From 8d601bd15e9046c7e4a716e0681f110cce876fb0 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 14 Mar 2018 14:50:53 +0100
Subject: [PATCH] structures for plugin data
---
.../lcsb/mapviewer/model/plugin/Plugin.java | 102 ++++++++++++++++++
.../model/plugin/PluginDataEntry.java | 90 ++++++++++++++++
...ix_db_20180206.sql => fix_db_20180311.sql} | 0
.../src/db/12.0.0~alpha.2/fix_db_20180314.sql | 49 +++++++++
.../lcsb/mapviewer/persist/dao/BaseDao.java | 10 +-
.../persist/dao/plugin/PluginDao.java | 20 ++++
.../dao/plugin/PluginDataEntryDao.java | 43 ++++++++
.../resources/applicationContext-persist.xml | 5 +
.../mapviewer/persist/dao/AllDaoTests.java | 16 +--
.../persist/dao/plugin/AllPluginTests.java | 12 +++
.../persist/dao/plugin/PluginDaoTest.java | 32 ++++++
.../dao/plugin/PluginDataEntryDaoTest.java | 65 +++++++++++
12 files changed, 435 insertions(+), 9 deletions(-)
create mode 100644 model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
rename persist/src/db/12.0.0~alpha.1/{fix_db_20180206.sql => fix_db_20180311.sql} (100%)
create mode 100644 persist/src/db/12.0.0~alpha.2/fix_db_20180314.sql
create mode 100644 persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
create mode 100644 persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java
create mode 100644 persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java
create mode 100644 persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java
create mode 100644 persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java
diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
new file mode 100644
index 0000000000..ad3fd50c8e
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
@@ -0,0 +1,102 @@
+package lcsb.mapviewer.model.plugin;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.Table;
+
+/**
+ * Meta data of the plugin used in the system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "plugin_table")
+public class Plugin implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Hash of the plugin code used as identifier to distinguish between plugins.
+ */
+ private String hash;
+
+ /**
+ * Name of the plugin.
+ */
+ private String name;
+
+ /**
+ * Version of the plugin.
+ */
+ private String version;
+
+ /**
+ * List of urls from which plugin can be downloaded.
+ */
+ @ElementCollection
+ @CollectionTable(name = "plugin_urls", joinColumns = @JoinColumn(name = "plugin_iddb"))
+ @Column(name = "url")
+ private Set<String> urls = new HashSet<>();
+
+ public String getHash() {
+ return hash;
+ }
+
+ public void setHash(String hash) {
+ this.hash = hash;
+ }
+
+ public Set<String> getUrls() {
+ return urls;
+ }
+
+ public void setUrls(Set<String> urls) {
+ this.urls = urls;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getVersion() {
+ return version;
+ }
+
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ public int getId() {
+ return id;
+ }
+
+ public void setId(int id) {
+ this.id = id;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
new file mode 100644
index 0000000000..3f661f5284
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
@@ -0,0 +1,90 @@
+package lcsb.mapviewer.model.plugin;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.model.user.User;
+
+/**
+ * Single entry of data stored by the plugin.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "plugin_data_entry")
+public class PluginDataEntry implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ @ManyToOne(fetch = FetchType.LAZY, optional = true)
+ private User user;
+
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private Plugin plugin;
+
+ @Column(name = "entry_key", nullable = false)
+ private String key;
+
+ @Column(name = "entry_value", nullable = false)
+ private String value;
+
+ public int getId() {
+ return id;
+ }
+
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ public User getUser() {
+ return user;
+ }
+
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ public Plugin getPlugin() {
+ return plugin;
+ }
+
+ public void setPlugin(Plugin plugin) {
+ this.plugin = plugin;
+ }
+
+ public String getKey() {
+ return key;
+ }
+
+ public void setKey(String key) {
+ this.key = key;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+}
diff --git a/persist/src/db/12.0.0~alpha.1/fix_db_20180206.sql b/persist/src/db/12.0.0~alpha.1/fix_db_20180311.sql
similarity index 100%
rename from persist/src/db/12.0.0~alpha.1/fix_db_20180206.sql
rename to persist/src/db/12.0.0~alpha.1/fix_db_20180311.sql
diff --git a/persist/src/db/12.0.0~alpha.2/fix_db_20180314.sql b/persist/src/db/12.0.0~alpha.2/fix_db_20180314.sql
new file mode 100644
index 0000000000..b5fc165fc1
