EVA-2217 Improve release api

.gitlab-ci.yml

@@ -5,6 +5,7 @@ stages:
 
 variables:
     WS_ARTIFACT_PATH: eva-server/target/eva-$ENVIRONMENT_NAME.war
+    WS_RS_RELEASE_ARTIFACT_PATH: eva-release/target/eva-release-$ENVIRONMENT_NAME.war
     MAVEN_SETTINGS: maven-settings.xml
     URL_MAVEN_SETTINGS: https://api.github.com/repos/EBIvariation/configuration/contents/eva-maven-settings.xml
     MEDIA_TYPE: application/vnd.github.raw
@@ -16,7 +17,7 @@ test:
         - mongo:4.0.18
     script:
         # Gitlab exposes services under their own hostnames. So test host should be "mongo" instead of "localhost".
-        - mvn clean test --projects 'eva-lib,eva-server' -Deva.mongo.host.test=mongo
+        - mvn clean test --projects 'eva-lib,eva-server,eva-release' -Deva.mongo.host.test=mongo
     only:
         - master
         - tags
@@ -34,11 +35,13 @@ test:
     script:
         - mvn package --projects 'eva-lib,eva-server' --settings $MAVEN_SETTINGS -P $MAVEN_PROFILE -DskipTests -Dtimestamp=$DATETIME
         - cp eva-server/target/eva-*.war $WS_ARTIFACT_PATH
+        - cp eva-release/target/eva-release-*.war $WS_RS_RELEASE_ARTIFACT_PATH
     after_script:
         - rm $MAVEN_SETTINGS
     artifacts:
         paths:
             - $WS_ARTIFACT_PATH
+            - $WS_RS_RELEASE_ARTIFACT_PATH
 
 package-internal:
     extends: .package
@@ -74,6 +77,7 @@ package-production:
         - DATETIME=$(date +%Y-%m-%dT%H-%M-%S)
         - apk add --update curl
         - curl -u $TOMCAT_USER:$TOMCAT_PASSWORD -T "$WS_ARTIFACT_PATH" "http://$TOMCAT_HOST/manager/text/deploy?update=true&path=/eva&version=$DATETIME" | grep "OK - Deployed application"
+        - curl -u $TOMCAT_USER:$TOMCAT_PASSWORD -T "$WS_RS_RELEASE_ARTIFACT_PATH" "http://$TOMCAT_HOST/manager/text/deploy?update=true&path=/eva/webservices/release&version=$DATETIME" | grep "OK - Deployed application"
 
 deploy-tomcat-internal:
     extends: .deploy-tomcat

eva-release/pom.xml

@@ -55,6 +55,10 @@
             <artifactId>springfox-swagger2</artifactId>
             <scope>compile</scope>
         </dependency>
+        <dependency>
+            <groupId>org.hsqldb</groupId>
+            <artifactId>hsqldb</artifactId>
+        </dependency>
     </dependencies>
 
     <build>

eva-release/src/main/java/uk/ac/ebi/eva/release/SwaggerConfiguration.java → eva-release/src/main/java/uk/ac/ebi/eva/release/configuration/SwaggerConfiguration.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package uk.ac.ebi.eva.release;
+package uk.ac.ebi.eva.release.configuration;
 
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -47,8 +47,8 @@ private ApiInfo getApiInfo() {
                 .licenseUrl("http://www.apache.org/licenses/LICENSE-2.0")
                 .title("EVA RS Release API")
                 .description(
-                        "API to retrieve information about clustered variant identifiers (usually called RefSNP or RS)" +
-                                "released by the EVA")
+                        "API to retrieve information about clustered variant identifiers (usually called RefSNP or " +
+                                "RS) released by the EVA")
                 .version("0.1")
                 .build();
     }

eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoController.java

@@ -16,6 +16,7 @@
 package uk.ac.ebi.eva.release.controllers;
 
 import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
@@ -24,7 +25,6 @@
 import uk.ac.ebi.eva.release.models.ReleaseInfo;
 import uk.ac.ebi.eva.release.repositories.ReleaseInfoRepository;
 
-import javax.websocket.server.PathParam;
 import java.util.Collections;
 
