/
TestValueSetResourceProvider.java
1060 lines (964 loc) · 59.6 KB
/
TestValueSetResourceProvider.java
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package org.openconceptlab.fhir.provider;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.*;
import org.junit.After;
import org.junit.Before;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.mockito.MockitoAnnotations;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
import org.mockito.stubbing.OngoingStubbing;
import org.openconceptlab.fhir.base.OclFhirTest;
import org.openconceptlab.fhir.model.*;
import org.openconceptlab.fhir.model.Collection;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.springframework.jdbc.core.BatchPreparedStatementSetter;
import java.sql.SQLException;
import java.time.LocalDate;
import java.time.ZoneId;
import java.util.*;
import static org.junit.Assert.assertEquals;
import static org.mockito.Mockito.*;
import static org.openconceptlab.fhir.util.OclFhirConstants.*;
public class TestValueSetResourceProvider extends OclFhirTest {
Collection collection1;
Collection collection2;
public static final String URL_COLLECTION_1 = "http://openconceptlab.org/collection1";
public static final String COLLECTION_1 = "collection1";
public static final String COLLECTION_1_NAME = "collection1 name";
public static final String COLLECTION_1_FULL_NAME = "collection1 full name";
public static final String COLLECTION_1_COPYRIGHT_TEXT = "collection1 copyright text";
public static final String TEST = "TEST";
public static final String URL_COLLECTION_2 = "http://openconceptlab.org/collection2";
public static final String COLLECTION_2 = "collection2";
public static final String COLLECTION_2_NAME = "collection2 name";
public static final String COLLECTION_2_FULL_NAME = "collection2 full name";
public static final String COLLECTION_2_COPYRIGHT_TEXT = "collection2 copyright text";
@BeforeEach
public void setUpBefore() {
MockitoAnnotations.initMocks(this);
when(requestDetails.getCompleteUrl()).thenReturn("http://test.org");
source1 = source(123L, "v1.0", concept1(), concept2(), concept3());
source2 = source(234L, "v2.0", concept1(), concept2(), concept3(), concept4());
source3 = source(345L, "v3.0", concept1(), concept2(), concept3(), concept4());
populateSource1(source1);
populateSource2(source2);
collection1 = new Collection();
populateCollection1(collection1);
collection2 = new Collection();
populateCollection2(collection2);
}
@AfterEach
public void after() {
source1 = null;
source2 = null;
source3 = null;
collection1 = null;
collection2 = null;
cs11 = null;
cs21 = null;
cs22 = null;
cs23 = null;
cs24 = null;
cs31 = null;
cs32 = null;
cs33 = null;
cs34 = null;
}
private void populateCollection2(Collection collection2) {
collection2.setMnemonic(COLLECTION_2);
collection2.setUri(URI_COLLECTION_2);
collection2.setCanonicalUrl(URL_COLLECTION_2);
collection2.setName(COLLECTION_2_NAME);
collection2.setFullName(COLLECTION_2_FULL_NAME);
collection2.setDescription(COLLECTION_2_NAME);
collection2.setIsActive(false);
collection2.setPublisher(TEST);
collection2.setContact("[{\"name\": \"Jon Doe 2\", \"telecom\": [{\"use\": \"work\", \"rank\": 1, \"value\": \"jondoe2@gmail.com\", \"period\": {\"end\": \"2022-10-29T10:26:15-04:00\", \"start\": \"2021-10-29T10:26:15-04:00\"}, \"system\": \"email\"}]}]");
collection2.setJurisdiction("[{\"coding\": [{\"code\": \"ETH\", \"system\": \"http://unstats.un.org/unsd/methods/m49/m49.htm\", \"display\": \"Ethiopia\"}]}]");
collection2.setPurpose(TEST);
collection2.setCopyright(COLLECTION_2_COPYRIGHT_TEXT);
collection2.setImmutable(true);
collection2.setRevisionDate(Date.from(LocalDate.of(2020, 12, 2).atStartOfDay(ZoneId.systemDefault()).toInstant()));
}
private void populateCollection1(Collection collection1) {
collection1.setMnemonic(COLLECTION_1);
collection1.setUri(URI_COLLECTION_1);
collection1.setCanonicalUrl(URL_COLLECTION_1);
collection1.setName(COLLECTION_1_NAME);
collection1.setFullName(COLLECTION_1_FULL_NAME);
collection1.setDescription(COLLECTION_1_NAME);
collection1.setIsActive(true);
collection1.setPublisher(TEST);
collection1.setContact("[{\"name\": \"Jon Doe 1\", \"telecom\": [{\"use\": \"work\", \"rank\": 1, \"value\": \"jondoe1@gmail.com\", \"period\": {\"end\": \"2025-10-29T10:26:15-04:00\", \"start\": \"2020-10-29T10:26:15-04:00\"}, \"system\": \"email\"}]}]");
collection1.setJurisdiction("[{\"coding\": [{\"code\": \"USA\", \"system\": \"http://unstats.un.org/unsd/methods/m49/m49.htm\", \"display\": \"United States of America\"}]}]");
collection1.setPurpose(TEST);
collection1.setCopyright(COLLECTION_1_COPYRIGHT_TEXT);
collection1.setImmutable(false);
collection1.setRevisionDate(Date.from(LocalDate.of(2020, 12, 1).atStartOfDay(ZoneId.systemDefault()).toInstant()));
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/source1/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/source2/v2.0/concepts/" + TUMOR_DISORDER + "/123/"
);
