Update jsbml
This commit is contained in:
Chris Myers
parent
73196545f6
commit
518bbc1383
3 changed files with 1 additions and 131 deletions
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@ -1,65 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
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<Properties>
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<Property name="filename">jsbml.log</Property>
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</Properties>
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<ThresholdFilter level="trace"/>
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<Appenders>
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<Console name="console">
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<PatternLayout pattern="%5p (%F:%L) - %m%n"/>
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</Console>
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<File name="file" fileName="${filename}">
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<PatternLayout>
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<pattern>%d %p %C{1.} [%t] %m%n</pattern>
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</PatternLayout>
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</File>
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</Appenders>
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<Loggers>
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<Logger name="org.sbml" level="info" additivity="false">
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<AppenderRef ref="console"/>
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<AppenderRef ref="file"/>
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</Logger>
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<!--
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<Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="debug" additivity="false">
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<AppenderRef ref="console"/>
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<AppenderRef ref="file"/>
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</Logger>
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<Logger name="org.sbml.jsbml.xml.stax.SBMLReader" level="debug" additivity="false">
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<AppenderRef ref="console"/>
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<AppenderRef ref="file"/>
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</Logger>
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-->
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<!--
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# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
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# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
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# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
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# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
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# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
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# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
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# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
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# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
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# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
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# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
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# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
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# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
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# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
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# org.sbml.jsbml.ASTNode - ERROR to DEBUG
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# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
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# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
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# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
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# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
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# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
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# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
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-->
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<Root level="info">
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<AppenderRef ref="file"/>
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</Root>
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</Loggers>
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</Configuration>
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@ -71,7 +71,7 @@
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<dependency>
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<groupId>org.sbml.jsbml</groupId>
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<artifactId>jsbml</artifactId>
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<version>1.6.1</version>
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<version>1.7-SNAPSHOT</version>
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</dependency>
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<dependency>
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65
log4j2.xml
65
log4j2.xml
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@ -1,65 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
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<Properties>
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<Property name="filename">jsbml.log</Property>
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</Properties>
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<ThresholdFilter level="trace"/>
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<Appenders>
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<Console name="console">
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<PatternLayout pattern="%5p (%F:%L) - %m%n"/>
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</Console>
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<File name="file" fileName="${filename}">
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<PatternLayout>
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<pattern>%d %p %C{1.} [%t] %m%n</pattern>
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</PatternLayout>
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</File>
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</Appenders>
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<Loggers>
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<Logger name="org.sbml" level="info" additivity="false">
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<AppenderRef ref="console"/>
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<AppenderRef ref="file"/>
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</Logger>
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<!--
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<Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="debug" additivity="false">
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<AppenderRef ref="console"/>
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<AppenderRef ref="file"/>
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</Logger>
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<Logger name="org.sbml.jsbml.xml.stax.SBMLReader" level="debug" additivity="false">
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<AppenderRef ref="console"/>
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<AppenderRef ref="file"/>
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</Logger>
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-->
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<!--
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# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
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# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
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# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
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# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
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# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
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# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
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# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
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# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
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# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
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# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
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# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
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# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
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# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
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# org.sbml.jsbml.ASTNode - ERROR to DEBUG
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# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
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# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
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# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
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# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
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# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
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# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
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-->
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<Root level="info">
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<AppenderRef ref="file"/>
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</Root>
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</Loggers>
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</Configuration>
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