Merge pull request #656 from overture-stack/rc/4.2.3

Release Candidate 4.2.3

Author: rtisma

pom.xml

@@ -21,7 +21,7 @@
     <groupId>bio.overture</groupId>
     <artifactId>song</artifactId>
     <packaging>pom</packaging>
-    <version>4.2.2</version>
+    <version>4.2.3</version>
     <modules>
         <module>song-core</module>
         <module>song-java-sdk</module>

song-client/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 
@@ -35,12 +35,12 @@
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-java-sdk</artifactId>
-			<version>4.2.2</version>
+			<version>4.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>bio.overture</groupId>
 			<artifactId>song-core</artifactId>
-			<version>4.2.2</version>
+			<version>4.2.3</version>
 		</dependency>
 
 		<!-- CLI -->

song-core/pom.xml

@@ -19,7 +19,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-java-sdk/pom.xml

@@ -18,7 +18,7 @@
 	<parent>
 		<artifactId>song</artifactId>
 		<groupId>bio.overture</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

song-server/pom.xml

@@ -19,7 +19,7 @@
     <parent>
         <artifactId>song</artifactId>
         <groupId>bio.overture</groupId>
-        <version>4.2.2</version>
+        <version>4.2.3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>bio.overture</groupId>
             <artifactId>song-core</artifactId>
-            <version>4.2.2</version>
+            <version>4.2.3</version>
         </dependency>
 
         <!-- Spring -->

song-server/src/main/java/bio/overture/song/server/config/NoSecurityConfig.java

@@ -0,0 +1,17 @@
+package bio.overture.song.server.config;
+
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Profile;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
+
+@Profile("noSecurityDev")
+@Configuration
+@EnableWebSecurity
+public class NoSecurityConfig extends WebSecurityConfigurerAdapter {
+  @Override
+  protected void configure(HttpSecurity http) throws Exception {
+    http.authorizeRequests().antMatchers("/").permitAll();
+  }
+}

song-server/src/main/java/bio/overture/song/server/controller/AnalysisController.java

@@ -25,14 +25,14 @@
 import bio.overture.song.server.model.analysis.Analysis;
 import bio.overture.song.server.model.entity.FileEntity;
 import bio.overture.song.server.repository.search.IdSearchRequest;
-import bio.overture.song.server.service.AnalysisService;
+import bio.overture.song.server.service.analysis.AnalysisService;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.google.common.collect.ImmutableSet;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
 import java.util.List;
-import lombok.RequiredArgsConstructor;
+import lombok.NonNull;
 import lombok.SneakyThrows;
 import lombok.val;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -50,7 +50,6 @@
 import org.springframework.web.bind.annotation.RestController;
 
 @RestController
-@RequiredArgsConstructor
 @RequestMapping("/studies/{studyId}/analysis")
 @Api(
     tags = "Analysis",
@@ -71,7 +70,12 @@ public class AnalysisController {
           + "}";
 
   /** Dependencies */
-  @Autowired private final AnalysisService analysisService;
+  private final AnalysisService analysisService;
+
+  @Autowired
+  public AnalysisController(@NonNull AnalysisService analysisService) {
+    this.analysisService = analysisService;
+  }
 
   @ApiOperation(
       value = "GetAnalysesForStudy",

song-server/src/main/java/bio/overture/song/server/controller/analysisType/AnalysisTypeController.java

@@ -86,7 +86,6 @@ public AnalysisType getAnalysisTypeVersion(
       @ApiParam(
               value = "Optionally, retrieve a specific version of the analysisType",
               type = "integer",
-              defaultValue = "false",
               required = false)
           @RequestParam(value = "version", required = false)
           Integer version) {

song-server/src/main/java/bio/overture/song/server/kafka/AnalysisMessage.java

@@ -21,13 +21,24 @@
 import static lombok.AccessLevel.PRIVATE;
 
 import bio.overture.song.core.model.enums.AnalysisStates;
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import lombok.AccessLevel;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.NoArgsConstructor;
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import lombok.Value;
 
