diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 4f74bc820c8d0834eeaba088d778faf5dc7f88bc..0507c49cb97f264e89ffeb146b549fefed93d6f2 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -25,18 +25,14 @@ import scala.concurrent.ExecutionContext;
import scala.concurrent.Future;
import java.io.IOException;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-
+import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
/**
* Created by habfast on 21/04/16.
*/
@RestController
-@RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
+@RequestMapping(value = "/experiments", produces = { APPLICATION_JSON_VALUE })
@Api(value = "/experiments", description = "the experiments API")
public class ExperimentApi extends WokenClientController {
@@ -44,11 +40,8 @@ public class ExperimentApi extends WokenClientController {
private static final Gson gson = new Gson();
- private static final Gson gsonOnlyExposed = new GsonBuilder()
- .serializeNulls()
- .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ")
- .excludeFieldsWithoutExposeAnnotation()
- .create();
+ private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
+ .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
@Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
public String miningExaremeQueryUrl;
@@ -76,25 +69,41 @@ public class ExperimentApi extends WokenClientController {
experiment.setName(expQuery.getName());
experiment.setCreatedBy(user);
experiment.setModel(modelRepository.findOne(expQuery.getModel()));
- experiment.setSource(expQuery.getSource());
experimentRepository.save(experiment);
LOGGER.info("Experiment saved");
+ sendExperiment(experiment);
- if (experiment.getSource() != "exareme") {
- 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);
+ }
+
+ @ApiOperation(value = "Create an experiment on Exareme", response = Experiment.class)
+ @RequestMapping(value = "/exareme", method = RequestMethod.POST)
+ public ResponseEntity<String> runExaremeExperiment(@RequestBody ExperimentQuery expQuery) {
+ LOGGER.info("sendExaremeExperiment");
+
+ Experiment experiment = new Experiment();
+ experiment.setUuid(UUID.randomUUID());
+ User user = userInfo.getUser();
+
+ experiment.setAlgorithms(gson.toJson(expQuery.getAlgorithms()));
+ experiment.setValidations(gson.toJson(expQuery.getValidations()));
+ experiment.setName(expQuery.getName());
+ experiment.setCreatedBy(user);
+ experiment.setModel(modelRepository.findOne(expQuery.getModel()));
+ experimentRepository.save(experiment);
+
+ 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);
}
@ApiOperation(value = "get an experiment", response = Experiment.class)
@RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
- public ResponseEntity<String> getExperiment(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ public ResponseEntity<String> getExperiment(
+ @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
LOGGER.info("Get an experiment");
Experiment experiment;
@@ -118,7 +127,8 @@ public class ExperimentApi extends WokenClientController {
@ApiOperation(value = "Mark an experiment as viewed", response = Experiment.class)
@RequestMapping(value = "/{uuid}/markAsViewed", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsViewed(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ public ResponseEntity<String> markExperimentAsViewed(
+ @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
LOGGER.info("Mark an experiment as viewed");
Experiment experiment;
@@ -145,7 +155,8 @@ public class ExperimentApi extends WokenClientController {
@ApiOperation(value = "Mark an experiment as shared", response = Experiment.class)
@RequestMapping(value = "/{uuid}/markAsShared", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsShared(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ public ResponseEntity<String> markExperimentAsShared(
+ @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
LOGGER.info("Mark an experiment as shared");
return doMarkExperimentAsShared(uuid, true);
@@ -153,72 +164,62 @@ public class ExperimentApi extends WokenClientController {
@ApiOperation(value = "Mark an experiment as unshared", response = Experiment.class)
@RequestMapping(value = "/{uuid}/markAsUnshared", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsUnshared(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ public ResponseEntity<String> markExperimentAsUnshared(
+ @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
LOGGER.info("Mark an experiment as unshared");
return doMarkExperimentAsShared(uuid, false);
}
@ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"maxResultCount"})
+ @RequestMapping(method = RequestMethod.GET, params = { "maxResultCount" })
public ResponseEntity<String> listExperiments(
- @ApiParam(value = "maxResultCount") @RequestParam int maxResultCount
- ) {
+ @ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
