diff --git a/README.md b/README.md
index 574f2a9736b79c44dbb176be1aece51797d1e84a..d1a47f05c43aa3d1da12a5b8708aaf81ba2adf34 100644
--- a/README.md
+++ b/README.md
@@ -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.
#### EXTERNAL SERVICES ###
-* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://localhost:5000" .
* 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_API_KEY: The api key to authorize galaxy requests.
* GALAXY_USERNAME: The username of galaxy user to be able to embed the frame.
diff --git a/config/application.tmpl b/config/application.tmpl
index 415e9f469edf2db038335109f933a898f48ed876..d128fe57132353390e95f95f597266b1912b05c4 100644
--- a/config/application.tmpl
+++ b/config/application.tmpl
@@ -35,10 +35,10 @@ spring:
### EXTERNAL SERVICES ###
services:
algorithmsUpdateInterval: {{ .Env.ALGORITHM_UPDATE_INTERVAL}}
- mipengine:
- algorithmsUrl: {{ .Env.MIPENGINE_URL}}/algorithms
- attributesUrl: {{ .Env.MIPENGINE_URL}}/data_models_attributes
- cdesMetadataUrl: {{ .Env.MIPENGINE_URL}}/cdes_metadata
+ exareme2:
+ algorithmsUrl: {{ .Env.EXAREME2_URL}}/algorithms
+ attributesUrl: {{ .Env.EXAREME2_URL}}/data_models_attributes
+ cdesMetadataUrl: {{ .Env.EXAREME2_URL}}/cdes_metadata
exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
index 4320f90c7d22f228f8423698b61d8d0a2f10a437..fa1826979cc414090db6376e1e22888f1403ea87 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
@@ -2,8 +2,8 @@ package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
-import eu.hbp.mip.models.DTOs.MIPEngineAttributesDTO;
-import eu.hbp.mip.models.DTOs.MIPEngineCommonDataElement;
+import eu.hbp.mip.models.DTOs.Exareme2AttributesDTO;
+import eu.hbp.mip.models.DTOs.Exareme2CommonDataElement;
import eu.hbp.mip.models.DTOs.PathologyDTO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.*;
@@ -32,11 +32,11 @@ public class PathologiesAPI {
@Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
- @Value("#{'${services.mipengine.attributesUrl}'}")
- private String mipengineAttributesUrl;
+ @Value("#{'${services.exareme2.attributesUrl}'}")
+ private String exareme2AttributesUrl;
- @Value("#{'${services.mipengine.cdesMetadataUrl}'}")
- private String mipengineCDEsMetadataUrl;
+ @Value("#{'${services.exareme2.cdesMetadataUrl}'}")
+ private String exareme2CDEsMetadataUrl;
private final ActiveUserService activeUserService;
public PathologiesAPI(ActiveUserService activeUserService) {
@@ -48,15 +48,15 @@ public class PathologiesAPI {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /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<>();
- for (String pathology : mipEnginePathologyAttributes.keySet()) {
+ for (String pathology : exareme2PathologyAttributes.keySet()) {
PathologyDTO newPathology;
try {
- newPathology = new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology));
+ newPathology = new PathologyDTO(pathology, exareme2PathologyAttributes.get(pathology), datasetsPerPathology.get(pathology));
}
catch(InternalServerError e) {
logger.LogUserAction(e.getMessage());
@@ -76,15 +76,15 @@ public class PathologiesAPI {
return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS)));
}
- public Map<String, List<PathologyDTO.EnumerationDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
- Map<String, Map<String, MIPEngineCommonDataElement>> mipEngineCDEsMetadata;
- // Get MIPEngine algorithms
+ public Map<String, List<PathologyDTO.EnumerationDTO>> getExareme2DatasetsPerPathology(Logger logger) {
+ Map<String, Map<String, Exareme2CommonDataElement>> exareme2CDEsMetadata;
+ // Get Exareme2 algorithms
try {
StringBuilder response = new StringBuilder();
