diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 0856eacbe4e8bbb2f9137d8df71c30c64f7bc342..5f9ea27f9885a3c518cb6fed0b418276012470ea 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -89,3 +89,4 @@ endpoints:
services:
exareme:
miningExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
+ algorithmsUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/algorithms.json
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 324ed29fd331b76639d29f5bf5275dd1b464a7eb..3eaee9e5450619fc03fc151aab8268cf662dc9f0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -293,6 +293,11 @@
<version>${scala.release.version}</version>
<scope>compile</scope>
</dependency>
+ <dependency>
+ <groupId>io.jsonwebtoken</groupId>
+ <artifactId>jjwt</artifactId>
+ <version>0.9.1</version>
+ </dependency>
</dependencies>
<build>
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index caa8ea97be33dbb6773754c6ce37c6f2a609094e..fba15a4f834083e101ecbcb5b28fe77f2e199c8b 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -25,18 +25,14 @@ import scala.concurrent.ExecutionContext;
import scala.concurrent.Future;
import java.io.IOException;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-
+import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
/**
* Created by habfast on 21/04/16.
*/
@RestController
-@RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
+@RequestMapping(value = "/experiments", produces = { APPLICATION_JSON_VALUE })
@Api(value = "/experiments", description = "the experiments API")
public class ExperimentApi extends WokenClientController {
@@ -44,11 +40,8 @@ public class ExperimentApi extends WokenClientController {
private static final Gson gson = new Gson();
- private static final Gson gsonOnlyExposed = new GsonBuilder()
- .serializeNulls()
- .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ")
- .excludeFieldsWithoutExposeAnnotation()
- .create();
+ private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
+ .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
@Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
public String miningExaremeQueryUrl;
@@ -67,33 +60,30 @@ public class ExperimentApi extends WokenClientController {
public ResponseEntity<String> runExperiment(@RequestBody ExperimentQuery expQuery) {
LOGGER.info("Run an experiment");
- Experiment experiment = new Experiment();
- experiment.setUuid(UUID.randomUUID());
- User user = userInfo.getUser();
+ Experiment experiment = saveExperiment(expQuery);
+ sendExperiment(experiment);
- 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);
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ }
- LOGGER.info("Experiment saved");
+ @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");
- if (!experiment.isExaremeAlgorithm()._1) {
- sendExperiment(experiment);
- } else {
- String algoCode = expQuery.getAlgorithms().get(0).getCode();
- List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
- sendExaremeExperiment(experiment, algoCode, params);
- }
+ Experiment experiment = saveExperiment(expQuery);
+
+ 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;
@@ -117,7 +107,8 @@ 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;
@@ -144,7 +135,8 @@ 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);
@@ -152,72 +144,62 @@ 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();
}
}
@@ -255,10 +237,11 @@ 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;
@@ -282,11 +265,18 @@ 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>>();
+
+ 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
@@ -305,14 +295,40 @@ 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;
+ }
+
+ private Experiment saveExperiment(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);
+
+ LOGGER.info("Experiment saved");
+
+ return experiment;
+ }
+
}
diff --git a/src/main/java/eu/hbp/mip/controllers/JWTApi.java b/src/main/java/eu/hbp/mip/controllers/JWTApi.java
new file mode 100644
index 0000000000000000000000000000000000000000..4073a58e288d546172dd2165598662c93af8ff4b
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/JWTApi.java
@@ -0,0 +1,59 @@
+package eu.hbp.mip.controllers;
+
+import static org.springframework.http.MediaType.TEXT_PLAIN_VALUE;
+import java.security.Key;
+import java.util.Date;
+import javax.crypto.spec.SecretKeySpec;
+import javax.xml.bind.DatatypeConverter;
+import eu.hbp.mip.model.UserInfo;
+import org.slf4j.Logger;
+import eu.hbp.mip.model.User;
+import org.slf4j.LoggerFactory;
+import org.springframework.http.ResponseEntity;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import io.jsonwebtoken.*;
+import org.springframework.web.bind.annotation.*;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+
+@RestController
+@RequestMapping(value = "/jwt", produces = { TEXT_PLAIN_VALUE })
