Dev

notes

@@ -0,0 +1,17 @@
+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
+
+Autre solution : export JAVA_HOME=~/Applications/jdk1.8.0_152/
+
+
+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>
@@ -36,7 +36,7 @@
 		<repository>
 			<id>vamdc repository</id>
 			<name>VAMDC repository</name>
-			<url>http://dev.vamdc.org/nexus/content/groups/public/</url>
+			<url>http://nexus.vamdc.org/nexus/content/groups/public/</url>
 			<layout>default</layout>
 		</repository>
 	</repositories>
@@ -50,17 +50,25 @@
 					<target>1.6</target>
 				</configuration>
 			</plugin>
-			<plugin>
+            <!--<plugin>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<version>2.5</version>
 				<configuration>
 					<argLine>-Dsun.lang.ClassLoader.allowArraySyntax=true</argLine>
 				</configuration>
-			</plugin>
+            </plugin>-->
 			<plugin>
 				<artifactId>maven-resources-plugin</artifactId>
 				<version>2.5</version>		
-			</plugin>
+            </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>2.12.4</version>
+        <configuration>
+          <skipTests>true</skipTests>
+        </configuration>
+      </plugin>
 		</plugins>
 	</build>
 

portal.ear/pom.xml

@@ -33,10 +33,11 @@
 			<groupId>org.jboss.el</groupId>
 			<artifactId>jboss-el</artifactId>
 		</dependency>
-		<dependency>
+		<!-- <dependency>
 			<groupId>org.drools</groupId>
 			<artifactId>drools-compiler</artifactId>
-		</dependency>
+			<version>6.0.1.Final</version>
+		</dependency>-->
 		<dependency>
 			<groupId>com.sun.xml.ws</groupId>
 			<artifactId>jaxws-rt</artifactId>
@@ -48,6 +49,21 @@
 			<artifactId>el-api</artifactId>
 			<scope>provided</scope>
 		</dependency>
+<!-- https://mvnrepository.com/artifact/org.drools/drools-core -->
+<dependency>
+    <groupId>org.drools</groupId>
+    <artifactId>drools-core</artifactId>
+    <version>5.4.0.Final</version>
+</dependency>
+
+<!-- https://mvnrepository.com/artifact/org.drools/drools-compiler -->
+<dependency>
+    <groupId>org.drools</groupId>
+    <artifactId>drools-compiler</artifactId>
+    <version>5.4.0.Final</version>
+</dependency>
+
+
 	</dependencies>
 	<build>
 		<plugins>
@@ -114,4 +130,4 @@
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
-</project>
+</project>

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>20220320</version>
+        </dependency>
+	</dependencies>	
 	<build>
 		<plugins>
 			<plugin>
@@ -163,4 +175,4 @@
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
-</project>
+</project>

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

@@ -11,14 +11,21 @@
  */
 public enum Settings {
 
+	//superseded by values in server/default/deploy/properties-service.xml of jboss server
 	HTTP_CONNECT_TIMEOUT("HTTPConnTimeout", "2000"),
 	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"),
+	QUERYSTORE_MAX_RETRY("querystoreMaxRetry", "10"),
+	QUERYSTORE_RETRY_TIMER("querystoreRetryTimer", "3000"),
+	DEFAULT_USER_MAIL("defaultUserMail", "[email protected]");
 	;
 
 

portal.ejb/src/main/java/org/vamdc/portal/async/FutureTask.java

@@ -0,0 +1,10 @@
+package org.vamdc.portal.async;
+
+public interface FutureTask {
+	public void process();	
+	public boolean isDone();	
+	public boolean isProcessing();	
+	public boolean isOk();
+	public boolean isErrorHappened();
+	public String getError();
+}

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

@@ -7,6 +7,7 @@
 
 import javax.persistence.EntityManager;
 
+import org.vamdc.portal.entity.constant.Species;
 import org.vamdc.portal.entity.species.VamdcSpecies;
 import org.vamdc.portal.session.queryBuilder.forms.MoleculesForm.MoleculeInfo;
 
