From c17eeea5515ddf149f5a1f5a5824af7f031ea119 Mon Sep 17 00:00:00 2001 From: Syphax Date: Mon, 19 Aug 2024 07:52:10 +0200 Subject: [PATCH 1/4] fix response description field to be a list not a string --- .gitignore | 2 ++ pom.xml | 13 ++++++++++++- .../apigateway/controller/GatewayController.java | 2 +- .../apigateway/model/DynTransformResponse.java | 3 ++- .../apigateway/service/ConfigurationLoader.java | 1 + .../{ => search}/SearchLocalIndexerService.java | 15 +++++++++------ 6 files changed, 27 insertions(+), 9 deletions(-) rename src/main/java/org/semantics/apigateway/service/{ => search}/SearchLocalIndexerService.java (87%) diff --git a/.gitignore b/.gitignore index 96acd52..a6d8afd 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,5 @@ build/ # System files .DS_Store + +/src/frontend/ \ No newline at end of file diff --git a/pom.xml b/pom.xml index 3969666..dc364c4 100644 --- a/pom.xml +++ b/pom.xml @@ -13,7 +13,7 @@ 0.0.1-SNAPSHOT jar API-Gateway - API-Gateway Federated Terminology Services  + API-Gateway Federated Terminology Services  11 @@ -81,6 +81,17 @@ + + org.mockito + mockito-core + test + + + org.mockito + mockito-inline + test + + org.springframework.integration spring-integration-core diff --git a/src/main/java/org/semantics/apigateway/controller/GatewayController.java b/src/main/java/org/semantics/apigateway/controller/GatewayController.java index 8d71675..a1d9ff0 100644 --- a/src/main/java/org/semantics/apigateway/controller/GatewayController.java +++ b/src/main/java/org/semantics/apigateway/controller/GatewayController.java @@ -5,7 +5,7 @@ import io.swagger.v3.oas.annotations.responses.ApiResponses; import org.apache.http.HttpStatus; import org.apache.jena.rdf.model.ResourceFactory; -import org.semantics.apigateway.service.DynSearchService; +import org.semantics.apigateway.service.search.DynSearchService; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.ResponseEntity; import org.springframework.web.bind.annotation.*; diff --git a/src/main/java/org/semantics/apigateway/model/DynTransformResponse.java b/src/main/java/org/semantics/apigateway/model/DynTransformResponse.java index 6ac0678..30cbbb3 100644 --- a/src/main/java/org/semantics/apigateway/model/DynTransformResponse.java +++ b/src/main/java/org/semantics/apigateway/model/DynTransformResponse.java @@ -95,7 +95,8 @@ private Map processItem(Map item, OntologyConfig } if (responseMapping.getDescription() != null && item.containsKey(responseMapping.getDescription())) { - newItem.put("description", item.get(responseMapping.getDescription())); + List list = (List) item.get(responseMapping.getDescription()); + newItem.put("description", list); } if (responseMapping.getOntology() != null && item.containsKey(responseMapping.getOntology())) { if (responseMapping.getOntology().equals("links")) { diff --git a/src/main/java/org/semantics/apigateway/service/ConfigurationLoader.java b/src/main/java/org/semantics/apigateway/service/ConfigurationLoader.java index d0761e8..e9f94fe 100644 --- a/src/main/java/org/semantics/apigateway/service/ConfigurationLoader.java +++ b/src/main/java/org/semantics/apigateway/service/ConfigurationLoader.java @@ -6,6 +6,7 @@ import org.semantics.apigateway.config.DatabaseConfig; import org.semantics.apigateway.config.OntologyConfig; import org.semantics.apigateway.model.DynTransformResponse; +import org.semantics.apigateway.service.search.DynSearchService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/semantics/apigateway/service/SearchLocalIndexerService.java b/src/main/java/org/semantics/apigateway/service/search/SearchLocalIndexerService.java similarity index 87% rename from src/main/java/org/semantics/apigateway/service/SearchLocalIndexerService.java rename to src/main/java/org/semantics/apigateway/service/search/SearchLocalIndexerService.java index e7be43e..986cf0b 100644 --- a/src/main/java/org/semantics/apigateway/service/SearchLocalIndexerService.java +++ b/src/main/java/org/semantics/apigateway/service/search/SearchLocalIndexerService.java @@ -1,5 +1,7 @@ -package org.semantics.apigateway.service; +package org.semantics.apigateway.service.search; +import com.google.gson.Gson; +import com.google.gson.reflect.TypeToken; import lombok.NoArgsConstructor; import org.apache.lucene.analysis.standard.StandardAnalyzer; import org.apache.lucene.document.Document; @@ -7,10 +9,6 @@ import org.apache.lucene.document.StringField; import org.apache.lucene.document.TextField; import org.apache.lucene.index.