From 91dd9f895a39e7ce2ac26f722e4e542d9e6a7067 Mon Sep 17 00:00:00 2001
From: Mirco Nasuti <mirco.nasuti@chuv.ch>
Date: Mon, 20 Jun 2016 11:42:46 +0200
Subject: [PATCH] add exareme GLR into mining catalog
---
config/application.yml | 1 +
config/application_hbps1.yml | 46 -------------------
pom.xml | 34 ++------------
.../org/hbp/mip/controllers/MiningApi.java | 25 +++++++++-
.../hbp/mip/model/algorithm/Algorithm.java | 10 ++++
5 files changed, 39 insertions(+), 77 deletions(-)
delete mode 100644 config/application_hbps1.yml
diff --git a/config/application.yml b/config/application.yml
index d8a9f7180..6f752d822 100644
--- a/config/application.yml
+++ b/config/application.yml
@@ -40,6 +40,7 @@ server:
timeout: 2592000
workflow:
+ 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/config/application_hbps1.yml b/config/application_hbps1.yml
deleted file mode 100644
index d8a9f7180..000000000
--- a/config/application_hbps1.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-# Configuration for the portal running inside a Docker container for development
-
-connection:
- url: "jdbc:postgresql://portaldb:5432/postgres"
- username: "postgres"
- password: "test"
-
-security:
- enabled: false
-
-hbp:
- client:
- clientId: 996f97c5-a3ca-460e-b18b-00df3e2be89a
- clientSecret: aD0Tueb3KkNkcZqZgQbNyDWgnM95IfZ0xPCQ_6Z9dQNHXY00RIrnAD_m7sNJh1oofYSX8aHkl72MkwI0K626Ug
- accessTokenUri: https://services.humanbrainproject.eu/oidc/token
- userAuthorizationUri: https://services.humanbrainproject.eu/oidc/authorize
- tokenName: oauth_token
- authenticationScheme: query
- clientAuthenticationScheme: form
- # use-current-uri: false # For both production and HBPS1 deployments
- # pre-established-redirect-uri: https://mip.humanbrainproject.eu/services/login/hbp # For production deployment
- # pre-established-redirect-uri: http://hbps1.chuv.ch/services/login/hbp # For HBPS1 deployment
- resource:
- userInfoUri: https://services.humanbrainproject.eu/oidc/userinfo
-
-logging:
- level:
- org.springframework.security: DEBUG
-
-spring:
- resources:
- chain:
- enabled: true
-
-server:
- contextPath: /services
- port: 8080
- use-forward-headers: true
- session:
- timeout: 2592000
-
-workflow:
- 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 74b2de554..859fadb7a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -18,25 +18,6 @@
<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>${connection.password}</flyway.password>
- </properties>
- </profile>
<profile>
<id>prod</id>
<properties>
@@ -48,9 +29,7 @@
<connection.password>iaezXODVLb1e70I</connection.password>
<hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
<schema.deploy>false</schema.deploy>
- <frontend.redirect>https://mip.humanbrainproject.eu/#/home</frontend.redirect>
- <workflow.experimentUrl>http://hbps1.chuv.ch:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://hbps1.chuv.ch:8087/list-methods</workflow.listMethodsUrl>
+ <frontend.redirect>https://mip.humanbrainproject.eu/home</frontend.redirect>
<flyway.url>${connection.url}</flyway.url>
<flyway.user>${connection.username}</flyway.user>
<flyway.password>${connection.password}</flyway.password>
@@ -68,10 +47,6 @@
<hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
<schema.deploy>false</schema.deploy>
<frontend.redirect>http://frontend/home</frontend.redirect>
- <workflow.experimentUrl>http://dockerhost:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://dockerhost:8087/list-methods</workflow.listMethodsUrl>
- <workflow.miningMipUrl>http://dockerhost:8087/mining</workflow.miningMipUrl>
- <workflow.miningExaremeUrl>http://dockerhost:8087/mining/query</workflow.miningExaremeUrl>
<flyway.url>${connection.url}</flyway.url>
<flyway.user>${connection.username}</flyway.user>
<flyway.password>${connection.password}</flyway.password>
@@ -89,8 +64,6 @@
<hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
<schema.deploy>false</schema.deploy>
<frontend.redirect>http://hbps1.chuv.ch/home</frontend.redirect>
- <workflow.experimentUrl>http://hbps1.chuv.ch:8087/experiment</workflow.experimentUrl>
- <workflow.listMethodsUrl>http://hbps1.chuv.ch:8087/list-methods</workflow.listMethodsUrl>
<flyway.url>${connection.url}</flyway.url>
<flyway.user>${connection.username}</flyway.user>
<flyway.password>${connection.password}</flyway.password>
@@ -189,7 +162,10 @@
<resources>
<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/MiningApi.java b/src/main/java/org/hbp/mip/controllers/MiningApi.java
index cc99c1fce..157ffc733 100644
--- a/src/main/java/org/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/org/hbp/mip/controllers/MiningApi.java
@@ -4,15 +4,22 @@
package org.hbp.mip.controllers;
+import com.google.gson.Gson;
import com.google.gson.JsonParser;
import io.swagger.annotations.*;
+import org.hbp.mip.model.algorithm.Algorithm;
+import org.hbp.mip.model.algorithm.Catalog;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
import java.io.BufferedReader;
import java.io.DataOutputStream;
+import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
@@ -23,6 +30,8 @@ import java.net.UnknownHostException;
@Api(value = "/mining", description = "Forward mining API")
public class MiningApi {
+ private static final String EXAREME_ALGO_JSON_FILE="data/exareme_algorithms.json";
+
@Value("#{'${workflow.listMethodsUrl:http://hbps1.chuv.ch:8087/list-methods}'}")
private String listMethodsUrl;
@@ -47,7 +56,19 @@ public class MiningApi {
return new ResponseEntity<>(response.toString(), HttpStatus.valueOf(code));
}
- return null;
+ Catalog catalog = new Gson().fromJson(response.toString(), Catalog.class);
+ for (Algorithm algo: catalog.getAlgorithms()) {
+ algo.setSource("ML");
+ }
+
+ InputStream is = MiningApi.class.getClassLoader().getResourceAsStream(EXAREME_ALGO_JSON_FILE);
+ InputStreamReader isr = new InputStreamReader(is);
+ BufferedReader br = new BufferedReader(isr);
+ Algorithm exaremeGLR = new Gson().fromJson(br, Algorithm.class);
+ exaremeGLR.setSource("exareme");
+ catalog.getAlgorithms().add(exaremeGLR);
+
+ return new ResponseEntity<>(new Gson().toJson(catalog), HttpStatus.valueOf(code));
}
private ResponseEntity<String> postMipMining(String query) throws Exception {
diff --git a/src/main/java/org/hbp/mip/model/algorithm/Algorithm.java b/src/main/java/org/hbp/mip/model/algorithm/Algorithm.java
index 2b2897c08..5e0aae5de 100644
--- a/src/main/java/org/hbp/mip/model/algorithm/Algorithm.java
+++ b/src/main/java/org/hbp/mip/model/algorithm/Algorithm.java
@@ -33,6 +33,8 @@ public class Algorithm {
private Boolean disable;
+ private String source;
+
public String getCode() {
return code;
@@ -105,4 +107,12 @@ public class Algorithm {
public void setDisable(Boolean disable) {
this.disable = disable;
}
+
+ public String getSource() {
+ return source;
+ }
+
+ public void setSource(String source) {
+ this.source = source;
+ }
}
--
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