From 6fa0f55fd64ca4d316d22c8c2bbdf3104661f27b Mon Sep 17 00:00:00 2001 From: rng Date: Tue, 7 Jan 2025 15:21:10 +1100 Subject: [PATCH 1/8] Refactor to split classes --- .../esindexer/configuration/AppConstants.java | 2 +- .../controller/IndexerController.java | 26 +-- .../service/IndexCloudOptimizedService.java | 11 ++ .../IndexCloudOptimizedServiceImpl.java | 89 +++++++++ .../aodn/esindexer/service/IndexService.java | 13 ++ .../esindexer/service/IndexServiceImpl.java | 112 ++++++++++++ ...rvice.java => IndexerMetadataService.java} | 6 +- ...l.java => IndexerMetadataServiceImpl.java} | 169 +++--------------- .../esindexer/service/IndexerServiceIT.java | 6 +- .../esindexer/service/IndexerServiceTest.java | 6 +- .../StacCollectionMapperServiceTest.java | 16 +- 11 files changed, 273 insertions(+), 183 deletions(-) create mode 100644 indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedService.java create mode 100644 indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java create mode 100644 indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java create mode 100644 indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java rename indexer/src/main/java/au/org/aodn/esindexer/service/{IndexerService.java => IndexerMetadataService.java} (80%) rename indexer/src/main/java/au/org/aodn/esindexer/service/{IndexerServiceImpl.java => IndexerMetadataServiceImpl.java} (76%) diff --git a/indexer/src/main/java/au/org/aodn/esindexer/configuration/AppConstants.java b/indexer/src/main/java/au/org/aodn/esindexer/configuration/AppConstants.java index df00f348..cfef4039 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/configuration/AppConstants.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/configuration/AppConstants.java @@ -2,7 +2,7 @@ public interface AppConstants { String PORTAL_RECORDS_MAPPING_JSON_FILE = "portal_records_index_schema.json"; - String DATASET_INDEX_MAPPING_JSON_FILE = "dataset_index_schema.json"; + String DATASET_INDEX_MAPPING_JSON_FILE = "data_index_schema.json"; String FORMAT_XML = "xml"; String FORMAT_ISO19115_3_2018 = "iso19115-3.2018"; diff --git a/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java b/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java index ac31331d..4215510d 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java @@ -2,7 +2,8 @@ import au.org.aodn.esindexer.service.DataAccessService; import au.org.aodn.esindexer.service.GeoNetworkService; -import au.org.aodn.esindexer.service.IndexerService; +import au.org.aodn.esindexer.service.IndexCloudOptimizedService; +import au.org.aodn.esindexer.service.IndexerMetadataService; import co.elastic.clients.elasticsearch.core.BulkResponse; import com.fasterxml.jackson.databind.node.ObjectNode; import io.swagger.v3.oas.annotations.Operation; @@ -22,7 +23,6 @@ import java.util.ArrayList; import java.util.List; import java.util.concurrent.CompletableFuture; -import java.util.concurrent.ExecutionException; @RestController @RequestMapping(value = "/api/v1/indexer/index") @@ -31,7 +31,10 @@ public class IndexerController { @Autowired - IndexerService indexerService; + IndexerMetadataService indexerMetadata; + + @Autowired + IndexCloudOptimizedService indexCloudOptimizedData; @Autowired GeoNetworkService geonetworkResourceService; @@ -51,7 +54,7 @@ public ResponseEntity getMetadataRecordFromGeoNetworkByUUID(@PathVariabl @Operation(description = "Get a document from portal index by UUID") public ResponseEntity getDocumentByUUID(@PathVariable("uuid") String uuid) throws IOException { log.info("getting a document form portal by UUID: {}", uuid); - ObjectNode response = indexerService.getDocumentByUUID(uuid).source(); + ObjectNode response = indexerMetadata.getDocumentByUUID(uuid).source(); return ResponseEntity.status(HttpStatus.OK).body(response); } /** @@ -69,13 +72,12 @@ public ResponseEntity indexAllMetadataRecords( @RequestParam(value = "confirm", defaultValue = "false") Boolean confirm, @RequestParam(value = "beginWithUuid", required=false) String beginWithUuid) throws IOException { - List responses = indexerService.indexAllMetadataRecordsFromGeoNetwork(beginWithUuid, confirm, null); + List responses = indexerMetadata.indexAllMetadataRecordsFromGeoNetwork(beginWithUuid, confirm, null); return ResponseEntity.ok(responses.toString()); } /** * Emit result to FE so it will not result in gateway time-out. You need to run it with postman or whatever tools * support server side event, the content type needs to be text/event-stream in order to work - * * Noted: There is a bug in postman desktop, so either you run postman using web-browser with agent directly * or you need to have version 10.2 or above in order to get the emitted result * @@ -91,7 +93,7 @@ public SseEmitter indexAllMetadataRecordsAsync( final SseEmitter emitter = new SseEmitter(0L); // 0L means no timeout; - IndexerService.Callback callback = new IndexerService.Callback() { + IndexerMetadataService.Callback callback = new IndexerMetadataService.Callback() { @Override public void onProgress(Object update) { try { @@ -130,7 +132,7 @@ public void onComplete(Object result) { new Thread(() -> { try { - indexerService.indexAllMetadataRecordsFromGeoNetwork(beginWithUuid, confirm, callback); + indexerMetadata.indexAllMetadataRecordsFromGeoNetwork(beginWithUuid, confirm, callback); } catch(IOException e) { emitter.completeWithError(e); @@ -142,10 +144,10 @@ public void onComplete(Object result) { @PostMapping(path="/{uuid}", produces = "application/json") @Operation(security = { @SecurityRequirement(name = "X-API-Key") }, description = "Index a metadata record by UUID") - public ResponseEntity addDocumentByUUID(@PathVariable("uuid") String uuid) throws IOException, FactoryException, JAXBException, TransformException, ExecutionException, InterruptedException { + public ResponseEntity addDocumentByUUID(@PathVariable("uuid") String uuid) throws IOException, FactoryException, JAXBException, TransformException { String metadataValues = geonetworkResourceService.searchRecordBy(uuid); - CompletableFuture> f = indexerService.indexMetadata(metadataValues); + CompletableFuture> f = indexerMetadata.indexMetadata(metadataValues); // Return when done make it back to sync instead of async return f.join(); } @@ -153,7 +155,7 @@ public ResponseEntity addDocumentByUUID(@PathVariable("uuid") String uui @DeleteMapping(path="/{uuid}", produces = "application/json") @Operation(security = { @SecurityRequirement(name = "X-API-Key") }, description = "Delete a metadata record by UUID") public ResponseEntity deleteDocumentByUUID(@PathVariable("uuid") String uuid) throws IOException { - return indexerService.deleteDocumentByUUID(uuid); + return indexerMetadata.deleteDocumentByUUID(uuid); } @PostMapping(path="/{uuid}/dataset", produces = "application/json") @@ -165,7 +167,7 @@ public ResponseEntity> indexDatasetByUUID(@PathVariable("uuid") Str var endDate = temporalExtents.getEndDate(); log.info("Indexing dataset with UUID: {} from {} to {}", uuid, startDate, endDate); - var responses = indexerService.indexDataset(uuid, startDate, endDate); + var responses = indexCloudOptimizedData.indexCloudOptimizedData(uuid, startDate, endDate); List result = new ArrayList<>(); for (BulkResponse response : responses) { diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedService.java new file mode 100644 index 00000000..77e5a61a --- /dev/null +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedService.java @@ -0,0 +1,11 @@ +package au.org.aodn.esindexer.service; + +import co.elastic.clients.elasticsearch.core.BulkResponse; + +import java.time.LocalDate; +import java.util.List; + +public interface IndexCloudOptimizedService extends IndexService { + List indexCloudOptimizedData(String uuid, LocalDate startDate, LocalDate endDate); + +} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java new file mode 100644 index 00000000..2f308a3e --- /dev/null +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java @@ -0,0 +1,89 @@ +package au.org.aodn.esindexer.service; + +import au.org.aodn.esindexer.model.DatasetProvider; +import co.elastic.clients.elasticsearch.ElasticsearchClient; +import co.elastic.clients.elasticsearch.core.BulkRequest; +import co.elastic.clients.elasticsearch.core.BulkResponse; +import com.fasterxml.jackson.databind.ObjectMapper; +import lombok.extern.slf4j.Slf4j; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.context.annotation.Lazy; +import org.springframework.context.annotation.Scope; +import org.springframework.context.annotation.ScopedProxyMode; +import org.springframework.stereotype.Service; + +import java.time.LocalDate; +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; + +@Slf4j +@Service +@Scope(proxyMode = ScopedProxyMode.TARGET_CLASS) +public class IndexCloudOptimizedServiceImpl extends IndexServiceImpl implements IndexCloudOptimizedService { + + protected DataAccessService dataAccessService; + protected ObjectMapper indexerObjectMapper; + protected String datasetIndexName; + + @Lazy + @Autowired + protected IndexCloudOptimizedServiceImpl self; + + @Autowired + public IndexCloudOptimizedServiceImpl( + @Value("${elasticsearch.dataset_index.name}") String datasetIndexName, + @Qualifier("portalElasticsearchClient") ElasticsearchClient elasticsearchClient, + ObjectMapper indexerObjectMapper, + DataAccessService dataAccessService) { + + super(elasticsearchClient, indexerObjectMapper); + + this.datasetIndexName = datasetIndexName; + this.indexerObjectMapper = indexerObjectMapper; + this.dataAccessService = dataAccessService; + } + + // TODO: Refactor this method later since it uses similar logic as indexAllMetadataRecordsFromGeoNetwork + @Override + public List indexCloudOptimizedData(String uuid, LocalDate startDate, LocalDate endDate) { + + BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); + List responses = new ArrayList<>(); + + long dataSize = 0; + final long maxSize = 5242880; // is 5mb + + var dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); + try { + for (var entry : dataset) { + if (entry == null) { + continue; + } + log.info("add dataset into b with UUID: {} and yearMonth: {}", entry.uuid(), entry.yearMonth()); + + bulkRequest.operations(operation -> operation.index( + indexReq -> indexReq + .id(entry.uuid() + entry.yearMonth()) + .index(datasetIndexName) + .document(entry) + )); + dataSize += indexerObjectMapper.writeValueAsBytes(entry).length; + if (dataSize > maxSize) { + log.info("Execute bulk request as bulk request is big enough {}", dataSize); + responses.add(reduceResponse(self.executeBulk(bulkRequest, (item) -> Optional.empty(), null))); + dataSize = 0; + bulkRequest = new BulkRequest.Builder(); + } + } + log.info("Finished execute bulk indexing records to index: {}", datasetIndexName); + responses.add(reduceResponse(self.executeBulk(bulkRequest, (item) -> Optional.empty(), null))); + } catch (Exception e) { + log.error("Failed", e); + throw new RuntimeException("Exception thrown while indexing dataset with UUID: " + uuid + " | " + e.getMessage(), e); + } + return responses; + } +} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java new file mode 100644 index 00000000..0cfa9de5 --- /dev/null +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java @@ -0,0 +1,13 @@ +package au.org.aodn.esindexer.service; + +import co.elastic.clients.elasticsearch.core.BulkRequest; +import co.elastic.clients.elasticsearch.core.BulkResponse; +import co.elastic.clients.elasticsearch.core.bulk.BulkResponseItem; + +import java.io.IOException; +import java.util.Optional; +import java.util.function.Function; + +public interface IndexService { + BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Function> mapper, IndexerMetadataService.Callback callback) throws IOException; +} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java new file mode 100644 index 00000000..71bf5aec --- /dev/null +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java @@ -0,0 +1,112 @@ +package au.org.aodn.esindexer.service; + +import co.elastic.clients.elasticsearch.ElasticsearchClient; +import co.elastic.clients.elasticsearch.core.BulkRequest; +import co.elastic.clients.elasticsearch.core.BulkResponse; +import co.elastic.clients.elasticsearch.core.bulk.BulkResponseItem; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import lombok.extern.slf4j.Slf4j; +import org.springframework.http.HttpStatus; +import org.springframework.retry.annotation.Backoff; +import org.springframework.retry.annotation.Retryable; +import org.springframework.web.client.HttpServerErrorException; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; +import java.util.function.Function; + +@Slf4j +public abstract class IndexServiceImpl implements IndexService { + + protected static final long DEFAULT_BACKOFF_TIME = 3000L; + protected ElasticsearchClient elasticClient; + protected ObjectMapper indexerObjectMapper; + + public IndexServiceImpl(ElasticsearchClient elasticClient, ObjectMapper indexerObjectMapper) { + this.elasticClient = elasticClient; + this.indexerObjectMapper = indexerObjectMapper; + } + + public static BulkResponse reduceResponse(BulkResponse in) { + List errors = in.items() + .stream() + .filter(p -> !(p.status() == HttpStatus.CREATED.value() || p.status() == HttpStatus.OK.value())) + .toList(); + + return errors.isEmpty() ? + BulkResponse.of(f -> f.items(new ArrayList<>()).errors(false).took(in.took())) : + BulkResponse.of(f -> f.items(errors).errors(true).took(in.took())); + } + + /** + * Keep retry until success, it is ok to insert docs to elastic again because we use _id as identifier. + * In case any service is not available, we will keep retry many times, with 100 retry we try 25 mins which is + * big enough for aws process restart. + * + * @param bulkRequest - The bulk request + * @param callback - The event call back to avoid timeout + * @return - The bulk insert result + * @throws IOException - Exceptions on error + * @throws HttpServerErrorException.ServiceUnavailable - Exceptions on geonetwork die or elastic not available + */ + @Retryable( + retryFor = {Exception.class, HttpServerErrorException.ServiceUnavailable.class}, + maxAttempts = 1000, + backoff = @Backoff(delay = DEFAULT_BACKOFF_TIME) + ) + @Override + public BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Function> mapper, IndexerMetadataService.Callback callback) throws IOException, HttpServerErrorException.ServiceUnavailable { + try { + // Keep retry until success + BulkResponse result = elasticClient.bulk(bulkRequest.build()); + + // Flush after insert, otherwise you need to wait for next auto-refresh. It is + // especially a problem with autotest, where assert happens very fast. + elasticClient.indices().refresh(); + + // Report status if success + if(callback != null) { + callback.onProgress(reduceResponse(result)); + } + + // Log errors, if any + if (!result.items().isEmpty()) { + if (result.errors()) { + log.error("Bulk load have errors? {}", true); + } else { + log.info("Bulk load have errors? {}", false); + } + for (BulkResponseItem item : result.items()) { + if (item.error() != null) { + Optional i = mapper.apply(item); + i.ifPresent(a -> { + try { + log.error("UUID {} {} {} {}", + item.id(), + item.error().reason(), + item.error().causedBy(), + indexerObjectMapper + .writerWithDefaultPrettyPrinter() + .writeValueAsString(a) + ); + } catch (JsonProcessingException e) { + log.error("Fail to convert item with json mapper, {}", item.id()); + } + }); + } + } + } + return result; + } + catch(Exception e) { + // Report status if not success, this help to keep connection + if(callback != null) { + callback.onProgress("Exception on bulk save, will retry : " + e.getMessage()); + } + throw e; + } + } +} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java similarity index 80% rename from indexer/src/main/java/au/org/aodn/esindexer/service/IndexerService.java rename to indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java index 3b8616fe..bd97732e 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerService.