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README.md
View file @ 2e6de1ad
...@@ -25,8 +25,8 @@ To use this image, you need a running instance of PostgreSQL and to configure th ...@@ -25,8 +25,8 @@ To use this image, you need a running instance of PostgreSQL and to configure th
* PORTAL_DB_PASSWORD: Password to use when connecting to the portal database. * PORTAL_DB_PASSWORD: Password to use when connecting to the portal database.
#### EXTERNAL SERVICES ### #### EXTERNAL SERVICES ###
* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://localhost:5000" .
* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" . * EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
* EXAREME2_URL: URL to Exareme2 server. Default is "http://localhost:5000" .
* GALAXY_URL: URL to Workflow server. Default is "http://localhost:8090/" . * GALAXY_URL: URL to Workflow server. Default is "http://localhost:8090/" .
* GALAXY_API_KEY: The api key to authorize galaxy requests. * GALAXY_API_KEY: The api key to authorize galaxy requests.
* GALAXY_USERNAME: The username of galaxy user to be able to embed the frame. * GALAXY_USERNAME: The username of galaxy user to be able to embed the frame.
......
config/application.tmpl
View file @ 2e6de1ad
...@@ -35,10 +35,10 @@ spring: ...@@ -35,10 +35,10 @@ spring:
### EXTERNAL SERVICES ### ### EXTERNAL SERVICES ###
services: services:
algorithmsUpdateInterval: {{ .Env.ALGORITHM_UPDATE_INTERVAL}} algorithmsUpdateInterval: {{ .Env.ALGORITHM_UPDATE_INTERVAL}}
mipengine: exareme2:
algorithmsUrl: {{ .Env.MIPENGINE_URL}}/algorithms algorithmsUrl: {{ .Env.EXAREME2_URL}}/algorithms
attributesUrl: {{ .Env.MIPENGINE_URL}}/data_models_attributes attributesUrl: {{ .Env.EXAREME2_URL}}/data_models_attributes
cdesMetadataUrl: {{ .Env.MIPENGINE_URL}}/cdes_metadata cdesMetadataUrl: {{ .Env.EXAREME2_URL}}/cdes_metadata
exareme: exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
......
src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
View file @ 2e6de1ad
...@@ -2,8 +2,8 @@ package eu.hbp.mip.controllers; ...@@ -2,8 +2,8 @@ package eu.hbp.mip.controllers;
import com.google.gson.Gson; import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken; import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.models.DTOs.MIPEngineAttributesDTO; import eu.hbp.mip.models.DTOs.Exareme2AttributesDTO;
import eu.hbp.mip.models.DTOs.MIPEngineCommonDataElement; import eu.hbp.mip.models.DTOs.Exareme2CommonDataElement;
import eu.hbp.mip.models.DTOs.PathologyDTO; import eu.hbp.mip.models.DTOs.PathologyDTO;
import eu.hbp.mip.services.ActiveUserService; import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.*; import eu.hbp.mip.utils.*;
...@@ -32,11 +32,11 @@ public class PathologiesAPI { ...@@ -32,11 +32,11 @@ public class PathologiesAPI {
@Value("#{'${authentication.enabled}'}") @Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled; private boolean authenticationIsEnabled;
@Value("#{'${services.mipengine.attributesUrl}'}") @Value("#{'${services.exareme2.attributesUrl}'}")
private String mipengineAttributesUrl; private String exareme2AttributesUrl;
@Value("#{'${services.mipengine.cdesMetadataUrl}'}") @Value("#{'${services.exareme2.cdesMetadataUrl}'}")
private String mipengineCDEsMetadataUrl; private String exareme2CDEsMetadataUrl;
private final ActiveUserService activeUserService; private final ActiveUserService activeUserService;
public PathologiesAPI(ActiveUserService activeUserService) { public PathologiesAPI(ActiveUserService activeUserService) {
...@@ -48,15 +48,15 @@ public class PathologiesAPI { ...@@ -48,15 +48,15 @@ public class PathologiesAPI {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies"); Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies");
logger.LogUserAction("Loading pathologies ..."); logger.LogUserAction("Loading pathologies ...");
Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = getMIPEngineDatasetsPerPathology(logger); Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = getExareme2DatasetsPerPathology(logger);
Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes = getMIPEnginePathologyAttributes(logger); Map<String, Exareme2AttributesDTO> exareme2PathologyAttributes = getExareme2PathologyAttributes(logger);
List<PathologyDTO> pathologyDTOS = new ArrayList<>(); List<PathologyDTO> pathologyDTOS = new ArrayList<>();
for (String pathology : mipEnginePathologyAttributes.keySet()) { for (String pathology : exareme2PathologyAttributes.keySet()) {
PathologyDTO newPathology; PathologyDTO newPathology;
try { try {
newPathology = new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology)); newPathology = new PathologyDTO(pathology, exareme2PathologyAttributes.get(pathology), datasetsPerPathology.get(pathology));
} }
catch(InternalServerError e) { catch(InternalServerError e) {
