Merge pull request #434 from SEEG-Oxford/healthmap-config-page

Add HealthMap config page

db/migrations/1511161054__allow_edits_for_subdiseases.sql

@@ -0,0 +1,4 @@
+-- Allow healthmap_subdisease to be edited by the platform.
+--
+-- Copyright (c) 2015 University of Oxford
+GRANT INSERT, UPDATE ON TABLE healthmap_subdisease TO ${application_username};

db/migrations/1511161511__allow_subdisease_without_parent.sql

@@ -0,0 +1,4 @@
+-- Allow healthmap_subdisease without parent healthmap_disease.
+--
+-- Copyright (c) 2015 University of Oxford
+ALTER TABLE healthmap_subdisease ALTER COLUMN healthmap_disease_id DROP NOT NULL;

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/config/beans-service.xml

@@ -24,6 +24,7 @@
     <bean id="expertService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.ExpertServiceImpl" autowire="constructor"/>
     <bean id="locationService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.LocationServiceImpl" autowire="constructor"/>
     <bean id="geometryService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.GeometryServiceImpl" autowire="constructor"/>
+    <bean id="healthMapService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.HealthMapServiceImpl" autowire="constructor"/>
     <bean id="modelRunService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.ModelRunServiceImpl" autowire="constructor"/>
     <bean id="reportingService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.ReportingServiceImpl" autowire="constructor"/>
     <bean id="validationParameterCacheService" class="uk.ac.ox.zoo.seeg.abraid.mp.common.service.core.ValidationParameterCacheServiceImpl" autowire="constructor"/>

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/dao/HealthMapDiseaseDao.java

@@ -10,19 +10,19 @@
  * Copyright (c) 2014 University of Oxford
  */
 public interface HealthMapDiseaseDao {
-    /**
-     * Gets all diseases.
-     * @return All diseases.
-     */
-    List<HealthMapDisease> getAll();
-
     /**
      * Gets a HealthMap disease by ID.
      * @param id The ID.
      * @return The HealthMap disease, or null if not found.
      */
     HealthMapDisease getById(Integer id);
 
+    /**
+     * Gets all diseases.
+     * @return All diseases.
+     */
+    List<HealthMapDisease> getAll();
+
     /**
      * Saves the specified HealthMap disease.
      * @param disease The disease to save.

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/dao/HealthMapSubDiseaseDao.java

@@ -10,16 +10,23 @@
  * Copyright (c) 2014 University of Oxford
  */
 public interface HealthMapSubDiseaseDao {
+    /**
+     * Gets a HealthMapSubDisease by ID.
+     *
+     * @param id The ID.
+     * @return The HealthMapSubDisease with the specified ID, or null if not found.
+     */
+    HealthMapSubDisease getById(Integer id);
+
     /**
      * Gets all sub-diseases.
      * @return All sub-diseases.
      */
     List<HealthMapSubDisease> getAll();
 
     /**
-     * Gets a HealthMap sub-disease by name.
-     * @param name The name.
-     * @return The HealthMap sub-disease, or null if not found.
+     * Saves the specified HealthMap subdisease.
+     * @param disease The disease to save.
      */
-    HealthMapSubDisease getByName(String name);
+    void save(HealthMapSubDisease disease);
 }

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/dao/HealthMapSubDiseaseDaoImpl.java

@@ -15,13 +15,4 @@ public class HealthMapSubDiseaseDaoImpl extends AbstractDao<HealthMapSubDisease,
     public HealthMapSubDiseaseDaoImpl(SessionFactory sessionFactory) {
         super(sessionFactory);
     }
-
-    /**
-     * Gets a HealthMap sub-disease by name.
-     * @param name The name.
-     * @return The HealthMap sub-disease, or null if not found.
-     */
-    public HealthMapSubDisease getByName(String name) {
-        return uniqueResultNamedQuery("getHealthMapSubDiseaseByName", "name", name);
-    }
 }

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/domain/HealthMapSubDisease.java

@@ -5,24 +5,15 @@
 
 import javax.persistence.*;
 import javax.persistence.Entity;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
 import javax.persistence.Table;
 
 /**
  * Represents a "sub-disease" as defined by HealthMap. This is specified in the comment field of a HealthMap alert.
  *
  * Copyright (c) 2014 University of Oxford
  */
-@NamedQueries({
-        @NamedQuery(
-                name = "getHealthMapSubDiseaseByName",
-                query = "from HealthMapSubDisease where name=:name"
-        )
-})
 @Entity
 @Table(name = "healthmap_subdisease")
-@Immutable
 public class HealthMapSubDisease {
     // The primary key.
     @Id
@@ -68,6 +59,10 @@ public HealthMapDisease getHealthMapDisease() {
         return healthMapDisease;
     }
 
