public class SolrCommandRunner extends TaxonCommandRunner
CommandRunnerBase.OptionException
bioentityDocument, eco, gafdoc
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
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SolrCommandRunner() |
Modifier and Type | Method and Description |
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void |
configRead(Opts opts)
Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
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void |
dumpShuntGraphs(Opts opts)
Used for generating output for units tests in other languages.
|
void |
experimentalLoadComplexAnnotationSolr(Opts opts)
Experimental method for trying out the loading of complex_annotation doc type
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void |
flexDumpOntologySolr(Opts opts)
Dump experimental flexible loader output to JSON(?) blob.
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void |
flexLoadOntologySolr(Opts opts)
Flexible loader for ontologies--uses the YAML config to find loading functions.
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void |
generalLoadOntologySolr(Opts opts)
Trivial hard-wired (and optional) method for loading collected
ontology information into the "general" schema (general-config.yaml) for GO.
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void |
loadComplexAnnotationSolr(Opts opts)
Experimental method for trying out the loading of complex_annotation doc type.
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void |
loadGAFsSolr(Opts opts)
Used for loading a list of GAFs into GOlr.
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void |
loadGPADsSolr(Opts opts)
Used for loading a list of GPAD pairs into GOlr.
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void |
loadModelAnnotations(Opts opts) |
void |
loadPANTHERGeneralSolr(Opts opts)
Requires the --read-panther argument (or something else that fills the pSet object).
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void |
loadPANTHERSolr(Opts opts)
Requires the --read-panther argument (or something else that fills the pSet object).
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void |
optimizeSolr(Opts opts)
Requires the --solr-url argument.
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void |
processCAFiles(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
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void |
processLegoCatalogs(Opts opts)
Used for reading the ontology catalogs to be used for loading complex annotations.
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void |
processLegoFiles(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
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void |
processModelFolder(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
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void |
processModelUrlPrefix(Opts opts) |
void |
processPantherTrees(Opts opts)
Used for applying the panther trees to the currently data run.
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void |
purgeSolr(Opts opts)
Manually purge the index to try again.
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void |
setSolrLogFile(Opts opts)
Set an optional file to use for logging load data (can be consumed by AmiGO 2).
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void |
setSolrUrl(Opts opts)
Set an optional Solr URL to use with Solr options so they don't have to
be specified separately for every option.
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void |
solrSchemaDump(Opts opts)
Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
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createDisjoint, createDisjoint, createDisjoint, createTaxonDisjointOverInTaxon, makeClassTaxonMatrix, makeTaxonSet
createExperimentalPredictions, createRdfXml, extractOntologySubsetByGaf, foldGafExtensions, gaCalculateSpecificity, gaf, gaf2oa, gaf2Owl, gaf2OwlSimple, gafCompareBasic, gafFoldInferences, gafQuery, gafRemoveRedundant, gafTermCounts, gafTermICValues, gafXpPredict, generateJsonGafStatistics, loadGpadGpi, mapToSlim, preCheckOntology, runGAFChecks, runOntologyPreCheck, setExperimentalGAFPredictionFile, setExperimentalGAFPredictionReportFile, setGAFPredictionFile, setGAFPredictionReportFile, setGAFReportFile, setGAFReportSummaryFile, setGAFTaxonModule, unfoldGafExtensions, writeGaf, writeGpad, writeGpi, writeXgmml
assertAboxInferences, assertInferredSubClassAxioms, createBioChebi, createExternalMappings, createPartOfLinks, createSlim, createSubsetTags, extractAnnotationValue, extractExtensionFile, filterExtensionFile, removeRedundantInferredSuperClassAxioms, removeRedundantInferredSVFs, removeRedundantSubclasses, removeRedundantSVFs, removeSubsetEntities, runDAGCheck, runSingleIteration, verifyChanges
exit, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, printVersion, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runSingleIteration, summarizeOntology
public void configRead(Opts opts)
opts
- public void solrSchemaDump(Opts opts)
opts
- public void setSolrUrl(Opts opts)
opts
- public void setSolrLogFile(Opts opts)
opts
- public void purgeSolr(Opts opts) throws Exception
opts
- Exception
public void flexLoadOntologySolr(Opts opts) throws Exception
opts
- Exception
public void generalLoadOntologySolr(Opts opts) throws Exception
opts
- Exception
public void processLegoCatalogs(Opts opts) throws Exception
opts
- Exception
public void processLegoFiles(Opts opts) throws Exception
opts
- Exception
public void processModelFolder(Opts opts) throws Exception
opts
- Exception
public void processModelUrlPrefix(Opts opts) throws Exception
Exception
public void processCAFiles(Opts opts) throws Exception
opts
- Exception
public void experimentalLoadComplexAnnotationSolr(Opts opts) throws Exception
opts
- Exception
public void loadComplexAnnotationSolr(Opts opts) throws Exception
opts
- Exception
public void flexDumpOntologySolr(Opts opts) throws Exception
opts
- Exception
public void loadGAFsSolr(Opts opts) throws Exception
opts
- Exception
public void loadPANTHERSolr(Opts opts) throws Exception
opts
- Exception
public void loadPANTHERGeneralSolr(Opts opts) throws Exception
opts
- Exception
public void loadGPADsSolr(Opts opts) throws Exception
opts
- Exception
public void processPantherTrees(Opts opts) throws Exception
opts
- Exception
public void optimizeSolr(Opts opts) throws Exception
opts
- Exception
public void dumpShuntGraphs(Opts opts) throws Exception
opts
- Exception
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