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1 SKOS API Support #625 #626

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1 SKOS API Support #625 #626

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bd25235
enabled all rest controllers
giraygi Dec 27, 2023
8811ab9
added imports
giraygi Dec 27, 2023
865418e
added skos tree generation controllers
giraygi Jan 3, 2024
5db94ef
enabled hastopconcept option by making conceptSchema a term
giraygi Jan 3, 2024
fb211c8
implemented graph definition call for visualization
giraygi Feb 15, 2024
d2df44f
removed yet to be introduced caching for now and moved graph method b…
giraygi Feb 15, 2024
c7f8de2
renamed call signatures with respect to EBI conventions in #625
giraygi Feb 16, 2024
5080ff8
handled null relations for some ontologies in EBISPOT#625 and TIBHann…
giraygi Feb 19, 2024
c249078
changed skos variable name in the config file
giraygi Feb 20, 2024
0f88d25
added skos tree configuration parameters for frontend in EBISPOT#625 …
giraygi Feb 20, 2024
e56e916
refactored and handled null cases
giraygi Mar 4, 2024
49b63a4
implemented skos v2 api for EBISPOT#625 and TIBHannover#1
giraygi Apr 3, 2024
e4205e7
refactored with enum for skos relations
giraygi Apr 10, 2024
60eb886
refactored the whole skos functionaliuty of v1 and v2 for EBISPOT#625…
giraygi Apr 11, 2024
6afd55f
reverted the get first method of olssolrclient
giraygi Apr 11, 2024
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7 changes: 7 additions & 0 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/TopConceptEnum.java
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@@ -0,0 +1,7 @@
package uk.ac.ebi.spot.ols.controller.api.v1;

public enum TopConceptEnum {
SCHEMA,
TOPCONCEPTOF_PROPERTY,
RELATIONSHIPS
}
5 changes: 2 additions & 3 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1ApiUnavailable.java
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Expand Up @@ -6,8 +6,7 @@
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.*;

import javax.servlet.http.HttpServletResponse;

Expand All @@ -16,7 +15,7 @@
* @date 27/09/2016
* Samples, Phenotypes and Ontologies Team, EMBL-EBI
*/
@Controller
@RestController
public class V1ApiUnavailable {

@RequestMapping(path = "/api/unavailable", produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)
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18 changes: 9 additions & 9 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1IndividualController.java
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Expand Up @@ -28,7 +28,7 @@
* @date 18/08/2015
* Samples, Phenotypes and Ontologies Team, EMBL-EBI
*/
@Controller
@RestController
@RequestMapping("/api/individuals")
@ExposesResourceFor(V1Individual.class)
public class V1IndividualController implements
Expand Down Expand Up @@ -81,7 +81,7 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividuals(

return new ResponseEntity<>(assembler.toModel(terms, individualAssembler), HttpStatus.OK);
}

@RequestMapping(path = "/findByIdAndIsDefiningOntology/{id}", produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, method = RequestMethod.GET)
HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
@PathVariable("id") String termId,
Expand All @@ -92,11 +92,11 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
decoded = UriUtils.decode(termId, "UTF-8");
return getAllIndividualsByIdAndIsDefiningOntology(decoded, null, null, lang, pageable, assembler);

}
@RequestMapping(path = "/findByIdAndIsDefiningOntology",
produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE},
}


@RequestMapping(path = "/findByIdAndIsDefiningOntology",
produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE},
method = RequestMethod.GET)
HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
@RequestParam(value = "iri", required = false) String iri,
Expand All @@ -120,11 +120,11 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(

return new ResponseEntity<>(assembler.toModel(terms, individualAssembler), HttpStatus.OK);
}


@ResponseStatus(value = HttpStatus.NOT_FOUND, reason = "EntityModel not found")
@ExceptionHandler(ResourceNotFoundException.class)
public void handleError(HttpServletRequest req, Exception exception) {
}

}
}
2 changes: 1 addition & 1 deletion backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyController.java
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Expand Up @@ -31,7 +31,7 @@
* @date 19/08/2015
* Samples, Phenotypes and Ontologies Team, EMBL-EBI
*/
@Controller
@RestController
@RequestMapping("/api/ontologies")
@ExposesResourceFor(V1Ontology.class)
public class V1OntologyController implements
Expand Down
2 changes: 1 addition & 1 deletion ...nd/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyIndividualController.java
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Expand Up @@ -34,7 +34,7 @@
* @date 02/11/15
* Samples, Phenotypes and Ontologies Team, EMBL-EBI
*/
@Controller
@RestController
@RequestMapping("/api/ontologies")
public class V1OntologyIndividualController {

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2 changes: 1 addition & 1 deletion backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyPropertyController.java
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Expand Up @@ -27,7 +27,7 @@
import javax.servlet.http.HttpServletRequest;
import java.util.Arrays;

@Controller
@RestController
@RequestMapping("/api/ontologies")
public class V1OntologyPropertyController {

Expand Down
348 changes: 348 additions & 0 deletions ...d/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologySKOSConceptController.java
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8 changes: 4 additions & 4 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1PropertyController.java
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Expand Up @@ -23,7 +23,7 @@

import javax.servlet.http.HttpServletRequest;