- HTTPUtil.sendGet(mipengineCDEsMetadataUrl, response);
- mipEngineCDEsMetadata = gson.fromJson(
+ HTTPUtil.sendGet(exareme2CDEsMetadataUrl, response);
+ exareme2CDEsMetadata = gson.fromJson(
response.toString(),
- new TypeToken<HashMap<String, Map<String, MIPEngineCommonDataElement>>>() {
+ new TypeToken<HashMap<String, Map<String, Exareme2CommonDataElement>>>() {
}.getType()
);
} catch (Exception e) {
@@ -94,7 +94,7 @@ public class PathologiesAPI {
Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = new HashMap<>();
- mipEngineCDEsMetadata.forEach( (pathology, cdePerDataset) -> {
+ exareme2CDEsMetadata.forEach( (pathology, cdePerDataset) -> {
List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS = new ArrayList<>();
Map datasetEnumerations = (Map) cdePerDataset.get("dataset").getEnumerations();
datasetEnumerations.forEach((code, label) -> pathologyDatasetDTOS.add(new PathologyDTO.EnumerationDTO((String) code, (String) label)));
@@ -106,15 +106,15 @@ public class PathologiesAPI {
return datasetsPerPathology;
}
- public Map<String, MIPEngineAttributesDTO> getMIPEnginePathologyAttributes(Logger logger) {
- Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes;
- // Get MIPEngine algorithms
+ public Map<String, Exareme2AttributesDTO> getExareme2PathologyAttributes(Logger logger) {
+ Map<String, Exareme2AttributesDTO> exareme2PathologyAttributes;
+ // Get Exareme2 algorithms
try {
StringBuilder response = new StringBuilder();
- HTTPUtil.sendGet(mipengineAttributesUrl, response);
- mipEnginePathologyAttributes = gson.fromJson(
+ HTTPUtil.sendGet(exareme2AttributesUrl, response);
+ exareme2PathologyAttributes = gson.fromJson(
response.toString(),
- new TypeToken<HashMap<String, MIPEngineAttributesDTO>>() {
+ new TypeToken<HashMap<String, Exareme2AttributesDTO>>() {
}.getType()
);
} catch (Exception e) {
@@ -123,6 +123,6 @@ public class PathologiesAPI {
}
- return mipEnginePathologyAttributes;
+ return exareme2PathologyAttributes;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java
similarity index 64%
rename from src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java
index b373ff3c7a0c45e92703871ebc285cc448324e5d..db5095359df8827a5839b4b0c2ee46c1b1f01a3a 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java
@@ -1,173 +1,173 @@
-package eu.hbp.mip.models.DTOs;
-
-import com.google.gson.annotations.SerializedName;
-import lombok.AllArgsConstructor;
-import lombok.Data;
-
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Optional;
-
-@Data
-@AllArgsConstructor
-public class MIPEngineAlgorithmDTO {
-
- @SerializedName("name")
- private String name;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("parameters")
- private Hashtable<String, MIPEngineAlgorithmParameterDTO> parameters;
-
- @SerializedName("crossvalidation")
- private String crossvalidation;
-
- @SerializedName("inputdata")
- private MIPEngineAlgorithmInputdataDTO inputdata;
-
- public Optional<Hashtable<String, MIPEngineAlgorithmParameterDTO>> getParameters() {
- return Optional.ofNullable(parameters);
- }
- @SerializedName("preprocessing")
- private List<MIPEngineTransformerDTO> preprocessing;
-
- public Optional<List<MIPEngineTransformerDTO>> getPreprocessing() {
- return Optional.ofNullable(preprocessing);
- }
-
-
- @Data
- @AllArgsConstructor
- public static class MIPEngineAlgorithmParameterDTO {
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("notblank")
- private String notblank;
-
- @SerializedName("multiple")
- private String multiple;
-
- @SerializedName("types")
- private List<String> types;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("min")
- private String min;
-
