owltools.cli
Class SolrCommandRunner

java.lang.Object
  extended by owltools.cli.CommandRunner
      extended by owltools.cli.GafCommandRunner
          extended by owltools.cli.TaxonCommandRunner
              extended by owltools.cli.SolrCommandRunner
Direct Known Subclasses:
SimCommandRunner

public class SolrCommandRunner
extends TaxonCommandRunner

Solr/GOlr loading.


Nested Class Summary
 
Nested classes/interfaces inherited from class owltools.cli.CommandRunner
CommandRunner.OptionException, CommandRunner.Opts
 
Field Summary
 
Fields inherited from class owltools.cli.GafCommandRunner
gafdoc
 
Fields inherited from class owltools.cli.CommandRunner
exitOnException, g, owlObjectCachedSet, owlpp, pw, queryOntology, reasoner, reasonerName
 
Constructor Summary
SolrCommandRunner()
           
 
Method Summary
 void configRead(CommandRunner.Opts opts)
          Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
 void dumpShuntGraphs(CommandRunner.Opts opts)
          Used for generating output for units tests in other languages.
 void flexDumpOntologySolr(CommandRunner.Opts opts)
          Dump experimental flexible loader output to JSON(?) blob.
 void flexLoadOntologySolr(CommandRunner.Opts opts)
          Experimental flexible loader.
 void loadGafSolr(CommandRunner.Opts opts)
          Requires the --gaf argument (or something else that fills the gafdoc object).
 void loadGafsSolr(CommandRunner.Opts opts)
          Used for loading a list of GAFs into GOlr.
 void loadGPADsSolr(CommandRunner.Opts opts)
          Used for loading a list of GPAD pairs into GOlr.
 void loadOntologySolr(CommandRunner.Opts opts)
          Deprecated. 
 void purgeSolr(CommandRunner.Opts opts)
          Manually purge the index to try again.
 void setSolrUrl(CommandRunner.Opts opts)
          Set an optional Solr URL to use with Solr options so they don't have to be specified separately for every option.
 void solrSchemaDump(CommandRunner.Opts opts)
          Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
 
Methods inherited from class owltools.cli.TaxonCommandRunner
makeClassTaxonMatrix, makeTaxonSet
 
Methods inherited from class owltools.cli.GafCommandRunner
createRdfXml, gaf, gaf2Owl, gafQuery, gafTermCounts, gafXpPredict, runGAFChecks, setGAFReportFile, writeXgmml
 
Methods inherited from class owltools.cli.CommandRunner
exit, help, helpFooter, parseArgString, resolveClass, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, run, run, summarizeOntology
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SolrCommandRunner

public SolrCommandRunner()
Method Detail

configRead

public void configRead(CommandRunner.Opts opts)
Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.

Parameters:
opts -

solrSchemaDump

public void solrSchemaDump(CommandRunner.Opts opts)
Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).

Parameters:
opts -

setSolrUrl

public void setSolrUrl(CommandRunner.Opts opts)
Set an optional Solr URL to use with Solr options so they don't have to be specified separately for every option.

Parameters:
opts -

purgeSolr

public void purgeSolr(CommandRunner.Opts opts)
               throws Exception
Manually purge the index to try again. Since this cascade is currently ordered, can be used to purge before we load.

Parameters:
opts -
Throws:
Exception

loadOntologySolr

@Deprecated
public void loadOntologySolr(CommandRunner.Opts opts)
                      throws Exception
Deprecated. 

Used for loading whatever ontology stuff we have into GOlr.

Parameters:
opts -
Throws:
Exception

flexLoadOntologySolr

public void flexLoadOntologySolr(CommandRunner.Opts opts)
                          throws Exception
Experimental flexible loader.

Parameters:
opts -
Throws:
Exception

flexDumpOntologySolr

public void flexDumpOntologySolr(CommandRunner.Opts opts)
                          throws Exception
Dump experimental flexible loader output to JSON(?) blob.

Parameters:
opts -
Throws:
Exception

loadGafsSolr

public void loadGafsSolr(CommandRunner.Opts opts)
                  throws Exception
Used for loading a list of GAFs into GOlr.

Parameters:
opts -
Throws:
Exception

loadGafSolr

public void loadGafSolr(CommandRunner.Opts opts)
                 throws Exception
Requires the --gaf argument (or something else that fills the gafdoc object).

Parameters:
opts -
Throws:
Exception

loadGPADsSolr

public void loadGPADsSolr(CommandRunner.Opts opts)
                   throws Exception
Used for loading a list of GPAD pairs into GOlr.

Parameters:
opts -
Throws:
Exception

dumpShuntGraphs

public void dumpShuntGraphs(CommandRunner.Opts opts)
                     throws Exception
Used for generating output for units tests in other languages. Output some JSON graph serializations. NOTE: In order to cut down on clutter, this method depends on relative resources in the test/resources. This may change later on--be warned.

Parameters:
opts -
Throws:
Exception


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