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@southeo
southeo committed Jul 18, 2024
1 parent 729e883 commit d23bf66
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Showing 11 changed files with 174 additions and 280 deletions.
14 changes: 7 additions & 7 deletions src/main/java/eu/dissco/core/handlemanager/controller/PidController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -54,11 +54,11 @@ public class PidController {
@GetMapping("/{prefix}/{suffix}")
public ResponseEntity<JsonApiWrapperRead> resolvePid(@PathVariable("prefix") String prefix,
@PathVariable("suffix") String suffix, HttpServletRequest r) throws PidResolutionException {
String path = applicationProperties.getUiUrl() + "/" + r.getRequestURI();
String link = applicationProperties.getUiUrl() + "/" + r.getRequestURI();
String handle = prefix + "/" + suffix;

if (prefix.equals(applicationProperties.getPrefix())) {
var node = service.resolveSingleRecord(handle, path);
var node = service.resolveSingleRecord(handle, link);
return ResponseEntity.status(HttpStatus.OK).body(node);
}
throw new PidResolutionException(
Expand All @@ -71,15 +71,15 @@ public ResponseEntity<JsonApiWrapperRead> resolvePid(@PathVariable("prefix") Str
public ResponseEntity<JsonApiWrapperRead> resolvePids(
@RequestParam List<String> handles,
HttpServletRequest r) throws InvalidRequestException {
String path = applicationProperties.getUiUrl() + "/" + r.getRequestURI();
String link = applicationProperties.getUiUrl() + "/" + r.getRequestURI();

if (handles.size() > applicationProperties.getMaxHandles()) {
throw new InvalidRequestException(
"Attempting to resolve more than maximum permitted PIDs in a single request. Maximum handles: "
+ applicationProperties.getMaxHandles());
}

return ResponseEntity.status(HttpStatus.OK).body(service.resolveBatchRecord(handles, path));
return ResponseEntity.status(HttpStatus.OK).body(service.resolveBatchRecord(handles, link));
}

@Operation(summary = "Given a physical identifier (i.e. local identifier), resolve PID record")
Expand Down Expand Up @@ -119,7 +119,7 @@ public ResponseEntity<JsonApiWrapperWrite> updateRecord(@PathVariable("prefix")
Authentication authentication) throws InvalidRequestException, UnprocessableEntityException {
log.info("Received single update request for PID {}/{} from user {}", prefix, suffix,
authentication.getName());
schemaValidator.validatePutRequest(request);
schemaValidator.validatePatchRequest(request);
var handle = (prefix + "/" + suffix);
var handleData = request.get(NODE_DATA).get(NODE_ID).asText();
if (!handle.equals(handleData)) {
Expand All @@ -137,7 +137,7 @@ public ResponseEntity<JsonApiWrapperWrite> updateRecords(@RequestBody List<JsonN
Authentication authentication) throws InvalidRequestException, UnprocessableEntityException {
log.info("Validating batch update request from user {}", authentication.getName());
for (JsonNode request : requests) {
schemaValidator.validatePutRequest(request);
schemaValidator.validatePatchRequest(request);
}
log.info("Received valid batch update request for {} PIDS", requests.size());
var result = service.updateRecords(requests, true);
Expand Down Expand Up @@ -192,7 +192,7 @@ public ResponseEntity<JsonApiWrapperWrite> rollbackHandleUpdate(

log.info("Validating rollback update request from user {}", authentication.getName());
for (JsonNode request : requests) {
schemaValidator.validatePutRequest(request);
schemaValidator.validatePatchRequest(request);
}
var handles = requests.stream().map(r -> r.get(NODE_DATA).get(NODE_ID).asText())
.limit(LOG_LIMIT).toList();
Expand Down
5 changes: 3 additions & 2 deletions src/main/java/eu/dissco/core/handlemanager/domain/repsitoryobjects/FdoAttribute.java
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Expand Up @@ -19,11 +19,12 @@ public class FdoAttribute {
int ttl;
Instant timestamp;

public FdoAttribute(FdoProfile fdoAttribute, Instant timestamp, String value) {
public FdoAttribute(FdoProfile fdoAttribute, Instant timestamp, Object value) {
this.index = fdoAttribute.index();
this.type = fdoAttribute.get();
this.timestamp = timestamp;
this.data = new StringHandleData(value);
value = value == null ? "" : value;
this.data = new StringHandleData(value.toString());
this.ttl = 86400;
}

