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Upsert specimens #73

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merged 3 commits into from
Dec 15, 2023
Merged

Upsert specimens #73

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01ac3d9
Upsert specimens
southeo Dec 12, 2023
7580c84
Vocab fixes
southeo Dec 12, 2023
ac60b49
Code review
southeo Dec 13, 2023
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2 changes: 1 addition & 1 deletion src/main/java/eu/dissco/core/handlemanager/domain/FdoProfile.java
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Expand Up @@ -97,7 +97,7 @@ public enum FdoProfile {
private final int index;


private FdoProfile(String attribute, int index) {
FdoProfile(String attribute, int index) {
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Way are these no longer private?

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"If you do not specify an access modifier the enum constructor it will be implicitly private."

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Slowly going to remove the private constructors when I touch enum files

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Good find 💯

this.attribute = attribute;
this.index = index;
}
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4 changes: 2 additions & 2 deletions .../eu/dissco/core/handlemanager/domain/requests/vocabulary/specimen/BaseTypeOfSpecimen.java
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Expand Up @@ -4,12 +4,12 @@

public enum BaseTypeOfSpecimen {
@JsonProperty("Material entity") MATERIAL("Material entity"),
@JsonProperty("Information artefact") INFO("informationArtefact");
@JsonProperty("Information artefact") INFO("Information Artefact");

private final String state;


private BaseTypeOfSpecimen(String state) {
BaseTypeOfSpecimen(String state) {
this.state = state;
}

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6 changes: 3 additions & 3 deletions .../eu/dissco/core/handlemanager/domain/requests/vocabulary/specimen/MaterialSampleType.java
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Expand Up @@ -7,12 +7,12 @@ public enum MaterialSampleType {
@JsonProperty("Whole organism specimen") WHOLE_ORG("Whole organism specimen"),
@JsonProperty("Organism part") ORG_PART("Organism part"),
@JsonProperty("Organism product") ORG_PRODUCT("Organism product"),
@JsonProperty("Biome aggegation") AGGR_BIOME("Biome aggegation"),
@JsonProperty("Biome aggregation") AGGR_BIOME("Biome aggregation"),
@JsonProperty("Bundle biome aggregation") BUNDLE_BIOME("Bundle biome aggregation"),
@JsonProperty("Fossil") FOSSIL("Fossil"),
@JsonProperty("Any biological specimen") ANY_BIO("Any biological specimen"),
@JsonProperty("Aggregation") AGGR("Aggregation"),
@JsonProperty("Slurry biome aggegation") SLURRY_BIOME("Slurry biome aggegation"),
@JsonProperty("Slurry biome aggregation") SLURRY_BIOME("Slurry biome aggregation"),
@JsonProperty("Other solid object") OTHER_SOLID("Other solid object"),
@JsonProperty("Fluid in container") FLUID("Fluid in container"),
@JsonProperty("Anthropogenic aggregation") ANTHRO_AGGR("Anthropogenic aggregation"),
Expand All @@ -22,7 +22,7 @@ public enum MaterialSampleType {

private final String state;

private MaterialSampleType(String state) {
MaterialSampleType(String state) {
this.state = state;
}

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15 changes: 13 additions & 2 deletions src/main/java/eu/dissco/core/handlemanager/repository/PidRepository.java
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Expand Up @@ -6,6 +6,7 @@
import static eu.dissco.core.handlemanager.domain.FdoProfile.PID_RECORD_ISSUE_NUMBER;
import static eu.dissco.core.handlemanager.domain.FdoProfile.PID_STATUS;
import static eu.dissco.core.handlemanager.domain.FdoProfile.PRIMARY_SPECIMEN_OBJECT_ID;
import static org.jooq.impl.DSL.select;

import eu.dissco.core.handlemanager.domain.repsitoryobjects.HandleAttribute;
import eu.dissco.core.handlemanager.exceptions.PidCreationException;
Expand Down Expand Up @@ -73,8 +74,18 @@ public List<HandleAttribute> resolveHandleAttributes(List<byte[]> handles) {

public List<HandleAttribute> searchByNormalisedPhysicalIdentifier(
List<byte[]> normalisedPhysicalIdentifiers) {

return searchByNormalisedPhysicalIdentifierQuery(normalisedPhysicalIdentifiers)
return context.select(HANDLES.IDX, HANDLES.HANDLE, HANDLES.TYPE, HANDLES.DATA)
.from(HANDLES)
.where(HANDLES.HANDLE.in(select(HANDLES.HANDLE).from(HANDLES)
.where(HANDLES.TYPE.eq(PID_STATUS.get().getBytes(StandardCharsets.UTF_8)))
.and(HANDLES.DATA.notEqual("ARCHIVED".getBytes(StandardCharsets.UTF_8)))
.and(HANDLES.HANDLE.in(
select(HANDLES.HANDLE).from(HANDLES)
.where(HANDLES.TYPE.eq(NORMALISED_SPECIMEN_OBJECT_ID.get().getBytes(
StandardCharsets.UTF_8)))
.and(HANDLES.DATA.in(normalisedPhysicalIdentifiers))
))))
.and(HANDLES.TYPE.eq(NORMALISED_SPECIMEN_OBJECT_ID.get().getBytes(StandardCharsets.UTF_8)))
.fetch(this::mapToAttribute);
}

