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Enable Version-Based File Type Validation for Analysis Submission #866

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Merged
merged 4 commits into from
Oct 15, 2024
Merged

Enable Version-Based File Type Validation for Analysis Submission #866

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4c94036
Validation of custom schema against the version
Azher2Ali Oct 2, 2024
e11d484
Updating the Validation of schema according to the feedback
Azher2Ali Oct 3, 2024
a5222fe
Removing extra spcaces from the code
Azher2Ali Oct 3, 2024
153461f
Reverting the changes related to schema in ValidationService
Azher2Ali Oct 4, 2024
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3 changes: 2 additions & 1 deletion song-server/src/main/java/bio/overture/song/server/repository/AnalysisSchemaRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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> {
Expand All @@ -32,5 +33,5 @@ public interface AnalysisSchemaRepository

Optional<AnalysisSchema> findByNameAndVersion(String name, Integer version);

List<AnalysisSchema> findByName(String name);
List<AnalysisSchema> findAllByName(String name);
}
22 changes: 22 additions & 0 deletions song-server/src/main/java/bio/overture/song/server/service/AnalysisTypeService.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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)
Expand Down
7 changes: 6 additions & 1 deletion song-server/src/main/java/bio/overture/song/server/service/ValidationService.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand Down