Bulk export reducer step fix mergeback (#4606)

* One more fix for #4467

* Enabling massIngestionMode causes incomplete resource deletion (#4476)

* Adding initial test.

* Adding fix and subsequent test.

* Adding changelog.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Provide the capability to request that the name of the subscription matching channel be unqualified (#4464)

* Adding initial test.

* Adding initial solution implementation.

* Adding change log and code clean up.

* addressing comments from 1st code review.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Change visibility of migration method (#4471)

* change migration visibility

* add empty migration method for 640

---------

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484)

* First commit:  Make SubscriptionValidatingInterceptor aware of which Pointcut is being called.  In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED.   Fix resulting compile errors in various unit tests.

* Fix/enhance unit tests.  Mark methods as deprecated instead of deleting them.  Add proper error code.  Complete changelog.

* Remove erroneous TODOs and tweak the validation logic.

* Enhance unit tests and fix changelog.

* Reindex batch job fails when processing deleted resources. (#4482)

* adding changelog.

* Providing solution and adding changelog.

* Adding new test.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* cleaning up checkstyle files (#4470)

* cleaning up checkstyle files

* One more fix for #4467 (#4469)

* added exlusions for files at base project level so checkstyle doesn't error out

* duplicate error code from merge

* changing lifecycle goal for all module checkstyle check

* moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code

* wip

* trying to figure out why pipeline cannot copy files

* removing modules that don't actually need to be built.

* I messed up the version

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* Bump core to 5.6.881 (#4496)

* Bump core to 5.6.881-SNAPSHOT

* Work on fixing tests

* Work on fixing tests 2

* Bump to core release

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>

* Issue 4486 mdm inconsistent possible match score values (#4487)

* Extract method for readability

* Save always normalized score values in POSSIBLE_MATCH links.

* Avoid setting properties to null values. Adjust test.

* Simplify fix

* Fix test. Add RangeTestHelper.

---------

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Revert "cleaning up checkstyle files (#4470)"

This reverts commit efae3b5d5f.

* core version fix

* Loosen rules for id helper

* License

* fix batch2 reduction step (#4499)

* fix bug where FINALIZE jobs are not cancellable

* moved reduction step to message hander

* moving reduction step to queue

* addingchangelog

* cleaning up

* review fixes

* review fix'

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* Scheduled batch 2 bulk export job and binary delete (#4492)

* First commit:  Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted.

* Refine solution and add a concrete unit test but still work to do.

* Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline.

* Unit tests complete.  New Msg code for new IJobPersistence.fetchInstances() method.  Cleanup TODOs and add others.

* Finish final touches on implementation.

* Add changelog.

* Various cleanup.

* Code review feedback.

* Small tweak to changelog.

* Last code review tweak.

* Address more code review comments.

* Reverse changes to consider work chunks.  Add a constant for write-to-binary.

* Change bulk import test for valueUri type (#4503)

* change tests

* suggested test change

* CVE resolutions (#4513)

* Bump Postgres for CVE

* Bump jetty

* Verison bump

* Remove comments

* Revrt bump

* Add check in scanner (#4518)

* 4516 create hapi fhir cli command to clear stale lock entries (#4517)

* Initial implementation

* better tests

* Add changelog and docs

* Forgotten files

* Code review comments

* Fix checkstyle

* Unable to Expunge CodeSystem (#4507)

* changes for GL-3943

* changes for GL-3943

---------

Co-authored-by: isaacwen <isaac.wen@smilecdr.com>

* New line::

* Update to documentation regarding narrative generation; (#4521)

Providing changelog;

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* changed what score is set for mdmlinks that created new golden resource (#4514)

* changed what score is set for mdmlinks that created new golden resource

* fix test

---------

Co-authored-by: Long Ma <long@smilecdr.com>

* REVERT: change to operationoutcome.html

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527)

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* added change log

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fix build (#4530)

* Making narrative_generation.md reference an html snippet (#4531)

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)

* fix + test

* minor fix

* Addressing suggestion

* Minor changes

* 4441 rel 6 4 bad references creation bug (#4519)

* adding a test

* fail in the case of ref enforce on type and on write and autocreate are all true

* update to code

* removing a line

* cleanup

* removing check on urn

* changing just to trigger a build

* adding a comment to the pom

* updating test for better information

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* fixed channel import null pointer exception from null header (#4534)

* retryCount 0 on null header + test + changelog

* suggested changes

* Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535)

This reverts commit 53252b8d15.

* Better error handling for when channel type is not supported (#4538)

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Avoid logging message payloads that contain sensitive data (#4537)

Don't log payloads - they may contain sensitive data.

* Bulk Export Bug With Many Resources and Low Max File Size (#4506)

* failing test

* fix + changelog

* tweak

* add method to IJobPersistence to use a Stream

* tweak

* tweak

* decrease test time

* clean up

* code review comments

* version bump

* Increase timeout limit to match BulkExportUseCaseTest

* shorten test

* maintenance pass

* add logging

* Revert "add logging"

This reverts commit b0453fd953.

* Revert "maintenance pass"

This reverts commit bbc7418d51.

* test

* trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp

* shorten tests

* logging

* move test location

* fixes a regression caused my change in hapi-fhir

* timeout

* Revert "fixes a regression caused my change in hapi-fhir"

This reverts commit 4b58013149.

* testing

* Revert "testing"

This reverts commit aafc95c2f3.

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

* bump ver

* License updates'

* Downgrade dep'

* Updating version to: 6.4.1 post release.

* Add javadocs and sources to our serviceloaders

* Reset version

* Change parent

* Remove bumped version

* License fixes, new parent

* Updating version to: 6.4.1 post release.

* Fix bad creation of versionenum

* Improve performance on bulk export

* Add changelog

* Start working on cleaned up reducer

* Clean up batch calls

* Work on issues

* Build fixes

* typedbundleprovider getallresources override (#4552)

* typedbundleprovider getallresources override

* added test to immunization tests that validates pagination does not result in null pointer if over default queryCount

* moved HapiFhirDal test to its own test class

* removed unused imports

* Update to use JpaStorageSettings

* adding changelog for issue 4551

* fix changelog spacing

* changelog type  to fix

---------

Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

* Add backport info

* Upgrade core to 5.6.97, make adjustments in hapi-fhir, and ensure that all tests pass (#4579)

* First commit:  Create new branch from the release branch with changes from James' branch.  This probably won't compile as the work is incomplete.

* Second round of changes from integrating James' branch.

* Mark most test failures with TODOs.

* Add whitespace

* Add changes to FhirPathR4 to set FHIRPathEngine to non-strict FP evaluation.

* Fix CreatePackageCommandTest to assert null instead of empty string.  Comments on tests that fail due to the double-quote encoding problem.

* Downgrade to core 5.6.97.

* Fix another test and remove TODOs.

* Fix changelog.

* Clean up some erroneous changes and TODOs.

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Fix up dal test

* Address leftover code review feedback from the upgrade to core 5.6.97. (#4585)

* Exclude pinned core deps

* Force pin structs

* Add model changes to IBaseCoding and related changes (#4587)

* Add IbaseCoding changes, and tinder changes

* Fix up tag definition

* converter addition

* Fix unit test and add changelog.

* Add jira to changelog.

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Fix changelog

* Tidy metadata

* Test fixing

* Test fixes

* Work on progress

* Add changelog

* Build tweak

* Fixes

* Disable intermittently failing tests. (#4593)

* rename tests to IT

* Disable more intermittently failing tests (#4595)

* Disable more intermittently failing tests.

* Disable another intermittently failing tests.

* ITify

* Disable yet another intermittently failing tests. (#4596)

* disable

* disables

* Fixes

* disables

* Fix compile

* Test fixes

* Updating version to: 6.4.2 post release.

* Bump to 6.4.2-SNAPSHOT

* Fix compile

* fix version

* Address review comments

* Review comments

* Version bump

* Compile fix

* Test fixes

* Compile fixes

* One more compile fix

* Test fixes

* Version bump

* Resolve fixme

---------

Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>
Co-authored-by: dotasek <dotasek.dev@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: samguntersmilecdr <123124187+samguntersmilecdr@users.noreply.github.com>
Co-authored-by: Isaac Wen <76772867+isaacwen@users.noreply.github.com>
Co-authored-by: isaacwen <isaac.wen@smilecdr.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.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: Jonathan Percival <jonathan.i.percival@gmail.com>
This commit is contained in:
James Agnew 2023-03-01 14:52:36 -05:00 committed by GitHub
parent 2083b7ca74
commit ae1d249d99
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
186 changed files with 854690 additions and 1076 deletions

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -133,6 +133,15 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-others.xml"); structureDefinitionResources.add("/org/hl7/fhir/r4/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4/model/extension/extension-definitions.xml"); structureDefinitionResources.add("/org/hl7/fhir/r4/model/extension/extension-definitions.xml");
break; break;
case R4B:
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/valuesets.xml");
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/v2-tables.xml");
terminologyResources.add("/org/hl7/fhir/r4b/model/valueset/v3-codesystems.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-types.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/profile/profiles-others.xml");
structureDefinitionResources.add("/org/hl7/fhir/r4b/model/extension/extension-definitions.xml");
break;
case R5: case R5:
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-resources.xml"); structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-resources.xml");
structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-types.xml"); structureDefinitionResources.add("/org/hl7/fhir/r5/model/profile/profiles-types.xml");
@ -221,15 +230,41 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
@Override @Override
public IBaseResource fetchStructureDefinition(String theUrl) { public IBaseResource fetchStructureDefinition(String theUrl) {
String url = theUrl; String url = theUrl;
if (url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) { if (!url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
// no change if (url.indexOf('/') == -1) {
} else if (url.indexOf('/') == -1) {
url = URL_PREFIX_STRUCTURE_DEFINITION + url; url = URL_PREFIX_STRUCTURE_DEFINITION + url;
} else if (StringUtils.countMatches(url, '/') == 1) { } else if (StringUtils.countMatches(url, '/') == 1) {
url = URL_PREFIX_STRUCTURE_DEFINITION_BASE + url; url = URL_PREFIX_STRUCTURE_DEFINITION_BASE + url;
} }
}
Map<String, IBaseResource> structureDefinitionMap = provideStructureDefinitionMap(); Map<String, IBaseResource> structureDefinitionMap = provideStructureDefinitionMap();
return structureDefinitionMap.get(url); IBaseResource retVal = structureDefinitionMap.get(url);
if (retVal == null) {
if (url.startsWith(URL_PREFIX_STRUCTURE_DEFINITION)) {
/*
* A few built-in R4 SearchParameters have the wrong casing for primitive
* search parameters eg "value.as(String)" when it should be
* "value.as(string)". This lets us be a bit lenient about this.
*/
if (myCtx.getVersion().getVersion() == FhirVersionEnum.R4 || myCtx.getVersion().getVersion() == FhirVersionEnum.R4B || myCtx.getVersion().getVersion() == FhirVersionEnum.R5) {
String end = url.substring(URL_PREFIX_STRUCTURE_DEFINITION.length());
if (Character.isUpperCase(end.charAt(0))) {
String newEnd = Character.toLowerCase(end.charAt(0)) + end.substring(1);
String alternateUrl = URL_PREFIX_STRUCTURE_DEFINITION + newEnd;
retVal = structureDefinitionMap.get(alternateUrl);
if (retVal != null) {
retVal = myCtx.newTerser().clone(retVal);
myCtx.newTerser().setElement(retVal, "type", end);
}
}
}
}
}
return retVal;
} }
@Override @Override

View File

@ -59,6 +59,8 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
private String myLabel; private String myLabel;
private String myScheme; private String myScheme;
private String myTerm; private String myTerm;
private String myVersion;
private boolean myUserSelected;
public Tag() { public Tag() {
} }
@ -124,6 +126,16 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
return false; return false;
} else if (!myTerm.equals(other.myTerm)) } else if (!myTerm.equals(other.myTerm))
return false; return false;
if (myVersion == null) {
if (other.getVersion() != null)
return false;
} else if (!myVersion.equals(other.getVersion()))
return false;
if (myUserSelected != other.getUserSelected())
return false;
return true; return true;
} }
@ -133,6 +145,8 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
int result = 1; int result = 1;
result = prime * result + ((myScheme == null) ? 0 : myScheme.hashCode()); result = prime * result + ((myScheme == null) ? 0 : myScheme.hashCode());
result = prime * result + ((myTerm == null) ? 0 : myTerm.hashCode()); result = prime * result + ((myTerm == null) ? 0 : myTerm.hashCode());
result = prime * result + ((myVersion == null) ? 0 : myVersion.hashCode());
result = prime * result + Boolean.hashCode(myUserSelected);
return result; return result;
} }
@ -174,6 +188,8 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
b.append("Scheme", myScheme); b.append("Scheme", myScheme);
b.append("Term", myTerm); b.append("Term", myTerm);
b.append("Label", myLabel); b.append("Label", myLabel);
b.append("Version", myVersion);
b.append("UserSelected", myUserSelected);
return b.toString(); return b.toString();
} }
@ -210,4 +226,22 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
return this; return this;
} }
@Override
public String getVersion() { return myVersion; }
@Override
public IBaseCoding setVersion(String theVersion) {
myVersion = theVersion;
return this;
}
@Override
public boolean getUserSelected() { return myUserSelected; }
@Override
public IBaseCoding setUserSelected(boolean theUserSelected) {
myUserSelected = theUserSelected;
return this;
}
} }

