diff --git a/pom.xml b/pom.xml
index 94ff7bd03760ff25fb31e65637b5d0a039da7b53..29af3cfb507310d34edbcef1d5d6a1c83b851e60 100644
--- a/pom.xml
+++ b/pom.xml
@@ -18,33 +18,33 @@
<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>
- </properties>
- </profile>
- <profile>
- <id>prod</id>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <java.version>1.8</java.version>
- <connection.driver_class>org.postgresql.Driver</connection.driver_class>
- <connection.url>jdbc:postgresql://hbpmdw1.chuv.ch:31432/portal</connection.url>
- <connection.username>portal</connection.username>
- <connection.password>iaezXODVLb1e70I</connection.password>
- <hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
- <schema.deploy>false</schema.deploy>
- </properties>
- </profile>
+ <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>
+ </properties>
+ </profile>
+ <profile>
+ <id>prod</id>
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <java.version>1.8</java.version>
+ <connection.driver_class>org.postgresql.Driver</connection.driver_class>
+ <connection.url>jdbc:postgresql://hbpmdw1.chuv.ch:31432/portal</connection.url>
+ <connection.username>portal</connection.username>
+ <connection.password>iaezXODVLb1e70I</connection.password>
+ <hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
+ <schema.deploy>false</schema.deploy>
+ </properties>
+ </profile>
<profile>
<id>dev</id>
<properties>
@@ -58,7 +58,7 @@
<schema.deploy>false</schema.deploy>
</properties>
</profile>
- </profiles>
+ </profiles>
<dependencies>
<dependency>
@@ -77,10 +77,10 @@
<groupId>org.springframework.security.oauth</groupId>
<artifactId>spring-security-oauth2</artifactId>
</dependency>
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-orm</artifactId>
- </dependency>
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-orm</artifactId>
+ </dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>angularjs</artifactId>
@@ -143,30 +143,30 @@
</dependencies>
<build>
- <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>
- <excludes><exclude>**/*.csv</exclude></excludes>
- <filtering>true</filtering>
- </resource>
- </resources>
-
+ <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>
+ <excludes><exclude>**/*.csv</exclude></excludes>
+ <filtering>true</filtering>
+ </resource>
+ </resources>
+
<plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-resources-plugin</artifactId>
- <version>2.3</version>
- <configuration>
- <!-- specify UTF-8, ISO-8859-1 or any other file encoding -->
- <encoding>UTF-8</encoding>
- </configuration>
- </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>2.3</version>
+ <configuration>
+ <!-- specify UTF-8, ISO-8859-1 or any other file encoding -->
+ <encoding>UTF-8</encoding>
+ </configuration>
+ </plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
@@ -184,6 +184,14 @@
</execution>
</executions>
</plugin>
+ <plugin>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>3.1</version>
+ <configuration>
+ <source>1.8</source>
+ <target>1.8</target>
+ </configuration>
+ </plugin>
</plugins>
</build>
diff --git a/src/docker/build/mip.sh b/src/docker/build/mip.sh
index 59bc112e1a1de37fae7c5a79b815aa9196d1b8aa..cfae68474c42a1e66b80edb0ea849911ddd8eef4 100644
--- a/src/docker/build/mip.sh
+++ b/src/docker/build/mip.sh
@@ -1,5 +1,3 @@
#!/usr/bin/env bash
-# Configuration is read in the config folder relative to current path
-cd /opt/portal/
-/usr/bin/java -jar /opt/portal/lib/mip.jar
+/usr/bin/java -DconfigFile=/opt/portal/config/application.yml -jar /opt/portal/lib/mip.jar