logger.LogUserAction(e.getMessage()); logger.LogUserAction(e.getMessage());
...@@ -76,15 +76,15 @@ public class PathologiesAPI { ...@@ -76,15 +76,15 @@ public class PathologiesAPI {
return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS))); return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS)));
} }
public Map<String, List<PathologyDTO.EnumerationDTO>> getMIPEngineDatasetsPerPathology(Logger logger) { public Map<String, List<PathologyDTO.EnumerationDTO>> getExareme2DatasetsPerPathology(Logger logger) {
Map<String, Map<String, MIPEngineCommonDataElement>> mipEngineCDEsMetadata; Map<String, Map<String, Exareme2CommonDataElement>> exareme2CDEsMetadata;
// Get MIPEngine algorithms // Get Exareme2 algorithms
try { try {
StringBuilder response = new StringBuilder(); StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(mipengineCDEsMetadataUrl, response); HTTPUtil.sendGet(exareme2CDEsMetadataUrl, response);
mipEngineCDEsMetadata = gson.fromJson( exareme2CDEsMetadata = gson.fromJson(
response.toString(), response.toString(),
new TypeToken<HashMap<String, Map<String, MIPEngineCommonDataElement>>>() { new TypeToken<HashMap<String, Map<String, Exareme2CommonDataElement>>>() {
}.getType() }.getType()
); );
} catch (Exception e) { } catch (Exception e) {
...@@ -94,7 +94,7 @@ public class PathologiesAPI { ...@@ -94,7 +94,7 @@ public class PathologiesAPI {
Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = new HashMap<>(); Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = new HashMap<>();
mipEngineCDEsMetadata.forEach( (pathology, cdePerDataset) -> { exareme2CDEsMetadata.forEach( (pathology, cdePerDataset) -> {
List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS = new ArrayList<>(); List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS = new ArrayList<>();
Map datasetEnumerations = (Map) cdePerDataset.get("dataset").getEnumerations(); Map datasetEnumerations = (Map) cdePerDataset.get("dataset").getEnumerations();
datasetEnumerations.forEach((code, label) -> pathologyDatasetDTOS.add(new PathologyDTO.EnumerationDTO((String) code, (String) label))); datasetEnumerations.forEach((code, label) -> pathologyDatasetDTOS.add(new PathologyDTO.EnumerationDTO((String) code, (String) label)));
...@@ -106,15 +106,15 @@ public class PathologiesAPI { ...@@ -106,15 +106,15 @@ public class PathologiesAPI {
return datasetsPerPathology; return datasetsPerPathology;
} }
public Map<String, MIPEngineAttributesDTO> getMIPEnginePathologyAttributes(Logger logger) { public Map<String, Exareme2AttributesDTO> getExareme2PathologyAttributes(Logger logger) {
Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes; Map<String, Exareme2AttributesDTO> exareme2PathologyAttributes;
// Get MIPEngine algorithms // Get Exareme2 algorithms
try { try {
StringBuilder response = new StringBuilder(); StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(mipengineAttributesUrl, response); HTTPUtil.sendGet(exareme2AttributesUrl, response);
mipEnginePathologyAttributes = gson.fromJson( exareme2PathologyAttributes = gson.fromJson(
response.toString(), response.toString(),
new TypeToken<HashMap<String, MIPEngineAttributesDTO>>() { new TypeToken<HashMap<String, Exareme2AttributesDTO>>() {
}.getType() }.getType()
); );
} catch (Exception e) { } catch (Exception e) {
...@@ -123,6 +123,6 @@ public class PathologiesAPI { ...@@ -123,6 +123,6 @@ public class PathologiesAPI {
} }
return mipEnginePathologyAttributes; return exareme2PathologyAttributes;
} }
} }
src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java → src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs; package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName; import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor; import lombok.AllArgsConstructor;
import lombok.Data; import lombok.Data;
import java.util.Hashtable; import java.util.Hashtable;
import java.util.List; import java.util.List;
import java.util.Optional; import java.util.Optional;
@Data @Data
@AllArgsConstructor @AllArgsConstructor
public class MIPEngineAlgorithmDTO { public class Exareme2AlgorithmDTO {
@SerializedName("name") @SerializedName("name")
private String name; private String name;
@SerializedName("desc") @SerializedName("desc")
private String desc; private String desc;
@SerializedName("label") @SerializedName("label")
private String label; private String label;
@SerializedName("type") @SerializedName("type")
private String type; private String type;
@SerializedName("parameters") @SerializedName("parameters")
private Hashtable<String, MIPEngineAlgorithmParameterDTO> parameters; private Hashtable<String, Exareme2AlgorithmParameterDTO> parameters;
@SerializedName("crossvalidation") @SerializedName("crossvalidation")
private String crossvalidation; private String crossvalidation;
@SerializedName("inputdata") @SerializedName("inputdata")
