diff --git a/config/application.yml b/config/application.yml
index aba6d24c8361d21d4e4a899afb617ef8dbd0595a..6f752d822bf63ecaf3bfb238dd920f177f05e2f3 100644
--- a/config/application.yml
+++ b/config/application.yml
@@ -40,7 +40,8 @@ server:
timeout: 2592000
workflow:
- miningUrl: http://mip.humanbrainproject.eu/services/mining
- exaremeListAlgoUrl: http://hbps2.chuv.ch:9090/mining/algorithms
- exaremeQueryUrl: http://hbps2.chuv.ch:9090/mining/query
+ experimentUrl: http://dockerhost:8087/experiment
+ listMethodsUrl: http://dockerhost:8087/list-methods
+ miningMipUrl: http://dockerhost:8087/mining
+ miningExaremeUrl: http://hbps2.chuv.ch:9090/mining/query
diff --git a/pom.xml b/pom.xml
index 7c627835778704f3a3d84b2fd11a293946d1c09d..af7c98035d8d7f354bf6730240deef5b94d9d464 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,25 +25,6 @@
<relativePath /> <!-- lookup parent from repository -->
</parent>
<profiles>
- <profile>
- <id>test</id>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <java.version>1.8</java.version>
- <connection.driver_class>org.h2.Driver</connection.driver_class>
- <connection.url>jdbc:h2:mem:test</connection.url>
- <connection.username>root</connection.username>
- <connection.password>root</connection.password>
- <hibernate.dialect>org.hibernate.dialect.H2Dialect</hibernate.dialect>
- <schema.deploy>true</schema.deploy>
- <frontend.redirect>http://frontend/#/home</frontend.redirect>
- <workflow.experimentUrl>http://hbps1.chuv.ch:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://hbps1.chuv.ch:8087/list-methods</workflow.listMethodsUrl>
- <flyway.url>${connection.url}</flyway.url>
- <flyway.user>${connection.username}</flyway.user>
- <flyway.password>${connection.password}</flyway.password>
- </properties>
- </profile>
<profile>
<id>prod</id>
<properties>
@@ -55,9 +36,7 @@
<connection.password>iaezXODVLb1e70I</connection.password>
<hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
<schema.deploy>false</schema.deploy>
- <frontend.redirect>https://mip.humanbrainproject.eu/#/home</frontend.redirect>
- <workflow.experimentUrl>http://hbps1.chuv.ch:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://hbps1.chuv.ch:8087/list-methods</workflow.listMethodsUrl>
+ <frontend.redirect>https://mip.humanbrainproject.eu/home</frontend.redirect>
<flyway.url>${connection.url}</flyway.url>
<flyway.user>${connection.username}</flyway.user>
<flyway.password>${connection.password}</flyway.password>
@@ -75,8 +54,6 @@
<hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
<schema.deploy>false</schema.deploy>
<frontend.redirect>http://frontend/home</frontend.redirect>
- <workflow.experimentUrl>http://hbps1.chuv.ch:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://hbps1.chuv.ch:8087/list-methods</workflow.listMethodsUrl>
<flyway.url>${connection.url}</flyway.url>
<flyway.user>${connection.username}</flyway.user>
<flyway.password>${connection.password}</flyway.password>
@@ -94,8 +71,6 @@
<hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
<schema.deploy>false</schema.deploy>
<frontend.redirect>http://hbps1.chuv.ch/home</frontend.redirect>
- <workflow.experimentUrl>http://hbps1.chuv.ch:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://hbps1.chuv.ch:8087/list-methods</workflow.listMethodsUrl>
<flyway.url>${connection.url}</flyway.url>
<flyway.user>${connection.username}</flyway.user>
<flyway.password>${connection.password}</flyway.password>
@@ -194,12 +169,10 @@
<resources>
<resource>
<directory>src/main/resources</directory>