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 6f52bc2b236f1f373b34b29956a97ea11ff6d346..59275a8798a9fec304a88d765216cf2b13005147 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -94,7 +94,8 @@ public class ModelsApi {
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
- } }
+ }
+ }
return new ResponseEntity<List<Model>>(HttpStatus.OK).ok(models);
}
@@ -112,7 +113,8 @@ public class ModelsApi {
User user = mipApplication.getUser(principal);
// Set up model
- model.setSlug(model.getTitle().toLowerCase());
+ model.setSlug(model.getConfig().getTitle().get("text").toLowerCase());
+ model.setTitle(model.getConfig().getTitle().get("text"));
model.setValid(true);
model.setCreatedBy(user);
model.setCreatedAt(new Date());
@@ -133,32 +135,6 @@ public class ModelsApi {
return new ResponseEntity<Void>(HttpStatus.OK);
}
- @ApiOperation(value = "Get SVG", response = Model.class)
- @ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
- @RequestMapping(value = "/{slug}.svg", produces = {"image/svg+xml"}, method = RequestMethod.GET)
- public ResponseEntity<String> getSVG(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
- ) {
-
- // Query DB
- Session session = sessionFactoryBean.getCurrentSession();
- Model model = null;
- try{
- session.beginTransaction();
- org.hibernate.Query query = session.createQuery("from Model where slug= :slug");
- query.setString("slug", slug);
- model = (Model) query.uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- } }
-
- return new ResponseEntity<String>(HttpStatus.OK).ok(model.getChart().getSvg());
- }
-
@ApiOperation(value = "Get a model", response = Model.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@RequestMapping(value = "/{slug}", method = RequestMethod.GET)
diff --git a/src/main/java/org/hbp/mip/controllers/VariablesApi.java b/src/main/java/org/hbp/mip/controllers/VariablesApi.java
index bf64e31079a6503ba9cb5e694278d2e58c0f0ef5..ee01a9dc53d9efa780add3646a4ac963c4cc7f9e 100644
--- a/src/main/java/org/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/VariablesApi.java
@@ -52,7 +52,8 @@ public class VariablesApi {
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
- } }
+ }
+ }
return new ResponseEntity<List<Variable>>(HttpStatus.OK).ok(variables);
}
diff --git a/src/main/java/org/hbp/mip/model/Config.java b/src/main/java/org/hbp/mip/model/Config.java
new file mode 100644
index 0000000000000000000000000000000000000000..2e6b081c20c39d287933410211f0567368815cfe
--- /dev/null
+++ b/src/main/java/org/hbp/mip/model/Config.java
@@ -0,0 +1,87 @@
+package org.hbp.mip.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import io.swagger.annotations.ApiModel;
+
+import javax.persistence.*;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Created by mirco on 25.02.16.
+ */
+@Entity
+@Table(name = "`config`")
+@ApiModel(description = "")
+@JsonIgnoreProperties(value = { "id" })
+public class Config {
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ private Long id = null;
+ private String type = null;
+ private Integer height = null;
+ @ElementCollection(fetch = FetchType.EAGER)
+ private List<String> yAxisVariables = new LinkedList<>();
+ private String xAxisVariable = null;
+ private Boolean hasXAxis = null;
+ @ElementCollection(fetch = FetchType.EAGER)
+ private Map<String, String> title = new HashMap<>();
+
+ public Long getId() {
+ return id;
+ }
+
+ public void setId(Long id) {
+ this.id = id;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public Integer getHeight() {
+ return height;
+ }
+
+ public void setHeight(Integer height) {
+ this.height = height;
+ }
+