- @SerializedName("max")
- private String max;
-
- @SerializedName("default")
- private String default_value;
-
- @SerializedName("enums")
- private MIPEngineAlgorithmEnumDTO enums;
-
- @SerializedName("dict_keys_enums")
- private MIPEngineAlgorithmEnumDTO dict_keys_enums;
-
- @SerializedName("dict_values_enums")
- private MIPEngineAlgorithmEnumDTO dict_values_enums;
-
- public Optional<MIPEngineAlgorithmEnumDTO> getEnums() {
- return Optional.ofNullable(enums);
- }
-
- @Data
- @AllArgsConstructor
- public static class MIPEngineAlgorithmEnumDTO {
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("source")
- private List<String> source;
-
- }
- }
-
- @Data
- @AllArgsConstructor
- public static class MIPEngineAlgorithmInputdataDTO {
-
- @SerializedName("x")
- private MIPEngineAlgorithmInputDataDetailDTO x;
-
- @SerializedName("y")
- private MIPEngineAlgorithmInputDataDetailDTO y;
-
- @SerializedName("data_model")
- private MIPEngineAlgorithmInputDataDetailDTO data_model;
-
- @SerializedName("datasets")
- private MIPEngineAlgorithmInputDataDetailDTO datasets;
-
- @SerializedName("filter")
- private MIPEngineAlgorithmInputDataDetailDTO filter;
-
- public Optional<MIPEngineAlgorithmInputDataDetailDTO> getY() {
- return Optional.ofNullable(y);
- }
-
- public Optional<MIPEngineAlgorithmInputDataDetailDTO> getX() {
- return Optional.ofNullable(x);
- }
- }
-
-
-
- @Data
- @AllArgsConstructor
- public static class MIPEngineAlgorithmInputDataDetailDTO {
-
- @SerializedName("stattypes")
- private List<String> stattypes;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("notblank")
- private String notblank;
-
- @SerializedName("enumslen")
- private Integer enumslen;
-
- @SerializedName("multiple")
- private String multiple;
-
- @SerializedName("types")
- private List<String> types;
-
- @SerializedName("desc")
- private String desc;
- }
-
- @Data
- @AllArgsConstructor
- public static class MIPEngineTransformerDTO {
- @SerializedName("name")
- private String name;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("parameters")
- private Hashtable<String, MIPEngineAlgorithmParameterDTO> parameters;
-
- }
-}
+package eu.hbp.mip.models.DTOs;
+
+import com.google.gson.annotations.SerializedName;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Optional;
+
+@Data
+@AllArgsConstructor
+public class Exareme2AlgorithmDTO {
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("parameters")
+ private Hashtable<String, Exareme2AlgorithmParameterDTO> parameters;
+
+ @SerializedName("crossvalidation")
+ private String crossvalidation;
+
+ @SerializedName("inputdata")
+ private Exareme2AlgorithmInputdataDTO inputdata;
+
+ public Optional<Hashtable<String, Exareme2AlgorithmParameterDTO>> getParameters() {
+ return Optional.ofNullable(parameters);
+ }
+ @SerializedName("preprocessing")
+ private List<Exareme2TransformerDTO> preprocessing;
+
+ public Optional<List<Exareme2TransformerDTO>> getPreprocessing() {
+ return Optional.ofNullable(preprocessing);
+ }
+
+
+ @Data
+ @AllArgsConstructor
+ public static class Exareme2AlgorithmParameterDTO {
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("notblank")
+ private String notblank;
+
+ @SerializedName("multiple")
+ private String multiple;
+
+ @SerializedName("types")
+ private List<String> types;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("min")
+ private String min;
+
+ @SerializedName("max")
+ private String max;
+
+ @SerializedName("default")
+ private String default_value;
+
+ @SerializedName("enums")
+ private Exareme2AlgorithmEnumDTO enums;
+
+ @SerializedName("dict_keys_enums")
+ private Exareme2AlgorithmEnumDTO dict_keys_enums;