collection1.setCollectionsReferences(references);
}
@Test
public void testSearchValueSet_return_1() {
collection1.setReleased(false);
when(collectionRepository.findAllLatest(anyList())).thenReturn(Collections.singletonList(collection1));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSets(null, null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertEquals(0, valueSet.getCompose().getInclude().size());
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
}
@Test
public void testSearchValueSet_return_2() {
collection1.setReleased(true);
collection2.setReleased(false);
when(collectionRepository.findAllLatest(anyList())).thenReturn(Arrays.asList(collection1, collection2));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSets(null, null, null, null, null,requestDetails);
assertEquals(2, bundle.getTotal());
ValueSet valueSet1 = (ValueSet) bundle.getEntry().get(0).getResource();
assertEquals(0, valueSet1.getCompose().getInclude().size());
assertBaseValueSet(valueSet1, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
ValueSet valueSet2 = (ValueSet) bundle.getEntry().get(1).getResource();
assertEquals(0, valueSet2.getCompose().getInclude().size());
assertBaseValueSet(valueSet2, URL_COLLECTION_2, COLLECTION_2_NAME, COLLECTION_2_FULL_NAME, "Jon Doe 2", "jondoe2@gmail.com",
"ETH", TEST, COLLECTION_2_COPYRIGHT_TEXT);
}
@Test
public void testSearchValueSet_return_empty() {
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSets(null, null, null, null, null,requestDetails);
assertEquals(0, bundle.getTotal());
}
@Test
public void testSearchValueSet_head_return_empty() {
collection1.setIsLatestVersion(true);
collection2.setIsLatestVersion(true);
collection1.setVersion("HEAD");
collection2.setVersion("HEAD");
when(collectionRepository.findAllLatest(anyList())).thenReturn(Arrays.asList(collection1, collection2));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSets(null, null, null, null, null,requestDetails);
assertEquals(0, bundle.getTotal());
}
@Test
public void testSearchValueSetByUrl_version_empty_return_most_recent() {
when(collectionRepository.findFirstByCanonicalUrlAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByUrl(newString(URL_COLLECTION_1), null, null, null,null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(0), URL_SOURCE_2, V_2_0, TM, TUMOR_DISORDER);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(1), URL_SOURCE_1, V_1_0, AD, ALLERGIC_DISORDER);
}
@Test
public void testSearchValueSetByUrl_version() {
when(collectionRepository.findFirstByCanonicalUrlAndVersionAndPublicAccessIn(anyString(), anyString(), anyList()))
.thenReturn(collection1);
collection1.setVersion(V_1_0);
when(sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByUrl(newString(URL_COLLECTION_1), newString(V_1_0), null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(0), URL_SOURCE_2, V_2_0, TM, TUMOR_DISORDER);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(1), URL_SOURCE_1, V_1_0, AD, ALLERGIC_DISORDER);
}
@Test
public void testSearchValueSetByUrl_version_all() {
collection1.setVersion(V_1_0);
Collection collection1V2 = new Collection();
populateCollection1(collection1V2);
collection1V2.setVersion("v1.1");
when(collectionRepository.findByCanonicalUrlAndPublicAccessIn(anyString(), anyList()))
.thenReturn(Arrays.asList(collection1, collection1V2));
when(sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByUrl(newString(URL_COLLECTION_1), newString("*"), null, null, null, null, requestDetails);
assertEquals(2, bundle.getTotal());
ValueSet valueSet1 = (ValueSet) bundle.getEntry().get(0).getResource();
ValueSet valueSet2 = (ValueSet) bundle.getEntry().get(1).getResource();
assertEquals(V_1_0, valueSet1.getVersion());
assertEquals("v1.1", valueSet2.getVersion());
}
@Test
public void testSearchValueSetByUrl_version_head() {
when(collectionRepository.findFirstByCanonicalUrlAndVersionAndPublicAccessIn(anyString(), anyString(), anyList()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
collection1.setVersion("HEAD");
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByUrl(newString(URL_COLLECTION_1), newString(V_1_0), null,null, null, null, requestDetails);
assertEquals(0, bundle.getTotal());
}
@Test
public void testSearchValueSetByUrl_not_found() {
ValueSetResourceProvider provider = valueSetProvider();
Assertions.assertThrows(ResourceNotFoundException.class, () -> {
provider.searchValueSetByUrl(newString(URL_COLLECTION_1), null,null, null, null, null, requestDetails);
});
}
@Test
public void testSearchValueSetByOwner() {
collection1.setReleased(true);
when(collectionRepository.findByOrganizationMnemonicAndPublicAccessInAndIsLatestVersionOrderByMnemonic(anyString(), anyList(), anyBoolean()))
.thenReturn(Collections.singletonList(collection1));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwner(newString("org:OCL"), null, null, null,null, null, requestDetails);
assertEquals(1, bundle.getTotal());