@Controller
@RestController
@RequestMapping("/api/properties")
@ExposesResourceFor(V1Property.class)
public class V1PropertyController implements
Expand Down Expand Up @@ -93,8 +93,8 @@ HttpEntity<PagedModel<V1Property>> getPropertiesByIriAndIsDefiningOntology(@Path
String decoded = null;
decoded = UriUtils.decode(termId, "UTF-8");
return getPropertiesByIdAndIsDefiningOntology(decoded, null, null, lang, pageable, assembler);
}
}

@RequestMapping(path = "/findByIdAndIsDefiningOntology", produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, method = RequestMethod.GET)
HttpEntity<PagedModel<V1Property>> getPropertiesByIdAndIsDefiningOntology(
@RequestParam(value = "iri", required = false) String iri,
Expand All @@ -121,7 +121,7 @@ else if (oboId != null) {

return new ResponseEntity<>( assembler.toModel(terms, termAssembler), HttpStatus.OK);
}

@ResponseStatus(value = HttpStatus.NOT_FOUND, reason = "EntityModel not found")
@ExceptionHandler(ResourceNotFoundException.class)
public void handleError(HttpServletRequest req, Exception exception) {
Expand Down
8 changes: 2 additions & 6 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java
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Expand Up @@ -5,15 +5,11 @@
import com.google.gson.JsonParser;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.impl.HttpSolrClient;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import uk.ac.ebi.spot.ols.repository.Validation;
import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
import uk.ac.ebi.spot.ols.repository.transforms.LocalizationTransform;
Expand All @@ -35,7 +31,7 @@
* @date 02/07/2015
* Samples, Phenotypes and Ontologies Team, EMBL-EBI
*/
@Controller
@RestController
public class V1SearchController {

Gson gson = new Gson();
Expand Down
6 changes: 2 additions & 4 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java
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Expand Up @@ -11,9 +11,7 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import uk.ac.ebi.spot.ols.repository.Validation;
import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
import uk.ac.ebi.spot.ols.repository.transforms.LocalizationTransform;
Expand All @@ -28,7 +26,7 @@
import java.util.function.Function;
import java.util.stream.Collectors;

@Controller
@RestController
public class V1SelectController {

Gson gson = new Gson();
Expand Down
6 changes: 2 additions & 4 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SuggestController.java
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Expand Up @@ -10,9 +10,7 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import uk.ac.ebi.spot.ols.repository.Validation;
import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
import uk.ac.ebi.spot.ols.repository.v1.V1OntologyRepository;
Expand All @@ -22,7 +20,7 @@
import java.nio.charset.StandardCharsets;
import java.util.*;

@Controller
@RestController
public class V1SuggestController {

Gson gson = new Gson();
Expand Down
9 changes: 3 additions & 6 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2ClassController.java
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Expand Up @@ -15,10 +15,7 @@
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.util.UriUtils;
import uk.ac.ebi.spot.ols.controller.api.v2.helpers.DynamicQueryHelper;
import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedAndFacetedResponse;
Expand All @@ -35,7 +32,7 @@
import java.util.List;
import java.util.Map;

@Controller
@RestController
@RequestMapping("/api/v2")
public class V2ClassController {

Expand Down Expand Up @@ -101,7 +98,7 @@ public HttpEntity<V2Entity> getClass(

iri = UriUtils.decode(iri, "UTF-8");

V2Entity entity = classRepository.getByOntologyIdAndIri(ontologyId, iri, lang);
V2Entity entity = classRepository.findByOntologyAndIri(ontologyId, iri, lang);
if (entity == null) throw new ResourceNotFoundException();
return new ResponseEntity<>( entity, HttpStatus.OK);
}
Expand Down
7 changes: 2 additions & 5 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2EntityController.java
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Expand Up @@ -10,10 +10,7 @@
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.util.UriUtils;
import uk.ac.ebi.spot.ols.controller.api.v2.helpers.DynamicQueryHelper;
import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedAndFacetedResponse;
Expand All @@ -28,7 +25,7 @@
import java.util.List;
import java.util.Map;

@Controller
@RestController
@RequestMapping("/api/v2")
public class V2EntityController {

Expand Down
7 changes: 2 additions & 5 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2IndividualController.java
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Expand Up @@ -11,10 +11,7 @@
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.util.UriUtils;
import uk.ac.ebi.spot.ols.controller.api.v2.helpers.DynamicQueryHelper;
import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedAndFacetedResponse;
Expand All @@ -29,7 +26,7 @@
import java.util.List;
import java.util.Map;

@Controller
@RestController
@RequestMapping("/api/v2")
public class V2IndividualController {

Expand Down
7 changes: 2 additions & 5 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2OntologyController.java
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Expand Up @@ -12,10 +12,7 @@
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.*;
import uk.ac.ebi.spot.ols.controller.api.v2.helpers.DynamicQueryHelper;
import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedAndFacetedResponse;
import uk.ac.ebi.spot.ols.model.v2.V2Entity;
Expand All @@ -29,7 +26,7 @@
import java.util.List;
import java.util.Map;

@Controller
@RestController
@RequestMapping("/api/v2/ontologies")
public class V2OntologyController {

Expand Down
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