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java @@ -1,6 +1,5 @@ package au.org.aodn.esindexer.service; -import co.elastic.clients.elasticsearch.core.BulkRequest; import co.elastic.clients.elasticsearch.core.BulkResponse; import co.elastic.clients.elasticsearch.core.search.Hit; import com.fasterxml.jackson.databind.node.ObjectNode; @@ -10,22 +9,19 @@ import org.springframework.http.ResponseEntity; import java.io.IOException; -import java.time.LocalDate; import java.util.List; import java.util.concurrent.CompletableFuture; -public interface IndexerService { +public interface IndexerMetadataService extends IndexService { // Event call back to notify caller, this avoid gateway timeout as we have message back to browser interface Callback { void onProgress(Object update); void onComplete(Object result); } CompletableFuture> indexMetadata(String metadataValues) throws IOException, FactoryException, TransformException, JAXBException; - List indexDataset(String uuid, LocalDate startDate, LocalDate endDate); ResponseEntity deleteDocumentByUUID(String uuid) throws IOException; List indexAllMetadataRecordsFromGeoNetwork(String beginWithUuid, boolean confirm, Callback callback) throws IOException; Hit getDocumentByUUID(String uuid) throws IOException; boolean isMetadataPublished(String uuid); boolean isGeoNetworkInstanceReinstalled(long portalIndexDocumentsCount); - BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Callback callback) throws IOException; } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java similarity index 76% rename from indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java rename to indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java index 3421d9e8..2d061286 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java @@ -3,7 +3,6 @@ import au.org.aodn.ardcvocabs.model.VocabModel; import au.org.aodn.esindexer.configuration.AppConstants; import au.org.aodn.esindexer.exception.*; -import au.org.aodn.esindexer.model.DatasetProvider; import au.org.aodn.esindexer.utils.GcmdKeywordUtils; import au.org.aodn.esindexer.utils.JaxbUtils; import au.org.aodn.metadata.iso19115_3_2018.MDMetadataType; @@ -27,36 +26,31 @@ import org.opengis.referencing.FactoryException; import org.opengis.referencing.operation.TransformException; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Lazy; import org.springframework.context.annotation.Scope; import org.springframework.context.annotation.ScopedProxyMode; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; -import org.springframework.retry.annotation.Backoff; -import org.springframework.retry.annotation.Retryable; import org.springframework.scheduling.annotation.Async; import org.springframework.stereotype.Service; -import org.springframework.web.client.HttpServerErrorException; import java.io.ByteArrayInputStream; import java.io.IOException; import java.io.InputStream; -import java.time.LocalDate; import java.util.*; import java.util.concurrent.*; -import java.util.stream.Collectors; -import java.util.stream.Stream; +import java.util.function.Function; import static au.org.aodn.esindexer.utils.CommonUtils.safeGet; @Slf4j @Service @Scope(proxyMode = ScopedProxyMode.TARGET_CLASS) -public class IndexerServiceImpl implements IndexerService { +public class IndexerMetadataServiceImpl extends IndexServiceImpl implements IndexerMetadataService { protected String indexName; - protected String datasetIndexName; protected String tokensAnalyserName; protected GeoNetworkService geoNetworkResourceService; protected ElasticsearchClient portalElasticsearchClient; @@ -66,42 +60,38 @@ public class IndexerServiceImpl implements IndexerService { protected JaxbUtils jaxbUtils; protected RankingService rankingService; protected VocabService vocabService; - protected DataAccessService dataAccessService; protected GcmdKeywordUtils gcmdKeywordUtils; - protected static final long DEFAULT_BACKOFF_TIME = 3000L; @Lazy @Autowired - protected IndexerService self; + protected IndexerMetadataService self; @Autowired - public IndexerServiceImpl( + public IndexerMetadataServiceImpl( @Value("${elasticsearch.index.name}") String indexName, - @Value("${elasticsearch.dataset_index.name}") String datasetIndexName, @Value("${elasticsearch.analyser.tokens.name}") String tokensAnalyserName, ObjectMapper indexerObjectMapper, JaxbUtils jaxbUtils, RankingService rankingService, GeoNetworkService geoNetworkResourceService, - ElasticsearchClient portalElasticsearchClient, + @Qualifier("portalElasticsearchClient") ElasticsearchClient elasticsearchClient, ElasticSearchIndexService elasticSearchIndexService, StacCollectionMapperService stacCollectionMapperService, VocabService vocabService, - DataAccessService dataAccessService, GcmdKeywordUtils gcmdKeywordUtils ) { + super(elasticsearchClient, indexerObjectMapper); + this.indexName = indexName; - this.datasetIndexName = datasetIndexName; this.tokensAnalyserName = tokensAnalyserName; this.indexerObjectMapper = indexerObjectMapper; this.jaxbUtils = jaxbUtils; this.rankingService = rankingService; this.geoNetworkResourceService = geoNetworkResourceService; - this.portalElasticsearchClient = portalElasticsearchClient; + this.portalElasticsearchClient = elasticsearchClient; this.elasticSearchIndexService = elasticSearchIndexService; this.stacCollectionMapperService = stacCollectionMapperService; this.vocabService = vocabService; - this.dataAccessService = dataAccessService; this.gcmdKeywordUtils = gcmdKeywordUtils; } @@ -173,7 +163,6 @@ protected StacCollectionModel getMappedMetadataValues(String metadataValues) thr StacCollectionModel stacCollectionModel = stacCollectionMapperService.mapToSTACCollection(metadataType); // evaluate completeness - Integer completeness = rankingService.evaluateCompleteness(stacCollectionModel); // TODO: in future, evaluate other aspects of the data such as relevance, quality, etc using NLP /* expand score with other aspect of the data such as relevance, quality, etc. @@ -182,7 +171,7 @@ protected StacCollectionModel getMappedMetadataValues(String metadataValues) thr * e.g completeness = 80, relevance = 90, quality = 100 * final score = (80 + 90 + 100) / 3 = 90 */ - Integer score = completeness; + Integer score = rankingService.evaluateCompleteness(stacCollectionModel); stacCollectionModel.getSummaries().setScore(score); @@ -293,48 +282,6 @@ public CompletableFuture> indexMetadata(String metadataVa } } - // TODO: Refactor this method later since it uses similar logic as indexAllMetadataRecordsFromGeoNetwork - @Override - public List indexDataset(String uuid, LocalDate startDate, LocalDate endDate) { - - BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); - List responses = new ArrayList<>(); - - long dataSize = 0; - final long maxSize = 5242880; // is 5mb - - var dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); - try { - for (var entry : dataset) { - if (entry == null) { - continue; - } - log.info("add dataset into b with UUID: {} and yearMonth: {}", entry.uuid(), entry.yearMonth()); - - bulkRequest.operations(operation -> operation.index( - indexReq -> indexReq - .id(entry.uuid() + entry.yearMonth()) - .index(datasetIndexName) - .document(entry) - )); - dataSize += indexerObjectMapper.writeValueAsBytes(entry).length; - if (dataSize > maxSize) { - log.info("Execute bulk request as bulk request is big enough {}", dataSize); - responses.add(reduceResponse(self.executeBulk(bulkRequest, null))); - dataSize = 0; - bulkRequest = new BulkRequest.Builder(); - } - } - log.info("Finished execute bulk indexing records to index: {}", datasetIndexName); - responses.add(reduceResponse(self.executeBulk(bulkRequest, null))); - } catch (Exception e) { - log.error("Failed", e); - throw new RuntimeException("Exception thrown while indexing dataset with UUID: " + uuid + " | " + e.getMessage(), e); - } - return responses; - } - - public ResponseEntity deleteDocumentByUUID(String uuid) throws IOException { log.info("Deleting document with UUID: {} from index: {}", uuid, indexName); try { @@ -374,6 +321,17 @@ public List indexAllMetadataRecordsFromGeoNetwork( log.info("Resume indexing records from GeoNetwork at {}", beginWithUuid); } + Function> mapper = (item) -> + { + try { + return Optional.of(this.getMappedMetadataValues( + geoNetworkResourceService.searchRecordBy(item.id()) + )); + } catch (IOException | FactoryException | TransformException | JAXBException e) { + return Optional.empty(); + } + }; + BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); List results = new ArrayList<>(); @@ -443,7 +401,7 @@ public List indexAllMetadataRecordsFromGeoNetwork( callback.onProgress(String.format("Execute batch as bulk request is big enough %s", dataSize + size)); } - results.add(reduceResponse(self.executeBulk(bulkRequest, callback))); + results.add(reduceResponse(self.executeBulk(bulkRequest, mapper, callback))); dataSize = 0; bulkRequest = new BulkRequest.Builder(); @@ -471,8 +429,9 @@ public List indexAllMetadataRecordsFromGeoNetwork( } } } + // In case there are residual, just report error - BulkResponse temp = reduceResponse(self.executeBulk(bulkRequest, callback)); + BulkResponse temp = reduceResponse(self.executeBulk(bulkRequest, mapper, callback)); results.add(temp); if(callback != null) { @@ -498,84 +457,4 @@ public List indexAllMetadataRecordsFromGeoNetwork( } return results; } - /** - * Keep retry until success, it is ok to insert docs to elastic again because we use _id as identifier. - * In case any service is not available, we will keep retry many times, with 100 retry we try 25 mins which is - * big enough for aws process restart. - * - * @param bulkRequest - The bulk request - * @param callback - The event call back to avoid timeout - * @return - The bulk insert result - * @throws IOException - Exceptions on error - * @throws HttpServerErrorException.ServiceUnavailable - Exceptions on geonetwork die or elastic not available - */ - @Retryable( - retryFor = {Exception.class, HttpServerErrorException.ServiceUnavailable.class}, - maxAttempts = 1000, - backoff = @Backoff(delay = DEFAULT_BACKOFF_TIME) - ) - @Override - public BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Callback callback) throws IOException, HttpServerErrorException.ServiceUnavailable { - try { - // Keep retry until success - BulkResponse result = portalElasticsearchClient.bulk(bulkRequest.build()); - - // Flush after insert, otherwise you need to wait for next auto-refresh. It is - // especially a problem with autotest, where assert happens very fast. - portalElasticsearchClient.indices().refresh(); - - // Report status if success - if(callback != null) { - callback.onProgress(reduceResponse(result)); - } - - // Log errors, if any - if (!result.items().isEmpty()) { - if (result.errors()) { - log.error("Bulk load have errors? {}", true); - } else { - log.info("Bulk load have errors? {}", false); - } - for (BulkResponseItem item : result.items()) { - if (item.error() != null) { - try { - log.error("UUID {} {} {} {}", - item.id(), - item.error().reason(), - item.error().causedBy(), - indexerObjectMapper - .writerWithDefaultPrettyPrinter() - .writeValueAsString( - this.getMappedMetadataValues( - geoNetworkResourceService.searchRecordBy(item.id()) - ) - ) - ); - } catch (FactoryException | TransformException | JAXBException e) { - log.warn("Parse error on display stac record"); - } - } - } - } - return result; - } - catch(Exception e) { - // Report status if not success, this help to keep connection - if(callback != null) { - callback.onProgress("Exception on bulk save, will retry : " + e.getMessage()); - } - throw e; - } - } - - protected static BulkResponse reduceResponse(BulkResponse in) { - List errors = in.items() - .stream() - .filter(p -> !(p.status() == HttpStatus.CREATED.value() || p.status() == HttpStatus.OK.value())) - .toList(); - - return errors.isEmpty() ? - BulkResponse.of(f -> f.items(new ArrayList<>()).errors(false).took(in.took())) : - BulkResponse.of(f -> f.items(errors).errors(true).took(in.took())); - } } diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java index da8f24d1..0c8e3dfb 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java @@ -3,8 +3,6 @@ import au.org.aodn.esindexer.BaseTestClass; import au.org.aodn.esindexer.configuration.GeoNetworkSearchTestConfig; import co.elastic.clients.elasticsearch.ElasticsearchClient; -import co.elastic.clients.elasticsearch.core.BulkResponse; -import co.elastic.clients.elasticsearch.core.bulk.BulkResponseItem; import co.elastic.clients.elasticsearch.core.search.Hit; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; @@ -17,7 +15,6 @@ import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.test.context.SpringBootTest; -import org.springframework.http.HttpStatus; import org.springframework.test.context.ActiveProfiles; import java.io.IOException; @@ -38,7 +35,7 @@ public class IndexerServiceIT extends BaseTestClass { ElasticsearchClient gn4ElasticsearchClient; @Autowired - protected IndexerService indexerService; + protected IndexerMetadataService indexerService; @Autowired protected ObjectMapper indexerObjectMapper; @@ -237,7 +234,6 @@ public void verifyThumbnailLinkAddedOnIndex() throws IOException { /** * This test is use to make sure if the geonetwork return an empty thumbnails [] array, we are still ok, * in the related/5905b3eb-aad0-4f9c-a03e-a02fb3488082.json, the thumbnails: [] is empty - * @throws IOException */ @Test public void verifyThumbnailLinkNullAdbbdedOnIndex() throws IOException { diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java index 9bdaa981..5f8100db 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java @@ -1,6 +1,5 @@ package au.org.aodn.esindexer.service; -import co.elastic.clients.elasticsearch._types.ErrorCause; import co.elastic.clients.elasticsearch.core.BulkResponse; import co.elastic.clients.elasticsearch.core.bulk.BulkResponseItem; import co.elastic.clients.elasticsearch.core.bulk.OperationType; @@ -14,6 +13,7 @@ */ @Slf4j public class IndexerServiceTest { + /** * Verify this function, it should only return error if items contains status no CREATED or OK */ @@ -34,7 +34,7 @@ public void verifyReduceResponse() { .errors(false).took(1) ); - bulkResponse = IndexerServiceImpl.reduceResponse(bulkResponse); + bulkResponse = IndexerMetadataServiceImpl.reduceResponse(bulkResponse); Assertions.assertFalse(bulkResponse.errors(), "Should not contain error"); bulkResponse = BulkResponse.of(b -> @@ -52,7 +52,7 @@ public void verifyReduceResponse() { .errors(false).took(1) ); - bulkResponse = IndexerServiceImpl.reduceResponse(bulkResponse); + bulkResponse = IndexerMetadataServiceImpl.reduceResponse(bulkResponse); Assertions.assertTrue(bulkResponse.errors(), "Should contain error"); } } diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java b/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java index 2b5ea9d2..88339f21 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java @@ -32,7 +32,6 @@ import java.io.IOException; import java.util.Collections; import java.util.Map; -import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicReference; import java.util.function.Function; @@ -63,9 +62,6 @@ public class StacCollectionMapperServiceTest { @MockBean protected VocabService vocabsService; - @MockBean - protected DataAccessService dataAccessService; - @MockBean protected RankingService rankingService; @@ -77,7 +73,7 @@ public class StacCollectionMapperServiceTest { protected AtomicReference> lastRequest = new AtomicReference<>(); - protected IndexerServiceImpl indexerService; + protected IndexerMetadataServiceImpl indexerService; @BeforeAll public static void preSetup() { @@ -111,9 +107,8 @@ public void cleanUp() { @BeforeEach public void createIndexerService() throws IOException { - indexerService = new IndexerServiceImpl( + indexerService = new IndexerMetadataServiceImpl( "any-works", - "any-works-dataset", "shingle_analyser", objectMapper, jaxbUtils, @@ -123,7 +118,6 @@ public void createIndexerService() throws IOException { elasticSearchIndexService, service, vocabsService, - dataAccessService, gcmdKeywordUtils ); indexerService = spy(indexerService); @@ -222,7 +216,7 @@ public void verifyLicenseCorrect() throws IOException, JSONException { } @Test - public void verifySummaryGeoCorrect1() throws IOException, JAXBException, JSONException { + public void verifySummaryGeoCorrect1() throws IOException, JSONException { // We only index one record, the String xml = readResourceFile("classpath:canned/sample9.xml"); String expected = readResourceFile("classpath:canned/sample9_stac.json"); @@ -285,9 +279,7 @@ public void verifyNullAbstractResponsibility() throws IOException, JSONException verify(expected); } - /** - * @throws IOException - */ + @Test public void verifyAbstractCIParty1() throws IOException, JSONException { String xml = readResourceFile("classpath:canned/sample12.xml"); From 