LOGGER.info("List experiments");
return doListExperiments(false, null);
}
@ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
- public ResponseEntity<String> listExperiments(
- @ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
- @ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount
- ) {
+ @RequestMapping(method = RequestMethod.GET, params = { "slug", "maxResultCount" })
+ public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
+ @ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
LOGGER.info("List experiments");
if (maxResultCount <= 0 && (modelSlug == null || "".equals(modelSlug))) {
- return new ResponseEntity<>("You must provide at least a slug or a limit of result", HttpStatus.BAD_REQUEST);
+ return new ResponseEntity<>("You must provide at least a slug or a limit of result",
+ HttpStatus.BAD_REQUEST);
}
return doListExperiments(false, modelSlug);
}
@ApiOperation(value = "list my experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"mine"})
- public ResponseEntity<String> listMyExperiments(
- @ApiParam(value = "mine") @RequestParam("mine") boolean mine
- ) {
+ @RequestMapping(method = RequestMethod.GET, params = { "mine" })
+ public ResponseEntity<String> listMyExperiments(@ApiParam(value = "mine") @RequestParam("mine") boolean mine) {
LOGGER.info("List my experiments");
return doListExperiments(true, null);
}
-
- private ResponseEntity<String> doListExperiments(
- boolean mine,
- String modelSlug
- ) {
+ private ResponseEntity<String> doListExperiments(boolean mine, String modelSlug) {
User user = userInfo.getUser();
Iterable<Experiment> myExperiments = experimentRepository.findByCreatedBy(user);
List<Experiment> expList = Lists.newLinkedList(myExperiments);
- if(!mine)
- {
+ if (!mine) {
Iterable<Experiment> sharedExperiments = experimentRepository.findByShared(true);
List<Experiment> sharedExpList = Lists.newLinkedList(sharedExperiments);
expList.addAll(sharedExpList);
}
if (modelSlug != null && !"".equals(modelSlug)) {
- for(Iterator<Experiment> it = expList.iterator(); it.hasNext();)
- {
+ for (Iterator<Experiment> it = expList.iterator(); it.hasNext();) {
Experiment e = it.next();
e.setResult(null);
e.setAlgorithms(null);
e.setValidations(null);
- if(!e.getModel().getSlug().equals(modelSlug))
- {
+ if (!e.getModel().getSlug().equals(modelSlug)) {
it.remove();
}
}
@@ -256,10 +257,11 @@ public class ExperimentApi extends WokenClientController {
User user = userInfo.getUser();
// this runs in the background. For future optimization: use a thread pool
- final ch.chuv.lren.woken.messages.query.ExperimentQuery experimentQuery = experiment.prepareQuery(user.getUsername());
+ final ch.chuv.lren.woken.messages.query.ExperimentQuery experimentQuery = experiment
+ .prepareQuery(user.getUsername());
final ExecutionContext ec = getExecutor();
- Future<Object> response = sendWokenQuery(experimentQuery, 24*3600);
+ Future<Object> response = sendWokenQuery(experimentQuery, 24 * 3600);
response.onSuccess(new OnSuccess<Object>() {
public void onSuccess(Object result) {
QueryResult queryResult = (QueryResult) result;
@@ -283,11 +285,27 @@ public class ExperimentApi extends WokenClientController {
}, ec);
}
- private void sendExaremeExperiment(Experiment experiment, String algoCode, List <AlgorithmParam> params) {
- // >> Temporary: we should integrate exareme in a proper way in the future
+ private void sendExaremeExperiment(Experiment experiment, String algoCode, List<AlgorithmParam> params) {
// this runs in the background. For future optimization: use a thread pool
new Thread(() -> {
- String query = ""; //experiment.computeExaremeQuery(params);
+ List<HashMap<String, String>> queryList = new ArrayList<HashMap<String, String>>();
+
+ Query modelQuery = experiment.getModel().getQuery();
+ queryList.add(makeObject("x", Variable.stringFromVariables(modelQuery.getVariables(), ",")));
+
+ List<Variable> mergedCovariables = new ArrayList<Variable>(modelQuery.getCovariables());
+ queryList.add(makeObject("y", Variable.stringFromVariables(mergedCovariables, ",")));
+
+ List<Variable> mergedDatasets = new ArrayList<Variable>(modelQuery.getTrainingDatasets());
+ queryList.add(makeObject("dataset", Variable.stringFromVariables(mergedDatasets, ",")));
+
+ if (params != null) {
+ for (AlgorithmParam p : params) {
+ queryList.add(makeObject(p.getName(), p.getValue()));
+ }
+ }
+
+ String query = gson.toJson(queryList);
String url = miningExaremeQueryUrl + "/" + algoCode;
// Results are stored in the experiment object
@@ -306,14 +324,21 @@ public class ExperimentApi extends WokenClientController {
}
finishExperiment(experiment);
}).start();
- // << Temporary
}
- private void finishExperiment(Experiment experiment)
- {
+ private void finishExperiment(Experiment experiment) {
experiment.setFinished(new Date());