+ public List<String> getyAxisVariables() {
+ return yAxisVariables;
+ }
+
+ public void setyAxisVariables(List<String> yAxisVariables) {
+ this.yAxisVariables = yAxisVariables;
+ }
+
+ public String getxAxisVariable() {
+ return xAxisVariable;
+ }
+
+ public void setxAxisVariable(String xAxisVariable) {
+ this.xAxisVariable = xAxisVariable;
+ }
+
+ public Boolean getHasXAxis() {
+ return hasXAxis;
+ }
+
+ public void setHasXAxis(Boolean hasXAxis) {
+ this.hasXAxis = hasXAxis;
+ }
+
+ public Map<String, String> getTitle() {
+ return title;
+ }
+
+ public void setTitle(Map<String, String> title) {
+ this.title = title;
+ }
+}
diff --git a/src/main/java/org/hbp/mip/model/Dataset.java b/src/main/java/org/hbp/mip/model/Dataset.java
index f7f63ec75a0c1840b21b5e888b5990eb276d1edc..d56a618c7499883aff36c37797dc6d8640b19583 100644
--- a/src/main/java/org/hbp/mip/model/Dataset.java
+++ b/src/main/java/org/hbp/mip/model/Dataset.java
@@ -21,9 +21,9 @@ public class Dataset {
private String code = null;
private Date date = null;
@ElementCollection(fetch = FetchType.EAGER)
- private List<String> header = new LinkedList<String>();
- @Transient
- private Map<String, List<Object>> data = new HashMap<>();
+ private List<String> header = new LinkedList<>();
+ @ElementCollection(fetch=FetchType.EAGER)
+ private Map<String, LinkedList<Object>> data = new HashMap<>();
public Dataset() {
}
@@ -67,11 +67,11 @@ public class Dataset {
this.header = header;
}
- public Map<String, List<Object>> getData() {
+ public Map<String, LinkedList<Object>> getData() {
return data;
}
- public void setData(Map<String, List<Object>> data) {
+ public void setData(Map<String, LinkedList<Object>> data) {
this.data = data;
}
@@ -83,7 +83,6 @@ public class Dataset {
sb.append(" code: ").append(code).append("\n");
sb.append(" date: ").append(date).append("\n");
sb.append(" header: ").append(header).append("\n");
- sb.append(" data: ").append(data).append("\n");
sb.append("}\n");
return sb.toString();
}
diff --git a/src/main/java/org/hbp/mip/model/Model.java b/src/main/java/org/hbp/mip/model/Model.java
index 13b1a61c34afc9a50767c26fe0c3729556c0f50b..53c0e6e9a476a8f886c288d70d285c7d4b5b675c 100644
--- a/src/main/java/org/hbp/mip/model/Model.java
+++ b/src/main/java/org/hbp/mip/model/Model.java
@@ -8,12 +8,10 @@ import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
-import org.hibernate.annotations.*;
+import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import javax.persistence.*;
-import javax.persistence.Entity;
-import javax.persistence.Table;
import java.util.Date;
@Entity
@@ -36,7 +34,7 @@ public class Model {
private Dataset dataset = null;
@ManyToOne
@Cascade(CascadeType.SAVE_UPDATE)
- private Chart chart = null;
+ private Config config = null;
@ManyToOne
private User createdBy = null;
@ManyToOne
@@ -124,17 +122,14 @@ public class Model {
this.valid = valid;
}
- /**
- * Chart
- **/
- @ApiModelProperty(value = "Chart")
- @JsonProperty("chart")
- public Chart getChart() {
- return chart;
+ @ApiModelProperty(value = "Config")
+ @JsonProperty("config")
+ public Config getConfig() {
+ return config;
}
- public void setChart(Chart chart) {
- this.chart = chart;
+ public void setConfig(Config config) {
+ this.config = config;
}
/**
@@ -211,9 +206,7 @@ public class Model {
sb.append(" slug: ").append(slug).append("\n");
sb.append(" description: ").append(description).append("\n");
sb.append(" query: ").append(query).append("\n");
- sb.append(" dataset: ").append(dataset).append("\n");
sb.append(" valid: ").append(valid).append("\n");