 @Value
-@RequiredArgsConstructor(access = PRIVATE)
+//Note: although the AllArgs and NoArgs combination below seems odd,
+// it allows Jackson to deserialize to an immutable object without using any additional annotations.
+@AllArgsConstructor
+@NoArgsConstructor(force = true, access = PRIVATE)
 public class AnalysisMessage {
+
   @NonNull private final String analysisId;
   @NonNull private final String studyId;
   @NonNull private final String state;

song-server/src/main/java/bio/overture/song/server/service/DonorService.java

@@ -31,6 +31,7 @@
 import bio.overture.song.server.model.entity.Donor;
 import bio.overture.song.server.model.entity.composites.DonorWithSpecimens;
 import bio.overture.song.server.repository.DonorRepository;
+import bio.overture.song.server.service.InfoService.DonorInfoService;
 import bio.overture.song.server.service.id.IdService;
 import java.util.ArrayList;
 import java.util.List;

song-server/src/main/java/bio/overture/song/server/service/ExportService.java

@@ -34,6 +34,7 @@
 import bio.overture.song.server.model.entity.FileEntity;
 import bio.overture.song.server.model.entity.Sample;
 import bio.overture.song.server.model.entity.Specimen;
+import bio.overture.song.server.service.analysis.AnalysisService;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.google.common.collect.ImmutableList;

song-server/src/main/java/bio/overture/song/server/service/FileModificationService.java

@@ -35,6 +35,7 @@
 import bio.overture.song.core.model.enums.FileUpdateTypes;
 import bio.overture.song.server.converter.FileConverter;
 import bio.overture.song.server.model.entity.FileEntity;
+import bio.overture.song.server.service.analysis.AnalysisService;
 import javax.transaction.Transactional;
 import lombok.NonNull;
 import lombok.val;

song-server/src/main/java/bio/overture/song/server/service/FileService.java

@@ -27,6 +27,7 @@
 import bio.overture.song.server.converter.FileConverter;
 import bio.overture.song.server.model.entity.FileEntity;
 import bio.overture.song.server.repository.FileRepository;
+import bio.overture.song.server.service.InfoService.FileInfoService;
 import bio.overture.song.server.service.id.IdService;
 import java.util.List;
 import java.util.Optional;

song-server/src/main/java/bio/overture/song/server/service/InfoService.java

@@ -44,7 +44,7 @@
 
 @Service
 @RequiredArgsConstructor
-abstract class InfoService {
+public abstract class InfoService {
 
   private final InfoTypes type;
   private final InfoRepository infoRepository;
@@ -119,60 +119,45 @@ private List<Info> findInfo(@NonNull Set<String> ids) {
     val searchRequest = ids.stream().map(this::buildPK).collect(toList());
     return infoRepository.findAllByInfoPKIn(searchRequest);
   }
-}
 
-@Service
-class StudyInfoService extends InfoService {
-  @Autowired
-  StudyInfoService(InfoRepository repo) {
-    super(InfoTypes.STUDY, repo);
+  @Service
+  public static class StudyInfoService extends InfoService {
+    @Autowired
+    StudyInfoService(InfoRepository repo) {
+      super(InfoTypes.STUDY, repo);
+    }
   }
-}
 
-@Service
-class DonorInfoService extends InfoService {
-  @Autowired
-  DonorInfoService(InfoRepository repo) {
-    super(InfoTypes.DONOR, repo);
+  @Service
+  public static class DonorInfoService extends InfoService {
+    @Autowired
+    DonorInfoService(InfoRepository repo) {
+      super(InfoTypes.DONOR, repo);
+    }
   }
-}
 
-@Service
-class SpecimenInfoService extends InfoService {
-  @Autowired
-  SpecimenInfoService(InfoRepository repo) {
-    super(InfoTypes.SPECIMEN, repo);
+  @Service
+  public static class SpecimenInfoService extends InfoService {
+    @Autowired
+    SpecimenInfoService(InfoRepository repo) {
+      super(InfoTypes.SPECIMEN, repo);
+    }
   }
-}
 
-@Service
-class SampleInfoService extends InfoService {
-  @Autowired
-  SampleInfoService(InfoRepository repo) {
-    super(InfoTypes.SAMPLE, repo);
+  @Service
+  public static class SampleInfoService extends InfoService {
+    @Autowired
+    SampleInfoService(InfoRepository repo) {
+      super(InfoTypes.SAMPLE, repo);
+    }
   }
-}
 
-@Service
-class FileInfoService extends InfoService {
-  @Autowired
-  FileInfoService(InfoRepository repo) {
-    super(InfoTypes.FILE, repo);
-  }
-}
-
-@Service
-class VariantCallInfoService extends InfoService {
-  @Autowired
-  VariantCallInfoService(InfoRepository repo) {
-    super(InfoTypes.VARIANT_CALL, repo);
+  @Service
+  public static class FileInfoService extends InfoService {
+    @Autowired
+    FileInfoService(InfoRepository repo) {
+      super(InfoTypes.FILE, repo);
+    }
   }
-}
 