View File

@ -115,6 +115,7 @@ public enum VersionEnum {
V6_3_0, V6_3_0,
V6_4_0, V6_4_0,
V6_4_1, V6_4_1,
V6_4_2,
V6_5_0, V6_5_0,
V6_6_0 V6_6_0
; ;

View File

@ -28,10 +28,19 @@ public interface IBaseCoding extends IBase {
String getSystem(); String getSystem();
boolean getUserSelected();
String getVersion();
IBaseCoding setCode(String theTerm); IBaseCoding setCode(String theTerm);
IBaseCoding setDisplay(String theLabel); IBaseCoding setDisplay(String theLabel);
IBaseCoding setSystem(String theScheme); IBaseCoding setSystem(String theScheme);
IBaseCoding setVersion(String theVersion);
IBaseCoding setUserSelected(boolean theUserSelected);
} }

View File

@ -27,7 +27,7 @@ public class TagTest {
@Test @Test
public void testHashCode() { public void testHashCode() {
Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label"); Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
assertEquals(1920714536, tag1.hashCode()); assertEquals(-1029266947, tag1.hashCode());
} }
@Test @Test

View File

@ -4,14 +4,14 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId> <artifactId>hapi-fhir-bom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<packaging>pom</packaging> <packaging>pom</packaging>
<name>HAPI FHIR BOM</name> <name>HAPI FHIR BOM</name>
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
@ -237,6 +237,11 @@
<artifactId>hapi-fhir-validation-resources-r4</artifactId> <artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>hapi-fhir-validation-resources-r4b</artifactId>
<version>${project.version}</version>
</dependency>
<dependency> <dependency>
<groupId>${project.groupId}</groupId> <groupId>${project.groupId}</groupId>
<artifactId>hapi-fhir-validation-resources-r5</artifactId> <artifactId>hapi-fhir-validation-resources-r5</artifactId>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -103,7 +103,7 @@ public class CreatePackageCommandTest extends BaseTest {
{ {
"name" : "com.example.ig", "name" : "com.example.ig",
"version" : "1.0.1", "version" : "1.0.1",
"description" : "", "description" : null,
"fhirVersions" : ["4.0.1"], "fhirVersions" : ["4.0.1"],
"dependencies" : { "dependencies" : {
"hl7.fhir.core" : "4.0.1", "hl7.fhir.core" : "4.0.1",
@ -158,7 +158,7 @@ public class CreatePackageCommandTest extends BaseTest {
{ {
"name" : "com.example.ig", "name" : "com.example.ig",
"version" : "1.0.1", "version" : "1.0.1",
"description" : "", "description" : null,
"fhirVersions" : ["4.0.1"] "fhirVersions" : ["4.0.1"]
} }
"""; """;

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId> <artifactId>hapi-fhir-cli</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath> <relativePath>../../hapi-deployable-pom</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -273,9 +273,8 @@ public class VersionCanonicalizer {
retVal.setSystem(coding.getSystem()); retVal.setSystem(coding.getSystem());
retVal.setDisplay(coding.getDisplay()); retVal.setDisplay(coding.getDisplay());
retVal.setVersion(coding.getVersion()); retVal.setVersion(coding.getVersion());
if (coding.getUserSelected() != null) { retVal.setUserSelected( ! coding.getUserSelectedElement().isEmpty() && coding.getUserSelected() );
retVal.setUserSelected(coding.getUserSelected());
}
return retVal; return retVal;
} }

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
@ -212,6 +212,11 @@
<artifactId>hapi-fhir-validation-resources-r4</artifactId> <artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4b</artifactId>
<version>${project.version}</version>
</dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -0,0 +1 @@
This release bumps the org.hl7.fhir core dependency up to 5.6.97, and modifies IBaseCoding

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@ -0,0 +1,3 @@
---
release-date: "2023-02-24"
codename: "Vishwa"

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@ -1,4 +1,5 @@
--- ---
type: fix type: fix
issue: 4551 issue: 4551
backport: 6.4.1
title: "The HapifhirDal search method required use of TypedBundleProvider.getallresources to avoid null pointer issue on searches that are greater than the default querycount" title: "The HapifhirDal search method required use of TypedBundleProvider.getallresources to avoid null pointer issue on searches that are greater than the default querycount"

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@ -0,0 +1,6 @@
---
type: perf
issue: 4569
backport: 6.4.1
title: "A race condition in the Bulk Export module sometimes resulted in bulk export jobs producing completion
reports that did not contain all generated output files. This has been corrected."

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@ -0,0 +1,7 @@
---
type: perf
issue: 4569
backport: 6.4.1
title: "An inefficient query in the JPA Bulk Export module was optimized. This query caused exports for resources
containing tags/security labels/profiles to perform a number of redundant database lookups, so this type of
export should be much faster now."

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@ -0,0 +1,5 @@
---
type: fix
issue: 4582
backport: 6.4.1
title: "Update IBaseCoding, Tag, and tinder Child to support new userSelected and version fields for resource tags."

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@ -0,0 +1,6 @@
---
type: fix
issue: 4582
jira: SMILE-4688
backport: 6.4.1
title: "Upgrade dependency on core to 5.6.97 including hapi-fhir code enhancements and unit test fixes."

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@ -11,7 +11,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
@ -132,6 +132,11 @@
<artifactId>hapi-fhir-validation-resources-r4</artifactId> <artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4b</artifactId>
<version>${project.version}</version>
</dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r5</artifactId> <artifactId>hapi-fhir-validation-resources-r5</artifactId>

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@ -47,6 +47,7 @@ import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition; import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional; import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate; import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull; import javax.annotation.Nonnull;
@ -61,6 +62,7 @@ import java.util.function.Consumer;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import static ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity.ERROR_MSG_MAX_LENGTH;
import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isBlank;
public class JpaJobPersistenceImpl implements IJobPersistence { public class JpaJobPersistenceImpl implements IJobPersistence {
@ -235,7 +237,8 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
@Override @Override
@Transactional(propagation = Propagation.REQUIRES_NEW) @Transactional(propagation = Propagation.REQUIRES_NEW)
public void markWorkChunkAsErroredAndIncrementErrorCount(String theChunkId, String theErrorMessage) { public void markWorkChunkAsErroredAndIncrementErrorCount(String theChunkId, String theErrorMessage) {
myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), theErrorMessage, StatusEnum.ERRORED); String errorMessage = truncateErrorMessage(theErrorMessage);
myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), errorMessage, StatusEnum.ERRORED);
} }
@Override @Override
@ -251,28 +254,39 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
@Transactional(propagation = Propagation.REQUIRES_NEW) @Transactional(propagation = Propagation.REQUIRES_NEW)
public void markWorkChunkAsFailed(String theChunkId, String theErrorMessage) { public void markWorkChunkAsFailed(String theChunkId, String theErrorMessage) {
ourLog.info("Marking chunk {} as failed with message: {}", theChunkId, theErrorMessage); ourLog.info("Marking chunk {} as failed with message: {}", theChunkId, theErrorMessage);
String errorMessage; String errorMessage = truncateErrorMessage(theErrorMessage);
if (theErrorMessage.length() > Batch2WorkChunkEntity.ERROR_MSG_MAX_LENGTH) {
ourLog.warn("Truncating error message that is too long to store in database: {}", theErrorMessage);
errorMessage = theErrorMessage.substring(0, Batch2WorkChunkEntity.ERROR_MSG_MAX_LENGTH);
} else {
errorMessage = theErrorMessage;
}
myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), errorMessage, StatusEnum.FAILED); myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), errorMessage, StatusEnum.FAILED);
} }
@Override @Nonnull
@Transactional(propagation = Propagation.REQUIRES_NEW) private static String truncateErrorMessage(String theErrorMessage) {
public void markWorkChunkAsCompletedAndClearData(String theChunkId, int theRecordsProcessed) { String errorMessage;
myWorkChunkRepository.updateChunkStatusAndClearDataForEndSuccess(theChunkId, new Date(), theRecordsProcessed, StatusEnum.COMPLETED); if (theErrorMessage != null && theErrorMessage.length() > ERROR_MSG_MAX_LENGTH) {
ourLog.warn("Truncating error message that is too long to store in database: {}", theErrorMessage);
errorMessage = theErrorMessage.substring(0, ERROR_MSG_MAX_LENGTH);
} else {
errorMessage = theErrorMessage;
}
return errorMessage;
} }
@Override @Override
@Transactional(propagation = Propagation.REQUIRES_NEW) @Transactional(propagation = Propagation.REQUIRES_NEW)
public void markWorkChunksWithStatusAndWipeData(String theInstanceId, List<String> theChunkIds, StatusEnum theStatus, String theErrorMsg) { public void markWorkChunkAsCompletedAndClearData(String theInstanceId, String theChunkId, int theRecordsProcessed) {
StatusEnum newStatus = StatusEnum.COMPLETED;
ourLog.debug("Marking chunk {} for instance {} to status {}", theChunkId, theInstanceId, newStatus);
myWorkChunkRepository.updateChunkStatusAndClearDataForEndSuccess(theChunkId, new Date(), theRecordsProcessed, newStatus);
}
@Override
public void markWorkChunksWithStatusAndWipeData(String theInstanceId, List<String> theChunkIds, StatusEnum theStatus, String theErrorMessage) {
assert TransactionSynchronizationManager.isActualTransactionActive();
ourLog.debug("Marking all chunks for instance {} to status {}", theInstanceId, theStatus);
String errorMessage = truncateErrorMessage(theErrorMessage);
List<List<String>> listOfListOfIds = ListUtils.partition(theChunkIds, 100); List<List<String>> listOfListOfIds = ListUtils.partition(theChunkIds, 100);
for (List<String> idList : listOfListOfIds) { for (List<String> idList : listOfListOfIds) {
myWorkChunkRepository.updateAllChunksForInstanceStatusClearDataAndSetError(idList, new Date(), theStatus, theErrorMsg); myWorkChunkRepository.updateAllChunksForInstanceStatusClearDataAndSetError(idList, new Date(), theStatus, errorMessage);
} }
} }
@ -285,6 +299,13 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
@Override @Override
@Transactional(propagation = Propagation.REQUIRES_NEW) @Transactional(propagation = Propagation.REQUIRES_NEW)
public boolean canAdvanceInstanceToNextStep(String theInstanceId, String theCurrentStepId) { public boolean canAdvanceInstanceToNextStep(String theInstanceId, String theCurrentStepId) {
Optional<Batch2JobInstanceEntity> instance = myJobInstanceRepository.findById(theInstanceId);
if (!instance.isPresent()) {
return false;
}
if (instance.get().getStatus().isEnded()) {
return false;
}
List<StatusEnum> statusesForStep = myWorkChunkRepository.getDistinctStatusesForStep(theInstanceId, theCurrentStepId); List<StatusEnum> statusesForStep = myWorkChunkRepository.getDistinctStatusesForStep(theInstanceId, theCurrentStepId);
ourLog.debug("Checking whether gated job can advanced to next step. [instanceId={}, currentStepId={}, statusesForStep={}]", theInstanceId, theCurrentStepId, statusesForStep); ourLog.debug("Checking whether gated job can advanced to next step. [instanceId={}, currentStepId={}, statusesForStep={}]", theInstanceId, theCurrentStepId, statusesForStep);
return statusesForStep.stream().noneMatch(StatusEnum::isIncomplete) && statusesForStep.stream().anyMatch(status -> status == StatusEnum.COMPLETED); return statusesForStep.stream().noneMatch(StatusEnum::isIncomplete) && statusesForStep.stream().anyMatch(status -> status == StatusEnum.COMPLETED);
@ -314,6 +335,11 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
return myTxTemplate.execute(tx -> myWorkChunkRepository.fetchAllChunkIdsForStepWithStatus(theInstanceId, theStepId, theStatusEnum)); return myTxTemplate.execute(tx -> myWorkChunkRepository.fetchAllChunkIdsForStepWithStatus(theInstanceId, theStepId, theStatusEnum));
} }
@Override
public void updateInstanceUpdateTime(String theInstanceId) {
myJobInstanceRepository.updateInstanceUpdateTime(theInstanceId, new Date());
}
private void fetchChunksForStep(String theInstanceId, String theStepId, int thePageSize, int thePageIndex, Consumer<WorkChunk> theConsumer) { private void fetchChunksForStep(String theInstanceId, String theStepId, int thePageSize, int thePageIndex, Consumer<WorkChunk> theConsumer) {
myTxTemplate.executeWithoutResult(tx -> { myTxTemplate.executeWithoutResult(tx -> {
List<Batch2WorkChunkEntity> chunks = myWorkChunkRepository.fetchChunksForStep(PageRequest.of(thePageIndex, thePageSize), theInstanceId, theStepId); List<Batch2WorkChunkEntity> chunks = myWorkChunkRepository.fetchChunksForStep(PageRequest.of(thePageIndex, thePageSize), theInstanceId, theStepId);
@ -380,6 +406,7 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
instanceEntity.setReport(theInstance.getReport()); instanceEntity.setReport(theInstance.getReport());
myJobInstanceRepository.save(instanceEntity); myJobInstanceRepository.save(instanceEntity);
return recordsChangedByStatusUpdate > 0; return recordsChangedByStatusUpdate > 0;
} }
@ -393,8 +420,9 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
@Override @Override
@Transactional(propagation = Propagation.REQUIRES_NEW) @Transactional(propagation = Propagation.REQUIRES_NEW)
public void deleteChunks(String theInstanceId) { public void deleteChunksAndMarkInstanceAsChunksPurged(String theInstanceId) {
ourLog.info("Deleting all chunks for instance ID: {}", theInstanceId); ourLog.info("Deleting all chunks for instance ID: {}", theInstanceId);
myJobInstanceRepository.updateWorkChunksPurgedTrue(theInstanceId);
myWorkChunkRepository.deleteAllForInstance(theInstanceId); myWorkChunkRepository.deleteAllForInstance(theInstanceId);
} }

