From e98b52a945f236e8eeacabf01c9395893af47b0f Mon Sep 17 00:00:00 2001
From: Manuel Spuhler <manuel.spuhler@chuv.ch>
Date: Wed, 18 Apr 2018 15:13:42 +0200
Subject: [PATCH] I/O for Exareme K_MEANS - wip
---
.../eu/hbp/mip/controllers/ExperimentApi.java | 24 ++--
.../java/eu/hbp/mip/model/Experiment.java | 123 ++++++++++++------
2 files changed, 88 insertions(+), 59 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index c1639df2d..3ede8eef8 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -6,6 +6,7 @@ import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import eu.hbp.mip.akka.WokenClientController;
import eu.hbp.mip.configuration.SecurityConfiguration;
+import eu.hbp.mip.model.AlgorithmParam;
import eu.hbp.mip.model.Experiment;
import eu.hbp.mip.model.ExperimentQuery;
import eu.hbp.mip.model.User;
@@ -83,12 +84,12 @@ public class ExperimentApi extends WokenClientController {
LOGGER.info("Experiment saved");
- if (isExaremeAlgo(expQuery)) {
- String algoCode = expQuery.getAlgorithms().get(0).getCode();
- sendExaremeExperiment(experiment, algoCode);
- }
- else {
+ if (!experiment.isExaremeAlgorithm()) {
sendExperiment(experiment);
+ } else {
+ String algoCode = expQuery.getAlgorithms().get(0).getCode();
+ List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
+ sendExaremeExperiment(experiment, algoCode, params);
}
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
@@ -286,11 +287,11 @@ public class ExperimentApi extends WokenClientController {
}, ec);
}
- private void sendExaremeExperiment(Experiment experiment, String algoCode) {
+ private void sendExaremeExperiment(Experiment experiment, String algoCode, List <AlgorithmParam> params) {
// >> Temporary: we should integrate exareme in a proper way in the future
// this runs in the background. For future optimization: use a thread pool
new Thread(() -> {
- String query = experiment.computeExaremeQuery();
+ String query = experiment.computeExaremeQuery(params);
String url = miningExaremeQueryUrl + "/" + algoCode;
// Results are stored in the experiment object
try {
@@ -322,13 +323,4 @@ public class ExperimentApi extends WokenClientController {
LOGGER.info("Experiment updated (finished)");
}
-
- private static boolean isExaremeAlgo(ExperimentQuery expQuery) {
- String code = expQuery.getAlgorithms().get(0).getCode();
- return expQuery.getAlgorithms().size() > 0
- && ("WP_".equals(code.substring(0, 3))
- || "glm_exareme".equals(code)
- || "K_MEANS".equals(code));
- }
-
}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index 38e535cb5..f4880376f 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -1,10 +1,7 @@
package eu.hbp.mip.model;
import ch.chuv.lren.mip.portal.WokenConversions;
-import com.google.gson.Gson;
-import com.google.gson.JsonArray;
-import com.google.gson.JsonObject;
-import com.google.gson.JsonParser;
+import com.google.gson.*;
import com.google.gson.annotations.Expose;
import com.google.gson.reflect.TypeToken;
import ch.chuv.lren.woken.messages.datasets.DatasetId;
@@ -21,10 +18,7 @@ import scala.collection.JavaConversions;
import javax.persistence.*;
import java.lang.reflect.Type;
-import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.UUID;
+import java.util.*;
/**
@@ -137,44 +131,60 @@ public class Experiment {
}
- public String computeExaremeQuery() {
+ public String computeExaremeQuery(List<AlgorithmParam> params) {
List<ExaremeQueryElement> queryElements = new LinkedList<>();
- for (Variable var : model.getQuery().getVariables())
+
+ // columns
+ List<String> columns = new ArrayList<>();
+ for (Variable var : model.getQuery().getVariables()) { columns.add(var.getCode()); }
+ for (Variable var : model.getQuery().getCovariables()) { columns.add(var.getCode()); }
