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Commit 9d81defd authored by Davide Lagoa's avatar Davide Lagoa
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neo4j upgrade to version 4

parent 723b01be
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.classpath
View file @ 9d81defd
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-10">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
......
.gitignore
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/target/
logs/
*.log
\ No newline at end of file
.settings/org.eclipse.jdt.core.prefs
View file @ 9d81defd
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=10
org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=10
org.eclipse.jdt.core.compiler.compliance=11
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
......@@ -11,6 +11,6 @@ org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
org.eclipse.jdt.core.compiler.release=enabled
org.eclipse.jdt.core.compiler.source=10
org.eclipse.jdt.core.compiler.source=11
dependency-reduced-pom.xml
View file @ 9d81defd
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>service</artifactId>
<name>service</name>
<version>0.0.5-SNAPSHOT</version>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<dependencies>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm</artifactId>
<version>6.2</version>
</dependency>
</dependencies>
<configuration>
<release>10</release>
</configuration>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
</transformer>
<transformer />
</transformers>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>nexus</id>
<name>Nexus BioSystems Server</name>
<url>https://www.bio.di.uminho.pt/nexus/content/groups/public/</url>
</repository>
<repository>
<id>ebi-repo</id>
<name>ebi-repo</name>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>service</artifactId>
<name>service</name>
<version>0.0.7-SNAPSHOT</version>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<dependencies>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm</artifactId>
<version>6.2</version>
</dependency>
</dependencies>
<configuration>
<release>11</release>
</configuration>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
</transformer>
<transformer />
</transformers>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>nexus</id>
<name>Nexus BioSystems Server</name>
<url>https://www.bio.di.uminho.pt/nexus/content/groups/public/</url>
</repository>
<repository>
<id>ebi-repo</id>
<name>ebi-repo</name>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.4.2.Final</version>
<type>pom</type>
<scope>compile</scope>
</dependency>
</dependencies>
<properties>
<hibernate.version>5.4.2.Final</hibernate.version>
</properties>
</project>
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pom.xml
View file @ 9d81defd
......@@ -4,10 +4,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>service</artifactId>
<version>0.0.5-SNAPSHOT</version>
<description>
</description>
<version>0.0.7-SNAPSHOT</version>
<properties>
<hibernate.version>5.4.2.Final</hibernate.version>
</properties>
<repositories>
......@@ -39,7 +42,7 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<release>10</release>
<release>11</release>
</configuration>
<dependencies>
<dependency>
......@@ -102,13 +105,13 @@
<dependency>
<groupId>org.neo4j.driver</groupId>
<artifactId>neo4j-java-driver</artifactId>
<version>1.7.2</version>
<version>4.0.0</version>
</dependency>
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>utilities</artifactId>
<version>0.0.5-SNAPSHOT</version>
<version>0.0.7-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
......@@ -138,7 +141,7 @@
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>scraper</artifactId>
<version>0.0.5-SNAPSHOT</version>
<version>0.0.7-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>uk.ac.ebi.uniprot</groupId>
......@@ -155,109 +158,38 @@
</dependency>
<!-- <dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-chebi</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>
pt.uminho.sysbio.biosynthframework
</groupId>
<artifactId>biosynth-biodb</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
</exclusions>
</dependency> -->
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-reactome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- <dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-chemanalysis</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency> -->
<dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-chebi</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId> pt.uminho.sysbio.biosynthframework </groupId>
<artifactId>biosynth-biodb</artifactId> </exclusion> <exclusion> <groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId> </exclusion> <exclusion> <groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId> </exclusion> </exclusions> </dependency>
