| Previous changeset 6:3740505b579c (2011-09-18) Next changeset 8:40adbcb2a7cc (2011-10-11) |
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Commit message:
Added (Properly) reasoner option (Pellet or HermiT) |
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modified:
OPPL/Tool.java OPPL/oppl.xml OPPL/oppl_galaxy_tool.jar |
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added:
OPPL/oppl_galaxy_tool_lib/HermiT.jar |
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| diff -r 3740505b579c -r 756f1f5798bf OPPL/Tool.java --- a/OPPL/Tool.java Sun Sep 18 12:35:18 2011 +0200 +++ b/OPPL/Tool.java Sun Sep 18 12:57:22 2011 +0200 |
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| @@ -125,7 +125,7 @@ // Parse the OPPL script ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner); Logger logger = Logger.getLogger(Tool.class.getName()); - Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null) +// Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null) ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); OPPLParser opplparser = parserFactory.build(errorListener); OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); |
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| diff -r 3740505b579c -r 756f1f5798bf OPPL/oppl.xml --- a/OPPL/oppl.xml Sun Sep 18 12:35:18 2011 +0200 +++ b/OPPL/oppl.xml Sun Sep 18 12:57:22 2011 +0200 |
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| @@ -1,4 +1,4 @@ -<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3"> +<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.4"> <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description> <!-- The command execution of the conditional is tacky, I think, but it works! --> @@ -6,12 +6,12 @@ <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --> <command> - #if $import_opts.imports_select==False #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null - #else #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null + #if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null + #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null #end if </command> - <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar--> + <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar --> <inputs> <param format="text" name="input" type="data" label="Input ontology file"/> |
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| diff -r 3740505b579c -r 756f1f5798bf OPPL/oppl_galaxy_tool.jar |
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| Binary file OPPL/oppl_galaxy_tool.jar has changed |
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| diff -r 3740505b579c -r 756f1f5798bf OPPL/oppl_galaxy_tool_lib/HermiT.jar |
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| Binary file OPPL/oppl_galaxy_tool_lib/HermiT.jar has changed |