--- /dev/null
+++ b/persist/src/db/12.0.0~alpha.2/fix_db_20180314.sql
@@ -0,0 +1,49 @@
+CREATE SEQUENCE plugin_table_iddb_seq
+ INCREMENT 1
+ MINVALUE 1
+ MAXVALUE 9223372036854775807
+ START 1
+ CACHE 1;
+
+CREATE TABLE plugin_table
+(
+ iddb integer NOT NULL DEFAULT nextval('plugin_table_iddb_seq'::regclass),
+ hash character varying(255) NOT NULL,
+ name character varying(255) NOT NULL,
+ version character varying(255) NOT NULL,
+ CONSTRAINT plugin_pkey PRIMARY KEY (iddb),
+ CONSTRAINT plugin_hash_unique UNIQUE (hash)
+);
+
+CREATE TABLE plugin_urls
+(
+ plugin_iddb integer NOT NULL,
+ url character varying(1024) NOT NULL,
+ CONSTRAINT plugin_urls_pkey PRIMARY KEY (plugin_iddb, url),
+ CONSTRAINT plugin_urls_fk FOREIGN KEY (plugin_iddb)
+ REFERENCES public.plugin_table (iddb) MATCH SIMPLE
+ ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+CREATE SEQUENCE plugin_data_entry_iddb_seq
+ INCREMENT 1
+ MINVALUE 1
+ MAXVALUE 9223372036854775807
+ START 1
+ CACHE 1;
+
+CREATE TABLE plugin_data_entry
+(
+ iddb integer NOT NULL DEFAULT nextval('plugin_table_iddb_seq'::regclass),
+ plugin_iddb integer NOT NULL,
+ user_iddb integer,
+ entry_key character varying(1024) NOT NULL,
+ entry_value character varying(2048) NOT NULL,
+ CONSTRAINT plugin_data_entry_pkey PRIMARY KEY (iddb),
+ CONSTRAINT plugin_data_entry_plugin_fk FOREIGN KEY (plugin_iddb)
+ REFERENCES public.plugin_table (iddb) MATCH SIMPLE
+ ON UPDATE CASCADE ON DELETE CASCADE,
+ CONSTRAINT plugin_data_entry_user_fk FOREIGN KEY (user_iddb)
+ REFERENCES public.user_table (iddb) MATCH SIMPLE
+ ON UPDATE CASCADE ON DELETE CASCADE
+);
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
index c6b2da5579..ff6e427890 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
@@ -220,7 +220,11 @@ public abstract class BaseDao<T> {
if (!firstParam) {
queryString += " AND ";
}
- queryString += key + " = :param_val_" + key + " ";
+ if (param.getRight() == null) {
+ queryString += key + " is null ";
+ } else {
+ queryString += key + " = :param_val_" + key + " ";
+ }
firstParam = false;
}
@@ -229,7 +233,9 @@ public abstract class BaseDao<T> {
for (Pair<String, Object> param : params) {
String key = param.getLeft();
Object value = param.getRight();
- query = query.setParameter("param_val_" + key, value);
+ if (value != null) {
+ query = query.setParameter("param_val_" + key, value);
+ }
}
List<?> list = query.list();
return (List<T>) list;
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
new file mode 100644
index 0000000000..d76e95bc25
--- /dev/null
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
@@ -0,0 +1,20 @@
+package lcsb.mapviewer.persist.dao.plugin;
+
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for {@link Plugin} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PluginDao extends BaseDao<Plugin> {
+ /**
+ * Default constructor.
+ */
+ public PluginDao() {
+ super(Plugin.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java
new file mode 100644
index 0000000000..34eaed2a25
--- /dev/null
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java
@@ -0,0 +1,43 @@
+package lcsb.mapviewer.persist.dao.plugin;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.model.plugin.PluginDataEntry;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for {@link PluginDataEntry} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PluginDataEntryDao extends BaseDao<PluginDataEntry> {
+ /**
+ * Default constructor.
+ */
+ public PluginDataEntryDao() {
+ super(PluginDataEntry.class);
+ }
+
+ public PluginDataEntry getByKey(Plugin plugin, String key, User user) {
+ List<Pair<String, Object>> params = new ArrayList<>();
+ params.add(new Pair<String, Object>("plugin_iddb", plugin.getId()));
+ params.add(new Pair<String, Object>("entry_key", key));
+ if (user == null) {
+ params.add(new Pair<String, Object>("user_iddb", null));
+ } else {
+ params.add(new Pair<String, Object>("user_iddb", user.getId()));
+ }
+ List<PluginDataEntry> entries = getElementsByParameters(params);
+ if (entries.size() > 0) {
+ return entries.get(0);
+ } else {
+ return null;
+ }
+ }
+
+}
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 7743d71430..623cbfdb71 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -25,6 +25,9 @@
<bean id="DataMiningSetDao" class="lcsb.mapviewer.persist.dao.map.graph.DataMiningSetDao" parent="BaseDao"/>
<bean id="ElementDao" class="lcsb.mapviewer.persist.dao.map.species.ElementDao" parent="BaseDao"/>
+
+ <bean id="PluginDao" class="lcsb.mapviewer.persist.dao.plugin.PluginDao" parent="BaseDao"/>
+ <bean id="PluginDataEntryDao" class="lcsb.mapviewer.persist.dao.plugin.PluginDataEntryDao" parent="BaseDao"/>
