Merge pull request #692 from EBISPOT/IsObsolete_Related_issues

Is obsolete related issues

.github/workflows/docker.yml

@@ -29,15 +29,13 @@ jobs:
 
       - name: Build and push ols4 dataload Docker image
         run: |
-          cd dataload
-          docker build -t ghcr.io/ebispot/ols4-dataload:${{ github.sha }} .
+          docker build -t ghcr.io/ebispot/ols4-dataload:${{ github.sha }} -f ./dataload/Dockerfile .
           docker tag ghcr.io/ebispot/ols4-dataload:${{github.sha}} ghcr.io/ebispot/ols4-dataload:${{ github.head_ref || github.ref_name }}
           docker push --all-tags ghcr.io/ebispot/ols4-dataload
 
       - name: Build and push ols4 backend Docker image
         run: |
-          cd backend
-          docker build -t ghcr.io/ebispot/ols4-backend:${{ github.sha }} .
+          docker build -t ghcr.io/ebispot/ols4-backend:${{ github.sha }} -f ./backend/Dockerfile .
           docker tag ghcr.io/ebispot/ols4-backend:${{github.sha}} ghcr.io/ebispot/ols4-backend:${{ github.head_ref || github.ref_name }}
           docker push --all-tags ghcr.io/ebispot/ols4-backend
 

README.md

@@ -189,7 +189,7 @@ Once the backend is up, you can start the frontend with:
 
 Once you are done testing, to stop everything:
 
-    ./stopall.sh
+    ./stopNeo4JSolr.sh
 
 ### Running the dataload locally
 
@@ -395,7 +395,7 @@ Ensure that all differences in this file can be explained and that they do make
 new expected output:
 
        rm -rf testcases_expected_output
-       cp -r testcases_output testcases_expected_output
+       cp -r testcases_output/testcases testcases_expected_output
 
 6. Now continue with API testing.
 
@@ -432,6 +432,6 @@ the old `testcases_expected_output_api` and replace with new expected output:
 
 12. You can stop the OLS4 backend with "Ctrl-C", and Solr and Neo4J with:
 
-        ./dev-testing/stopall.sh
+        ./dev-testing/stopNeo4JSolr.sh
 
 

backend/Dockerfile

@@ -1,11 +1,17 @@
 
-FROM maven:3.6.3-adoptopenjdk-14
+#FROM maven:3.6.3-adoptopenjdk-14
+FROM maven:3.8-jdk-11
 
-RUN mkdir /opt/ols
-COPY . /opt/ols/ 
-RUN cd /opt/ols && ls && mvn clean package -DskipTests
+RUN mkdir /opt/ols && mkdir /opt/ols/backend && mkdir /opt/ols/ols-shared
+COPY ./backend /opt/ols/backend
+COPY ./ols-shared /opt/ols/ols-shared
+
+RUN cd /opt/ols/ols-shared && mvn package
+
+RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/ols/ols-shared/target/ols4-shared-1.0.0-SNAPSHOT.jar -DgroupId=uk.ac.ebi.spot.ols -DartifactId=ols4-shared -Dversion=1.0.0-SNAPSHOT
+RUN cd /opt/ols/backend && ls && mvn clean package -DskipTests
 
 EXPOSE 8080
-ENTRYPOINT ["java", "-jar", "/opt/ols/target/ols4-backend-4.0.0-SNAPSHOT.jar"]
+ENTRYPOINT ["java", "-jar", "/opt/ols/backend/target/ols4-backend-4.0.0-SNAPSHOT.jar"]
 
 

backend/pom.xml

@@ -21,7 +21,11 @@
     </properties>
 
     <dependencies>
-
+        <dependency>
+            <groupId>uk.ac.ebi.spot.ols</groupId>
+            <artifactId>ols4-shared</artifactId>
+            <version>1.0.0-SNAPSHOT</version>
+        </dependency>
     	<dependency>
     		<groupId>com.google.code.gson</groupId>
     		<artifactId>gson</artifactId>

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java

@@ -25,7 +25,6 @@
 import org.slf4j.LoggerFactory;
 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;
@@ -44,11 +43,9 @@
 import uk.ac.ebi.spot.ols.repository.v1.V1OntologyRepository;
 import uk.ac.ebi.spot.ols.repository.v1.mappers.AnnotationExtractor;
 
-/**
- * @author Simon Jupp
- * @date 02/07/2015
- * Samples, Phenotypes and Ontologies Team, EMBL-EBI
- */
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
+
+
 @Tag(name = "Search Controller")
 @RestController
 public class V1SearchController {
@@ -186,7 +183,7 @@ public void search(
             }
         }
 