<!-- <dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-core</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency> -->
<dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-reactome</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId>ch.qos.logback</groupId> <artifactId>logback-classic</artifactId>
</exclusion> </exclusions> </dependency> <dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-chemanalysis</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId>ch.qos.logback</groupId> <artifactId>logback-classic</artifactId>
</exclusion> <exclusion> <groupId>log4j</groupId> <artifactId>log4j</artifactId>
</exclusion> </exclusions> </dependency>
<!-- <dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-genome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
</exclusion>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency> -->
<dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-core</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId>ch.qos.logback</groupId> <artifactId>logback-classic</artifactId>
</exclusion> </exclusions> </dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-integration</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.neo4j</groupId>
<artifactId>neo4j</artifactId>
</exclusion>
<exclusion>
<groupId>
pt.uminho.sysbio.biosynthframework
</groupId>
<artifactId>biosynth-biodb</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-genome</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId>org.biojava</groupId> <artifactId>biojava-alignment</artifactId>
</exclusion> <exclusion> <groupId>org.biojava</groupId> <artifactId>biojava-core</artifactId>
</exclusion> <exclusion> <groupId>ch.qos.logback</groupId> <artifactId>logback-classic</artifactId>
</exclusion> </exclusions> </dependency> <dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-integration</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId>org.neo4j</groupId> <artifactId>neo4j</artifactId>
</exclusion> <exclusion> <groupId> pt.uminho.sysbio.biosynthframework </groupId>
<artifactId>biosynth-biodb</artifactId> </exclusion> <exclusion> <groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId> </exclusion> </exclusions> </dependency>
<dependency>
<groupId>org.neo4j</groupId>
......@@ -273,17 +205,10 @@
</dependency>
<!-- <dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-visualization</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency> -->
<dependency> <groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-visualization</artifactId> <version>0.9.0-SNAPSHOT</version>
<exclusions> <exclusion> <groupId>ch.qos.logback</groupId> <artifactId>logback-classic</artifactId>
</exclusion> </exclusions> </dependency>
<dependency>
<groupId>org.apache.poi</groupId>
......@@ -291,11 +216,8 @@
<version>3.17</version>
</dependency>
<!-- <dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>6.0.6</version>
</dependency> -->
<!-- <dependency> <groupId>mysql</groupId> <artifactId>mysql-connector-java</artifactId>
<version>6.0.6</version> </dependency> -->
<dependency>
<groupId>org.jsoup</groupId>
......@@ -334,6 +256,30 @@
<version>1.2.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
<type>pom</type>
</dependency>
<!-- http://mvnrepository.com/artifact/org.hibernate/hibernate-entitymanager%20 -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>${hibernate.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.springframework/spring-core -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>5.2.2.RELEASE</version>
</dependency>
</dependencies>
<name>service</name>
</project>
src/main/java/pt/uminho/ceb/biosystems/transyt/service/biosynth/BIGG1.java
View file @ 9d81defd
......@@ -70,7 +70,7 @@ public class BIGG1 {
etlPipeline.exclude.add("D05511");
etlPipeline.setSkipLoad(false);
etlPipeline.setGraphDatabaseService(graphDatabaseService);
etlPipeline.setSessionFactory(null);
// etlPipeline.setSessionFactory(null);
etlPipeline.setEtlDataCleasingSubsystem(new CentralMetaboliteEtlDataCleansing(new CdkWrapper()));
etlPipeline.setExtractSubsystem(new DefaultMetaboliteEtlExtract<M>(src));
etlPipeline.setLoadSubsystem(new HeterogenousMetaboliteEtlLoad<GraphMetaboliteEntity>(dst));
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/blast/BlastAlignmentTransyt.java
View file @ 9d81defd
......@@ -157,6 +157,9 @@ public class BlastAlignmentTransyt extends Observable implements ModelAlignments
// System.out.println(outputFile.getAbsolutePath());
if(forceBlast) {
System.out.println("blastp -query " + this.queryFasta + " -subject "
+ this.subjectFasta + " -out " + outputFile.getAbsolutePath() + " -outfmt 5");