assertBaseValueSet((ValueSet) bundle.getEntryFirstRep().getResource(), URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(0, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
}
@Test
public void testSearchValueSetByOwner_user() {
collection1.setReleased(true);
when(collectionRepository.findByUserIdUsernameAndPublicAccessInAndIsLatestVersionOrderByMnemonic(anyString(), anyList(), anyBoolean()))
.thenReturn(Collections.singletonList(collection1));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwner(newString("user:test"), null, null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
assertBaseValueSet((ValueSet) bundle.getEntryFirstRep().getResource(), URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(0, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
}
@Test
public void testSearchValueSetByOwnerAndId_version_empty() {
when(collectionRepository.findFirstByMnemonicAndPublicAccessInAndOrganizationMnemonicAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyString(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwnerAndId(newString("org:OCL"), newString("123"), null, null, null, null,null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(0), URL_SOURCE_2, V_2_0, TM, TUMOR_DISORDER);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(1), URL_SOURCE_1, V_1_0, AD, ALLERGIC_DISORDER);
}
@Test
public void testSearchValueSetByOwnerAndId_expression_owner_user() {
List<CollectionsReference> references = newReferences(
"/users/test/sources/source1/v1.0/concepts/" + AD + "/123/",
"/users/test/sources/source2/v2.0/concepts/" + TUMOR_DISORDER + "/123/"
);
collection1.setCollectionsReferences(references);
when(collectionRepository.findFirstByMnemonicAndPublicAccessInAndUserIdUsernameAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyString(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndUserIdUsernameAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwnerAndId(newString("user:test"), newString("123"), null, null, null, null, null,requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(2, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
assertConceptComponent(0, valueSet.getCompose().getInclude().get(0), URL_SOURCE_2, V_2_0, TM, TUMOR_DISORDER);
assertConceptComponent(0, valueSet.getCompose().getInclude().get(1), URL_SOURCE_1, V_1_0, AD, ALLERGIC_DISORDER);
}
@Test
public void testSearchValueSetByOwnerAndId_expression_source_version_not_found() {
List<CollectionsReference> references = newReferences(
"/users/test/sources/source1/v1111.0/concepts/" + AD + "/123/",
"/users/test/sources/source2/v2222.0/concepts/" + TUMOR_DISORDER + "/123/"
);
collection1.setCollectionsReferences(references);
when(collectionRepository.findFirstByMnemonicAndPublicAccessInAndUserIdUsernameAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyString(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndUserIdUsernameAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwnerAndId(newString("user:test"), newString("123"), null, null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(0, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
}
@Test
public void testSearchValueSetByOwnerAndId_expression_source_not_found() {
List<CollectionsReference> references = newReferences(
"/users/test/sources/source111/v1.0/concepts/" + AD + "/123/",
"/users/test/sources/source222/v2.0/concepts/" + TUMOR_DISORDER + "/123/"
);
collection1.setCollectionsReferences(references);
when(collectionRepository.findFirstByMnemonicAndPublicAccessInAndUserIdUsernameAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyString(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndUserIdUsernameAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwnerAndId(newString("user:test"), newString("123"), null, null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(0, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
}
@Test
public void testSearchValueSetByOwnerAndId_expression_owner_not_found() {
List<CollectionsReference> references = newReferences(
"/users/OCL/sources/source111/v1.0/concepts/" + AD + "/123/",
"/users/OCL/sources/source222/v2.0/concepts/" + TUMOR_DISORDER + "/123/"
);
collection1.setCollectionsReferences(references);
when(collectionRepository.findFirstByMnemonicAndPublicAccessInAndUserIdUsernameAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyString(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndUserIdUsernameAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList())).thenReturn(Collections.singletonList(cs22))
.thenReturn(Collections.singletonList(cs11));
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwnerAndId(newString("user:test"), newString("123"), null, null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(0, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
}
@Test
public void testSearchValueSetByOwnerAndId_expression_concept_not_found() {
List<CollectionsReference> references = newReferences(
"/users/OCL/sources/source1/v1.0/concepts/" + AD + "/123/",