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@ -35,6 +35,7 @@ import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.util.Batch2JobDefinitionConstants; import ca.uhn.fhir.util.Batch2JobDefinitionConstants;
import ca.uhn.fhir.util.JsonUtil; import ca.uhn.fhir.util.JsonUtil;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils; import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBaseBinary; import org.hl7.fhir.instance.model.api.IBaseBinary;
@ -54,6 +55,7 @@ import javax.annotation.PostConstruct;
import java.time.LocalDateTime; import java.time.LocalDateTime;
import java.time.ZoneId; import java.time.ZoneId;
import java.util.Date; import java.util.Date;
import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Optional; import java.util.Optional;

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@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.packages.loader.PackageLoaderSvc; import ca.uhn.fhir.jpa.packages.loader.PackageLoaderSvc;
import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc; import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
import org.hl7.fhir.utilities.npm.PackageClient; import org.hl7.fhir.utilities.npm.PackageClient;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
@ -34,8 +35,8 @@ public class PackageLoaderConfig {
public PackageLoaderSvc packageLoaderSvc() { public PackageLoaderSvc packageLoaderSvc() {
PackageLoaderSvc svc = new PackageLoaderSvc(); PackageLoaderSvc svc = new PackageLoaderSvc();
svc.getPackageServers().clear(); svc.getPackageServers().clear();
svc.getPackageServers().add(PackageClient.PRIMARY_SERVER); svc.getPackageServers().add(PackageServer.primaryServer());
svc.getPackageServers().add(PackageClient.SECONDARY_SERVER); svc.getPackageServers().add(PackageServer.secondaryServer());
return svc; return svc;
} }

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@ -159,7 +159,7 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
String codeSystemUrl; String codeSystemUrl;
if (theCodeSystemId != null) { if (theCodeSystemId != null) {
IBaseResource codeSystem = read(theCodeSystemId, theRequestDetails); IBaseResource codeSystem = read(theCodeSystemId, theRequestDetails);
codeSystemUrl = CommonCodeSystemsTerminologyService.getCodeSystemUrl(codeSystem); codeSystemUrl = CommonCodeSystemsTerminologyService.getCodeSystemUrl(myFhirContext, codeSystem);
} else if (isNotBlank(toStringValue(theCodeSystemUrl))) { } else if (isNotBlank(toStringValue(theCodeSystemUrl))) {
codeSystemUrl = toStringValue(theCodeSystemUrl); codeSystemUrl = toStringValue(theCodeSystemUrl);
} else { } else {

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@ -176,8 +176,8 @@ public class JpaResourceDaoValueSet<T extends IBaseResource> extends BaseHapiFhi
String valueSetIdentifier; String valueSetIdentifier;
if (theValueSetId != null) { if (theValueSetId != null) {
IBaseResource valueSet = read(theValueSetId, theRequestDetails); IBaseResource valueSet = read(theValueSetId, theRequestDetails);
StringBuilder valueSetIdentifierBuilder = new StringBuilder(CommonCodeSystemsTerminologyService.getValueSetUrl(valueSet)); StringBuilder valueSetIdentifierBuilder = new StringBuilder(CommonCodeSystemsTerminologyService.getValueSetUrl(myFhirContext, valueSet));
String valueSetVersion = CommonCodeSystemsTerminologyService.getValueSetVersion(valueSet); String valueSetVersion = CommonCodeSystemsTerminologyService.getValueSetVersion(myFhirContext, valueSet);
if (valueSetVersion != null) { if (valueSetVersion != null) {
valueSetIdentifierBuilder.append("|").append(valueSetVersion); valueSetIdentifierBuilder.append("|").append(valueSetVersion);
} }

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@ -38,13 +38,17 @@ public interface IBatch2JobInstanceRepository extends JpaRepository<Batch2JobIns
@Query("UPDATE Batch2JobInstanceEntity e SET e.myStatus = :status WHERE e.myId = :id and e.myStatus <> :status") @Query("UPDATE Batch2JobInstanceEntity e SET e.myStatus = :status WHERE e.myId = :id and e.myStatus <> :status")
int updateInstanceStatus(@Param("id") String theInstanceId, @Param("status") StatusEnum theStatus); int updateInstanceStatus(@Param("id") String theInstanceId, @Param("status") StatusEnum theStatus);
@Modifying
@Query("UPDATE Batch2JobInstanceEntity e SET e.myUpdateTime = :updated WHERE e.myId = :id")
int updateInstanceUpdateTime(@Param("id") String theInstanceId, @Param("updated") Date theUpdated);
@Modifying @Modifying
@Query("UPDATE Batch2JobInstanceEntity e SET e.myCancelled = :cancelled WHERE e.myId = :id") @Query("UPDATE Batch2JobInstanceEntity e SET e.myCancelled = :cancelled WHERE e.myId = :id")
int updateInstanceCancelled(@Param("id") String theInstanceId, @Param("cancelled") boolean theCancelled); int updateInstanceCancelled(@Param("id") String theInstanceId, @Param("cancelled") boolean theCancelled);
@Modifying @Modifying
@Query("UPDATE Batch2JobInstanceEntity e SET e.myCurrentGatedStepId = :currentGatedStepId WHERE e.myId = :id") @Query("UPDATE Batch2JobInstanceEntity e SET e.myWorkChunksPurged = true WHERE e.myId = :id")
void updateInstanceCurrentGatedStepId(@Param("id") String theInstanceId, @Param("currentGatedStepId") String theCurrentGatedStepId); int updateWorkChunksPurgedTrue(@Param("id") String theInstanceId);
@Query("SELECT b from Batch2JobInstanceEntity b WHERE b.myDefinitionId = :defId AND b.myParamsJson = :params AND b.myStatus IN( :stats )") @Query("SELECT b from Batch2JobInstanceEntity b WHERE b.myDefinitionId = :defId AND b.myParamsJson = :params AND b.myStatus IN( :stats )")
List<Batch2JobInstanceEntity> findInstancesByJobIdParamsAndStatus( List<Batch2JobInstanceEntity> findInstancesByJobIdParamsAndStatus(

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@ -144,8 +144,6 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.online(true) .online(true)
.withColumns("SEARCH_PID") .withColumns("SEARCH_PID")
.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS); .onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
;
} }
private void init620() { private void init620() {

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@ -60,6 +60,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType; import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager; import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage; import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
@ -129,9 +130,9 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
private IBinaryStorageSvc myBinaryStorageSvc; private IBinaryStorageSvc myBinaryStorageSvc;
@Override @Override
public void addPackageServer(@Nonnull String theUrl) { public void addPackageServer(@Nonnull PackageServer thePackageServer) {
assert myPackageLoaderSvc != null; assert myPackageLoaderSvc != null;
myPackageLoaderSvc.addPackageServer(theUrl); myPackageLoaderSvc.addPackageServer(thePackageServer);
} }
@Override @Override
@ -150,7 +151,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
} }
@Override @Override
public List<String> getPackageServers() { public List<PackageServer> getPackageServers() {
return myPackageLoaderSvc.getPackageServers(); return myPackageLoaderSvc.getPackageServers();
} }

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@ -116,7 +116,7 @@ class JpaJobPersistenceImplTest {
String jobId = "jobid"; String jobId = "jobid";
// test // test
mySvc.deleteChunks(jobId); mySvc.deleteChunksAndMarkInstanceAsChunksPurged(jobId);
// verify // verify
verify(myWorkChunkRepository) verify(myWorkChunkRepository)

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -16,6 +16,8 @@ import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Meta; import org.hl7.fhir.r4.model.Meta;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.RepeatedTest;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;

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@ -3,7 +3,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
@ -92,6 +92,11 @@
<artifactId>hapi-fhir-validation-resources-r4</artifactId> <artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4b</artifactId>
<version>${project.version}</version>
</dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r5</artifactId> <artifactId>hapi-fhir-validation-resources-r5</artifactId>

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@ -87,6 +87,7 @@ import static ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum.DATE;
import static ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum.REFERENCE; import static ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum.REFERENCE;
import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.startsWith;
import static org.apache.commons.lang3.StringUtils.trim; import static org.apache.commons.lang3.StringUtils.trim;
public abstract class BaseSearchParamExtractor implements ISearchParamExtractor { public abstract class BaseSearchParamExtractor implements ISearchParamExtractor {
@ -829,6 +830,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
try { try {
allValues = allValuesFunc.get(); allValues = allValuesFunc.get();
} catch (Exception e) { } catch (Exception e) {
e.printStackTrace();
String msg = getContext().getLocalizer().getMessage(BaseSearchParamExtractor.class, "failedToExtractPaths", nextPath, e.toString()); String msg = getContext().getLocalizer().getMessage(BaseSearchParamExtractor.class, "failedToExtractPaths", nextPath, e.toString());
throw new InternalErrorException(Msg.code(504) + msg, e); throw new InternalErrorException(Msg.code(504) + msg, e);
} }
@ -1294,7 +1296,30 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
} }
private <T> SearchParamSet<T> extractSearchParams(IBaseResource theResource, IExtractor<T> theExtractor, RestSearchParameterTypeEnum theSearchParamType, boolean theWantLocalReferences) { /**
* Ignore any of the Resource-level search params. This is kind of awkward, but here is why
* we do it:
* <p>
* The ReadOnlySearchParamCache supplies these params, and they have paths associated with
* them. E.g. HAPI's SearchParamRegistryImpl will know about the _id search parameter and
* assigns it the path "Resource.id". All of these parameters have indexing code paths in the
* server that don't rely on the existence of the SearchParameter. For example, we have a
* dedicated column on ResourceTable that handles the _id parameter.
* <p>
* Until 6.2.0 the FhirPath evaluator didn't actually resolve any values for these paths
* that started with Resource instead of the actual resource name, so it never actually
* made a difference that these parameters existed because they'd never actually result
* in any index rows. In 6.4.0 that bug was fixed in the core FhirPath engine. We don't
* want that fix to result in pointless index rows for things like _id and _tag, so we
* ignore them here.
* <p>
* Note that you can still create a search parameter that includes a path like
* "meta.tag" if you really need to create an SP that actually does index _tag. This
* is needed if you want to search for tags in <code>INLINE</code> tag storage mode.
* This is the only way you could actually specify a FhirPath expression for those
* prior to 6.2.0 so this isn't a breaking change.
*/
<T> SearchParamSet<T> extractSearchParams(IBaseResource theResource, IExtractor<T> theExtractor, RestSearchParameterTypeEnum theSearchParamType, boolean theWantLocalReferences) {
SearchParamSet<T> retVal = new SearchParamSet<>(); SearchParamSet<T> retVal = new SearchParamSet<>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource); Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
@ -1306,6 +1331,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
continue; continue;
} }
// See the method javadoc for an explanation of this
if (startsWith(nextSpDef.getPath(), "Resource.")) {
continue;
}
extractSearchParam(nextSpDef, theResource, theExtractor, retVal, theWantLocalReferences); extractSearchParam(nextSpDef, theResource, theExtractor, retVal, theWantLocalReferences);
} }
return retVal; return retVal;