private MIPEngineAlgorithmInputdataDTO inputdata; private Exareme2AlgorithmInputdataDTO inputdata;
public Optional<Hashtable<String, MIPEngineAlgorithmParameterDTO>> getParameters() { public Optional<Hashtable<String, Exareme2AlgorithmParameterDTO>> getParameters() {
return Optional.ofNullable(parameters); return Optional.ofNullable(parameters);
} }
@SerializedName("preprocessing")
private List<Exareme2TransformerDTO> preprocessing;
@Data
@AllArgsConstructor public Optional<List<Exareme2TransformerDTO>> getPreprocessing() {
public static class MIPEngineAlgorithmParameterDTO { return Optional.ofNullable(preprocessing);
}
@SerializedName("label")
private String label;
@Data
@SerializedName("notblank") @AllArgsConstructor
private String notblank; public static class Exareme2AlgorithmParameterDTO {
@SerializedName("multiple") @SerializedName("label")
private String multiple; private String label;
@SerializedName("types") @SerializedName("notblank")
private List<String> types; private String notblank;
@SerializedName("desc") @SerializedName("multiple")
private String desc; private String multiple;
@SerializedName("min") @SerializedName("types")
private String min; private List<String> types;
@SerializedName("max") @SerializedName("desc")
private String max; private String desc;
@SerializedName("default") @SerializedName("min")
private String default_value; private String min;
@SerializedName("enums") @SerializedName("max")
private MIPEngineAlgorithmEnumDTO enums; private String max;
@SerializedName("dict_keys_enums") @SerializedName("default")
private MIPEngineAlgorithmEnumDTO dict_keys_enums; private String default_value;
@SerializedName("dict_values_enums") @SerializedName("enums")
private MIPEngineAlgorithmEnumDTO dict_values_enums; private Exareme2AlgorithmEnumDTO enums;
public Optional<MIPEngineAlgorithmEnumDTO> getEnums() { @SerializedName("dict_keys_enums")
return Optional.ofNullable(enums); private Exareme2AlgorithmEnumDTO dict_keys_enums;
}
@SerializedName("dict_values_enums")
@Data private Exareme2AlgorithmEnumDTO dict_values_enums;
@AllArgsConstructor
public static class MIPEngineAlgorithmEnumDTO { public Optional<Exareme2AlgorithmEnumDTO> getEnums() {
return Optional.ofNullable(enums);
@SerializedName("type") }
private String type;
@Data
@SerializedName("source") @AllArgsConstructor
private List<String> source; public static class Exareme2AlgorithmEnumDTO {
} @SerializedName("type")
} private String type;
@Data @SerializedName("source")
@AllArgsConstructor private List<String> source;
public static class MIPEngineAlgorithmInputdataDTO {
}
@SerializedName("x") }
private MIPEngineAlgorithmInputDataDetailDTO x;
@Data
@SerializedName("y") @AllArgsConstructor
private MIPEngineAlgorithmInputDataDetailDTO y; public static class Exareme2AlgorithmInputdataDTO {
@SerializedName("data_model") @SerializedName("x")
private MIPEngineAlgorithmInputDataDetailDTO data_model; private Exareme2AlgorithmInputDataDetailDTO x;
@SerializedName("datasets") @SerializedName("y")
private MIPEngineAlgorithmInputDataDetailDTO datasets; private Exareme2AlgorithmInputDataDetailDTO y;
@SerializedName("filter") @SerializedName("data_model")
private MIPEngineAlgorithmInputDataDetailDTO filter; private Exareme2AlgorithmInputDataDetailDTO data_model;
public Optional<MIPEngineAlgorithmInputDataDetailDTO> getY() { @SerializedName("datasets")
return Optional.ofNullable(y); private Exareme2AlgorithmInputDataDetailDTO datasets;
}
@SerializedName("filter")
public Optional<MIPEngineAlgorithmInputDataDetailDTO> getX() { private Exareme2AlgorithmInputDataDetailDTO filter;
return Optional.ofNullable(x);
} public Optional<Exareme2AlgorithmInputDataDetailDTO> getY() {
} return Optional.ofNullable(y);
}
@Data
@AllArgsConstructor public Optional<Exareme2AlgorithmInputDataDetailDTO> getX() {
public static class MIPEngineAlgorithmInputDataDetailDTO { return Optional.ofNullable(x);
}
@SerializedName("stattypes") }
private List<String> stattypes;
@SerializedName("label")
private String label; @Data
@AllArgsConstructor
@SerializedName("notblank") public static class Exareme2AlgorithmInputDataDetailDTO {
private String notblank;
@SerializedName("stattypes")
@SerializedName("enumslen") private List<String> stattypes;
private Integer enumslen;
@SerializedName("label")
@SerializedName("multiple") private String label;
private String multiple;
@SerializedName("notblank")
@SerializedName("types") private String notblank;
private List<String> types;
@SerializedName("enumslen")
@SerializedName("desc") private Integer enumslen;
private String desc;
} @SerializedName("multiple")
} private String multiple;
@SerializedName("types")
private List<String> types;
@SerializedName("desc")
private String desc;
}
@Data
@AllArgsConstructor
public static class Exareme2TransformerDTO {
@SerializedName("name")
