Merge pull request #60 from nicolasmoreau/master

Dev to prod commit

notes

@@ -0,0 +1,14 @@
+03/04/2017:
+Problème avec le clic sur les liens vers les fichiers xsams pour declencher l'association des requêtes dans le querystore.
+Le javascript rafraichissant la page ne fonctionnait pas sous firefox. Les liens ont été remplacés par des boutons.
+
+
+13/02/2017:
+SEAM retourne des erreurs d'exécution lorsqu'il est lancé avec java8 :
+Could not instantiate Seam component: registration
+
+Le fichier ~/.mavenrc a été édité pour que JAVA_HOME pointe sur java7
+JAVA_HOME est défini dans deploy.sh pour que jboss utilise java7
+
+Utilise JSF en version 1.x
+

portal.ejb/pom.xml

@@ -111,6 +111,17 @@
             <artifactId>slf4j-log4j12</artifactId>
             <version>1.4.2</version>
         </dependency> 
+		<dependency>
+		    <groupId>org.apache.httpcomponents</groupId>
+		    <artifactId>httpclient</artifactId>
+		    <version>4.5.3</version>
+		</dependency>
+		<!-- https://mvnrepository.com/artifact/org.json/json -->
+		<dependency>
+		    <groupId>org.json</groupId>
+		    <artifactId>json</artifactId>
+		    <version>20160810</version>
+		</dependency>
 	</dependencies>	
 	<build>
 		<plugins>

portal.ejb/src/main/java/org/vamdc/portal/Settings.java

@@ -15,10 +15,13 @@ public enum Settings {
 	HTTP_DATA_TIMEOUT("HTTPDataTimeout","30000"),
 	REGISTRY_URL("registryURL","http://registry.vamdc.eu/registry-12.07/services/RegistryQueryv1_0"),
 	REGISTRY_UPDATE_INTERVAL("registryUpdateInterval","300000"),
+	QUERYSTORE_ASSOCIATION_URL("querystoreAssociationUrl","http://querystore.vamdc.eu/PortalAssociationService?"),
 	AVAILABILITY_MONITOR_INTERVAL("availabilityMonitorInterval","300000"),
 	REGISTRY_RETRY_INTERVAL("registryRetryInterval","10000"),
 	HTTP_HEAD_TIMEOUT("HTTPHeadTimeout","60000"),
 	PDL_SERVER_URL("pdlServerURL", "http://vm-euhoutestc62.obspm.fr/vamdc/OnlineCode?"),
+	PORTAL_USER_AGENT("userAgent", "VAMDC Portal Dev"),
+	PORTAL_VERSION("version", "2017_02")
 	;
 
 

portal.ejb/src/main/java/org/vamdc/portal/entity/EntityFacade.java

@@ -17,6 +17,8 @@
  *
  */
 public class EntityFacade {
+
+	private EntityFacade(){}
 
 	public static Collection<String> suggestMoleculeStoichiometricFormula(
 			EntityManager entityManager, String value) {
@@ -34,15 +36,6 @@ public static Collection<String> suggestMoleculeOrdinaryFormula(
 
 		return EntityQuery.suggestMoleculeStructForm(entityManager, value);
 	}
-
-
-	/*public static Collection<String> suggestChemicalName(
-			EntityManager entityManager, String value) {
-		if (!checkValue(value) || entityManager==null)
-			return Collections.emptyList();
-
-		return EntityQuery.suggestMoleculeName(entityManager, value.trim());
-	}*/
 
 	public static Collection<String> suggestMoleculeName(
 			EntityManager entityManager, String value) {
@@ -64,14 +57,16 @@ public static List<MoleculeInfo> loadMoleculesFromName(EntityManager em,String v
 
 	public static List<MoleculeInfo> loadMoleculesFromStoichForm(EntityManager em,String value){
 		String query = "SELECT distinct vs FROM VamdcSpecies vs " +
-				"WHERE vs.stoichiometricFormula = :Value";
+				"WHERE vs.stoichiometricFormula = :Value " +
+				"AND vs.speciesType = 2";
 		return loadElements(em,query,value);
 	}
 
 	public static List<MoleculeInfo> loadMoleculesFromOrdForm(EntityManager em, String value) {
 		String query = "SELECT distinct vs FROM VamdcSpecies vs " +
 				"INNER JOIN vs.vamdcSpeciesStructFormulaes vsf "   +
-				"WHERE vsf.formula = :Value";
+				"WHERE vsf.formula = :Value " +
+				"AND vs.speciesType = 2";
 		return loadElements(em,query,value);
 	}
 

portal.ejb/src/main/java/org/vamdc/portal/entity/EntityQuery.java

@@ -9,6 +9,8 @@
  *
  */
 class EntityQuery{
+
+	private EntityQuery(){}
 
 	@SuppressWarnings("unchecked")
 	static Collection<String> suggestSpeciesName(EntityManager em,
@@ -83,15 +85,4 @@ private static Collection<String> suggestRestrictedStructForm(EntityManager em,
 				.getResultList();
 	}
 
