diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 68eb313401323f94d237374bf5aacbbfb4971a8f..6385d89d5e1309cda7ea8b28aa5ab0b33f19c2f6 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -78,7 +78,11 @@ public class AlgorithmsAPI {
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
- algorithms.addAll(exaremeAlgorithms);
+ //algorithms.addAll(exaremeAlgorithms);
+ exaremeAlgorithms.forEach(algorithmDTO -> {
+ if(algorithmDTO.getName().equals("LOGISTIC_REGRESSION"))
+ algorithms.add(algorithmDTO);
+ });
} else {
logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
index 216140ba22f24332a862605404e94b84f5cf113c..6d70c021567ddf258f2dc4e716cb030f27949518 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -98,7 +98,7 @@ public class AlgorithmDTO {
@Getter
@Setter
- public static class Filters
+ public static class Filter
{
@SerializedName("condition")
private String condition;
@@ -109,7 +109,7 @@ public class AlgorithmDTO {
@SerializedName("valid")
private boolean valid;
- public Filters(String condition, List<Object> rules, boolean valid) {
+ public Filter(String condition, List<Object> rules, boolean valid) {
this.condition = condition;
this.rules = rules;
this.valid = valid;
@@ -121,36 +121,42 @@ public class AlgorithmDTO {
{
MIPEngineBody mipEngineBody = new MIPEngineBody();
MIPEngineBody.InputData inputData = new MIPEngineBody.InputData();
+ Hashtable<String, Object> mipEngineParameters = new Hashtable<>();
List<Object> rules = new ArrayList<>();
this.parameters.forEach(parameter -> {
+
if(parameter.getName().equals("x")) {
+ System.out.println("x");
List<String> x = Arrays.asList(parameter.getValue().split(","));
x.forEach(column -> rules.add(new Rule(column, parameter.getColumnValuesSQLType(), "is_not_null", null)));
inputData.setX(x);
}
- if(parameter.getName().equals("y")) {
+ else if(parameter.getName().equals("y")) {
List<String> y = Arrays.asList(parameter.getValue().split(","));
y.forEach(column -> rules.add(new Rule(column, parameter.getColumnValuesSQLType(), "is_not_null", null)));
inputData.setY(y);
}
- if(parameter.getName().equals("dataset")){
+ else if(parameter.getName().equals("dataset")){
List<String> datasets = Arrays.asList(parameter.getValue().split(","));
rules.add(new Rule("dataset","string", "in", datasets));
inputData.setDatasets(datasets);
}
- String pathology;
- if(parameter.getName().equals("pathology"))
+ else if(parameter.getName().equals("pathology"))
inputData.setPathology(parameter.getValue());
- if(parameter.getName().equals("filter")){
+ else if(parameter.getName().equals("filter")){
if (parameter.getValue() != "")
- rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), Filters.class));
+ rules.add(JsonConverters.convertJsonStringToObject(parameter.getValue(), Filter.class));
+ }
+ else{
+ mipEngineParameters.put(parameter.getName(), Arrays.asList(parameter.getValue().split(",")));
}
});
- Filters filters = new Filters("AND", rules, true);
- inputData.setFilters(filters);
+ Filter filter = new Filter("AND", rules, true);
+ inputData.setFilters(filter);
mipEngineBody.setInputdata(inputData);
+ mipEngineBody.setParameters(mipEngineParameters);
return mipEngineBody;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
index f253bab6d76e156a34a59947108bb0d8866b8662..d391492d7615e6ef5892fa78c5a83227207d4afb 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -1,6 +1,7 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.utils.JsonConverters;
import lombok.Getter;
import lombok.Setter;
@@ -26,7 +27,7 @@ public class MIPEngineAlgorithmDTO {
private String type;
@SerializedName("parameters")
- private InputDataParamDTO parameters;
+ private Hashtable<String, ParameterDTO> parameters;
@SerializedName("crossvalidation")
private String crossvalidation;
