Merge pull request #177 from tcezard/EVA3475_release_count_v2

EVA-3475 - Release count endpoints v2

eva-release/pom.xml

@@ -55,6 +55,10 @@
             <artifactId>springfox-swagger2</artifactId>
             <scope>compile</scope>
         </dependency>
+        <dependency>
+            <groupId>io.hypersistence</groupId>
+            <artifactId>hypersistence-utils-hibernate-52</artifactId>
+        </dependency>
     </dependencies>
 
     <build>

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

@@ -24,7 +24,6 @@
 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

eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsV2Controller.java

@@ -0,0 +1,62 @@
+/*
+ * 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 io.swagger.annotations.Api;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import uk.ac.ebi.eva.release.dto.ReleaseStatsPerAssemblyV2Dto;
+import uk.ac.ebi.eva.release.dto.ReleaseStatsPerSpeciesV2Dto;
+import uk.ac.ebi.eva.release.services.ReleaseStatsServiceV2;
+
+@RestController
+@RequestMapping(value = "/v2/stats", produces = "application/json")
+@Api(tags = {"RS Release Statistics"})
+public class ReleaseStatsV2Controller {
+
+    private final ReleaseStatsServiceV2 releaseStatsService;
+
+    public ReleaseStatsV2Controller(ReleaseStatsServiceV2 releaseStatsService) {
+        this.releaseStatsService = releaseStatsService;
+    }
+
+    @GetMapping("/per-species")
+    public Iterable<ReleaseStatsPerSpeciesV2Dto> getReleaseStatsPerSpecies(
+            @RequestParam(name = "releaseVersion", required = false) Integer releaseVersion,
+            @RequestParam(name = "excludeUnmappedOnly", required = false) boolean excludeUnmappedOnly) {
+        return releaseStatsService.getReleaseStatsPerSpecies(releaseVersion, excludeUnmappedOnly);
+    }
+
+    @GetMapping("/per-species/new")
+    public Iterable<ReleaseStatsPerSpeciesV2Dto> getSpeciesWithNewRsIds(
+            @RequestParam(name = "releaseVersion") Integer releaseVersion) {
+        return releaseStatsService.getSpeciesWithNewRsIds(releaseVersion);
+    }
+
+    @GetMapping("/per-assembly")
+    public Iterable<ReleaseStatsPerAssemblyV2Dto> getReleaseStatsPerAssemblies(
+            @RequestParam(name = "releaseVersion", required = false) Integer releaseVersion) {
+        return releaseStatsService.getReleaseStatsPerAssembly(releaseVersion);
+    }
+
+    @GetMapping("/per-assembly/new")
+    public Iterable<ReleaseStatsPerAssemblyV2Dto> getAssembliesWithNewRsIds(
+            @RequestParam(name = "releaseVersion") Integer releaseVersion) {
+        return releaseStatsService.getReleaseStatsPerAssemblyWithNewRsIds(releaseVersion);
+    }
+}

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerAssemblyV2Dto.java

@@ -0,0 +1,91 @@
+/*
+ * Copyright 2022 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.dto;
+
+import java.util.Objects;
+
+public class ReleaseStatsPerAssemblyV2Dto extends ReleaseStatsV2Dto {
+
+    private String assemblyAccession;
+
+    private int[] taxonomyIds;
+
+    private String[] taxonomyLinks;
+
+    public ReleaseStatsPerAssemblyV2Dto() {
+    }
+
+    public int[] getTaxonomyIds() {
+        return taxonomyIds;
+    }
+
+    public void setTaxonomyIds(int[] taxonomyIds) {
+        this.taxonomyIds = taxonomyIds;
+    }
+
+    public String getAssemblyAccession() {
+        return assemblyAccession;
+    }
+
+    public void setAssemblyAccession(String assemblyAccession) {
+        this.assemblyAccession = assemblyAccession;
+    }
+
+    public String[] getTaxonomyLinks() {
+        return taxonomyLinks;
+    }
+
+    public void setTaxonomyLinks(String[] taxonomyLinks) {
+        this.taxonomyLinks = taxonomyLinks;
+    }
+
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        ReleaseStatsPerAssemblyV2Dto that = (ReleaseStatsPerAssemblyV2Dto) o;
+        return releaseVersion == that.releaseVersion &&
+                Objects.equals(assemblyAccession, that.assemblyAccession);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(assemblyAccession, releaseVersion);
+    }
+
+    @Override
+    public String toString() {
+        return "ReleaseStatsPerAssemblyDto{" +
+                "assemblyAccession='" + assemblyAccession + '\'' +
+                ", releaseVersion=" + releaseVersion +
+                ", taxonomyIds=" + taxonomyIds +
+                ", releaseFolder='" + releaseFolder + '\'' +
+                ", currentRs=" + getCurrentRs() +
+                ", multiMappedRs=" + getMultiMappedRs() +
+                ", mergedRs=" + getMergedRs() +
+                ", deprecatedRs=" + getDeprecatedRs() +
+                ", mergedDeprecatedRs=" + getMergedDeprecatedRs() +
+                ", newCurrentRs=" + getNewCurrentRs() +
+                ", newMultiMappedRs=" + getNewMultiMappedRs() +
+                ", newMergedRs=" + getNewMergedRs() +
+                ", newDeprecatedRs=" + getNewDeprecatedRs() +
+                ", newMergedDeprecatedRs=" + getNewMergedDeprecatedRs() +
+                ", releaseLink='" + releaseLink + '\'' +
+                ", taxonomyLinks='" + taxonomyLinks + '\'' +
+                '}';
+    }
+}