2aef5a3e0802c04ca4e186448ecc25a778f99cca Mon Sep 17 00:00:00 2001 From: rng Date: Tue, 7 Jan 2025 17:26:40 +1100 Subject: [PATCH 2/8] Checkpoint refactor bulk operation --- .../IndexCloudOptimizedServiceImpl.java | 2 +- .../aodn/esindexer/service/IndexService.java | 6 ++ .../esindexer/service/IndexServiceImpl.java | 78 +++++++++++++++++++ .../service/IndexerMetadataService.java | 6 +- .../service/IndexerMetadataServiceImpl.java | 60 ++++---------- ...dex_schema.json => data_index_schema.json} | 7 +- 6 files changed, 101 insertions(+), 58 deletions(-) rename indexer/src/main/resources/config_files/{dataset_index_schema.json => data_index_schema.json} (80%) diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java index 2f308a3e..c6305411 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java @@ -54,7 +54,7 @@ public List indexCloudOptimizedData(String uuid, LocalDate startDa List responses = new ArrayList<>(); long dataSize = 0; - final long maxSize = 5242880; // is 5mb + final long maxSize = this.getBatchSize(); var dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); try { diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java index 0cfa9de5..b0f7ab84 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexService.java @@ -9,5 +9,11 @@ import java.util.function.Function; public interface IndexService { + // Event call back to notify caller, this avoid gateway timeout as we have message back to browser + interface Callback { + void onProgress(Object update); + void onComplete(Object result); + } + long getBatchSize(); BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Function> mapper, IndexerMetadataService.Callback callback) throws IOException; } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java index 71bf5aec..f1533366 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java @@ -25,6 +25,79 @@ public abstract class IndexServiceImpl implements IndexService { protected ElasticsearchClient elasticClient; protected ObjectMapper indexerObjectMapper; + /** + * This processor help to shield the complexity of bulk save of Elastic search where the batch size cannot be + * too large. You keep calling the processItem by adding it new item. Once it reached the max size it will flush + * to the Elastic, then it will reset and allow adding new item. + * You must call flush at the end so that any remain item will get push + * @param + */ + protected class BulkRequestProcessor { + BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); + IndexService proxyImpl; + Callback callback; + Function> mapper; + String indexName; + long dataSize = 0; + long total = 0; + + BulkRequestProcessor(String indexName, Function> mapper, IndexService proxyImpl, Callback callback) { + this.indexName = indexName; + this.proxyImpl = proxyImpl; + this.mapper = mapper; + this.callback = callback; + } + + Optional processItem(String id, T item) throws IOException { + if(item != null) { + int size = indexerObjectMapper.writeValueAsBytes(item).length; + + // We need to split the batch into smaller size to avoid data too large error in ElasticSearch, + // the limit is 10mb, so to make check before document add and push batch if size is too big + // + // dataSize = 0 is init case, just in case we have a very big doc that exceed the limit + // and we have not add it to the bulkRequest, hardcode to 5M which should be safe, + // usually it is 5M - 15M + // + if (dataSize + size > IndexServiceImpl.this.getBatchSize() && dataSize != 0) { + if (callback != null) { + callback.onProgress(String.format("Execute batch as bulk request is big enough %s", dataSize + size)); + } + + dataSize = 0; + bulkRequest = new BulkRequest.Builder(); + + return Optional.of(reduceResponse(proxyImpl.executeBulk(bulkRequest, mapper, callback))); + } + // Add item to bulk request to Elasticsearch + bulkRequest.operations(op -> op + .index(idx -> idx + .id(id) + .index(indexName) + .document(item) + ) + ); + dataSize += size; + total++; + + if (callback != null) { + callback.onProgress( + String.format( + "Add uuid %s to batch, batch size is %s, total is %s", + id, + dataSize, + total) + ); + } + } + return Optional.empty(); + } + + Optional flush() throws IOException { + return Optional.of(reduceResponse(proxyImpl.executeBulk(bulkRequest, mapper, callback))); + } + } + public IndexServiceImpl(ElasticsearchClient elasticClient, ObjectMapper indexerObjectMapper) { this.elasticClient = elasticClient; this.indexerObjectMapper = indexerObjectMapper; @@ -41,6 +114,10 @@ public static BulkResponse reduceResponse(BulkResponse in) { BulkResponse.of(f -> f.items(errors).errors(true).took(in.took())); } + @Override + public long getBatchSize() { + return 5242880; + } /** * Keep retry until success, it is ok to insert docs to elastic again because we use _id as identifier. * In case any service is not available, we will keep retry many times, with 100 retry we try 25 mins which is @@ -109,4 +186,5 @@ public BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Function> indexMetadata(String metadataValues) throws IOException, FactoryException, TransformException, JAXBException; ResponseEntity deleteDocumentByUUID(String uuid) throws IOException; List indexAllMetadataRecordsFromGeoNetwork(String beginWithUuid, boolean confirm, Callback callback) throws IOException; diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java index 2d061286..0333867f 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java @@ -332,11 +332,9 @@ public List indexAllMetadataRecordsFromGeoNetwork( } }; - BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); List results = new ArrayList<>(); + BulkRequestProcessor bulkRequestProcessor = new BulkRequestProcessor<>(indexName, mapper, self, callback); - long dataSize = 0; - long total = 0; // We need to keep sending messages to client to avoid timeout on long processing ExecutorService executor = Executors.newFixedThreadPool(2); @@ -387,56 +385,24 @@ public List indexAllMetadataRecordsFromGeoNetwork( final StacCollectionModel mappedMetadataValues = value.get(); if(mappedMetadataValues != null) { - int size = indexerObjectMapper.writeValueAsBytes(mappedMetadataValues).length; - - // We need to split the batch into smaller size to avoid data too large error in ElasticSearch, - // the limit is 10mb, so to make check before document add and push batch if size is too big - // - // dataSize = 0 is init case, just in case we have a very big doc that exceed the limit - // and we have not add it to the bulkRequest, hardcode to 5M which should be safe, - // usually it is 5M - 15M - // - if (dataSize + size > 5242880 && dataSize != 0) { - if (callback != null) { - callback.onProgress(String.format("Execute batch as bulk request is big enough %s", dataSize + size)); - } - - results.add(reduceResponse(self.executeBulk(bulkRequest, mapper, callback))); - - dataSize = 0; - bulkRequest = new BulkRequest.Builder(); - } - // Add item to bulk request to Elasticsearch - bulkRequest.operations(op -> op - .index(idx -> idx - .id(mappedMetadataValues.getUuid()) - .index(indexName) - .document(mappedMetadataValues) - ) - ); - dataSize += size; - total++; - - if (callback != null) { - callback.onProgress( - String.format( - "Add uuid %s to batch, batch size is %s, total is %s", - mappedMetadataValues.getUuid(), - dataSize, - total) - ); - } + bulkRequestProcessor + .processItem(mappedMetadataValues.getUuid(), mappedMetadataValues) + .ifPresent(results::add); } } } // In case there are residual, just report error - BulkResponse temp = reduceResponse(self.executeBulk(bulkRequest, mapper, callback)); - results.add(temp); + bulkRequestProcessor + .flush() + .ifPresent(response -> { + results.add(response); + + if(callback != null) { + callback.onComplete(response); + } + }); - if(callback != null) { - callback.onComplete(temp); - } // TODO now processing for record_suggestions index log.info("Finished execute bulk indexing records to index: {}",indexName); diff --git a/indexer/src/main/resources/config_files/dataset_index_schema.json b/indexer/src/main/resources/config_files/data_index_schema.json similarity index 80% rename from indexer/src/main/resources/config_files/dataset_index_schema.json rename to indexer/src/main/resources/config_files/data_index_schema.json index 6e427ea2..968566fb 100644 --- a/indexer/src/main/resources/config_files/dataset_index_schema.json +++ b/indexer/src/main/resources/config_files/data_index_schema.json @@ -14,11 +14,8 @@ "type": "date", "format": "yyyy-MM-dd" }, - "longitude": { - "type": "float" - }, - "latitude": { - "type": "float" + "location": { + "type": "geo_shape" }, "depth": { "type": "float" From aaa53954c0afeddd223d7d451ac6ed0d0c9b2d50 Mon Sep 17 00:00:00 2001 From: rng Date: Tue, 7 Jan 2025 17:33:38 +1100 Subject: [PATCH 3/8] Bug fix --- .../java/au/org/aodn/esindexer/service/IndexServiceImpl.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java index f1533366..0448f0be 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java @@ -64,10 +64,12 @@ Optional processItem(String id, T item) throws IOException { callback.onProgress(String.format("Execute batch as bulk request is big enough %s", dataSize + size)); } + Optional result = Optional.of(reduceResponse(proxyImpl.executeBulk(bulkRequest, mapper, callback))); + dataSize = 0; bulkRequest = new BulkRequest.Builder(); - return Optional.of(reduceResponse(proxyImpl.executeBulk(bulkRequest, mapper, callback))); + return result; } // Add item to bulk request to Elasticsearch bulkRequest.operations(op -> op From 10cfa8ef68dda709cb42bdaadfc0c212917281a4 Mon Sep 17 00:00:00 2001 From: rng Date: Thu, 9 Jan 2025 15:29:05 +1100 Subject: [PATCH 4/8] Refactor and checkpoint on add test case --- geonetwork4-api/pom.xml | 5 + .../metadata/geonetwork}/GeoNetworkField.java | 2 +- .../configuration/DatasetAccessConfig.java | 15 +- .../controller/IndexerController.java | 30 +- .../aodn/esindexer/model/DatasetProvider.java | 5 +- .../au/org/aodn/esindexer/model/Datum.java | 40 +- .../org/aodn/esindexer/model/MediaType.java | 17 - .../aodn/esindexer/model/RelationType.java | 2 +- .../aodn/esindexer/model/TemporalExtent.java | 28 +- .../esindexer/service/DataAccessService.java | 9 +- .../service/DataAccessServiceImpl.java | 59 +- .../IndexCloudOptimizedServiceImpl.java | 58 +- .../esindexer/service/IndexServiceImpl.java | 32 +- .../service/StacCollectionMapperService.java | 15 +- .../utils/AssociatedRecordsUtil.java | 4 +- .../src/main/resources/application-dev.yaml | 3 - indexer/src/main/resources/application.yaml | 4 + .../config_files/data_index_schema.json | 2 +- .../configuration/CommonTestConfig.java | 21 + .../DatasetAccessTestConfig.java | 19 + .../org/aodn/esindexer/model/MockServer.java | 13 + .../esindexer/model/TemporalExtentTest.java | 25 + .../service/DataAccessServiceIT.java | 79 + .../service/GeoNetworkServiceIT.java | 2 +- .../2024-01.json | 106893 +++++++++++++++ .../2024-02.json | 61074 ++++++++ .../aodn/stac/configuration/AppConstants.java | 6 +- .../au/org/aodn/stac/model/AssetModel.java | 48 + .../aodn/stac/model/StacCollectionModel.java | 2 +- .../au/org/aodn/stac/model/StacItemModel.java | 75 + 30 files changed, 168430 insertions(+), 157 deletions(-) rename {indexer/src/main/java/au/org/aodn/esindexer/model => geonetwork4-api/src/main/java/au/org/aodn/metadata/geonetwork}/GeoNetworkField.java (72%) delete mode 100644 indexer/src/main/java/au/org/aodn/esindexer/model/MediaType.java create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/configuration/CommonTestConfig.java create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/configuration/DatasetAccessTestConfig.java create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/model/MockServer.java create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/model/TemporalExtentTest.java create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java create mode 100644 indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json create mode 100644 indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json create mode 100644 stacmodel/src/main/java/au/org/aodn/stac/model/AssetModel.java create mode 100644 stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java diff --git a/geonetwork4-api/pom.xml b/geonetwork4-api/pom.xml index 288016de..7c5e2e1d 100644 --- a/geonetwork4-api/pom.xml +++ b/geonetwork4-api/pom.xml @@ -28,6 +28,11 @@ org.glassfish.jaxb jaxb-runtime + + org.projectlombok + lombok + true + diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java b/geonetwork4-api/src/main/java/au/org/aodn/metadata/geonetwork/GeoNetworkField.java similarity index 72% rename from indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java rename to geonetwork4-api/src/main/java/au/org/aodn/metadata/geonetwork/GeoNetworkField.java index 7da75110..8fa66f6d 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java +++ b/geonetwork4-api/src/main/java/au/org/aodn/metadata/geonetwork/GeoNetworkField.java @@ -1,4 +1,4 @@ -package au.org.aodn.esindexer.model; +package au.org.aodn.metadata.geonetwork; import lombok.Getter; diff --git a/indexer/src/main/java/au/org/aodn/esindexer/configuration/DatasetAccessConfig.java b/indexer/src/main/java/au/org/aodn/esindexer/configuration/DatasetAccessConfig.java index 6e88bfdf..c6439dcd 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/configuration/DatasetAccessConfig.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/configuration/DatasetAccessConfig.java @@ -1,17 +1,24 @@ package au.org.aodn.esindexer.configuration; +import au.org.aodn.esindexer.service.DataAccessService; import au.org.aodn.esindexer.service.DataAccessServiceImpl; +import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; +import org.springframework.web.client.RestTemplate; @Configuration public class DatasetAccessConfig { - @Bean(name = "DataAccessService") + @Bean + @ConditionalOnMissingBean(DataAccessService.class) public DataAccessServiceImpl createDataAccessService( - @Value("${dataaccess.host:defaultForTesting}") String serverUrl - ){ - return new DataAccessServiceImpl(serverUrl); + @Value("${dataaccess.host:http://localhost:5000}") String serverUrl, + @Value("${dataaccess.baseUrl:/api/v1/das/}") String baseUrl, + @Autowired RestTemplate template){ + + return new DataAccessServiceImpl(serverUrl, baseUrl, template); } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java b/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java index 4215510d..cc32fec4 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/controller/IndexerController.java @@ -1,5 +1,6 @@ package au.org.aodn.esindexer.controller; +import au.org.aodn.esindexer.model.TemporalExtent; import au.org.aodn.esindexer.service.DataAccessService; import au.org.aodn.esindexer.service.GeoNetworkService; import au.org.aodn.esindexer.service.IndexCloudOptimizedService; @@ -20,6 +21,7 @@ import org.springframework.web.servlet.mvc.method.annotation.SseEmitter; import java.io.IOException; +import java.time.LocalDate; import java.util.ArrayList; import java.util.List; import java.util.concurrent.CompletableFuture; @@ -160,20 +162,26 @@ public ResponseEntity deleteDocumentByUUID(@PathVariable("uuid") String @PostMapping(path="/{uuid}/dataset", produces = "application/json") @Operation(security = {@SecurityRequirement(name = "X-API-Key") }, description = "Index a dataset by UUID") - public ResponseEntity> indexDatasetByUUID(@PathVariable("uuid") String uuid) { + public ResponseEntity indexDatasetByUUID(@PathVariable("uuid") String uuid) { - var temporalExtents = dataAccessService.getTemporalExtentOf(uuid); - var startDate = temporalExtents.getStartDate(); - var endDate = temporalExtents.getEndDate(); - log.info("Indexing dataset with UUID: {} from {} to {}", uuid, startDate, endDate); + List temporalExtents = dataAccessService.getTemporalExtentOf(uuid); + if(!temporalExtents.isEmpty()) { + // Only first block works from dataservice api + LocalDate startDate = temporalExtents.get(0).getLocalStartDate(); + LocalDate endDate = temporalExtents.get(0).getLocalEndDate(); + log.info("Indexing dataset with UUID: {} from {} to {}", uuid, startDate, endDate); - var responses = indexCloudOptimizedData.indexCloudOptimizedData(uuid, startDate, endDate); + var responses = indexCloudOptimizedData.indexCloudOptimizedData(uuid, startDate, endDate); - List result = new ArrayList<>(); - for (BulkResponse response : responses) { - result.add(response.toString()); - } + List