+ for (Variable var : model.getQuery().getGrouping()) { columns.add(var.getCode()); }
+ StringBuilder sb = new StringBuilder();
+ int i = 0;
+ for (String s : columns)
{
- ExaremeQueryElement el = new ExaremeQueryElement();
- el.setName("variable");
- el.setDesc("");
- el.setValue(var.getCode());
- queryElements.add(el);
+ i++;
+ sb.append(s);
+ if (i < columns.size()) {
+ sb.append(",");
+ }
}
- for (Variable var : model.getQuery().getCovariables())
- {
- ExaremeQueryElement el = new ExaremeQueryElement();
- el.setName("covariables");
- el.setDesc("");
- el.setValue(var.getCode());
- queryElements.add(el);
+ ExaremeQueryElement columnsEl = new ExaremeQueryElement();
+ columnsEl.setName("columns");
+ columnsEl.setDesc("");
+ columnsEl.setValue(sb.toString());
+ queryElements.add(columnsEl);
+
+ // parameters
+ if (params != null) {
+ for (AlgorithmParam p : params)
+ {
+ ExaremeQueryElement paramEl = new ExaremeQueryElement();
+ paramEl.setName(p.getCode());
+ paramEl.setDesc("");
+ paramEl.setValue(p.getValue());
+ queryElements.add(paramEl);
+ }
}
- for (Variable var : model.getQuery().getGrouping())
+
+ // datasets
+ StringBuilder datasets = new StringBuilder();
+ List<Variable> trainingDatasets = model.getQuery().getTrainingDatasets();
+ int j = 0;
+ for (Variable var : trainingDatasets)
{
- ExaremeQueryElement el = new ExaremeQueryElement();
- el.setName("groupings");
- el.setDesc("");
- el.setValue(var.getCode());
- queryElements.add(el);
+ j++;
+ datasets.append(var.getCode());
+ if (j < trainingDatasets.size() ) {
+ datasets.append(",");
+ }
}
- ExaremeQueryElement tableEl = new ExaremeQueryElement();
- tableEl.setName("showtable");
- tableEl.setDesc("");
- tableEl.setValue("TotalResults");
- queryElements.add(tableEl);
-
- ExaremeQueryElement formatEl = new ExaremeQueryElement();
- formatEl.setName("format");
- formatEl.setDesc("");
- formatEl.setValue("True");
- queryElements.add(formatEl);
+ ExaremeQueryElement datasetsEl = new ExaremeQueryElement();
+ datasetsEl.setName("dataset");
+ datasetsEl.setDesc("");
+ datasetsEl.setValue(datasets.toString());
+ queryElements.add(datasetsEl);
return gson.toJson(queryElements);
}
@@ -197,11 +207,30 @@ public class Experiment {
exp.add("validations", jsonValidations);
}
- if (this.result != null && !this.hasServerError)
- {
+ if (this.result != null && !this.hasServerError) {
exp.remove("result");
- JsonArray jsonResult = parser.parse(this.result).getAsJsonArray();
- exp.add("result", jsonResult);
+
+ if (!this.isExaremeAlgorithm()) {
+ JsonArray jsonResult = parser.parse(this.result).getAsJsonArray();
+ exp.add("result", jsonResult);
+ } else {
+ JsonArray jsonArrayResult = new JsonArray();
+ JsonObject jsonObjectResult = new JsonObject();
+ exp.remove("result");
+
+ JsonObject jsonData = parser.parse(this.result).getAsJsonArray().get(0).getAsJsonObject();
+ jsonObjectResult.add("data", jsonData);
+
+ JsonObject algoObject = parser.parse(this.algorithms).getAsJsonArray().get(0).getAsJsonObject();
+ jsonObjectResult.add("algorithm", algoObject.get("name"));
+ jsonObjectResult.add("code", algoObject.get("code"));
+
+ jsonObjectResult.add("type", new JsonPrimitive("application/vnd.highcharts+json"));
+
+ jsonArrayResult.add(jsonObjectResult);
+
+ exp.add("result", jsonArrayResult);
+ }
}
return exp;
@@ -310,4 +339,12 @@ public class Experiment {
public void setShared(boolean shared) {
this.shared = shared;
}
+
+ public boolean isExaremeAlgorithm() {
+ String algorithms = this.algorithms;
+ Boolean isExareme = algorithms.contains("WP_")
+ || algorithms.contains("K_MEANS");
+
+ return isExareme;
+ }
}
--
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