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerSpeciesV2Dto.java

@@ -0,0 +1,130 @@
+/*
+ * 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.dto;
+
+import java.util.Objects;
+
+public class ReleaseStatsPerSpeciesV2Dto extends ReleaseStatsV2Dto {
+
+    private int taxonomyId;
+
+    private String[] assemblyAccessions;
+
+    private String taxonomyLink;
+
+    private String scientificName;
+
+    private String commonName;
+
+    public ReleaseStatsPerSpeciesV2Dto() {
+    }
+
+    public int getTaxonomyId() {
+        return taxonomyId;
+    }
+
+    public void setTaxonomyId(int taxonomyId) {
+        this.taxonomyId = taxonomyId;
+    }
+
+    public String getScientificName() {
+        return scientificName;
+    }
+
+    public void setScientificName(String scientificName) {
+        this.scientificName = scientificName;
+    }
+
+    public String getCommonName() {
+        return commonName;
+    }
+
+    public void setCommonName(String commonName) {
+        this.commonName = commonName;
+    }
+
+    public String getTaxonomyLink() {
+        return taxonomyLink;
+    }
+
+    public void setTaxonomyLink(String taxonomyLink) {
+        this.taxonomyLink = taxonomyLink;
+    }
+
+    public String[] getAssemblyAccessions() {
+        return assemblyAccessions;
+    }
+
+    public void setAssemblyAccessions(String[] assemblyAccessions) {
+        this.assemblyAccessions = assemblyAccessions;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        ReleaseStatsPerSpeciesV2Dto that = (ReleaseStatsPerSpeciesV2Dto) o;
+        return taxonomyId == that.taxonomyId &&
+                releaseVersion == that.releaseVersion &&
+                Objects.equals(scientificName, that.scientificName) &&
+                Objects.equals(releaseFolder, that.releaseFolder) &&
+                Objects.equals(currentRs, that.currentRs) &&
+                Objects.equals(multiMappedRs, that.multiMappedRs) &&
+                Objects.equals(mergedRs, that.mergedRs) &&
+                Objects.equals(deprecatedRs, that.deprecatedRs) &&
+                Objects.equals(mergedDeprecatedRs, that.mergedDeprecatedRs) &&
+                Objects.equals(unmappedRs, that.unmappedRs) &&
+                Objects.equals(newCurrentRs, that.newCurrentRs) &&
+                Objects.equals(newMultiMappedRs, that.newMultiMappedRs) &&
+                Objects.equals(newMergedRs, that.newMergedRs) &&
+                Objects.equals(newDeprecatedRs, that.newDeprecatedRs) &&
+                Objects.equals(newMergedDeprecatedRs, that.newMergedDeprecatedRs) &&
+                Objects.equals(newUnmappedRs, that.newUnmappedRs) &&
+                Objects.equals(releaseLink, that.releaseLink) &&
+                Objects.equals(taxonomyLink, that.taxonomyLink);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(taxonomyId, releaseVersion, scientificName, releaseFolder, currentRs, multiMappedRs,
+                mergedRs, deprecatedRs, mergedDeprecatedRs, unmappedRs, newCurrentRs, newMultiMappedRs, newMergedRs,
+                newDeprecatedRs, newMergedDeprecatedRs, newUnmappedRs, releaseLink, taxonomyLink);
+    }
+
+    @Override
+    public String toString() {
+        return "ReleaseStatsPerSpeciesDto{" +
+                "taxonomyId=" + taxonomyId +
+                ", releaseVersion=" + releaseVersion +
+                ", scientificName='" + scientificName + '\'' +
+                ", releaseFolder='" + releaseFolder + '\'' +
+                ", currentRs=" + getCurrentRs() +
+                ", multiMappedRs=" + getMultiMappedRs() +
+                ", mergedRs=" + getMergedRs() +
+                ", deprecatedRs=" + getDeprecatedRs() +
+                ", mergedDeprecatedRs=" + getMergedDeprecatedRs() +
+                ", unmappedRs=" + getUnmappedRs() +
+                ", newCurrentRs=" + getNewCurrentRs() +
+                ", newMultiMappedRs=" + getNewMultiMappedRs() +
+                ", newMergedRs=" + getNewMergedRs() +
+                ", newDeprecatedRs=" + getNewDeprecatedRs() +
+                ", newMergedDeprecatedRs=" + getNewMergedDeprecatedRs() +
+                ", newUnmappedRs=" + getNewUnmappedRs() +
+                ", releaseLink='" + releaseLink + '\'' +
+                ", taxonomyLink='" + taxonomyLink + '\'' +
+                '}';
+    }
+}