View File

@ -32,6 +32,7 @@ import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.instance.model.api.IBase; import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.r4.context.IWorkerContext; import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext; import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.hl7.fhir.r4.model.Base; import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.ExpressionNode; import org.hl7.fhir.r4.model.ExpressionNode;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
@ -133,7 +134,7 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
@Override @Override
public Base resolveReference(Object theAppContext, String theUrl) throws FHIRException { public Base resolveReference(Object theAppContext, String theUrl, Base theRefContext) throws FHIRException {
/* /*
* When we're doing resolution within the SearchParamExtractor, if we want * When we're doing resolution within the SearchParamExtractor, if we want

View File

@ -95,6 +95,8 @@ public class ReadOnlySearchParamCache {
IBaseBundle allSearchParameterBundle = null; IBaseBundle allSearchParameterBundle = null;
if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R4) { if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R4) {
allSearchParameterBundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4/model/sp/search-parameters.json")); allSearchParameterBundle = (IBaseBundle) theFhirContext.newJsonParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4/model/sp/search-parameters.json"));
} else if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R4B) {
allSearchParameterBundle = (IBaseBundle) theFhirContext.newXmlParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r4b/model/sp/search-parameters.xml"));
} else if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R5) { } else if (theFhirContext.getVersion().getVersion() == FhirVersionEnum.R5) {
allSearchParameterBundle = (IBaseBundle) theFhirContext.newXmlParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r5/model/sp/search-parameters.xml")); allSearchParameterBundle = (IBaseBundle) theFhirContext.newXmlParser().parseResource(ClasspathUtil.loadResourceAsStream("org/hl7/fhir/r5/model/sp/search-parameters.xml"));
} }

View File

@ -79,6 +79,7 @@ public class SearchParameterCanonicalizer {
retVal = canonicalizeSearchParameterDstu3((org.hl7.fhir.dstu3.model.SearchParameter) theSearchParameter); retVal = canonicalizeSearchParameterDstu3((org.hl7.fhir.dstu3.model.SearchParameter) theSearchParameter);
break; break;
case R4: case R4:
case R4B:
case R5: case R5:
retVal = canonicalizeSearchParameterR4Plus(theSearchParameter); retVal = canonicalizeSearchParameterR4Plus(theSearchParameter);
break; break;

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -15,6 +15,9 @@ import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder; import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseBinary; import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.utilities.npm.IPackageCacheManager;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -66,7 +69,7 @@ public class IgInstallerDstu3Test extends BaseJpaDstu3Test {
myPort = JettyUtil.getPortForStartedServer(myServer); myPort = JettyUtil.getPortForStartedServer(myServer);
jpaPackageCache.getPackageServers().clear(); jpaPackageCache.getPackageServers().clear();
jpaPackageCache.addPackageServer("http://localhost:" + myPort); jpaPackageCache.addPackageServer(new PackageServer("http://localhost:" + myPort));
myFakeNpmServlet.getResponses().clear(); myFakeNpmServlet.getResponses().clear();
} }

View File

@ -15,6 +15,7 @@ import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.OperationOutcome; import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.StructureDefinition; import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet; import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -61,7 +62,7 @@ public class NpmDstu3Test extends BaseJpaDstu3Test {
int port = JettyUtil.getPortForStartedServer(myServer); int port = JettyUtil.getPortForStartedServer(myServer);
jpaPackageCache.getPackageServers().clear(); jpaPackageCache.getPackageServers().clear();
jpaPackageCache.addPackageServer("http://localhost:" + port); jpaPackageCache.addPackageServer(new PackageServer("http://localhost:" + port));
myResponses.clear(); myResponses.clear();
} }

View File

@ -18,6 +18,7 @@
<logger name="org.eclipse" level="error"/> <logger name="org.eclipse" level="error"/>
<logger name="ca.uhn.fhir.rest.client" level="info"/> <logger name="ca.uhn.fhir.rest.client" level="info"/>
<logger name="ca.uhn.fhir.jpa.dao" level="info"/> <logger name="ca.uhn.fhir.jpa.dao" level="info"/>
<logger name="ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor" level="debug"/>
<!-- set to debug to enable term expansion logs --> <!-- set to debug to enable term expansion logs -->

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -33,6 +33,7 @@ import ca.uhn.test.concurrency.PointcutLatch;
import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.annotation.JsonProperty;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource; import org.junit.jupiter.params.provider.ValueSource;

View File

@ -41,6 +41,7 @@ import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.hasSize; import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse; import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull; import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
@ -55,6 +56,7 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
public static final int JOB_DEF_VER = 1; public static final int JOB_DEF_VER = 1;
public static final int SEQUENCE_NUMBER = 1; public static final int SEQUENCE_NUMBER = 1;
public static final String CHUNK_DATA = "{\"key\":\"value\"}"; public static final String CHUNK_DATA = "{\"key\":\"value\"}";
public static final String INSTANCE_ID = "instance-id";
@Autowired @Autowired
private IJobPersistence mySvc; private IJobPersistence mySvc;
@ -102,7 +104,7 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
// Execute // Execute
mySvc.deleteChunks(instanceId); mySvc.deleteChunksAndMarkInstanceAsChunksPurged(instanceId);
// Verify // Verify
@ -216,19 +218,6 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
.collect(Collectors.toUnmodifiableSet())); .collect(Collectors.toUnmodifiableSet()));
} }
/**
* Returns a set of statuses, and whether they should be successfully picked up and started by a consumer.
* @return
*/
public static List<Arguments> provideStatuses() {
return List.of(
Arguments.of(StatusEnum.QUEUED, true),
Arguments.of(StatusEnum.IN_PROGRESS, true),
Arguments.of(StatusEnum.ERRORED, true),
Arguments.of(StatusEnum.FAILED, false),
Arguments.of(StatusEnum.COMPLETED, false)
);
}
@ParameterizedTest @ParameterizedTest
@MethodSource("provideStatuses") @MethodSource("provideStatuses")
public void testStartChunkOnlyWorksOnValidChunks(StatusEnum theStatus, boolean theShouldBeStartedByConsumer) { public void testStartChunkOnlyWorksOnValidChunks(StatusEnum theStatus, boolean theShouldBeStartedByConsumer) {
@ -335,6 +324,24 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
empty()); empty());
} }
@Test
public void testUpdateTime() {
// Setup
JobInstance instance = createInstance();
String instanceId = mySvc.storeNewInstance(instance);
Date updateTime = runInTransaction(() -> new Date(myJobInstanceRepository.findById(instanceId).orElseThrow().getUpdateTime().getTime()));
sleepUntilTimeChanges();
// Test
runInTransaction(() -> mySvc.updateInstanceUpdateTime(instanceId));
// Verify
Date updateTime2 = runInTransaction(() -> new Date(myJobInstanceRepository.findById(instanceId).orElseThrow().getUpdateTime().getTime()));
assertNotEquals(updateTime, updateTime2);
}
@Test @Test
public void testFetchUnknownWork() { public void testFetchUnknownWork() {
assertFalse(myWorkChunkRepository.findById("FOO").isPresent()); assertFalse(myWorkChunkRepository.findById("FOO").isPresent());
@ -393,7 +400,7 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
sleepUntilTimeChanges(); sleepUntilTimeChanges();
mySvc.markWorkChunkAsCompletedAndClearData(chunkId, 50); mySvc.markWorkChunkAsCompletedAndClearData(INSTANCE_ID, chunkId, 50);
runInTransaction(() -> { runInTransaction(() -> {
Batch2WorkChunkEntity entity = myWorkChunkRepository.findById(chunkId).orElseThrow(IllegalArgumentException::new); Batch2WorkChunkEntity entity = myWorkChunkRepository.findById(chunkId).orElseThrow(IllegalArgumentException::new);
assertEquals(StatusEnum.COMPLETED, entity.getStatus()); assertEquals(StatusEnum.COMPLETED, entity.getStatus());
@ -427,13 +434,14 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
assertEquals(1, chunks.size()); assertEquals(1, chunks.size());
assertEquals(5, chunks.get(0).getErrorCount()); assertEquals(5, chunks.get(0).getErrorCount());
} }
@Test @Test
public void testGatedAdvancementByStatus() { public void testGatedAdvancementByStatus() {
// Setup // Setup
JobInstance instance = createInstance(); JobInstance instance = createInstance();
String instanceId = mySvc.storeNewInstance(instance); String instanceId = mySvc.storeNewInstance(instance);
String chunkId = storeWorkChunk(DEF_CHUNK_ID, STEP_CHUNK_ID, instanceId, SEQUENCE_NUMBER, null); String chunkId = storeWorkChunk(DEF_CHUNK_ID, STEP_CHUNK_ID, instanceId, SEQUENCE_NUMBER, null);
mySvc.markWorkChunkAsCompletedAndClearData(chunkId, 0); mySvc.markWorkChunkAsCompletedAndClearData(INSTANCE_ID, chunkId, 0);
boolean canAdvance = mySvc.canAdvanceInstanceToNextStep(instanceId, STEP_CHUNK_ID); boolean canAdvance = mySvc.canAdvanceInstanceToNextStep(instanceId, STEP_CHUNK_ID);
assertTrue(canAdvance); assertTrue(canAdvance);
@ -445,7 +453,7 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
assertFalse(canAdvance); assertFalse(canAdvance);
//Toggle it to complete //Toggle it to complete
mySvc.markWorkChunkAsCompletedAndClearData(newChunkId, 0); mySvc.markWorkChunkAsCompletedAndClearData(INSTANCE_ID, newChunkId, 0);
canAdvance = mySvc.canAdvanceInstanceToNextStep(instanceId, STEP_CHUNK_ID); canAdvance = mySvc.canAdvanceInstanceToNextStep(instanceId, STEP_CHUNK_ID);
assertTrue(canAdvance); assertTrue(canAdvance);
@ -456,7 +464,7 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
assertFalse(canAdvance); assertFalse(canAdvance);
//Toggle IN_PROGRESS to complete //Toggle IN_PROGRESS to complete
mySvc.markWorkChunkAsCompletedAndClearData(newerChunkId, 0); mySvc.markWorkChunkAsCompletedAndClearData(INSTANCE_ID, newerChunkId, 0);
canAdvance = mySvc.canAdvanceInstanceToNextStep(instanceId, STEP_CHUNK_ID); canAdvance = mySvc.canAdvanceInstanceToNextStep(instanceId, STEP_CHUNK_ID);
assertTrue(canAdvance); assertTrue(canAdvance);
} }
@ -609,7 +617,7 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
chunkIds.add(id); chunkIds.add(id);
} }
mySvc.markWorkChunksWithStatusAndWipeData(instance.getInstanceId(), chunkIds, StatusEnum.COMPLETED, null); runInTransaction(() -> mySvc.markWorkChunksWithStatusAndWipeData(instance.getInstanceId(), chunkIds, StatusEnum.COMPLETED, null));
Iterator<WorkChunk> reducedChunks = mySvc.fetchAllWorkChunksIterator(instanceId, true); Iterator<WorkChunk> reducedChunks = mySvc.fetchAllWorkChunksIterator(instanceId, true);
@ -631,7 +639,6 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
return instance; return instance;
} }
@Nonnull @Nonnull
private String storeJobInstanceAndUpdateWithEndTime(StatusEnum theStatus, int minutes) { private String storeJobInstanceAndUpdateWithEndTime(StatusEnum theStatus, int minutes) {
final JobInstance jobInstance = new JobInstance(); final JobInstance jobInstance = new JobInstance();
@ -656,4 +663,17 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
return id; return id;
} }
/**
* Returns a set of statuses, and whether they should be successfully picked up and started by a consumer.
*/
public static List<Arguments> provideStatuses() {
return List.of(
Arguments.of(StatusEnum.QUEUED, true),
Arguments.of(StatusEnum.IN_PROGRESS, true),
Arguments.of(StatusEnum.ERRORED, true),
Arguments.of(StatusEnum.FAILED, false),
Arguments.of(StatusEnum.COMPLETED, false)
);
}
} }