+
+ @SerializedName("dict_values_enums")
+ private Exareme2AlgorithmEnumDTO dict_values_enums;
+
+ public Optional<Exareme2AlgorithmEnumDTO> getEnums() {
+ return Optional.ofNullable(enums);
+ }
+
+ @Data
+ @AllArgsConstructor
+ public static class Exareme2AlgorithmEnumDTO {
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("source")
+ private List<String> source;
+
+ }
+ }
+
+ @Data
+ @AllArgsConstructor
+ public static class Exareme2AlgorithmInputdataDTO {
+
+ @SerializedName("x")
+ private Exareme2AlgorithmInputDataDetailDTO x;
+
+ @SerializedName("y")
+ private Exareme2AlgorithmInputDataDetailDTO y;
+
+ @SerializedName("data_model")
+ private Exareme2AlgorithmInputDataDetailDTO data_model;
+
+ @SerializedName("datasets")
+ private Exareme2AlgorithmInputDataDetailDTO datasets;
+
+ @SerializedName("filter")
+ private Exareme2AlgorithmInputDataDetailDTO filter;
+
+ public Optional<Exareme2AlgorithmInputDataDetailDTO> getY() {
+ return Optional.ofNullable(y);
+ }
+
+ public Optional<Exareme2AlgorithmInputDataDetailDTO> getX() {
+ return Optional.ofNullable(x);
+ }
+ }
+
+
+
+ @Data
+ @AllArgsConstructor
+ public static class Exareme2AlgorithmInputDataDetailDTO {
+
+ @SerializedName("stattypes")
+ private List<String> stattypes;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("notblank")
+ private String notblank;
+
+ @SerializedName("enumslen")
+ private Integer enumslen;
+
+ @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;
+
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java
similarity index 83%
rename from src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java
index 6d71623d434034836315fb5a01273e4d812c915d..7df8a3cc516fa1f00102875497b7778dc0de93d9 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java
@@ -9,7 +9,7 @@ import java.util.*;
@Data
@AllArgsConstructor
-public class MIPEngineAlgorithmRequestDTO {
+public class Exareme2AlgorithmRequestDTO {
@SerializedName("request_id")
private String request_id;
@SerializedName("inputdata")
@@ -19,11 +19,11 @@ public class MIPEngineAlgorithmRequestDTO {
@SerializedName("preprocessing")
private HashMap<String, Object> preprocessing;
- public MIPEngineAlgorithmRequestDTO(UUID experimentUUID, List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOs, List<ExaremeAlgorithmDTO.Transformer> exaremeTransformers) {
+ public Exareme2AlgorithmRequestDTO(UUID experimentUUID, List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOs, List<ExaremeAlgorithmDTO.Transformer> exaremeTransformers) {
this.request_id = experimentUUID.toString();
- MIPEngineAlgorithmRequestDTO.InputData inputData = new MIPEngineAlgorithmRequestDTO.InputData();
- HashMap<String, Object> mipEngineParameters = new HashMap<>();
- HashMap<String, Object> mipEnginePreprocessing = new HashMap<>();
+ Exareme2AlgorithmRequestDTO.InputData inputData = new Exareme2AlgorithmRequestDTO.InputData();
+ HashMap<String, Object> exareme2Parameters = new HashMap<>();
+ HashMap<String, Object> exareme2Preprocessing = new HashMap<>();
exaremeAlgorithmRequestParamDTOs.forEach(parameter -> {
@@ -45,10 +45,10 @@ public class MIPEngineAlgorithmRequestDTO {
break;
case "filter":
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;
default:
- mipEngineParameters.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
+ exareme2Parameters.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
}
});
if (exaremeTransformers.size() > 0) {
@@ -64,12 +64,12 @@ public class MIPEngineAlgorithmRequestDTO {
transformerParameterDTOs.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
}
}
- mipEnginePreprocessing.put(transformer.getName(), transformerParameterDTOs);
