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Merge pull request #576 from EBISPOT/dev
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#170, #559, #567, #568, #549, #319, #575
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@henrietteharmse
henrietteharmse authored Nov 14, 2023
2 parents a347700 + a6292e1 commit 0636f18
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Showing 32 changed files with 2,025 additions and 1,871 deletions.
15 changes: 9 additions & 6 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2ClassController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import org.springframework.http.MediaType;
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;
Expand All @@ -29,7 +30,9 @@

import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

@Controller
Expand All @@ -48,12 +51,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getClasses(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String, Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand All @@ -74,12 +77,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getClasses(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String,Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand Down
15 changes: 9 additions & 6 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2EntityController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import org.springframework.http.MediaType;
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;
Expand All @@ -22,7 +23,9 @@

import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

@Controller
Expand All @@ -42,12 +45,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getEntities(
@RequestParam(value = "facetFields", required = false) String facetFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String,Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand All @@ -68,12 +71,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getTerms(
@RequestParam(value = "facetFields", required = false) String facetFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String,Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand Down
15 changes: 9 additions & 6 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2IndividualController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import org.springframework.http.MediaType;
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;
Expand All @@ -23,7 +24,9 @@

import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

@Controller
Expand All @@ -42,12 +45,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getIndividuals(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String, Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand All @@ -67,12 +70,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getIndividuals(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String, Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand Down
8 changes: 5 additions & 3 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2OntologyController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,9 @@
import uk.ac.ebi.spot.ols.repository.v2.V2OntologyRepository;

import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

@Controller
Expand All @@ -47,12 +49,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getOntologies(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam Map<String, Collection<String>> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String,Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand Down
15 changes: 9 additions & 6 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2PropertyController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.util.UriUtils;
import uk.ac.ebi.spot.ols.controller.api.v2.helpers.DynamicQueryHelper;
Expand All @@ -19,7 +20,9 @@

import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

@Controller
Expand All @@ -38,12 +41,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getProperties(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam Map<String, Collection<String>> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String,Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand All @@ -63,12 +66,12 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getProperties(
@RequestParam(value = "boostFields", required = false) String boostFields,
@RequestParam(value = "exactMatch", required = false, defaultValue = "false") boolean exactMatch,
@RequestParam(value = "includeObsoleteEntities", required = false, defaultValue = "false") boolean includeObsoleteEntities,
@RequestParam Map<String,String> searchProperties
@RequestParam MultiValueMap<String,String> searchProperties
) throws ResourceNotFoundException, IOException {

Map<String,String> properties = new HashMap<>();
Map<String,Collection<String>> properties = new HashMap<>();
if(!includeObsoleteEntities)
properties.put("isObsolete", "false");
properties.put("isObsolete", List.of("false"));
properties.putAll(searchProperties);

return new ResponseEntity<>(
Expand Down
9 changes: 4 additions & 5 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/helpers/DynamicQueryHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,25 +4,24 @@

import java.util.HashMap;
import java.util.Map;
import java.util.Collection;

public class DynamicQueryHelper {

public static Map<String,String> filterProperties(Map<String,String> properties) {
public static Map<String,Collection<String>> filterProperties(Map<String,Collection<String>> properties) {

Map<String,String> newProps = new HashMap<>();
Map<String,Collection<String>> newProps = new HashMap<>();

for(String k : properties.keySet()) {

String value = properties.get(k);

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

if(k.equals("lang") || k.equals("search") || k.equals("searchFields")
|| k.equals("boostFields") || k.equals("page") || k.equals("size") || k.equals("exactMatch")
|| k.equals("includeObsoleteEntities"))
continue;

newProps.put(k, value);
newProps.put(k, properties.get(k));
}

return newProps;
Expand Down
12 changes: 9 additions & 3 deletions backend/src/main/java/uk/ac/ebi/spot/ols/repository/solr/OlsSolrClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@

import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.net.URLDecoder;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.stream.Collectors;
Expand All @@ -39,6 +40,7 @@ public class OlsSolrClient {
private Gson gson = new Gson();

private static final Logger logger = LoggerFactory.getLogger(OlsSolrClient.class);
public static final int MAX_ROWS = 1000;

public Map<String,Object> getCoreStatus() throws IOException {
try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
Expand Down Expand Up @@ -111,11 +113,13 @@ public QueryResponse runSolrQuery(SolrQuery query, Pageable pageable) {

if(pageable != null) {
query.setStart((int)pageable.getOffset());
query.setRows(pageable.getPageSize());
query.setRows(pageable.getPageSize() > MAX_ROWS ? MAX_ROWS : pageable.getPageSize());
}

System.out.println("solr query: " + query.toQueryString());
System.out.println("solr host: " + host);
logger.debug("solr rows: {} ", query.getRows());
logger.debug("solr query: {} ", query.toQueryString());
logger.debug("solr query urldecoded: {}",URLDecoder.decode(query.toQueryString()));
logger.debug("solr host: {}", host);

org.apache.solr.client.solrj.SolrClient mySolrClient = new HttpSolrClient.Builder(host + "/solr/ols4_entities").build();

Expand All @@ -139,6 +143,8 @@ public QueryResponse runSolrQuery(SolrQuery query, Pageable pageable) {

public QueryResponse dispatchSearch(SolrQuery query, String core) throws IOException, SolrServerException {
org.apache.solr.client.solrj.SolrClient mySolrClient = new HttpSolrClient.Builder(host + "/solr/" + core).build();
final int rows = query.getRows().intValue() > MAX_ROWS ? MAX_ROWS : query.getRows().intValue();
query.setRows(rows);
QueryResponse qr = mySolrClient.query(query);
mySolrClient.close();
return qr;
Expand Down
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