont use new API for a bit (#5190) * licenses * wip * Fix API usage * wip * Version bump --------- Co-authored-by: dotasek <[email protected]> Co-authored-by: TynerGjs <[email protected]> Co-authored-by: Steve Corbett <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: Ken Stevens <[email protected]> Co-authored-by: peartree <[email protected]> Co-authored-by: jdar8 <[email protected]> Co-authored-by: justindar <[email protected]> Co-authored-by: volodymyr-korzh <[email protected]> Co-authored-by: Nathan Doef <[email protected]> Co-authored-by: Etienne Poirier <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: leif stawnyczy <[email protected]> Co-authored-by: michaelabuckley <[email protected]> Co-authored-by: Luke deGruchy <[email protected]> Co-authored-by: jmarchionatto <[email protected]> Co-authored-by: juan.marchionatto <[email protected]> Co-authored-by: Justin McKelvy <[email protected]> Co-authored-by: justin.mckelvy <[email protected]> Co-authored-by: LalithE <[email protected]>
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‎hapi-deployable-pom/pom.xml

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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir</artifactId>
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<version>6.9.2-SNAPSHOT</version>
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<version>6.9.3-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>

‎hapi-fhir-android/pom.xml

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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>6.9.2-SNAPSHOT</version>
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<version>6.9.3-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</parent>

‎hapi-fhir-base/pom.xml

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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
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<version>6.9.2-SNAPSHOT</version>
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<version>6.9.3-SNAPSHOT</version>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</parent>

‎hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/UriParamQualifierEnum.java

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* Value <code>:below</code>
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* </p>
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*/
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BELOW(":below");
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BELOW(":below"),
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/**
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* The contains modifier allows clients to indicate that a supplied URI input should be matched
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* as a case-insensitive and combining-character insensitive match anywhere in the target URI.
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* <p>
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* Value <code>:contains</code>
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* </p>
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*/
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CONTAINS(":contains");
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private static final Map<String, UriParamQualifierEnum> KEY_TO_VALUE;
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‎hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlUtil.java

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import java.net.URISyntaxException;
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import java.net.URL;
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import java.net.URLDecoder;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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return parameters;
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}
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/**
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* Creates list of sub URIs candidates for search with :above modifier
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* Example input: http://[host]/[pathPart1]/[pathPart2]
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* Example output: http://[host], http://[host]/[pathPart1], http://[host]/[pathPart1]/[pathPart2]
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*
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* @param theUri String URI parameter
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* @return List of URI candidates
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*/
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public static List<String> getAboveUriCandidates(String theUri) {
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try {
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URI uri = new URI(theUri);
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if (uri.getScheme() == null || uri.getHost() == null) {
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throwInvalidRequestExceptionForNotValidUri(theUri, null);
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}
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} catch (URISyntaxException theCause) {
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throwInvalidRequestExceptionForNotValidUri(theUri, theCause);
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}
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List<String> candidates = new ArrayList<>();
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Path path = Paths.get(theUri);
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candidates.add(path.toString().replace(":/", "://"));
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while (path.getParent() != null && path.getParent().toString().contains("/")) {
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candidates.add(path.getParent().toString().replace(":/", "://"));
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path = path.getParent();
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}
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return candidates;
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}
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private static void throwInvalidRequestExceptionForNotValidUri(String theUri, Exception theCause) {
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throw new InvalidRequestException(
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Msg.code(2419) + String.format("Provided URI is not valid: %s", theUri), theCause);
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}
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public static class UrlParts {
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private String myParams;
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private String myResourceId;

‎hapi-fhir-bom/pom.xml

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<modelVersion>4.0.0</modelVersion>
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<artifactId>hapi-fhir-bom</artifactId>
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<version>6.9.2-SNAPSHOT</version>
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<packaging>pom</packaging>
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<name>HAPI FHIR BOM</name>
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<version>6.9.2-SNAPSHOT</version>
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<version>6.9.3-SNAPSHOT</version>
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‎hapi-fhir-checkstyle/pom.xml

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<relativePath>../pom.xml</relativePath>
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‎hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

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‎hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

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<version>6.9.2-SNAPSHOT</version>
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‎hapi-fhir-cli/pom.xml

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<version>6.9.2-SNAPSHOT</version>
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<version>6.9.3-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>

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