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Commit 17ffbaaf authored by jcapels's avatar jcapels
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[FIX] models reactions mapping

parent 75845165
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.classpath
View file @ 17ffbaaf
<?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-11">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" output="target/classes" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
......@@ -23,6 +18,11 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<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>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
......
.gitignore
View file @ 17ffbaaf
lib/
/target/
logs/
*.log
\ No newline at end of file
*.log
dependency-reduced-pom.xml
View file @ 17ffbaaf
......@@ -43,6 +43,14 @@
</excludes>
</filter>
</filters>
<archive>
<manifest>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<transformers>
<transformer>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
......@@ -51,13 +59,35 @@
</transformers>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</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>
<url>https://nexus.bio.di.uminho.pt/content/groups/public/</url>
</repository>
<repository>
<id>ebi-repo</id>
......@@ -72,6 +102,306 @@
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
<exclusion>
<artifactId>spring-context</artifactId>
<groupId>org.springframework</groupId>
</exclusion>
<exclusion>
<artifactId>spring-tx</artifactId>
<groupId>org.springframework</groupId>
</exclusion>
<exclusion>
<artifactId>okhttp</artifactId>
<groupId>com.squareup.okhttp</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-chebi</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>biosynth-biodb</artifactId>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
</exclusion>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>logback-core</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-reactome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-chemanalysis</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
</exclusion>
<exclusion>
<artifactId>jni-inchi</artifactId>
<groupId>net.sf.jni-inchi</groupId>
</exclusion>
<exclusion>
<artifactId>opsin-core</artifactId>
<groupId>uk.ac.cam.ch.opsin</groupId>
</exclusion>
<exclusion>
<artifactId>opsin-inchi</artifactId>
<groupId>uk.ac.cam.ch.opsin</groupId>
</exclusion>
<exclusion>
<artifactId>openbabel</artifactId>
<groupId>openbabel</groupId>
</exclusion>
<exclusion>
<artifactId>cdk-bundle</artifactId>
<groupId>org.openscience.cdk</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-core</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-genome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>biojava-alignment</artifactId>
<groupId>org.biojava</groupId>
</exclusion>
<exclusion>
<artifactId>biojava-core</artifactId>
<groupId>org.biojava</groupId>
</exclusion>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-integration</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>neo4j</artifactId>
<groupId>org.neo4j</groupId>
</exclusion>
<exclusion>
<artifactId>biosynth-biodb</artifactId>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
</exclusion>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>jung-algorithms</artifactId>
<groupId>net.sf.jung</groupId>
</exclusion>
<exclusion>
<artifactId>jung-graph-impl</artifactId>
<groupId>net.sf.jung</groupId>
</exclusion>
<exclusion>
<artifactId>ahocorasick</artifactId>
<groupId>org.ahocorasick</groupId>
</exclusion>
<exclusion>
<artifactId>jgrapht-core</artifactId>
<groupId>org.jgrapht</groupId>
</exclusion>
<exclusion>
<artifactId>jgrapht-ext</artifactId>
<groupId>org.jgrapht</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-visualization</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>logback-classic</artifactId>
<groupId>ch.qos.logback</groupId>
</exclusion>
<exclusion>
<artifactId>joda-time</artifactId>
<groupId>joda-time</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-datatype-joda</artifactId>
<groupId>com.fasterxml.jackson.datatype</groupId>
</exclusion>
<exclusion>
<artifactId>jackson-dataformat-xml</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
</exclusion>
<exclusion>
<artifactId>usertype.core</artifactId>
<groupId>org.jadira.usertype</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
......
pom.xml
View file @ 17ffbaaf
......@@ -17,10 +17,14 @@
<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> -->
<url>https://www.bio.di.uminho.pt/nexus/content/groups/public/</url>
<url>https://nexus.bio.di.uminho.pt/content/groups/public/</url>
</repository>
<!-- <repository>
<id>local</id>
<name>local</name>
<url>/home/joao/Desktop/TRANSYT/biosynth_dependencies/</url>
</repository> -->
<repository>
......@@ -75,15 +79,14 @@
</excludes>
</filter>
</filters>
<!-- <archive> uncomment if not working -->
<!-- <manifest> -->
<!-- <addClasspath>true</addClasspath> -->
<!-- <mainClass>pt.uminho.ceb.biosystems.transyt.service.internalDB.WriteByMetabolitesID</mainClass> -->
<!-- </manifest> -->
<!-- </archive> -->
<!-- <descriptorRefs> -->
<!-- <descriptorRef>jar-with-dependencies</descriptorRef> -->
<!-- </descriptorRefs> -->
<archive>
<manifest>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
......@@ -93,6 +96,29 @@
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
</transformers>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>pt.uminho.ceb.biosystems.transyt.service.transyt.TransytMain</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
......@@ -108,35 +134,14 @@
<version>4.0.0</version>
</dependency>
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>validation</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>pt.uminho.ceb.biosystems.transyt</groupId> <artifactId>validation</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>pt.uminho.ceb.biosystems.transyt</groupId>
......@@ -187,11 +192,18 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId> pt.uminho.sysbio.biosynthframework </groupId>
<artifactId>biosynth-biodb</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-chebi</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId> pt.uminho.sysbio.biosynthframework </groupId>
......@@ -207,11 +219,11 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-reactome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
......@@ -223,6 +235,7 @@
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-chemanalysis</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
......@@ -234,11 +247,11 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-core</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
......@@ -246,11 +259,11 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-genome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>org.biojava</groupId>
......@@ -270,13 +283,15 @@
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-integration</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>org.neo4j</groupId>
<artifactId>neo4j</artifactId>
</exclusion>
<exclusion>
<groupId> pt.uminho.sysbio.biosynthframework </groupId>
<groupId> pt.uminho.sysbio.biosynthframework
</groupId>
<artifactId>biosynth-biodb</artifactId>
</exclusion>
<exclusion>
......@@ -285,6 +300,54 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-visualization</artifactId>
<version>0.9.0-SNAPSHOT</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</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-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>
......@@ -300,18 +363,10 @@
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-visualization</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>