Added generation of pom to converter
This commit is contained in:
leandrohw
parent
f111971d3d
commit
a5545947c2
5 changed files with 109 additions and 89 deletions
|
|
@ -1,6 +1,5 @@
|
|||
<?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"
|
||||
<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>
|
||||
<artifactId>conversion</artifactId>
|
||||
|
|
@ -11,6 +10,57 @@
|
|||
<relativePath>../</relativePath>
|
||||
</parent>
|
||||
<packaging>jar</packaging>
|
||||
<build>
|
||||
<plugins>
|
||||
<!-- Build an executable JAR -->
|
||||
<plugin>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>build-converter</id>
|
||||
<configuration>
|
||||
<archive>
|
||||
<manifest>
|
||||
<mainClass>edu.utah.ece.async.Converter</mainClass>
|
||||
</manifest>
|
||||
</archive>
|
||||
<descriptorRefs>
|
||||
<descriptorRef>jar-with-dependencies</descriptorRef>
|
||||
</descriptorRefs>
|
||||
</configuration>
|
||||
<phase>package</phase>
|
||||
<goals>
|
||||
<goal>assembly</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-javadoc-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>attach-javadoc</id>
|
||||
<goals>
|
||||
<goal>jar</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-source-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>attach-source</id>
|
||||
<goals>
|
||||
<goal>jar</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>edu.utah.ece.async</groupId>
|
||||
|
|
|
|||
|
|
@ -48,8 +48,58 @@ import edu.utah.ece.async.biomodel.util.SBMLutilities;
|
|||
import edu.utah.ece.async.util.GlobalConstants;
|
||||
|
||||
/**
|
||||
* Provides functionality for validating SBOL data models.
|
||||
* Command line method for reading an input file and producing an output file.
|
||||
* --jar libSBOLj.jar [options] inputFile [-o outputFile -e compareFile]
|
||||
* <p>
|
||||
* By default, validations on compliance and completeness are performed, and types
|
||||
* for top-level objects are not used in URIs.
|
||||
* <p>
|
||||
* Requirements:
|
||||
* <p>
|
||||
* inputfile
|
||||
* <p>
|
||||
* "-e" specifies a file to compare if equal to
|
||||
* <p>
|
||||
* "-o" specifies an output filename
|
||||
* <p>
|
||||
*
|
||||
* Options:
|
||||
* <p>
|
||||
* "-b" check best practices
|
||||
* <p>
|
||||
* "-cf" second SBOL file if file diff. option is selected
|
||||
* <p>
|
||||
* "-d" display detailed error trace
|
||||
* <p>
|
||||
* "-esf" export single SBML file
|
||||
* <p>
|
||||
* "-f" fail on first error
|
||||
* <p>
|
||||
* "-i" allow SBOL document to be incomplete
|
||||
* <p>
|
||||
* "-l" indicates the language for output (default=SBOL2, other options SBOL1, GenBank, FASTA, SBML)
|
||||
* <p>
|
||||
* "-mf" main SBOL file if file diff. option is selected
|
||||
* <p>
|
||||
* "-n" allow non-compliant URIs
|
||||
* <p>
|
||||
* "-no" indicate no output file to be generated from validation
|
||||
* <p>
|
||||
* "-oDir" output directory of resulting conversion and validation file
|
||||
* <p>
|
||||
* "-p" specifies the default URI prefix for converted objects
|
||||
* <p>
|
||||
* "-rsbml" The full path of external SBML files to be referenced in the SBML2SBOL conversion
|
||||
* <p>
|
||||
* "-rsbol" The full path of external SBOL files to be referenced in the SBML2SBOL conversion
|
||||
* <p>
|
||||
* "-s" select only this topLevel object and those it references
|
||||
* <p>
|
||||
* "-t" uses types in URIs
|
||||
* <p>
|
||||
* "-v" specifies version to use for converted objects
|
||||
* <p>
|
||||
*
|
||||
* @author Zhen Zhang
|
||||
* @author Tramy Nguyen
|
||||
* @author Chris Myers
|
||||
|
|
@ -97,61 +147,6 @@ public class Converter {
|
|||
System.exit(1);
|
||||
}
|
||||
|
||||
/**
|
||||
* Command line method for reading an input file and producing an output file.
|
||||
* --jar libSBOLj.jar [options] <inputFile> [-o <outputFile> -e <compareFile>]
|
||||
* <p>
|
||||
* By default, validations on compliance and completeness are performed, and types
|
||||
* for top-level objects are not used in URIs.