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16 changes: 2 additions & 14 deletions src/main/java/eu/dissco/core/handlemanager/service/PidService.java
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Expand Up @@ -344,13 +344,9 @@ private ProcessedDigitalSpecimenRequest processSpecimenRequests(
var registeredPhysicalIdentiferMap = registeredPhysicalIdentifiers.stream()
.collect(Collectors.toMap(row -> new String(row.getData(), StandardCharsets.UTF_8),
row -> new String(row.getHandle(), StandardCharsets.UTF_8)));
var writableHandles = pidRepository.checkHandlesWritable(
registeredPhysicalIdentiferMap.values().stream().map(s -> s.getBytes(
StandardCharsets.UTF_8)).toList()).stream()
.map(h -> new String(h, StandardCharsets.UTF_8)).collect(Collectors.toSet());
var updates = specimenRequests.stream()
.filter(request -> requestExistsAndIsWriteable(request, registeredPhysicalIdentiferMap,
writableHandles))
.filter(request -> registeredPhysicalIdentiferMap.containsKey(
request.getNormalisedPrimarySpecimenObjectId()))
.map(request -> new DigitalSpecimenUpdateWrapper(
registeredPhysicalIdentiferMap.get(request.getNormalisedPrimarySpecimenObjectId()),
request
Expand All @@ -366,14 +362,6 @@ private ProcessedDigitalSpecimenRequest processSpecimenRequests(
return new ProcessedDigitalSpecimenRequest(specimenRequests, updates);
}

private boolean requestExistsAndIsWriteable(DigitalSpecimenRequest request,
Map<String, String> registeredPhysicalIdentifiers, Set<String> writableHandles) {
return registeredPhysicalIdentifiers.containsKey(request.getNormalisedPrimarySpecimenObjectId())
&&
writableHandles.contains(
registeredPhysicalIdentifiers.get(request.getNormalisedPrimarySpecimenObjectId()));
}

protected List<HandleAttribute> createMediaObject(List<JsonNode> requestAttributes,
Iterator<byte[]> handleIterator)
throws InvalidRequestException, JsonProcessingException, PidResolutionException {
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18 changes: 18 additions & 0 deletions src/test/java/eu/dissco/core/handlemanager/repository/PidRepositoryIT.java
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Expand Up @@ -322,6 +322,24 @@ void testSearchByPhysicalSpecimenId() throws Exception {
assertThat(response).isEqualTo(expected);
}

@Test
void testSearchByPhysicalSpecimenIdIsArchived() {
//Given
var handle = HANDLE.getBytes(StandardCharsets.UTF_8);
var record = List.of(new HandleAttribute(NORMALISED_SPECIMEN_OBJECT_ID, handle,
NORMALISED_PRIMARY_SPECIMEN_OBJECT_ID_TESTVAL),
new HandleAttribute(PID_STATUS, handle, "ARCHIVED"));

postAttributes(record);

// When
var response = pidRepository.searchByNormalisedPhysicalIdentifier(
List.of(NORMALISED_PRIMARY_SPECIMEN_OBJECT_ID_TESTVAL.getBytes(StandardCharsets.UTF_8)));

// Then
assertThat(response).isEmpty();
}

@Test
void testUpdateRecord() throws Exception {
// Given
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32 changes: 0 additions & 32 deletions src/test/java/eu/dissco/core/handlemanager/service/HandleServiceTest.java
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Expand Up @@ -378,7 +378,6 @@ void testCreateDigitalSpecimenSpecimenExists() throws Exception {
ObjectType.DIGITAL_SPECIMEN);

given(pidNameGeneratorService.genHandleList(1)).willReturn(new ArrayList<>(List.of(handle)));
given(pidRepository.checkHandlesWritable(anyList())).willReturn(List.of(handle));
given(profileProperties.getDomain()).willReturn(HANDLE_DOMAIN);
given(pidRepository.searchByNormalisedPhysicalIdentifier(anyList())).willReturn(List.of(
new HandleAttribute(FdoProfile.NORMALISED_SPECIMEN_OBJECT_ID, handle,
Expand All @@ -395,37 +394,6 @@ void testCreateDigitalSpecimenSpecimenExists() throws Exception {
assertThat(result).isEqualTo(responseExpected);
}

@Test
void testCreateDigitalSpecimenSpecimenExistsNotWritable() throws Exception {
// Given
byte[] handle = handles.get(0);
var digitalSpecimen = givenDigitalSpecimenRequestObjectNullOptionals();
var request = genCreateRecordRequest(digitalSpecimen,
RECORD_TYPE_DS);
List<HandleAttribute> digitalSpecimenAttributes = genDigitalSpecimenAttributes(handle);
var digitalSpecimenSublist = digitalSpecimenAttributes.stream()
.filter(row -> row.getType().equals(PRIMARY_SPECIMEN_OBJECT_ID.get())).toList();
var responseExpected = givenRecordResponseWriteSmallResponse(digitalSpecimenSublist,
List.of(handle),
ObjectType.DIGITAL_SPECIMEN);

given(pidNameGeneratorService.genHandleList(1)).willReturn(new ArrayList<>(List.of(handle)));
given(profileProperties.getDomain()).willReturn(HANDLE_DOMAIN);
given(pidRepository.searchByNormalisedPhysicalIdentifier(anyList())).willReturn(List.of(
new HandleAttribute(FdoProfile.NORMALISED_SPECIMEN_OBJECT_ID, handle,
digitalSpecimen.getNormalisedPrimarySpecimenObjectId())));
given(fdoRecordService.prepareDigitalSpecimenRecordAttributes(digitalSpecimen,
handle)).willReturn(digitalSpecimenAttributes);

// When
var result = service.createRecords(List.of(request));

// Then
then(pidRepository).should()
.postAttributesToDb(CREATED.getEpochSecond(), digitalSpecimenAttributes);
assertThat(result).isEqualTo(responseExpected);
}

@Test
void testCreateMediaObjectRecord() throws Exception {
// Given
Expand Down