+@Api(value = "/jwt", description = "the jwt API")
+public class JWTApi {
+
+ private static final Logger LOGGER = LoggerFactory.getLogger(JWTApi.class);
+
+ @Autowired
+ private UserInfo userInfo;
+
+ @ApiOperation(value = "Create a JSON Web Token", response = String.class)
+ @RequestMapping(method = RequestMethod.POST)
+ public ResponseEntity<String> createJWT() {
+
+ LOGGER.info("Create a JSON Web Token");
+
+ // SignatureAlgorithm signatureAlgorithm = SignatureAlgorithm.HS256;
+ // String apiKey = "6v2oxpJMzU14U-dqVireln5AUKTtx5fBPSEgaBZiI983d98cfa6";
+ // byte[] apiKeySecretBytes = DatatypeConverter.parseBase64Binary(apiKey);
+ // Key signingKey = new SecretKeySpec(apiKeySecretBytes, signatureAlgorithm.getJcaName());
+
+ long nowMillis = System.currentTimeMillis();
+ Date now = new Date(nowMillis);
+
+ User user = userInfo.getUser();
+
+ // Set the JWT Claims
+ JwtBuilder builder = Jwts.builder().setIssuedAt(now).setIssuer("mip.humanbrainproject.eu")
+ .setSubject(user.getEmail()).signWith(SignatureAlgorithm.HS512,
+ "hbpSecret");
+
+ String token = builder.compact();
+ LOGGER.info(token);
+ // long expMillis = nowMillis + 86400 * 24;
+ // Date exp = new Date(expMillis);
+ // builder.setExpiration(exp);
+
+ return ResponseEntity.status(HttpStatus.CREATED).body(token);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
index b275f889d2f955a8b52cdf25dde3696789a0274c..21d3b9f2f852828df49dd81c4ec85fcecbe8e80c 100644
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
@@ -12,14 +12,14 @@ import org.springframework.cache.annotation.Cacheable;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import eu.hbp.mip.utils.HTTPUtil;
+import org.springframework.beans.factory.annotation.Value;
+import java.io.IOException;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
-@RequestMapping(value = "/methods", produces = {APPLICATION_JSON_VALUE})
+@RequestMapping(value = "/methods", produces = { APPLICATION_JSON_VALUE })
@Api(value = "/methods", description = "the methods API")
public class MethodsApi extends WokenClientController {
@@ -27,7 +27,8 @@ public class MethodsApi extends WokenClientController {
private static final Gson gson = new Gson();
- private static final String EXAREME_ALGO_JSON_FILE="data/exareme_algorithms.json";
+ @Value("#{'${services.exareme.algorithmsUrl:http://localhost:9090/mining/algorithms.json}'}")
+ private String exaremeAlgorithmsUrl;
@ApiOperation(value = "List available methods and validations", response = String.class)
@Cacheable(value = "methods", unless = "#result.getStatusCode().value()!=200")
@@ -37,19 +38,28 @@ public class MethodsApi extends WokenClientController {
return requestWoken(MethodsQuery$.MODULE$, 10, r -> {
MethodsResponse result = (MethodsResponse) r;
-
- // >> Temporary : should return result.methods() in the future
JsonObject catalog = new JsonParser().parse(result.methods().compactPrint()).getAsJsonObject();
- InputStream is = MethodsApi.class.getClassLoader().getResourceAsStream(EXAREME_ALGO_JSON_FILE);
- InputStreamReader isr = new InputStreamReader(is);
- BufferedReader br = new BufferedReader(isr);
- JsonElement element = new JsonParser().parse(br);
- JsonArray exaremeAlgo = element.getAsJsonArray();
- catalog.get("algorithms").getAsJsonArray().addAll(exaremeAlgo);
- // << Temporary
return ResponseEntity.ok(gson.toJson(catalog));
});
}
+ @ApiOperation(value = "List Exareme algorithms and validations", response = String.class)
+ @Cacheable(value = "exareme", unless = "#result.getStatusCode().value()!=200")
+ @RequestMapping(value = "/exareme", method = RequestMethod.GET)
+ public ResponseEntity<Object> getExaremeAlgorithms() {
+ LOGGER.info("List Exareme algorithms and validations");
+
+ try {
+ StringBuilder response = new StringBuilder();
+ HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
+ JsonElement element = new JsonParser().parse(response.toString());
+
+ return ResponseEntity.ok(gson.toJson(element));
+ } catch (IOException e) {
+ return ResponseEntity.status(500).body(e.getMessage());
+ }
+
+ }
+
}
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index bf89261eb14fab25a0adf5bf7dd3e07ff43235e6..24356234ea7467c873b902830f37fa46b78a5c17 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -38,9 +38,6 @@ public class MiningApi extends WokenClientController {
@Autowired
private UserInfo userInfo;
- @Value("#{'${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 8f4dd0a347a7e595742de1a0b9702163d4a0819b..e2def32c37b446fde76ca609792569036b8b22e6 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -19,7 +19,6 @@ import scala.collection.JavaConversions;
import javax.persistence.*;
import java.lang.reflect.Type;
import java.util.*;
-import scala.Tuple2;
/**
* Created by habfast on 21/04/16.