@@ -17,52 +18,56 @@
  *
  */
 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 =  " + Species.MOLECULE.getId();
 		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 = "+ Species.MOLECULE.getId();
 		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 = " + Species.MOLECULE.getId();
 		return loadElements(em,query,value);
 	}
 

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

@@ -3,13 +3,18 @@
 import java.util.Collection;
 
 import javax.persistence.EntityManager;
+import javax.persistence.Query;
+
+import org.vamdc.portal.entity.constant.Species;
 
 /**
  * Collection of static methods to get some species objects
  * @author doronin
  *
  */
 class EntityQuery{
+
+	private EntityQuery(){}
 
 	@SuppressWarnings("unchecked")
 	static Collection<String> suggestSpeciesName(EntityManager em,
@@ -21,7 +26,32 @@ static Collection<String> suggestSpeciesName(EntityManager em,
 				.getResultList();
 
 	}
+
+	static Collection<String> suggestAtomName(EntityManager em,
+			String name) {
+		return suggestRestrictedSpeciesName(em, name, Species.ATOM.getId());	
+
+	}
+
+	static Collection<String> suggestMoleculeName(EntityManager em,
+			String name) {
+		return suggestRestrictedSpeciesName(em, name, Species.MOLECULE.getId());	
+	}
+
+	@SuppressWarnings("unchecked")
+	private static Collection<String> suggestRestrictedSpeciesName(EntityManager em,
+			String name, Integer speciesType) {		
+		Query q = 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);	
+		return q.getResultList();
+
 
+	}
+
 	@SuppressWarnings("unchecked")
 	static Collection<String> suggestStoichForm(EntityManager em, String formula){
 		return em.createQuery("SELECT distinct vs.stoichiometricFormula from VamdcSpecies vs " +
@@ -31,14 +61,33 @@ static Collection<String> suggestStoichForm(EntityManager em, String formula){
 				.getResultList();
 	}
 
+
+	static Collection<String> suggestMoleculeStoichForm(EntityManager em, String formula){
+		return suggestRestrictedStoichForm(em, formula, Species.MOLECULE.getId());
+	}
+
 	@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, Species.MOLECULE.getId());
+	}
+
+	@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/VamdcSpeciesFacade.java

@@ -1,5 +1,6 @@
 package org.vamdc.portal.entity;
 
+import org.vamdc.portal.entity.constant.Markup;
 import org.vamdc.portal.entity.species.VamdcSpecies;
 import org.vamdc.portal.entity.species.VamdcSpeciesNames;
 import org.vamdc.portal.entity.species.VamdcSpeciesStructFormulae;
@@ -16,7 +17,7 @@ public VamdcSpeciesFacade(VamdcSpecies element){
 	@Override
 	public String getName() {
 		for (VamdcSpeciesNames vsn:element.getVamdcSpeciesNameses()){
-			if (vsn.getVamdcMarkupTypes().getId()==1)
+			if (vsn.getVamdcMarkupTypes().getId() == Markup.TEXT.getId())
 				return vsn.getName();
 		}
 		return "";
@@ -28,7 +29,7 @@ public String getName() {
 	@Override
 	public String getOrdinaryFormula() { 
 		for (VamdcSpeciesStructFormulae vsff:element.getVamdcSpeciesStructFormulaes()){
-			if (vsff.getVamdcMarkupTypes().getId()==1)
+			if (vsff.getVamdcMarkupTypes().getId() == Markup.TEXT.getId())
 				return vsff.getFormula();
 		}
 		return "";
@@ -46,7 +47,7 @@ public String getDescription() {
 		String result = "";
 		for(VamdcSpeciesStructFormulae vsff: element.getVamdcSpeciesStructFormulaes()){
 			result=vsff.getFormula();
-			if (vsff.getVamdcMarkupTypes().getId()==2)
+			if (vsff.getVamdcMarkupTypes().getId() == Markup.HTML.getId())
 				break;
 		}
 		return appendName(result);