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Don't thrash delta links (#1721) 

* Don't thrash delta links

* Add changelog

* Remove commented out code
This commit is contained in:
James Agnew 2020-02-19 17:46:54 -05:00 committed by GitHub
parent ab8dfa5a03
commit a05c4ce9eb
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3 changed files with 94 additions and 76 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1721-dont-thrash-delta-links.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 1721
title: When performing a terminology delta ADD operation, existing parent-child links were often
deleted and recrreated needlessly during operations, which could result in a deadlock. This has
been resolved.

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
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@ -451,48 +451,40 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
String nextCodeToAdd = conceptToAdd.getCode();
String parentDescription = "(root concept)";
Set<TermConcept> parentConcepts = new HashSet<>();
if (!theParentCodes.isEmpty()) {
parentDescription = "[" + String.join(", ", theParentCodes) + "]";
for (String nextParentCode : theParentCodes) {
Optional<TermConcept> nextParentOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextParentCode);
if (nextParentOpt.isPresent() == false) {
throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
}
parentConcepts.add(nextParentOpt.get());
}
}
ourLog.info("Saving concept {} with parent {}", theStatisticsTracker.getUpdatedConceptCount(), parentDescription);
Optional<TermConcept> existingCodeOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextCodeToAdd);
List<TermConceptParentChildLink> existingParentLinks;
if (existingCodeOpt.isPresent()) {
TermConcept existingCode = existingCodeOpt.get();
existingCode.setIndexStatus(null);
existingCode.setDisplay(conceptToAdd.getDisplay());
conceptToAdd = existingCode;
existingParentLinks = conceptToAdd.getParents();
} else {
existingParentLinks = Collections.emptyList();
}
Set<TermConcept> parentConceptsWeShouldLinkTo = new HashSet<>();
for (String nextParentCode : theParentCodes) {
// Don't add parent links that already exist for the code
if (existingParentLinks.stream().anyMatch(t->t.getParent().getCode().equals(nextParentCode))) {
continue;
}
Optional<TermConcept> nextParentOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextParentCode);
if (nextParentOpt.isPresent() == false) {
throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
}
parentConceptsWeShouldLinkTo.add(nextParentOpt.get());
}
if (conceptToAdd.getSequence() == null) {
conceptToAdd.setSequence(theSequence);
}
// Drop any old parent-child links if they aren't explicitly specified in the
// hierarchy being added
if (!theRootConcept) {
for (Iterator<TermConceptParentChildLink> iter = conceptToAdd.getParents().iterator(); iter.hasNext(); ) {
TermConceptParentChildLink nextLink = iter.next();
String parentCode = nextLink.getParent().getCode();
ourLog.info("Dropping existing parent/child link from {} -> {}", parentCode, nextCodeToAdd);
myConceptParentChildLinkDao.delete(nextLink);
iter.remove();
List<TermConceptParentChildLink> parentChildrenList = nextLink.getParent().getChildren();
parentChildrenList.remove(nextLink);
}
}
// Null out the hierarchy PIDs for this concept always. We do this because we're going to
// force a reindex, and it'll be regenerated then
conceptToAdd.setParentPids(null);
@ -504,7 +496,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
theStatisticsTracker.incrementUpdatedConceptCount();
// Add link to new child to the parent
for (TermConcept nextParentConcept : parentConcepts) {
for (TermConcept nextParentConcept : parentConceptsWeShouldLinkTo) {
TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
parentLink.setParent(nextParentConcept);
parentLink.setChild(conceptToAdd);

116
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java
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@ -156,6 +156,8 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAAA seq=0",
"RootB seq=0",
" ChildAA seq=0",
" ChildAAA seq=0"
@ -164,6 +166,72 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
}
@Test
public void testReAddingConceptsDoesntRecreateExistingLinks() {
createNotPresentCodeSystem();
assertHierarchyContains();
UploadStatistics outcome;
CustomTerminologySet delta;
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
delta.addRootConcept("RootA", "Root A")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0"
);
myCaptureQueriesListener.logDeleteQueries();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
myCaptureQueriesListener.logInsertQueries();
// 2 concepts, 1 link
assertEquals(3, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
delta.addRootConcept("RootA", "Root A")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAAA seq=0"
);
myCaptureQueriesListener.logDeleteQueries();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
myCaptureQueriesListener.logInsertQueries();
// 1 concept, 1 link
assertEquals(2, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
delta.addRootConcept("RootA", "Root A")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAAA").setDisplay("Child AAAA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAAA seq=0",
" ChildAAAA seq=0"
);
myCaptureQueriesListener.logDeleteQueries();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
myCaptureQueriesListener.logInsertQueries();
// 1 concept, 1 link
assertEquals(2, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.clear();
}
@Test
public void testAddNotPermittedForNonExternalCodeSystem() {
@ -307,54 +375,6 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
assertEquals("CODEA1", myTermSvc.lookupCode(myFhirCtx, "http://foo", "codea").getCodeDisplay());
}
@Test
public void testAddRelocateHierarchy() {
createNotPresentCodeSystem();
// Add code hierarchy
CustomTerminologySet delta = new CustomTerminologySet();
TermConcept codeA = delta.addRootConcept("CodeA", "Code A");
TermConcept codeAA = codeA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
codeAA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAAA").setDisplay("Code AAA");
codeAA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAAB").setDisplay("Code AAB");
TermConcept codeB = delta.addRootConcept("CodeB", "Code B");
TermConcept codeBA = codeB.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBA").setDisplay("Code BA");
codeBA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBAA").setDisplay("Code BAA");
codeBA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBAB").setDisplay("Code BAB");
UploadStatistics outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertEquals(8, outcome.getUpdatedConceptCount());
assertHierarchyContains(
"CodeA seq=0",
" CodeAA seq=0",
" CodeAAA seq=0",
" CodeAAB seq=1",
"CodeB seq=0",
" CodeBA seq=0",
" CodeBAA seq=0",
" CodeBAB seq=1"
);
// Move a single child code to a new spot and make sure the hierarchy comes along
// for the ride..
delta = new CustomTerminologySet();
delta
.addRootConcept("CodeB", "Code B")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertEquals(2, outcome.getUpdatedConceptCount());
assertHierarchyContains(
"CodeA seq=0",
"CodeB seq=0",
" CodeBA seq=0",
" CodeBAA seq=0",
" CodeBAB seq=1",
" CodeAA seq=0", // <-- CodeAA got added here so it comes second
" CodeAAA seq=0",
" CodeAAB seq=1"
);
}
@Test
@Ignore
public void testAddWithPropertiesAndDesignations() {