 @RestController
@@ -40,6 +40,7 @@ public ReleaseInfoController(ReleaseInfoRepository releaseInfoRepository) {
 
     @GetMapping
     public Iterable<ReleaseInfo> getReleaseInfo(
+            @ApiParam(value = "Version of the RS Release, e.g.: 2")
             @RequestParam(name = "releaseVersion", required = false) Integer releaseVersion) {
         if (releaseVersion != null) {
             return Collections.singleton(releaseInfoRepository.findById(releaseVersion).get());

eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsController.java

@@ -16,6 +16,7 @@
 package uk.ac.ebi.eva.release.controllers;
 
 import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
@@ -37,13 +38,16 @@ public ReleaseStatsController(ReleaseStatsService releaseStatsService) {
 
     @GetMapping("/per-species")
     public Iterable<ReleaseStatsPerSpeciesDto> getReleaseStatsPerSpecies(
+            @ApiParam(value = "Version of the RS Release, e.g.: 2")
             @RequestParam(name = "releaseVersion", required = false) Integer releaseVersion,
+            @ApiParam(value = "Flag to indicate if unmapped variants should be excluded from statistics")
             @RequestParam(name = "excludeUnmappedOnly", required = false) boolean excludeUnmappedOnly) {
         return releaseStatsService.getReleaseStatsPerSpecies(releaseVersion, excludeUnmappedOnly);
     }
 
     @GetMapping("/per-species/new")
     public Iterable<ReleaseStatsPerSpeciesDto> getSpeciesWithNewRsIds(
+            @ApiParam(value = "Version of the RS Release, e.g.: 2")
             @RequestParam(name = "releaseVersion") Integer releaseVersion) {
         return releaseStatsService.getSpeciesWithNewRsIds(releaseVersion);
     }

eva-release/src/main/java/uk/ac/ebi/eva/release/repositories/ReleaseStatsPerSpeciesRepository.java

@@ -15,6 +15,7 @@
  */
 package uk.ac.ebi.eva.release.repositories;
 
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.stereotype.Repository;
 
@@ -27,17 +28,21 @@ public interface ReleaseStatsPerSpeciesRepository extends CrudRepository<Release
 
     Iterable<ReleaseStatsPerSpecies> findAllByReleaseVersion(int releaseVersion);
 
-    //All release data excluding rows with only unmapped data
-    Iterable<ReleaseStatsPerSpecies> findByCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan(
-            long currentRs, long multiMappedRs, long mergedRs, long deprecatedRs, long mergedDeprecatedRs,
-            long unmappedRs);
-
-    //Data by release version excluding rows with only unmapped data
-    Iterable<ReleaseStatsPerSpecies> findByReleaseVersionAndCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan(
-            int releaseVersion, long currentRs, long multiMappedRs, long mergedRs, long deprecatedRs,
-            long mergedDeprecatedRs, long unmappedRs);
-
-    Iterable<ReleaseStatsPerSpecies> findByNewCurrentRsGreaterThan(long currentRs);
-
-    Iterable<ReleaseStatsPerSpecies> findByReleaseVersionAndNewCurrentRsGreaterThan(int releaseVersion, long currentRs);
+    //All released species stats excluding the unmapped only
+    @Query(value = "select * from release_rs_statistics_per_species " +
+            "where not (current_rs = 0 and multi_mapped_rs = 0 and merged_rs = 0 and deprecated_rs = 0 " +
+            "and merged_deprecated_rs = 0 and unmapped_rs > 0)", nativeQuery=true)
+    Iterable<ReleaseStatsPerSpecies> getAllExcludingUnmappedOnly();
+
+    //Species stats by release version excluding the unmapped only
+    @Query(value = "select * from release_rs_statistics_per_species " +
+            "where release_version = ?1 and not (current_rs = 0 and multi_mapped_rs = 0 and merged_rs = 0 " +
+            "and deprecated_rs = 0  and merged_deprecated_rs = 0 and unmapped_rs > 0)", nativeQuery=true)
+    Iterable<ReleaseStatsPerSpecies> getAllByVersionExcludingUnmappedOnly(int releaseVersion);
+
+    //Species that introduced new variants in specified release
+    @Query(value = "select * from release_rs_statistics_per_species where release_version = ?1 " +
+            "and (new_current_rs > 0 or new_merged_rs > 0 or new_deprecated_rs > 0 or new_merged_deprecated_rs > 0 " +
+            "or new_unmapped_rs > 0)", nativeQuery=true)
+    Iterable<ReleaseStatsPerSpecies> getSpeciesWithVariantsInRelease(int releaseVersion);
 }

eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsService.java

@@ -44,32 +44,20 @@ public Iterable<ReleaseStatsPerSpeciesDto> getReleaseStatsPerSpecies(Integer rel
         Iterable<ReleaseStatsPerSpecies> releaseData;
         if (releaseVersion != null) {
             if (excludeUnmappedOnly) {
-                releaseData = getReleaseDataByVersionExcludingUnmappedOnly(releaseVersion);
+                releaseData = releaseStatsPerSpeciesRepository.getAllByVersionExcludingUnmappedOnly(releaseVersion);
             } else {
                 releaseData = releaseStatsPerSpeciesRepository.findAllByReleaseVersion(releaseVersion);
             }
         } else {
             if (excludeUnmappedOnly) {
-                releaseData = getReleaseDataExcludingUnmappedOnly();
+                releaseData = releaseStatsPerSpeciesRepository.getAllExcludingUnmappedOnly();
             } else {
                 releaseData = releaseStatsPerSpeciesRepository.findAll();
             }
         }
         return toDto(releaseData);
     }
 
-    private Iterable<ReleaseStatsPerSpecies> getReleaseDataByVersionExcludingUnmappedOnly(Integer releaseVersion) {
-        return releaseStatsPerSpeciesRepository
-                .findByReleaseVersionAndCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan(
-                        releaseVersion, 0, 0, 0, 0, 0, 0);
-    }
-
-    private Iterable<ReleaseStatsPerSpecies> getReleaseDataExcludingUnmappedOnly() {
-        return releaseStatsPerSpeciesRepository
-                .findByCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan(
-                        0, 0, 0, 0, 0, 0);
-    }
-
     private Iterable<ReleaseStatsPerSpeciesDto> toDto(Iterable<ReleaseStatsPerSpecies> releaseStatsPerSpecies) {
         List<ReleaseStatsPerSpeciesDto> releaseStatsPerSpeciesDtos = new ArrayList();
         for (ReleaseStatsPerSpecies species : releaseStatsPerSpecies) {
@@ -105,11 +93,6 @@ private ReleaseStatsPerSpeciesDto toDto(ReleaseStatsPerSpecies releaseStatsPerSp
     }
 
     public Iterable<ReleaseStatsPerSpeciesDto> getSpeciesWithNewRsIds(Integer releaseVersion) {
-        if (releaseVersion != null) {
-            return toDto(releaseStatsPerSpeciesRepository
-                                 .findByReleaseVersionAndNewCurrentRsGreaterThan(releaseVersion, 0L));
-        } else {
-            return toDto(releaseStatsPerSpeciesRepository.findByNewCurrentRsGreaterThan(0L));
-        }
+        return toDto(releaseStatsPerSpeciesRepository.getSpeciesWithVariantsInRelease(releaseVersion));
     }
 }

eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoControllerTest.java

@@ -0,0 +1,57 @@
+/*
+ * Copyright 2020 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.release.controllers;
+
+import org.assertj.core.util.IterableUtil;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import uk.ac.ebi.eva.release.Application;
+import uk.ac.ebi.eva.release.models.ReleaseInfo;
+
+import static org.junit.Assert.assertEquals;
+
+@SpringBootTest(classes = Application.class)
+@RunWith(SpringRunner.class)
+public class ReleaseInfoControllerTest {
+
+    @Autowired
+    private ReleaseInfoController releaseInfoController;
+
+    @Test
+    public void getOneReleaseInfo() {
+        int releaseVersion = 1;
+        Iterable<ReleaseInfo> releaseInfo = releaseInfoController.getReleaseInfo(releaseVersion);
+        assertEquals(releaseVersion, releaseInfo.iterator().next().getReleaseVersion());
+    }
+
+    @Test
+    public void getAllReleasesInfo() {
+        Integer releaseVersion = null;
+        Iterable<ReleaseInfo> releaseInfo = releaseInfoController.getReleaseInfo(releaseVersion);
+        assertEquals(2, IterableUtil.sizeOf(releaseInfo));
+    }
+
+    @Test
+    public void getLatestReleaseInfo() {
+        int latestReleaseVersion = 2;
+        ReleaseInfo latestReleaseInfo = releaseInfoController.getLatestReleaseInfo();
+        assertEquals(latestReleaseVersion, latestReleaseInfo.getReleaseVersion());
+    }
+}

eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java

@@ -0,0 +1,72 @@
+/*
+ * Copyright 2020 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.release.controllers;
+
+import org.assertj.core.util.IterableUtil;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import uk.ac.ebi.eva.release.Application;
+import uk.ac.ebi.eva.release.dto.ReleaseStatsPerSpeciesDto;
+
+import static org.junit.Assert.assertEquals;
+
+@SpringBootTest(classes = Application.class)
+@RunWith(SpringRunner.class)
+public class ReleaseStatsControllerTest {
+
+    @Autowired
+    private ReleaseStatsController releaseStatsController;
+
+    @Test
+    public void getAllSpeciesStats() {
+        int totalNumberOfRecords = 417;
+        Iterable<ReleaseStatsPerSpeciesDto> allRecords = releaseStatsController.getReleaseStatsPerSpecies(null, false);
+        assertEquals(totalNumberOfRecords, IterableUtil.sizeOf(allRecords));
+    }
+
+    @Test
+    public void getStatsByReleaseVersion() {
+        int speciesInRelease2 = 218;
+        Iterable<ReleaseStatsPerSpeciesDto> allRecords = releaseStatsController.getReleaseStatsPerSpecies(2, false);
+        assertEquals(speciesInRelease2, IterableUtil.sizeOf(allRecords));
+    }
+
+    @Test
+    public void getStatsByReleaseVersionNoUnmapped() {
+        int speciesInRelease1ExcludingUnmapped = 58;
+        Iterable<ReleaseStatsPerSpeciesDto> release1 = releaseStatsController.getReleaseStatsPerSpecies(1, true);
+        assertEquals(speciesInRelease1ExcludingUnmapped, IterableUtil.sizeOf(release1));
+
+        int speciesInRelease2ExcludingUnmapped = 79;
+        Iterable<ReleaseStatsPerSpeciesDto> release2 = releaseStatsController.getReleaseStatsPerSpecies(2, true);
+        assertEquals(speciesInRelease2ExcludingUnmapped, IterableUtil.sizeOf(release2));
+    }
+
+    @Test
+    public void getStatsForNewVariantsOnlyInSpecificRelease() {
+        int numberOfSpeciesWithNewVariantsRelease1 = 199;
+        Iterable<ReleaseStatsPerSpeciesDto> Release1 = releaseStatsController.getSpeciesWithNewRsIds(1);
+        assertEquals(numberOfSpeciesWithNewVariantsRelease1, IterableUtil.sizeOf(Release1));
+
+        int numberOfSpeciesWithNewVariantsRelease2 = 29;
+        Iterable<ReleaseStatsPerSpeciesDto> Release2 = releaseStatsController.getSpeciesWithNewRsIds(2);
+        assertEquals(numberOfSpeciesWithNewVariantsRelease2, IterableUtil.sizeOf(Release2));
+    }
+}

eva-release/src/test/resources/application.properties

@@ -0,0 +1,10 @@
+spring.datasource.driver-class-name=org.hsqldb.jdbcDriver
+spring.datasource.url=jdbc:hsqldb:mem:db;sql.syntax_pgs=true;DB_CLOSE_DELAY=-1
+spring.datasource.username=SA
+spring.datasource.password=
+
+spring.jpa.generate-ddl=true
+spring.jpa.show-sql=true
+
+# See https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.1-Release-Notes#bean-overriding
+spring.main.allow-bean-definition-overriding=true