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Refactor project structure from Package by Layer to Package by Feature #74

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merged 1 commit into from
Dec 12, 2023
Merged

Refactor project structure from Package by Layer to Package by Feature #74

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5 changes: 1 addition & 4 deletions ...va/hbp/mip/services/AlgorithmService.java → ...a/hbp/mip/algorithm/AlgorithmService.java
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@@ -1,11 +1,8 @@
package hbp.mip.services;
package hbp.mip.algorithm;

import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import hbp.mip.models.DTOs.AlgorithmSpecificationDTO;
import hbp.mip.models.DTOs.exareme2.Exareme2AlgorithmSpecificationDTO;
import hbp.mip.utils.CustomResourceLoader;
import hbp.mip.utils.Exareme2AlgorithmsSpecs;
import hbp.mip.utils.HTTPUtil;
import hbp.mip.utils.Logger;
import org.springframework.beans.factory.annotation.Value;
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323 changes: 161 additions & 162 deletions ...odels/DTOs/AlgorithmSpecificationDTO.java → .../algorithm/AlgorithmSpecificationDTO.java
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package hbp.mip.models.DTOs;

import hbp.mip.models.DTOs.exareme2.Exareme2AlgorithmSpecificationDTO;
import hbp.mip.utils.Exceptions.InternalServerError;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;


public record AlgorithmSpecificationDTO(
String name,
String label,
String desc,
List<AlgorithmParameterSpecificationDTO> parameters,
List<TransformerSpecificationDTO> preprocessing
){
public record TransformerSpecificationDTO(String name, String label, String desc,
List<AlgorithmParameterSpecificationDTO> parameters) {
public TransformerSpecificationDTO(Exareme2AlgorithmSpecificationDTO.Exareme2TransformerSpecificationDTO transformerDTO) {
this(
transformerDTO.name(),
transformerDTO.label(),
transformerDTO.desc(),
getAlgorithmParameterSpecifications(transformerDTO.parameters())
);
}

private static List<AlgorithmParameterSpecificationDTO> getAlgorithmParameterSpecifications(
Map<String, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO> exareme2Parameters
) {
List<AlgorithmParameterSpecificationDTO> parameters = new ArrayList<>();
exareme2Parameters.forEach((name, parameterDTO)
-> parameters.add(new AlgorithmParameterSpecificationDTO(name, parameterDTO)));
return parameters;
}

}

public record AlgorithmParameterSpecificationDTO(
String name,
String label,
String desc,
String type,
String columnValuesSQLType,
String columnValuesIsCategorical,
String defaultValue,
String valueType,
String valueNotBlank,
String valueMultiple,
String valueMin,
String valueMax,
List<String> valueEnumerations
) {
public AlgorithmParameterSpecificationDTO(String name, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO parameter) {
this(
name,
parameter.label(),
parameter.desc(),
"other",
"",
"",
parameter.default_value(),
parameter.types().get(0),
parameter.notblank(),
parameter.multiple(),
parameter.min(),
parameter.max(),
parameter.enums() != null ? parameter.enums().source() : null
);
}

public AlgorithmParameterSpecificationDTO(String name, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmInputDataDetailSpecificationDTO inputDataDetail) {
this(
name,
inputDataDetail.label(),
inputDataDetail.desc(),
getParameterType(name),
getParameterColumnValuesSQLType(name, inputDataDetail.types()),
getParameterColumnValuesIsCategorical(name, inputDataDetail.stattypes()),
"",
getParameterValueType(name, inputDataDetail.types()),
inputDataDetail.notblank(),
inputDataDetail.multiple(),
"",
"",
null
);
}

private static String getParameterType(String inputDataDetailName){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return inputDataDetailName;
}
return "column";
}

private static String getParameterValueType(String inputDataDetailName, List<String> types){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return types.get(0);
}
return "";
}

private static String getParameterColumnValuesSQLType(String inputDataDetailName, List<String> types){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return "";
}
return String.join(", ", types);
}

private static String getParameterColumnValuesIsCategorical(String inputDataDetailName, List<String> stattypes){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return "";
}

if (stattypes.contains("nominal") && stattypes.contains("numerical")) {
return "";
} else if (stattypes.contains("nominal")) {
return "true";
} else if (stattypes.contains("numerical")) {
return "false";
} else {
throw new InternalServerError("Invalid stattypes: " + stattypes);
}
}
}

public AlgorithmSpecificationDTO(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){
this(
exareme2Algorithm.name(),
exareme2Algorithm.label(),
exareme2Algorithm.desc(),
getAlgorithmParameters(exareme2Algorithm),
getTransformers(exareme2Algorithm.preprocessing())
);
}