*; -import org.apache.lucene.queries.spans.SpanMultiTermQueryWrapper; -import org.apache.lucene.queries.spans.SpanNearQuery; -import org.apache.lucene.queries.spans.SpanQuery; -import org.apache.lucene.queries.spans.SpanTermQuery; import org.apache.lucene.queryparser.classic.ParseException; import org.apache.lucene.search.*; import org.apache.lucene.store.ByteBuffersDirectory; @@ -19,7 +17,9 @@ import org.springframework.stereotype.Service; import java.io.IOException; +import java.lang.reflect.Type; import java.util.*; +import java.util.stream.Collectors; @Service @NoArgsConstructor @@ -31,7 +31,10 @@ public class SearchLocalIndexerService { public List> reIndexResults(String query, List> combinedResults , Logger logger) throws IOException, ParseException { Directory index = indexResults(combinedResults); - return localIndexSearch(query, logger, index, INDEXED_FIELD); + List> localIndexedResult = localIndexSearch(query, logger, index, INDEXED_FIELD); + + return localIndexedResult.stream().map(x -> combinedResults.stream().filter(y -> y.get("iri").equals(x.get("iri")) && y.get("backend_type").equals(x.get("backend_type"))) + .findFirst().orElse(null)).collect(Collectors.toList()); } private static List> localIndexSearch(String query, Logger logger, Directory index, String field) throws IOException { From 914132b7edf1fca68c23699fe0d732cba4825e47 Mon Sep 17 00:00:00 2001 From: Syphax Date: Mon, 19 Aug 2024 07:55:58 +0200 Subject: [PATCH 2/4] handle the case when the federated services are down --- .../{ => search}/DynSearchService.java | 42 ++++++++++++++++--- src/main/resources/response-config.json | 2 +- 2 files changed, 37 insertions(+), 7 deletions(-) rename src/main/java/org/semantics/apigateway/service/{ => search}/DynSearchService.java (90%) diff --git a/src/main/java/org/semantics/apigateway/service/DynSearchService.java b/src/main/java/org/semantics/apigateway/service/search/DynSearchService.java similarity index 90% rename from src/main/java/org/semantics/apigateway/service/DynSearchService.java rename to src/main/java/org/semantics/apigateway/service/search/DynSearchService.java index c6112a6..274de11 100644 --- a/src/main/java/org/semantics/apigateway/service/DynSearchService.java +++ b/src/main/java/org/semantics/apigateway/service/search/DynSearchService.java @@ -1,24 +1,27 @@ -package org.semantics.apigateway.service; +package org.semantics.apigateway.service.search; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; +import lombok.Setter; +import org.apache.http.HttpStatus; import org.semantics.apigateway.config.OntologyConfig; import org.semantics.apigateway.model.DynDatabaseTransform; import org.semantics.apigateway.model.DynTransformResponse; import org.semantics.apigateway.model.JsonLdTransform; +import org.semantics.apigateway.service.ConfigurationLoader; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.core.io.ClassPathResource; import org.springframework.http.ResponseEntity; +import org.springframework.http.client.SimpleClientHttpRequestFactory; import org.springframework.scheduling.annotation.Async; import org.springframework.stereotype.Service; import org.springframework.web.client.RestTemplate; import java.io.IOException; import java.io.InputStream; -import java.nio.charset.StandardCharsets; import java.util.HashMap; import java.util.List; import java.util.Map; @@ -26,23 +29,45 @@ import java.util.stream.Collectors; import java.util.stream.Stream; + + + + @Service public class DynSearchService { + + + @Autowired private ConfigurationLoader configurationLoader; + + @Autowired + private SearchLocalIndexerService localIndexer; + + + @Setter + private RestTemplate restTemplate; + + private static final Logger logger = LoggerFactory.getLogger(DynSearchService.class); - private final RestTemplate restTemplate = new RestTemplate(); + + + private final DynTransformResponse dynTransformResponse = new DynTransformResponse(); + private List ontologyConfigs; + private Map> responseMappings; - private SearchLocalIndexerService localIndexer; - @Autowired public DynSearchService(ConfigurationLoader configurationLoader, SearchLocalIndexerService localIndexer) { this.configurationLoader = configurationLoader; this.ontologyConfigs = configurationLoader.getOntologyConfigs(); this.responseMappings = configurationLoader.getResponseMappings(); this.localIndexer = localIndexer; + SimpleClientHttpRequestFactory factory = new SimpleClientHttpRequestFactory(); + factory.setConnectTimeout(5000); + factory.setReadTimeout(5000); + this.restTemplate = new RestTemplate(factory); } // Constructs the URL for the API call based on the query and configuration @@ -68,7 +93,12 @@ public CompletableFuture>> search(String query, Ontolog try { String url = constructUrl(query, config); logger.info("Accessing URL: {}", url); - ResponseEntity response = restTemplate.getForEntity(url, Map.class); + ResponseEntity response; + try { + response = restTemplate.getForEntity(url, Map.class); + }catch (Exception e) { + response = ResponseEntity.status(404).body(new HashMap<>()); + } if (response.getStatusCode().is2xxSuccessful() && response.getBody() != null) { logger.info("Raw API Response: {}", response.getBody()); diff --git a/src/main/resources/response-config.json b/src/main/resources/response-config.json index 155e721..64b50ec 100644 --- a/src/main/resources/response-config.json +++ b/src/main/resources/response-config.json @@ -16,7 +16,7 @@ }, { "database": "ols", - "url": "https://www.ebi.ac.uk/ols4/api/search?q=%s", + "url": "https://ebi.ac.uk/ols4/api/search?q=%s", "apiKey": "", "responseMapping": { "nestedJson": "response", From d94f71dba98199adb1a4b76b0ea1e4580c35136e Mon Sep 17 00:00:00 2001 From: Syphax Date: Mon, 19 Aug 2024 07:56:16 +0200 Subject: [PATCH 3/4] add search service integration test --- .../apigateway/SearchServiceTest.java | 115 + src/test/resources/mocks/search/ols.json | 763 +++++ .../resources/mocks/search/ontoportal.json | 2801 +++++++++++++++++ src/test/resources/mocks/search/skosmos.json | 1007 ++++++ 4 files changed, 4686 insertions(+) create mode 100644 src/test/java/org/semantics/apigateway/SearchServiceTest.java create mode 100644 src/test/resources/mocks/search/ols.json create mode 100644 src/test/resources/mocks/search/ontoportal.json create mode 100644 src/test/resources/mocks/search/skosmos.json diff --git a/src/test/java/org/semantics/apigateway/SearchServiceTest.java b/src/test/java/org/semantics/apigateway/SearchServiceTest.java new file mode 100644 index 0000000..ff47c17 --- /dev/null +++ b/src/test/java/org/semantics/apigateway/SearchServiceTest.java @@ -0,0 +1,115 @@ +package org.semantics.apigateway; + +import com.google.gson.Gson; +import com.google.gson.reflect.TypeToken; +import org.junit.jupiter.api.Test; +import org.mockito.Mock; +import org.semantics.apigateway.config.OntologyConfig; +import org.semantics.apigateway.service.ConfigurationLoader; +import org.semantics.apigateway.service.search.DynSearchService; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.ResponseEntity; +import org.springframework.web.client.RestTemplate; + +import java.lang.reflect.Type; +import java.net.URL; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.concurrent.CompletableFuture; +import java.util.stream.Collectors; + +import static org.assertj.core.api.Assertions.assertThat; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.Mockito.when; + +@AutoConfigureMockMvc +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +public class SearchServiceTest { + + @Autowired + private DynSearchService searchService; + + @Mock + private RestTemplate restTemplate; // Mock RestTemplate + + @Autowired + private ConfigurationLoader configurationLoader; // Autowire the real ConfigurationLoader + + + + + @Test + public void testSearchAllDatabases() { + + searchService.setRestTemplate(restTemplate); + + List configs = configurationLoader.getOntologyConfigs(); + + when(restTemplate.getForEntity( + anyString(), + any(Class.class))) + .thenAnswer(invocation -> { + String url = invocation.getArgument(0, String.class); + ResponseEntity> response = ResponseEntity.status(404).body(new HashMap<>()); + + for (OntologyConfig config : configs) { + String serviceName = String.format("src/test/resources/mocks/search/%s.json", config.getDatabase()); + String jsonResponse = new String(Files.readAllBytes(Paths.get(serviceName))); + + String configHost = new URL(config.getUrl()).getHost(); + String currentURLHost = new URL(url).getHost(); + + + if (configHost.equals(currentURLHost)) { + + Gson gson = new Gson(); + Type mapType = new TypeToken>() {}.getType(); + Map map = gson.fromJson(jsonResponse, mapType); + + response = ResponseEntity.status(200).body(map); + return response; + } + } + return response; + }); + + + // Perform the search + CompletableFuture r = searchService.performDynFederatedSearch("plant", "", "", ""); + + List> responseList = (List>) r.join(); + + assertThat(responseList).hasSize(100); + + Map firstPlant = responseList.get(0); + assertThat(firstPlant.get("iri")).isEqualTo("http://sweetontology.net/matrPlant/Plant"); + assertThat(firstPlant.get("backend_type")).isEqualTo("ontoportal"); + assertThat(firstPlant.get("short_form")).isEqualTo("plant"); + assertThat(firstPlant.get("label")).isEqualTo("plant"); + assertThat(firstPlant.get("source")).isEqualTo("https://data.biodivportal.gfbio.dev"); + assertThat(firstPlant.get("type")).isEqualTo("class"); + assertThat(firstPlant.get("ontology")).isEqualTo("sweet"); + + Map secondPlant = responseList.get(1); + assertThat(secondPlant.get("iri")).isEqualTo("http://purl.obolibrary.org/obo/NCIT_C14258"); + assertThat(secondPlant.get("backend_type")).isEqualTo("ols"); + assertThat(secondPlant.get("short_form")).isEqualTo("NCIT_C14258"); + assertThat(secondPlant.get("description")) + .isEqualTo(new ArrayList(List.of(new String[]{"Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (EPA Terminology Reference System)"}))); + assertThat(secondPlant.get("label")).isEqualTo("Plant"); + assertThat(secondPlant.get("source")).isEqualTo("https://ebi.ac.uk/ols4/api"); + assertThat(secondPlant.get("type")).isEqualTo("class"); + assertThat(secondPlant.get("ontology")).isEqualTo("ncit"); + + + assertThat(responseList.stream().map(x -> x.get("backend_type")).distinct().sorted().collect(Collectors.toList())) + .isEqualTo(configs.stream().map(OntologyConfig::getDatabase).sorted().collect(Collectors.toList())); + } +} diff --git a/src/test/resources/mocks/search/ols.json b/src/test/resources/mocks/search/ols.json new file mode 100644 index 0000000..407a877 --- /dev/null +++ b/src/test/resources/mocks/search/ols.json @@ -0,0 +1,763 @@ +{ + "response": { + "docs": [ + { + "iri": "http://purl.obolibrary.org/obo/NCIT_C14258", + "ontology_name": "ncit", + "ontology_prefix": "NCIT", + "short_form": "NCIT_C14258", + "description": [ + "Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (EPA Terminology Reference System)" + ], + "label": "Plant", + "obo_id": "NCIT:C14258", + "type": "class" + }, + { + "iri": "http://purl.obolibrary.org/obo/BTO_0001481", + "ontology_name": "bto", + "ontology_prefix": "BTO", + "short_form": "BTO_0001481", + "description": [ + "Any of a kingdom (Plantae) of living things typically lacking locomotive movement or obvious nervous or sensory organs and possessing cellulose cell walls." + ], + "label": "plant", + "obo_id": "BTO:0001481", + "type": "class" + }, + { + "iri": "http://www.bioassayontology.org/bao#BAO_0000605", + "ontology_name": "bao", + "ontology_prefix": "BAO", + "short_form": "BAO_0000605", + "description": [ + "They are living organisms which derive their energy from photosynthesis, with the exception of parasitic plants. Plants include herbs, shrubs, trees, grasses, vines, etc." + ], + "label": "plant", + "obo_id": "BAO:0000605", + "type": "class" + }, + { + "iri": "http://purl.obolibrary.org/obo/BTO_0001481", + "ontology_name": "ado", + "ontology_prefix": "ADO", + "short_form": "BTO_0001481", + "description": [ + "Any of a kingdom (Plantae) of living things typically lacking locomotive movement or obvious nervous or sensory organs and possessing cellulose cell walls." + ], + "label": "plant", + "obo_id": "BTO:0001481", + "type": "class" + }, + { + "iri": "https://w3id.org/biolink/vocab/Plant", + "ontology_name": "biolink", + "short_form": "Plant", + "description": [], + "label": "plant", + "obo_id": "Plant", + "type": "class" + }, + { + "iri": "http://purl.obolibrary.org/obo/IDOMAL_6000005", + "ontology_name": "idomal", + "short_form": "IDOMAL_6000005", + "description": [ + "Any of various photosynthetic, eukaryotic, multicellular organisms of the kingdom Plantae characteristically producing embryos, containing chloroplasts, having cellulose cell walls, and lacking the power of locomotion." + ], + "label": "plant", + "obo_id": "IDOMAL:6000005", + "type": "class" + }, + { + "iri": "http://edamontology.org/topic_0780", + "ontology_name": "edam", + "ontology_prefix": "EDAM", + "short_form": "EDAM_0780", + "description": [ + "Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.", + "The