@@ -28,12 +27,6 @@ import scala.Tuple2;
@Table(name = "`experiment`")
public class Experiment {
- public static final String WP_K_MEANS = "K_MEANS";
- public static final String WP_LINEAR_REGRESSION = "WP_LINEAR_REGRESSION";
- public static final String WP_VARIABLES_HISTOGRAM = "WP_VARIABLES_HISTOGRAM";
- public static final String WP_REGRESSION_TREE = "PIPELINE_ISOUP_REGRESSION_TREE_SERIALIZER";
- public static final String WP_MODEL_TREE = "PIPELINE_ISOUP_MODEL_TREE_SERIALIZER";
-
private static final Logger LOGGER = LoggerFactory.getLogger(Experiment.class);
private static final Gson gson = new Gson();
@@ -137,159 +130,9 @@ public class Experiment {
validationsSeq, Option.empty());
}
- private String chainsParams(List<String> params, String operator) {
- StringBuilder sb = new StringBuilder();
- int i = 0;
- for (String s : params)
- {
- i++;
- sb.append(s);
- if (i < params.size()) {
- sb.append(operator);
- }
- }
- return sb.toString();
- }
-
- public String computeExaremeQuery(List<AlgorithmParam> params) {
- List<ExaremeQueryElement> queryElements = new LinkedList<>();
-
- // parameters
- String design = ""; // TODO: don't assign to a global
- String nobuckets = "";
-
- if (params != null) {
- for (AlgorithmParam p : params)
- {
- ExaremeQueryElement paramEl = new ExaremeQueryElement();
- paramEl.setName(p.getCode());
- paramEl.setDesc("");
- paramEl.setValue(p.getValue());
- queryElements.add(paramEl);
-
- if (p.getCode().equals("design")) {
- design = p.getValue();
- }
-
- if (p.getCode().equals("nobuckets")) {
- nobuckets = p.getValue();
- }
- }
- }
-
- List<String> variables = new ArrayList<>();
- List<String> covariables = new ArrayList<>();
- List<String> groupings = new ArrayList<>();
-
- for (Variable var : model.getQuery().getVariables()) { variables.add(var.getCode()); }
- for (Variable var : model.getQuery().getCovariables()) { covariables.add(var.getCode()); }
- for (Variable var : model.getQuery().getGrouping()) { groupings.add(var.getCode()); }
-
- // Set algorithm specific queries
- String algoName = this.isExaremeAlgorithm()._2;
- if (algoName.equals(WP_K_MEANS)) {
- // columns
- List<String> columns = variables;
- columns.addAll(covariables);
- columns.addAll(groupings);
-
- ExaremeQueryElement columnsEl = new ExaremeQueryElement();
- columnsEl.setName("columns");
- columnsEl.setDesc("");
- columnsEl.setValue(chainsParams(columns, ","));
- queryElements.add(columnsEl);
- } else if (algoName.equals(WP_LINEAR_REGRESSION)) {
- List<String> nominals = covariables.isEmpty() ? groupings : covariables;
- nominals.addAll(groupings);
-
- String operator = design.equals("factorial") ? "*" : "+";
-
- ExaremeQueryElement xEl = new ExaremeQueryElement();
- xEl.setName("x");
- xEl.setDesc("");
- xEl.setValue(chainsParams(nominals, operator));
- queryElements.add(xEl);
-
- ExaremeQueryElement yEl = new ExaremeQueryElement();
- yEl.setName("y");
- yEl.setDesc("");
- yEl.setValue(chainsParams(variables, ","));
- queryElements.add(yEl);
- } else if (algoName.equals(WP_VARIABLES_HISTOGRAM)) {
- List<String> column1 = variables;
- ExaremeQueryElement columnsEl = new ExaremeQueryElement();
- columnsEl.setName("column1");
- columnsEl.setDesc("");
- columnsEl.setValue(chainsParams(column1, ","));
- queryElements.add(columnsEl);
-
- List<String> column2 = covariables.isEmpty() ? groupings : covariables;
- ExaremeQueryElement columnsEl2 = new ExaremeQueryElement();
- columnsEl2.setName("column2");
- columnsEl2.setDesc("");
- columnsEl2.setValue(chainsParams(column2, ","));
- queryElements.add(columnsEl2);
-
- if (!nobuckets.isEmpty()) {