"/users/OCL/sources/source2/v2.0/concepts/" + TUMOR_DISORDER + "/123/"
);
collection1.setCollectionsReferences(references);
when(collectionRepository.findFirstByMnemonicAndPublicAccessInAndUserIdUsernameAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyString(), anyBoolean()))
.thenReturn(collection1);
when(sourceRepository.findFirstByMnemonicAndVersionAndUserIdUsernameAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source1).thenReturn(source2);
ValueSetResourceProvider provider = valueSetProvider();
Bundle bundle = provider.searchValueSetByOwnerAndId(newString("user:test"), newString("123"), null, null, null, null, null, requestDetails);
assertEquals(1, bundle.getTotal());
ValueSet valueSet = (ValueSet) bundle.getEntryFirstRep().getResource();
assertBaseValueSet(valueSet, URL_COLLECTION_1, COLLECTION_1_NAME, COLLECTION_1_FULL_NAME, "Jon Doe 1", "jondoe1@gmail.com",
"USA", TEST, COLLECTION_1_COPYRIGHT_TEXT);
assertEquals(0, ((ValueSet) bundle.getEntryFirstRep().getResource()).getCompose().getInclude().size());
}
private void assertConceptComponent(int index, ValueSet.ConceptSetComponent component, String systemUrl, String systemVersion, String code, String display) {
assertEquals(systemUrl, component.getSystem());
assertEquals(systemVersion, component.getVersion());
assertEquals(code, component.getConcept().get(index).getCode());
assertEquals(display, component.getConcept().get(index).getDisplay());
}
private void assertBaseValueSet(ValueSet valueSet, String url, String name, String fullName,
String contactName, String contactEmail, String jurisdictionCode, String purpose,
String copyright) {
assertEquals(url, valueSet.getUrl());
assertEquals(name, valueSet.getName());
assertEquals(fullName, valueSet.getTitle());
assertEquals(contactName, valueSet.getContactFirstRep().getName());
assertEquals(contactEmail, valueSet.getContactFirstRep().getTelecomFirstRep().getValue());
assertEquals(jurisdictionCode, valueSet.getJurisdictionFirstRep().getCodingFirstRep().getCode());
assertEquals(purpose, valueSet.getPurpose());
assertEquals(copyright, valueSet.getCopyright());
}
@Test
public void testValidateCode_url_null() {
Assertions.assertThrows(InvalidRequestException.class, () -> {
validateCode(null, V_11_1, CS_URL, V_21_1, AD, null, null, null, OWNER_VAL);
});
}
@Test
public void testValidateCode_code_null() {
Assertions.assertThrows(InvalidRequestException.class, () -> {
validateCode(VS_URL, V_11_1, CS_URL, V_21_1, null, null, null, null, OWNER_VAL);
});
}
@Test
public void testValidateCode_system_null() {
Assertions.assertThrows(InvalidRequestException.class, () -> {
validateCode(VS_URL, V_11_1, null, V_21_1, AD, null, null, null, OWNER_VAL);
});
}
@Test
public void testValidateCode_code_coding() {
Assertions.assertThrows(InvalidRequestException.class, () -> {
validateCode(VS_URL, V_11_1, CS_URL, null, AD, null, null,
new Coding("ABC", "ABC", "ABC"), OWNER_VAL);
});
}
@Test
public void testValidateCode_systemversion_unmatch() {
assertFalse(validateCode(VS_URL, V_11_1, CS_URL, V_21_1, AD, null, null, null, OWNER_VAL));
}
@Test
public void testValidateCode_systemversion_match1() {
assertTrue(validateCode(VS_URL, V_11_1, CS_URL, null, AD, null, null, null, OWNER_VAL));
}
@Test
public void testValidateCode_systemversion_match2() {
assertTrue(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, null, null, null, OWNER_VAL));
}
@Test
public void testValidateCode_display_match1() {
assertTrue(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, ALLERGIC_DISORDER, null, null, OWNER_VAL));
}
@Test
public void testValidateCode_display_match2() {
assertTrue(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, TRASTORNO_ALERGICO, null, null, OWNER_VAL));
}
@Test
public void testValidateCode_display_dl_match1() {
assertTrue(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, ALLERGIC_DISORDER, EN, null, OWNER_VAL));
}
@Test
public void testValidateCode_display_dl_match2() {
assertTrue(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, TRASTORNO_ALERGICO, ES, null, OWNER_VAL));
}
@Test
public void testValidateCode_display_dl_unmatch1() {
assertFalse(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, ALLERGIC_DISORDER, ES, null, OWNER_VAL));
}
@Test
public void testValidateCode_display_dl_unmatch2() {
assertFalse(validateCode(VS_URL, V_11_1, CS_URL, V_21_2, AD, TRASTORNO_ALERGICO, EN, null, OWNER_VAL));
}
@Test
public void testExpand() {
// all match
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + LUNG_PROCEDURE + "/123/"
);
source1.setCanonicalUrl(CS_URL);
source1.setMnemonic(CS);
source2.setCanonicalUrl(CS_URL);
source2.setMnemonic(CS);
ValueSet vs = runExpand(references, Collections.singletonList(cs11), Arrays.asList(cs21, cs22, cs23, cs24), null, 0, 50, "");
assertEquals(5, vs.getExpansion().getContains().size());
assertContains(vs, 0, CS_URL, "v2.0", AD, ALLERGIC_DISORDER);
assertContains(vs, 4, CS_URL, "v1.0", AD, ALLERGIC_DISORDER);