-        solrQuery.addFilterQuery("isObsolete:" + queryObsoletes);
+        solrQuery.addFilterQuery(IS_OBSOLETE.getText() + ":" + queryObsoletes);
 
         solrQuery.setStart(start);
         solrQuery.setRows(rows);
@@ -206,7 +203,12 @@ public void search(
 		 *
 		 */
 		// TODO: Need to check and add additional faceted fields if required
-		solrQuery.addFacetField("ontologyId", "ontologyIri", "ontologyPreferredPrefix", "type", "isDefiningOntology", "isObsolete");
+		solrQuery.addFacetField("ontologyId",
+                "ontologyIri",
+                "ontologyPreferredPrefix",
+                "type",
+                "isDefiningOntology",
+                IS_OBSOLETE.getText());
 		/*
 		 * Fix: End
 		 */

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java

@@ -6,14 +6,12 @@
 import io.swagger.v3.oas.annotations.tags.Tag;
 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.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 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;
@@ -32,6 +30,7 @@
 import java.util.*;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 @Tag(name = "Select Controller")
 @RestController
@@ -112,7 +111,7 @@ public void select(
             solrQuery.addFilterQuery("hierarchicalAncestor: (" + result + ")");
         }
 
-        solrQuery.addFilterQuery("isObsolete:" + queryObsoletes);
+        solrQuery.addFilterQuery(IS_OBSOLETE.getText() + ":" + queryObsoletes);
         solrQuery.setStart(start);
         solrQuery.setRows(rows);
         solrQuery.setHighlight(true);

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2ClassController.java

@@ -1,14 +1,9 @@
 package uk.ac.ebi.spot.ols.controller.api.v2;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
-import org.springframework.data.rest.webmvc.RepositoryLinksResource;
 import org.springframework.data.rest.webmvc.ResourceNotFoundException;
 import org.springframework.data.web.PageableDefault;
-import org.springframework.data.web.PagedResourcesAssembler;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
@@ -24,9 +19,7 @@
 import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedAndFacetedResponse;
 import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedResponse;
 import uk.ac.ebi.spot.ols.model.v2.V2Entity;
-import uk.ac.ebi.spot.ols.repository.solr.OlsFacetedResultsPage;
 import uk.ac.ebi.spot.ols.repository.v2.V2ClassRepository;
-import uk.ac.ebi.spot.ols.repository.v2.V2EntityRepository;
 
 import javax.validation.constraints.NotNull;
 import java.io.IOException;
@@ -35,6 +28,8 @@
 import java.util.List;
 import java.util.Map;
 
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
+
 @Controller
 @RequestMapping("/api/v2")
 public class V2ClassController {
@@ -56,7 +51,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getClasses(
 
 	Map<String, Collection<String>> properties = new HashMap<>();
     if(!includeObsoleteEntities)
-        properties.put("isObsolete", List.of("false"));
+        properties.put(IS_OBSOLETE.getText(), List.of("false"));
 	properties.putAll(searchProperties);
 
         return new ResponseEntity<>(
@@ -82,7 +77,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getClasses(
 
         Map<String,Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2EntityController.java

@@ -18,7 +18,6 @@
 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;
-import uk.ac.ebi.spot.ols.repository.solr.OlsFacetedResultsPage;
 import uk.ac.ebi.spot.ols.repository.v2.V2EntityRepository;
 
 import javax.validation.constraints.NotNull;
@@ -28,6 +27,8 @@
 import java.util.List;
 import java.util.Map;
 
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
+
 @Controller
 @RequestMapping("/api/v2")
 public class V2EntityController {
@@ -50,7 +51,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getEntities(
 
         Map<String,Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(
@@ -76,7 +77,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getTerms(
 
         Map<String,Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2IndividualController.java

@@ -21,6 +21,7 @@
 import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedResponse;
 import uk.ac.ebi.spot.ols.model.v2.V2Entity;
 import uk.ac.ebi.spot.ols.repository.v2.V2IndividualRepository;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 import javax.validation.constraints.NotNull;
 import java.io.IOException;
@@ -50,7 +51,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getIndividuals(
 
         Map<String, Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(
@@ -75,7 +76,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getIndividuals(
 
         Map<String, Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2OntologyController.java

@@ -19,9 +19,8 @@
 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;
-import uk.ac.ebi.spot.ols.repository.solr.OlsFacetedResultsPage;
-import uk.ac.ebi.spot.ols.repository.v2.V2EntityRepository;
 import uk.ac.ebi.spot.ols.repository.v2.V2OntologyRepository;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 import java.io.IOException;
 import java.util.Collection;
@@ -54,7 +53,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getOntologies(
 
         Map<String,Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/V2PropertyController.java