Expand Down
2 changes: 1 addition & 1 deletion ...lemanager/domain/requests/PutRequest.java → ...manager/domain/requests/PatchRequest.java
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Expand Up @@ -2,6 +2,6 @@

import com.fasterxml.jackson.annotation.JsonProperty;

public record PutRequest(@JsonProperty(required = true) PutRequestData data) {
public record PatchRequest(@JsonProperty(required = true) PutRequestData data) {

}
2 changes: 1 addition & 1 deletion src/main/java/eu/dissco/core/handlemanager/domain/requests/PostRequestData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
import eu.dissco.core.handlemanager.domain.fdo.FdoType;

public record PostRequestData(
@JsonProperty(required = true)
//@JsonProperty(required = true)
@JsonPropertyDescription("type of object")
FdoType type,
@JsonProperty(required = true)
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/eu/dissco/core/handlemanager/domain/requests/PutRequestData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,11 @@
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyDescription;
import com.fasterxml.jackson.databind.JsonNode;
import eu.dissco.core.handlemanager.domain.fdo.FdoType;

public record PutRequestData(
@JsonProperty(required = true) @JsonPropertyDescription("DiSSCo Identifier of object") String id,
@JsonProperty(required = true) JsonNode attributes) {
@JsonProperty(required = true) JsonNode attributes,
FdoType type) {

}
5 changes: 5 additions & 0 deletions src/main/java/eu/dissco/core/handlemanager/domain/requests/TombstoneRequest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
package eu.dissco.core.handlemanager.domain.requests;

public record TombstoneRequest(TombstoneRequestData data) {

}
12 changes: 12 additions & 0 deletions src/main/java/eu/dissco/core/handlemanager/domain/requests/TombstoneRequestData.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
package eu.dissco.core.handlemanager.domain.requests;

import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyDescription;
import com.fasterxml.jackson.databind.JsonNode;

public record TombstoneRequestData(
@JsonProperty(required = true) @JsonPropertyDescription("DiSSCo Identifier of object") String id,
@JsonProperty(required = true) JsonNode attributes
) {

}
147 changes: 75 additions & 72 deletions src/main/java/eu/dissco/core/handlemanager/domain/validation/JsonSchemaValidator.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package eu.dissco.core.handlemanager.domain.validation;

import static eu.dissco.core.handlemanager.domain.fdo.FdoType.TOMBSTONE;
import static eu.dissco.core.handlemanager.domain.jsonapi.JsonApiFields.NODE_ATTRIBUTES;
import static eu.dissco.core.handlemanager.domain.jsonapi.JsonApiFields.NODE_DATA;
import static eu.dissco.core.handlemanager.domain.jsonapi.JsonApiFields.NODE_TYPE;
Expand Down Expand Up @@ -28,8 +29,9 @@
import eu.dissco.core.handlemanager.domain.fdo.OrganisationRequest;
import eu.dissco.core.handlemanager.domain.fdo.SourceSystemRequest;
import eu.dissco.core.handlemanager.domain.fdo.TombstoneRecordRequest;
import eu.dissco.core.handlemanager.domain.requests.PatchRequest;
import eu.dissco.core.handlemanager.domain.requests.PostRequest;
import eu.dissco.core.handlemanager.domain.requests.PutRequest;
import eu.dissco.core.handlemanager.domain.requests.TombstoneRequest;
import eu.dissco.core.handlemanager.exceptions.InvalidRequestException;
import jakarta.validation.constraints.NotEmpty;
import java.util.Arrays;
Expand All @@ -46,31 +48,33 @@ public class JsonSchemaValidator {