-	//@SuppressWarnings("unchecked")
-	/*static Collection<String> suggestStructForm(EntityManager em, String formula){
-		return em.createQuery("SELECT distinct vssf.formula from VamdcSpeciesStructFormulae vssf JOIN vssf.vamdcSpecies vs" +
-				"WHERE vssf.formula LIKE :formula and vssf.vamdcMarkupTypes.id=1 order by length(vssf.formula), vssf.searchPriority")
-				.setParameter("formula", "%"+formula+"%")
-				.setMaxResults(20)
-				.getResultList();
-	}*/
-
-
-
 }

portal.ejb/src/main/java/org/vamdc/portal/entity/query/HttpHeadResponse.java

@@ -42,6 +42,7 @@ public String getDescription(){
 	private Response status;
 	private Date lastmodified;
 	private Query query;
+	private String requestToken;
 
 	private Integer recordID;
 
@@ -76,6 +77,7 @@ private void retrieveHeaders(HttpURLConnection connection) {
 		processes = collisions+radiative+nonRadiative;
 		truncated = getTruncatedValue(connection,"VAMDC-TRUNCATED");
 		lastmodified = extractLastModified(connection);
+		requestToken = connection.getHeaderField("VAMDC-REQUEST-TOKEN");		
 	}
 
 	private Date extractLastModified(HttpURLConnection connection) {
@@ -152,6 +154,8 @@ public boolean isLastModSet(){
 	public int getRadiative() { return radiative; }
 	public int getNonRadiative() { return nonRadiative; }
 	public int getCollisions() { return collisions; }
+	public String getRequestToken(){ return requestToken; }
+
 	@Transient
 	public int getTruncated() { return truncated; }
 
@@ -161,7 +165,7 @@ public boolean isLastModSet(){
 	public void setRadiative(int radiative) { this.radiative = radiative; }
 	public void setNonRadiative(int nonRadiative) { this.nonRadiative = nonRadiative; }
 	public void setCollisions(int collisions) { this.collisions = collisions; }
-
+	public void setRequestToken(String token){ this.requestToken = token; }
 
 	@Lob 
 	public String getFullQueryURL() { return fullQueryURL; }

portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcInchikeyExceptions.java

@@ -6,18 +6,22 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+
 import static javax.persistence.GenerationType.IDENTITY;
+
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
+
 import org.hibernate.validator.NotNull;
+import org.vamdc.portal.Settings;
 
 /**
  * VamdcInchikeyExceptions generated by hbm2java
  */
 @Entity
-@Table(name = "vamdc_inchikey_exceptions", catalog = "vamdc_species")
+@Table(name = "vamdc_inchikey_exceptions", catalog = "vamdc_species_dev")
 public class VamdcInchikeyExceptions implements java.io.Serializable {
 
 	private Integer id;

portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMarkupTypes.java

@@ -17,7 +17,7 @@
  * VamdcMarkupTypes generated by hbm2java
  */
 @Entity
-@Table(name = "vamdc_markup_types", catalog = "vamdc_species")
+@Table(name = "vamdc_markup_types", catalog = "vamdc_species_dev")
 public class VamdcMarkupTypes implements java.io.Serializable {
 
 	private int id;

portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabaseIdentifiers.java

@@ -19,7 +19,7 @@
  * VamdcMemberDatabaseIdentifiers generated by hbm2java
  */
 @Entity
-@Table(name = "vamdc_member_database_identifiers", catalog = "vamdc_species", uniqueConstraints = @UniqueConstraint(columnNames = {
+@Table(name = "vamdc_node_species", catalog = "vamdc_species_dev", uniqueConstraints = @UniqueConstraint(columnNames = {
 		"species_id", "database_species_id", "member_database_id" }))
 public class VamdcMemberDatabaseIdentifiers implements java.io.Serializable {
 

portal.ejb/src/main/java/org/vamdc/portal/entity/species/VamdcMemberDatabases.java

@@ -19,7 +19,7 @@
  * VamdcMemberDatabases generated by hbm2java
  */
 @Entity
-@Table(name = "vamdc_member_databases", catalog = "vamdc_species")
+@Table(name = "vamdc_nodes", catalog = "vamdc_species_dev")
 public class VamdcMemberDatabases implements java.io.Serializable {
 
 	private Integer id;