@@ -34,6 +35,54 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("inputdata")
private Hashtable<String, InputDataParamDTO> inputdata;
+ @Getter
+ @Setter
+ public static class ParameterDTO {
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("notblank")
+ private String notblank;
+
+ @SerializedName("multiple")
+ private String multiple;
+
+ @SerializedName("types")
+ private String type;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("min")
+ private String min;
+
+ @SerializedName("max")
+ private String max;
+
+ @SerializedName("default_value")
+ private String default_value;
+
+ @SerializedName("enums")
+ private List<String> enums;
+
+ public AlgorithmDTO.AlgorithmParamDTO convertToAlgorithmParamDTO(String name) throws Exception {
+ AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
+ algorithmParamDTO.setName(name);
+ algorithmParamDTO.setDesc(this.desc);
+ algorithmParamDTO.setValueType(this.type);
+ algorithmParamDTO.setType("other");
+ algorithmParamDTO.setDefaultValue(this.default_value);
+ algorithmParamDTO.setValueNotBlank(this.notblank);
+ algorithmParamDTO.setLabel(this.label);
+ algorithmParamDTO.setValueEnumerations(this.enums);
+ algorithmParamDTO.setValueMultiple(this.multiple);
+ algorithmParamDTO.setValueMin(this.min);
+ algorithmParamDTO.setValueMax(this.max);
+ return algorithmParamDTO;
+ }
+ }
+
@Getter
@Setter
public static class InputDataParamDTO {
@@ -63,16 +112,13 @@ public class MIPEngineAlgorithmDTO {
AlgorithmDTO.AlgorithmParamDTO algorithmParamDTO = new AlgorithmDTO.AlgorithmParamDTO();
algorithmParamDTO.setName(name);
algorithmParamDTO.setDesc(this.desc);
- if(name.equals("datasets") || name.equals("filters") || name.equals("pathology")){
- algorithmParamDTO.setValueType(this.types.get(0));
- if(name.equals("filters")){
- algorithmParamDTO.setName("filter");
- algorithmParamDTO.setType("filter");
- }
+
+ if(name.equals("datasets") || name.equals("filter") || name.equals("pathology")){
if(name.equals("datasets")){
algorithmParamDTO.setName("dataset");
- algorithmParamDTO.setType("dataset");
}
+ algorithmParamDTO.setValueType(this.types.get(0));
+ algorithmParamDTO.setType(algorithmParamDTO.getName());
}
else{
algorithmParamDTO.setType("column");
@@ -84,7 +130,8 @@ public class MIPEngineAlgorithmDTO {
algorithmParamDTO.setValueMultiple(this.multiple);
String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
algorithmParamDTO.setLabel(Arrays.asList(hidden).contains(algorithmParamDTO.getName()) ? algorithmParamDTO.getName():this.label);
-
+ System.out.println("-------------------------------------------------------->");
+ System.out.println(JsonConverters.convertObjectToJsonString(algorithmParamDTO));
return algorithmParamDTO;
}
private String getColumnValuesIsCategorical(List<String> stattypes) throws Exception {
@@ -120,6 +167,14 @@ public class MIPEngineAlgorithmDTO {
e.printStackTrace();
}
});
+ this.parameters.forEach((name, parameterDTO) -> {
+ try {
+ AlgorithmDTO.AlgorithmParamDTO parameter = parameterDTO.convertToAlgorithmParamDTO(name);
+ parameters.add(parameter);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ });
algorithmDTO.setParameters(parameters);
return algorithmDTO;
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
index b8b2f957a166467890296f35baa5e55b89f2b184..1572eb7daed817717bfff4c03d1a8524e2e498eb 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineBody.java
@@ -4,6 +4,7 @@ import com.google.gson.annotations.SerializedName;
import lombok.Getter;
import lombok.Setter;
+import java.util.Hashtable;
import java.util.List;
@Getter
@@ -12,7 +13,7 @@ public class MIPEngineBody {
@SerializedName("inputdata")
private InputData inputdata;
@SerializedName("parameters")
- private Object parameters;
+ private Hashtable<String, Object> parameters;