- <includes><include>**/*.csv</include></includes>
- <excludes><exclude>**/*.xml</exclude></excludes>
- </resource>
- <resource>
- <directory>src/main/resources</directory>
- <includes><include>**/*.xml</include></includes>
+ <includes>
+ <include>**/*.xml</include>
+ <include>**/*.json</include>
+ </includes>
<excludes><exclude>**/*.csv</exclude></excludes>
<filtering>true</filtering>
</resource>
diff --git a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
index e71ee947f6a46583f375c52e680f9c865afffd49..868b7ed860f08eb63d1bb88a572355d00f30c486 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -1,13 +1,10 @@
package org.hbp.mip.controllers;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-import com.google.gson.JsonObject;
+import com.google.gson.*;
import io.swagger.annotations.*;
import org.hbp.mip.MIPApplication;
-import org.hbp.mip.model.Experiment;
-import org.hbp.mip.model.Model;
-import org.hbp.mip.model.User;
+import org.hbp.mip.model.*;
+import org.hbp.mip.utils.HTTPUtil;
import org.hbp.mip.utils.HibernateUtil;
import org.hibernate.Query;
import org.hibernate.Session;
@@ -20,11 +17,11 @@ import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import java.io.*;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.ProtocolException;
-import java.net.URL;
-import java.util.*;
+import java.net.*;
+import java.util.Date;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.UUID;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -37,19 +34,23 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
public class ExperimentApi {
+ private static final String EXAREME_ALGO_JSON_FILE="data/exareme_algorithms.json";
+
private static final Gson gson = new GsonBuilder()
.serializeNulls()
.setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ")
.excludeFieldsWithoutExposeAnnotation()
.create();
- @Value("#{'${workflow.experimentUrl:http://hbps1.chuv.ch:8087/experiment}'}")
+ @Value("#{'${workflow.experimentUrl:http://dockerhost:8087/experiment}'}")
private String experimentUrl;
-
- @Value("#{'${workflow.listMethodsUrl:http://hbps1.chuv.ch:8087/list-methods}'}")
+ @Value("#{'${workflow.listMethodsUrl:http://dockerhost:8087/list-methods}'}")
private String listMethodsUrl;
+ @Value("#{'${workflow.miningExaremeUrl:http://hbps2.chuv.ch:9090/mining/query}'}")
+ private String miningExaremeQueryUrl;
+
@Autowired
MIPApplication mipApplication;
@@ -155,12 +156,117 @@ public class ExperimentApi {
}
try {
- sendPost(experiment);
+ if(isExaremeAlgo(experiment))
+ {
+ sendExaremePost(experiment);
+ }
+ else
+ {
+ sendPost(experiment);
+ }
} catch (MalformedURLException mue) {} // ignore
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
+ private void sendExaremePost(Experiment experiment) {
+
+ Model model = experiment.getModel();
+ String algoCode = "WP_LINEAR_REGRESSION";
+
+ LinkedList<ExaremeQueryElement> queryElements = new LinkedList<>();
+ for (Variable var : model.getQuery().getVariables())
+ {
+ ExaremeQueryElement el = new ExaremeQueryElement();
+ el.setName("variable");
+ el.setDesc("");
+ el.setValue(var.getCode());
+ queryElements.add(el);
+ }
+ for (Variable var : model.getQuery().getCovariables())
+ {
+ ExaremeQueryElement el = new ExaremeQueryElement();
+ el.setName("covariables");
+ el.setDesc("");
+ el.setValue(var.getCode());
+ queryElements.add(el);
+ }
+ for (Variable var : model.getQuery().getGrouping())
+ {
+ ExaremeQueryElement el = new ExaremeQueryElement();
+ el.setName("groupings");