+ exareme2Preprocessing.put(transformer.getName(), transformerParameterDTOs);
});
}
this.inputdata = inputData;
- this.parameters = mipEngineParameters;
- this.preprocessing = mipEnginePreprocessing;
+ this.parameters = exareme2Parameters;
+ this.preprocessing = exareme2Preprocessing;
}
private static Object convertStringToMultipleValues(String str) {
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java
similarity index 79%
rename from src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java
index 1da25fe9197571387aeb223c498e04a8b53e6dfc..aaaa627db9582dee2c970ad2a7a4271dcf33d37e 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java
@@ -4,14 +4,12 @@ import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
-import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
@Data
@AllArgsConstructor
-public class MIPEngineAttributesDTO {
+public class Exareme2AttributesDTO {
@SerializedName("properties")
private Map<String, List<MetadataHierarchyDTO>> properties;
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java
similarity index 95%
rename from src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java
rename to src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java
index 9d81a3c77a944c63cbc53cb510264c19e77dd9c0..786bf76308803119ffc3c22299fc91922127602a 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java
@@ -7,7 +7,7 @@ import lombok.Data;
@Data
@AllArgsConstructor
-public class MIPEngineCommonDataElement {
+public class Exareme2CommonDataElement {
@SerializedName("is_categorical")
private Boolean is_categorical;
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
index cfa6ca97d26011d740ca84151a377b7431951bcf..16d68771a4c305b5334a40f12a5e5dbbd5b56b36 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java
@@ -33,32 +33,32 @@ public class ExaremeAlgorithmDTO {
}
- public ExaremeAlgorithmDTO(MIPEngineAlgorithmDTO mipEngineAlgorithm) {
- this.name = mipEngineAlgorithm.getName().toUpperCase();
- this.label = mipEngineAlgorithm.getLabel();
- this.desc = mipEngineAlgorithm.getDesc();
- this.type = "mipengine";
+ public ExaremeAlgorithmDTO(Exareme2AlgorithmDTO exareme2Algorithm) {
+ this.name = exareme2Algorithm.getName().toUpperCase();
+ this.label = exareme2Algorithm.getLabel();
+ this.desc = exareme2Algorithm.getDesc();
+ this.type = "exareme2";
List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
- if (mipEngineAlgorithm.getInputdata().getY().isPresent()) {
- parameters.add(new ExaremeAlgorithmRequestParamDTO("y", mipEngineAlgorithm.getInputdata().getY().get()));
+ if (exareme2Algorithm.getInputdata().getY().isPresent()) {
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("y", exareme2Algorithm.getInputdata().getY().get()));
}
- if (mipEngineAlgorithm.getInputdata().getX().isPresent()) {
- parameters.add(new ExaremeAlgorithmRequestParamDTO("x", mipEngineAlgorithm.getInputdata().getX().get()));
+ if (exareme2Algorithm.getInputdata().getX().isPresent()) {
+ parameters.add(new ExaremeAlgorithmRequestParamDTO("x", exareme2Algorithm.getInputdata().getX().get()));
}
- 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()) {
- mipEngineAlgorithm.getParameters().get().forEach((name, parameterDTO) -> {
+ 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);
});
}
this.parameters = parameters;
List<Transformer> preprocessing = new ArrayList<>();
- if (mipEngineAlgorithm.getPreprocessing().isPresent()) {
- mipEngineAlgorithm.getPreprocessing().get().forEach(mipEngineTransformerDTO -> {
- Transformer transformer = new Transformer(mipEngineTransformerDTO);
+ if (exareme2Algorithm.getPreprocessing().isPresent()) {
