Merge pull request #866 from overture-stack/feature/schema_version_fix

Enable Version-Based File Type Validation for Analysis Submission

Author: Azher2Ali

Diff for: song-server/src/main/java/bio/overture/song/server/repository/AnalysisSchemaRepository.java

@@ -22,6 +22,7 @@
 import java.util.Optional;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
+import org.springframework.data.jpa.repository.Query;
 
 public interface AnalysisSchemaRepository
     extends JpaRepository<AnalysisSchema, Integer>, JpaSpecificationExecutor<AnalysisSchema> {
@@ -32,5 +33,5 @@ public interface AnalysisSchemaRepository
 
   Optional<AnalysisSchema> findByNameAndVersion(String name, Integer version);
 
-  List<AnalysisSchema> findByName(String name);
+  List<AnalysisSchema> findAllByName(String name);
 }

Diff for: song-server/src/main/java/bio/overture/song/server/service/AnalysisTypeService.java

@@ -99,6 +99,10 @@ public Schema getAnalysisTypeRegistrationSchema() {
     return analysisTypeRegistrationSchema;
   }
 
+  public List<AnalysisSchema> getAllAnalysisSchemas(String name) {
+    return analysisSchemaRepository.findAllByName(name);
+  }
+
   public AnalysisType getAnalysisType(
       @NonNull String name, @Nullable Integer version, boolean unrenderedOnly) {
     val resolvedVersion = isNull(version) ? getLatestVersionNumber(name) : version;
@@ -265,6 +269,24 @@ private AnalysisType commitAnalysisType(
     if (options != null && CollectionUtils.isNotEmpty(options.getFileTypes())) {
       fileTypes = options.getFileTypes();
     }
+
+    // checking if file types is empty
+    // if the version is new version of the schema , we are checking the previous version allowed file types
+    // if it is new then it is empty
+    if(fileTypes.isEmpty()){
+      List<AnalysisSchema> analysisSchemaList = analysisSchemaRepository.findAllByName(analysisTypeName);
+
+      if(!analysisSchemaList.isEmpty()){
+        Optional<AnalysisSchema> latestSchemaOptional =  analysisSchemaList.stream()
+                .filter(schema -> schema.getVersion() != null)
+                .max(Comparator.comparingInt(AnalysisSchema::getVersion));
+
+        if(latestSchemaOptional.isPresent()){
+          fileTypes = latestSchemaOptional.get().getFileTypes();
+        }
+      }
+    }
+
     val analysisSchema =
         AnalysisSchema.builder()
             .name(analysisTypeName)

Diff for: song-server/src/main/java/bio/overture/song/server/service/ValidationService.java

@@ -30,15 +30,18 @@
 
 import bio.overture.song.core.model.AnalysisTypeId;
 import bio.overture.song.core.model.FileData;
+import bio.overture.song.server.model.entity.AnalysisSchema;
 import bio.overture.song.server.model.enums.UploadStates;
 import bio.overture.song.server.repository.UploadRepository;
 import bio.overture.song.server.validation.SchemaValidator;
 import bio.overture.song.server.validation.ValidationResponse;
 import com.fasterxml.jackson.databind.JsonNode;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 import lombok.NonNull;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
@@ -96,7 +99,9 @@ public Optional<String> validate(@NonNull JsonNode payload) {
         fileTypes = analysisType.getOptions().getFileTypes();
       }
 
-      validateFileType(fileTypes, payload);
+      if (!fileTypes.isEmpty()) {
+        validateFileType(fileTypes, payload);
+      }
 
       val schema = buildSchema(analysisType.getSchema());
       validateWithSchema(schema, payload);