View File

@ -0,0 +1,222 @@
package ca.uhn.fhir.jpa.bulk;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.model.BulkExportJobResults;
import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.jpa.util.BulkExportUtils;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.JsonUtil;
import com.google.common.collect.Sets;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.BufferedReader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Future;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.emptyOrNullString;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
/**
* A test to poke at our job framework and induce errors.
*/
public class BulkDataErrorAbuseTest extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(BulkDataErrorAbuseTest.class);
@Autowired
private IBatch2JobRunner myJobRunner;
@AfterEach
void afterEach() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
}
@Test
public void testGroupBulkExportNotInGroup_DoesNotShowUp() throws InterruptedException, ExecutionException {
duAbuseTest(100);
}
/**
* This test is disabled because it never actually exists. Run it if you want to ensure
* that changes to the Bulk Export Batch2 task haven't affected our ability to successfully
* run endless parallel jobs. If you run it for a few minutes, and it never stops on its own,
* you are good.
* <p>
* The enabled test above called {@link #testGroupBulkExportNotInGroup_DoesNotShowUp()} does
* run with the build and runs 100 jobs.
*/
@Test
@Disabled
public void testNonStopAbuseBatch2BulkExportStressTest() throws InterruptedException, ExecutionException {
duAbuseTest(Integer.MAX_VALUE);
}
private void duAbuseTest(int taskExecutions) throws InterruptedException, ExecutionException {
// Create some resources
Patient patient = new Patient();
patient.setId("PING1");
patient.setGender(Enumerations.AdministrativeGender.FEMALE);
patient.setActive(true);
myClient.update().resource(patient).execute();
patient = new Patient();
patient.setId("PING2");
patient.setGender(Enumerations.AdministrativeGender.MALE);
patient.setActive(true);
myClient.update().resource(patient).execute();
patient = new Patient();
patient.setId("PNING3");
patient.setGender(Enumerations.AdministrativeGender.MALE);
patient.setActive(true);
myClient.update().resource(patient).execute();
Group group = new Group();
group.setId("Group/G2");
group.setActive(true);
group.addMember().getEntity().setReference("Patient/PING1");
group.addMember().getEntity().setReference("Patient/PING2");
myClient.update().resource(group).execute();
// set the export options
BulkDataExportOptions options = new BulkDataExportOptions();
options.setResourceTypes(Sets.newHashSet("Patient"));
options.setGroupId(new IdType("Group", "G2"));
options.setFilters(new HashSet<>());
options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
options.setOutputFormat(Constants.CT_FHIR_NDJSON);
BlockingQueue<Runnable> workQueue = new LinkedBlockingQueue<>();
ExecutorService executorService = new ThreadPoolExecutor(10, 10,
0L, TimeUnit.MILLISECONDS,
workQueue);
ourLog.info("Starting task creation");
List<Future<Boolean>> futures = new ArrayList<>();
for (int i = 0; i < taskExecutions; i++) {
futures.add(executorService.submit(() -> {
String instanceId = null;
try {
instanceId = startJob(options);
// Run a scheduled pass to build the export
myBatch2JobHelper.awaitJobCompletion(instanceId, 60);
verifyBulkExportResults(instanceId, List.of("Patient/PING1", "Patient/PING2"), Collections.singletonList("Patient/PNING3"));
return true;
} catch (Throwable theError) {
ourLog.error("Caught an error during processing instance {}", instanceId, theError);
throw new InternalErrorException("Caught an error during processing instance " + instanceId, theError);
}
}));
// Don't let the list of futures grow so big we run out of memory
if (futures.size() > 200) {
while (futures.size() > 100) {
// This should always return true, but it'll throw an exception if we failed
assertTrue(futures.remove(0).get());
}
}
}
ourLog.info("Done creating tasks, waiting for task completion");
for (var next : futures) {
// This should always return true, but it'll throw an exception if we failed
assertTrue(next.get());
}
ourLog.info("Finished task execution");
}
private void verifyBulkExportResults(String theInstanceId, List<String> theContainedList, List<String> theExcludedList) {
// Iterate over the files
String report = myJobRunner.getJobInfo(theInstanceId).getReport();
ourLog.debug("Export job {} report: {}", theInstanceId, report);
if (!theContainedList.isEmpty()) {
assertThat("report for instance " + theInstanceId + " is empty", report, not(emptyOrNullString()));
}
BulkExportJobResults results = JsonUtil.deserialize(report, BulkExportJobResults.class);
Set<String> foundIds = new HashSet<>();
for (Map.Entry<String, List<String>> file : results.getResourceTypeToBinaryIds().entrySet()) {
String resourceType = file.getKey();
List<String> binaryIds = file.getValue();
for (var nextBinaryId : binaryIds) {
Binary binary = myBinaryDao.read(new IdType(nextBinaryId), mySrd);
assertEquals(Constants.CT_FHIR_NDJSON, binary.getContentType());
String nextNdJsonFileContent = new String(binary.getContent(), Constants.CHARSET_UTF8);
ourLog.trace("Export job {} file {} contents: {}", theInstanceId, nextBinaryId, nextNdJsonFileContent);
List<String> lines = new BufferedReader(new StringReader(nextNdJsonFileContent))
.lines().toList();
ourLog.debug("Export job {} file {} line-count: {}", theInstanceId, nextBinaryId, lines.size());
lines.stream()
.map(line -> myFhirContext.newJsonParser().parseResource(line))
.map(r -> r.getIdElement().toUnqualifiedVersionless())
.forEach(nextId -> {
if (!resourceType.equals(nextId.getResourceType())) {
fail("Found resource of type " + nextId.getResourceType() + " in file for type " + resourceType);
} else {
if (!foundIds.add(nextId.getValue())) {
fail("Found duplicate ID: " + nextId.getValue());
}
}
});
}
}
ourLog.debug("Export job {} exported resources {}", theInstanceId, foundIds);
for (String containedString : theContainedList) {
assertThat("export has expected ids", foundIds, hasItem(containedString));
}
for (String excludedString : theExcludedList) {
assertThat("export doesn't have expected ids", foundIds, not(hasItem(excludedString)));
}
}
private String startJob(BulkDataExportOptions theOptions) {
Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(theOptions));
assertNotNull(startResponse);
return startResponse.getInstanceId();
}
}

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@ -18,7 +18,6 @@ import org.hl7.fhir.r4.model.*;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.MethodOrderer; import org.junit.jupiter.api.MethodOrderer;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestMethodOrder; import org.junit.jupiter.api.TestMethodOrder;
import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.ParameterizedTest;
@ -38,12 +37,14 @@ import java.util.Set;
import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeUnit;
import java.util.stream.Stream; import java.util.stream.Stream;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TagsInlineTest.createSearchParameterForInlineSecurity;
import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.awaitility.Awaitility.await; import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasItem; import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.not; import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.fail; import static org.junit.jupiter.api.Assertions.fail;
@ -57,6 +58,7 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
@AfterEach @AfterEach
void afterEach() { void afterEach() {
myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED); myStorageSettings.setIndexMissingFields(JpaStorageSettings.IndexEnabledEnum.DISABLED);
myStorageSettings.setTagStorageMode(new JpaStorageSettings().getTagStorageMode());
} }
@BeforeEach @BeforeEach
@ -96,8 +98,45 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
verifyBulkExportResults(options, Collections.singletonList("Patient/PF"), Collections.singletonList("Patient/PM")); verifyBulkExportResults(options, Collections.singletonList("Patient/PF"), Collections.singletonList("Patient/PM"));
} }
@Test
public void testGroupBulkExportWithTypeFilter_OnTags_InlineTagMode() {
myStorageSettings.setTagStorageMode(JpaStorageSettings.TagStorageModeEnum.INLINE);
mySearchParameterDao.update(createSearchParameterForInlineSecurity(), mySrd);
mySearchParamRegistry.forceRefresh();
// Create some resources
Patient patient = new Patient();
patient.setId("PF");
patient.getMeta().addSecurity("http://security", "val0", null);
patient.setActive(true);
myClient.update().resource(patient).execute();
patient = new Patient();
patient.setId("PM");
patient.getMeta().addSecurity("http://security", "val1", null);
patient.setActive(true);
myClient.update().resource(patient).execute();
Group group = new Group();
group.setId("Group/G");
group.setActive(true);
group.addMember().getEntity().setReference("Patient/PF");
group.addMember().getEntity().setReference("Patient/PM");
myClient.update().resource(group).execute();
// set the export options
BulkDataExportOptions options = new BulkDataExportOptions();
options.setResourceTypes(Sets.newHashSet("Patient"));
options.setGroupId(new IdType("Group", "G"));
options.setFilters(Sets.newHashSet("Patient?_security=http://security|val1"));
options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
options.setOutputFormat(Constants.CT_FHIR_NDJSON);
verifyBulkExportResults(options, Collections.singletonList("Patient/PM"), Collections.singletonList("Patient/PF"));
}
@Test @Test
@Order(0)
public void testGroupBulkExportNotInGroup_DoesNotShowUp() { public void testGroupBulkExportNotInGroup_DoesNotShowUp() {
// Create some resources // Create some resources
Patient patient = new Patient(); Patient patient = new Patient();
@ -652,7 +691,7 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(theOptions)); Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(theOptions));
assertNotNull(startResponse); assertNotNull(startResponse);
assertEquals(false, startResponse.isUsesCachedResult()); assertFalse(startResponse.isUsesCachedResult());
// Run a scheduled pass to build the export // Run a scheduled pass to build the export
myBatch2JobHelper.awaitJobCompletion(startResponse.getInstanceId(), 120); myBatch2JobHelper.awaitJobCompletion(startResponse.getInstanceId(), 120);
@ -701,10 +740,10 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
} }
for (String containedString : theContainedList) { for (String containedString : theContainedList) {
assertThat(foundIds, hasItem(containedString)); assertThat("Didn't find expected ID " + containedString + " in IDS: " + foundIds, foundIds, hasItem(containedString));
} }
for (String excludedString : theExcludedList) { for (String excludedString : theExcludedList) {
assertThat(foundIds, not(hasItem(excludedString))); assertThat("Didn't want unexpected ID " + excludedString + " in IDS: " + foundIds, foundIds, not(hasItem(excludedString)));
} }
} }