+    public void setHealthMapDisease(HealthMapDisease healthMapDisease) {
+        this.healthMapDisease = healthMapDisease;
+    }
+
     public String getName() {
         return name;
     }
@@ -76,6 +71,10 @@ public DiseaseGroup getDiseaseGroup() {
         return diseaseGroup;
     }
 
+    public void setDiseaseGroup(DiseaseGroup diseaseGroup) {
+        this.diseaseGroup = diseaseGroup;
+    }
+
     public DateTime getCreatedDate() {
         return createdDate;
     }

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/dto/json/JsonHealthMapDisease.java

@@ -0,0 +1,25 @@
+package uk.ac.ox.zoo.seeg.abraid.mp.common.dto.json;
+
+/**
+ * A JSON DTO used identify a HealthMap disease.
+ * Copyright (c) 2015 University of Oxford
+ */
+public class JsonHealthMapDisease extends JsonNamedEntry {
+    private JsonNamedEntry abraidDisease;
+
+    public JsonHealthMapDisease() {
+    }
+
+    public JsonHealthMapDisease(Integer id, String name, JsonNamedEntry abraidDisease) {
+        super(id, name);
+        setAbraidDisease(abraidDisease);
+    }
+
+    public JsonNamedEntry getAbraidDisease() {
+        return abraidDisease;
+    }
+
+    public void setAbraidDisease(JsonNamedEntry abraidDisease) {
+        this.abraidDisease = abraidDisease;
+    }
+}

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/dto/json/JsonHealthMapSubDisease.java

@@ -0,0 +1,26 @@
+package uk.ac.ox.zoo.seeg.abraid.mp.common.dto.json;
+
+/**
+ * A JSON DTO used identify a HealthMap subdisease.
+ * Copyright (c) 2015 University of Oxford
+ */
+public class JsonHealthMapSubDisease extends JsonHealthMapDisease {
+    private JsonNamedEntry parent;
+
+    public JsonHealthMapSubDisease() {
+    }
+
+    public JsonHealthMapSubDisease(
+            Integer id, String name, JsonNamedEntry abraidDisease, JsonNamedEntry parent) {
+        super(id, name, abraidDisease);
+        setParent(parent);
+    }
+
+    public JsonNamedEntry getParent() {
+        return parent;
+    }
+
+    public void setParent(JsonNamedEntry parent) {
+        this.parent = parent;
+    }
+}

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/dto/json/JsonNamedEntry.java

@@ -0,0 +1,34 @@
+package uk.ac.ox.zoo.seeg.abraid.mp.common.dto.json;
+
+/**
+ * A base JSON dto to represent any object with an ID and name.
+ * Copyright (c) 2015 University of Oxford
+ */
+public class JsonNamedEntry {
+    private Integer id;
+    private String name;
+
+    public JsonNamedEntry() {
+    }
+
+    public JsonNamedEntry(Integer id, String name) {
+        setId(id);
+        setName(name);
+    }
+
+    public Integer getId() {
+        return id;
+    }
+
+    public void setId(Integer id) {
+        this.id = id;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+}

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/service/core/DiseaseService.java

@@ -13,18 +13,6 @@
  * Copyright (c) 2014 University of Oxford
  */
 public interface DiseaseService {
-    /**
-     * Gets all HealthMap diseases.
-     * @return All HealthMap diseases.
-     */
-    List<HealthMapDisease> getAllHealthMapDiseases();
-
-    /**
-     * Gets all HealthMap sub-diseases.
-     * @return All HealthMap sub-diseases.
-     */
-    List<HealthMapSubDisease> getAllHealthMapSubDiseases();
-
     /**
      * Gets all disease groups.
      * @return All disease groups.
@@ -223,12 +211,6 @@ List<DiseaseOccurrenceReview> getDiseaseOccurrenceReviewsForOccurrencesInValidat
      */
     void saveDiseaseGroup(DiseaseGroup diseaseGroup);
 
-    /**
-     * Saves a HealthMap disease.
-     * @param disease The disease to save.
-     */
-    void saveHealthMapDisease(HealthMapDisease disease);
-
     /**
      * Saves a disease extent class that is associated with an admin unit (global or tropical).
      * @param adminUnitDiseaseExtentClass The object to save.