result = new ArrayList<>(); + for (BulkResponse response : responses) { + result.add(response.toString()); + } - return ResponseEntity.ok(result); + return ResponseEntity.ok(result); + } + else { + return ResponseEntity.notFound().build(); + } } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java index fd3aae2b..23ca176d 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java @@ -5,7 +5,6 @@ import java.time.LocalDate; import java.time.YearMonth; -import java.util.Arrays; import java.util.Iterator; import java.util.List; import java.util.NoSuchElementException; @@ -40,11 +39,11 @@ public DatasetEsEntry next() { throw new NoSuchElementException(); } - List data = Arrays.stream(dataAccessService.getIndexingDatasetBy( + List data = dataAccessService.getIndexingDatasetBy( uuid, LocalDate.of(currentYearMonth.getYear(), currentYearMonth.getMonthValue(), 1), LocalDate.of(currentYearMonth.getYear(), currentYearMonth.getMonthValue(), currentYearMonth.lengthOfMonth()) - )).toList(); + ); currentYearMonth = currentYearMonth.plusMonths(1); if (data.isEmpty()) { return null; diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java b/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java index 0a403d5a..929d1d95 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java @@ -5,6 +5,9 @@ import com.fasterxml.jackson.annotation.JsonProperty; import lombok.Data; +import java.util.Objects; +import java.util.Optional; + // If more fields are needed to be filtered, please add more columns here // and don't forget updating the override equals() method @Data @@ -42,17 +45,34 @@ public boolean equals(Object obj) { if (this == obj) { return true; } - if (obj == null || getClass() != obj.getClass()) { + else if (obj instanceof Datum that) { + int compareLong = Optional + .ofNullable(that.longitude) + .orElse(Double.NEGATIVE_INFINITY) + .compareTo(Optional.ofNullable(longitude) + .orElse(Double.NEGATIVE_INFINITY)); + + int compareLat = Optional + .ofNullable(that.latitude) + .orElse(Double.NEGATIVE_INFINITY) + .compareTo(Optional.ofNullable(latitude) + .orElse(Double.NEGATIVE_INFINITY)); + + int compareDepth = Optional + .ofNullable(that.depth) + .orElse(Double.NEGATIVE_INFINITY) + .compareTo(Optional.ofNullable(depth) + .orElse(Double.NEGATIVE_INFINITY)); + + boolean compareTime = Objects.equals(that.time, time); + + return compareLong == 0 && + compareLat == 0 && + compareDepth == 0 && + compareTime; + } + else { return false; } - Datum that = (Datum) obj; - - return Double.compare(that.longitude, longitude) == 0 && - Double.compare(that.latitude, latitude) == 0 && - Double.compare( - that.depth != null? that.depth : 0.0, - depth != null? depth : 0.0 - ) == 0 && - time.equals(that.time); } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/MediaType.java b/indexer/src/main/java/au/org/aodn/esindexer/model/MediaType.java deleted file mode 100644 index b1253621..00000000 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/MediaType.java +++ /dev/null @@ -1,17 +0,0 @@ -package au.org.aodn.esindexer.model; - -import lombok.Getter; - -@Getter -public enum MediaType { - TEXT_HTML("text/html"), - IMAGE_PNG("image/png"), - APPLICATION_JSON("application/json"), - ; - - private final String value; - - MediaType(String value) { - this.value = value; - } -} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/RelationType.java b/indexer/src/main/java/au/org/aodn/esindexer/model/RelationType.java index 74869845..546072b3 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/RelationType.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/RelationType.java @@ -1,7 +1,7 @@ package au.org.aodn.esindexer.model; import lombok.Getter; - +// TODO: Should use some lib provide value or move it to stacmodel folder @Getter public enum RelationType { SELF("self"), diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/TemporalExtent.java b/indexer/src/main/java/au/org/aodn/esindexer/model/TemporalExtent.java index eac9d51d..31af6f39 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/TemporalExtent.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/TemporalExtent.java @@ -1,23 +1,35 @@ package au.org.aodn.esindexer.model; +import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; +import lombok.Builder; +import lombok.Getter; +import lombok.Setter; import java.time.LocalDate; +import java.time.ZonedDateTime; import java.time.format.DateTimeFormatter; +@Builder +@Setter +@Getter public class TemporalExtent{ + + static DateTimeFormatter DATE_FORMAT = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ssZ"); + @JsonProperty("start_date") - String startDate; + protected String startDate; + @JsonProperty("end_date") - String endDate; + protected String endDate; - public LocalDate getStartDate() { - DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd"); - return LocalDate.parse(startDate, formatter); + @JsonIgnore + public LocalDate getLocalStartDate() { + return ZonedDateTime.parse(startDate, DATE_FORMAT).toLocalDate(); } - public LocalDate getEndDate() { - DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd"); - return LocalDate.parse(endDate, formatter); + @JsonIgnore + public LocalDate getLocalEndDate() { + return ZonedDateTime.parse(endDate, DATE_FORMAT).toLocalDate(); } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java index cb782643..061aff70 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java @@ -4,12 +4,9 @@ import au.org.aodn.esindexer.model.TemporalExtent; import java.time.LocalDate; +import java.util.List; public interface DataAccessService { - Datum[] getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate); - String getServiceUrl(); - void setServiceUrl(String url); - - - TemporalExtent getTemporalExtentOf(String uuid); + List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate); + List getTemporalExtentOf(String uuid); } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java index 73f81e14..3a3779cd 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java @@ -3,7 +3,8 @@ import au.org.aodn.esindexer.exception.MetadataNotFoundException; import au.org.aodn.esindexer.model.Datum; import au.org.aodn.esindexer.model.TemporalExtent; -import org.springframework.beans.factory.annotation.Autowired; +import lombok.Getter; +import org.springframework.core.ParameterizedTypeReference; import org.springframework.http.*; import org.springframework.web.client.HttpClientErrorException; import org.springframework.web.client.RestTemplate; @@ -15,29 +16,19 @@ import java.util.List; import java.util.Map; +@Getter public class DataAccessServiceImpl implements DataAccessService { - private String serverUrl; + protected String accessEndPoint; + protected RestTemplate restTemplate; - @Override - public String getServiceUrl() { - return serverUrl; - } - - @Override - public void setServiceUrl(String url) { - this.serverUrl = url; + public DataAccessServiceImpl(String serverUrl, String baseUrl, RestTemplate restTemplate) { + this.accessEndPoint = serverUrl + baseUrl; + this.restTemplate = restTemplate; } - public DataAccessServiceImpl(String serverUrl) { - setServiceUrl(serverUrl); - } - - @Autowired - private RestTemplate restTemplate; - @Override - public Datum[] getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate) { + public List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate) { // currently, we force to get data in the same year to simplify the logic if (startDate.getYear() != endDate.getYear()) { @@ -57,33 +48,31 @@ public Datum[] getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate .buildAndExpand(uuid) .toUriString(); - ResponseEntity responseEntity = restTemplate.exchange( + ResponseEntity> responseEntity = restTemplate.exchange( url, HttpMethod.GET, request, - Datum[].class, + new ParameterizedTypeReference<>() {}, params ); if (responseEntity.getStatusCode().is2xxSuccessful()) { - List data = new ArrayList<>(); if (responseEntity.getBody() != null) { - data = List.of(responseEntity.getBody()); + return aggregateData(responseEntity.getBody()); } - var dataToIndex = aggregateData(data); - return dataToIndex.toArray(new Datum[0]); } throw new RuntimeException("Unable to retrieve dataset with UUID: " + uuid ); - - } catch (HttpClientErrorException.NotFound e) { + } + catch (HttpClientErrorException.NotFound e) { throw new MetadataNotFoundException("Unable to find dataset with UUID: " + uuid + " in GeoNetwork"); - } catch (Exception e) { + } + catch (Exception e) { throw new RuntimeException("Exception thrown while retrieving dataset with UUID: " + uuid + e.getMessage(), e); } } @Override - public TemporalExtent getTemporalExtentOf(String uuid) { + public List getTemporalExtentOf(String uuid) { try { HttpEntity request = getRequestEntity(null, null); @@ -94,11 +83,11 @@ public TemporalExtent getTemporalExtentOf(String uuid) { .buildAndExpand(uuid) .toUriString(); - ResponseEntity responseEntity = restTemplate.exchange( + ResponseEntity> responseEntity = restTemplate.exchange( url, HttpMethod.GET, request, - TemporalExtent.class, + new ParameterizedTypeReference<>() {}, params ); @@ -110,13 +99,12 @@ public TemporalExtent getTemporalExtentOf(String uuid) { throw new RuntimeException("Exception thrown while retrieving dataset with UUID: " + uuid + e.getMessage(), e); } } - /** * Summarize the data by counting the number if all the concerned fields are the same * @param data the data to summarize * @return the summarized data */ - private List aggregateData(List data) { + protected List aggregateData(List data) { var aggregatedData = new ArrayList(); for (var datum: data) { if (aggregatedData.contains(datum)) { @@ -129,11 +117,10 @@ private List aggregateData(List data) { return aggregatedData; } - private String getDataAccessEndpoint() { - return getServiceUrl() + "/api/v1/das/"; + protected String getDataAccessEndpoint() { + return this.accessEndPoint; } - // parameters are not in use for now. May be useful in the future so just keep it protected HttpEntity getRequestEntity(MediaType accept, String body) { HttpHeaders headers = new HttpHeaders(); @@ -143,6 +130,6 @@ protected HttpEntity getRequestEntity(MediaType accept, String body) { MediaType.valueOf("application/*+json"), MediaType.ALL )); - return body == null ? new org.springframework.http.HttpEntity<>(headers) : new org.springframework.http.HttpEntity<>(body, headers); + return body == null ? new HttpEntity<>(headers) : new HttpEntity<>(body, headers); } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java index c6305411..763ca2b1 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java @@ -1,8 +1,8 @@ package au.org.aodn.esindexer.service; +import au.org.aodn.esindexer.model.DatasetEsEntry; import au.org.aodn.esindexer.model.DatasetProvider; import co.elastic.clients.elasticsearch.ElasticsearchClient; -import co.elastic.clients.elasticsearch.core.BulkRequest; import co.elastic.clients.elasticsearch.core.BulkResponse; import com.fasterxml.jackson.databind.ObjectMapper; import lombok.extern.slf4j.Slf4j; @@ -26,7 +26,7 @@ public class IndexCloudOptimizedServiceImpl extends IndexServiceImpl implements protected DataAccessService dataAccessService; protected ObjectMapper indexerObjectMapper; - protected String datasetIndexName; + protected String indexName; @Lazy @Autowired @@ -34,53 +34,49 @@ public class IndexCloudOptimizedServiceImpl extends IndexServiceImpl implements @Autowired public IndexCloudOptimizedServiceImpl( - @Value("${elasticsearch.dataset_index.name}") String datasetIndexName, + @Value("${elasticsearch.dataset_index.name}") String indexName, @Qualifier("portalElasticsearchClient") ElasticsearchClient elasticsearchClient, ObjectMapper indexerObjectMapper, DataAccessService dataAccessService) { super(elasticsearchClient, indexerObjectMapper); - this.datasetIndexName = datasetIndexName; + this.indexName = indexName; this.indexerObjectMapper = indexerObjectMapper; this.dataAccessService = dataAccessService; } - - // TODO: Refactor this method later since it uses similar logic as indexAllMetadataRecordsFromGeoNetwork + /** + * + * @param uuid + * @param startDate + * @param endDate + * @return + */ @Override public List indexCloudOptimizedData(String uuid, LocalDate startDate, LocalDate endDate) { - BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); List responses = new ArrayList<>(); - long dataSize = 0; - final long maxSize = this.getBatchSize(); + Iterable dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); + BulkRequestProcessor bulkRequestProcessor = new BulkRequestProcessor<>( + indexName, (item) -> Optional.empty(),self, null + ); - var dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); try { - for (var entry : dataset) { - if (entry == null) { - continue; - } - log.info("add dataset into b with UUID: {} and yearMonth: {}", entry.uuid(), entry.yearMonth()); - - bulkRequest.operations(operation -> operation.index( - indexReq -> indexReq - .id(entry.uuid() + entry.yearMonth()) - .index(datasetIndexName) - .document(entry) - )); - dataSize += indexerObjectMapper.writeValueAsBytes(entry).length; - if (dataSize > maxSize) { - log.info("Execute bulk request as bulk request is big enough {}", dataSize); - responses.add(reduceResponse(self.executeBulk(bulkRequest, (item) -> Optional.empty(), null))); - dataSize = 0; - bulkRequest = new BulkRequest.Builder(); + for (DatasetEsEntry entry : dataset) { + if (entry != null) { + log.info("add dataset into b with UUID: {} and yearMonth: {}", entry.uuid(), entry.yearMonth()); + bulkRequestProcessor.processItem(entry.uuid(), entry) + .ifPresent(responses::add); } } - log.info("Finished execute bulk indexing records to index: {}", datasetIndexName); - responses.add(reduceResponse(self.executeBulk(bulkRequest, (item) -> Optional.empty(), null))); - } catch (Exception e) { + bulkRequestProcessor + .flush() + .ifPresent(responses::add); + + log.info("Finished execute bulk indexing records to index: {}", indexName); + } + catch (Exception e) { log.error("Failed", e); throw new RuntimeException("Exception thrown while indexing dataset with UUID: " + uuid + " | " + e.getMessage(), e); } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java index 0448f0be..2c77f682 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java @@ -7,6 +7,7 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import lombok.extern.slf4j.Slf4j; +import org.springframework.aop.support.AopUtils; import org.springframework.http.HttpStatus; import org.springframework.retry.annotation.Backoff; import org.springframework.retry.annotation.Retryable; @@ -33,19 +34,32 @@ public abstract class IndexServiceImpl implements IndexService { * @param */ protected class BulkRequestProcessor { - BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); - IndexService proxyImpl; - Callback callback; - Function> mapper; - String indexName; - long dataSize = 0; - long total = 0; - + private final IndexService proxyImpl; + private final Callback callback; + private final Function> mapper; + private final String indexName; + + private BulkRequest.Builder bulkRequest = new BulkRequest.Builder(); + private long dataSize = 0; + private long total = 0; + /** + * A class the use to write request by batch to improve writing speed and not to flood the Elastic by too many call. + * @param indexName - The elastic index name that store the output json. + * @param mapper - An optional mapper to find the original object from source given some input + * @param proxyImpl - Must be a IndexService wrapper by the proxy so that the @Retryable call of the executeBulk can be use + * @param callback - A callback to the front end to avoid timeout on aws gateway on long run process + */ BulkRequestProcessor(String indexName, Function> mapper, IndexService proxyImpl, Callback callback) { this.indexName = indexName; - this.proxyImpl = proxyImpl; this.mapper = mapper; this.callback = callback; + + if(AopUtils.isAopProxy(proxyImpl) || AopUtils.isJdkDynamicProxy(proxyImpl)) { + this.proxyImpl = proxyImpl; + } + else { + throw new RuntimeException("Spring AOP component expected, please pass the Autowrired instance"); + } } Optional processItem(String id, T item) throws IOException { diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/StacCollectionMapperService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/StacCollectionMapperService.java index 95b7a5b2..e5d02c15 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/StacCollectionMapperService.