- Deep change to data structures. Inclusion of the ExperimentContext. All the domain, administration and repository classes where refactored

- The importing of excel files is now complete with all the available information
- Database operations where put into transactions
- Add total of records to results page
- Some libraries were updated in the build.gradle file
- Sql initialization files have now an initial version of the compendium

Author: odizeuz

build.gradle

@@ -13,7 +13,7 @@ buildscript {
         // Spring boot integration with gradle
         classpath("org.springframework.boot:spring-boot-gradle-plugin:1.2.3.RELEASE")
         // Plugin to reload changed classes with out restarting
-        classpath("org.springframework:springloaded:1.2.1.RELEASE")
+        classpath("org.springframework:springloaded:1.2.3.RELEASE")
         // Plugin to include optional dependencies
         classpath("org.springframework.build.gradle:propdeps-plugin:0.0.7")
         // Plugin to deploy the war file to a remote Tomcat
@@ -48,7 +48,6 @@ bootRun {
 repositories {
     //mavenLocal()
     mavenCentral()
-    maven { url "http://lightadmin.org/nexus/content/repositories/snapshots" }
     maven { url "http://repository.primefaces.org" }
 }
 
@@ -60,7 +59,7 @@ repositories {
  */
 dependencies {
 
-    def springBootVersion = "1.2.3.RELEASE"
+    def springBootVersion = "1.2.4.RELEASE"
     def springVersion = "4.1.6.RELEASE"
 
     compile "org.springframework.boot:spring-boot-starter:$springBootVersion"
@@ -72,8 +71,8 @@ dependencies {
     compile "org.springframework:spring-orm:$springVersion"
 
     // Includes tomcat-embed-core, tomcat-embed-el, ecj
-    providedCompile "org.apache.tomcat.embed:tomcat-embed-jasper:8.0.22"
-    providedCompile "org.apache.tomcat.embed:tomcat-embed-logging-juli:8.0.22"
+    providedCompile "org.apache.tomcat.embed:tomcat-embed-jasper:8.0.23"
+    providedCompile "org.apache.tomcat.embed:tomcat-embed-logging-juli:8.0.23"
 
     compile("org.springframework.data:spring-data-jpa:1.7.2.RELEASE") {
         // Requests an older version with different name
@@ -108,7 +107,7 @@ dependencies {
     compile "com.fasterxml.jackson.core:jackson-databind:2.5.1"
 
     // For backend administration. Excludes some apache tiles extras
-    compile ("org.lightadmin:lightadmin:1.2.0.BUILD-SNAPSHOT") {
+    compile ("org.lightadmin:lightadmin:1.2.0.RC1") {
         exclude module: "tiles-freemarker"
         exclude module: "tiles-request-mustache"
         exclude module: "tiles-velocity"

src/main/java/org/cgiar/ccafs/csa/domain/AbstractInformationEntity.java

@@ -1,25 +1,30 @@
 package org.cgiar.ccafs.csa.domain;
 
+import com.google.common.base.Joiner;
+
 import javax.persistence.Column;
-import javax.persistence.Lob;
 import javax.persistence.MappedSuperclass;
 import java.io.Serializable;
+import java.util.Objects;
 
 /**
  * Super class for those entities that have four basic translatable fields
  */
 @MappedSuperclass
 public abstract class AbstractInformationEntity implements Serializable {
+
+    protected static final Joiner joiner = Joiner.on(";").skipNulls();
+
     private static final long serialVersionUID = 1L;
 
     private String code;
 
     private String name;
 
-    @Column(length=100000)
+    @Column(length = 100000)
     private String description;
 
-    @Column(length=100000)
+    @Column(length = 100000)
     private String documentation;
 
     public abstract Integer getId();
@@ -56,4 +61,18 @@ public void setDocumentation(String documentation) {
         this.documentation = documentation;
     }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || !(o instanceof AbstractInformationEntity)) return false;
+        AbstractInformationEntity that = (AbstractInformationEntity) o;
+        return Objects.equals(this.code, that.code) && Objects.equals(this.name, that.name);
+    }
+
+    @Override
+    public int hashCode() {
+        int result = code != null ? code.hashCode() : super.hashCode();
+        result = 31 * result + (name != null ? name.hashCode() : 0);
+        return result;
+    }
 }

src/main/java/org/cgiar/ccafs/csa/domain/ContextValue.java

@@ -1,6 +1,8 @@
 package org.cgiar.ccafs.csa.domain;
 
 import javax.persistence.*;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * The persistent class for the context_filters database table.
@@ -18,6 +20,9 @@ public class ContextValue extends AbstractInformationEntity {
     @JoinColumn(name = "context_variable_id")
     private ContextVariable contextVariable;
 