Process p = Runtime.getRuntime().exec("blastp -query " + this.queryFasta + " -subject "
+ this.subjectFasta + " -out " + outputFile.getAbsolutePath() + " -outfmt 5");
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/internalDB/WriteByMetabolitesID.java
View file @ 9d81defd
......@@ -50,8 +50,8 @@ public class WriteByMetabolitesID {
Map<String, BiosynthMetaboliteProperties> data = getBiosynthDBData(service);
// Map<String, BiosynthMetaboliteProperties> data = null;
@SuppressWarnings("resource")
Scanner reader = new Scanner(System.in);
// @SuppressWarnings("resource")
// Scanner reader = new Scanner(System.in);
// System.out.println("Writing Excel...");
// WriteExcel.writeNeo4jKeggInfo(data);
......@@ -75,11 +75,11 @@ public class WriteByMetabolitesID {
//
// Map<String, String[]> forChildsSearch = metabolitesIdentification.getforChildsSearch();
int n = 1;
// int n = 1;
while (n != 99) {
n = 99;
// while (n != 99) {
//
// n = 99;
test(namesAndIDsContainer, data, service, null, reactionsData, null, properties); //uncomment
//
......@@ -87,15 +87,15 @@ public class WriteByMetabolitesID {
//
// System.out.println("Enter a random number to repeat (100 to repeat data retrieval) or 99 to finish: ");
try {
n = reader.nextInt();
} catch (Exception e) {
e.printStackTrace();
n = reader.nextInt();
}
}
// try {
// n = reader.nextInt();
// } catch (Exception e) {
// e.printStackTrace();
//
// n = reader.nextInt();
// }
//
// }
dataTx.failure();
dataTx.close();
service.shutdown();
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/neo4jRest/RestNeo4jGraphDatabase.java
View file @ 9d81defd
......@@ -9,14 +9,22 @@ import java.util.Set;
import org.codehaus.jackson.JsonParseException;
import org.codehaus.jackson.map.JsonMappingException;
import org.neo4j.driver.v1.AccessMode;
import org.neo4j.driver.v1.AuthTokens;
import org.neo4j.driver.v1.Driver;
import org.neo4j.driver.v1.GraphDatabase;
import org.neo4j.driver.v1.Record;
import org.neo4j.driver.v1.Session;
import org.neo4j.driver.v1.Statement;
import org.neo4j.driver.v1.StatementResult;
import org.neo4j.driver.AccessMode;
import org.neo4j.driver.AuthTokens;
import org.neo4j.driver.Driver;
import org.neo4j.driver.GraphDatabase;
import org.neo4j.driver.Record;
import org.neo4j.driver.Result;
import org.neo4j.driver.Session;
import org.neo4j.driver.SessionConfig;
//import org.neo4j.driver.v1.AccessMode;
//import org.neo4j.driver.v1.AuthTokens;
//import org.neo4j.driver.v1.Driver;
//import org.neo4j.driver.v1.GraphDatabase;
//import org.neo4j.driver.v1.Record;
//import org.neo4j.driver.v1.Session;
//import org.neo4j.driver.v1.Statement;
//import org.neo4j.driver.v1.StatementResult;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
......@@ -69,6 +77,8 @@ public class RestNeo4jGraphDatabase implements AutoCloseable{
temporaryCompoundsNames = new HashMap<>();
temporaryCompoundsFormulas = new HashMap<>();
// driver = GraphDatabase.driver(uri);
driver = GraphDatabase.driver( uri, AuthTokens.basic(username, password ) );
}
......@@ -79,12 +89,34 @@ public class RestNeo4jGraphDatabase implements AutoCloseable{
}
/**
* This method is used to change neo4j's database password. This step might be needed when using a default password.
*
* @param currentPassword
* @param newPassword
*/
public void changePassword(String currentPassword, String newPassword) {
Session session = driver.session();
this.password = newPassword;
session.run("ALTER CURRENT USER SET PASSWORD FROM + '" + currentPassword + "' TO '" + newPassword + "'");
logger.info("Neo4j password changed!");
restartDriver();
session.close();
}
/**
* Create constraints to avoid duplicated data.
*/
public void createContraints() {
Session session = driver.session(AccessMode.WRITE);
Session session = driver.session();
session.run("CREATE CONSTRAINT ON (a:" + TransytNodeLabel.Uniprot_Accession + ") assert a." + TransytGeneralProperties.Accession_Number + " IS UNIQUE");
session.run("CREATE CONSTRAINT ON (a:" + TransytNodeLabel.TC_Number + ") assert a." + TransytGeneralProperties.TC_Number + " IS UNIQUE");
......@@ -110,7 +142,7 @@ public class RestNeo4jGraphDatabase implements AutoCloseable{
*/
public void createIndexes(TransytNodeLabel label, TransytGeneralProperties property) {
Session session = driver.session(AccessMode.WRITE);
Session session = driver.session();
session.run("CREATE INDEX ON :" + label + "(" + property + ")");
......@@ -145,15 +177,13 @@ public class RestNeo4jGraphDatabase implements AutoCloseable{
*/
public TransytNode createNode(TransytNodeLabel label, Map<String, String> properties) {
Session session = driver.session(AccessMode.WRITE);
Session session = driver.session();
String auxString = buildPropertiesQuery(properties);