diff --git a/config/application.tmpl b/config/application.tmpl
index e6af51b24f0c74934e7c83c63fe518387d14a959..e42153df2e203acedcf657c7f73ed8578826c442 100644
--- a/config/application.tmpl
+++ b/config/application.tmpl
@@ -36,6 +36,8 @@ spring:
services:
mipengine:
algorithmsUrl: {{ .Env.MIPENGINE_URL}}/algorithms
+ attributesUrl: {{ .Env.MIPENGINE_URL}}/data_models_attributes
+ cdesMetadataUrl: {{ .Env.MIPENGINE_URL}}/cdes_metadata
exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
@@ -83,4 +85,4 @@ endpoints:
health:
enabled: true
endpoint: /health
- sensitive: false
\ No newline at end of file
+ sensitive: false
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 1fb02b09de4f10fc3534870966ae377a3a863d8e..44e40651d9042fac87a547c4c50d885217c089e7 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -78,9 +78,12 @@ public class AlgorithmsAPI {
// Remove Exareme algorithms that exist in the Exareme2
if (mipengineAlgorithms != null && exaremeAlgorithms != null){
+ int old_exareme_algorithm_size = exaremeAlgorithms.size();
+
for (ExaremeAlgorithmDTO algorithm : mipengineAlgorithms) {
exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName()));
}
+ logger.LogUserAction("Removed "+ (old_exareme_algorithm_size - exaremeAlgorithms.size()) +" deprecated exareme algorithms");
}
if (exaremeAlgorithms != null) {
@@ -109,8 +112,6 @@ public class AlgorithmsAPI {
logger.LogUserAction("The disabled algorithms could not be loaded.");
}
-
-
// Remove any disabled algorithm
ArrayList<ExaremeAlgorithmDTO> allowedAlgorithms = new ArrayList<>();
for (ExaremeAlgorithmDTO algorithm : algorithms) {
@@ -118,6 +119,9 @@ public class AlgorithmsAPI {
allowedAlgorithms.add(algorithm);
}
}
+
+ logger.LogUserAction("Removed "+ (algorithms.size() - allowedAlgorithms.size()) +" disabled algorithms");
+
logger.LogUserAction("Successfully listed " + allowedAlgorithms.size() + " algorithms");
return ResponseEntity.ok(allowedAlgorithms);
}
@@ -138,15 +142,12 @@ public class AlgorithmsAPI {
new TypeToken<ArrayList<ExaremeAlgorithmDTO>>() {
}.getType()
);
- } catch (ConnectException e) {
- logger.LogUserAction("An exception occurred: " + e.getMessage());
- return null;
- } catch (IOException e) {
+ } catch (Exception e) {
logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
}
- logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
+ logger.LogUserAction("Completed, returned " + algorithms.size() + " Exareme algorithms.");
return algorithms;
}
@@ -166,10 +167,7 @@ public class AlgorithmsAPI {
new TypeToken<ArrayList<MIPEngineAlgorithmDTO>>() {
}.getType()
);
- } catch (ConnectException e) {
- logger.LogUserAction("An exception occurred: " + e.getMessage());
- return null;
- } catch (IOException e) {
+ } catch (Exception e) {
logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
}
@@ -177,7 +175,7 @@ public class AlgorithmsAPI {
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
mipEngineAlgorithms.forEach(mipEngineAlgorithm -> algorithms.add(new ExaremeAlgorithmDTO(mipEngineAlgorithm)));
- logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
+ logger.LogUserAction("Completed, returned " + algorithms.size() + " Exareme2 algorithms.");
return algorithms;
}
@@ -256,4 +254,4 @@ public class AlgorithmsAPI {
}.getType()
);
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
index 5e9a9d34452f81ff5293bccaf3a5a5aca0624057..e53d8d354c98f36db958492e72302612e806878c 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
@@ -2,16 +2,13 @@ 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.MetadataHierarchyDTO;
import eu.hbp.mip.models.DTOs.PathologyDTO;
import eu.hbp.mip.services.ActiveUserService;
-import eu.hbp.mip.utils.ClaimUtils;
-import eu.hbp.mip.utils.CustomResourceLoader;
-import eu.hbp.mip.utils.Exceptions.BadRequestException;
-import eu.hbp.mip.utils.InputStreamConverter;
-import eu.hbp.mip.utils.Logger;
+import eu.hbp.mip.utils.*;
import io.swagger.annotations.Api;
import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -19,7 +16,8 @@ import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import java.io.IOException;
-import java.util.List;
+import java.net.ConnectException;
+import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -35,16 +33,15 @@ public class PathologiesAPI {
@Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
- @Value("#{'${files.pathologies_json}'}")
- private String pathologiesFilePath;
+ @Value("#{'${services.mipengine.attributesUrl}'}")
+ private String mipengineAttributesUrl;
+ @Value("#{'${services.mipengine.cdesMetadataUrl}'}")
+ private String mipengineCDEsMetadataUrl;
private final ActiveUserService activeUserService;
- private final CustomResourceLoader resourceLoader;
-