private static List<AlgorithmParameterSpecificationDTO> getAlgorithmParameters(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){
List<AlgorithmParameterSpecificationDTO> parameters = new ArrayList<>();
if (exareme2Algorithm.inputdata().y() != null) {
parameters.add(new AlgorithmParameterSpecificationDTO("y", exareme2Algorithm.inputdata().y()));
}
if (exareme2Algorithm.inputdata().x() != null) {
parameters.add(new AlgorithmParameterSpecificationDTO("x", exareme2Algorithm.inputdata().x()));
}
parameters.add(new AlgorithmParameterSpecificationDTO("pathology", exareme2Algorithm.inputdata().data_model()));
parameters.add(new AlgorithmParameterSpecificationDTO("dataset", exareme2Algorithm.inputdata().datasets()));
parameters.add(new AlgorithmParameterSpecificationDTO("filter", exareme2Algorithm.inputdata().filter()));
exareme2Algorithm.parameters().forEach((name, parameterDTO)
-> parameters.add(new AlgorithmParameterSpecificationDTO(name, parameterDTO)));
return parameters;
}

private static List<TransformerSpecificationDTO> getTransformers(List<Exareme2AlgorithmSpecificationDTO.Exareme2TransformerSpecificationDTO> exareme2Transformers){
List<TransformerSpecificationDTO> preprocessing = new ArrayList<>();
exareme2Transformers.forEach(exareme2TransformerSpecificationDTO
-> preprocessing.add(new TransformerSpecificationDTO(exareme2TransformerSpecificationDTO)));
return preprocessing;
}

}
package hbp.mip.algorithm;

import hbp.mip.utils.Exceptions.InternalServerError;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;


public record AlgorithmSpecificationDTO(
String name,
String label,
String desc,
List<AlgorithmParameterSpecificationDTO> parameters,
List<TransformerSpecificationDTO> preprocessing
){
public record TransformerSpecificationDTO(String name, String label, String desc,
List<AlgorithmParameterSpecificationDTO> parameters) {
public TransformerSpecificationDTO(Exareme2AlgorithmSpecificationDTO.Exareme2TransformerSpecificationDTO transformerDTO) {
this(
transformerDTO.name(),
transformerDTO.label(),
transformerDTO.desc(),
getAlgorithmParameterSpecifications(transformerDTO.parameters())
);
}

private static List<AlgorithmParameterSpecificationDTO> getAlgorithmParameterSpecifications(
Map<String, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO> exareme2Parameters
) {
List<AlgorithmParameterSpecificationDTO> parameters = new ArrayList<>();
exareme2Parameters.forEach((name, parameterDTO)
-> parameters.add(new AlgorithmParameterSpecificationDTO(name, parameterDTO)));
return parameters;
}

}

public record AlgorithmParameterSpecificationDTO(
String name,
String label,
String desc,
String type,
String columnValuesSQLType,
String columnValuesIsCategorical,
String defaultValue,
String valueType,
String valueNotBlank,
String valueMultiple,
String valueMin,
String valueMax,
List<String> valueEnumerations
) {
public AlgorithmParameterSpecificationDTO(String name, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO parameter) {
this(
name,
parameter.label(),
parameter.desc(),
"other",
"",
"",
parameter.default_value(),
parameter.types().get(0),
parameter.notblank(),
parameter.multiple(),
parameter.min(),
parameter.max(),
parameter.enums() != null ? parameter.enums().source() : null
);
}

public AlgorithmParameterSpecificationDTO(String name, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmInputDataDetailSpecificationDTO inputDataDetail) {
this(
name,
inputDataDetail.label(),
inputDataDetail.desc(),
getParameterType(name),
getParameterColumnValuesSQLType(name, inputDataDetail.types()),
getParameterColumnValuesIsCategorical(name, inputDataDetail.stattypes()),
"",
getParameterValueType(name, inputDataDetail.types()),
inputDataDetail.notblank(),
inputDataDetail.multiple(),
"",
"",
null
);
}

private static String getParameterType(String inputDataDetailName){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return inputDataDetailName;
}
return "column";
}

private static String getParameterValueType(String inputDataDetailName, List<String> types){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return types.get(0);
}
return "";
}

private static String getParameterColumnValuesSQLType(String inputDataDetailName, List<String> types){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return "";
}
return String.join(", ", types);
}

private static String getParameterColumnValuesIsCategorical(String inputDataDetailName, List<String> stattypes){
if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) {
return "";
}

if (stattypes.contains("nominal") && stattypes.contains("numerical")) {
return "";
} else if (stattypes.contains("nominal")) {
return "true";
} else if (stattypes.contains("numerical")) {
return "false";
} else {
throw new InternalServerError("Invalid stattypes: " + stattypes);
}
}
}

