Dev

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
+

pom.xml

@@ -26,7 +26,7 @@
 		<jaxb.version>2.2.11</jaxb.version>
 		<jaxws.version>2.2.10</jaxws.version>
 		<hibernate-commons-annotations.version>3.3.0.ga</hibernate-commons-annotations.version>
-		<registry-client.version>12.07r2-SNAPSHOT</registry-client.version>
+		<registry-client.version>12.07r3-SNAPSHOT</registry-client.version>
 		<query-parser.version>12.07</query-parser.version>
 		<dictionary.version>12.07r2-SNAPSHOT</dictionary.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

portal.ejb/pom.xml

@@ -55,11 +55,7 @@
 			<groupId>javax.ejb</groupId>
 			<artifactId>ejb-api</artifactId>
 			<scope>provided</scope>
-		</dependency>
-
-
-
-
+		</dependency>		
 		<dependency>
 			<groupId>javax.measure</groupId>
 			<artifactId>jsr-275</artifactId>
@@ -110,7 +106,23 @@
 			<artifactId>servlet-api</artifactId>
 			<scope>provided</scope>
 		</dependency>
-	</dependencies>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <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>
 			<plugin>

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","https://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_06")
 	;
 
 

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

@@ -17,52 +17,56 @@
  *
  */
 public class EntityFacade {
+
+	private EntityFacade(){}
 
-	public static Collection<String> suggestStoichiometricFormula(
+	public static Collection<String> suggestMoleculeStoichiometricFormula(
 			EntityManager entityManager, String value) {
 		if (!checkValue(value) || entityManager==null)
 			return Collections.emptyList();
 
-		return EntityQuery.suggestStoichForm(entityManager, value.trim());
+		return EntityQuery.suggestMoleculeStoichForm(entityManager, value.trim());
 	}
 
 
-	public static Collection<String> suggestOrdinaryFormula(
+	public static Collection<String> suggestMoleculeOrdinaryFormula(
 			EntityManager entityManager, String value) {
 		if (!checkValue(value) || entityManager==null)
 			return Collections.emptyList();
 
-		return EntityQuery.suggestStructForm(entityManager, value);
+		return EntityQuery.suggestMoleculeStructForm(entityManager, value);
 	}
-
-
-	public static Collection<String> suggestChemicalName(
+
+	public static Collection<String> suggestMoleculeName(
 			EntityManager entityManager, String value) {
 		if (!checkValue(value) || entityManager==null)
 			return Collections.emptyList();
 
-		return EntityQuery.suggestSpeciesName(entityManager, value.trim());
+		return EntityQuery.suggestMoleculeName(entityManager, value.trim());
 	}
 
 
 	public static List<MoleculeInfo> loadMoleculesFromName(EntityManager em,String value){
 		String query = "SELECT distinct vs FROM VamdcSpecies vs " +
 				"INNER JOIN vs.vamdcSpeciesNameses vsn " +
-				"WHERE vsn.name = :Value";
+				"WHERE vsn.name = :Value " +
+				"AND vs.speciesType = 2 ";
 		return loadElements(em,query,value);
 	}
 
 
 	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

@@ -1,7 +1,6 @@
 package org.vamdc.portal.entity;
 
 import java.util.Collection;
-
 import javax.persistence.EntityManager;
 
 /**
@@ -10,6 +9,8 @@
  *
  */
 class EntityQuery{
+
+	private EntityQuery(){}
 
 	@SuppressWarnings("unchecked")
 	static Collection<String> suggestSpeciesName(EntityManager em,
@@ -21,7 +22,31 @@ static Collection<String> suggestSpeciesName(EntityManager em,
 				.getResultList();
 
 	}
+
+	static Collection<String> suggestAtomName(EntityManager em,
+			String name) {
+		return suggestRestrictedSpeciesName(em, name, 1);	
+
+	}
+
+	static Collection<String> suggestMoleculeName(EntityManager em,
+			String name) {
+		return suggestRestrictedSpeciesName(em, name, 2);	
+	}
+
+	@SuppressWarnings("unchecked")
+	private static Collection<String> suggestRestrictedSpeciesName(EntityManager em,
+			String name, Integer speciesType) {		
+		return em.createQuery("SELECT DISTINCT vsn.name from VamdcSpeciesNames vsn JOIN vsn.vamdcSpecies vsp " +
+				"WHERE vsn.name LIKE :speciesName and vsn.vamdcMarkupTypes.id=1 and vsp.speciesType=:speciesType "
+				+ " order by length(vsn.name), vsn.searchPriority")
+				.setParameter("speciesName", "%"+name+"%")
+				.setParameter("speciesType", speciesType)
+				.setMaxResults(20)
+				.getResultList();		
 
+	}
+
 	@SuppressWarnings("unchecked")
 	static Collection<String> suggestStoichForm(EntityManager em, String formula){
 		return em.createQuery("SELECT distinct vs.stoichiometricFormula from VamdcSpecies vs " +
@@ -31,14 +56,33 @@ static Collection<String> suggestStoichForm(EntityManager em, String formula){
 				.getResultList();
 	}
 
+
+	static Collection<String> suggestMoleculeStoichForm(EntityManager em, String formula){
+		return suggestRestrictedStoichForm(em, formula, 2);
+	}
+
 	@SuppressWarnings("unchecked")
-	static Collection<String> suggestStructForm(EntityManager em, String formula){
-		return em.createQuery("SELECT distinct vssf.formula from VamdcSpeciesStructFormulae vssf " +
-				"WHERE vssf.formula LIKE :formula and vssf.vamdcMarkupTypes.id=1 order by length(vssf.formula), vssf.searchPriority")
+	private static Collection<String> suggestRestrictedStoichForm(EntityManager em, String formula, Integer speciesType){
+		return em.createQuery("SELECT distinct vs.stoichiometricFormula from VamdcSpecies vs " +
+				"WHERE vs.stoichiometricFormula LIKE :formula AND vs.speciesType=:speciesType  order by length(vs.stoichiometricFormula)")
 				.setParameter("formula", "%"+formula+"%")
+				.setParameter("speciesType", speciesType)
 				.setMaxResults(20)
 				.getResultList();
 	}
 
+	static Collection<String> suggestMoleculeStructForm(EntityManager em, String formula){
+		return suggestRestrictedStructForm(em, formula, 2);
+	}
+
+	@SuppressWarnings("unchecked")
+	private static Collection<String> suggestRestrictedStructForm(EntityManager em, String formula, Integer speciesType){
+		return em.createQuery("SELECT distinct vssf.formula from VamdcSpeciesStructFormulae vssf JOIN vssf.vamdcSpecies vs " +
+				"WHERE vssf.formula LIKE :formula and vssf.vamdcMarkupTypes.id=1 and vs.speciesType=:speciesType order by length(vssf.formula), vssf.searchPriority")
+				.setParameter("formula", "%"+formula+"%")
+				.setParameter("speciesType", speciesType)
+				.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;