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@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.bulk; package ca.uhn.fhir.jpa.bulk;
import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
import ca.uhn.fhir.batch2.api.IJobPersistence; import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.model.JobInstance; import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings; import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
@ -8,6 +9,10 @@ import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse; import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum; import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson; import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test; import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.BulkExportUtils; import ca.uhn.fhir.jpa.util.BulkExportUtils;
@ -16,6 +21,7 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails; import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions; import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.JsonUtil; import ca.uhn.fhir.util.JsonUtil;
import ca.uhn.fhir.util.SearchParameterUtil; import ca.uhn.fhir.util.SearchParameterUtil;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
@ -33,22 +39,25 @@ import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations; import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Group; import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation; import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference; import org.hl7.fhir.r4.model.Reference;
import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import java.io.IOException; import java.io.IOException;
import java.nio.charset.StandardCharsets; import java.nio.charset.StandardCharsets;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.Date;
import java.util.HashMap; import java.util.HashMap;
import java.util.HashSet; import java.util.HashSet;
import java.util.List; import java.util.List;
@ -82,6 +91,12 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
@Autowired @Autowired
private IJobPersistence myJobPersistence; private IJobPersistence myJobPersistence;
@Autowired
private IJobMaintenanceService myJobMaintenanceService;
@Autowired
private IBatch2JobInstanceRepository myJobInstanceRepository;
@Autowired
private IBatch2WorkChunkRepository myWorkChunkRepository;
@BeforeEach @BeforeEach
public void beforeEach() { public void beforeEach() {
@ -114,6 +129,7 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
myBatch2JobHelper.awaitJobCompletion(secondJobId); myBatch2JobHelper.awaitJobCompletion(secondJobId);
} }
@Test @Test
public void testPollingLocationContainsAllRequiredAttributesUponCompletion() throws IOException { public void testPollingLocationContainsAllRequiredAttributesUponCompletion() throws IOException {
@ -146,7 +162,7 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
} }
} }
@NotNull @Nonnull
private String getJobIdFromPollingLocation(String pollingLocation) { private String getJobIdFromPollingLocation(String pollingLocation) {
return pollingLocation.substring(pollingLocation.indexOf("_jobId=") + 7); return pollingLocation.substring(pollingLocation.indexOf("_jobId=") + 7);
} }
@ -369,6 +385,8 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM); options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM);
options.setOutputFormat(Constants.CT_FHIR_NDJSON); options.setOutputFormat(Constants.CT_FHIR_NDJSON);
myCaptureQueriesListener.clear();
Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(options)); Batch2JobStartResponse startResponse = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(options));
assertNotNull(startResponse); assertNotNull(startResponse);
@ -378,6 +396,23 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
// Run a scheduled pass to build the export // Run a scheduled pass to build the export
myBatch2JobHelper.awaitJobCompletion(startResponse.getInstanceId()); myBatch2JobHelper.awaitJobCompletion(startResponse.getInstanceId());
String queries = myCaptureQueriesListener
.getUpdateQueries()
.stream()
.filter(t -> t.getSql(false, false).toUpperCase().contains(" BT2_JOB_INSTANCE "))
.map(t -> new InstantType(new Date(t.getQueryTimestamp())) + " - " + t.getSql(true, false))
.collect(Collectors.joining("\n * "));
ourLog.info("Update queries:\n * " + queries);
runInTransaction(() -> {
String entities = myJobInstanceRepository
.findAll()
.stream()
.map(t -> t.toString())
.collect(Collectors.joining("\n * "));
ourLog.info("Entities:\n * " + entities);
});
final Optional<JobInstance> optJobInstance = myJobPersistence.fetchInstance(jobId); final Optional<JobInstance> optJobInstance = myJobPersistence.fetchInstance(jobId);
assertNotNull(optJobInstance); assertNotNull(optJobInstance);
@ -502,25 +537,28 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
@Test @Test
public void testVeryLargeGroup() { public void testVeryLargeGroup() {
BundleBuilder bb = new BundleBuilder(myFhirContext);
Group group = new Group(); Group group = new Group();
group.setId("Group/G"); group.setId("Group/G");
group.setActive(true); group.setActive(true);
bb.addTransactionUpdateEntry(group);
for (int i = 0; i < 600; i++) { for (int i = 0; i < 600; i++) {
Patient patient = new Patient(); Patient patient = new Patient();
patient.setId("PING-" + i); patient.setId("PING-" + i);
patient.setGender(Enumerations.AdministrativeGender.FEMALE); patient.setGender(Enumerations.AdministrativeGender.FEMALE);
patient.setActive(true); patient.setActive(true);
myClient.update().resource(patient).execute(); bb.addTransactionUpdateEntry(patient);
group.addMember().getEntity().setReference("Patient/PING-" + i); group.addMember().getEntity().setReference("Patient/PING-" + i);
Observation obs = new Observation(); Observation obs = new Observation();
obs.setId("obs-" + i); obs.setId("obs-" + i);
obs.setSubject(new Reference("Patient/PING-" + i)); obs.setSubject(new Reference("Patient/PING-" + i));
myClient.update().resource(obs).execute(); bb.addTransactionUpdateEntry(obs);
} }
myClient.update().resource(group).execute(); myClient.transaction().withBundle(bb.getBundle()).execute();
HashSet<String> resourceTypes = Sets.newHashSet("Group", "Patient", "Observation"); HashSet<String> resourceTypes = Sets.newHashSet("Group", "Patient", "Observation");
BulkExportJobResults bulkExportJobResults = startGroupBulkExportJobAndAwaitCompletion(resourceTypes, new HashSet<>(), "G"); BulkExportJobResults bulkExportJobResults = startGroupBulkExportJobAndAwaitCompletion(resourceTypes, new HashSet<>(), "G");
@ -567,7 +605,6 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
@Test @Test
public void testDifferentTypesDoNotUseCachedResults() { public void testDifferentTypesDoNotUseCachedResults() {
Patient patient = new Patient(); Patient patient = new Patient();
patient.setId("PING1"); patient.setId("PING1");
patient.setGender(Enumerations.AdministrativeGender.FEMALE); patient.setGender(Enumerations.AdministrativeGender.FEMALE);
@ -601,6 +638,13 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
Map<String, List<IBaseResource>> secondMap = convertJobResultsToResources(altBulkExportResults); Map<String, List<IBaseResource>> secondMap = convertJobResultsToResources(altBulkExportResults);
assertThat(secondMap.get("Patient"), hasSize(1)); assertThat(secondMap.get("Patient"), hasSize(1));
assertThat(secondMap.get("Coverage"), hasSize(1)); assertThat(secondMap.get("Coverage"), hasSize(1));
runInTransaction(() -> {
List<Batch2JobInstanceEntity> instances = myJobInstanceRepository.findAll();
ourLog.info("Job instance states:\n * {}", instances.stream().map(Object::toString).collect(Collectors.joining("\n * ")));
List<Batch2WorkChunkEntity> workChunks = myWorkChunkRepository.findAll();
ourLog.info("Work chunks instance states:\n * {}", workChunks.stream().map(Object::toString).collect(Collectors.joining("\n * ")));
});
} }
@ -1014,7 +1058,7 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
} }
@Nested @Nested
public class WithClientIdStrategyEnumANY { public class WithClientIdStrategyEnumANYTest {
@BeforeEach @BeforeEach
void setUp() { void setUp() {

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@ -3,12 +3,14 @@ package ca.uhn.fhir.jpa.bulk;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings; import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
public class BulkExportUseCaseTestAnyMode extends BulkExportUseCaseTest { @Disabled
private static final Logger ourLog = LoggerFactory.getLogger(BulkExportUseCaseTestAnyMode.class); public class BulkExportUseCaseTestAnyModeIT extends BulkExportUseCaseTest {
private static final Logger ourLog = LoggerFactory.getLogger(BulkExportUseCaseTestAnyModeIT.class);
@BeforeEach @BeforeEach

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@ -0,0 +1,104 @@
package ca.uhn.fhir.jpa.bulk.export;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.jobs.export.ExpandResourcesStep;
import ca.uhn.fhir.batch2.jobs.export.models.BulkExportJobParameters;
import ca.uhn.fhir.batch2.jobs.export.models.ExpandedResourcesList;
import ca.uhn.fhir.batch2.jobs.export.models.ResourceIdList;
import ca.uhn.fhir.batch2.jobs.models.BatchResourceId;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import java.util.stream.IntStream;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
public class ExpandResourcesStepJpaTest extends BaseJpaR4Test {
@Autowired
private ExpandResourcesStep myExpandResourcesStep;
@Mock
private IJobDataSink<ExpandedResourcesList> mySink;
@Captor
private ArgumentCaptor<ExpandedResourcesList> myWorkChunkCaptor;
@Override
public void afterCleanupDao() {
super.afterCleanupDao();
myStorageSettings.setTagStorageMode(new JpaStorageSettings().getTagStorageMode());
}
/**
* Make sure we load inline tags efficiently when generating bulk export
*/
@ParameterizedTest
@CsvSource({"INLINE,2", "NON_VERSIONED,3", "VERSIONED,3"})
public void testBulkExportExpandResourcesStep(JpaStorageSettings.TagStorageModeEnum theTagStorageMode, int theExpectedSelectQueries) {
// Setup
myStorageSettings.setTagStorageMode(theTagStorageMode);
int count = 10;
List<Long> ids = IntStream.range(0, count)
.boxed()
.map(t -> {
Patient p = new Patient();
p.getMeta().addTag().setSystem("http://static").setCode("tag");
p.getMeta().addTag().setSystem("http://dynamic").setCode("tag" + t);
return myPatientDao.create(p, mySrd).getId().getIdPartAsLong();
}).toList();
assertEquals(count, ids.size());
ResourceIdList resourceList = new ResourceIdList();
resourceList.setResourceType("Patient");
resourceList.setIds(ids.stream().map(t -> new BatchResourceId().setResourceType("Patient").setId(Long.toString(t))).toList());
BulkExportJobParameters params = new BulkExportJobParameters();
JobInstance jobInstance = new JobInstance();
String chunkId = "ABC";
StepExecutionDetails<BulkExportJobParameters, ResourceIdList> details = new StepExecutionDetails<>(params, resourceList, jobInstance, chunkId);
// Test
myCaptureQueriesListener.clear();
myExpandResourcesStep.run(details, mySink);
// Verify
verify(mySink, times(1)).accept(myWorkChunkCaptor.capture());
ExpandedResourcesList expandedResourceList = myWorkChunkCaptor.getValue();
assertEquals(10, expandedResourceList.getStringifiedResources().size());
assertThat(expandedResourceList.getStringifiedResources().get(0), containsString("{\"system\":\"http://static\",\"code\":\"tag\"}"));
assertThat(expandedResourceList.getStringifiedResources().get(0), containsString("{\"system\":\"http://dynamic\",\"code\":\"tag0\"}"));
assertThat(expandedResourceList.getStringifiedResources().get(1), containsString("{\"system\":\"http://static\",\"code\":\"tag\"}"));
assertThat(expandedResourceList.getStringifiedResources().get(1), containsString("{\"system\":\"http://dynamic\",\"code\":\"tag1\"}"));
// Verify query counts
assertEquals(theExpectedSelectQueries, myCaptureQueriesListener.countSelectQueries());
assertEquals(0, myCaptureQueriesListener.countInsertQueries());
assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(2, myCaptureQueriesListener.countCommits());
assertEquals(0, myCaptureQueriesListener.countRollbacks());
}
}

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@ -37,6 +37,7 @@ import org.hl7.fhir.r4.model.DecimalType;
import org.hl7.fhir.r4.model.Encounter; import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations; import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation; import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization; import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
@ -87,6 +88,32 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
myStorageSettings.setInlineResourceTextBelowSize(new JpaStorageSettings().getInlineResourceTextBelowSize()); myStorageSettings.setInlineResourceTextBelowSize(new JpaStorageSettings().getInlineResourceTextBelowSize());
} }
@Test
public void testCreateDoesntIndexForMetaSearchTags() {
Observation obs = new Observation();
obs.setId("A");
obs.addNote().setText("A non indexed value");
obs.getMeta().setLastUpdatedElement(InstantType.now());
obs.getMeta().addTag().setSystem("http://foo").setCode("blah");
obs.getMeta().addTag().setSystem("http://foo").setCode("blah2");
obs.getMeta().addSecurity().setSystem("http://foo").setCode("blah");
obs.getMeta().addSecurity().setSystem("http://foo").setCode("blah2");
obs.getMeta().addProfile("http://blah");
obs.getMeta().addProfile("http://blah2");
obs.getMeta().setSource("http://foo#bar");
myObservationDao.update(obs, new SystemRequestDetails());
runInTransaction(()->{
logAllTokenIndexes();
logAllStringIndexes();
assertEquals(0, myResourceIndexedSearchParamStringDao.count());
assertEquals(0, myResourceIndexedSearchParamTokenDao.count());
assertEquals(0, myResourceIndexedSearchParamUriDao.count());
});
}
@Test @Test
public void testCreateLinkCreatesAppropriatePaths() { public void testCreateLinkCreatesAppropriatePaths() {

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@ -17,8 +17,13 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID; import java.util.UUID;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString; import static org.hamcrest.Matchers.containsString;
@ -109,7 +114,8 @@ public class FhirResourceDaoR4SearchSqlTest extends BaseJpaR4Test {
boolean reindexParamCache = myStorageSettings.isMarkResourcesForReindexingUponSearchParameterChange(); boolean reindexParamCache = myStorageSettings.isMarkResourcesForReindexingUponSearchParameterChange();
myStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false); myStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false);
SearchParameter searchParameter = FhirResourceDaoR4TagsTest.createSearchParamForInlineResourceProfile(); // SearchParameter searchParameter = FhirResourceDaoR4TagsTest.createSearchParamForInlineResourceProfile();
SearchParameter searchParameter = FhirResourceDaoR4TagsInlineTest.createSearchParameterForInlineProfile();
ourLog.debug("SearchParam:\n{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter)); ourLog.debug("SearchParam:\n{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
mySearchParameterDao.update(searchParameter, mySrd); mySearchParameterDao.update(searchParameter, mySrd);
mySearchParamRegistry.forceRefresh(); mySearchParamRegistry.forceRefresh();