+ el.setDesc("");
+ el.setValue(var.getCode());
+ queryElements.add(el);
+ }
+
+ 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);
+
+ String jsonQuery = new Gson().toJson(queryElements);
+
+ new Thread() {
+ public void run() {
+ try {
+ String url = miningExaremeQueryUrl + "/" + algoCode;
+ StringBuilder results = new StringBuilder();
+ int code = HTTPUtil.sendPost(url, jsonQuery, results);
+
+ experiment.setResult(results.toString().replace("\0", ""));
+ experiment.setHasError(code >= 400);
+ experiment.setHasServerError(code >= 500);
+
+ if(!isJSONValid(experiment.getResult()))
+ {
+ experiment.setResult("Unsupported variables !");
+ }
+ } catch (Exception e) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ experiment.setResult(e.getMessage());
+ }
+
+ experiment.setFinished(new Date());
+
+ try {
+ Session session = HibernateUtil.getSessionFactory().openSession();
+ Transaction transaction = session.beginTransaction();
+ session.update(experiment);
+ transaction.commit();
+ session.close();
+ } catch (DataException e) {
+ throw e;
+ }
+
+ }
+ }.start();
+ }
+
+ public boolean isJSONValid(String test) {
+ try {
+ new JsonParser().parse(test);
+ } catch (JsonParseException jpe)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ private boolean isExaremeAlgo(Experiment experiment) {
+ JsonArray algorithms = new JsonParser().parse(experiment.getAlgorithms()).getAsJsonArray();
+ String algoCode = algorithms.get(0).getAsJsonObject().get("code").getAsString();
+ return algoCode.equals("glm_exareme");
+ }
+
@ApiOperation(value = "get an experiment", response = Experiment.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
@@ -371,22 +477,22 @@ public class ExperimentApi {
@RequestMapping(path = "/methods", method = RequestMethod.GET)
public ResponseEntity<String> listAvailableMethodsAndValidations() throws Exception {
- URL obj = new URL(listMethodsUrl);
- HttpURLConnection con = (HttpURLConnection) obj.openConnection();
- con.setRequestMethod("GET");
+ StringBuilder response = new StringBuilder();
- int respCode = con.getResponseCode();
+ int code = HTTPUtil.sendGet(listMethodsUrl, response);
+ if (code < 200 || code > 299) {
+ return new ResponseEntity<>(response.toString(), HttpStatus.valueOf(code));
+ }
- BufferedReader in = new BufferedReader(new InputStreamReader(respCode == 200 ? con.getInputStream() : con.getErrorStream()));
+ JsonObject catalog = new JsonParser().parse(response.toString()).getAsJsonObject();
- String inputLine;
- StringBuilder response = new StringBuilder();
+ InputStream is = ExperimentApi.class.getClassLoader().getResourceAsStream(EXAREME_ALGO_JSON_FILE);
+ InputStreamReader isr = new InputStreamReader(is);
+ BufferedReader br = new BufferedReader(isr);
+ JsonObject exaremeAlgo = new JsonParser().parse(br).getAsJsonObject();
- while ((inputLine = in.readLine()) != null) {
- response.append(inputLine);
- }
- in.close();
+ catalog.get("algorithms").getAsJsonArray().add(exaremeAlgo);
- return new ResponseEntity<>(response.toString(), HttpStatus.valueOf(respCode));
+ return new ResponseEntity<>(new Gson().toJson(catalog), HttpStatus.valueOf(code));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/MiningApi.java b/src/main/java/org/hbp/mip/controllers/MiningApi.java
deleted file mode 100644
index 2fc2882d7ee1a9e401c02b879dcb598a1dcb9407..0000000000000000000000000000000000000000
--- a/src/main/java/org/hbp/mip/controllers/MiningApi.java
+++ /dev/null
@@ -1,172 +0,0 @@
-/**
- * Created by mirco on 02.03.16.