private String name;
@SerializedName("desc")
private String desc;
@SerializedName("label")
private String label;
@SerializedName("parameters")
private Hashtable<String, Exareme2AlgorithmParameterDTO> parameters;
}
}
src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java → src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java
View file @ 2e6de1ad
...@@ -9,18 +9,21 @@ import java.util.*; ...@@ -9,18 +9,21 @@ import java.util.*;
@Data @Data
@AllArgsConstructor @AllArgsConstructor
public class MIPEngineAlgorithmRequestDTO { public class Exareme2AlgorithmRequestDTO {
@SerializedName("request_id") @SerializedName("request_id")
private String request_id; private String request_id;
@SerializedName("inputdata") @SerializedName("inputdata")
private InputData inputdata; private InputData inputdata;
@SerializedName("parameters") @SerializedName("parameters")
private HashMap<String, Object> parameters; private HashMap<String, Object> parameters;
@SerializedName("preprocessing")
private HashMap<String, Object> preprocessing;
public MIPEngineAlgorithmRequestDTO(UUID experimentUUID, List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOs) { public Exareme2AlgorithmRequestDTO(UUID experimentUUID, List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOs, List<ExaremeAlgorithmDTO.ExaremeTransformerDTO> exaremeTransformers) {
this.request_id = experimentUUID.toString(); this.request_id = experimentUUID.toString();
MIPEngineAlgorithmRequestDTO.InputData inputData = new MIPEngineAlgorithmRequestDTO.InputData(); Exareme2AlgorithmRequestDTO.InputData inputData = new Exareme2AlgorithmRequestDTO.InputData();
HashMap<String, Object> mipEngineParameters = new HashMap<>(); HashMap<String, Object> exareme2Parameters = new HashMap<>();
HashMap<String, Object> exareme2Preprocessing = new HashMap<>();
exaremeAlgorithmRequestParamDTOs.forEach(parameter -> { exaremeAlgorithmRequestParamDTOs.forEach(parameter -> {
...@@ -42,14 +45,31 @@ public class MIPEngineAlgorithmRequestDTO { ...@@ -42,14 +45,31 @@ public class MIPEngineAlgorithmRequestDTO {
break; break;
case "filter": case "filter":
if (parameter.getValue() != null && !parameter.getValue().equals("")) if (parameter.getValue() != null && !parameter.getValue().equals(""))
inputData.setFilters(JsonConverters.convertJsonStringToObject(parameter.getValue(), MIPEngineAlgorithmRequestDTO.Filter.class)); inputData.setFilters(JsonConverters.convertJsonStringToObject(parameter.getValue(), Exareme2AlgorithmRequestDTO.Filter.class));
break; break;
default: default:
mipEngineParameters.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue())); exareme2Parameters.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
} }
}); });
if (exaremeTransformers != null) {
exaremeTransformers.forEach(transformer -> {
HashMap<String, Object> transformerParameterDTOs = new HashMap<>();
for (ExaremeAlgorithmRequestParamDTO parameter : transformer.getParameters()) {
if (parameter.getName().equals("strategies")){
transformerParameterDTOs.put(parameter.getName(),
JsonConverters.convertJsonStringToObject(parameter.getValue(), HashMap.class)
);
}
else {
transformerParameterDTOs.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
}
}
exareme2Preprocessing.put(transformer.getName(), transformerParameterDTOs);
});
}
this.inputdata = inputData; this.inputdata = inputData;
this.parameters = mipEngineParameters; this.parameters = exareme2Parameters;
this.preprocessing = exareme2Preprocessing;
} }
private static Object convertStringToMultipleValues(String str) { private static Object convertStringToMultipleValues(String str) {
......
src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java → src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java
View file @ 2e6de1ad
...@@ -4,14 +4,12 @@ import com.google.gson.annotations.SerializedName; ...@@ -4,14 +4,12 @@ import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor; import lombok.AllArgsConstructor;
import lombok.Data; import lombok.Data;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@Data @Data
@AllArgsConstructor @AllArgsConstructor
public class MIPEngineAttributesDTO { public class Exareme2AttributesDTO {
@SerializedName("properties") @SerializedName("properties")
private Map<String, List<MetadataHierarchyDTO>> properties; private Map<String, List<MetadataHierarchyDTO>> properties;
......
src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java → src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java
View file @ 2e6de1ad
...@@ -7,7 +7,7 @@ import lombok.Data; ...@@ -7,7 +7,7 @@ import lombok.Data;
@Data @Data
@AllArgsConstructor @AllArgsConstructor
public class MIPEngineCommonDataElement { public class Exareme2CommonDataElement {
@SerializedName("is_categorical") @SerializedName("is_categorical")
private Boolean is_categorical; private Boolean is_categorical;
......
