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Commit 006ee099 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

major refactoring

parent e436e271
Pipeline #4 failed with stages
......@@ -18,11 +18,7 @@
<attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-10">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
......
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=9
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=10
org.eclipse.jdt.core.compiler.compliance=9
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
......@@ -11,4 +11,4 @@ org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.release=enabled
org.eclipse.jdt.core.compiler.source=10
org.eclipse.jdt.core.compiler.source=9
......@@ -2,8 +2,8 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>Biosynth</groupId>
<artifactId>biosynth</artifactId>
<groupId>transyt</groupId>
<artifactId>transyt-service</artifactId>
<version>0.0.1-SNAPSHOT</version>
<description>
......@@ -51,8 +51,8 @@
<dependencies>
<dependency>
<groupId>utilities</groupId>
<artifactId>triage-utilities</artifactId>
<groupId>transyt</groupId>
<artifactId>transyt-utilities</artifactId>
<version>0.0.1-SNAPSHOT</version>
<exclusions>
<exclusion>
......@@ -81,8 +81,8 @@
</dependency>
<dependency>
<groupId>tcdb</groupId>
<artifactId>triage</artifactId>
<groupId>transyt</groupId>
<artifactId>transyt-scraper</artifactId>
<version>0.0.1-SNAPSHOT</version>
<exclusions>
<exclusion>
......@@ -279,4 +279,5 @@
</dependency>
</dependencies>
<name>transyt-service</name>
</project>
......@@ -267,7 +267,7 @@ public class ProvideTransportReactionsToGenes {
}
else {
//IMPLEMENTAR METODO QUE PEDE PESSOA PARA INSERIR MANUALMENTE
//IMPLEMENTAR METODO QUE PEDE PESSOA PARA INSERIR MANUALMENTE
logger.error("Taxonomy ID not recognized by UniProt! Please insert a valid TaxonomyID!");
logger.info("SHUTING DOWN TRIAGE...");
System.exit(0);
......
......@@ -20,7 +20,6 @@ import org.biojava.nbio.ontology.Synonym;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Transaction;
import compartments.CompartmentsProvider;
import containers.BiosynthMetabolites;
import dictionary.Synonyms;
import enumerators.CompartmentsSource;
......@@ -383,22 +382,6 @@ class Test {
FilesUtils.saveMapInFile3("C:\\Users\\Davide\\Desktop\\KEGG_To_ModelSEED.txt", res);
}
// @org.junit.jupiter.api.Test
void text2() {
File file = new File("C:\\Users\\Davide\\OneDrive - Universidade do Minho\\UMinho\\Tese\\KBase\\Genomes\\Escherichia coli str. K-12 substr. MG1655 - NCBI\\Compartments.txt");
CompartmentsProvider provider = new CompartmentsProvider(file, CompartmentsSource.PSortb);
Map<String, CompartmentResult> results = provider.getCompartments();
for(String gene : results.keySet()) {
System.out.println(results.get(gene).getCompartments());
}
}
// @org.junit.jupiter.api.Test
void readMap() {
......
Manifest-Version: 1.0
Built-By: davidelagoa
Build-Jdk: 11.0.1
Created-By: Maven Integration for Eclipse
#Generated by Maven Integration for Eclipse
#Thu Nov 08 17:50:50 WET 2018
m2e.projectLocation=/Users/davidelagoa/TranSyT/transyt-service
m2e.projectName=transyt-service
groupId=Biosynth
artifactId=biosynth
version=0.0.1-SNAPSHOT
<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>Biosynth</groupId>
<artifactId>biosynth</artifactId>
<version>0.0.1-SNAPSHOT</version>
<description>
</description>
<repositories>
<repository>
<id>nexus</id>
<name>Nexus BioSystems Server</name>
<!-- <url>http://192.168.1.99/nexus/content/groups/public/</url> -->
<url>http://193.137.11.210/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>
<build>
<plugins>
<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version> <configuration> <source>9</source> <target>9</target>
</configuration> </plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<release>10</release>
</configuration>
<dependencies>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm</artifactId>
<version>6.2</version> <!-- Use newer version of ASM -->
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>utilities</groupId>
<artifactId>triage-utilities</artifactId>
<version>0.0.1-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<exclusion>
<groupId>
uk.ac.ebi.chebi.webapps.chebiWS.client
</groupId>
<artifactId>chebiWS-client</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.axis</groupId>
<artifactId>axis-saaj</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>tcdb</groupId>
<artifactId>triage</artifactId>
<version>0.0.1-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>uk.ac.ebi.uniprot</groupId>
<artifactId>japi</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</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-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-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>
<artifactId>neo4j</artifactId>
<version>3.4.1</version>
</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>
<artifactId>poi-ooxml</artifactId>
<version>3.17</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>6.0.6</version>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.11.2</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>5.0.0</version>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.25</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-classic -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/uk.ac.ebi.chebi.webapps.chebiWS.client/chebiWS-client -->
<dependency>
<groupId>uk.ac.ebi.chebi.webapps.chebiWS.client</groupId>
<artifactId>chebiWS-client</artifactId>
<version>2.4</version>
</dependency>
</dependencies>
</project>
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