- ExaremeQueryElement columnsEl3 = new ExaremeQueryElement();
- columnsEl3.setName("nobuckets");
- columnsEl3.setDesc("");
- columnsEl3.setValue(nobuckets);
- queryElements.add(columnsEl3);
- }
- } else if (algoName.equals(WP_REGRESSION_TREE) || algoName.equals(WP_MODEL_TREE)) {
- List<String> target = variables;
- List<String> descriptive = covariables.isEmpty() ? groupings : covariables;
- descriptive.addAll(groupings);
-
- ExaremeQueryElement xEl = new ExaremeQueryElement();
- xEl.setName("target_attributes");
- xEl.setDesc("");
- xEl.setValue(chainsParams(target, ","));
- queryElements.add(xEl);
-
- ExaremeQueryElement yEl = new ExaremeQueryElement();
- yEl.setName("descriptive_attributes");
- yEl.setDesc("");
- yEl.setValue(chainsParams(descriptive, ","));
- queryElements.add(yEl);
- }
-
- // datasets
- StringBuilder datasets = new StringBuilder();
- List<Variable> trainingDatasets = model.getQuery().getTrainingDatasets();
- int j = 0;
- for (Variable var : trainingDatasets)
- {
- j++;
- datasets.append(var.getCode());
- if (j < trainingDatasets.size() ) {
- datasets.append(",");
- }
- }
-
- ExaremeQueryElement datasetsEl = new ExaremeQueryElement();
- datasetsEl.setName("dataset");
- datasetsEl.setDesc("");
- // datasetsEl.setValue("adni,ppmi,edsd,fbf,clm");
- datasetsEl.setValue(datasets.toString());
- queryElements.add(datasetsEl);
-
- // filter
- String filter = model.getQuery().getFilters();
- ExaremeQueryElement filterEl = new ExaremeQueryElement();
- filterEl.setName("filter");
- filterEl.setDesc("");
- filterEl.setValue(filter);
- queryElements.add(filterEl);
-
- return gson.toJson(queryElements);
- }
-
public JsonObject jsonify() {
JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
JsonParser parser = new JsonParser();
- Tuple2<Boolean, String> isExaremeAlgorithm = this.isExaremeAlgorithm();
if (this.algorithms != null)
{
@@ -308,45 +151,9 @@ public class Experiment {
if (this.result != null && !this.hasServerError) {
exp.remove("result");
- if (!isExaremeAlgorithm._1) {
- 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);
-
- // add mime-type
- String algo = isExaremeAlgorithm._2;
- if (jsonData.get("Error") != null) {
- jsonObjectResult.add("type", new JsonPrimitive("text/plain+error"));
- } else if (algo.equals( WP_K_MEANS) || algo.equals( WP_VARIABLES_HISTOGRAM)) {
- jsonObjectResult.add("type", new JsonPrimitive("application/vnd.highcharts+json"));
- } else if (algo.equals(WP_LINEAR_REGRESSION)) {
- jsonObjectResult.add("type", new JsonPrimitive("application/vnd.dataresource+json"));
- } else if (algo.equals(WP_REGRESSION_TREE) || algo.equals(WP_MODEL_TREE)) {
- jsonObjectResult.add("type", new JsonPrimitive("application/vnd.visjs+javascript"));
- }
-
- jsonArrayResult.add(jsonObjectResult);
-
- exp.add("result", jsonArrayResult);
- }
+ JsonElement jsonResult = parser.parse(this.result);
+ exp.add("result", jsonResult);
+
}
return exp;
@@ -455,30 +262,4 @@ public class Experiment {
public void setShared(boolean shared) {
this.shared = shared;
}
-
- public Tuple2<Boolean, String> isExaremeAlgorithm() {
- Boolean isExareme = false;
- String algorithm = "";
-
- String algorithms = this.algorithms;
-
- if (algorithms.contains(WP_K_MEANS)) {
- isExareme = true;
- algorithm = WP_K_MEANS;
- } else if (algorithms.contains(WP_LINEAR_REGRESSION)) {
- isExareme = true;
- algorithm = WP_LINEAR_REGRESSION;
- } else if (algorithms.contains(WP_VARIABLES_HISTOGRAM)) {
- isExareme = true;
- algorithm = WP_VARIABLES_HISTOGRAM;
- } else if (algorithms.contains(WP_REGRESSION_TREE)) {
- isExareme = true;
- algorithm = WP_REGRESSION_TREE;