assertContains(vs, 1, CS_URL, "v2.0", LUNG_PROCEDURE, LUNG_PROCEDURE_1);
assertContains(vs, 2, CS_URL, "v2.0", TM, TUMOR_DISORDER);
assertContains(vs, 3, CS_URL, "v2.0", VEIN_PROCEDURE, VEIN_PROCEDURE_1);
}
@Test
public void testExpand_partial() {
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + LUNG_PROCEDURE + "/123/"
);
source1.setCanonicalUrl(CS_URL);
source1.setMnemonic(CS);
source2.setCanonicalUrl(CS_URL);
source2.setMnemonic(CS);
ValueSet vs = runExpand(references, Collections.singletonList(cs11), Arrays.asList(cs24, cs22, cs23), null, 2, 50, "");
assertEquals(3, vs.getExpansion().getContains().size());
assertContains(vs, 0, CS_URL, "v2.0", LUNG_PROCEDURE, LUNG_PROCEDURE_1);
assertContains(vs, 1, CS_URL, "v2.0", TM, TUMOR_DISORDER);
assertContains(vs, 2, CS_URL, "v2.0", VEIN_PROCEDURE, VEIN_PROCEDURE_1);
}
@Test
public void testExpand_count_0() {
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + LUNG_PROCEDURE + "/123/"
);
ValueSet vs = runExpand(references, Collections.singletonList(cs11), Collections.singletonList(cs21), null, 0, 0, "");
assertEquals(5, vs.getExpansion().getTotal());
assertEquals(0, vs.getExpansion().getContains().size());
}
@Test
public void testExpand_count_negative() {
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + LUNG_PROCEDURE + "/123/"
);
Assertions.assertThrows(InvalidRequestException.class, () -> {
runExpand(references, Collections.singletonList(cs11), Collections.singletonList(cs21), null, 0, -2, "");
});
}
@Test
public void testExpand_missing_url() {
ValueSetResourceProvider provider = valueSetProvider();
Assertions.assertThrows(InvalidRequestException.class, () -> {
provider.valueSetExpand(null, null, new IntegerType(0), new IntegerType(10),
null, null, null, null, null, null, null, newString(OWNER_VAL), requestDetails);
});
}
@Test
public void testExpand_unknown_systemversion() {
// all match
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + LUNG_PROCEDURE + "/123/"
);
Assertions.assertThrows(InvalidRequestException.class, () -> {
runExpand(references, Collections.singletonList(cs11), Arrays.asList(cs21, cs22, cs23, cs24),
null, 0, 50, CS_URL + "|unk");
});
}
@Test
public void testExpand_known_systemversion() {
// all match
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/concepts/" + LUNG_PROCEDURE + "/123/"
);
ValueSet vs = runExpand(references, Collections.singletonList(cs11), Arrays.asList(cs21, cs22, cs23, cs24),
Arrays.asList(cs31, cs32, cs33, cs34), 0, 50, CS_URL + "|v3.0");
assertEquals(4, vs.getExpansion().getContains().size());
assertContains(vs, 0, CS_URL, "v3.0", AD, ALLERGIC_DISORDER);
assertContains(vs, 1, CS_URL, "v3.0", LUNG_PROCEDURE, LUNG_PROCEDURE_1);
assertContains(vs, 2, CS_URL, "v3.0", TM, TUMOR_DISORDER);
assertContains(vs, 3, CS_URL, "v3.0", VEIN_PROCEDURE, VEIN_PROCEDURE_1);
}
@Test
public void testExpand_known_systemversion_no_head_in_expression() {
// all match
List<CollectionsReference> references = newReferences(
"/orgs/OCL/sources/" + CS + "/v1.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + TM + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + VEIN_PROCEDURE + "/123/",
"/orgs/OCL/sources/" + CS + "/v2.0/concepts/" + LUNG_PROCEDURE + "/123/"
);
ValueSet vs = runExpand(references, Collections.singletonList(cs11), Arrays.asList(cs21, cs22, cs23, cs24),
Arrays.asList(cs31, cs32, cs33, cs34), 0, 50, CS_URL + "|v3.0");
assertEquals(0, vs.getExpansion().getContains().size());
}
@Test
public void testCreateValueSet_null() {
ValueSetResourceProvider provider = valueSetProvider();
Assertions.assertThrows(InvalidRequestException.class, () -> {
provider.createValueSet(null, requestDetails);
});
}
@Test
public void testCreateValueSet_accessionId_null() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
valueSet.setIdentifier(null);
Assertions.assertThrows(InvalidRequestException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
}
@Test
public void testCreateValueSet_url_null() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
valueSet.setUrl(null);
Assertions.assertThrows(InvalidRequestException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
}
@Test
public void testCreateValueSet_invalid_org() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(organizationRepository.findByMnemonic(anyString())).thenReturn(null);
Assertions.assertThrows(InvalidRequestException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(organizationRepository, times(1)).findByMnemonic(anyString());
}
@Test
public void testCreateValueSet_invalid_user() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
valueSet.getIdentifierFirstRep().setValue("/users/testuser/ValueSet/testsource/2.0");
when(userRepository.findByUsername(anyString())).thenReturn(null);
Assertions.assertThrows(InvalidRequestException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(userRepository, times(1)).findByUsername(anyString());
}
@Test