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/StacCollectionMapperService.java @@ -1,12 +1,11 @@ package au.org.aodn.esindexer.service; import au.org.aodn.esindexer.utils.AssociatedRecordsUtil; -import au.org.aodn.esindexer.model.GeoNetworkField; -import au.org.aodn.esindexer.model.MediaType; import au.org.aodn.esindexer.model.RelationType; import au.org.aodn.esindexer.utils.*; import au.org.aodn.stac.model.*; +import au.org.aodn.metadata.geonetwork.GeoNetworkField; import au.org.aodn.metadata.iso19115_3_2018.*; import au.org.aodn.stac.util.JsonUtil; import jakarta.xml.bind.JAXBElement; @@ -15,6 +14,7 @@ import org.mapstruct.*; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; +import org.springframework.http.MediaType; import org.springframework.stereotype.Service; import java.io.IOException; @@ -26,7 +26,6 @@ import java.util.regex.Pattern; import java.util.stream.Collectors; -import static au.org.aodn.esindexer.model.GeoNetworkField.*; import static au.org.aodn.esindexer.utils.CommonUtils.safeGet; import static au.org.aodn.esindexer.utils.StringUtil.capitalizeFirstLetter; @@ -318,14 +317,14 @@ List> mapSummariesTemporal(MDMetadataType source) { String mapSummariesCreation(MDMetadataType source) { var dateSources = MapperUtils.findMDDateInfo(source); var dateMap = getMetadataDateInfoFrom(dateSources); - return safeGet(() -> dateMap.get(creation)).orElse(null); + return safeGet(() -> dateMap.get(GeoNetworkField.creation)).orElse(null); } @Named("mapSummaries.revision") String mapSummariesRevision(MDMetadataType source) { var dateSources = MapperUtils.findMDDateInfo(source); var dateMap = getMetadataDateInfoFrom(dateSources); - return safeGet(() -> dateMap.get(revision)).orElse(null); + return safeGet(() -> dateMap.get(GeoNetworkField.revision)).orElse(null); } private HashMap getMetadataDateInfoFrom(List dateSources) { @@ -640,7 +639,7 @@ else if (LinkUtils.isWfs(protocol)) { LinkModel linkModel = LinkModel.builder() .href(url) .rel(RelationType.DESCRIBEDBY.getValue()) - .type(MediaType.TEXT_HTML.getValue()) + .type(MediaType.TEXT_HTML.toString()) .title("Full metadata link") .build(); results.add(linkModel); @@ -708,7 +707,7 @@ private LinkModel getLicenseGraphic(MDLegalConstraintsType legalConstraints) { return graphic.map(graphicUrl -> LinkModel.builder() .href(graphicUrl) .rel(RelationType.LICENSE.getValue()) - .type(MediaType.IMAGE_PNG.getValue()) + .type(MediaType.IMAGE_PNG.toString()) .build()).orElse(null); } @@ -728,7 +727,7 @@ private LinkModel getLicenseUrl(MDLegalConstraintsType legalConstraints) { return LinkModel.builder() .href(url.get()) .rel(RelationType.LICENSE.getValue()) - .type(MediaType.TEXT_HTML.getValue()) + .type(MediaType.TEXT_HTML.toString()) .build(); } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/utils/AssociatedRecordsUtil.java b/indexer/src/main/java/au/org/aodn/esindexer/utils/AssociatedRecordsUtil.java index 378c023b..b08ca1d2 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/utils/AssociatedRecordsUtil.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/utils/AssociatedRecordsUtil.java @@ -1,9 +1,9 @@ package au.org.aodn.esindexer.utils; -import au.org.aodn.esindexer.model.MediaType; import au.org.aodn.esindexer.model.RelationType; import au.org.aodn.stac.model.LinkModel; import au.org.aodn.stac.util.JsonUtil; +import org.springframework.http.MediaType; import java.util.*; @@ -55,7 +55,7 @@ private static LinkModel buildLink(Map record, RelationType rela .href(href) .rel(relationType.getValue()) .title(JsonUtil.toJsonString(titleWithAbstract)) - .type(MediaType.APPLICATION_JSON.getValue()) + .type(MediaType.APPLICATION_JSON.toString()) .build(); }).orElse(null); } diff --git a/indexer/src/main/resources/application-dev.yaml b/indexer/src/main/resources/application-dev.yaml index 10891bab..d0a56878 100644 --- a/indexer/src/main/resources/application-dev.yaml +++ b/indexer/src/main/resources/application-dev.yaml @@ -19,9 +19,6 @@ geonetwork: index: "records" endpoint: /geonetwork/srv/api/search -dataaccess: - host: http://localhost:5000 - logging: level: au.org.aodn.indexer: DEBUG diff --git a/indexer/src/main/resources/application.yaml b/indexer/src/main/resources/application.yaml index ebaf6972..c73d4f18 100644 --- a/indexer/src/main/resources/application.yaml +++ b/indexer/src/main/resources/application.yaml @@ -53,6 +53,10 @@ geonetwork: index: "records" endpoint: /geonetwork/srv/api/search +dataaccess: + host: http://localhost:5000 + baseUrl: "/api/v1/das/" + springdoc: api-docs: enabled: true diff --git a/indexer/src/main/resources/config_files/data_index_schema.json b/indexer/src/main/resources/config_files/data_index_schema.json index 968566fb..3b9de990 100644 --- a/indexer/src/main/resources/config_files/data_index_schema.json +++ b/indexer/src/main/resources/config_files/data_index_schema.json @@ -1,7 +1,7 @@ { "mappings": { "properties": { - "uuid": { + "id": { "type": "keyword" }, "year_month": { diff --git a/indexer/src/test/java/au/org/aodn/esindexer/configuration/CommonTestConfig.java b/indexer/src/test/java/au/org/aodn/esindexer/configuration/CommonTestConfig.java new file mode 100644 index 00000000..9db48c14 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/configuration/CommonTestConfig.java @@ -0,0 +1,21 @@ +package au.org.aodn.esindexer.configuration; + +import au.org.aodn.esindexer.model.MockServer; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.http.client.SimpleClientHttpRequestFactory; +import org.springframework.test.web.client.MockRestServiceServer; +import org.springframework.web.client.RestTemplate; + +@Configuration +public class CommonTestConfig { + + @Bean + public MockServer createMockServer() { + RestTemplate template = new RestTemplate(new SimpleClientHttpRequestFactory()); + return MockServer.builder() + .server(MockRestServiceServer.createServer(template)) + .restTemplate(template) + .build(); + } +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/configuration/DatasetAccessTestConfig.java b/indexer/src/test/java/au/org/aodn/esindexer/configuration/DatasetAccessTestConfig.java new file mode 100644 index 00000000..5b619cb0 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/configuration/DatasetAccessTestConfig.java @@ -0,0 +1,19 @@ +package au.org.aodn.esindexer.configuration; + +import au.org.aodn.esindexer.model.MockServer; +import au.org.aodn.esindexer.service.DataAccessServiceImpl; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +@Configuration +public class DatasetAccessTestConfig { + /** + * + * @return A bean with rest template mocked, so we need to + */ + @Bean + public DataAccessServiceImpl createDataAccessService(MockServer serviceServer){ + return new DataAccessServiceImpl("http://localhost", "/api/v1/das/", serviceServer.getRestTemplate()); + } + +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/model/MockServer.java b/indexer/src/test/java/au/org/aodn/esindexer/model/MockServer.java new file mode 100644 index 00000000..defe84d7 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/model/MockServer.java @@ -0,0 +1,13 @@ +package au.org.aodn.esindexer.model; + +import lombok.Builder; +import lombok.Getter; +import org.springframework.test.web.client.MockRestServiceServer; +import org.springframework.web.client.RestTemplate; + +@Getter +@Builder +public class MockServer { + protected MockRestServiceServer server; + protected RestTemplate restTemplate; +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/model/TemporalExtentTest.java b/indexer/src/test/java/au/org/aodn/esindexer/model/TemporalExtentTest.java new file mode 100644 index 00000000..b463b3b9 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/model/TemporalExtentTest.java @@ -0,0 +1,25 @@ +package au.org.aodn.esindexer.model; + +import org.junit.jupiter.api.Test; + +import java.time.LocalDate; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +public class TemporalExtentTest { + + @Test + public void verifyTemporalExtent() { + TemporalExtent temporalExtent = TemporalExtent.builder() + .startDate("2020-09-01T00:00:00+0000") + .endDate("2024-06-01T00:00:00+0000") + .build(); + + // No error on calling getLocalDate so parse correct + LocalDate d = temporalExtent.getLocalStartDate(); + assertNotNull(d); + + d = temporalExtent.getLocalEndDate(); + assertNotNull(d); + } +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java new file mode 100644 index 00000000..61a9b7b1 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java @@ -0,0 +1,79 @@ +package au.org.aodn.esindexer.service; + +import au.org.aodn.esindexer.controller.IndexerController; +import au.org.aodn.esindexer.model.MockServer; +import au.org.aodn.esindexer.model.TemporalExtent; +import org.junit.jupiter.api.MethodOrderer; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.TestInstance; +import org.junit.jupiter.api.TestMethodOrder; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpMethod; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.test.context.ActiveProfiles; +import org.testcontainers.shaded.com.fasterxml.jackson.databind.ObjectMapper; + +import java.io.IOException; +import java.util.List; + +import static au.org.aodn.esindexer.BaseTestClass.readResourceFile; +import static org.springframework.test.web.client.ExpectedCount.once; +import static org.springframework.test.web.client.match.MockRestRequestMatchers.method; +import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo; +import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess; + +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +@ActiveProfiles("test") +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +@TestInstance(TestInstance.Lifecycle.PER_CLASS) +public class DataAccessServiceIT { + + @Autowired + protected MockServer mockServer; + + @Autowired + protected IndexerController controller; + + protected ObjectMapper objectMapper = new ObjectMapper(); + + @Test + public void verifyConversion1() throws IOException { + try { + // This set the time range of the mock data range. + TemporalExtent temporalExtent = TemporalExtent.builder() + .startDate("2024-01-01T00:00:00+0000") + .endDate("2024-04-01T00:00:00+0000") + .build(); + + mockServer.getServer().expect(once(), requestTo("http://localhost/api/v1/das/data/35234913-aa3c-48ec-b9a4-77f822f66ef8/temporal_extent")) + .andExpect(method(HttpMethod.GET)) + .andRespond(withSuccess(objectMapper.writeValueAsString(List.of(temporalExtent)), MediaType.APPLICATION_JSON)); + + // Mimic the api call given the range above + String canned_2024_01= readResourceFile("classpath:canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json"); + mockServer.getServer().expect(once(), requestTo("http://localhost/api/v1/das/data/35234913-aa3c-48ec-b9a4-77f822f66ef8?is_to_index=true&start_date=2024-01-01&end_date=2024-01-31")) + .andExpect(method(HttpMethod.GET)) + .andRespond(withSuccess(canned_2024_01, MediaType.APPLICATION_JSON)); + + String canned_2024_02= readResourceFile("classpath:canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json"); + mockServer.getServer().expect(once(), requestTo("http://localhost/api/v1/das/data/35234913-aa3c-48ec-b9a4-77f822f66ef8?is_to_index=true&start_date=2024-02-01&end_date=2024-02-29")) + .andExpect(method(HttpMethod.GET)) + .andRespond(withSuccess(canned_2024_02, MediaType.APPLICATION_JSON)); + + mockServer.getServer().expect(once(), requestTo("http://localhost/api/v1/das/data/35234913-aa3c-48ec-b9a4-77f822f66ef8?is_to_index=true&start_date=2024-03-01&end_date=2024-03-31")) + .andExpect(method(HttpMethod.GET)) + .andRespond(withSuccess("[]", MediaType.APPLICATION_JSON)); + + mockServer.getServer().expect(once(), requestTo("http://localhost/api/v1/das/data/35234913-aa3c-48ec-b9a4-77f822f66ef8?is_to_index=true&start_date=2024-04-01&end_date=2024-04-30")) + .andExpect(method(HttpMethod.GET)) + .andRespond(withSuccess("[]", MediaType.APPLICATION_JSON)); + + ResponseEntity v = controller.indexDatasetByUUID("35234913-aa3c-48ec-b9a4-77f822f66ef8"); + } + finally { + mockServer.getServer().reset(); + } + } +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java b/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java index 713ac89d..6e7684c9 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java @@ -5,8 +5,8 @@ import au.org.aodn.esindexer.configuration.GeoNetworkSearchTestConfig; import au.org.aodn.esindexer.exception.MetadataNotFoundException; -import au.org.aodn.esindexer.utils.AssociatedRecordsUtil; import au.org.aodn.esindexer.model.RelationType; +import au.org.aodn.esindexer.utils.AssociatedRecordsUtil; import au.org.aodn.esindexer.utils.JaxbUtils; import au.org.aodn.metadata.iso19115_3_2018.MDMetadataType; import co.elastic.clients.elasticsearch.ElasticsearchClient; diff --git a/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json new file mode 100644 index 00000000..1e4c862b --- /dev/null +++ b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json @@ -0,0 +1,106893 @@ +[ + { + "TIME": "2024-01-28 14:07:00", + "LATITUDE": -33.02584, + "LONGITUDE": 153.684, + "DEPTH": 912.95, + "DEPTH_quality_control": 9.0, + "TEMP": 6.73, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240128T140700Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1704067200, + "polygon": "01030000000100000005000000000000000020624000000000008041C0000000000060634000000000008041C0000000000060634000000000000039C0000000000020624000000000000039C0000000000020624000000000008041C0" + }, + { + "TIME": "2024-01-28 14:07:00", + "LATITUDE": -33.02584, + "LONGITUDE": 153.684, + "DEPTH": 913.68, + "DEPTH_quality_control": 9.0, + "TEMP": 6.72, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240128T140700Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1704067200, + "polygon": "01030000000100000005000000000000000020624000000000008041C0000000000060634000000000008041C0000000000060634000000000000039C0000000000020624000000000000039C0000000000020624000000000008041C0" + }, + { + "TIME": "2024-01-28 14:07:00", + "LATITUDE": -33.02584, + "LONGITUDE": 153.684, + "DEPTH": 914.41, + "DEPTH_quality_control": 9.0, + "TEMP": 6.71, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240128T140700Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1704067200, + "polygon": "01030000000100000005000000000000000020624000000000008041C0000000000060634000000000008041C0000000000060634000000000000039C0000000000020624000000000000039C0000000000020624000000000008041C0" + }, + { + "TIME": "2024-01-28 14:07:00", + "LATITUDE": -33.02584, + "LONGITUDE": 153.684, + "DEPTH": 915.13, + "DEPTH_quality_control": 9.0, + "TEMP": 6.7, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240128T140700Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1704067200, + "polygon": "01030000000100000005000000000000000020624000000000008041C0000000000060634000000000008041C0000000000060634000000000000039C0000000000020624000000000000039C0000000000020624000000000008041C0" + }, + { + "TIME": "2024-01-28 14:07:00", + "LATITUDE": -33.02584, + "LONGITUDE": 153.684, + "DEPTH": 915.86, + "DEPTH_quality_control": 9.0, + "TEMP": 6.69, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240128T140700Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1704067200, + "polygon": "01030000000100000005000000000000000020624000000000008041C0000000000060634000000000008041C0000000000060634000000000000039C0000000000020624000000000000039C0000000000020624000000000008041C0" + }, + { + "TIME": "2024-01-28 14:07:00", + "LATITUDE": -33.02584, + "LONGITUDE": 153.684, + "DEPTH": 916.59, + "DEPTH_quality_control": 9.0, + "TEMP": 6.68, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + 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"2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 443.02, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 443.72, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 444.42, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 445.12, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 445.82, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 446.52, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 447.22, + "DEPTH_quality_control": 9.0, + "TEMP": 9.6, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 447.91, + "DEPTH_quality_control": 9.0, + "TEMP": 9.59, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 448.61, + "DEPTH_quality_control": 9.0, + "TEMP": 9.59, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 449.31, + "DEPTH_quality_control": 9.0, + "TEMP": 