experimentRepository.save(experiment);
LOGGER.info("Experiment updated (finished)");
}
+
+ private HashMap<String, String> makeObject(String name, String value) {
+ HashMap<String, String> o = new HashMap<String, String>();
+ o.put("name", name);
+ o.put("value", value);
+
+ return o;
+ }
+
}
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index bf89261eb14fab25a0adf5bf7dd3e07ff43235e6..24356234ea7467c873b902830f37fa46b78a5c17 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -38,9 +38,6 @@ public class MiningApi extends WokenClientController {
@Autowired
private UserInfo userInfo;
- @Value("#{'${services.query.miningExaremeUrl:http://localhost:9090/mining/query}'}")
- public String queryUrl;
-
@ApiOperation(value = "Run an algorithm", response = String.class)
@Cacheable(value = "mining",
condition = "#query != null and (#query.getAlgorithm().getCode() == 'histograms' or #query.getAlgorithm().getCode() == 'histograms')",
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmParam.java b/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
index e4e5eac8ddcb77ea6e5c4af7837af547c2ba6efd..62c48ba13b4cffcf647d4da97a0509735f18cac4 100644
--- a/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
+++ b/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
@@ -11,6 +11,15 @@ public class AlgorithmParam {
public String getCode() {
return code;
+
+ }
+
+ public void setName(String name) {
+ this.code = name;
+ }
+
+ public String getName() {
+ return this.code;
}
public void setCode(String code) {
diff --git a/src/main/java/eu/hbp/mip/model/ExaremeQueryElement.java b/src/main/java/eu/hbp/mip/model/ExaremeQueryElement.java
deleted file mode 100644
index 0b7005c19dd985d4ae639768053df2c61f836ac7..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExaremeQueryElement.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-/**
- * Created by mirco on 20.06.16.
- */
-
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class ExaremeQueryElement {
-
- private String name;
-
- private String desc;
-
- private String value;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getDesc() {
- return desc;
- }
-
- public void setDesc(String desc) {
- this.desc = desc;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index c0a1799097a3aff5ffba52bf24c5708c780f27c5..c84ec57ed37bfd699ad167c361cceaa241ba88fc 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -137,7 +137,6 @@ public class Experiment {
public JsonObject jsonify() {
JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
JsonParser parser = new JsonParser();
- Boolean isExaremeAlgorithm = this.getSource() == "exareme";
if (this.algorithms != null)
{
@@ -156,33 +155,9 @@ public class Experiment {
if (this.result != null && !this.hasServerError) {
exp.remove("result");
- if (!isExaremeAlgorithm) {
- JsonElement jsonResult = parser.parse(this.result);
- exp.add("result", jsonResult);
- } else {
- JsonArray jsonArrayResult = new JsonArray();
- JsonObject jsonObjectResult = new JsonObject();
-
- JsonObject algoObject = parser.parse(this.algorithms).getAsJsonArray().get(0).getAsJsonObject();
- jsonObjectResult.add("algorithm", algoObject.get("name"));
- jsonObjectResult.add("code", algoObject.get("code"));
-
- exp.remove("result");
- JsonObject tryJson;
- try {
- tryJson = parser.parse(this.result).getAsJsonArray().get(0).getAsJsonObject();
- } catch(JsonParseException e) {
- tryJson = new JsonObject();
- tryJson.add("result", new JsonPrimitive(this.result));
- }
-
- JsonObject jsonData = tryJson;
- jsonObjectResult.add("data", jsonData);
-
- jsonArrayResult.add(jsonObjectResult);
-
- exp.add("result", jsonArrayResult);
- }
+ JsonElement jsonResult = parser.parse(this.result);
+ exp.add("result", jsonResult);
+
}
return exp;
@@ -291,12 +266,4 @@ public class Experiment {
public void setShared(boolean shared) {
this.shared = shared;
}
-
- public String getSource() {
- return this.source;
- }
-
- public void setSource(String source) {
- this.source = source;
- }
}
diff --git a/src/main/java/eu/hbp/mip/model/Variable.java b/src/main/java/eu/hbp/mip/model/Variable.java
index 0947cdd7db753d27741a2e0b32fb4239c166cbac..1fcce2e48e89dc8e94a935bfc803ada086cd53f5 100644
--- a/src/main/java/eu/hbp/mip/model/Variable.java
+++ b/src/main/java/eu/hbp/mip/model/Variable.java
@@ -12,6 +12,7 @@ import io.swagger.annotations.ApiModel;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
+import java.util.List;
@Entity
@Table(name = "`variable`")
@@ -42,6 +43,17 @@ public class Variable {
this.code = code;
}
-
+ public static String stringFromVariables(List<Variable> variables, String operator) {
+ StringBuilder sb = new StringBuilder();
+ int i = 0;
+ for (Variable s : variables) {
+ i++;
+ sb.append(s.getCode());
+ if (i < variables.size()) {
+ sb.append(operator);
+ }
+ }
+ return sb.toString();
+ }
}