src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
View file @ 2e6de1ad
...@@ -3,6 +3,7 @@ package eu.hbp.mip.models.DTOs; ...@@ -3,6 +3,7 @@ package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName; import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor; import lombok.AllArgsConstructor;
import lombok.Data; import lombok.Data;
import lombok.NoArgsConstructor;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
...@@ -26,32 +27,73 @@ public class ExaremeAlgorithmDTO { ...@@ -26,32 +27,73 @@ public class ExaremeAlgorithmDTO {
@SerializedName("parameters") @SerializedName("parameters")
private List<ExaremeAlgorithmRequestParamDTO> parameters; private List<ExaremeAlgorithmRequestParamDTO> parameters;
@SerializedName("preprocessing")
private List<ExaremeTransformerDTO> preprocessing;
public ExaremeAlgorithmDTO() { public ExaremeAlgorithmDTO() {
} }
public ExaremeAlgorithmDTO(MIPEngineAlgorithmDTO mipEngineAlgorithm) { public ExaremeAlgorithmDTO(Exareme2AlgorithmDTO exareme2Algorithm) {
this.name = mipEngineAlgorithm.getName().toUpperCase(); this.name = exareme2Algorithm.getName().toUpperCase();
this.label = mipEngineAlgorithm.getLabel(); this.label = exareme2Algorithm.getLabel();
this.desc = mipEngineAlgorithm.getDesc(); this.desc = exareme2Algorithm.getDesc();
this.type = "mipengine"; this.type = "exareme2";
List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>(); List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
if (mipEngineAlgorithm.getInputdata().getY().isPresent()) { if (exareme2Algorithm.getInputdata().getY().isPresent()) {
parameters.add(new ExaremeAlgorithmRequestParamDTO("y", mipEngineAlgorithm.getInputdata().getY().get())); parameters.add(new ExaremeAlgorithmRequestParamDTO("y", exareme2Algorithm.getInputdata().getY().get()));
}
if (exareme2Algorithm.getInputdata().getX().isPresent()) {
parameters.add(new ExaremeAlgorithmRequestParamDTO("x", exareme2Algorithm.getInputdata().getX().get()));
}
parameters.add(new ExaremeAlgorithmRequestParamDTO("pathology", exareme2Algorithm.getInputdata().getData_model()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("dataset", exareme2Algorithm.getInputdata().getDatasets()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("filter", exareme2Algorithm.getInputdata().getFilter()));
if (exareme2Algorithm.getParameters().isPresent()) {
exareme2Algorithm.getParameters().get().forEach((name, parameterDTO) -> {
ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
parameters.add(parameter);
});
} }
if (mipEngineAlgorithm.getInputdata().getX().isPresent()) { this.parameters = parameters;
parameters.add(new ExaremeAlgorithmRequestParamDTO("x", mipEngineAlgorithm.getInputdata().getX().get())); List<ExaremeTransformerDTO> preprocessing = new ArrayList<>();
if (exareme2Algorithm.getPreprocessing().isPresent()) {
exareme2Algorithm.getPreprocessing().get().forEach(exareme2TransformerDTO -> {
ExaremeTransformerDTO transformer = new ExaremeTransformerDTO(exareme2TransformerDTO);
preprocessing.add(transformer);
});
this.preprocessing = preprocessing;
} }
parameters.add(new ExaremeAlgorithmRequestParamDTO("pathology", mipEngineAlgorithm.getInputdata().getData_model())); }
parameters.add(new ExaremeAlgorithmRequestParamDTO("dataset", mipEngineAlgorithm.getInputdata().getDatasets()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("filter", mipEngineAlgorithm.getInputdata().getFilter()));
if (mipEngineAlgorithm.getParameters().isPresent()) { @Data
mipEngineAlgorithm.getParameters().get().forEach((name, parameterDTO) -> { @NoArgsConstructor
@AllArgsConstructor
public static class ExaremeTransformerDTO {
@SerializedName("name")
private String name;
@SerializedName("desc")
private String desc;
@SerializedName("label")
private String label;
@SerializedName("parameters")
private List<ExaremeAlgorithmRequestParamDTO> parameters;
public ExaremeTransformerDTO(Exareme2AlgorithmDTO.Exareme2TransformerDTO transformerDTO) {
this.name = transformerDTO.getName().toUpperCase();
this.label = transformerDTO.getLabel();
this.desc = transformerDTO.getDesc();
List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
transformerDTO.getParameters().forEach((name, parameterDTO) -> {
ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO); ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
parameters.add(parameter); parameters.add(parameter);
}); });
this.parameters = parameters;
} }
this.setParameters(parameters);
} }
@Data @Data
......
src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
View file @ 2e6de1ad
...@@ -55,7 +55,7 @@ public class ExaremeAlgorithmRequestParamDTO { ...@@ -55,7 +55,7 @@ public class ExaremeAlgorithmRequestParamDTO {
private List<String> valueEnumerations; private List<String> valueEnumerations;
public ExaremeAlgorithmRequestParamDTO (){} public ExaremeAlgorithmRequestParamDTO (){}
public ExaremeAlgorithmRequestParamDTO (String name, MIPEngineAlgorithmDTO.MIPEngineAlgorithmParameterDTO parameter){ public ExaremeAlgorithmRequestParamDTO (String name, Exareme2AlgorithmDTO.Exareme2AlgorithmParameterDTO parameter){
this.name = name; this.name = name;
this.desc = parameter.getDesc(); this.desc = parameter.getDesc();
this.valueType = parameter.getTypes().get(0); this.valueType = parameter.getTypes().get(0);
...@@ -69,7 +69,7 @@ public class ExaremeAlgorithmRequestParamDTO { ...@@ -69,7 +69,7 @@ public class ExaremeAlgorithmRequestParamDTO {
this.valueMin = parameter.getMin(); this.valueMin = parameter.getMin();
} }
public ExaremeAlgorithmRequestParamDTO (String name, MIPEngineAlgorithmDTO.MIPEngineAlgorithmInputDataDetailDTO inputDataDetail){ public ExaremeAlgorithmRequestParamDTO (String name, Exareme2AlgorithmDTO.Exareme2AlgorithmInputDataDetailDTO inputDataDetail){
this.name = name; this.name = name;
this.desc = inputDataDetail.getDesc(); this.desc = inputDataDetail.getDesc();
this.value = ""; this.value = "";
......