resource may be specific to a plant, a group of plants or all plants." + ], + "label": "Plant biology", + "obo_id": "EDAM:0780", + "type": "class" + }, + { + "iri": "http://purl.obolibrary.org/obo/FOODON_03412066", + "ontology_name": "foodon", + "ontology_prefix": "FOODON", + "short_form": "FOODON_03412066", + "description": [], + "label": "niger (plant) plant", + "obo_id": "FOODON:03412066", + "type": "class" + }, + { + "iri": "http://purl.obolibrary.org/obo/FLOPO_0005767", + "ontology_name": "flopo", + "ontology_prefix": "FLOPO", + "short_form": "FLOPO_0005767", + "description": [], + "label": "whole plant evergreen (plant)", + "obo_id": "FLOPO:0005767", + "type": "class" + }, + { + "iri": "http://snomed.info/id/37202001", + "ontology_name": "snomed", + "ontology_prefix": "SNOMED", + "short_form": "SNOMED_37202001", + "description": [], + "label": "Plant fiber (substance)", + "obo_id": "SNOMED:37202001", + "type": "class" + } + ], + "numFound": 14510, + "start": 0 + }, + "responseHeader": { + "QTime": 8, + "status": 0 + }, + "facet_counts": { + "facet_fields": { + "ontologyPreferredPrefix": [ + "foodon", + "4299", + "ncit", + "1306", + "flopo", + "1013", + "to", + "913", + "go", + "442", + "po", + "437", + "ecto", + "404", + "ncbitaxon", + "387", + "pr", + "296", + "peco", + "288", + "chebi", + "259", + "slm", + "259", + "ppo", + "249", + "cco", + "246", + "snomed", + "228", + "agro", + "214", + "pso", + "207", + "envo", + "184", + "efo", + "174", + "bto", + "131", + "maxo", + "128", + "micro", + "126", + "fideo", + "87", + "omit", + "83", + "enm", + "81", + "oba", + "72", + "gallont", + "71", + "rbo", + "70", + "gexo", + "67", + "rexo", + "67", + "reto", + "66", + "ecocore", + "65", + "slso", + "59", + "dron", + "58", + "genepio", + "52", + "mondo", + "52", + "mp", + "39", + "hp", + "29", + "gsso", + "28", + "fypo", + "27", + "occo", + "27", + "hcao", + "25", + "uberon", + "25", + "cdno", + "24", + "cmo", + "24", + "xco", + "23", + "planp", + "22", + "chiro", + "21", + "pato", + "21", + "cido", + "20", + "phipo", + "19", + "doid", + "18", + "cl", + "17", + "pcl", + "16", + "fobi", + "15", + "mco", + "15", + "ontoneo", + "15", + "fovt", + "14", + "srao", + "14", + "wbphenotype", + "14", + "zp", + "14", + "aism", + "13", + "bco", + "13", + "ohpi", + "13", + "xpo", + "13", + "eupath", + "12", + "fbcv", + "12", + "ons", + "12", + "ngbo", + "11", + "obi", + "11", + "bao", + "10", + "clo", + "10", + "pw", + "10", + "aro", + "9", + "one", + "9", + "edam", + "8", + "mfmo", + "8", + "mi", + "8", + "nbo", + "8", + 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+ "rexo", + "67", + "reto", + "66", + "ecocore", + "65", + "slso", + "59", + "dron", + "58", + "genepio", + "52", + "mondo", + "52", + "mp", + "39", + "idomal", + "34", + "upa", + "33", + "hp", + "29", + "gsso", + "28", + "fypo", + "27", + "occo", + "27", + "hcao", + "25", + "uberon", + "25", + "cdno", + "24", + "cmo", + "24", + "xco", + "23", + "planp", + "22", + "chiro", + "21", + "pato", + "21", + "cido", + "20", + "phipo", + "19", + "doid", + "18", + "cl", + "17", + "pcl", + "16", + "fobi", + "15", + "mco", + "15", + "ontoneo", + "15", + "fovt", + "14", + "srao", + "14", + "wbphenotype", + "14", + "zp", + "14", + "aism", + "13", + "bco", + "13", + "ohpi", + "13", + "xpo", + "13", + "eupath", + "12", + "ons", + "12", + "ngbo", + "11", + "obi", + "11", + "bao", + "10", + "clo", + "10", + "pw", + "10", + "aro", + "9", + "one", + "9", + "bcgo", + "8", + "edam", + "8", + "mfmo", + "8", + "mi", + "8", + "nbo", + "8", + "ro", + "8", + "dpo", + "7", + "fbbt", + "7", + "pco", + "7", + "vo", 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May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003)." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/PO_0009008", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/OBA", + "children": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/parents", + "descendants": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/descendants", + "ancestors": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/ancestors", + "instances": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/instances", + "tree": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/tree", + "notes": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/notes", + "mappings": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008/mappings", + "ui": "http://biodivportal.gfbio.dev/ontologies/OBA?