+ exareme2Algorithm.getPreprocessing().get().forEach(exareme2TransformerDTO -> {
+ Transformer transformer = new Transformer(exareme2TransformerDTO);
preprocessing.add(transformer);
});
this.preprocessing = preprocessing;
@@ -82,7 +82,7 @@ public class ExaremeAlgorithmDTO {
private List<ExaremeAlgorithmRequestParamDTO> parameters;
- public Transformer(MIPEngineAlgorithmDTO.MIPEngineTransformerDTO transformerDTO) {
+ public Transformer(Exareme2AlgorithmDTO.Exareme2TransformerDTO transformerDTO) {
this.name = transformerDTO.getName().toUpperCase();
this.label = transformerDTO.getLabel();
this.desc = transformerDTO.getDesc();
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
index 5d9c354409461add8007a7b3f4cd2f4b09cd7d82..ab80e2852bb8ef777ef68c4400c33304ad71a27e 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java
@@ -55,7 +55,7 @@ public class ExaremeAlgorithmRequestParamDTO {
private List<String> valueEnumerations;
public ExaremeAlgorithmRequestParamDTO (){}
- public ExaremeAlgorithmRequestParamDTO (String name, MIPEngineAlgorithmDTO.MIPEngineAlgorithmParameterDTO parameter){
+ public ExaremeAlgorithmRequestParamDTO (String name, Exareme2AlgorithmDTO.Exareme2AlgorithmParameterDTO parameter){
this.name = name;
this.desc = parameter.getDesc();
this.valueType = parameter.getTypes().get(0);
@@ -69,7 +69,7 @@ public class ExaremeAlgorithmRequestParamDTO {
this.valueMin = parameter.getMin();
}
- public ExaremeAlgorithmRequestParamDTO (String name, MIPEngineAlgorithmDTO.MIPEngineAlgorithmInputDataDetailDTO inputDataDetail){
+ public ExaremeAlgorithmRequestParamDTO (String name, Exareme2AlgorithmDTO.Exareme2AlgorithmInputDataDetailDTO inputDataDetail){
this.name = name;
this.desc = inputDataDetail.getDesc();
this.value = "";
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
index de85a0fa22bea20e9f8f2892ab0e27ecee422ae4..127f1eb2d38a1bdd42c761d52d4ec343d95a334f 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -33,8 +33,8 @@ public class PathologyDTO {
}
- public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<EnumerationDTO> pathologyDatasetDTOS) {
- MetadataHierarchyDTO metadataHierarchyDTO = mipEngineAttributesDTO.getProperties().get("cdes").get(0);
+ public PathologyDTO(String pathology, Exareme2AttributesDTO exareme2AttributesDTO, List<EnumerationDTO> pathologyDatasetDTOS) {
+ MetadataHierarchyDTO metadataHierarchyDTO = exareme2AttributesDTO.getProperties().get("cdes").get(0);
if (!metadataHierarchyDTO.isDatasetCDEPresent()) throw new InternalServerError("CommonDataElement Dataset was not present in the pathology:" + pathology);
metadataHierarchyDTO.updateDatasetCde(pathologyDatasetDTOS);
diff --git a/src/main/java/eu/hbp/mip/services/AlgorithmService.java b/src/main/java/eu/hbp/mip/services/AlgorithmService.java
index cf5d797f0d6c46dc0bfc2eda09bc5fb9ee977a18..93e22a297f33404c6aa1ee66e677ee34ca42ad5a 100644
--- a/src/main/java/eu/hbp/mip/services/AlgorithmService.java
+++ b/src/main/java/eu/hbp/mip/services/AlgorithmService.java
@@ -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.RetrofitClientInstance;
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.utils.CustomResourceLoader;
import eu.hbp.mip.utils.Exceptions.BadRequestException;
@@ -38,8 +38,8 @@ public class AlgorithmService {
private ArrayList<ExaremeAlgorithmDTO> algorithmDTOS = new ArrayList<>();
- @Value("#{'${services.mipengine.algorithmsUrl}'}")
- private String mipengineAlgorithmsUrl;
+ @Value("#{'${services.exareme2.algorithmsUrl}'}")
+ private String exareme2AlgorithmsUrl;
@Value("#{'${services.exareme.algorithmsUrl}'}")
private String exaremeAlgorithmsUrl;
@@ -62,16 +62,16 @@ public class AlgorithmService {