- */
-
-package org.hbp.mip.controllers;
-
-import com.google.gson.JsonParser;
-import io.swagger.annotations.*;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-
-import java.io.BufferedReader;
-import java.io.DataOutputStream;
-import java.io.InputStreamReader;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.net.UnknownHostException;
-
-@RestController
-@RequestMapping(value = "/mining")
-@Api(value = "/mining", description = "Forward mining API")
-public class MiningApi {
-
- @Value("#{'${workflow.miningUrl:http://localhost:8087/mining}'}")
- private String miningUrl;
-
- @Value("#{'${workflow.exaremeListAlgoUrl:http://localhost:9090/mining/algorithms}'}")
- private String exaremeListAlgoUrl;
-
- @Value("#{'${workflow.exaremeQueryUrl:http://localhost:9090/mining/query}'}")
- private String exaremeQueryUrl;
-
- @ApiOperation(value = "Send a request to the workflow for data mining", response = String.class)
- @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<String> postMining(
- @RequestBody @ApiParam(value = "Query for the data mining", required = true) String query
- ) throws Exception {
- try {
- StringBuilder results = new StringBuilder();
- int code = sendPost(miningUrl, query, results);
-
- return new ResponseEntity<>(results.toString(), HttpStatus.valueOf(code));
- }
- catch(UnknownHostException uhe) {
- uhe.printStackTrace();
- return new ResponseEntity<>(HttpStatus.BAD_GATEWAY);
- }
- }
-
- @ApiOperation(value = "Send a request to the Exareme service to list available algorithms", response = String.class)
- @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
- @RequestMapping(path = "/exareme/algorithms", method = RequestMethod.GET)
- public ResponseEntity<String> getExaremeAlgoList(
- ) throws Exception {
- try {
- StringBuilder results = new StringBuilder();
- int code = sendGet(exaremeListAlgoUrl, results);
-
- return new ResponseEntity<>(results.toString(), HttpStatus.valueOf(code));
- }
- catch(UnknownHostException uhe) {
- uhe.printStackTrace();
- return new ResponseEntity<>(HttpStatus.BAD_GATEWAY);
- }
- }
-
- @ApiOperation(value = "Send a request to the Exareme service to run an algorithm", response = String.class)
- @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
- @RequestMapping(path = "/exareme/query/{algo}", method = RequestMethod.POST)
- public ResponseEntity<String> postExaremeQuery(
- @ApiParam(value = "algo", required = true) @PathVariable("algo") String algo,
- @RequestBody(required = false) @ApiParam(value = "Query for the data mining") String query
- ) throws Exception {
- try {
-
- /* Launch computation */
-
- String url = exaremeQueryUrl+"/"+algo+"/?format=true";
- StringBuilder results = new StringBuilder();
- int code = sendPost(url, query, results);
- if (code < 200 || code > 299)
- {
- return new ResponseEntity<>(results.toString(), HttpStatus.valueOf(code));
- }
-
- JsonParser parser = new JsonParser();
- String key = parser.parse(results.toString()).getAsJsonObject().get("queryKey").getAsString();
-
- /* Wait for result */
-
- url = exaremeQueryUrl+"/"+key+"/status";
- double progress = 0;
-
- while (progress < 100) {
- Thread.sleep(200);
- results = new StringBuilder();
- code = sendPost(url, query, results);
- if (code < 200 || code > 299)
- {
- return new ResponseEntity<>(results.toString(), HttpStatus.valueOf(code));
- }
- progress = parser.parse(results.toString()).getAsJsonObject().get("status").getAsDouble();
- }
-
- /* Get result */
-
- url = exaremeQueryUrl+"/"+key+"/result";
- results = new StringBuilder();
- code = sendPost(url, query, results);
-
- return new ResponseEntity<>(results.toString(), HttpStatus.valueOf(code));
- }
- catch(UnknownHostException uhe) {
- uhe.printStackTrace();
- return new ResponseEntity<>(HttpStatus.BAD_GATEWAY);
- }
- }
-
- private static int sendGet(String url, StringBuilder resp) throws Exception {
- return sendHTTP(url, "", resp, "GET");
- }
-
- private static int sendPost(String url, String query, StringBuilder resp) throws Exception {