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009008", + + "@context": { + "self": "http://www.w3.org/2002/07/owl#Class", + "ontology": "http://data.bioontology.org/metadata/Ontology", + "children": "http://www.w3.org/2002/07/owl#Class", + "parents": "http://www.w3.org/2002/07/owl#Class", + "descendants": "http://www.w3.org/2002/07/owl#Class", + "ancestors": "http://www.w3.org/2002/07/owl#Class", + "instances": "http://data.bioontology.org/metadata/Instance", + "tree": "http://www.w3.org/2002/07/owl#Class", + "notes": "http://data.bioontology.org/metadata/Note", + "mappings": "http://data.bioontology.org/metadata/Mapping", + "ui": "http://www.w3.org/2002/07/owl#Class" + } + + }, + + "@context": { + "@vocab": "http://data.bioontology.org/metadata/", + "prefLabel": "http://www.w3.org/2004/02/skos/core#prefLabel", + "definition": "http://www.w3.org/2004/02/skos/core#definition", + "obsolete": "http://www.w3.org/2002/07/owl#deprecated", + "@language": "en" + } + + }, + { + + "prefLabel": "plant embryo", + + "definition": [ + + "A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010)." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/PO_0009009", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/OBA", + "children": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/parents", + "descendants": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/descendants", + "ancestors": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/ancestors", + "instances": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/instances", + "tree": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/tree", + "notes": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/notes", + "mappings": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009/mappings", + "ui": "http://biodivportal.gfbio.dev/ontologies/OBA?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009009", + + "@context": { + "self": "http://www.w3.org/2002/07/owl#Class", + "ontology": "http://data.bioontology.org/metadata/Ontology", + "children": "http://www.w3.org/2002/07/owl#Class", + "parents": "http://www.w3.org/2002/07/owl#Class", + "descendants": "http://www.w3.org/2002/07/owl#Class", + "ancestors": "http://www.w3.org/2002/07/owl#Class", + "instances": "http://data.bioontology.org/metadata/Instance", + "tree": "http://www.w3.org/2002/07/owl#Class", + "notes": "http://data.bioontology.org/metadata/Note", + "mappings": "http://data.bioontology.org/metadata/Mapping", + "ui": "http://www.w3.org/2002/07/owl#Class" + } + + }, + + "@context": { + "@vocab": "http://data.bioontology.org/metadata/", + "prefLabel": "http://www.w3.org/2004/02/skos/core#prefLabel", + "definition": "http://www.w3.org/2004/02/skos/core#definition", + "obsolete": "http://www.w3.org/2002/07/owl#deprecated", + "@language": "en" + } + + }, + { + + "prefLabel": "plant ovule", + + "definition": [ + + "A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352)." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/PO_0020003", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/OBA", + "children": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/parents", + "descendants": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/descendants", + "ancestors": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/ancestors", + "instances": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/instances", + "tree": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/tree", + "notes": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/notes", + "mappings": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003/mappings", + "ui": "http://biodivportal.gfbio.dev/ontologies/OBA?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0020003", + + "@context": { + "self": "http://www.w3.org/2002/07/owl#Class", + "ontology": "http://data.bioontology.org/metadata/Ontology", + "children": "http://www.w3.org/2002/07/owl#Class", + "parents": "http://www.w3.org/2002/07/owl#Class", + "descendants": "http://www.w3.org/2002/07/owl#Class", + "ancestors": "http://www.w3.org/2002/07/owl#Class", + "instances": "http://data.bioontology.org/metadata/Instance", + "tree": "http://www.w3.org/2002/07/owl#Class", + "notes": "http://data.bioontology.org/metadata/Note", + "mappings": "http://data.bioontology.org/metadata/Mapping", + "ui": "http://www.w3.org/2002/07/owl#Class" + } + + }, + + "@context": { + "@vocab": "http://data.bioontology.org/metadata/", + "prefLabel": "http://www.w3.org/2004/02/skos/core#prefLabel", + "definition": "http://www.w3.org/2004/02/skos/core#definition", + "obsolete": "http://www.w3.org/2002/07/owl#deprecated", + "@language": "en" + } + + }, + { + + "prefLabel": "plant cell", + + "definition": [ + + "Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: \"The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope\". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/PO_0009002", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/OBA", + "children": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/parents", + "descendants": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/descendants", + "ancestors": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/ancestors", + "instances": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/instances", + "tree": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/tree", + "notes": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/notes", + "mappings": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002/mappings", + "ui": "http://biodivportal.gfbio.dev/ontologies/OBA?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009002", + + "@context": { + "self": "http://www.w3.org/2002/07/owl#Class", + "ontology": "http://data.bioontology.org/metadata/Ontology", + "children": "http://www.w3.org/2002/07/owl#Class", + "parents": "http://www.w3.org/2002/07/owl#Class", + "descendants": "http://www.w3.org/2002/07/owl#Class", + "ancestors": "http://www.w3.org/2002/07/owl#Class", + "instances": "http://data.bioontology.org/metadata/Instance", + "tree": "http://www.w3.org/2002/07/owl#Class", + "notes": "http://data.bioontology.org/metadata/Note", + "mappings": "http://data.bioontology.org/metadata/Mapping", + "ui": "http://www.w3.org/2002/07/owl#Class" + } + + }, + + "@context": { + "@vocab": "http://data.bioontology.org/metadata/", + "prefLabel": "http://www.w3.org/2004/02/skos/core#prefLabel", + "definition": "http://www.w3.org/2004/02/skos/core#definition", + "obsolete": "http://www.w3.org/2002/07/owl#deprecated", + "@language": "en" + } + + }, + { + + "prefLabel": "plant structure", + + "definition": [ + + "'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/PO_0009011", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009011", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/OBA", + "children": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009011/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009011/parents", + "descendants": 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The term includes endogenous and non-endogenous compounds (e.g. active compounds produced by bacteria on the leaf surface) as well as semi-synthetic and fully synthetic compounds." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/CHEBI_37848", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI", + "children": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/parents", + "descendants": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/descendants", + "ancestors": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/ancestors", + "instances": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/instances", + "tree": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/tree", + "notes": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/notes", + "mappings": "https://data.biodivportal.gfbio.dev/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848/mappings", + "ui": "http://biodivportal.gfbio.dev/ontologies/CHEBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37848", + + "@context": { + "self": "http://www.w3.org/2002/07/owl#Class", + "ontology": "http://data.bioontology.org/metadata/Ontology", + "children": "http://www.w3.org/2002/07/owl#Class", + "parents": "http://www.w3.org/2002/07/owl#Class", + "descendants": "http://www.w3.org/2002/07/owl#Class", + "ancestors": "http://www.w3.org/2002/07/owl#Class", + "instances": "http://data.bioontology.org/metadata/Instance", + "tree": "http://www.w3.org/2002/07/owl#Class", + "notes": "http://data.bioontology.org/metadata/Note", + "mappings": "http://data.bioontology.org/metadata/Mapping", + "ui": "http://www.w3.org/2002/07/owl#Class" + } + + }, + + "@context": { + "@vocab": "http://data.bioontology.org/metadata/", + "prefLabel": "http://www.w3.org/2004/02/skos/core#prefLabel", + "synonym": "http://www.w3.org/2004/02/skos/core#altLabel", + "definition": "http://www.w3.org/2004/02/skos/core#definition", + "obsolete": "http://www.w3.org/2002/07/owl#deprecated", + "@language": "en" + } + + }, + { + + "prefLabel": "plant