9.59, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 450.01, + "DEPTH_quality_control": 9.0, + "TEMP": 9.59, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 450.71, + "DEPTH_quality_control": 9.0, + "TEMP": 9.59, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 451.41, + "DEPTH_quality_control": 9.0, + "TEMP": 9.59, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 452.11, + "DEPTH_quality_control": 9.0, + "TEMP": 9.58, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + }, + { + "TIME": "2024-02-01 07:50:00", + "LATITUDE": -33.89783, + "LONGITUDE": 171.00021, + "DEPTH": 452.8, + "DEPTH_quality_control": 9.0, + "TEMP": 9.58, + "TEMP_quality_control": 1.0, + "imo_number": 9358022, + "ship_name": "Pacific-Sun", + "Callsign": "9HA2479", + "filename": "IMOS_SOOP-XBT_T_20240201T075000Z_PX34_FV00_ID_9358022.nc", + "XBT_line": "PX34", + "timestamp": 1706745600, + "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" + } +] \ No newline at end of file diff --git a/stacmodel/src/main/java/au/org/aodn/stac/configuration/AppConstants.java b/stacmodel/src/main/java/au/org/aodn/stac/configuration/AppConstants.java index f26e0a6c..5573a13b 100644 --- a/stacmodel/src/main/java/au/org/aodn/stac/configuration/AppConstants.java +++ b/stacmodel/src/main/java/au/org/aodn/stac/configuration/AppConstants.java @@ -1,9 +1,7 @@ package au.org.aodn.stac.configuration; -import java.util.Arrays; -import java.util.List; - public interface AppConstants { String STAC_VERSION = "1.0.0"; - String STAC_TYPE = "Collection"; + String STAC_COLLECTION = "Collection"; + String STAC_FEATURE = "Feature"; } diff --git a/stacmodel/src/main/java/au/org/aodn/stac/model/AssetModel.java b/stacmodel/src/main/java/au/org/aodn/stac/model/AssetModel.java new file mode 100644 index 00000000..a0cd09dc --- /dev/null +++ b/stacmodel/src/main/java/au/org/aodn/stac/model/AssetModel.java @@ -0,0 +1,48 @@ +package au.org.aodn.stac.model; + +import com.fasterxml.jackson.annotation.JsonInclude; +import lombok.Builder; +import lombok.Data; + +@Data +@Builder +@JsonInclude(JsonInclude.Include.NON_NULL) +public class AssetModel { + // https://github.com/radiantearth/stac-spec/blob/master/best-practices.md#list-of-asset-roles + public enum Role { + DATA("data"), + METADATA("metadata"), + THUMBNAIL("thumbnail"), + OVERVIEW("overview"), + VISUAL("visual"), + DATE("date"), + GRAPHIC("graphic"), + DATA_MASK("data-mask"), + SNOW_ICE("snow-ice"), + LAND_WATER("land-water"), + WATER_MASK("water-mask"), + ISO_19115("iso-19115"); + + private final String role; + + Role(String role) { + this.role = role; + } + + @Override + public String toString() { + return role; + } + } + /** + * REQUIRED. URI to the asset object. Relative and absolute URI are both allowed. Trailing slashes are significant. + */ + protected String href; + protected String title; + protected String description; + protected String type; + /** + * The semantic roles of the asset, similar to the use of rel in links. + */ + protected Role role; +} diff --git a/stacmodel/src/main/java/au/org/aodn/stac/model/StacCollectionModel.java b/stacmodel/src/main/java/au/org/aodn/stac/model/StacCollectionModel.java index 3f0df2c6..f8b87194 100644 --- a/stacmodel/src/main/java/au/org/aodn/stac/model/StacCollectionModel.java +++ b/stacmodel/src/main/java/au/org/aodn/stac/model/StacCollectionModel.java @@ -42,7 +42,7 @@ public String getStacVersion() { @JsonProperty("type") public String getType() { - return AppConstants.STAC_TYPE; + return AppConstants.STAC_COLLECTION; } @JsonProperty("stac_extensions") diff --git a/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java b/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java new file mode 100644 index 00000000..c15fcd13 --- /dev/null +++ b/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java @@ -0,0 +1,75 @@ +package au.org.aodn.stac.model; + +import au.org.aodn.stac.configuration.AppConstants; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.annotation.JsonProperty; +import lombok.Builder; +import lombok.Data; + +import java.math.BigDecimal; +import java.util.List; +import java.util.Map; + +@Data +@Builder +@JsonInclude(JsonInclude.Include.NON_NULL) +public class StacItemModel { + + @JsonProperty("type") + public String getType() { + return AppConstants.STAC_FEATURE; + } + /** + * REQUIRED. Provider identifier. The ID should be unique within the Collection that contains the Item. + */ + @JsonProperty("id") + protected String uuid; + /** + * REQUIRED. Defines the full footprint of the asset represented by this item, formatted according to RFC 7946, + * section 3.1 if a geometry is provided or section 3.2 if no geometry is provided. + * Use to generate the vector tile, the STAC format is not optimized and hard to work with for Elastic search + */ + @JsonProperty("geometry") + protected Map geometry; + /** + * REQUIRED if geometry is not null, prohibited if geometry is null. Bounding Box of the asset represented by + * this Item, formatted according to RFC 7946, section 5. + */ + @JsonProperty("bbox") + protected List> bbox; + /** + * REQUIRED. A dictionary of additional metadata for the Item. + */ + @JsonProperty("properties") + protected Map properties; + /** + * REQUIRED. List of link objects to resources and related URLs. See the best practices for details on when the + * use self links is strongly recommended. + */ + protected List links; + + protected Map assets; + /** + * The id of the STAC Collection this Item references to. This field is required if a link with a collection relation type is present and is not allowed otherwise. + */ + @JsonProperty("collection") + protected String collection; + + @JsonProperty("stac_version") + public String getStacVersion() { + return AppConstants.STAC_VERSION; + } + + @JsonProperty("stac_extensions") + public String[] getStacExtension() { + return new String[] { + "https://stac-extensions.github.io/scientific/v1.0.0/schema.json", + "https://stac-extensions.github.io/contacts/v0.1.1/schema.json", + "https://stac-extensions.github.io/projection/v1.1.0/schema.json", + "https://stac-extensions.github.io/language/v1.0.0/schema.json", + "https://stac-extensions.github.io/themes/v1.0.0/schema.json", + "https://stac-extensions.github.io/web-map-links/v1.2.0/schema.json" + }; + } + +} From de067842059b6fcb4f2bb298df6282aad7d2bb0b Mon Sep 17 00:00:00 2001 From: rng Date: Fri, 10 Jan 2025 13:46:52 +1100 Subject: [PATCH 5/8] Add first test to the cloud optimized data and refactor --- .../esindexer/model/CloudOptimizedEntry.java | 115 ++++++++++++++++++ .../CloudOptimizedEntryReducePrecision.java | 50 ++++++++ .../aodn/esindexer/model/DatasetEsEntry.java | 2 +- .../aodn/esindexer/model/DatasetProvider.java | 22 ++-- .../au/org/aodn/esindexer/model/Datum.java | 78 ------------ .../esindexer/service/DataAccessService.java | 4 +- .../service/DataAccessServiceImpl.java | 60 ++++++--- .../IndexCloudOptimizedServiceImpl.java | 28 +++-- .../esindexer/service/IndexServiceImpl.java | 7 +- .../aodn/esindexer/utils/GeometryUtils.java | 38 ++++++ .../service/DataAccessServiceTest.java | 84 +++++++++++++ .../esindexer/utils/GeometryUtilsTest.java | 31 ++++- 12 files changed, 395 insertions(+), 124 deletions(-) create mode 100644 indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java create mode 100644 indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java delete mode 100644 indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java new file mode 100644 index 00000000..a2fb5417 --- /dev/null +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java @@ -0,0 +1,115 @@ +package au.org.aodn.esindexer.model; + +import com.fasterxml.jackson.annotation.*; +import lombok.Data; + +import java.time.LocalDateTime; +import java.time.ZoneOffset; +import java.time.ZonedDateTime; +import java.time.format.DateTimeFormatter; +import java.time.temporal.Temporal; +import java.util.Objects; +import java.util.Optional; + +/** + * A container that represent the data entry from cloud optimize, if you add fields, please + * update the hashCode() and equals() + */ +@Data +@JsonInclude(JsonInclude.Include.NON_NULL) +@JsonIgnoreProperties(ignoreUnknown = true) +public class CloudOptimizedEntry { + + @JsonIgnore + protected DateTimeFormatter DATE_FORMATTER = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss"); + + @JsonIgnore + protected Temporal time; + + @JsonIgnore + protected Double longitude; + + @JsonIgnore + protected Double latitude; + + @JsonIgnore + protected Double depth; + + @JsonIgnore + public ZonedDateTime getZonedDateTime() { + return ((LocalDateTime)this.time).atZone(ZoneOffset.UTC); + } + + @JsonProperty("DEPTH") + public void setDepth(Double v) { + this.depth = v; + } + + @JsonProperty("LONGITUDE") + public void setLongitude(Double v) { + this.longitude = v; + } + + @JsonProperty("LATITUDE") + public void setLatitude(Double v) { + this.latitude = v; + } + + @JsonProperty("TIME") + public void setTime(String time) { + this.time = LocalDateTime.parse(time, DATE_FORMATTER); + } + /** + * Must use function as child class may override functions + * @return - The hashcode + */ + @Override + public int hashCode() { + return Objects.hash( + this.getTime(), + this.getLongitude(), + this.getLatitude(), + this.getDepth() + ); + } + /** + * Must use function as child class may override functions + * @param obj - Input + * @return - Compare result + */ + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + else if (obj instanceof CloudOptimizedEntry that) { + int compareLong = Optional + .ofNullable(that.getLongitude()) + .orElse(Double.NEGATIVE_INFINITY) + .compareTo(Optional.ofNullable(getLongitude()) + .orElse(Double.NEGATIVE_INFINITY)); + + int compareLat = Optional + .ofNullable(that.getLatitude()) + .orElse(Double.NEGATIVE_INFINITY) + .compareTo(Optional.ofNullable(getLatitude()) + .orElse(Double.NEGATIVE_INFINITY)); + + int compareDepth = Optional + .ofNullable(that.getDepth()) + .orElse(Double.NEGATIVE_INFINITY) + .compareTo(Optional.ofNullable(getDepth()) + .orElse(Double.NEGATIVE_INFINITY)); + + boolean compareTime = Objects.equals(that.getTime(), getTime()); + + return compareLong == 0 && + compareLat == 0 && + compareDepth == 0 && + compareTime; + } + else { + return false; + } + } +} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java new file mode 100644 index 00000000..d9ca3bbe --- /dev/null +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java @@ -0,0 +1,50 @@ +package au.org.aodn.esindexer.model; + +import java.math.BigDecimal; +import java.math.RoundingMode; +import java.time.LocalDateTime; +import java.time.YearMonth; +import java.time.ZoneOffset; +import java.time.ZonedDateTime; + +/** + * This class modified the time entry and consider the Year and Month only, and reduce precision it is used + * later to aggregate data based on year ond month only + */ +public class CloudOptimizedEntryReducePrecision extends CloudOptimizedEntry { + + @Override + public void setTime(String time) { + LocalDateTime l = LocalDateTime.parse(time, DATE_FORMATTER); + this.time = YearMonth.of(l.getYear(), l.getMonth()); + } + + @Override + public void setLongitude(Double v) { + super.setLongitude(new BigDecimal(v).setScale(2, RoundingMode.HALF_UP).doubleValue()); + } + + @Override + public void setLatitude(Double v) { + super.setLatitude(new BigDecimal(v).setScale(2, RoundingMode.HALF_UP).doubleValue()); + } + /** + * Round to 10 digit not decimal place + * @param v - Input + */ + @Override + public void setDepth(Double v) { + super.setDepth(new BigDecimal(v / 10).setScale(0, RoundingMode.HALF_UP).doubleValue() * 10); + } + /** + * Return a zoned datetime in this case because we use YearMonth internally, we set the day to 1 and all time zero + * @return - A ZonedDateTime at day 1 time 0 + */ + @Override + public ZonedDateTime getZonedDateTime() { + return ((YearMonth)this.time) + .atDay(1) + .atTime(0,0,0) + .atZone(ZoneOffset.UTC); + } +} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetEsEntry.java b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetEsEntry.java index 5b91fc98..f8514fe6 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetEsEntry.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetEsEntry.java @@ -5,6 +5,6 @@ public record DatasetEsEntry( String uuid, String yearMonth, - List data) { + List data) { } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java index 23ca176d..a593d174 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java @@ -1,6 +1,9 @@ package au.org.aodn.esindexer.model; import au.org.aodn.esindexer.service.DataAccessService; +import au.org.aodn.stac.model.StacItemModel; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.springframework.util.StopWatch; import java.time.LocalDate; @@ -11,10 +14,11 @@ public class DatasetProvider { - private final String uuid; - private YearMonth currentYearMonth; - private final YearMonth endYearMonth; - private final DataAccessService dataAccessService; + protected Logger log = LoggerFactory.getLogger(DatasetProvider.class); + protected final String uuid; + protected YearMonth currentYearMonth; + protected final YearMonth endYearMonth; + protected final DataAccessService dataAccessService; public DatasetProvider(String uuid, LocalDate startDate, LocalDate endDate, DataAccessService dataAccessService) { this.uuid = uuid; @@ -23,7 +27,7 @@ public DatasetProvider(String uuid, LocalDate startDate, LocalDate endDate, Data this.endYearMonth = YearMonth.from(endDate); } - public Iterable getIterator() { + public Iterable> getIterator() { return () -> new Iterator<>() { @Override public boolean hasNext() { @@ -31,7 +35,7 @@ public boolean hasNext() { } @Override - public DatasetEsEntry next() { + public List next() { // please keep it for a while since it benefits the performance optimisation StopWatch timer = new StopWatch(); timer.start("Data querying"); @@ -39,7 +43,7 @@ public DatasetEsEntry next() { throw new NoSuchElementException(); } - List data = dataAccessService.getIndexingDatasetBy( + List data = dataAccessService.getIndexingDatasetBy( uuid, LocalDate.of(currentYearMonth.getYear(), currentYearMonth.getMonthValue(), 1), LocalDate.of(currentYearMonth.getYear(), currentYearMonth.getMonthValue(), currentYearMonth.lengthOfMonth()) @@ -50,8 +54,8 @@ public DatasetEsEntry next() { } timer.stop(); - System.out.println(timer.prettyPrint()); - return new DatasetEsEntry(uuid, currentYearMonth.toString(), data); + log.info(timer.prettyPrint()); + return data; } }; } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java b/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java deleted file mode 100644 index 929d1d95..00000000 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/Datum.java +++ /dev/null @@ -1,78 +0,0 @@ -package au.org.aodn.esindexer.model; - -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -import java.util.Objects; -import java.util.Optional; - -// If more fields are needed to be filtered, please add more columns here -// and don't forget updating the override equals() method -@Data -@JsonInclude(JsonInclude.Include.NON_NULL) -public class Datum { - - private String time; - private Double longitude; - private Double latitude; - private Double depth; - - private long count; - - @JsonCreator - public Datum( - @JsonProperty("time") String time, - @JsonProperty("longitude") Double longitude, - @JsonProperty("latitude") Double latitude, - @JsonProperty("depth") Double depth) { - this.time = time; - this.longitude = longitude; - this.latitude = latitude; - this.depth = depth; - this.count = 1L; - } - - // putting all same record into one instance and increment the count is more efficient - public void incrementCount() { - count++; - } - - // Don't include variable "count" in the equals() method. - @Override - public boolean equals(Object obj) { - if (this == obj) { - return true; - } - else if (obj instanceof Datum that) { - int compareLong = Optional - .ofNullable(that.longitude) - .orElse(Double.NEGATIVE_INFINITY) - .compareTo(Optional.ofNullable(longitude) - .orElse(Double.NEGATIVE_INFINITY)); - - int compareLat = Optional - .ofNullable(that.latitude) - .orElse(Double.NEGATIVE_INFINITY) - .compareTo(Optional.ofNullable(latitude) - .orElse(Double.NEGATIVE_INFINITY)); - - int compareDepth = Optional - .ofNullable(that.depth) - .orElse(Double.NEGATIVE_INFINITY) - .compareTo(Optional.ofNullable(depth) - .orElse(Double.NEGATIVE_INFINITY)); - - boolean compareTime = Objects.equals(that.time, time); - - return compareLong == 0 && - compareLat == 0 && - compareDepth == 0 && - compareTime; - } - else { - return false; - } - } -} diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java index 061aff70..4030d211 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessService.java @@ -1,12 +1,12 @@ package au.org.aodn.esindexer.service; -import au.org.aodn.esindexer.model.Datum; import au.org.aodn.esindexer.model.TemporalExtent; +import au.org.aodn.stac.model.StacItemModel; import java.time.LocalDate; import java.util.List; public interface DataAccessService { - List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate); + List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate); List getTemporalExtentOf(String uuid); } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java index 3a3779cd..49e3b72a 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java @@ -1,8 +1,11 @@ package au.org.aodn.esindexer.service; import au.org.aodn.esindexer.exception.MetadataNotFoundException; -import au.org.aodn.esindexer.model.Datum; +import au.org.aodn.esindexer.model.CloudOptimizedEntry; +import au.org.aodn.esindexer.model.CloudOptimizedEntryReducePrecision; import au.org.aodn.esindexer.model.TemporalExtent; +import au.org.aodn.esindexer.utils.GeometryUtils; +import au.org.aodn.stac.model.StacItemModel; import lombok.Getter; import org.springframework.core.ParameterizedTypeReference; import org.springframework.http.