<bean id="ReferenceGenomeDao" class="lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao" parent="BaseDao"/>
<bean id="ReferenceGenomeGeneMappingDao" class="lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeGeneMappingDao" parent="BaseDao"/>
@@ -49,6 +52,8 @@
<property name="dataSource" ref="DataSource" />
<property name="annotatedClasses">
<list>
+ <value>lcsb.mapviewer.model.plugin.Plugin</value>
+ <value>lcsb.mapviewer.model.plugin.PluginDataEntry</value>
<value>lcsb.mapviewer.model.map.graph.DataMining</value>
<value>lcsb.mapviewer.model.map.graph.DataMiningSet</value>
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
index f289c4e122..50e07ae2b1 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
@@ -7,17 +7,19 @@ import lcsb.mapviewer.persist.dao.cache.AllCacheDbTests;
import lcsb.mapviewer.persist.dao.graphics.AllGraphicsDaoTests;
import lcsb.mapviewer.persist.dao.log.AllLogTests;
import lcsb.mapviewer.persist.dao.map.AllMapDaoTests;
+import lcsb.mapviewer.persist.dao.plugin.AllPluginTests;
import lcsb.mapviewer.persist.dao.user.AllUserTests;
@RunWith(Suite.class)
@Suite.SuiteClasses({ AllCacheDbTests.class, //
- AllGraphicsDaoTests.class, //
- AllLogTests.class, //
- AllMapDaoTests.class, //
- AllUserTests.class, //
- BaseDaoTest.class, //
- ConfigurationDaoTest.class, //
- ProjectDaoTest.class, //
+ AllGraphicsDaoTests.class, //
+ AllLogTests.class, //
+ AllMapDaoTests.class, //
+ AllPluginTests.class, //
+ AllUserTests.class, //
+ BaseDaoTest.class, //
+ ConfigurationDaoTest.class, //
+ ProjectDaoTest.class, //
})
public class AllDaoTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java
new file mode 100644
index 0000000000..75664e9ccb
--- /dev/null
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/AllPluginTests.java
@@ -0,0 +1,12 @@
+package lcsb.mapviewer.persist.dao.plugin;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ PluginDaoTest.class, //
+ PluginDataEntryDaoTest.class })
+public class AllPluginTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java
new file mode 100644
index 0000000000..571c4dc906
--- /dev/null
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDaoTest.java
@@ -0,0 +1,32 @@
+package lcsb.mapviewer.persist.dao.plugin;
+
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class PluginDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ PluginDao pluginDao;
+
+ @Test
+ public void testGetPlugins() {
+ assertTrue(pluginDao.getAll().size() >= 0);
+ }
+
+ @Test
+ public void testAddPlugin() {
+ Plugin plugin =new Plugin();
+ plugin.setHash("x");
+ plugin.setName("Plugin name");
+ plugin.setVersion("0.0.1");
+ plugin.getUrls().add("htpp://google.pl/");
+ pluginDao.add(plugin);
+ assertTrue(pluginDao.getAll().size() > 0);
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java
new file mode 100644
index 0000000000..ca4893275e
--- /dev/null
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDaoTest.java
@@ -0,0 +1,65 @@
+package lcsb.mapviewer.persist.dao.plugin;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.model.plugin.PluginDataEntry;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class PluginDataEntryDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ PluginDataEntryDao pluginDataEntryDao;
+
+ @Autowired
+ PluginDao pluginDao;
+
+ @Test
+ public void testGetByKeyForGlobalParam() {
+ Plugin plugin =new Plugin();
+ plugin.setHash("x");
+ plugin.setName("Plugin name");
+ plugin.setVersion("0.0.1");
+ pluginDao.add(plugin);
+
+ PluginDataEntry entry = new PluginDataEntry();
+ entry.setPlugin(plugin);
+ entry.setKey("x");
+ entry.setValue("y");
+
+ pluginDataEntryDao.add(entry);
+
+ PluginDataEntry entry2 = pluginDataEntryDao.getByKey(entry.getPlugin(), entry.getKey(), entry.getUser());
+ assertEquals(entry, entry2);
+ assertNull(pluginDataEntryDao.getByKey(entry.getPlugin(), "blabla", entry.getUser()));
+ }
+
+ @Test
+ public void testGetByKeyForUserParam() {
+ createUser();
+ Plugin plugin =new Plugin();
+ plugin.setHash("x");
+ plugin.setName("Plugin name");
+ plugin.setVersion("0.0.1");
+ pluginDao.add(plugin);
+
+ PluginDataEntry entry = new PluginDataEntry();
+ entry.setPlugin(plugin);
+ entry.setUser(user);
+ entry.setKey("x");
+ entry.setValue("y");
+
+ pluginDataEntryDao.add(entry);
+
+ PluginDataEntry entry2 = pluginDataEntryDao.getByKey(entry.getPlugin(), entry.getKey(), user);
+ assertEquals(entry, entry2);
+
+ assertNull(pluginDataEntryDao.getByKey(entry.getPlugin(), "blabla", user));
+ assertNull(pluginDataEntryDao.getByKey(entry.getPlugin(), entry.getKey(), null));
+ }
+
+}
--
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