ovary", + + "definition": [ + + "If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352)." + + ], + "obsolete": false, + "matchType": "prefLabel", + "ontologyType": "ONTOLOGY", + "@id": "http://purl.obolibrary.org/obo/PO_0009072", + "@type": "http://www.w3.org/2002/07/owl#Class", + "links": { + + "self": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009072", + "ontology": "https://data.biodivportal.gfbio.dev/ontologies/OBA", + "children": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009072/children", + "parents": "https://data.biodivportal.gfbio.dev/ontologies/OBA/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPO_0009072/parents", + "descendants": 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"prefLabel": "plant propagation", + "lang": "en", + "vocab": "agrovoc" + }, + { + "uri": "http:\/\/aims.fao.org\/aos\/agrovoc\/c_5978", + "type": [ + "skos:Concept" + ], + "prefLabel": "plant protection", + "lang": "en", + "vocab": "agrovoc" + }, + { + "uri": "http:\/\/aims.fao.org\/aos\/agrovoc\/c_25760", + "type": [ + "skos:Concept" + ], + "prefLabel": "plant protection equipment", + "lang": "en", + "vocab": "agrovoc" + }, + { + "uri": "http:\/\/aims.fao.org\/aos\/agrovoc\/c_8172", + "type": [ + "skos:Concept" + ], + "prefLabel": "plant protein", + "lang": "en", + "vocab": "agrovoc" + }, + { + "uri": "http:\/\/aims.fao.org\/aos\/agrovoc\/c_25398", + "type": [ + "skos:Concept" + ], + "prefLabel": "plant health", + "lang": "en", + "altLabel": "plant quality", + "vocab": "agrovoc" + }, + { + "uri": "http:\/\/aims.fao.org\/aos\/agrovoc\/c_13811", + "type": [ + "skos:Concept" + ], + "prefLabel": "replanting", + "lang": "en", + "altLabel": "plant replacement", + "vocab": "agrovoc" + }, + { + "uri": "http:\/\/aims.fao.org\/aos\/agrovoc\/c_27986", + "type": [ + "skos:Concept" + ], + "prefLabel": "plant reproductive organs", + "lang": "en", + "vocab": "agrovoc" + } + ] +} \ No newline at end of file From 7a1cc4570a9147f42986a84f05dde8b5c3063162 Mon Sep 17 00:00:00 2001 From: Syphax Date: Mon, 19 Aug 2024 08:15:29 +0200 Subject: [PATCH 4/4] fix ols database transformer type field --- .../java/org/semantics/apigateway/api/OlsTransformer.java | 8 +------- .../apigateway/service/search/DynSearchService.java | 2 +- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/src/main/java/org/semantics/apigateway/api/OlsTransformer.java b/src/main/java/org/semantics/apigateway/api/OlsTransformer.java index f5301e2..8e03413 100644 --- a/src/main/java/org/semantics/apigateway/api/OlsTransformer.java +++ b/src/main/java/org/semantics/apigateway/api/OlsTransformer.java @@ -48,13 +48,7 @@ public Map transformItem(Map item) { transformedItem.put("backend_type", item.get("backend_type")); } if (item.containsKey("type") && item.get("type") != null) { - // the value of the key @type in OntoPortal is saved as an IRI - if (item.containsKey("backend_type") && String.valueOf(item.get("backend_type")).equals("ontoportal")) { - transformedItem.put("type", - ResourceFactory.createResource(String.valueOf(item.get("type"))).getLocalName().toLowerCase()); - } else { - transformedItem.put("type", item.get("type")); - } + transformedItem.put("type", item.get("type")); } return transformedItem; } diff --git a/src/main/java/org/semantics/apigateway/service/search/DynSearchService.java b/src/main/java/org/semantics/apigateway/service/search/DynSearchService.java index 274de11..65b219c 100644 --- a/src/main/java/org/semantics/apigateway/service/search/DynSearchService.java +++ b/src/main/java/org/semantics/apigateway/service/search/DynSearchService.java @@ -152,7 +152,7 @@ public CompletableFuture performDynFederatedSearch( logger.info("Combined results before transformation: {}", combinedResults); - List> newResults = this.localIndexer.reIndexResults(query, combinedResults, logger); + List> newResults = this.localIndexer.reIndexResults(query.replace("*",""), combinedResults, logger); if (targetDbSchema != null && !targetDbSchema.isEmpty()) { Object transformedResults = transformAndStructureResults(newResults, targetDbSchema);