@Getter
@Setter
@@ -22,7 +23,7 @@ public class MIPEngineBody {
@SerializedName("datasets")
private List<String> datasets;
@SerializedName("filters")
- private AlgorithmDTO.Filters filters;
+ private AlgorithmDTO.Filter filters;
@SerializedName("x")
private List<String> x;
@SerializedName("y")
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index bc7f4dd11343e26bb888c28e5d987ec3916632ac..a48beb3aa9a975d71ad3c1bbeb0dad03cc191ebc 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -27,6 +27,9 @@ import eu.hbp.mip.utils.Exceptions.*;
import eu.hbp.mip.utils.HTTPUtil;
import eu.hbp.mip.utils.JsonConverters;
import eu.hbp.mip.utils.Logger;
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Value;
@@ -386,7 +389,7 @@ public class ExperimentService {
.append("\n"));
logger.LogUserAction("Executing " + algorithmName + parametersLogMessage);
}
-
+
/**
* The getDatasetFromExperimentParameters will retrieve the dataset from the experiment parameters
*
@@ -508,19 +511,9 @@ public class ExperimentService {
}
private List<Object> formattingMIPEngienResult(String result) {
- List<List<String>> resultJson = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<String>>().getClass());
- String schema_json = "{\"fields\":[{\"type\":\"string\",\"name\":\"node\"},{\"type\":\"number\",\"name\":\"row-id\"},{\"type\":\"number\",\"name\":\"alzheimerbroadcategory_bin\"}]}";
- LinkedTreeMap<String,List<Object>> schema = JsonConverters.convertJsonStringToObject(schema_json, new LinkedTreeMap<String,ArrayList<Object>>().getClass());
-
-
- LinkedTreeMap<String,Object> data_data = new LinkedTreeMap<>();
- data_data.put("data", resultJson);
- data_data.put("profile", "tabular-data-resource");
- data_data.put("schema", schema);
- data_data.put("name","Logistic Regression Stuff");
-
+ MIPVisualization mipVisualization = JsonConverters.convertJsonStringToObject(result, MIPVisualization.class);
LinkedTreeMap<String,Object> data = new LinkedTreeMap<>();
- data.put("data", data_data);
+ data.put("data", mipVisualization.convertToVisualization());
data.put("type", "application/vnd.dataresource+json");
List<Object> finalObject = new ArrayList<>();
finalObject.add(data);
@@ -601,6 +594,7 @@ public class ExperimentService {
} catch (Exception e) {
throw new InternalServerError("Error occurred : " + e.getMessage());
}
+ System.out.println(results);
// Results are stored in the experiment object
List<Object> resultDTOS = formattingMIPEngienResult(String.valueOf(results));
@@ -1045,6 +1039,8 @@ public class ExperimentService {
return returnError;
}
+ @Getter
+ @Setter
static class ExperimentResult {
private final int code;
private final List<Object> results;
@@ -1053,13 +1049,43 @@ public class ExperimentService {
this.code = code;
this.results = results;
}
+ }
- public int getCode() {
- return code;
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ static class Visualization {
+ private final String title;
+ private final String profile;
+ private final List<Field> columns;
+ private final List<List<Object>> data;
+ }
+
+ @Getter
+ @Setter
+ @AllArgsConstructor
+ static class MIPVisualization {
+ private final String title;
+ private final List<String> columns;
+ private final List<List<Object>> data;
+
+ public Visualization convertToVisualization() {
+ ArrayList<Field> fields = new ArrayList<>();
+ this.columns.forEach(header_name -> fields.add(new Field(header_name, "number")));
+ return new Visualization(this.title, "tabular-data-resource", fields, this.data);
}
- public List<Object> getResults() {
- return results;
+ }
+
+ @Getter
+ @Setter
+ static class Field {
+ private final String name;
+ private final String type;
+
+ Field(String name, String type) {
+ this.name = name;
+ this.type = type;
}
}
}