src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
View file @ 2e6de1ad
...@@ -33,8 +33,8 @@ public class PathologyDTO { ...@@ -33,8 +33,8 @@ public class PathologyDTO {
} }
public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<EnumerationDTO> pathologyDatasetDTOS) { public PathologyDTO(String pathology, Exareme2AttributesDTO exareme2AttributesDTO, List<EnumerationDTO> pathologyDatasetDTOS) {
MetadataHierarchyDTO metadataHierarchyDTO = mipEngineAttributesDTO.getProperties().get("cdes").get(0); MetadataHierarchyDTO metadataHierarchyDTO = exareme2AttributesDTO.getProperties().get("cdes").get(0);
if (!metadataHierarchyDTO.isDatasetCDEPresent()) throw new InternalServerError("CommonDataElement Dataset was not present in the pathology:" + pathology); if (!metadataHierarchyDTO.isDatasetCDEPresent()) throw new InternalServerError("CommonDataElement Dataset was not present in the pathology:" + pathology);
metadataHierarchyDTO.updateDatasetCde(pathologyDatasetDTOS); metadataHierarchyDTO.updateDatasetCde(pathologyDatasetDTOS);
......
src/main/java/eu/hbp/mip/services/AlgorithmService.java
View file @ 2e6de1ad
...@@ -9,7 +9,7 @@ import com.google.gson.reflect.TypeToken; ...@@ -9,7 +9,7 @@ import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients; import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance; import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO; import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO;
import eu.hbp.mip.models.DTOs.MIPEngineAlgorithmDTO; import eu.hbp.mip.models.DTOs.Exareme2AlgorithmDTO;
import eu.hbp.mip.models.galaxy.WorkflowDTO; import eu.hbp.mip.models.galaxy.WorkflowDTO;
import eu.hbp.mip.utils.CustomResourceLoader; import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.Exceptions.BadRequestException; import eu.hbp.mip.utils.Exceptions.BadRequestException;
...@@ -38,8 +38,8 @@ public class AlgorithmService { ...@@ -38,8 +38,8 @@ public class AlgorithmService {
private ArrayList<ExaremeAlgorithmDTO> algorithmDTOS = new ArrayList<>(); private ArrayList<ExaremeAlgorithmDTO> algorithmDTOS = new ArrayList<>();
@Value("#{'${services.mipengine.algorithmsUrl}'}") @Value("#{'${services.exareme2.algorithmsUrl}'}")
private String mipengineAlgorithmsUrl; private String exareme2AlgorithmsUrl;
@Value("#{'${services.exareme.algorithmsUrl}'}") @Value("#{'${services.exareme.algorithmsUrl}'}")
private String exaremeAlgorithmsUrl; private String exaremeAlgorithmsUrl;
...@@ -62,16 +62,16 @@ public class AlgorithmService { ...@@ -62,16 +62,16 @@ public class AlgorithmService {
} }
public void update(Logger logger) { public void update(Logger logger) {
ArrayList<ExaremeAlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger); ArrayList<ExaremeAlgorithmDTO> exareme2Algorithms = getExareme2Algorithms(logger);
ArrayList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger); ArrayList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
ArrayList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger); ArrayList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>(); ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
// Remove Exareme algorithms that exist in the Exareme2 // Remove Exareme algorithms that exist in the Exareme2
if (mipengineAlgorithms != null && exaremeAlgorithms != null){ if (exareme2Algorithms != null && exaremeAlgorithms != null){
int old_exareme_algorithm_size = exaremeAlgorithms.size(); int old_exareme_algorithm_size = exaremeAlgorithms.size();
for (ExaremeAlgorithmDTO algorithm : mipengineAlgorithms) { for (ExaremeAlgorithmDTO algorithm : exareme2Algorithms) {
exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName())); exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName()));
} }
logger.LogUserAction("Removed "+ (old_exareme_algorithm_size - exaremeAlgorithms.size()) +" deprecated exareme algorithms"); logger.LogUserAction("Removed "+ (old_exareme_algorithm_size - exaremeAlgorithms.size()) +" deprecated exareme algorithms");
...@@ -83,11 +83,11 @@ public class AlgorithmService { ...@@ -83,11 +83,11 @@ public class AlgorithmService {
} else { } else {
logger.LogUserAction("Fetching exareme algorithms failed"); logger.LogUserAction("Fetching exareme algorithms failed");
} }
if (mipengineAlgorithms != null) { if (exareme2Algorithms != null) {
algorithms.addAll(mipengineAlgorithms); algorithms.addAll(exareme2Algorithms);
logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms"); logger.LogUserAction("Loaded " + exareme2Algorithms.size() + " exareme2 algorithms");
} else { } else {
logger.LogUserAction("Fetching mipengine algorithms failed"); logger.LogUserAction("Fetching exareme2 algorithms failed");
} }
if (galaxyAlgorithms != null) { if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms); algorithms.addAll(galaxyAlgorithms);
...@@ -143,8 +143,8 @@ public class AlgorithmService { ...@@ -143,8 +143,8 @@ public class AlgorithmService {
private String getAlgorithmEngineType(ExaremeAlgorithmDTO algorithmDTO){ private String getAlgorithmEngineType(ExaremeAlgorithmDTO algorithmDTO){
switch (algorithmDTO.getType()) { switch (algorithmDTO.getType()) {
case "mipengine": case "exareme2":
return "MIP-Engine"; return "Exareme2";
case "workflow": case "workflow":