- sb.append(" chart: ").append(chart).append("\n");
sb.append(" createdAt: ").append(createdAt).append("\n");
sb.append(" updatedAt: ").append(updatedAt).append("\n");
sb.append(" createdBy: ").append(createdBy).append("\n");
@@ -222,4 +215,5 @@ public class Model {
sb.append("}\n");
return sb.toString();
}
+
}
diff --git a/src/main/java/org/hbp/mip/utils/CSVUtil.java b/src/main/java/org/hbp/mip/utils/CSVUtil.java
index 756479051dc201c641952c5e572e5085c86c8a53..cfbcded29c30e69721d738ad4419779896da83a7 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -27,7 +27,7 @@ public class CSVUtil {
String code = GenerateDSCode(query);
Date date = new Date();
List<String> header = new LinkedList<>();
- Map<String, List<Object>> data = new HashMap<>();
+ Map<String, LinkedList<Object>> data = new HashMap<>();
List<Variable> variables = new LinkedList<>();
//variables.addAll(query.getVariables()); // TODO : check that
@@ -50,6 +50,7 @@ public class CSVUtil {
String c = v.getCode();
int idx = find(c, firstRow);
List<Object> l = new LinkedList<>();
+ LinkedList<Object> ll = new LinkedList<>();
for (String[] row : rows) {
switch (type) {
case "T": {
@@ -122,10 +123,9 @@ public class CSVUtil {
// TODO : Remove this limit -> only to avoid bug with Virtua's front-end
if(l.size() > 50)
{
- l = l.subList(0, 49);
+ ll.addAll(l.subList(0,49));
}
- data.put(c, l);
- System.out.println("Adding "+l.size()+" values to "+c);
+ data.put(c, ll);
}
} catch (IOException e) {
e.printStackTrace();
@@ -302,10 +302,19 @@ public class CSVUtil {
private static String getTypeFromDB(Variable v)
{
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- session.beginTransaction();
- org.hibernate.Query q = session.createQuery("SELECT type FROM Variable where code= :code").setString("code", v.getCode());
- String type = (String) q.uniqueResult();
- session.getTransaction().commit();
+ String type = null;
+ try{
+ session.beginTransaction();
+ org.hibernate.Query q = session.createQuery("SELECT type FROM Variable where code= :code").setString("code", v.getCode());
+ type = (String) q.uniqueResult();
+ session.getTransaction().commit();
+ } catch (Exception e)
+ {
+ if(session.getTransaction() != null)
+ {
+ session.getTransaction().rollback();
+ }
+ }
if(type == null)
{
diff --git a/src/main/resources/hibernate.cfg.xml b/src/main/resources/hibernate.cfg.xml
index 044c40c229c1a9a5aa0b6ae7b795db994c0f7213..7b290ac701bd5b408fd3421db8f6a37f398ec284 100644
--- a/src/main/resources/hibernate.cfg.xml
+++ b/src/main/resources/hibernate.cfg.xml
@@ -17,18 +17,5 @@
<property name="hibernate.show_sql">false</property>
<property name="hibernate.hbm2ddl.auto">update</property>
- <mapping class="org.hbp.mip.model.Article"/>
- <mapping class="org.hbp.mip.model.Chart"/>
- <mapping class="org.hbp.mip.model.ChartConfigSet"/>
- <mapping class="org.hbp.mip.model.Dataset"/>
- <mapping class="org.hbp.mip.model.Model"/>
- <mapping class="org.hbp.mip.model.Query"/>
- <mapping class="org.hbp.mip.model.Tag"/>
- <mapping class="org.hbp.mip.model.User"/>
- <mapping class="org.hbp.mip.model.Value"/>
- <mapping class="org.hbp.mip.model.Variable"/>
- <mapping class="org.hbp.mip.model.Filter"/>
- <mapping class="org.hbp.mip.model.Group"/>
-
</session-factory>
</hibernate-configuration>
diff --git a/src/test/db b/src/test/db
index af28ed02d855345f286e171c758758283c742dff..0484f708e74764f1072ac8f7da67c94f7b38c386 160000
--- a/src/test/db
+++ b/src/test/db
@@ -1 +1 @@
-Subproject commit af28ed02d855345f286e171c758758283c742dff
+Subproject commit 0484f708e74764f1072ac8f7da67c94f7b38c386