Commit 00e75b98 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch '1009-add-support-for-colors-in-sbgn-parser' into 'master'

Resolve "add support for colors in sbgn parser"

Closes #1009

See merge request !1012
parents 572e14c0 a9706c50
minerva (15.0.0~alpha.1) stable; urgency=medium
* Improvement: support for rendering colors in SBGNML added (#1009)
* Small improvement: sort order of tables in admin panel is preserved among
sessions (#836)
* Small improvement: simple molecules in sbgn compliant view are drawn as
......
<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>
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>1.0</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
<description>Module used for preparing annotations for model and connect to external resources.</description>
<repositories>
<!-- Main repository of ebi -->
<repository>
<id>central</id>
<url>http://repo.maven.apache.org/maven2/</url>
</repository>
<!-- Repository used for chebi -->
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<dependencies>
<!-- dependency from the MapViewer model -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>1.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>1.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
to parsing functions for rdf) -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>1.0</version>
</dependency>
<!-- Log4J2 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j2.version}</version>
</dependency>
<!-- Spring uses commons-logging, so: https://stackoverflow.com/a/41475146/1127920 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-jcl</artifactId>
<version>${log4j-jcl-version}</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>${mail-version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<!-- XML parser -->
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>${xercesImp.version}</version>
</dependency>
<!-- Chebi API -->
<dependency>
<groupId>uk.ac.ebi.chebi.webapps.chebiWS.client</groupId>
<artifactId>chebiWS-client</artifactId>
<version>${chebi-ws.version}</version>
<exclusions>
<exclusion>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-rt</artifactId>
</exclusion>
<exclusion>
<groupId>javax.xml.ws</groupId>
<artifactId>jaxws-api</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-tools</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.messaging.saaj</groupId>
<artifactId>saaj-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/com.sun.xml.ws/jaxws-rt -->
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-rt</artifactId>
<version>${jaxws.version}</version>
<type>pom</type>
<exclusions>
<exclusion>
<groupId>org.jvnet.mimepull</groupId>
<artifactId>mimepull</artifactId>
</exclusion>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>txw2</artifactId>
</exclusion>
<exclusion>
<groupId>org.jvnet.staxex</groupId>
<artifactId>stax-ex</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/org.glassfish.jaxb/txw2 -->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>txw2</artifactId>
<version>${txw2.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/javax.xml.ws/jaxws-api -->
<dependency>
<groupId>javax.xml.ws</groupId>
<artifactId>jaxws-api</artifactId>
<version>${jaxws-api.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.sun.xml.ws/jaxws-tools -->
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-tools</artifactId>
<version>${jaxws.version}</version>
<type>pom</type>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${springframework.version}</version>
</dependency>
<!-- Utils used for connection via http -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${apache.httpcomponents.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
<version>${apache.httpcomponents.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>${apache.httpcomponents-core.version}</version>
<scope>compile</scope>
</dependency>
<!-- Java xml serialization -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>${jaxb.version}</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${jaxb.version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<!-- mockito used for testing -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>1.0</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
<description>Module used for preparing annotations for model and connect to external resources.</description>
<repositories>
<!-- Main repository of ebi -->
<repository>
<id>central</id>
<url>http://repo.maven.apache.org/maven2/</url>
</repository>
<!-- Repository used for chebi -->
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<dependencies>
<!-- dependency from the MapViewer model -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>1.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>1.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
to parsing functions for rdf) -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>1.0</version>
</dependency>
<!-- Log4J2 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j2.version}</version>
</dependency>
<!-- Spring uses commons-logging, so: https://stackoverflow.com/a/41475146/1127920 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-jcl</artifactId>
<version>${log4j-jcl-version}</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>${mail-version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<!-- XML parser -->
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>${xercesImp.version}</version>
</dependency>
<!-- Chebi API -->
<dependency>
<groupId>uk.ac.ebi.chebi.webapps.chebiWS.client</groupId>
<artifactId>chebiWS-client</artifactId>
<version>${chebi-ws.version}</version>
<exclusions>
<exclusion>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-rt</artifactId>
</exclusion>
<exclusion>
<groupId>javax.xml.ws</groupId>
<artifactId>jaxws-api</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-tools</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.messaging.saaj</groupId>
<artifactId>saaj-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/com.sun.xml.ws/jaxws-rt -->
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-rt</artifactId>
<version>${jaxws.version}</version>
<type>pom</type>
<exclusions>
<exclusion>
<groupId>org.jvnet.mimepull</groupId>
<artifactId>mimepull</artifactId>
</exclusion>
<exclusion>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>txw2</artifactId>
</exclusion>
<exclusion>
<groupId>org.jvnet.staxex</groupId>
<artifactId>stax-ex</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/org.glassfish.jaxb/txw2 -->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>txw2</artifactId>
<version>${txw2.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/javax.xml.ws/jaxws-api -->
<dependency>
<groupId>javax.xml.ws</groupId>
<artifactId>jaxws-api</artifactId>
<version>${jaxws-api.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.sun.xml.ws/jaxws-tools -->
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-tools</artifactId>
<version>${jaxws.version}</version>
<type>pom</type>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${springframework.version}</version>
</dependency>
<!-- Utils used for connection via http -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${apache.httpcomponents.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
<version>${apache.httpcomponents.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>${apache.httpcomponents-core.version}</version>
<scope>compile</scope>
</dependency>
<!-- Java xml serialization -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>${jaxb.version}</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${jaxb.version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<!-- mockito used for testing -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
\ No newline at end of file
<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>
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>1.0</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
<description>Common classes and configuration files</description>
<dependencies>
<!-- Log4J2-->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>${apache.commons-text.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${apache.commons-lang3.version}</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>${xercesImp.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
</dependency>
</dependencies>
<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>
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>1.0</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
<description>Common classes and configuration files</description>
<dependencies>