public class SolrCommandRunner extends TaxonCommandRunner
Modifier and Type | Field and Description |
---|---|
boolean |
exitOnException |
OWLGraphWrapper |
g |
boolean |
isDisposeReasonerOnExit |
Set<org.semanticweb.owlapi.model.OWLObject> |
owlObjectCachedSet |
protected ParserWrapper |
pw |
org.semanticweb.owlapi.model.OWLOntology |
queryOntology |
org.semanticweb.owlapi.reasoner.OWLReasoner |
reasoner |
String |
reasonerName |
bioentityDocument, eco, gafdoc
Constructor and Description |
---|
SolrCommandRunner() |
Modifier and Type | Method and Description |
---|---|
void |
configRead(Opts opts)
Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
|
void |
dumpShuntGraphs(Opts opts)
Used for generating output for units tests in other languages.
|
protected void |
exit(int code) |
void |
experimentalLoadComplexAnnotationSolr(Opts opts)
Experimental method for trying out the loading of complex_annotation doc type
|
void |
flexDumpOntologySolr(Opts opts)
Dump experimental flexible loader output to JSON(?) blob.
|
void |
flexLoadOntologySolr(Opts opts)
Flexible loader for ontologies--uses the YAML config to find loading functions.
|
void |
generalLoadOntologySolr(Opts opts)
Trivial hard-wired (and optional) method for loading collected
ontology information into the "general" schema (general-config.yaml) for GO.
|
protected OWLPrettyPrinter |
getPrettyPrinter() |
void |
handlePrettyPrinter(Opts opts) |
void |
help() |
void |
helpFooter() |
void |
loadComplexAnnotationSolr(Opts opts)
Experimental method for trying out the loading of complex_annotation doc type.
|
void |
loadGAFsSolr(Opts opts)
Used for loading a list of GAFs into GOlr.
|
void |
loadGPADsSolr(Opts opts)
Used for loading a list of GPAD pairs into GOlr.
|
void |
loadPANTHERGeneralSolr(Opts opts)
Requires the --read-panther argument (or something else that fills the pSet object).
|
void |
loadPANTHERSolr(Opts opts)
Requires the --read-panther argument (or something else that fills the pSet object).
|
void |
optimizeSolr(Opts opts)
Requires the --solr-url argument.
|
void |
processCAFiles(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
|
void |
processLegoCatalogs(Opts opts)
Used for reading the ontology catalogs to be used for loading complex annotations.
|
void |
processLegoFiles(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
|
void |
processPantherTrees(Opts opts)
Used for applying the panther trees to the currently data run.
|
void |
purgeSolr(Opts opts)
Manually purge the index to try again.
|
org.semanticweb.owlapi.model.OWLClass |
resolveClass(String id) |
List<org.semanticweb.owlapi.model.OWLClass> |
resolveClassList(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(String id) |
Set<org.semanticweb.owlapi.model.OWLObject> |
resolveEntityList(Opts opts) |
org.semanticweb.owlapi.model.OWLObjectProperty |
resolveObjectProperty(String id) |
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyList(Opts opts) |
List<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyListAsList(Opts opts) |
void |
run(Opts opts) |
void |
run(String[] args) |
void |
runSingleIteration(String[] args) |
void |
setSolrLogFile(Opts opts)
Set an optional file to use for logging load data (can be consumed by AmiGO 2).
|
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.
|
void |
solrSchemaDump(Opts opts)
Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
|
void |
summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont) |
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, jsonLdToRdf, rdfToJsonLd, removeRedundantInferredSuperClassAxioms, removeRedundantSubclasses, removeSubsetEntities, runDAGCheck, runSingleIteration, verifyChanges
public OWLGraphWrapper g
public org.semanticweb.owlapi.model.OWLOntology queryOntology
public boolean exitOnException
public boolean isDisposeReasonerOnExit
public org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
public String reasonerName
public Set<org.semanticweb.owlapi.model.OWLObject> owlObjectCachedSet
protected ParserWrapper pw
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 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
protected void exit(int code)
protected OWLPrettyPrinter getPrettyPrinter()
public void summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont)
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyList(Opts opts)
public List<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyListAsList(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(String id)
public org.semanticweb.owlapi.model.OWLObjectProperty resolveObjectProperty(String id)
public org.semanticweb.owlapi.model.OWLClass resolveClass(String id)
public void help()
public void helpFooter()
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