- return sendHTTP(url, query, resp, "POST");
- }
-
- private static int sendHTTP(String url, String query, StringBuilder resp, String httpVerb) throws Exception {
-
- URL obj = new URL(url);
- HttpURLConnection con = (HttpURLConnection) obj.openConnection();
-
- if(!httpVerb.equals("GET")) {
- con.setRequestMethod(httpVerb);
- if(query != null && query.length() > 0)
- {
- con.addRequestProperty("Content-Type", "application/json");
- con.setRequestProperty("Content-Length", Integer.toString(query.length()));
-
- con.setDoOutput(true);
- DataOutputStream wr = new DataOutputStream(con.getOutputStream());
- wr.write(query.getBytes("UTF8"));
- wr.flush();
- wr.close();
- }
- }
-
- int respCode = con.getResponseCode();
-
- BufferedReader in;
- if(respCode == 200) {
- in = new BufferedReader(new InputStreamReader(con.getInputStream()));
- }
- else
- {
- in = new BufferedReader(new InputStreamReader(con.getErrorStream()));
- }
- String inputLine;
- StringBuilder response = new StringBuilder();
-
- while ((inputLine = in.readLine()) != null) {
- response.append(inputLine);
- }
- in.close();
- resp.append(response.toString());
-
- return respCode;
- }
-
-}
diff --git a/src/main/java/org/hbp/mip/model/ExaremeQueryElement.java b/src/main/java/org/hbp/mip/model/ExaremeQueryElement.java
new file mode 100644
index 0000000000000000000000000000000000000000..dba6d6269da25986a0d39028d927f61563b39ae8
--- /dev/null
+++ b/src/main/java/org/hbp/mip/model/ExaremeQueryElement.java
@@ -0,0 +1,43 @@
+package org.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/org/hbp/mip/utils/HTTPUtil.java b/src/main/java/org/hbp/mip/utils/HTTPUtil.java
new file mode 100644
index 0000000000000000000000000000000000000000..92beffaf45e7f48e8c71d51e36414fb78ce827ae
--- /dev/null
+++ b/src/main/java/org/hbp/mip/utils/HTTPUtil.java
@@ -0,0 +1,63 @@
+package org.hbp.mip.utils;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
+
+/**
+ * Created by mirco on 20.06.16.
+ */
+public class HTTPUtil {
+
+ public static int sendGet(String url, StringBuilder resp) throws Exception {
+ return sendHTTP(url, "", resp, "GET");
+ }
+
+ public static int sendPost(String url, String query, StringBuilder resp) throws Exception {
+ return sendHTTP(url, query, resp, "POST");
+ }
+
+ public static int sendHTTP(String url, String query, StringBuilder resp, String httpVerb) throws Exception {
+
+ URL obj = new URL(url);
+ HttpURLConnection con = (HttpURLConnection) obj.openConnection();
+
+ if(!httpVerb.equals("GET")) {
+ con.setRequestMethod(httpVerb);
+ if(query != null && query.length() > 0)
+ {
+ con.addRequestProperty("Content-Type", "application/json");
+ con.setRequestProperty("Content-Length", Integer.toString(query.length()));
+
+ con.setDoOutput(true);
+ DataOutputStream wr = new DataOutputStream(con.getOutputStream());
+ wr.write(query.getBytes("UTF8"));
+ wr.flush();
+ wr.close();
+ }
+ }
+
+ int respCode = con.getResponseCode();
+
+ BufferedReader in;
+ if(respCode == 200) {
+ in = new BufferedReader(new InputStreamReader(con.getInputStream()));
+ }
+ else
+ {
+ in = new BufferedReader(new InputStreamReader(con.getErrorStream()));
+ }
+ String inputLine;
+ StringBuilder response = new StringBuilder();
+
+ while ((inputLine = in.readLine()) != null) {
+ response.append(inputLine);
+ }
+ in.close();
+ resp.append(response.toString());
+
+ return respCode;
+ }
+}
diff --git a/src/main/resources/data/exareme_algorithms.json b/src/main/resources/data/exareme_algorithms.json
new file mode 100644
index 0000000000000000000000000000000000000000..3fc6a34713fd110758b4c59032254cf292439775
--- /dev/null
+++ b/src/main/resources/data/exareme_algorithms.json
@@ -0,0 +1,14 @@
+{
+ "code": "glm_exareme",
+ "label": "GLM (exareme)",
+ "type": ["statistics"],
+ "environment": "Exareme",
+ "description": "Linear Regression using Exareme services",
+ "constraints": {
+ "variable": {
+ "real": true,
+ "binominal": false,
+ "polynominal": false
+ }
+ }
+}
\ No newline at end of file