+    @ManyToMany(mappedBy="contextValues")
+    private List<ExperimentArticle> experimentArticles = new ArrayList<>();
+
     @Override
     public Integer getId() {
         return this.id;
@@ -30,4 +35,8 @@ public ContextVariable getContextVariable() {
     public void setContextVariable(ContextVariable contextVariable) {
         this.contextVariable = contextVariable;
     }
+
+    public List<ExperimentArticle> getExperimentArticles() {
+        return experimentArticles;
+    }
 }

src/main/java/org/cgiar/ccafs/csa/domain/ContextVariable.java

@@ -25,18 +25,12 @@ public class ContextVariable extends AbstractInformationEntity {
 
     @Override
     public boolean equals(Object o) {
-        if (this == o) return true;
-        if (!(o instanceof ContextVariable)) return false;
-
-        ContextVariable that = (ContextVariable) o;
-
-        return id.equals(that.id);
-
+        return super.equals(o) && o instanceof ContextVariable && id.equals(((ContextVariable) o).getId());
     }
 
     @Override
     public int hashCode() {
-        return id.hashCode();
+        return id * super.hashCode();
     }
 
     @Override

src/main/java/org/cgiar/ccafs/csa/domain/ExperimentArticle.java

@@ -1,6 +1,5 @@
 package org.cgiar.ccafs.csa.domain;
 
-import org.apache.commons.lang3.StringUtils;
 import org.joda.time.LocalDate;
 import org.springframework.format.annotation.DateTimeFormat;
 
@@ -11,6 +10,7 @@
 import java.util.Date;
 import java.util.List;
 
+import static org.cgiar.ccafs.csa.domain.AbstractInformationEntity.joiner;
 import static org.springframework.format.annotation.DateTimeFormat.ISO.DATE;
 
 
@@ -31,27 +31,23 @@ public class ExperimentArticle implements Serializable {
 
     private String code;
 
-    @Column(length=100000)
+    @Column(length = 100000)
     private String title;
 
-    @Column(length=100000)
+    @Column(length = 100000)
     private String outline;
 
     private String link;
 
     private Integer rating;
 
-    @ManyToOne
-    @JoinColumn(name = "farming_system_id")
-    private FarmingSystem farmingSystem;
-
-    @Column(length=100000)
+    @Column(length = 100000)
     private String authors;
 
     @Transient
     private List<String> authorsList = new ArrayList<>();
 
-    @Column(length=100000)
+    @Column(length = 100000)
     private String contacts;
 
     @Transient
@@ -68,14 +64,7 @@ public class ExperimentArticle implements Serializable {
 
     @ManyToOne
     @JoinColumn(name = "theme_id")
-    private PracticeTheme practiceTheme;
-
-    @ManyToOne
-    @JoinColumn(name = "location_id")
-    private Location location;
-
-    @OneToMany(mappedBy = "experimentArticle", fetch = FetchType.EAGER)
-    private List<InitialCondition> initialConditions = new ArrayList<>();
+    private PracticeTheme theme;
 
     @ManyToMany(fetch = FetchType.EAGER)
     @JoinTable(
@@ -89,8 +78,8 @@ public class ExperimentArticle implements Serializable {
     )
     private List<ContextValue> contextValues = new ArrayList<>();
 
-    @OneToMany(mappedBy = "experimentArticle", fetch = FetchType.EAGER)
-    private List<Treatment> treatments;
+    @OneToMany(mappedBy = "experiment", fetch = FetchType.EAGER)
+    private List<ExperimentContext> contexts = new ArrayList<>();
 
     // Methods //
 
@@ -122,43 +111,20 @@ public void setOutline(String outline) {
         this.outline = outline;
     }
 
-    public Integer getRating() {
-        return this.rating;
-    }
-
-    public void setRating(Integer rating) {
-        this.rating = rating;
-    }
-
-    public FarmingSystem getFarmingSystem() {
-        return farmingSystem;
-    }
-
-    public void setFarmingSystem(FarmingSystem farmingSystem) {
-        this.farmingSystem = farmingSystem;
+    public String getLink() {
+        return link;
     }
 