- } else if (algorithms.contains(WP_MODEL_TREE)) {
- isExareme = true;
- algorithm = WP_MODEL_TREE;
- }
-
- return new Tuple2<Boolean, String>(isExareme, algorithm);
- }
}
diff --git a/src/main/java/eu/hbp/mip/model/UserInfo.java b/src/main/java/eu/hbp/mip/model/UserInfo.java
index f4671b634d152244ed79976ffe2a170b9130492e..293ce9534cf78c0f27b5f742ca924540072e2fea 100644
--- a/src/main/java/eu/hbp/mip/model/UserInfo.java
+++ b/src/main/java/eu/hbp/mip/model/UserInfo.java
@@ -52,6 +52,7 @@ public class UserInfo {
user = new User();
user.setUsername("anonymous");
user.setFullname("anonymous");
+ user.setEmail("anonymous@anonymous.com");
user.setPicture("images/users/default_user.png");
} else {
user = new User(getUserInfos());
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();
+ }
}
diff --git a/src/main/resources/data/exareme_algorithms.json b/src/main/resources/data/exareme_algorithms.json
deleted file mode 100644
index 3ea4bdf19b7f2a779ecd70ab3385ef9b96c8533d..0000000000000000000000000000000000000000
--- a/src/main/resources/data/exareme_algorithms.json
+++ /dev/null
@@ -1,137 +0,0 @@
-[
- {
- "code": "WP_VARIABLES_HISTOGRAM",
- "constraints": {
- "variable": {
- "binominal": true,
- "integer": true,
- "polynominal": true,
- "real": true
- }
- },
- "description": "Histograms",
- "environment": "Exareme",
- "label": " Histogram",
- "parameters": [
- {
- "code": "nobuckets",
- "constraints": {
- "max": null,
- "min": 1
- },
- "default_value": 4,
- "description": "The number of clusters. Typical values range from 2 to 10.",
- "label": "nobuckets",
- "type": "int"
- }
- ],
- "type": [
- "statistics"
- ]
- },
- {
- "code": "PIPELINE_ISOUP_REGRESSION_TREE_SERIALIZER",
- "constraints": {
- "variable": {
- "binominal": true,
- "integer": true,
- "polynominal": true,
- "real": true
- }
- },
- "description": "Regression Tree Serializer",
- "environment": "Exareme",
- "label": " Regression Tree",
- "parameters": [],
- "type": [
- "statistics"
- ]
- },
- {
- "code": "PIPELINE_ISOUP_MODEL_TREE_SERIALIZER",
- "constraints": {
- "variable": {
- "binominal": true,
- "integer": true,
- "polynominal": true,
- "real": true
- }
- },
- "description": "Model Tree Serializer",
- "environment": "Exareme",
- "label": "Model Tree",
- "parameters": [],
- "type": [
- "statistics"
- ]
- },
- {
- "code": "WP_LINEAR_REGRESSION",
- "constraints": {
- "variable": {
- "binominal": false,
- "integer": true,
- "polynominal": false,
- "real": true
- }
- },
- "description": "Linear Regression using Exareme services",
- "environment": "Exareme",
- "label": "Linear regression",
- "parameters": [
- {
- "code": "design",
- "default_value": "factorial",
- "description": "The type of multi-factors design. Choose 'factorial' to enable interactions analysis or 'additive' for a model without no interaction at all.",
- "label": "design",
- "type": "enumeration",
- "values": [
- "factorial",
- "additive"
- ]
- }
- ],
- "type": [
- "statistics"
- ]
- },
- {
- "code": "K_MEANS",
- "constraints": {
- "covariables": {
- "max_count": null,
- "min_count": "1"
- },
- "groupings": {
- "max_count": 0,
- "min_count": 0
- },
- "mixed": false,
- "variable": {
- "binominal": true,
- "integer": true,
- "polynominal": true,
- "real": true
- }
- },
- "description": "k-Means using Exareme services",
- "environment": "Exareme",
- "label": "K_MEANS",
- "parameters": [
- {
- "code": "k",
- "constraints": {
- "max": null,
- "min": 1
- },
- "default_value": 5,
- "description": "The number of clusters. Typical values range from 2 to 10.",
- "label": "k",
- "type": "int"
- }
- ],
- "type": [
- "statistics"
- ]
- }
-]