// JsonNodes
private JsonNode postReqJsonNode;
private JsonNode patchReqJsonNode;
private JsonNode putReqJsonNode;
private JsonNode handlePostReqJsonNode;
private JsonNode doiPostReqJsonNode;
private JsonNode digitalSpecimenPostReqJsonNode;
private JsonNode digitalMediaPostReqJsonNode;
private JsonNode handleJsonNode;
private JsonNode doiJsonNode;
private JsonNode digitalSpecimenJsonNode;
private JsonNode digitalMediaJsonNode;
private JsonNode tombstoneReqJsonNode;
private JsonNode annotationPostReqJsonNode;
private JsonNode mappingPostReqJsonNode;
private JsonNode sourceSystemPostReqJsonNode;
private JsonNode organisationPostReqJsonNode;
private JsonNode masPostReqJsonNode;
private JsonNode annotationJsonNode;
private JsonNode mappingJsonNode;
private JsonNode sourceSystemJsonNode;
private JsonNode organisationJsonNode;
private JsonNode masJsonNode;

// Schemas
private JsonSchema postReqSchema;
private JsonSchema patchReqSchema;
private JsonSchema putReqSchema;
private JsonSchema handlePostReqSchema;
private JsonSchema doiPostReqSchema;
private JsonSchema digitalSpecimenPostReqSchema;
private JsonSchema digitalMediaPostReqSchema;
private JsonSchema handleSchema;
private JsonSchema doiSchema;
private JsonSchema digitalSpecimenSchema;
private JsonSchema digitalMediaSchema;
private JsonSchema tombstoneReqSchema;
private JsonSchema annotationPostReqSchema;
private JsonSchema mappingPostReqSchema;
private JsonSchema sourceSystemPostReqSchema;
private JsonSchema organisationPostReqSchema;
private JsonSchema masPostReqSchema;
private JsonSchema annotationSchema;
private JsonSchema dataMappingSchema;
private JsonSchema sourceSystemSchema;
private JsonSchema organisationSchema;
private JsonSchema masSchema;

public JsonSchemaValidator() {
setPostRequestAttributesJsonNodes();
Expand All @@ -80,16 +84,16 @@ public JsonSchemaValidator() {

private void setPostRequestAttributesJsonNodes() {
var schemaGenerator = new SchemaGenerator(jacksonModuleSchemaConfig());
handlePostReqJsonNode = schemaGenerator.generateSchema(HandleRecordRequest.class);
doiPostReqJsonNode = schemaGenerator.generateSchema(DoiRecordRequest.class);
digitalSpecimenPostReqJsonNode = schemaGenerator.generateSchema(DigitalSpecimenRequest.class);
digitalMediaPostReqJsonNode = schemaGenerator.generateSchema(DigitalMediaRequest.class);
handleJsonNode = schemaGenerator.generateSchema(HandleRecordRequest.class);
doiJsonNode = schemaGenerator.generateSchema(DoiRecordRequest.class);
digitalSpecimenJsonNode = schemaGenerator.generateSchema(DigitalSpecimenRequest.class);
digitalMediaJsonNode = schemaGenerator.generateSchema(DigitalMediaRequest.class);
tombstoneReqJsonNode = schemaGenerator.generateSchema(TombstoneRecordRequest.class);
annotationPostReqJsonNode = schemaGenerator.generateSchema(AnnotationRequest.class);
mappingPostReqJsonNode = schemaGenerator.generateSchema(DataMappingRequest.class);
sourceSystemPostReqJsonNode = schemaGenerator.generateSchema(SourceSystemRequest.class);
organisationPostReqJsonNode = schemaGenerator.generateSchema(OrganisationRequest.class);
masPostReqJsonNode = schemaGenerator.generateSchema(MasRequest.class);
annotationJsonNode = schemaGenerator.generateSchema(AnnotationRequest.class);
mappingJsonNode = schemaGenerator.generateSchema(DataMappingRequest.class);
sourceSystemJsonNode = schemaGenerator.generateSchema(SourceSystemRequest.class);
organisationJsonNode = schemaGenerator.generateSchema(OrganisationRequest.class);
masJsonNode = schemaGenerator.generateSchema(MasRequest.class);
}