-    public List<Treatment> getTreatments() {
-        if (treatments == null) {
-            treatments = new ArrayList<>();
-        }
-        return treatments;
+    public void setLink(String link) {
+        this.link = link;
     }
 
-    public void setTreatments(List<Treatment> treatments) {
-        this.treatments = treatments;
-    }
-
-    public Treatment addTreatment(Treatment treatment) {
-        getTreatments().add(treatment);
-        treatment.setExperiment(this);
-        return treatment;
+    public Integer getRating() {
+        return this.rating;
     }
 
-    public Treatment removeTreatment(Treatment treatment) {
-        getTreatments().remove(treatment);
-        treatment.setExperiment(null);
-        return treatment;
+    public void setRating(Integer rating) {
+        this.rating = rating;
     }
 
     public List<String> getAuthorsList() {
@@ -173,30 +139,38 @@ public List<String> getContactsList() {
         return this.contactsList;
     }
 
-    public void addContact(String author) {
-        getContactsList().add(author);
+    public void addContact(String contactEmail) {
+        getContactsList().add(contactEmail);
     }
 
     @PrePersist
     @PreUpdate
     protected void recordSaved() {
-        authors = StringUtils.join(getAuthorsList(), ";");
-        contacts = StringUtils.join(getAuthorsList(), ";");
+        authors = joiner.join(getAuthorsList());
+        contacts = joiner.join(getContactsList());
     }
 
     @PostLoad
     protected void recordLoaded() {
-        if (authors != null && authors.trim().length() == 0) {
+        if (authors != null && authors.trim().length() != 0) {
             String[] data = authors.split(";");
             authorsList = Arrays.asList(data);
         }
 
-        if (contacts != null && contacts.trim().length() == 0) {
+        if (contacts != null && contacts.trim().length() != 0) {
             String[] data = contacts.split(";");
             contactsList = Arrays.asList(data);
         }
     }
 
+    public Language getLanguage() {
+        return language;
+    }
+
+    public void setLanguage(Language language) {
+        this.language = language;
+    }
+
     public LocalDate getPublicationDate() {
         return new LocalDate(this.publicationDate);
     }
@@ -205,40 +179,40 @@ public void setPublicationDate(LocalDate publicationDate) {
         this.publicationDate = publicationDate.toDate();
     }
 
-    public PracticeTheme getPracticeTheme() {
-        return practiceTheme;
+    public PracticeTheme getTheme() {
+        return theme;
     }
 
-    public void setPracticeTheme(PracticeTheme practiceTheme) {
-        this.practiceTheme = practiceTheme;
+    public void setTheme(PracticeTheme theme) {
+        this.theme = theme;
     }
 
-    public Location getLocation() {
-        return this.location;
+    public List<ContextValue> getContextValues() {
+        return this.contextValues;
     }
 
-    public void setLocation(Location location) {
-        this.location = location;
+    public ContextValue setContextVariable(ContextValue contextValue) {
+        if (contextValue != null) getContextValues().add(contextValue);
+        return contextValue;
     }
 
-    public List<ContextValue> getContextValues() {
-        return this.contextValues;
+    public boolean unsetContextVariable(ContextValue contextValue) {
+        return getContextValues().remove(contextValue);
     }
 
-    public List<InitialCondition> getInitialConditions() {
-        return this.initialConditions;
+    public List<ExperimentContext> getContexts() {
+        return contexts;
     }
 
-    public InitialCondition addInitialCondition(InitialCondition initialCondition) {
-        getInitialConditions().add(initialCondition);
-        initialCondition.setExperiment(this);
-        return initialCondition;
+    public ExperimentContext addContext(ExperimentContext context) {
+        getContexts().add(context);
+        context.setExperiment(this);
+        return context;
     }
 
-    public InitialCondition removeInitialCondition(InitialCondition initialCondition) {
-        getInitialConditions().remove(initialCondition);
-        initialCondition.setExperiment(null);
-        return initialCondition;
+    public ExperimentContext removeExperimentContext(ExperimentContext context) {
+        getContexts().remove(context);
+        context.setExperiment(null);
+        return context;
     }
-
 }