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Refactor project structure from Package by Layer to Package by Feature
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5 changes: 1 addition & 4 deletions
5
...va/hbp/mip/services/AlgorithmService.java → ...a/hbp/mip/algorithm/AlgorithmService.java
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323 changes: 161 additions & 162 deletions
323
...odels/DTOs/AlgorithmSpecificationDTO.java → .../algorithm/AlgorithmSpecificationDTO.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,162 +1,161 @@ | ||
| 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; | ||
|
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|
|
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| 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()) | ||
| ); | ||
| } | ||
|
|
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| 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; | ||
| } | ||
|
|
||
| } | ||
|
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| 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 ""; | ||
| } | ||
|
|
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| private static String getParameterColumnValuesSQLType(String inputDataDetailName, List<String> types){ | ||
| if (inputDataDetailName.equals("dataset") || inputDataDetailName.equals("filter") || inputDataDetailName.equals("pathology")) { | ||
| return ""; | ||
| } | ||
| return String.join(", ", types); | ||
| } | ||
|
|
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| 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); | ||
| } | ||
| } | ||
| } | ||
|
|
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| public AlgorithmSpecificationDTO(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){ | ||
| this( | ||
| exareme2Algorithm.name(), | ||
| exareme2Algorithm.label(), | ||
| exareme2Algorithm.desc(), | ||
| getAlgorithmParameters(exareme2Algorithm), | ||
| getTransformers(exareme2Algorithm.preprocessing()) | ||
| ); | ||
| } | ||
|
|
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| 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; | ||
| } | ||
|
|
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| 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; | ||
|
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||
|
|
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| 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; | ||
| } | ||
|
|
||
| } | ||
|
|
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| 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 | ||
| ); | ||
| } | ||
|
|
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| 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 | ||
| ); | ||
| } | ||
|
|
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| 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 ""; | ||
| } | ||
|
|
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| 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); | ||
| } | ||
| } | ||
| } | ||
|
|
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| public AlgorithmSpecificationDTO(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){ | ||
| this( | ||
| exareme2Algorithm.name(), | ||
| exareme2Algorithm.label(), | ||
| exareme2Algorithm.desc(), | ||
| getAlgorithmParameters(exareme2Algorithm), | ||
| getTransformers(exareme2Algorithm.preprocessing()) | ||
| ); | ||
| } | ||
|
|
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| 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; | ||
| } | ||
|
|
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| 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
6
...va/hbp/mip/controllers/AlgorithmsAPI.java → ...java/hbp/mip/algorithm/AlgorithmsAPI.java
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4 changes: 2 additions & 2 deletions
4
...exareme2/Exareme2AlgorithmRequestDTO.java → ...lgorithm/Exareme2AlgorithmRequestDTO.java
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2 changes: 1 addition & 1 deletion
2
...e2/Exareme2AlgorithmSpecificationDTO.java → ...hm/Exareme2AlgorithmSpecificationDTO.java
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15 changes: 15 additions & 0 deletions
15
src/main/java/hbp/mip/algorithm/Exareme2AlgorithmsSpecs.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| package hbp.mip.algorithm; | ||
|
|
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| import lombok.Getter; | ||
| import lombok.Setter; | ||
| import org.springframework.stereotype.Component; | ||
|
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
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| @Getter | ||
| @Setter | ||
| @Component | ||
| public class Exareme2AlgorithmsSpecs { | ||
| private List<Exareme2AlgorithmSpecificationDTO> algorithms = new ArrayList<>(); | ||
| } |
8 changes: 2 additions & 6 deletions
8
...va/hbp/mip/controllers/ExperimentAPI.java → ...ava/hbp/mip/experiment/ExperimentAPI.java
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