private SchemaGeneratorConfig jacksonModuleSchemaConfig() {
Expand Down Expand Up @@ -132,7 +136,8 @@ private SchemaGeneratorConfig jacksonModuleSchemaConfig() {
private void setRequestJsonNodes() {
var schemaGenerator = new SchemaGenerator(requestSchemaConfig());
postReqJsonNode = schemaGenerator.generateSchema(PostRequest.class);
putReqJsonNode = schemaGenerator.generateSchema(PutRequest.class);
patchReqJsonNode = schemaGenerator.generateSchema(PatchRequest.class);
putReqJsonNode = schemaGenerator.generateSchema(TombstoneRequest.class);
}

public SchemaGeneratorConfig requestSchemaConfig() {
Expand Down Expand Up @@ -163,74 +168,72 @@ public SchemaGeneratorConfig requestSchemaConfig() {

private void setJsonSchemas() {
JsonSchemaFactory factory = JsonSchemaFactory.getInstance(VersionFlag.V202012);

postReqSchema = factory.getSchema(postReqJsonNode);
patchReqSchema = factory.getSchema(patchReqJsonNode);
putReqSchema = factory.getSchema(putReqJsonNode);

handlePostReqSchema = factory.getSchema(handlePostReqJsonNode);
doiPostReqSchema = factory.getSchema(doiPostReqJsonNode);
digitalSpecimenPostReqSchema = factory.getSchema(digitalSpecimenPostReqJsonNode);
digitalMediaPostReqSchema = factory.getSchema(digitalMediaPostReqJsonNode);
annotationPostReqSchema = factory.getSchema(annotationPostReqJsonNode);
mappingPostReqSchema = factory.getSchema(mappingPostReqJsonNode);
sourceSystemPostReqSchema = factory.getSchema(sourceSystemPostReqJsonNode);
organisationPostReqSchema = factory.getSchema(organisationPostReqJsonNode);
masPostReqSchema = factory.getSchema(masPostReqJsonNode);
handleSchema = factory.getSchema(handleJsonNode);
doiSchema = factory.getSchema(doiJsonNode);
digitalSpecimenSchema = factory.getSchema(digitalSpecimenJsonNode);
digitalMediaSchema = factory.getSchema(digitalMediaJsonNode);
annotationSchema = factory.getSchema(annotationJsonNode);
dataMappingSchema = factory.getSchema(mappingJsonNode);
sourceSystemSchema = factory.getSchema(sourceSystemJsonNode);
organisationSchema = factory.getSchema(organisationJsonNode);
masSchema = factory.getSchema(masJsonNode);
tombstoneReqSchema = factory.getSchema(tombstoneReqJsonNode);

}

public void validatePostRequest(JsonNode requestRoot) throws InvalidRequestException {
var validationErrors = postReqSchema.validate(requestRoot);
if (!validationErrors.isEmpty()) {
throw new InvalidRequestException(setErrorMessage(validationErrors, "POST"));
throw new InvalidRequestException(setErrorMessage(validationErrors, "CREATE"));
}
var fdoType = FdoType.fromString(requestRoot.get(NODE_DATA).get(NODE_TYPE).asText());
validateAttributes(requestRoot, fdoType);
}