-@Service
-class SequencingReadInfoService extends InfoService {
-  @Autowired
-  SequencingReadInfoService(InfoRepository repo) {
-    super(SEQUENCING_READ, repo);
-  }
 }

song-server/src/main/java/bio/overture/song/server/service/SampleService.java

@@ -32,6 +32,7 @@
 import bio.overture.song.server.model.entity.Sample;
 import bio.overture.song.server.repository.BusinessKeyRepository;
 import bio.overture.song.server.repository.SampleRepository;
+import bio.overture.song.server.service.InfoService.SampleInfoService;
 import bio.overture.song.server.service.id.IdService;
 import java.util.List;
 import javax.transaction.Transactional;

song-server/src/main/java/bio/overture/song/server/service/SpecimenService.java

@@ -32,6 +32,7 @@
 import bio.overture.song.server.model.entity.composites.SpecimenWithSamples;
 import bio.overture.song.server.repository.BusinessKeyRepository;
 import bio.overture.song.server.repository.SpecimenRepository;
+import bio.overture.song.server.service.InfoService.SpecimenInfoService;
 import bio.overture.song.server.service.id.IdService;
 import java.util.ArrayList;
 import java.util.List;

song-server/src/main/java/bio/overture/song/server/service/StudyService.java

@@ -25,6 +25,7 @@
 
 import bio.overture.song.server.model.entity.Study;
 import bio.overture.song.server.repository.StudyRepository;
+import bio.overture.song.server.service.InfoService.StudyInfoService;
 import java.util.List;
 import javax.transaction.Transactional;
 import lombok.NonNull;

song-server/src/main/java/bio/overture/song/server/service/SubmitService.java

@@ -30,9 +30,9 @@
 import bio.overture.song.core.model.AnalysisTypeId;
 import bio.overture.song.core.model.SubmitResponse;
 import bio.overture.song.server.model.dto.Payload;
+import bio.overture.song.server.service.analysis.AnalysisService;
 import com.fasterxml.jackson.databind.JsonNode;
 import java.io.IOException;
-import javax.transaction.Transactional;
 import lombok.NonNull;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
@@ -58,7 +58,6 @@ public SubmitService(
     this.studyService = studyService;
   }
 
-  @Transactional
   public SubmitResponse submit(@NonNull String studyId, String payloadString) {
     // Check study exists
     studyService.checkStudyExist(studyId);

song-server/src/main/java/bio/overture/song/server/service/analysis/AnalysisService.java

@@ -0,0 +1,61 @@
+package bio.overture.song.server.service.analysis;
+
+import bio.overture.song.core.model.enums.AnalysisStates;
+import bio.overture.song.server.model.analysis.Analysis;
+import bio.overture.song.server.model.dto.Payload;
+import bio.overture.song.server.model.entity.FileEntity;
+import bio.overture.song.server.model.entity.composites.CompositeEntity;
+import bio.overture.song.server.repository.search.IdSearchRequest;
+import com.fasterxml.jackson.databind.JsonNode;
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+import lombok.NonNull;
+import org.springframework.http.ResponseEntity;
+
+public interface AnalysisService {
+
+  String create(String studyId, Payload payload);
+
+  void updateAnalysis(String studyId, String analysisId, JsonNode updateAnalysisRequest);
+
+  List<Analysis> getAnalysis(String studyId, Set<String> analysisStates);
+
+  List<Analysis> idSearch(String studyId, IdSearchRequest request);
+
+  boolean isAnalysisExist(String id);
+
+  void checkAnalysisExists(String id);
+
+  void checkAnalysisAndStudyRelated(String studyId, String id);
+
+  List<Analysis> unsecuredDeepReads(Collection<String> ids);
+
+  Analysis unsecuredDeepRead(String id);
+
+  List<FileEntity> unsecuredReadFiles(String id);
+
+  ResponseEntity<String> publish(String studyId, String id, boolean ignoreUndefinedMd5);
+
+  ResponseEntity<String> unpublish(String studyId, String id);
+
+  ResponseEntity<String> suppress(String studyId, String id);
+
+  List<CompositeEntity> readSamples(String id);
+
+  AnalysisStates readState(String id);
+
+  default List<FileEntity> securedReadFiles(@NonNull String studyId, String id) {
+    checkAnalysisAndStudyRelated(studyId, id);
+    return unsecuredReadFiles(id);
+  }
+
+  /**
+   * Securely reads an analysis WITH all of its files, samples and info, and verifies the input
+   * studyId is related to the requested analysisId
+   */
+  default Analysis securedDeepRead(@NonNull String studyId, String id) {
+    checkAnalysisAndStudyRelated(studyId, id);
+    return unsecuredDeepRead(id);
+  }
+}