- public PathologiesAPI(ActiveUserService activeUserService, CustomResourceLoader resourceLoader) {
+ public PathologiesAPI(ActiveUserService activeUserService) {
this.activeUserService = activeUserService;
- this.resourceLoader = resourceLoader;
}
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
@@ -52,24 +49,72 @@ public class PathologiesAPI {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies");
logger.LogUserAction("Loading pathologies ...");
- // Load pathologies from file
- Resource resource = resourceLoader.getResource(pathologiesFilePath);
- List<PathologyDTO> allPathologies;
- try {
- allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
- }.getType());
- } catch (IOException e) {
- logger.LogUserAction("Unable to load pathologies");
- throw new BadRequestException("The pathologies could not be loaded.");
+ Map<String, List<PathologyDTO.PathologyDatasetDTO>> datasetsPerPathology = getMIPEngineDatasetsPerPathology(logger);
+ System.out.println(datasetsPerPathology);
+
+ Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes = getMIPEnginePathologyAttributes(logger);
+ System.out.println(mipEnginePathologyAttributes);
+
+ List<PathologyDTO> pathologyDTOS = new ArrayList<>();
+ for (String pathology : mipEnginePathologyAttributes.keySet()) {
+ pathologyDTOS.add(new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology)));
}
+ System.out.println(pathologyDTOS);
// If authentication is disabled return everything
if (!authenticationIsEnabled) {
- logger.LogUserAction("Successfully loaded " + allPathologies.size() + " pathologies");
- return ResponseEntity.ok().body(gson.toJson(allPathologies));
+ logger.LogUserAction("Successfully loaded " + pathologyDTOS.size() + " pathologies");
+ return ResponseEntity.ok().body(gson.toJson(pathologyDTOS));
}
logger.LogUserAction("Successfully loaded all authorized pathologies");
- return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(logger, authentication, allPathologies));
+ return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS)));
+ }
+
+ public Map<String, List<PathologyDTO.PathologyDatasetDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
+ Map<String, Map<String, MetadataHierarchyDTO.CommonDataElement>> mipEngineCDEsMetadata;
+ // Get MIPEngine algorithms
+ try {
+ StringBuilder response = new StringBuilder();
+ HTTPUtil.sendGet(mipengineCDEsMetadataUrl, response);
+ mipEngineCDEsMetadata = gson.fromJson(
+ response.toString(),
+ new TypeToken<HashMap<String, Map<String, MetadataHierarchyDTO.CommonDataElement>>>() {
+ }.getType()
+ );
+ } catch (Exception e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ return null;
+ }
+
+ Map<String, List<PathologyDTO.PathologyDatasetDTO>> datasetsPerPathology = new HashMap<>();
+
+ mipEngineCDEsMetadata.forEach( (pathology, cdePerDataset) -> {
+ List<PathologyDTO.PathologyDatasetDTO> pathologyDatasetDTOS = new ArrayList<>();
+ cdePerDataset.forEach((dataset, cde) -> pathologyDatasetDTOS.add(new PathologyDTO.PathologyDatasetDTO(dataset, cde.getLabel())));
+ datasetsPerPathology.put(pathology, pathologyDatasetDTOS);
+ });
+
+
+ return datasetsPerPathology;
+ }
+
+ public Map<String, MIPEngineAttributesDTO> getMIPEnginePathologyAttributes(Logger logger) {
+ Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes;
+ // Get MIPEngine algorithms
+ try {
+ StringBuilder response = new StringBuilder();
+ HTTPUtil.sendGet(mipengineAttributesUrl, response);
+ mipEnginePathologyAttributes = gson.fromJson(
+ response.toString(),
+ new TypeToken<HashMap<String, MIPEngineAttributesDTO>>() {
+ }.getType()
+ );
+ } catch (Exception e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ return null;
+ }
+
+ return mipEnginePathologyAttributes;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..2f81aee6a9044396960d1b940f36cb350340d13a
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
@@ -0,0 +1,20 @@
+package eu.hbp.mip.models.DTOs;
+
+import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.models.DTOs.MetadataHierarchyDTO;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+
+import java.util.List;
+import java.util.Map;
+
+@Data
+@AllArgsConstructor
+public class MIPEngineAttributesDTO {
+ @SerializedName("properties")
+ private Map<String, List<MetadataHierarchyDTO>> properties;
+
+ @SerializedName("tags")
+ private Object tags;
+
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..e0db0c70d9430cf21b8a92c9ec70e4d8f46aa10a
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
@@ -0,0 +1,57 @@
+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 MetadataHierarchyDTO {
+
+ @SerializedName("variables")
+ private List<CommonDataElement> variables;
+
+ @SerializedName("code")
+ private String code;
+
+ @SerializedName("groups")
+ private Object groups;
+
+ @SerializedName("label")