public AlgorithmSpecificationDTO(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){
this(
exareme2Algorithm.name(),
exareme2Algorithm.label(),
exareme2Algorithm.desc(),
getAlgorithmParameters(exareme2Algorithm),
getTransformers(exareme2Algorithm.preprocessing())
);
}

private static List<AlgorithmParameterSpecificationDTO> getAlgorithmParameters(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){
List<AlgorithmParameterSpecificationDTO> parameters = new ArrayList<>();
if (exareme2Algorithm.inputdata().y() != null) {
parameters.add(new AlgorithmParameterSpecificationDTO("y", exareme2Algorithm.inputdata().y()));
}
if (exareme2Algorithm.inputdata().x() != null) {
parameters.add(new AlgorithmParameterSpecificationDTO("x", exareme2Algorithm.inputdata().x()));
}
parameters.add(new AlgorithmParameterSpecificationDTO("pathology", exareme2Algorithm.inputdata().data_model()));
parameters.add(new AlgorithmParameterSpecificationDTO("dataset", exareme2Algorithm.inputdata().datasets()));
parameters.add(new AlgorithmParameterSpecificationDTO("filter", exareme2Algorithm.inputdata().filter()));
exareme2Algorithm.parameters().forEach((name, parameterDTO)
-> parameters.add(new AlgorithmParameterSpecificationDTO(name, parameterDTO)));
return parameters;
}

private static List<TransformerSpecificationDTO> getTransformers(List<Exareme2AlgorithmSpecificationDTO.Exareme2TransformerSpecificationDTO> exareme2Transformers){
List<TransformerSpecificationDTO> preprocessing = new ArrayList<>();
exareme2Transformers.forEach(exareme2TransformerSpecificationDTO
-> preprocessing.add(new TransformerSpecificationDTO(exareme2TransformerSpecificationDTO)));
return preprocessing;
}

}
6 changes: 2 additions & 4 deletions ...va/hbp/mip/controllers/AlgorithmsAPI.java → ...java/hbp/mip/algorithm/AlgorithmsAPI.java
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package hbp.mip.controllers;
package hbp.mip.algorithm;

import hbp.mip.models.DTOs.AlgorithmSpecificationDTO;
import hbp.mip.services.ActiveUserService;
import hbp.mip.services.AlgorithmService;
import hbp.mip.user.ActiveUserService;
import hbp.mip.utils.Logger;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
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4 changes: 2 additions & 2 deletions ...exareme2/Exareme2AlgorithmRequestDTO.java → ...lgorithm/Exareme2AlgorithmRequestDTO.java
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package hbp.mip.models.DTOs.exareme2;
package hbp.mip.algorithm;

import com.google.gson.JsonSyntaxException;
import hbp.mip.models.DTOs.ExperimentExecutionDTO;
import hbp.mip.experiment.ExperimentExecutionDTO;
import hbp.mip.utils.Exceptions.InternalServerError;
import hbp.mip.utils.JsonConverters;

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2 changes: 1 addition & 1 deletion ...e2/Exareme2AlgorithmSpecificationDTO.java → ...hm/Exareme2AlgorithmSpecificationDTO.java
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package hbp.mip.models.DTOs.exareme2;
package hbp.mip.algorithm;

import com.google.gson.annotations.SerializedName;

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15 changes: 15 additions & 0 deletions src/main/java/hbp/mip/algorithm/Exareme2AlgorithmsSpecs.java
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package hbp.mip.algorithm;

import lombok.Getter;
import lombok.Setter;
import org.springframework.stereotype.Component;

import java.util.ArrayList;
import java.util.List;

@Getter
@Setter
@Component
public class Exareme2AlgorithmsSpecs {
private List<Exareme2AlgorithmSpecificationDTO> algorithms = new ArrayList<>();
}
8 changes: 2 additions & 6 deletions ...va/hbp/mip/controllers/ExperimentAPI.java → ...ava/hbp/mip/experiment/ExperimentAPI.java
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package hbp.mip.controllers;
package hbp.mip.experiment;


import hbp.mip.models.DTOs.ExperimentDTO;
import hbp.mip.models.DTOs.ExperimentExecutionDTO;
import hbp.mip.models.DTOs.ExperimentsDTO;
import hbp.mip.services.ActiveUserService;
import hbp.mip.services.ExperimentService;
import hbp.mip.user.ActiveUserService;
import hbp.mip.utils.JsonConverters;
import hbp.mip.utils.Logger;
import org.springframework.http.HttpStatus;
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