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/service/core/DiseaseServiceImpl.java

@@ -22,8 +22,6 @@ public class DiseaseServiceImpl implements DiseaseService {
     private DiseaseOccurrenceDao diseaseOccurrenceDao;
     private DiseaseOccurrenceReviewDao diseaseOccurrenceReviewDao;
     private DiseaseGroupDao diseaseGroupDao;
-    private HealthMapDiseaseDao healthMapDiseaseDao;
-    private HealthMapSubDiseaseDao healthMapSubDiseaseDao;
     private ValidatorDiseaseGroupDao validatorDiseaseGroupDao;
     private AdminUnitDiseaseExtentClassDao adminUnitDiseaseExtentClassDao;
 
@@ -35,8 +33,6 @@ public class DiseaseServiceImpl implements DiseaseService {
     public DiseaseServiceImpl(DiseaseOccurrenceDao diseaseOccurrenceDao,
                               DiseaseOccurrenceReviewDao diseaseOccurrenceReviewDao,
                               DiseaseGroupDao diseaseGroupDao,
-                              HealthMapDiseaseDao healthMapDiseaseDao,
-                              HealthMapSubDiseaseDao healthMapSubDiseaseDao,
                               ValidatorDiseaseGroupDao validatorDiseaseGroupDao,
                               AdminUnitDiseaseExtentClassDao adminUnitDiseaseExtentClassDao,
                               ModelRunDao modelRunDao,
@@ -46,8 +42,6 @@ public DiseaseServiceImpl(DiseaseOccurrenceDao diseaseOccurrenceDao,
         this.diseaseOccurrenceDao = diseaseOccurrenceDao;
         this.diseaseOccurrenceReviewDao = diseaseOccurrenceReviewDao;
         this.diseaseGroupDao = diseaseGroupDao;
-        this.healthMapDiseaseDao = healthMapDiseaseDao;
-        this.healthMapSubDiseaseDao = healthMapSubDiseaseDao;
         this.validatorDiseaseGroupDao = validatorDiseaseGroupDao;
         this.adminUnitDiseaseExtentClassDao = adminUnitDiseaseExtentClassDao;
         this.modelRunDao = modelRunDao;
@@ -56,24 +50,6 @@ public DiseaseServiceImpl(DiseaseOccurrenceDao diseaseOccurrenceDao,
         this.nativeSQL = nativeSQL;
     }
 
-    /**
-     * Gets all HealthMap diseases.
-     * @return All HealthMap diseases.
-     */
-    @Override
-    public List<HealthMapDisease> getAllHealthMapDiseases() {
-        return healthMapDiseaseDao.getAll();
-    }
-
-    /**
-     * Gets all HealthMap sub-diseases.
-     * @return All HealthMap sub-diseases.
-     */
-    @Override
-    public List<HealthMapSubDisease> getAllHealthMapSubDiseases() {
-        return healthMapSubDiseaseDao.getAll();
-    }
-
     /**
      * Gets all disease groups.
      * @return All disease groups.
@@ -424,15 +400,6 @@ public void saveDiseaseGroup(DiseaseGroup diseaseGroup) {
         diseaseGroupDao.save(diseaseGroup);
     }
 
-    /**
-     * Saves a HealthMap disease.
-     * @param disease The disease to save.
-     */
-    @Override
-    public void saveHealthMapDisease(HealthMapDisease disease) {
-        healthMapDiseaseDao.save(disease);
-    }
-
     /**
      * Saves a disease extent class that is associated with an admin unit (global or tropical).
      * @param adminUnitDiseaseExtentClass The object to save.

src/Common/src/uk/ac/ox/zoo/seeg/abraid/mp/common/service/core/HealthMapService.java

@@ -0,0 +1,50 @@
+package uk.ac.ox.zoo.seeg.abraid.mp.common.service.core;
+
+import uk.ac.ox.zoo.seeg.abraid.mp.common.domain.HealthMapDisease;
+import uk.ac.ox.zoo.seeg.abraid.mp.common.domain.HealthMapSubDisease;
+
+import java.util.List;
+
+/**
+ * Service interface for HealthMap configuration.
+ * Copyright (c) 2015 University of Oxford
+ */
+public interface HealthMapService {
+    /**
+     * Gets a HealthMap disease by ID.
+     * @param id The ID.
+     * @return The HealthMap disease, or null if not found.
+     */
+    HealthMapDisease getHealthMapDiseasesById(Integer id);
+
+    /**
+     * Gets a HealthMap subdisease by ID.
+     * @param id The ID.
+     * @return The HealthMap subdisease, or null if not found.
+     */
+    HealthMapSubDisease getHealthMapSubDiseasesById(Integer id);
+
+    /**
+     * Gets all HealthMap diseases.
+     * @return All HealthMap diseases.
+     */
+    List<HealthMapDisease> getAllHealthMapDiseases();
+
+    /**
+     * Gets all HealthMap sub-diseases.
+     * @return All HealthMap sub-diseases.
+     */
+    List<HealthMapSubDisease> getAllHealthMapSubDiseases();
+
+    /**
+     * Saves a HealthMap disease.
+     * @param disease The disease to save.
+     */
+    void saveHealthMapDisease(HealthMapDisease disease);
+
+    /**
+     * Saves a HealthMap subdisease.
+     * @param disease The disease to save.
+     */
+    void saveHealthMapSubDisease(HealthMapSubDisease disease);
+}