+ private String label;
+ @Data
+ @AllArgsConstructor
+ public static class CommonDataElement {
+ @SerializedName("isCategorical")
+ private Boolean isCategorical;
+
+ @SerializedName("code")
+ private String code;
+
+ @SerializedName("sql_type")
+ private String sql_type;
+
+ @SerializedName("description")
+ private String description;
+
+ @SerializedName("enumerations")
+ private Object enumerations;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("units")
+ private String units;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("methodology")
+ private String methodology;
+
+ }
+}
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 c1b0f434fac9c68772b38fb62d221fa8d2bdbbff..8771aefd1aad8ad173982c4b2b0fdb9b8bce17a9 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -4,7 +4,9 @@ import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
+import java.util.Arrays;
import java.util.List;
+import java.util.Optional;
@Data
@AllArgsConstructor
@@ -21,7 +23,7 @@ public class PathologyDTO {
private String label;
@SerializedName("metadataHierarchy")
- private Object metadataHierarchy;
+ private MetadataHierarchyDTO metadataHierarchyDTO;
@SerializedName("datasets")
private List<PathologyDatasetDTO> datasets;
@@ -29,6 +31,23 @@ public class PathologyDTO {
public PathologyDTO(){
}
+
+
+ public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<PathologyDatasetDTO> pathologyDatasetDTOS) {
+ MetadataHierarchyDTO metadataHierarchyDTO = mipEngineAttributesDTO.getProperties().get("cdes").get(0);
+ List<MetadataHierarchyDTO.CommonDataElement> variables = metadataHierarchyDTO.getVariables();
+ variables.stream().filter(cde -> cde.getCode().equals("dataset")).
+ findAny().ifPresent(cde -> cde.setEnumerations(pathologyDatasetDTOS));
+ metadataHierarchyDTO.setVariables(variables);
+
+ List<String> pathology_info = Arrays.asList(pathology.split(":", 2));
+ this.code = pathology_info.get(0);
+ this.version = pathology_info.get(1);
+ this.metadataHierarchyDTO = metadataHierarchyDTO;
+ this.label = metadataHierarchyDTO.getLabel();
+ this.datasets = pathologyDatasetDTOS;
+ }
+
@Data
@AllArgsConstructor
public static class PathologyDatasetDTO {
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 12d923f12a30a6144925c7a4b12cfd5efbb85b32..de27f46fef43aae8426668f6227549c1238bd76d 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -124,7 +124,7 @@ public class ExperimentService {
logger.LogUserAction("Loading Experiment with uuid : " + uuid);
experimentDAO = experimentRepository.loadExperiment(uuid, logger);
- if (
+ if (
authenticationIsEnabled
&& !experimentDAO.isShared()
&& !experimentDAO.getCreatedBy().getUsername().equals(user.getUsername())
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index f5676b52c130f0b4be1c79d939567f74b752c0db..df2a75abf5d4a509b3bb6ee534ff1ed0de4555cd 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -54,8 +54,8 @@ public class ClaimUtils {
return hasRoleAccess(authorities, ClaimUtils.allExperimentsAllowedClaim(), logger);
}
- public static String getAuthorizedPathologies(Logger logger, Authentication authentication,
- List<PathologyDTO> allPathologies) {
+ public static List<PathologyDTO> getAuthorizedPathologies(Logger logger, Authentication authentication,
+ List<PathologyDTO> allPathologies) {
// --- Providing only the allowed pathologies/datasets to the user ---
logger.LogUserAction("Filter out the unauthorised datasets.");
@@ -63,7 +63,7 @@ public class ClaimUtils {
// If the "dataset_all" claim exists then return everything
if (hasRoleAccess(authorities, ClaimUtils.allDatasetsAllowedClaim(), logger)) {
- return gson.toJson(allPathologies);
+ return allPathologies;
}
List<PathologyDTO> userPathologies = new ArrayList<>();
@@ -83,13 +83,13 @@ public class ClaimUtils {
PathologyDTO userPathology = new PathologyDTO();
userPathology.setCode(curPathology.getCode());
userPathology.setLabel(curPathology.getLabel());
- userPathology.setMetadataHierarchy(curPathology.getMetadataHierarchy());
+ userPathology.setMetadataHierarchyDTO(curPathology.getMetadataHierarchyDTO());
userPathology.setDatasets(userPathologyDatasets);
userPathologies.add(userPathology);
}
}
- return gson.toJson(userPathologies);
+ return userPathologies;
}
private static boolean hasRoleAccess(ArrayList<String> authorities, String role, Logger logger)
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 32ed7ce849a5ad568c572289fb8cf0cf823b7e66..e301494d6f5a1ab32380a3b707a59ffb49c60d7b 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -36,6 +36,8 @@ spring:
services:
mipengine:
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"
exareme:
queryExaremeUrl: "http://127.0.0.1:9090/mining/query"
algorithmsUrl: "http://127.0.0.1:9090/mining/algorithms.json"