}
public void update(Logger logger) {
- ArrayList<ExaremeAlgorithmDTO> mipengineAlgorithms = getMIPEngineAlgorithms(logger);
+ ArrayList<ExaremeAlgorithmDTO> exareme2Algorithms = getExareme2Algorithms(logger);
ArrayList<ExaremeAlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
ArrayList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
// 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();
- for (ExaremeAlgorithmDTO algorithm : mipengineAlgorithms) {
+ for (ExaremeAlgorithmDTO algorithm : exareme2Algorithms) {
exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName()));
}
logger.LogUserAction("Removed "+ (old_exareme_algorithm_size - exaremeAlgorithms.size()) +" deprecated exareme algorithms");
@@ -83,11 +83,11 @@ public class AlgorithmService {
} else {
logger.LogUserAction("Fetching exareme algorithms failed");
}
- if (mipengineAlgorithms != null) {
- algorithms.addAll(mipengineAlgorithms);
- logger.LogUserAction("Loaded " + mipengineAlgorithms.size() + " mipengine algorithms");
+ if (exareme2Algorithms != null) {
+ algorithms.addAll(exareme2Algorithms);
+ logger.LogUserAction("Loaded " + exareme2Algorithms.size() + " exareme2 algorithms");
} else {
- logger.LogUserAction("Fetching mipengine algorithms failed");
+ logger.LogUserAction("Fetching exareme2 algorithms failed");
}
if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
@@ -143,8 +143,8 @@ public class AlgorithmService {
private String getAlgorithmEngineType(ExaremeAlgorithmDTO algorithmDTO){
switch (algorithmDTO.getType()) {
- case "mipengine":
- return "MIP-Engine";
+ case "exareme2":
+ return "Exareme2";
case "workflow":
return "Galaxy";
default:
@@ -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
*/
- public ArrayList<ExaremeAlgorithmDTO> getMIPEngineAlgorithms(Logger logger) {
- ArrayList<MIPEngineAlgorithmDTO> mipEngineAlgorithms;
- // Get MIPEngine algorithms
+ public ArrayList<ExaremeAlgorithmDTO> getExareme2Algorithms(Logger logger) {
+ ArrayList<Exareme2AlgorithmDTO> exareme2Algorithms;
+ // Get Exareme2 algorithms
try {
StringBuilder response = new StringBuilder();
- HTTPUtil.sendGet(mipengineAlgorithmsUrl, response);
- mipEngineAlgorithms = gson.fromJson(
+ HTTPUtil.sendGet(exareme2AlgorithmsUrl, response);
+ exareme2Algorithms = gson.fromJson(
response.toString(),
- new TypeToken<ArrayList<MIPEngineAlgorithmDTO>>() {
+ new TypeToken<ArrayList<Exareme2AlgorithmDTO>>() {
}.getType()
);
} catch (Exception e) {
@@ -199,7 +199,7 @@ public class AlgorithmService {
}
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.");
return algorithms;
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 7dc7d16b5dd88521fe98f3c470107e8a3a0f7bc4..9fe7e4cf9e507f3ed8b2ae4895bf7b098330a304 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -32,8 +32,8 @@ public class ExperimentService {
@Value("#{'${services.exareme.queryExaremeUrl}'}")
private String queryExaremeUrl;
- @Value("#{'${services.mipengine.algorithmsUrl}'}")
- private String mipengineAlgorithmsUrl;
+ @Value("#{'${services.exareme2.algorithmsUrl}'}")
+ private String exareme2AlgorithmsUrl;
@Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
@@ -410,7 +410,7 @@ public class ExperimentService {
/**
* 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 logger contains username and the endpoint.
@@ -454,15 +454,15 @@ public class ExperimentService {
}
/**
- * Runs the experiment to exareme or MIPEngine, waiting for the response from them.
- * Exareme and MIP-Engine do not support async fetching of an algorithm result.
+ * Runs the experiment to exareme or Exareme2, waiting for the response from them.