FdoType type = FdoType.fromString(requestRoot.get(NODE_DATA).get(NODE_TYPE).asText());
var attributes = requestRoot.get(NODE_DATA).get(NODE_ATTRIBUTES);
switch (type) {
case HANDLE -> validateRequestAttributes(attributes, handlePostReqSchema, type);
case DOI -> validateRequestAttributes(attributes, doiPostReqSchema, type);
case DIGITAL_SPECIMEN ->
validateRequestAttributes(attributes, digitalSpecimenPostReqSchema, type);
case DIGITAL_MEDIA -> validateRequestAttributes(attributes, digitalMediaPostReqSchema, type);
case ANNOTATION -> validateRequestAttributes(attributes, annotationPostReqSchema, type);
case DATA_MAPPING -> validateRequestAttributes(attributes, mappingPostReqSchema, type);
case SOURCE_SYSTEM -> validateRequestAttributes(attributes, sourceSystemPostReqSchema, type);
case ORGANISATION -> validateRequestAttributes(attributes, organisationPostReqSchema, type);
case MAS -> validateRequestAttributes(attributes, masPostReqSchema, type);
default ->
throw new InvalidRequestException("Invalid Request. Reason: Invalid type: " + type);
public void validatePatchRequest(JsonNode requestRoot) throws InvalidRequestException {
var validationErrors = patchReqSchema.validate(requestRoot);
if (!validationErrors.isEmpty()) {
throw new InvalidRequestException(
setErrorMessage(validationErrors, "UPDATE"));
}
var fdoType = FdoType.fromString(requestRoot.get(NODE_DATA).get(NODE_TYPE).asText());
validateAttributes(requestRoot, fdoType);
}

public void validatePutRequest(JsonNode requestRoot) throws InvalidRequestException {
var validationErrors = putReqSchema.validate(requestRoot);
if (!validationErrors.isEmpty()) {
throw new InvalidRequestException(
setErrorMessage(validationErrors, "PUT (tombstone)"));
setErrorMessage(validationErrors, "TOMBSTONE"));
}
var attributes = requestRoot.get(NODE_DATA).get(NODE_ATTRIBUTES);
validateTombstoneRequestAttributes(attributes);
validateAttributes(requestRoot, TOMBSTONE);
}


private void validateTombstoneRequestAttributes(JsonNode requestAttributes)
private void validateAttributes(JsonNode requestRoot, FdoType fdoType)
throws InvalidRequestException {
var validationErrors = tombstoneReqSchema.validate(requestAttributes);
if (!validationErrors.isEmpty()) {
throw new InvalidRequestException(
setErrorMessage(validationErrors, FdoType.TOMBSTONE.getDigitalObjectName(),
requestAttributes));
var requestAttributes = requestRoot.get(NODE_DATA).get(NODE_ATTRIBUTES);
JsonSchema schema;
switch (fdoType) {
case HANDLE -> schema = handleSchema;
case DOI -> schema = doiSchema;
case DIGITAL_SPECIMEN -> schema = digitalSpecimenSchema;
case DIGITAL_MEDIA -> schema = digitalMediaSchema;
case ANNOTATION -> schema = annotationSchema;
case DATA_MAPPING -> schema = dataMappingSchema;
case SOURCE_SYSTEM -> schema = sourceSystemSchema;
case ORGANISATION -> schema = organisationSchema;
case MAS -> schema = masSchema;
case TOMBSTONE -> schema = tombstoneReqSchema;
default ->
throw new InvalidRequestException("Invalid Request. Reason: Invalid type: " + fdoType);
}
}

private void validateRequestAttributes(JsonNode requestAttributes, JsonSchema schema,
FdoType type) throws InvalidRequestException {
var validationErrors = schema.validate(requestAttributes);
if (!validationErrors.isEmpty()) {
throw new InvalidRequestException(
setErrorMessage(validationErrors, type.getDigitalObjectName(), requestAttributes));
setErrorMessage(validationErrors, fdoType.getDigitalObjectName(),
requestAttributes));
}
}

Expand Down
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