*; @@ -11,10 +14,11 @@ import org.springframework.web.util.UriComponentsBuilder; import java.time.LocalDate; -import java.util.ArrayList; +import java.time.format.DateTimeFormatter; import java.util.HashMap; import java.util.List; import java.util.Map; +import java.util.stream.Collectors; @Getter public class DataAccessServiceImpl implements DataAccessService { @@ -28,7 +32,7 @@ public DataAccessServiceImpl(String serverUrl, String baseUrl, RestTemplate rest } @Override - public List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate) { + public List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalDate endDate) { // currently, we force to get data in the same year to simplify the logic if (startDate.getYear() != endDate.getYear()) { @@ -48,7 +52,7 @@ public List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalD .buildAndExpand(uuid) .toUriString(); - ResponseEntity> responseEntity = restTemplate.exchange( + ResponseEntity> responseEntity = restTemplate.exchange( url, HttpMethod.GET, request, @@ -58,7 +62,7 @@ public List getIndexingDatasetBy(String uuid, LocalDate startDate, LocalD if (responseEntity.getStatusCode().is2xxSuccessful()) { if (responseEntity.getBody() != null) { - return aggregateData(responseEntity.getBody()); + return toStacItemModel(uuid, aggregateData(responseEntity.getBody())); } } throw new RuntimeException("Unable to retrieve dataset with UUID: " + uuid ); @@ -104,17 +108,41 @@ public List getTemporalExtentOf(String uuid) { * @param data the data to summarize * @return the summarized data */ - protected List aggregateData(List data) { - var aggregatedData = new ArrayList(); - for (var datum: data) { - if (aggregatedData.contains(datum)) { - var existingDatum = aggregatedData.get(aggregatedData.indexOf(datum)); - existingDatum.incrementCount(); - } else { - aggregatedData.add(datum); - } - } - return aggregatedData; + protected Map aggregateData(List data) { + return data.parallelStream() + .collect(Collectors.groupingBy( + d -> d, + Collectors.counting() + )); + } + /** + * Group and count the entries based on user object equals/hashcode + * @param uuid - The parent uuid that associate with input + * @param data - The aggregated data + * @return + */ + protected List toStacItemModel(String uuid, Map data) { + return data.entrySet().parallelStream() + .filter(d -> d.getKey().getLongitude() != null && d.getKey().getLatitude() != null) + .map(d -> + StacItemModel.builder() + .collection(uuid) // collection point to the uuid of parent + .uuid(String + .join("|", + uuid, + d.getKey().getTime().toString(), + d.getKey().getLongitude().toString(), + d.getKey().getLatitude().toString(), + d.getKey().getDepth().toString() + ) + ) + .geometry(GeometryUtils.createGeoJson(d.getKey().getLongitude(), d.getKey().getLatitude(), d.getKey().getDepth())) + .properties(Map.of( + "count", d.getValue(), + "time", d.getKey().getZonedDateTime().format(DateTimeFormatter.ISO_ZONED_DATE_TIME))) + .build() + ) + .toList(); } protected String getDataAccessEndpoint() { diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java index 763ca2b1..49d711f6 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexCloudOptimizedServiceImpl.java @@ -1,7 +1,7 @@ package au.org.aodn.esindexer.service; -import au.org.aodn.esindexer.model.DatasetEsEntry; import au.org.aodn.esindexer.model.DatasetProvider; +import au.org.aodn.stac.model.StacItemModel; import co.elastic.clients.elasticsearch.ElasticsearchClient; import co.elastic.clients.elasticsearch.core.BulkResponse; import com.fasterxml.jackson.databind.ObjectMapper; @@ -46,28 +46,30 @@ public IndexCloudOptimizedServiceImpl( this.dataAccessService = dataAccessService; } /** - * - * @param uuid - * @param startDate - * @param endDate - * @return + * Index the cloud optimized data + * @param uuid - The UUID of data you want to index + * @param startDate - The start range to index + * @param endDate - THe end range to index + * @return - The index result */ @Override public List indexCloudOptimizedData(String uuid, LocalDate startDate, LocalDate endDate) { List responses = new ArrayList<>(); - Iterable dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); - BulkRequestProcessor bulkRequestProcessor = new BulkRequestProcessor<>( + Iterable> dataset = new DatasetProvider(uuid, startDate, endDate, dataAccessService).getIterator(); + BulkRequestProcessor bulkRequestProcessor = new BulkRequestProcessor<>( indexName, (item) -> Optional.empty(),self, null ); try { - for (DatasetEsEntry entry : dataset) { - if (entry != null) { - log.info("add dataset into b with UUID: {} and yearMonth: {}", entry.uuid(), entry.yearMonth()); - bulkRequestProcessor.processItem(entry.uuid(), entry) - .ifPresent(responses::add); + for (List entries : dataset) { + if (entries != null) { + for(StacItemModel entry: entries) { + log.debug("add dataset into b with UUID: {} and props: {}", entry.getUuid(), entry.getProperties()); + bulkRequestProcessor.processItem(entry.getUuid(), entry) + .ifPresent(responses::add); + } } } bulkRequestProcessor diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java index 2c77f682..f9c36103 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexServiceImpl.java @@ -110,7 +110,12 @@ Optional processItem(String id, T item) throws IOException { } Optional flush() throws IOException { - return Optional.of(reduceResponse(proxyImpl.executeBulk(bulkRequest, mapper, callback))); + if(total != 0) { + return Optional.of(reduceResponse(proxyImpl.executeBulk(bulkRequest, mapper, callback))); + } + else { + return Optional.empty(); + } } } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java b/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java index b20e9800..4788ffb6 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java @@ -101,6 +101,44 @@ public static synchronized void init() { throw new RuntimeException(ioe); } } + /** + * Although GeoJson point support 3D, however our target Elastic Search do not, so we need to use point2D plus + * a properties call depth. + * @param lng - lng + * @param lat - lat + * @param depth - depth + * @return + */ + public static Map createGeoJson(double lng, double lat, double depth) { + Point point = factory.createPoint(new Coordinate(lng, lat)); + + try (StringWriter writer = new StringWriter()) { + geometryJson.write(point, writer); + + Map values = objectMapper.readValue(writer.toString(), HashMap.class); + + if(values == null) { + logger.warn("Convert geometry to JSON result in null, {}", writer.toString()); + } + else { + logger.debug("Created geometry {}", values); + } + + Map feature = new HashMap<>(); + Map properties = new HashMap<>(); + + properties.put("depth", depth); + + feature.put("type", "Feature"); + feature.put("properties", properties); + feature.put("geometry", values); + + return feature; + } + catch(Exception e) { + return null; + } + } /** * @param polygons - Assume to be EPSG:4326, as GeoJson always use this encoding. * @return diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java new file mode 100644 index 00000000..ce64ef80 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java @@ -0,0 +1,84 @@ +package au.org.aodn.esindexer.service; + +import au.org.aodn.esindexer.model.CloudOptimizedEntry; +import au.org.aodn.esindexer.model.CloudOptimizedEntryReducePrecision; +import au.org.aodn.stac.model.StacItemModel; +import lombok.extern.slf4j.Slf4j; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.testcontainers.shaded.com.fasterxml.jackson.core.type.TypeReference; +import org.testcontainers.shaded.com.fasterxml.jackson.databind.ObjectMapper; + +import java.io.IOException; +import java.io.StringReader; +import java.util.List; +import java.util.Map; +import java.util.Optional; + +import static au.org.aodn.esindexer.BaseTestClass.readResourceFile; + +@Slf4j +public class DataAccessServiceTest { + + protected ObjectMapper objectMapper = new ObjectMapper(); + /** + * We test CloudOptimizedEntryReducePrecision to reduce precision so that we can group accordingly + * @throws IOException - Not expect to throw. + */ + @Test + public void verifyAggregateCorrect() throws IOException { + // Our test do not care, pass null is ok + DataAccessServiceImpl impl = new DataAccessServiceImpl(null, null, null); + String canned_2024_01= readResourceFile("classpath:canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json"); + + List l = objectMapper.readValue( + new StringReader(canned_2024_01), + new TypeReference>() {} + ); + Map result = impl.aggregateData(l); + + Assertions.assertEquals(478, result.size()); + + // Find a target object and check its count + CloudOptimizedEntryReducePrecision target = new CloudOptimizedEntryReducePrecision(); + target.setLongitude(155.0); + target.setLatitude(-33.21); + target.setDepth(500.0); + target.setTime("2024-01-28 00:12:12"); + + Assertions.assertEquals(14L, result.get(target), "Count is correct 1"); + + target.setDepth(530.0); + Assertions.assertEquals(15L, result.get(target), "Count is correct 2"); + } + + @Test + public void verifyToStacItemModel() throws IOException { + DataAccessServiceImpl impl = new DataAccessServiceImpl(null, null, null); + String canned_2024_01= readResourceFile("classpath:canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json"); + + List l = objectMapper.readValue( + new StringReader(canned_2024_01), + new TypeReference>() {} + ); + + Map result = impl.aggregateData(l); + List models = impl.toStacItemModel("35234913-aa3c-48ec-b9a4-77f822f66ef8", result); + + Assertions.assertEquals(270, models.size(), "Count correct"); + + // StacItemModel(uuid=35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.0, geometry={geometry={coordinates=[170.33, -33.87], type=Point}, type=Feature, properties={depth=530.0}}, bbox=null, properties={time=2024-02, count=15}, links=null, assets=null, collection=35234913-aa3c-48ec-b9a4-77f822f66ef8) + Optional t = models.stream() + .filter(f -> f.getUuid().equalsIgnoreCase("35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.0")) + .findFirst(); + + Assertions.assertTrue(t.isPresent(), "Target found"); + Assertions.assertEquals(15L, t.get().getProperties().get("count")); + + Assertions.assertNotNull(t.get().getGeometry().get("properties"), "geometry properties no null"); + Assertions.assertInstanceOf(Map.class, t.get().getGeometry().get("properties")); + + Map properties = (Map)t.get().getGeometry().get("properties"); + Assertions.assertEquals(530.0, properties.get("depth")); + } +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java b/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java index ebeda929..f8e0b28c 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java @@ -2,6 +2,7 @@ import au.org.aodn.metadata.iso19115_3_2018.MDMetadataType; import jakarta.xml.bind.JAXBException; +import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.locationtech.jts.geom.*; @@ -10,6 +11,7 @@ import java.io.IOException; import java.util.List; +import java.util.Map; import java.util.Objects; import static au.org.aodn.esindexer.BaseTestClass.readResourceFile; @@ -44,8 +46,8 @@ public void verifyLandStrippedFromSpatialExtents() throws IOException, JAXBExcep List> l = Objects.requireNonNull(withLand); - assertEquals(l.size(),1, "Land have 1 polygon array"); - assertEquals(l.get(0).size(),8, "Size 8 with land"); + assertEquals(1, l.size(), "Land have 1 polygon array"); + assertEquals(8, l.get(0).size(), "Size 8 with land"); Geometry le = l.get(0).get(0); Coordinate[] coors = le.getCoordinates(); @@ -70,7 +72,7 @@ public void verifyLandStrippedFromSpatialExtents() throws IOException, JAXBExcep List> nl = Objects.requireNonNull(noLand); - assertEquals(nl.size(),1, "No Land have 1 polygon array"); + assertEquals(1, nl.size(), "No Land have 1 polygon array"); assertEquals(11, nl.get(0).size(), "Size 11 with land"); Geometry nle = nl.get(0).get(0).getEnvelope(); @@ -114,7 +116,7 @@ public void verifyLandStrippedFromSpatialExtentsWithReducerOn() throws IOExcepti List> nl = Objects.requireNonNull(noLand); - assertEquals(nl.size(),1, "No Land have 1 polygon array"); + assertEquals(1, nl.size(), "No Land have 1 polygon array"); assertEquals(16, nl.get(0).size(), "Size 16 with land"); Geometry nle = nl.get(0).get(0).getEnvelope(); @@ -136,4 +138,25 @@ public void verifyLandStrippedFromSpatialExtentsWithReducerOn() throws IOExcepti assertEquals(118.0, ncoors[4].getX(), 0.00); assertEquals(-36.0, ncoors[4].getY(), 0.00); } + + @Test + public void verifyCreateJsonPoint() { + Map item = GeometryUtils.createGeoJson(1.2, 2.2, 3.0); + + Assertions.assertNotNull(item); + Assertions.assertEquals("Feature", item.get("type")); + Assertions.assertInstanceOf(Map.class, item.get("geometry")); + + Map geometry = (Map)item.get("geometry"); + Assertions.assertInstanceOf(List.class, geometry.get("coordinates")); + + Assertions.assertInstanceOf(List.class, geometry.get("coordinates")); + List coors = (List)geometry.get("coordinates"); + Assertions.assertEquals(1.2, coors.get(0)); + Assertions.assertEquals(2.2, coors.get(1)); + + Assertions.assertInstanceOf(Map.class, item.get("properties")); + Map properties = (Map)item.get("properties"); + Assertions.assertEquals(3.0, properties.get("depth")); + } } From c8bea365b7af0594bec17ec6cd70b867d4a3f470 Mon Sep 17 00:00:00 2001 From: rng Date: Fri, 10 Jan 2025 16:44:45 +1100 Subject: [PATCH 6/8] Add IT test to check output result --- .../esindexer/model/CloudOptimizedEntry.java | 27 ++++++------ .../CloudOptimizedEntryReducePrecision.java | 12 ++++-- .../aodn/esindexer/model/DatasetProvider.java | 2 +- .../service/DataAccessServiceImpl.java | 6 +-- .../service/IndexerMetadataService.java | 1 + .../service/IndexerMetadataServiceImpl.java | 4 ++ .../aodn/esindexer/utils/GeometryUtils.java | 11 ++--- .../config_files/data_index_schema.json | 41 ++++++++++++------- .../service/DataAccessServiceIT.java | 34 ++++++++++++--- .../service/DataAccessServiceTest.java | 6 ++- .../esindexer/utils/GeometryUtilsTest.java | 7 +++- .../StacItem1.json | 31 ++++++++++++++ .../au/org/aodn/stac/model/StacItemModel.java | 2 +- 13 files changed, 135 insertions(+), 49 deletions(-) create mode 100644 indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/StacItem1.json diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java index a2fb5417..8aaafed6 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntry.java @@ -3,6 +3,7 @@ import com.fasterxml.jackson.annotation.