|
||||
* <p>
|
||||
* Requirements:
|
||||
* <p>
|
||||
* inputfile
|
||||
* <p>
|
||||
* "-e" specifies a file to compare if equal to
|
||||
* <p>
|
||||
* "-o" specifies an output filename
|
||||
* <p>
|
||||
*
|
||||
* Options:
|
||||
* <p>
|
||||
* "-b" check best practices
|
||||
* <p>
|
||||
* "-cf" second SBOL file if file diff. option is selected
|
||||
* <p>
|
||||
* "-d" display detailed error trace
|
||||
* <p>
|
||||
* "-esf" export single SBML file
|
||||
* <p>
|
||||
* "-f" fail on first error
|
||||
* <p>
|
||||
* "-i" allow SBOL document to be incomplete
|
||||
* <p>
|
||||
* "-l" indicates the language for output (default=SBOL2, other options SBOL1, GenBank, FASTA, SBML)
|
||||
* <p>
|
||||
* "-mf" main SBOL file if file diff. option is selected
|
||||
* <p>
|
||||
* "-n" allow non-compliant URIs
|
||||
* <p>
|
||||
* "-no" indicate no output file to be generated from validation
|
||||
* <p>
|
||||
* "-oDir" output directory of resulting conversion and validation file
|
||||
* <p>
|
||||
* "-p" specifies the default URI prefix for converted objects
|
||||
* <p>
|
||||
* "-rsbml" The full path of external SBML files to be referenced in the SBML2SBOL conversion
|
||||
* <p>
|
||||
* "-rsbol" The full path of external SBOL files to be referenced in the SBML2SBOL conversion
|
||||
* <p>
|
||||
* "-s" select only this topLevel object and those it references
|
||||
* <p>
|
||||
* "-t" uses types in URIs
|
||||
* <p>
|
||||
* "-v" specifies version to use for converted objects
|
||||
* <p>
|
||||
*
|
||||
* @param args arguments supplied at command line
|
||||
*/
|
||||
public static void main(String[] args) {
|
||||
|
||||
//-----REQUIRED FIELD-----
|
||||
|
|
|
|||
|
|
@ -143,10 +143,10 @@ public class SBML2SBOL {
|
|||
* @param fileName - The name of the input SBML file
|
||||
* @param sbolFiles - The set of SBOL files to use for the conversion to reference from. If no ref_sbolInputfilePath is given, then null should be set to indicate no referencing SBOL files are given for conversion.
|
||||
* @param sbolURIPrefix - The URI prefix to be set on the SBOLDocument.
|
||||
* @throws SBOLValidationException
|
||||
* @throws XMLStreamException
|
||||
* @throws IOException
|
||||
* @throws SBOLConversionException
|
||||
* @throws SBOLValidationException -
|
||||
* @throws XMLStreamException -
|
||||
* @throws IOException -
|
||||
* @throws SBOLConversionException -
|
||||
*/
|
||||
public static void convert_SBML2SBOL(SBOLDocument sbolDoc, String externalSBMLPath, SBMLDocument sbmlDoc, String fileName, HashSet<String> sbolFiles, String sbolURIPrefix) throws SBOLValidationException, XMLStreamException, IOException, SBOLConversionException {
|
||||
|
||||
|
|
|
|||
|
|
@ -102,8 +102,8 @@ public class SBOL2SBML {
|
|||
* @param moduleDef - the current ModuleDefinition to convert all SBML object within the ModuleDefinition to its equivalent SBML component.
|
||||
* @param sbolDoc - The SBOL document to be converted to its equivalent SBML model.
|
||||
* @return The list of SBML models converted from SBOL ModuleDefinition. Each of the converted SBML model are stored within iBioSim's BioModel object.
|
||||
* @throws XMLStreamException
|
||||
* @throws IOException
|
||||
* @throws XMLStreamException -
|
||||
* @throws IOException -
|
||||
*/
|
||||
public static List<BioModel> generateModel(String projectDirectory, ModuleDefinition moduleDef, SBOLDocument sbolDoc) throws XMLStreamException, IOException {
|
||||
|
||||
|
|
|
|||
25
pom.xml
25
pom.xml
|
|
@ -64,32 +64,7 @@
|
|||
</testExcludes>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<!-- Build an executable JAR -->
|
||||
<plugin>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>build-converter</id>
|
||||
<configuration>
|
||||
<archive>
|
||||
<manifest>
|
||||
<mainClass>edu.utah.ece.async.Converter</mainClass>
|
||||
</manifest>
|
||||
</archive>
|
||||
<descriptorRefs>
|
||||
<descriptorRef>jar-with-dependencies</descriptorRef>
|
||||
</descriptorRefs>
|
||||
<finalName>converter</finalName>
|
||||
</configuration>
|
||||
<phase>package</phase>
|
||||
<goals>
|
||||
<goal>assembly</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
<!-- todo: add any other plugins needed here -->
|
||||
|
||||
</build>
|
||||
</project>
|
||||
Loading…
Add table
Add a link
Reference in a new issue