return "Galaxy"; return "Galaxy";
default: default:
...@@ -178,19 +178,19 @@ public class AlgorithmService { ...@@ -178,19 +178,19 @@ public class AlgorithmService {
} }
/** /**
* This method gets all the available mipengine algorithms and * This method gets all the available exareme2 algorithms and
* *
* @return a list of AlgorithmDTOs or null if something fails * @return a list of AlgorithmDTOs or null if something fails
*/ */
public ArrayList<ExaremeAlgorithmDTO> getMIPEngineAlgorithms(Logger logger) { public ArrayList<ExaremeAlgorithmDTO> getExareme2Algorithms(Logger logger) {
ArrayList<MIPEngineAlgorithmDTO> mipEngineAlgorithms; ArrayList<Exareme2AlgorithmDTO> exareme2Algorithms;
// Get MIPEngine algorithms // Get Exareme2 algorithms
try { try {
StringBuilder response = new StringBuilder(); StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(mipengineAlgorithmsUrl, response); HTTPUtil.sendGet(exareme2AlgorithmsUrl, response);
mipEngineAlgorithms = gson.fromJson( exareme2Algorithms = gson.fromJson(
response.toString(), response.toString(),
new TypeToken<ArrayList<MIPEngineAlgorithmDTO>>() { new TypeToken<ArrayList<Exareme2AlgorithmDTO>>() {
}.getType() }.getType()
); );
} catch (Exception e) { } catch (Exception e) {
...@@ -199,7 +199,7 @@ public class AlgorithmService { ...@@ -199,7 +199,7 @@ public class AlgorithmService {
} }
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>(); ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(new ExaremeAlgorithmDTO(mipEngineAlgorithm))); exareme2Algorithms.forEach(exareme2Algorithm -> algorithms.add(new ExaremeAlgorithmDTO(exareme2Algorithm)));
logger.LogUserAction("Completed, returned " + algorithms.size() + " Exareme2 algorithms."); logger.LogUserAction("Completed, returned " + algorithms.size() + " Exareme2 algorithms.");
return algorithms; return algorithms;
......
src/main/java/eu/hbp/mip/services/ExperimentService.java
View file @ 2e6de1ad
...@@ -32,8 +32,8 @@ public class ExperimentService { ...@@ -32,8 +32,8 @@ public class ExperimentService {
@Value("#{'${services.exareme.queryExaremeUrl}'}") @Value("#{'${services.exareme.queryExaremeUrl}'}")
private String queryExaremeUrl; private String queryExaremeUrl;
@Value("#{'${services.mipengine.algorithmsUrl}'}") @Value("#{'${services.exareme2.algorithmsUrl}'}")
private String mipengineAlgorithmsUrl; private String exareme2AlgorithmsUrl;
@Value("#{'${authentication.enabled}'}") @Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled; private boolean authenticationIsEnabled;
...@@ -356,13 +356,37 @@ public class ExperimentService { ...@@ -356,13 +356,37 @@ public class ExperimentService {
private void algorithmParametersLogging(ExperimentDTO experimentDTO, Logger logger) { private void algorithmParametersLogging(ExperimentDTO experimentDTO, Logger logger) {
String algorithmName = experimentDTO.getAlgorithm().getName(); String algorithmName = experimentDTO.getAlgorithm().getName();
StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n"); StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
experimentDTO.getAlgorithm().getParameters().forEach( if (experimentDTO.getAlgorithm().getParameters() != null){
params -> parametersLogMessage experimentDTO.getAlgorithm().getParameters().forEach(
params -> parametersLogMessage
.append(" ")
.append(params.getLabel())
.append(" -> ")
.append(params.getValue())
.append("\n"));
}
if (experimentDTO.getAlgorithm().getPreprocessing() != null) {
experimentDTO.getAlgorithm().getPreprocessing().forEach(transformer ->
{
parametersLogMessage
.append(" ") .append(" ")
.append(params.getLabel()) .append(transformer.getLabel())
.append(" -> ") .append(" -> ")
.append(params.getValue()) .append("\n");
.append("\n"));
if (transformer.getParameters() != null) {
transformer.getParameters().forEach(
transformerParams -> parametersLogMessage
.append(" ")
.append(transformerParams.getLabel())
.append(" -> ")
.append(transformerParams.getValue())
.append("\n"));
parametersLogMessage.append("\n");
}
});
}
logger.LogUserAction("Executing " + algorithmName + parametersLogMessage); logger.LogUserAction("Executing " + algorithmName + parametersLogMessage);
} }
...@@ -392,7 +416,7 @@ public class ExperimentService { ...@@ -392,7 +416,7 @@ public class ExperimentService {
/** /**
* Creates an experiment and runs it on the background. * Creates an experiment and runs it on the background.
* Uses the exareme or mip-engine engine that run an experiment synchronously. * Uses the exareme or exareme2 engine that run an experiment synchronously.
* *
* @param experimentDTO is the request with the experiment information * @param experimentDTO is the request with the experiment information
* @param logger contains username and the endpoint. * @param logger contains username and the endpoint.
...@@ -436,15 +460,15 @@ public class ExperimentService { ...@@ -436,15 +460,15 @@ public class ExperimentService {
} }
/** /**
* Runs the experiment to exareme or MIPEngine, waiting for the response from them. * Runs the experiment to exareme or Exareme2, waiting for the response from them.
* Exareme and MIP-Engine do not support async fetching of an algorithm result. * Exareme and Exareme2 do not support async fetching of an algorithm result.