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@ -0,0 +1,236 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.rest.gclient.TokenClientParam;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TagsTest.toProfiles;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TagsTest.toSecurityLabels;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TagsTest.toTags;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
@SuppressWarnings({"Duplicates"})
public class FhirResourceDaoR4TagsInlineTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4TagsInlineTest.class);
@Override
@AfterEach
public final void after() throws Exception {
super.after();
myStorageSettings.setTagStorageMode(JpaStorageSettings.DEFAULT_TAG_STORAGE_MODE);
}
@Test
public void testInlineTags_StoreAndRetrieve() {
myStorageSettings.setTagStorageMode(JpaStorageSettings.TagStorageModeEnum.INLINE);
// Store a first version
Patient patient = new Patient();
patient.setId("Patient/A");
patient.getMeta().addProfile("http://profile1");
patient.getMeta().addTag("http://tag1", "vtag1", "dtag1");
patient.getMeta().addSecurity("http://sec1", "vsec1", "dsec1");
patient.setActive(true);
myPatientDao.update(patient, mySrd);
runInTransaction(() -> {
assertEquals(0, myResourceTagDao.count());
assertEquals(0, myResourceHistoryTagDao.count());
assertEquals(0, myTagDefinitionDao.count());
});
// Read it back
patient = myPatientDao.read(new IdType("Patient/A/_history/1"), mySrd);
assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
// Store a second version
patient = new Patient();
patient.setId("Patient/A");
patient.getMeta().addProfile("http://profile2");
patient.getMeta().addTag("http://tag2", "vtag2", "dtag2");
patient.getMeta().addSecurity("http://sec2", "vsec2", "dsec2");
patient.setActive(true);
myPatientDao.update(patient, mySrd);
runInTransaction(() -> {
assertEquals(0, myResourceTagDao.count());
assertEquals(0, myResourceHistoryTagDao.count());
assertEquals(0, myTagDefinitionDao.count());
});
// First version should have only the initial tags
patient = myPatientDao.read(new IdType("Patient/A/_history/1"), mySrd);
assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
// Second version should have the new set of tags
// TODO: We could copy these forward like we do for non-inline mode. Perhaps in the future.
patient = myPatientDao.read(new IdType("Patient/A/_history/2"), mySrd);
assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile2"));
assertThat(toTags(patient).toString(), toTags(patient), containsInAnyOrder("http://tag2|vtag2|dtag2"));
assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), containsInAnyOrder("http://sec2|vsec2|dsec2"));
}
@Test
public void testInlineTags_Search_Tag() {
myStorageSettings.setTagStorageMode(JpaStorageSettings.TagStorageModeEnum.INLINE);
SearchParameter searchParameter = createSearchParameterForInlineTag();
ourLog.debug("SearchParam:\n{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
mySearchParameterDao.update(searchParameter, mySrd);
mySearchParamRegistry.forceRefresh();
createPatientsForInlineSearchTests();
logAllTokenIndexes();
// Perform a search
Bundle outcome = myClient.search().forResource("Patient").where(new TokenClientParam("_tag").exactly().systemAndCode("http://tag1", "vtag1")).returnBundle(Bundle.class).execute();
assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder("Patient/A", "Patient/B"));
validatePatientSearchResultsForInlineTags(outcome);
}
@Test
public void testInlineTags_Search_Profile() {
myStorageSettings.setTagStorageMode(JpaStorageSettings.TagStorageModeEnum.INLINE);
SearchParameter searchParameter = createSearchParameterForInlineProfile();
ourLog.debug("SearchParam:\n{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
mySearchParameterDao.update(searchParameter, mySrd);
mySearchParamRegistry.forceRefresh();
createPatientsForInlineSearchTests();
logAllTokenIndexes();
// Perform a search
Bundle outcome = myClient.search().forResource("Patient").where(new TokenClientParam("_profile").exactly().code("http://profile1")).returnBundle(Bundle.class).execute();
assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder("Patient/A", "Patient/B"));
validatePatientSearchResultsForInlineTags(outcome);
}
@Test
public void testInlineTags_Search_Security() {
myStorageSettings.setTagStorageMode(JpaStorageSettings.TagStorageModeEnum.INLINE);
SearchParameter searchParameter = createSearchParameterForInlineSecurity();
ourLog.debug("SearchParam:\n{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
mySearchParameterDao.update(searchParameter, mySrd);
mySearchParamRegistry.forceRefresh();
createPatientsForInlineSearchTests();
logAllTokenIndexes();
// Perform a search
Bundle outcome = myClient.search().forResource("Patient").where(new TokenClientParam("_security").exactly().systemAndCode("http://sec1", "vsec1")).returnBundle(Bundle.class).execute();
assertThat(toUnqualifiedVersionlessIdValues(outcome), containsInAnyOrder("Patient/A", "Patient/B"));
validatePatientSearchResultsForInlineTags(outcome);
}
private void validatePatientSearchResultsForInlineTags(Bundle outcome) {
Patient patient;
patient = (Patient) outcome.getEntry().get(0).getResource();
assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
patient = (Patient) outcome.getEntry().get(1).getResource();
assertThat(toProfiles(patient).toString(), toProfiles(patient), contains("http://profile1"));
assertThat(toTags(patient).toString(), toTags(patient), contains("http://tag1|vtag1|dtag1"));
assertThat(toSecurityLabels(patient).toString(), toSecurityLabels(patient), contains("http://sec1|vsec1|dsec1"));
}
private void createPatientsForInlineSearchTests() {
Patient patient = new Patient();
patient.setId("Patient/A");
patient.getMeta().addProfile("http://profile1");
patient.getMeta().addTag("http://tag1", "vtag1", "dtag1");
patient.getMeta().addSecurity("http://sec1", "vsec1", "dsec1");
patient.setActive(true);
myPatientDao.update(patient, mySrd);
patient = new Patient();
patient.setId("Patient/B");
patient.getMeta().addProfile("http://profile1");
patient.getMeta().addTag("http://tag1", "vtag1", "dtag1");
patient.getMeta().addSecurity("http://sec1", "vsec1", "dsec1");
patient.setActive(true);
myPatientDao.update(patient, mySrd);
patient = new Patient();
patient.setId("Patient/NO");
patient.getMeta().addProfile("http://profile99");
patient.getMeta().addTag("http://tag99", "vtag99", "dtag99");
patient.getMeta().addSecurity("http://sec99", "vsec99", "dsec99");
patient.setActive(true);
myPatientDao.update(patient, mySrd);
}
@Nonnull
public static SearchParameter createSearchParameterForInlineTag() {
SearchParameter searchParameter = new SearchParameter();
searchParameter.setId("SearchParameter/resource-tag");
for (String next : FhirContext.forR4Cached().getResourceTypes().stream().sorted().toList()) {
searchParameter.addBase(next);
}
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameter.setType(Enumerations.SearchParamType.TOKEN);
searchParameter.setCode("_tag");
searchParameter.setName("Tag");
searchParameter.setExpression("meta.tag");
return searchParameter;
}
@Nonnull
public static SearchParameter createSearchParameterForInlineSecurity() {
SearchParameter searchParameter = new SearchParameter();
searchParameter.setId("SearchParameter/resource-security");
for (String next : FhirContext.forR4Cached().getResourceTypes().stream().sorted().toList()) {
searchParameter.addBase(next);
}
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameter.setType(Enumerations.SearchParamType.TOKEN);
searchParameter.setCode("_security");
searchParameter.setName("Security");
searchParameter.setExpression("meta.security");
return searchParameter;
}
@Nonnull
public static SearchParameter createSearchParameterForInlineProfile() {
SearchParameter searchParameter = new SearchParameter();
searchParameter.setId("SearchParameter/resource-profile");
for (String next : FhirContext.forR4Cached().getResourceTypes().stream().sorted().toList()) {
searchParameter.addBase(next);
}
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameter.setType(Enumerations.SearchParamType.URI);
searchParameter.setCode("_profile");
searchParameter.setName("Profile");
searchParameter.setExpression("meta.profile");
return searchParameter;
}
}

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@ -595,32 +595,32 @@ public class FhirResourceDaoR4TagsTest extends BaseResourceProviderR4Test {
} }
@Nonnull @Nonnull
private List<String> toTags(Patient patient) { static List<String> toTags(Patient patient) {
return toTags(patient.getMeta()); return toTags(patient.getMeta());
} }
@Nonnull @Nonnull
private List<String> toSecurityLabels(Patient patient) { static List<String> toSecurityLabels(Patient patient) {
return toSecurityLabels(patient.getMeta()); return toSecurityLabels(patient.getMeta());
} }
@Nonnull @Nonnull
private List<String> toProfiles(Patient patient) { static List<String> toProfiles(Patient patient) {
return toProfiles(patient.getMeta()); return toProfiles(patient.getMeta());
} }
@Nonnull @Nonnull
private static List<String> toTags(Meta meta) { static List<String> toTags(Meta meta) {
return meta.getTag().stream().map(t -> t.getSystem() + "|" + t.getCode() + "|" + t.getDisplay()).collect(Collectors.toList()); return meta.getTag().stream().map(t -> t.getSystem() + "|" + t.getCode() + "|" + t.getDisplay()).collect(Collectors.toList());
} }
@Nonnull @Nonnull
private static List<String> toSecurityLabels(Meta meta) { static List<String> toSecurityLabels(Meta meta) {
return meta.getSecurity().stream().map(t -> t.getSystem() + "|" + t.getCode() + "|" + t.getDisplay()).collect(Collectors.toList()); return meta.getSecurity().stream().map(t -> t.getSystem() + "|" + t.getCode() + "|" + t.getDisplay()).collect(Collectors.toList());
} }
@Nonnull @Nonnull
private static List<String> toProfiles(Meta meta) { static List<String> toProfiles(Meta meta) {
return meta.getProfile().stream().map(t -> t.getValue()).collect(Collectors.toList()); return meta.getProfile().stream().map(t -> t.getValue()).collect(Collectors.toList());
} }

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@ -32,6 +32,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SortOrderEnum; import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec; import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId; import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.DateParam; import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam; import ca.uhn.fhir.rest.param.DateRangeParam;
@ -49,6 +50,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException; import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.BundleBuilder;
import com.google.common.base.Charsets; import com.google.common.base.Charsets;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -62,6 +64,7 @@ import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.instance.model.api.IAnyResource; import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Address;
import org.hl7.fhir.r4.model.Age; import org.hl7.fhir.r4.model.Age;
import org.hl7.fhir.r4.model.Attachment; import org.hl7.fhir.r4.model.Attachment;
import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle;
@ -99,6 +102,7 @@ import org.hl7.fhir.r4.model.OperationOutcome.IssueType;
import org.hl7.fhir.r4.model.Organization; import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period; import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Provenance; import org.hl7.fhir.r4.model.Provenance;
import org.hl7.fhir.r4.model.Quantity; import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Quantity.QuantityComparator; import org.hl7.fhir.r4.model.Quantity.QuantityComparator;
@ -334,7 +338,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
assertEquals("#", observation.getSubject().getReference()); assertEquals("#", observation.getSubject().getReference());
} }
@Tag("intermittent") @Tag("intermittent")
// @Test // @Test
public void testTermConceptReindexingDoesntDuplicateData() { public void testTermConceptReindexingDoesntDuplicateData() {

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@ -41,6 +41,7 @@ import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.SearchParameter; import org.hl7.fhir.r4.model.SearchParameter;
import org.hl7.fhir.r4.model.StructureDefinition; import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.utilities.npm.NpmPackage; import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Disabled;
@ -116,7 +117,7 @@ public class NpmR4Test extends BaseJpaR4Test {
int port = JettyUtil.getPortForStartedServer(myServer); int port = JettyUtil.getPortForStartedServer(myServer);
jpaPackageCache.getPackageServers().clear(); jpaPackageCache.getPackageServers().clear();
jpaPackageCache.addPackageServer("http://localhost:" + port); jpaPackageCache.addPackageServer(new PackageServer("http://localhost:" + port));
myFakeNpmServlet.responses.clear(); myFakeNpmServlet.responses.clear();
} }
@ -138,7 +139,7 @@ public class NpmR4Test extends BaseJpaR4Test {
public void testInstallUsCore() { public void testInstallUsCore() {
JpaPackageCache jpaPackageCache = ProxyUtil.getSingletonTarget(myPackageCacheManager, JpaPackageCache.class); JpaPackageCache jpaPackageCache = ProxyUtil.getSingletonTarget(myPackageCacheManager, JpaPackageCache.class);
jpaPackageCache.getPackageServers().clear(); jpaPackageCache.getPackageServers().clear();
jpaPackageCache.addPackageServer("https://packages.fhir.org"); jpaPackageCache.addPackageServer(new PackageServer("https://packages.fhir.org"));
PackageInstallationSpec spec = new PackageInstallationSpec() PackageInstallationSpec spec = new PackageInstallationSpec()
.setName("hl7.fhir.us.core") .setName("hl7.fhir.us.core")

