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Added a bunch of tests for ancestor/descendant filters.

This commit is contained in:
Diederik Muylwyk 2019-09-25 16:52:08 -04:00
parent 729d3a3d3b
commit 9b4671c05e
1 changed files with 577 additions and 44 deletions
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621
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
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@ -19,7 +19,9 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.ExpectedException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.transaction.TransactionStatus;
@ -38,6 +40,9 @@ import static org.junit.Assert.*;
public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcImplDstu3Test.class);
@Rule
public final ExpectedException expectedException = ExpectedException.none();
private static final String CS_URL = "http://example.com/my_code_system";
private static final String CS_URL_2 = "http://example.com/my_code_system2";
@ -306,7 +311,6 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, empty());
}
@Test
@ -485,12 +489,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("LOINC");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle op=ISA on property copyright", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property copyright");
myTermSvc.expandValueSet(vs);
}
@Test
@ -504,18 +506,16 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("LOINC");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Invalid filter, property copyright is LOINC-specific and cannot be used with system: http://example.com/my_code_system", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property copyright is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
@ -534,12 +534,281 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("bogus");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle value=bogus on property copyright", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle value=bogus on property copyright");
myTermSvc.expandValueSet(vs);
}
/*
FIXME: DM 2019-09-25 - Remove this comment once ancestor/descendant filters are working.
code1 = 50015-7
code2 = 43343-3
code3 = 43343-4
code4 = 47239-9
code1
-code2
-code3
-code4
testExpandValueSetPropertyFilterLoincAncestorWithExcludeAndEqual
exclude
ancestor = code1->[code1]
ancestor = code2->[code1,code2]
ancestor = code3->[code1,code2,code3,code4]
ancestor = code4->[code1,code2,code3,code4]
testExpandValueSetPropertyFilterLoincAncestorWithExcludeAndIn
exclude
ancestor in code1,code2,code3,code4->[code1]
testExpandValueSetPropertyFilterLoincAncestorWithIncludeAndEqual
include
ancestor = code1->[code2,code3,code4]
ancestor = code2->[code3,code4]
ancestor = code3->[]
ancestor = code4->[]
testExpandValueSetPropertyFilterLoincAncestorWithIncludeAndIn
include
ancestor in code1,code2,code3,code4->[code2,code3,code4]
testExpandValueSetPropertyFilterLoincAncestorWithUnsupportedOp
testExpandValueSetPropertyFilterLoincAncestorWithUnsupportedSystem
*/
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithExcludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithExcludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithIncludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
assertEquals(0, outcome.getExpansion().getContains().size());
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
assertEquals(0, outcome.getExpansion().getContains().size());
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithIncludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithUnsupportedOp() {
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property ancestor");
myTermSvc.expandValueSet(vs);
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithUnsupportedSystem() {
createCodeSystem();
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property ancestor is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
@ -747,12 +1016,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("child")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle op=ISA on property child", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property child");
myTermSvc.expandValueSet(vs);
}
@Test
@ -772,12 +1039,282 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("child")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Invalid filter, property child is LOINC-specific and cannot be used with system: http://example.com/my_code_system", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property child is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
/*
FIXME: DM 2019-09-25 - Remove this comment once ancestor/descendant filters are working.
code1 = 50015-7
code2 = 43343-3
code3 = 43343-4
code4 = 47239-9
code1
-code2
-code3
-code4
testExpandValueSetPropertyFilterLoincDescendantWithExcludeAndEqual
exclude
descendant = code1->[code1,code2,code3,code4]
descendant = code2->[code2,code3,code4]
descendant = code3->[code3,code4]
descendant = code4->[code3,code4]
testExpandValueSetPropertyFilterLoincDescendantWithExcludeAndIn
exclude
descendant in code1,code2,code3,code4->[code3,code4]
testExpandValueSetPropertyFilterLoincDescendantWithIncludeAndEqual
include
descendant = code1->[]
descendant = code2->[code1]
descendant = code3->[code1,code2]
descendant = code4->[code1,code2]
testExpandValueSetPropertyFilterLoincDescendantWithIncludeAndIn
include
descendant in code1,code2,code3,code4->[code1,code2]
testExpandValueSetPropertyFilterLoincDescendantWithUnsupportedOp
testExpandValueSetPropertyFilterLoincDescendantWithUnsupportedSystem
*/
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithExcludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithExcludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithIncludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
assertEquals(0, outcome.getExpansion().getContains().size());
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithIncludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithUnsupportedOp() {
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property descendant");
myTermSvc.expandValueSet(vs);
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithUnsupportedSystem() {
createCodeSystem();
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property descendant is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
@ -984,12 +1521,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("parent")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle op=ISA on property parent", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property parent");
myTermSvc.expandValueSet(vs);
}
@Test
@ -1009,12 +1544,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("parent")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Invalid filter, property parent is LOINC-specific and cannot be used with system: http://example.com/my_code_system", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property parent is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test