* *
* @param experimentDTO is the request with the experiment information * @param experimentDTO is the request with the experiment information
* @return the result of experiment as well as the http status that was retrieved * @return the result of experiment as well as the http status that was retrieved
*/ */
private ExaremeAlgorithmResultDTO runSynchronousExperiment(ExperimentDTO experimentDTO, String algorithmEngineName, Logger logger) { private ExaremeAlgorithmResultDTO runSynchronousExperiment(ExperimentDTO experimentDTO, String algorithmEngineName, Logger logger) {
if (algorithmEngineName.equals("MIP-Engine")) { if (algorithmEngineName.equals("Exareme2")) {
return runMIPEngineExperiment(experimentDTO, logger); return runExareme2Experiment(experimentDTO, logger);
} else { } else {
return runExaremeExperiment(experimentDTO, logger); return runExaremeExperiment(experimentDTO, logger);
} }
...@@ -499,22 +523,22 @@ public class ExperimentService { ...@@ -499,22 +523,22 @@ public class ExperimentService {
} }
/** /**
* The runMIPEngineExperiment will run an experiment using the MIP-Engine * The runExareme2Experiment will run an experiment using the Exareme2
* *
* @param experimentDTO contains the information needed to run the experiment * @param experimentDTO contains the information needed to run the experiment
* @param logger is used to log * @param logger is used to log
* @return the result of the algorithm * @return the result of the algorithm
*/ */
private ExaremeAlgorithmResultDTO runMIPEngineExperiment(ExperimentDTO experimentDTO, Logger logger) { private ExaremeAlgorithmResultDTO runExareme2Experiment(ExperimentDTO experimentDTO, Logger logger) {
String algorithmName = experimentDTO.getAlgorithm().getName(); String algorithmName = experimentDTO.getAlgorithm().getName();
logger.LogUserAction("Starting MIP-Engine algorithm execution, algorithm: " + algorithmName); logger.LogUserAction("Starting Exareme2 algorithm execution, algorithm: " + algorithmName);
String algorithmEndpoint = mipengineAlgorithmsUrl + "/" + algorithmName.toLowerCase(); String algorithmEndpoint = exareme2AlgorithmsUrl + "/" + algorithmName.toLowerCase();
MIPEngineAlgorithmRequestDTO mipEngineAlgorithmRequestDTO = Exareme2AlgorithmRequestDTO exareme2AlgorithmRequestDTO =
new MIPEngineAlgorithmRequestDTO(experimentDTO.getUuid(), experimentDTO.getAlgorithm().getParameters()); new Exareme2AlgorithmRequestDTO(experimentDTO.getUuid(), experimentDTO.getAlgorithm().getParameters(), experimentDTO.getAlgorithm().getPreprocessing());
String algorithmBody = JsonConverters.convertObjectToJsonString(mipEngineAlgorithmRequestDTO); String algorithmBody = JsonConverters.convertObjectToJsonString(exareme2AlgorithmRequestDTO);
logger.LogUserAction("MIP-Engine algorithm execution. Endpoint: " + algorithmEndpoint); logger.LogUserAction("Exareme2 algorithm execution. Endpoint: " + algorithmEndpoint);
logger.LogUserAction("MIP-Engine algorithm execution. Body: " + algorithmBody); logger.LogUserAction("Exareme2 algorithm execution. Body: " + algorithmBody);
StringBuilder requestResponseBody = new StringBuilder(); StringBuilder requestResponseBody = new StringBuilder();
int requestResponseCode; int requestResponseCode;
...@@ -527,9 +551,9 @@ public class ExperimentService { ...@@ -527,9 +551,9 @@ public class ExperimentService {
List<Object> exaremeAlgorithmResult = new ArrayList<>(); List<Object> exaremeAlgorithmResult = new ArrayList<>();
if (requestResponseCode == 200) { if (requestResponseCode == 200) {
Object mipEngineResult = Object exareme2Result =
JsonConverters.convertJsonStringToObject(String.valueOf(requestResponseBody), Object.class); JsonConverters.convertJsonStringToObject(String.valueOf(requestResponseBody), Object.class);
exaremeAlgorithmResult.add(mipEngineResult); exaremeAlgorithmResult.add(exareme2Result);
} else if (requestResponseCode == 400) { } else if (requestResponseCode == 400) {
Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>(); Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>();
...@@ -565,7 +589,7 @@ public class ExperimentService { ...@@ -565,7 +589,7 @@ public class ExperimentService {
} else { } else {
logger.LogUserAction( logger.LogUserAction(
"MIP-Engine execution responded with an unexpected status code: " + requestResponseCode "Exareme2 execution responded with an unexpected status code: " + requestResponseCode
); );
throw new InternalServerError(""); throw new InternalServerError("");
} }
......
src/main/resources/application.yml
View file @ 2e6de1ad
...@@ -35,7 +35,7 @@ spring: ...@@ -35,7 +35,7 @@ spring:
### EXTERNAL SERVICES ### ### EXTERNAL SERVICES ###
services: services:
algorithmsUpdateInterval: 100 algorithmsUpdateInterval: 100
mipengine: exareme2:
algorithmsUrl: "http://127.0.0.1:5000/algorithms" algorithmsUrl: "http://127.0.0.1:5000/algorithms"
attributesUrl: "http://127.0.0.1:5000/data_models_attributes" attributesUrl: "http://127.0.0.1:5000/data_models_attributes"
cdesMetadataUrl: "http://127.0.0.1:5000/cdes_metadata" cdesMetadataUrl: "http://127.0.0.1:5000/cdes_metadata"
......