public void testCreateValueSet_token_null() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(requestDetails.getHeader(anyString())).thenReturn(null);
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
Assertions.assertThrows(AuthenticationException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(requestDetails, times(1)).getHeader(anyString());
verify(organizationRepository, times(1)).findByMnemonic(anyString());
}
@Test
public void testCreateValueSet_invalid_token() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(requestDetails.getHeader(anyString())).thenReturn("Token 678423578911230985");
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
when(authtokenRepository.findByKey(anyString())).thenReturn(null);
Assertions.assertThrows(AuthenticationException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(requestDetails, times(1)).getHeader(anyString());
verify(organizationRepository, times(1)).findByMnemonic(anyString());
verify(authtokenRepository, times(1)).findByKey(anyString());
}
@Test
public void testCreateValueSet_user_not_org_member_invalid_user() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(requestDetails.getHeader(anyString())).thenReturn("Token 12345");
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
when(authtokenRepository.findByKey(anyString())).thenReturn(newToken(test_user));
when(userProfilesOrganizationRepository.findByOrganizationMnemonic(anyString()))
.thenReturn(Collections.singletonList(newUserOrg("otheruser")));
Assertions.assertThrows(AuthenticationException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(requestDetails, times(1)).getHeader(anyString());
verify(organizationRepository, times(1)).findByMnemonic(anyString());
verify(authtokenRepository, times(1)).findByKey(anyString());
verify(userProfilesOrganizationRepository, times(1)).findByOrganizationMnemonic(anyString());
}
@Test
public void testCreateValueSet_valueset_id_exists() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(requestDetails.getHeader(anyString())).thenReturn("Token 12345");
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
when(authtokenRepository.findByKey(anyString())).thenReturn(newToken(test_user));
when(userProfilesOrganizationRepository.findByOrganizationMnemonic(anyString()))
.thenReturn(Collections.singletonList(newUserOrg(test_user)));
when(collectionRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonic(anyString(), anyString(), anyString()))
.thenReturn(new Collection());
Assertions.assertThrows(ResourceVersionConflictException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(requestDetails, times(1)).getHeader(anyString());
verify(organizationRepository, times(1)).findByMnemonic(anyString());
verify(authtokenRepository, times(1)).findByKey(anyString());
verify(userProfilesOrganizationRepository, times(1)).findByOrganizationMnemonic(anyString());
verify(collectionRepository, times(1)).findFirstByMnemonicAndVersionAndOrganizationMnemonic(anyString(), anyString(), anyString());
}
@Test
public void testCreateValueSet_valueset_url_exists() {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(requestDetails.getHeader(anyString())).thenReturn("Token 12345");
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
when(authtokenRepository.findByKey(anyString())).thenReturn(newToken(test_user));
when(userProfilesOrganizationRepository.findByOrganizationMnemonic(anyString()))
.thenReturn(Collections.singletonList(newUserOrg(test_user)));
when(collectionRepository.findFirstByCanonicalUrlAndVersionAndOrganizationMnemonic(anyString(), anyString(), anyString()))
.thenReturn(new Collection());
Assertions.assertThrows(ResourceVersionConflictException.class, () -> {
provider.createValueSet(valueSet, requestDetails);
});
verify(requestDetails, times(1)).getHeader(anyString());
verify(organizationRepository, times(1)).findByMnemonic(anyString());
verify(authtokenRepository, times(1)).findByKey(anyString());
verify(userProfilesOrganizationRepository, times(1)).findByOrganizationMnemonic(anyString());
verify(collectionRepository, times(1)).findFirstByCanonicalUrlAndVersionAndOrganizationMnemonic(anyString(), anyString(), anyString());
}
@Test
public void testCreateValueSet() throws SQLException {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
when(requestDetails.getHeader(anyString())).thenReturn("Token 12345");
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
when(authtokenRepository.findByKey(anyString())).thenReturn(newToken(test_user));
when(userProfilesOrganizationRepository.findByOrganizationMnemonic(anyString()))
.thenReturn(Collections.singletonList(newUserOrg(test_user)));
doAnswer(new Answer() {
@Override
public Object answer(InvocationOnMock invocation) throws Throwable {
Object[] args = invocation.getArguments();
((Collection) args[0]).setId(123L);
return args[0];
}
}).when(collectionRepository).saveAndFlush(any(Collection.class));
when(insertCollectionReference.executeAndReturnKeyHolder(anyMap())).thenReturn(newKey());
doAnswer(new Answer() {