*; import lombok.Data; +import java.math.BigDecimal; import java.time.LocalDateTime; import java.time.ZoneOffset; import java.time.ZonedDateTime; @@ -20,6 +21,8 @@ @JsonIgnoreProperties(ignoreUnknown = true) public class CloudOptimizedEntry { + static final BigDecimal MIN = new BigDecimal(Double.MIN_VALUE); + @JsonIgnore protected DateTimeFormatter DATE_FORMATTER = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss"); @@ -27,13 +30,13 @@ public class CloudOptimizedEntry { protected Temporal time; @JsonIgnore - protected Double longitude; + protected BigDecimal longitude; @JsonIgnore - protected Double latitude; + protected BigDecimal latitude; @JsonIgnore - protected Double depth; + protected BigDecimal depth; @JsonIgnore public ZonedDateTime getZonedDateTime() { @@ -42,17 +45,17 @@ public ZonedDateTime getZonedDateTime() { @JsonProperty("DEPTH") public void setDepth(Double v) { - this.depth = v; + this.depth = new BigDecimal(v); } @JsonProperty("LONGITUDE") public void setLongitude(Double v) { - this.longitude = v; + this.longitude = new BigDecimal(v); } @JsonProperty("LATITUDE") public void setLatitude(Double v) { - this.latitude = v; + this.latitude = new BigDecimal(v); } @JsonProperty("TIME") @@ -85,21 +88,21 @@ public boolean equals(Object obj) { else if (obj instanceof CloudOptimizedEntry that) { int compareLong = Optional .ofNullable(that.getLongitude()) - .orElse(Double.NEGATIVE_INFINITY) + .orElse(MIN) .compareTo(Optional.ofNullable(getLongitude()) - .orElse(Double.NEGATIVE_INFINITY)); + .orElse(MIN)); int compareLat = Optional .ofNullable(that.getLatitude()) - .orElse(Double.NEGATIVE_INFINITY) + .orElse(MIN) .compareTo(Optional.ofNullable(getLatitude()) - .orElse(Double.NEGATIVE_INFINITY)); + .orElse(MIN)); int compareDepth = Optional .ofNullable(that.getDepth()) - .orElse(Double.NEGATIVE_INFINITY) + .orElse(MIN) .compareTo(Optional.ofNullable(getDepth()) - .orElse(Double.NEGATIVE_INFINITY)); + .orElse(MIN)); boolean compareTime = Objects.equals(that.getTime(), getTime()); diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java index d9ca3bbe..59cf6bd6 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/CloudOptimizedEntryReducePrecision.java @@ -21,20 +21,24 @@ public void setTime(String time) { @Override public void setLongitude(Double v) { - super.setLongitude(new BigDecimal(v).setScale(2, RoundingMode.HALF_UP).doubleValue()); + this.longitude = new BigDecimal(v).setScale(2, RoundingMode.HALF_UP); } @Override public void setLatitude(Double v) { - super.setLatitude(new BigDecimal(v).setScale(2, RoundingMode.HALF_UP).doubleValue()); + this.latitude = new BigDecimal(v).setScale(2, RoundingMode.HALF_UP); } /** - * Round to 10 digit not decimal place + * Round to 10th position, with two decimal place so later parse will generate .00 * @param v - Input */ @Override public void setDepth(Double v) { - super.setDepth(new BigDecimal(v / 10).setScale(0, RoundingMode.HALF_UP).doubleValue() * 10); + this.depth = new BigDecimal(v) + .divide(BigDecimal.TEN, RoundingMode.HALF_UP) + .setScale(0, RoundingMode.HALF_UP) + .multiply(BigDecimal.TEN) + .setScale(2, RoundingMode.HALF_UP); } /** * Return a zoned datetime in this case because we use YearMonth internally, we set the day to 1 and all time zero diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java index a593d174..85903605 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/DatasetProvider.java @@ -38,7 +38,7 @@ public boolean hasNext() { public List next() { // please keep it for a while since it benefits the performance optimisation StopWatch timer = new StopWatch(); - timer.start("Data querying"); + timer.start(String.format("Data querying for %s %s", currentYearMonth.getYear(), currentYearMonth.getMonth())); if (!hasNext()) { throw new NoSuchElementException(); } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java index 49e3b72a..8d91b902 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/DataAccessServiceImpl.java @@ -109,7 +109,7 @@ public List getTemporalExtentOf(String uuid) { * @return the summarized data */ protected Map aggregateData(List data) { - return data.parallelStream() + return data.stream() .collect(Collectors.groupingBy( d -> d, Collectors.counting() @@ -119,10 +119,10 @@ protected Map aggregateData(List toStacItemModel(String uuid, Map data) { - return data.entrySet().parallelStream() + return data.entrySet().stream() .filter(d -> d.getKey().getLongitude() != null && d.getKey().getLatitude() != null) .map(d -> StacItemModel.builder() diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java index 3531b8d3..d7ca1536 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataService.java @@ -18,6 +18,7 @@ public interface IndexerMetadataService extends IndexService { ResponseEntity deleteDocumentByUUID(String uuid) throws IOException; List indexAllMetadataRecordsFromGeoNetwork(String beginWithUuid, boolean confirm, Callback callback) throws IOException; Hit getDocumentByUUID(String uuid) throws IOException; + Hit getDocumentByUUID(String uuid, String indexName) throws IOException; boolean isMetadataPublished(String uuid); boolean isGeoNetworkInstanceReinstalled(long portalIndexDocumentsCount); } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java index 0333867f..851148f2 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerMetadataServiceImpl.java @@ -96,6 +96,10 @@ public IndexerMetadataServiceImpl( } public Hit getDocumentByUUID(String uuid) throws IOException { + return getDocumentByUUID(uuid, indexName); + } + + public Hit getDocumentByUUID(String uuid, String indexName) throws IOException { try { SearchResponse response = portalElasticsearchClient .search(s -> s diff --git a/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java b/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java index 4788ffb6..ac74efa3 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/utils/GeometryUtils.java @@ -20,6 +20,7 @@ import org.opengis.feature.simple.SimpleFeature; import java.io.*; +import java.math.BigDecimal; import java.net.URL; import java.util.*; import java.util.function.BiFunction; @@ -107,10 +108,10 @@ public static synchronized void init() { * @param lng - lng * @param lat - lat * @param depth - depth - * @return + * @return - The map that represent the geoJson */ - public static Map createGeoJson(double lng, double lat, double depth) { - Point point = factory.createPoint(new Coordinate(lng, lat)); + public static Map createGeoJson(BigDecimal lng, BigDecimal lat, BigDecimal depth) { + Point point = factory.createPoint(new Coordinate(lng.doubleValue(), lat.doubleValue())); try (StringWriter writer = new StringWriter()) { geometryJson.write(point, writer); @@ -141,7 +142,7 @@ public static Map createGeoJson(double lng, double lat, double depth) { } /** * @param polygons - Assume to be EPSG:4326, as GeoJson always use this encoding. - * @return + * @return - Map that represent the geojson */ protected static Map createGeoJson(List> polygons) { @@ -375,7 +376,7 @@ protected static List> createGeometryWithoutLand(List createGeometryFrom(List> rawInput, Integer gridSize) { // The return polygon is in EPSG:4326, so we can call createGeoJson directly diff --git a/indexer/src/main/resources/config_files/data_index_schema.json b/indexer/src/main/resources/config_files/data_index_schema.json index 3b9de990..d520b2a5 100644 --- a/indexer/src/main/resources/config_files/data_index_schema.json +++ b/indexer/src/main/resources/config_files/data_index_schema.json @@ -4,24 +4,35 @@ "id": { "type": "keyword" }, - "year_month": { - "type": "keyword" + "stac_version": { "type": "text" }, + "stac_extensions": { "type": "text" }, + "type": { "type": "text" }, + "collection": { "type": "text" }, + "geometry": { + "type": "geo_shape" + }, + "bbox" : { + "type": "double" + }, + "properties" : { + "type": "nested", + "properties" : { + "count": { "type": "double" }, + "time": { "type": "date" } + } }, - "data": { + "links": { "type": "nested", "properties": { - "time": { - "type": "date", - "format": "yyyy-MM-dd" - }, - "location": { - "type": "geo_shape" - }, - "depth": { - "type": "float" - }, - "count": { - "type": "integer" + "link" : { + "type": "nested", + "properties": { + "href": { "type": "text" }, + "rel": { "type": "text" }, + "type": { "type": "text" }, + "title": { "type": "text" }, + "description": { "type": "text" } + } } } } diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java index 61a9b7b1..31131342 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceIT.java @@ -3,11 +3,14 @@ import au.org.aodn.esindexer.controller.IndexerController; import au.org.aodn.esindexer.model.MockServer; import au.org.aodn.esindexer.model.TemporalExtent; -import org.junit.jupiter.api.MethodOrderer; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.TestInstance; -import org.junit.jupiter.api.TestMethodOrder; +import co.elastic.clients.elasticsearch.core.search.Hit; +import com.fasterxml.jackson.databind.node.ObjectNode; +import org.json.JSONException; +import org.junit.jupiter.api.*; +import org.skyscreamer.jsonassert.JSONAssert; +import org.skyscreamer.jsonassert.JSONCompareMode; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.test.context.SpringBootTest; import org.springframework.http.HttpMethod; import org.springframework.http.MediaType; @@ -30,16 +33,25 @@ @TestInstance(TestInstance.Lifecycle.PER_CLASS) public class DataAccessServiceIT { + @Value("${elasticsearch.dataset_index.name}") + protected String INDEX_NAME; + @Autowired protected MockServer mockServer; @Autowired protected IndexerController controller; + @Autowired + protected IndexerMetadataService indexerService; + + @Autowired + protected ElasticSearchIndexService elasticSearchIndexService; + protected ObjectMapper objectMapper = new ObjectMapper(); @Test - public void verifyConversion1() throws IOException { + public void verifyConversion1() throws IOException, JSONException { try { // This set the time range of the mock data range. TemporalExtent temporalExtent = TemporalExtent.builder() @@ -71,6 +83,18 @@ public void verifyConversion1() throws IOException { .andRespond(withSuccess("[]", MediaType.APPLICATION_JSON)); ResponseEntity v = controller.indexDatasetByUUID("35234913-aa3c-48ec-b9a4-77f822f66ef8"); + + Assertions.assertInstanceOf(List.class, v.getBody()); + + // Insert value correctly + Assertions.assertTrue(v.getBody().toString().contains("\"errors\":false"), "Return result OK"); + Assertions.assertEquals(747L, elasticSearchIndexService.getDocumentsCount(INDEX_NAME), "Doc count correct"); + + Hit hit = indexerService.getDocumentByUUID("35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.00", INDEX_NAME); + + String stac1= readResourceFile("classpath:canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/StacItem1.json"); + Assertions.assertNotNull(hit.source(), "Source not null"); + JSONAssert.assertEquals(stac1, hit.source().toString(), JSONCompareMode.STRICT); } finally { mockServer.getServer().reset(); diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java index ce64ef80..6b5d498d 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/DataAccessServiceTest.java @@ -69,7 +69,7 @@ public void verifyToStacItemModel() throws IOException { // StacItemModel(uuid=35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.0, geometry={geometry={coordinates=[170.33, -33.87], type=Point}, type=Feature, properties={depth=530.0}}, bbox=null, properties={time=2024-02, count=15}, links=null, assets=null, collection=35234913-aa3c-48ec-b9a4-77f822f66ef8) Optional t = models.stream() - .filter(f -> f.getUuid().equalsIgnoreCase("35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.0")) + .filter(f -> f.getUuid().equalsIgnoreCase("35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.00")) .findFirst(); Assertions.assertTrue(t.isPresent(), "Target found"); @@ -79,6 +79,8 @@ public void verifyToStacItemModel() throws IOException { Assertions.assertInstanceOf(Map.class, t.get().getGeometry().get("properties")); Map properties = (Map)t.get().getGeometry().get("properties"); - Assertions.assertEquals(530.0, properties.get("depth")); + // The depth is a BigDecimal, so we do a toString() will force it print the .00 which is what we want + // to check it contains two decimal + Assertions.assertEquals("530.00", properties.get("depth").toString()); } } diff --git a/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java b/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java index f8e0b28c..d367af21 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java @@ -10,6 +10,7 @@ import org.slf4j.LoggerFactory; import java.io.IOException; +import java.math.BigDecimal; import java.util.List; import java.util.Map; import java.util.Objects; @@ -141,7 +142,11 @@ public void verifyLandStrippedFromSpatialExtentsWithReducerOn() throws IOExcepti @Test public void verifyCreateJsonPoint() { - Map item = GeometryUtils.createGeoJson(1.2, 2.2, 3.0); + Map item = GeometryUtils.createGeoJson( + BigDecimal.valueOf(1.2), + BigDecimal.valueOf(2.2), + BigDecimal.valueOf(3.0) + ); Assertions.assertNotNull(item); Assertions.assertEquals("Feature", item.get("type")); diff --git a/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/StacItem1.json b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/StacItem1.json new file mode 100644 index 00000000..4884862b --- /dev/null +++ b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/StacItem1.json @@ -0,0 +1,31 @@ +{ + "id": "35234913-aa3c-48ec-b9a4-77f822f66ef8|2024-02|170.33|-33.87|530.00", + "geometry": { + "geometry": { + "coordinates": [ + 170.33, + -33.87 + ], + "type": "Point" + }, + "type": "Feature", + "properties": { + "depth": 530.0 + } + }, + "properties": { + "count": 15, + "time": "2024-02-01T00:00:00Z" + }, + "collection": "35234913-aa3c-48ec-b9a4-77f822f66ef8", + "stac_version": "1.0.0", + "stac_extensions": [ + "https://stac-extensions.github.io/scientific/v1.0.0/schema.json", + "https://stac-extensions.github.io/contacts/v0.1.1/schema.json", + "https://stac-extensions.github.io/projection/v1.1.0/schema.json", + "https://stac-extensions.github.io/language/v1.0.0/schema.json", + "https://stac-extensions.github.io/themes/v1.0.0/schema.json", + "https://stac-extensions.github.io/web-map-links/v1.2.0/schema.json" + ], + "type": "Feature" +} diff --git a/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java b/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java index c15fcd13..aa352c5a 100644 --- a/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java +++ b/stacmodel/src/main/java/au/org/aodn/stac/model/StacItemModel.java @@ -30,7 +30,7 @@ public String getType() { * Use to generate the vector tile, the STAC format is not optimized and hard to work with for Elastic search */ @JsonProperty("geometry") - protected Map geometry; + protected Map geometry; /** * REQUIRED if geometry is not null, prohibited if geometry is null. Bounding Box of the asset represented by * this Item, formatted according to RFC 7946, section 5. From eea986380887a99514bb0220624fd60c770b1e33 Mon Sep 17 00:00:00 2001 From: rng Date: Fri, 10 Jan 2025 16:54:41 +1100 Subject: [PATCH 7/8] pre-commit fix --- .../35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json | 2 +- .../35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json index 1e4c862b..1c67e132 100644 --- a/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json +++ b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-01.json @@ -106890,4 +106890,4 @@ "timestamp": 1704067200, "polygon": "010300000001000000050000000000000000C0624000000000008041C0000000000000644000000000008041C0000000000000644000000000000039C00000000000C0624000000000000039C00000000000C0624000000000008041C0" } -] \ No newline at end of file +] diff --git a/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json index b9a2cba3..a4df4faa 100644 --- a/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json +++ b/indexer/src/test/resources/canned/dataservice/35234913-aa3c-48ec-b9a4-77f822f66ef8/2024-02.json @@ -61071,4 +61071,4 @@ "timestamp": 1706745600, "polygon": "010300000001000000050000000000000000A0644000000000008041C00000000000E0654000000000008041C00000000000E0654000000000000039C00000000000A0644000000000000039C00000000000A0644000000000008041C0" } -] \ No newline at end of file +] From 460b93ab076bb802f6ccd10d15de7d85163d64df Mon Sep 17 00:00:00 2001 From: rng Date: Fri, 10 Jan 2025 17:22:46 +1100 Subject: [PATCH 8/8] fix build error --- .../java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java b/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java index d367af21..0d26d668 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/utils/GeometryUtilsTest.java @@ -162,6 +162,6 @@ public void verifyCreateJsonPoint() { Assertions.assertInstanceOf(Map.class, item.get("properties")); Map properties = (Map)item.get("properties"); - Assertions.assertEquals(3.0, properties.get("depth")); + Assertions.assertEquals(BigDecimal.valueOf(3.0), properties.get("depth")); } }