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@ -10,6 +10,7 @@ import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder; import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.npm.NpmPackage; import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -55,7 +56,7 @@ public class PackageLoaderSvcIT {
int port = JettyUtil.getPortForStartedServer(myServer); int port = JettyUtil.getPortForStartedServer(myServer);
myPackageLoaderSvc.getPackageServers().clear(); myPackageLoaderSvc.getPackageServers().clear();
myPackageLoaderSvc.addPackageServer("http://localhost:" + port); myPackageLoaderSvc.addPackageServer(new PackageServer("http://localhost:" + port));
myFakeNpmServlet.getResponses().clear(); myFakeNpmServlet.getResponses().clear();
} }

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@ -765,10 +765,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">hello</div>"); patient.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">hello</div>");
patient = (Patient) myClient.create().resource(patient).execute().getResource(); patient = (Patient) myClient.create().resource(patient).execute().getResource();
ourLog.info("Patient: {}", myFhirContext.newJsonParser().encodeResourceToString(patient));
assertEquals(1, patient.getIdElement().getVersionIdPartAsLong()); assertEquals(1, patient.getIdElement().getVersionIdPartAsLong());
// Read Patient // Read Patient
patient = (Patient) myClient.read().resource("Patient").withId(patient.getIdElement()).execute(); patient = (Patient) myClient.read().resource("Patient").withId(patient.getIdElement()).execute();
ourLog.info("Patient: {}", myFhirContext.newJsonParser().encodeResourceToString(patient));
assertEquals(1, patient.getIdElement().getVersionIdPartAsLong()); assertEquals(1, patient.getIdElement().getVersionIdPartAsLong());
// Update Patient with no changes // Update Patient with no changes

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@ -284,6 +284,8 @@ public class GiantTransactionPerfTest {
mySystemDao.transaction(requestDetails, input); mySystemDao.transaction(requestDetails, input);
ourLog.info("Merges:\n * " + myEntityManager.myMergeCount.stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
assertThat(myEntityManager.myPersistCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.contains("ResourceTable")); assertThat(myEntityManager.myPersistCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.contains("ResourceTable"));
assertThat(myEntityManager.myMergeCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.containsInAnyOrder("ResourceTable", "ResourceIndexedSearchParamToken", "ResourceIndexedSearchParamToken")); assertThat(myEntityManager.myMergeCount.stream().map(t -> t.getClass().getSimpleName()).collect(Collectors.toList()), Matchers.containsInAnyOrder("ResourceTable", "ResourceIndexedSearchParamToken", "ResourceIndexedSearchParamToken"));
assertEquals(1, myEntityManager.myFlushCount); assertEquals(1, myEntityManager.myFlushCount);

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@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc; import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy; import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator; import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer; import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionValidatingInterceptor; import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionValidatingInterceptor;

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -123,11 +123,12 @@ public class Batch2JobHelper {
return myJobCoordinator.getInstance(theBatchJobId); return myJobCoordinator.getInstance(theBatchJobId);
} }
private boolean checkStatusWithMaintenancePass(String theBatchJobId, StatusEnum... theExpectedStatuses) { private boolean checkStatusWithMaintenancePass(String theBatchJobId, StatusEnum... theExpectedStatuses) throws InterruptedException {
if (hasStatus(theBatchJobId, theExpectedStatuses)) { if (hasStatus(theBatchJobId, theExpectedStatuses)) {
return true; return true;
} }
myJobMaintenanceService.runMaintenancePass(); myJobMaintenanceService.runMaintenancePass();
Thread.sleep(1000);
return hasStatus(theBatchJobId, theExpectedStatuses); return hasStatus(theBatchJobId, theExpectedStatuses);
} }

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -7,7 +7,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
@ -20,7 +20,7 @@
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId> <artifactId>hapi-fhir-caching-api</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.github.ben-manes.caffeine</groupId> <groupId>com.github.ben-manes.caffeine</groupId>

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@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId> <artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId> <artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>6.5.3-SNAPSHOT</version> <version>6.5.4-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

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@ -57,13 +57,13 @@ public class BulkExportCreateReportStep implements IReductionStepWorker<BulkExpo
results.setOriginalRequestUrl(requestUrl); results.setOriginalRequestUrl(requestUrl);
if (myResourceToBinaryIds != null) { if (myResourceToBinaryIds != null) {
ourLog.info("Bulk Export Report creation step"); ourLog.info("Bulk Export Report creation step for instance: {}", theStepExecutionDetails.getInstance().getInstanceId());
results.setResourceTypeToBinaryIds(myResourceToBinaryIds); results.setResourceTypeToBinaryIds(myResourceToBinaryIds);
myResourceToBinaryIds = null; myResourceToBinaryIds = null;
} else { } else {
String msg = "Export complete, but no data to generate report."; String msg = "Export complete, but no data to generate report for job instance: " + theStepExecutionDetails.getInstance().getInstanceId();
ourLog.warn(msg); ourLog.warn(msg);
results.setReportMsg(msg); results.setReportMsg(msg);

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@ -28,14 +28,20 @@ import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.batch2.jobs.export.models.BulkExportJobParameters; import ca.uhn.fhir.batch2.jobs.export.models.BulkExportJobParameters;
import ca.uhn.fhir.batch2.jobs.export.models.ExpandedResourcesList; import ca.uhn.fhir.batch2.jobs.export.models.ExpandedResourcesList;
import ca.uhn.fhir.batch2.jobs.export.models.ResourceIdList; import ca.uhn.fhir.batch2.jobs.export.models.ResourceIdList;
import ca.uhn.fhir.batch2.jobs.models.BatchResourceId;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao; import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService; import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkExportProcessor; import ca.uhn.fhir.jpa.bulk.export.api.IBulkExportProcessor;
import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
import ca.uhn.fhir.jpa.model.entity.StorageSettings; import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.parser.IParser; import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc; import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc;
import com.google.common.collect.ArrayListMultimap; import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap; import com.google.common.collect.ListMultimap;
@ -47,7 +53,11 @@ import org.springframework.context.ApplicationContext;
import javax.annotation.Nonnull; import javax.annotation.Nonnull;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAM_ID;
import static org.slf4j.LoggerFactory.getLogger; import static org.slf4j.LoggerFactory.getLogger;
public class ExpandResourcesStep implements IJobStepWorker<BulkExportJobParameters, ResourceIdList, ExpandedResourcesList> { public class ExpandResourcesStep implements IJobStepWorker<BulkExportJobParameters, ResourceIdList, ExpandedResourcesList> {
@ -71,6 +81,9 @@ public class ExpandResourcesStep implements IJobStepWorker<BulkExportJobParamete
@Autowired @Autowired
private IIdHelperService myIdHelperService; private IIdHelperService myIdHelperService;
@Autowired
private IHapiTransactionService myTransactionService;
private volatile ResponseTerminologyTranslationSvc myResponseTerminologyTranslationSvc; private volatile ResponseTerminologyTranslationSvc myResponseTerminologyTranslationSvc;
@Nonnull @Nonnull
@ -102,7 +115,7 @@ public class ExpandResourcesStep implements IJobStepWorker<BulkExportJobParamete
terminologyTranslationSvc.processResourcesForTerminologyTranslation(allResources); terminologyTranslationSvc.processResourcesForTerminologyTranslation(allResources);
} }
// encode them // encode them - Key is resource type, Value is a collection of serialized resources of that type
ListMultimap<String, String> resources = encodeToString(allResources, jobParameters); ListMultimap<String, String> resources = encodeToString(allResources, jobParameters);
// set to datasink // set to datasink
@ -125,12 +138,46 @@ public class ExpandResourcesStep implements IJobStepWorker<BulkExportJobParamete
} }
private List<IBaseResource> fetchAllResources(ResourceIdList theIds) { private List<IBaseResource> fetchAllResources(ResourceIdList theIds) {
List<IBaseResource> resources = new ArrayList<>(); ArrayListMultimap<String, String> typeToIds = ArrayListMultimap.create();
theIds.getIds().forEach(t -> typeToIds.put(t.getResourceType(), t.getId()));
List<IBaseResource> resources = new ArrayList<>(theIds.getIds().size());
for (String resourceType : typeToIds.keySet()) {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
List<String> allIds = typeToIds.get(resourceType);
while (!allIds.isEmpty()) {
// Load in batches in order to avoid having too many PIDs go into a
// single SQ statement at once
int batchSize = Math.min(500, allIds.size());
Set<IResourcePersistentId> nextBatchOfPids =
allIds
.subList(0, batchSize)
.stream()
.map(t -> myIdHelperService.newPidFromStringIdAndResourceName(t, resourceType))
.collect(Collectors.toSet());
allIds = allIds.subList(batchSize, allIds.size());
PersistentIdToForcedIdMap nextBatchOfResourceIds = myTransactionService
.withRequest(null)
.execute(() -> myIdHelperService.translatePidsToForcedIds(nextBatchOfPids));
TokenOrListParam idListParam = new TokenOrListParam();
for (IResourcePersistentId nextPid : nextBatchOfPids) {
Optional<String> resourceId = nextBatchOfResourceIds.get(nextPid);
idListParam.add(resourceId.orElse(nextPid.getId().toString()));
}
SearchParameterMap spMap = SearchParameterMap
.newSynchronous()
.add(PARAM_ID, idListParam);
IBundleProvider outcome = dao.search(spMap, new SystemRequestDetails());
resources.addAll(outcome.getAllResources());
}
for (BatchResourceId batchResourceId : theIds.getIds()) {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(batchResourceId.getResourceType());
// This should be a query, but we have PIDs, and we don't have a _pid search param. TODO GGG, figure out how to make this search by pid.
resources.add(dao.readByPid(myIdHelperService.newPidFromStringIdAndResourceName(batchResourceId.getId(), batchResourceId.getResourceType())));
} }
return resources; return resources;

View File

@ -12,12 +12,17 @@ import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao; import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService; import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkExportProcessor; import ca.uhn.fhir.jpa.bulk.export.api.IBulkExportProcessor;
import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
import ca.uhn.fhir.jpa.dao.tx.NonTransactionalHapiTransactionService;
import ca.uhn.fhir.jpa.model.dao.JpaPid; import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.StorageSettings; import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions; import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId; import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc; import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
@ -32,6 +37,10 @@ import org.mockito.junit.jupiter.MockitoExtension;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.Date; import java.util.Date;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse; import static org.junit.jupiter.api.Assertions.assertFalse;
@ -62,6 +71,9 @@ public class ExpandResourcesStepTest {
@Spy @Spy
private StorageSettings myStorageSettings = new StorageSettings(); private StorageSettings myStorageSettings = new StorageSettings();
@Spy
private IHapiTransactionService myTransactionService = new NonTransactionalHapiTransactionService();
@InjectMocks @InjectMocks
private ExpandResourcesStep mySecondStep; private ExpandResourcesStep mySecondStep;
@ -122,9 +134,17 @@ public class ExpandResourcesStepTest {
createParameters(), createParameters(),
instance instance
); );
ArrayList<IBaseResource> clone = new ArrayList<>(resources); when(patientDao.search(any(), any())).thenReturn(new SimpleBundleProvider(resources));
when(patientDao.readByPid(any(BaseResourcePersistentId.class))).thenAnswer(i -> clone.remove(0));
when(myIdHelperService.newPidFromStringIdAndResourceName(anyString(), anyString())).thenReturn(JpaPid.fromId(1L)); when(myIdHelperService.newPidFromStringIdAndResourceName(anyString(), anyString())).thenReturn(JpaPid.fromId(1L));
when(myIdHelperService.translatePidsToForcedIds(any())).thenAnswer(t->{
Set<IResourcePersistentId<?>> inputSet = t.getArgument(0, Set.class);
Map<IResourcePersistentId<?>, Optional<String>> map = new HashMap<>();
for (var next : inputSet) {
map.put(next, Optional.empty());
}
return new PersistentIdToForcedIdMap<>(map);
});
// test // test
RunOutcome outcome = mySecondStep.run(input, sink); RunOutcome outcome = mySecondStep.run(input, sink);

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