@Override
public Object answer(InvocationOnMock invocation) throws Throwable {
return null;
}
}).when(jdbcTemplate).batchUpdate(anyString(), any(BatchPreparedStatementSetter.class));
populateSource1(source1);
source1.setOrganization(newOrganization());
when(sourceRepository.findFirstByCanonicalUrlAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyBoolean()))
.thenReturn(source1);
provider.createValueSet(valueSet, requestDetails);
verify(requestDetails, times(1)).getHeader(anyString());
verify(organizationRepository, times(1)).findByMnemonic(anyString());
verify(authtokenRepository, times(1)).findByKey(anyString());
verify(userProfilesOrganizationRepository, times(1)).findByOrganizationMnemonic(anyString());
verify(collectionRepository, times(2)).saveAndFlush(any(Collection.class));
verify(insertCollectionReference, times(2)).executeAndReturnKeyHolder(anyMap());
}
@Test
public void testUpdateValueSet() throws SQLException {
ValueSetResourceProvider provider = valueSetProvider();
ValueSet valueSet = valueSet();
valueSet.setName("Updated Name");
when(requestDetails.getHeader(AUTHORIZATION)).thenReturn("Token 12345");
when(requestDetails.getHeader(OWNER)).thenReturn("org:OCL");
when(organizationRepository.findByMnemonic(anyString())).thenReturn(newOrganization());
when(authtokenRepository.findByKey(anyString())).thenReturn(newToken(test_user));
when(userProfilesOrganizationRepository.findByOrganizationMnemonic(anyString()))
.thenReturn(Collections.singletonList(newUserOrg(test_user)));
when(collectionRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(
anyString(), anyString(), anyString(), anyList()
)).thenReturn(collection1);
doAnswer(new Answer() {
@Override
public Object answer(InvocationOnMock invocation) throws Throwable {
Object[] args = invocation.getArguments();
((Collection) args[0]).setId(123L);
return args[0];
}
}).when(collectionRepository).saveAndFlush(any(Collection.class));
when(insertCollectionReference.executeAndReturnKeyHolder(anyMap())).thenReturn(newKey());
doAnswer(new Answer() {
@Override
public Object answer(InvocationOnMock invocation) throws Throwable {
return null;
}
}).when(jdbcTemplate).batchUpdate(anyString(), any(BatchPreparedStatementSetter.class));
populateSource1(source1);
source1.setOrganization(newOrganization());
when(sourceRepository.findFirstByCanonicalUrlAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyList(), anyBoolean()))
.thenReturn(source1);
IdType type = new IdType();
type.setParts("", "ValueSet", "testcollection", "2.0");
provider.updateValueSet(type, valueSet, requestDetails);
assertEquals("Updated Name", collection1.getName());
verify(requestDetails, times(1)).getHeader(AUTHORIZATION);
verify(requestDetails, times(1)).getHeader(OWNER);
verify(organizationRepository, times(1)).findByMnemonic(anyString());
verify(authtokenRepository, times(1)).findByKey(anyString());
verify(userProfilesOrganizationRepository, times(1)).findByOrganizationMnemonic(anyString());
verify(collectionRepository, times(1)).saveAndFlush(any(Collection.class));
verify(insertCollectionReference, times(1)).executeAndReturnKeyHolder(anyMap());
}
private ValueSet valueSet() {
ValueSet valueSet = new ValueSet();
valueSet.setUrl(URL_COLLECTION_1);
Identifier identifier = valueSet.getIdentifierFirstRep();
identifier.getType().getCodingFirstRep().setSystem(ACSN_SYSTEM).setCode(ACSN);
identifier.setSystem("http://test.org");
identifier.setValue("/orgs/OCL/ValueSet/testcollection/2.0");
valueSet.setName("Test Value Set");
valueSet.setStatus(Enumerations.PublicationStatus.DRAFT);
valueSet.setCopyright("Test copy right");
valueSet.setPurpose("Test purpose");
valueSet.setPublisher("Test publisher");
valueSet.setDescription("Test description");
valueSet.setTitle("Test title");
valueSet.setDate(date1);
valueSet.getContactFirstRep().setName("Jon Doe").getTelecomFirstRep().setSystem(ContactPoint.ContactPointSystem.EMAIL)
.setValue("jondoe@gmail.com").setUse(ContactPoint.ContactPointUse.WORK).setRank(1);
valueSet.getJurisdictionFirstRep().getCodingFirstRep().setSystem("http://unstats.un.org/unsd/methods/m49/m49.htm")
.setCode("USA").setDisplay("United States of America");
addCodes(valueSet, URL_SOURCE_1, "TEST");
return valueSet;
}
private void addCodes(ValueSet valueSet, String system, String code) {
ValueSet.ValueSetComposeComponent compose = valueSet.getCompose();
ValueSet.ConceptSetComponent conceptSetComponent = compose.getIncludeFirstRep();
conceptSetComponent.setSystem(system);
ValueSet.ConceptReferenceComponent referenceComponent = new ValueSet.ConceptReferenceComponent();
referenceComponent.setCode(code);
conceptSetComponent.getConcept().add(referenceComponent);
}
private void assertContains(ValueSet valueSet, int index, String system, String version, String code, String display) {
assertEquals(system, valueSet.getExpansion().getContains().get(index).getSystem());
assertEquals(version, valueSet.getExpansion().getContains().get(index).getVersion());