@@ -18,6 +18,9 @@
 import uk.ac.ebi.spot.ols.model.v2.V2Entity;
 import uk.ac.ebi.spot.ols.repository.v2.V2PropertyRepository;
 
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
+
+
 import javax.validation.constraints.NotNull;
 import java.io.IOException;
 import java.util.Collection;
@@ -46,7 +49,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getProperties(
 
         Map<String,Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(
@@ -71,7 +74,7 @@ public HttpEntity<V2PagedAndFacetedResponse<V2Entity>> getProperties(
 
         Map<String,Collection<String>> properties = new HashMap<>();
         if(!includeObsoleteEntities)
-            properties.put("isObsolete", List.of("false"));
+            properties.put(IS_OBSOLETE.getText(), List.of("false"));
         properties.putAll(searchProperties);
 
         return new ResponseEntity<>(

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1PropertyRepository.java

@@ -15,6 +15,7 @@
 import uk.ac.ebi.spot.ols.repository.solr.OlsSolrQuery;
 import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
 import uk.ac.ebi.spot.ols.repository.v1.mappers.V1PropertyMapper;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 @Component
 public class V1PropertyRepository {
@@ -97,7 +98,7 @@ public Page<V1Property> getRoots(String ontologyId, boolean obsolete, String lan
         query.addFilter("hasHierarchicalParent", List.of("false"), SearchType.WHOLE_FIELD);
 
         if(!obsolete)
-            query.addFilter("isObsolete", List.of("false"), SearchType.WHOLE_FIELD);
+            query.addFilter(IS_OBSOLETE.getOls3Text(), List.of("false"), SearchType.WHOLE_FIELD);
 
         return solrClient.searchSolrPaginated(query, pageable)
                 .map(result -> V1PropertyMapper.mapProperty(result, lang));

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1TermRepository.java

@@ -15,6 +15,7 @@
 import uk.ac.ebi.spot.ols.repository.solr.OlsSolrQuery;
 import uk.ac.ebi.spot.ols.repository.solr.SearchType;
 import uk.ac.ebi.spot.ols.repository.v1.mappers.V1TermMapper;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 import java.util.Arrays;
 import java.util.List;
@@ -134,7 +135,7 @@ public Page<V1Term> findAllByOntology(String ontologyId, Boolean obsoletes, Stri
         OlsSolrQuery query = new OlsSolrQuery();
         query.addFilter("type", List.of("class"), SearchType.WHOLE_FIELD);
         query.addFilter("ontologyId", List.of(ontologyId), SearchType.WHOLE_FIELD);
-        if (obsoletes != null) query.addFilter("isObsolete", List.of(Boolean.toString(obsoletes)), SearchType.WHOLE_FIELD);
+        if (obsoletes != null) query.addFilter(IS_OBSOLETE.getOls3Text(), List.of(Boolean.toString(obsoletes)), SearchType.WHOLE_FIELD);
 
         return solrClient.searchSolrPaginated(query, pageable)
                 .map(result -> V1TermMapper.mapTerm(result, lang));
@@ -184,7 +185,7 @@ public Page<V1Term> getRoots(String ontologyId, boolean obsolete, String lang, P
         query.addFilter("hasHierarchicalParent", List.of("false"), SearchType.WHOLE_FIELD);
 
         if (!obsolete)
-            query.addFilter("isObsolete", List.of("false"), SearchType.WHOLE_FIELD);
+            query.addFilter(IS_OBSOLETE.getOls3Text(), List.of("false"), SearchType.WHOLE_FIELD);
 
         return solrClient.searchSolrPaginated(query, pageable)
                 .map(result -> V1TermMapper.mapTerm(result, lang));

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/mappers/V1TermMapper.java

@@ -5,6 +5,7 @@
 import uk.ac.ebi.spot.ols.model.v1.*;
 import uk.ac.ebi.spot.ols.repository.transforms.LocalizationTransform;
 import uk.ac.ebi.spot.ols.repository.v1.JsonHelper;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 import java.util.*;
 
@@ -54,7 +55,7 @@ public static V1Term mapTerm(JsonElement json, String lang) {
                         Boolean.parseBoolean(JsonHelper.getString(localizedJson, "hasHierarchicalParent"))
         );
 
-        term.isObsolete = Boolean.parseBoolean(JsonHelper.getString(localizedJson, "isObsolete"));
+        term.isObsolete = Boolean.parseBoolean(JsonHelper.getString(localizedJson, IS_OBSOLETE.getText()));
 
 
         List<JsonElement> replacedBy = JsonHelper.getValues(localizedJson, "http://purl.obolibrary.org/obo/IAO_0100001");