+ * Exareme and Exareme2 do not support async fetching of an algorithm result.
*
* @param experimentDTO is the request with the experiment information
* @return the result of experiment as well as the http status that was retrieved
*/
private ExaremeAlgorithmResultDTO runSynchronousExperiment(ExperimentDTO experimentDTO, String algorithmEngineName, Logger logger) {
- if (algorithmEngineName.equals("MIP-Engine")) {
- return runMIPEngineExperiment(experimentDTO, logger);
+ if (algorithmEngineName.equals("Exareme2")) {
+ return runExareme2Experiment(experimentDTO, logger);
} else {
return runExaremeExperiment(experimentDTO, logger);
}
@@ -517,22 +517,22 @@ 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 logger is used to log
* @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();
- logger.LogUserAction("Starting MIP-Engine algorithm execution, algorithm: " + algorithmName);
+ logger.LogUserAction("Starting Exareme2 algorithm execution, algorithm: " + algorithmName);
- String algorithmEndpoint = mipengineAlgorithmsUrl + "/" + algorithmName.toLowerCase();
- MIPEngineAlgorithmRequestDTO mipEngineAlgorithmRequestDTO =
- new MIPEngineAlgorithmRequestDTO(experimentDTO.getUuid(), experimentDTO.getAlgorithm().getParameters(), experimentDTO.getAlgorithm().getPreprocessing());
- String algorithmBody = JsonConverters.convertObjectToJsonString(mipEngineAlgorithmRequestDTO);
- logger.LogUserAction("MIP-Engine algorithm execution. Endpoint: " + algorithmEndpoint);
- logger.LogUserAction("MIP-Engine algorithm execution. Body: " + algorithmBody);
+ String algorithmEndpoint = exareme2AlgorithmsUrl + "/" + algorithmName.toLowerCase();
+ Exareme2AlgorithmRequestDTO exareme2AlgorithmRequestDTO =
+ new Exareme2AlgorithmRequestDTO(experimentDTO.getUuid(), experimentDTO.getAlgorithm().getParameters(), experimentDTO.getAlgorithm().getPreprocessing());
+ String algorithmBody = JsonConverters.convertObjectToJsonString(exareme2AlgorithmRequestDTO);
+ logger.LogUserAction("Exareme2 algorithm execution. Endpoint: " + algorithmEndpoint);
+ logger.LogUserAction("Exareme2 algorithm execution. Body: " + algorithmBody);
StringBuilder requestResponseBody = new StringBuilder();
int requestResponseCode;
@@ -545,9 +545,9 @@ public class ExperimentService {
List<Object> exaremeAlgorithmResult = new ArrayList<>();
if (requestResponseCode == 200) {
- Object mipEngineResult =
+ Object exareme2Result =
JsonConverters.convertJsonStringToObject(String.valueOf(requestResponseBody), Object.class);
- exaremeAlgorithmResult.add(mipEngineResult);
+ exaremeAlgorithmResult.add(exareme2Result);
} else if (requestResponseCode == 400) {
Map<String, Object> exaremeAlgorithmResultElement = new HashMap<>();
@@ -583,7 +583,7 @@ public class ExperimentService {
} else {
logger.LogUserAction(
- "MIP-Engine execution responded with an unexpected status code: " + requestResponseCode
+ "Exareme2 execution responded with an unexpected status code: " + requestResponseCode
);
throw new InternalServerError("");
}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 6d59ce9cbf057dd21b7c9ddf2c44963def747273..ae29362afd45bb1751b189cf2b3f838fce12705b 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -35,7 +35,7 @@ spring:
### EXTERNAL SERVICES ###
services:
algorithmsUpdateInterval: 100
- mipengine:
+ exareme2:
algorithmsUrl: "http://127.0.0.1:5000/algorithms"
attributesUrl: "http://127.0.0.1:5000/data_models_attributes"
cdesMetadataUrl: "http://127.0.0.1:5000/cdes_metadata"