assertEquals(code, valueSet.getExpansion().getContains().get(index).getCode());
assertEquals(display, valueSet.getExpansion().getContains().get(index).getDisplay());
}
public ValueSet runExpand(List<CollectionsReference> references, List<ConceptsSource> list1, List<ConceptsSource> list2,
List<ConceptsSource> list3, Integer offset, Integer count, String systemVersion) {
// set up
ValueSetResourceProvider provider = valueSetProvider();
Collection collection = collection(references);
when(sourceRepository.findFirstByMnemonicAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList()))
.thenReturn(source2).thenReturn(source1);
OngoingStubbing<List<ConceptsSource>> stub1 = when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(eq(123L), anyList()));
for (ConceptsSource cs1 : list1) {
stub1 = stub1.thenReturn(Collections.singletonList(cs1));
}
OngoingStubbing<List<ConceptsSource>> stub2 = when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(eq(234L), anyList()));
for (ConceptsSource cs2 : list2) {
stub2 = stub2.thenReturn(Collections.singletonList(cs2));
}
if (isValid(systemVersion) & !systemVersion.contains("unk")) {
when(sourceRepository.findFirstByCanonicalUrlAndVersionAndPublicAccessIn(anyString(), anyString(), anyList())).thenReturn(source3);
OngoingStubbing<List<ConceptsSource>> stub3 = when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(eq(345L), anyList()));
if (list3 != null) {
for (ConceptsSource cs3 : list3) {
stub3 = stub3.thenReturn(Collections.singletonList(cs3));
}
}
}
when(collectionRepository.findFirstByCanonicalUrlAndOrganizationMnemonicAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(
anyString(), anyString(), anyList(), anyBoolean())).thenReturn(collection);
return provider.valueSetExpand(newUrl(VS_URL), null, new IntegerType(offset), new IntegerType(count),
null, null, null, null, null, Sets.newHashSet(new CanonicalType(systemVersion)), null, newString(OWNER_VAL), requestDetails);
}
public Parameters validateCode(String url, String version, String system, String systemVersion, String code,
String display, String language, Coding coding, String owner) {
// set up
ValueSetResourceProvider provider = valueSetProvider();
Concept concept1 = concept1();
Concept concept2 = concept2();
Source source = source(123L, systemVersion, concept1, concept2);
Collection collection = collection(newReferences(
"/orgs/OCL/sources/" + CS + "/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/" + V_21_2 + "/concepts/" + AD + "/123/",
"/orgs/OCL/sources/" + CS + "/" + V_21_1 + "/concepts/" + TM + "/123/"
));
ConceptsSource cs1 = conceptsSource(concept1, source);
ConceptsSource cs2 = conceptsSource(concept2, source);
// mocks
if (StringUtils.isNotBlank(version)) {
when(collectionRepository.findFirstByCanonicalUrlAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(),
anyString(), anyString(), anyList())).thenReturn(collection);
} else {
when(collectionRepository.findFirstByCanonicalUrlAndOrganizationMnemonicAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(
anyString(), anyString(), anyList(), anyBoolean())).thenReturn(collection);
}
if (StringUtils.isNotBlank(systemVersion)) {
when(sourceRepository.findFirstByCanonicalUrlAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(),
anyString(), anyString(), anyList())).thenReturn(source);
} else {
when(sourceRepository.findFirstByCanonicalUrlAndOrganizationMnemonicAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(
anyString(), anyString(), anyList(), anyBoolean())).thenReturn(source);
}
when(conceptsSourceRepository.findBySourceIdAndConceptIdInOrderByConceptIdDesc(anyLong(), anyList()))
.thenReturn(Arrays.asList(cs1, cs2));
when(conceptRepository.findByMnemonic(anyString())).thenReturn(Arrays.asList(concept1, concept2));
// call to test method
Parameters output = provider.valueSetValidateCode(newUrl(url), newString(version), newCode(code), newUrl(system), newString(systemVersion),
newString(display), newCode(language), coding, newString(owner), requestDetails);
// verify
if (StringUtils.isNotBlank(version)) {
verify(collectionRepository, times(1))
.findFirstByCanonicalUrlAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList());
} else {
verify(collectionRepository, times(1))
.findFirstByCanonicalUrlAndOrganizationMnemonicAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyString(), anyList(), anyBoolean());
}
if (StringUtils.isNotBlank(systemVersion)) {
verify(sourceRepository, times(1))
.findFirstByCanonicalUrlAndVersionAndOrganizationMnemonicAndPublicAccessIn(anyString(), anyString(), anyString(), anyList());
} else {
verify(sourceRepository, times(1))
.findFirstByCanonicalUrlAndOrganizationMnemonicAndPublicAccessInAndIsLatestVersionOrderByCreatedAtDesc(anyString(), anyString(), anyList(), anyBoolean());
}
return output;
}
@Test
public void testToOclUri() {
assertEquals("/orgs/OCL/sources/test/1.0/", OclFhirUtil.toOclUri("/orgs/OCL/CodeSystem/test/version/1.0"));