Package ubic.gemma.core.apps
Class PubMedLoaderCli
- java.lang.Object
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- ubic.gemma.core.util.AbstractCLI
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- ubic.gemma.core.util.AbstractAuthenticatedCLI
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- ubic.gemma.core.apps.PubMedLoaderCli
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- All Implemented Interfaces:
org.springframework.beans.factory.InitializingBean
,CLI
public class PubMedLoaderCli extends AbstractAuthenticatedCLI
Load PubMed files from XML files -- not used routinely!- Author:
- pavlidis
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Nested Class Summary
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Nested classes/interfaces inherited from interface ubic.gemma.core.util.CLI
CLI.CommandGroup
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Field Summary
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Fields inherited from class ubic.gemma.core.util.AbstractCLI
ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS
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Constructor Summary
Constructors Constructor Description PubMedLoaderCli()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
buildOptions(org.apache.commons.cli.Options options)
Build option implementation.protected void
doAuthenticatedWork()
CLI.CommandGroup
getCommandGroup()
Obtain the command group for this CLI.String
getCommandName()
A short memorable name for the command that can be used to locate this class.String
getShortDesc()
Obtain a short description for this command explaining what it does.protected void
processOptions(org.apache.commons.cli.CommandLine commandLine)
Process command line options.-
Methods inherited from class ubic.gemma.core.util.AbstractAuthenticatedCLI
afterPropertiesSet, createBatchTaskExecutorService, doWork, setRequireLogin
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Methods inherited from class ubic.gemma.core.util.AbstractCLI
abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getBatchTaskExecutor, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments
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Method Detail
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getCommandName
public String getCommandName()
Description copied from interface:CLI
A short memorable name for the command that can be used to locate this class.- Specified by:
getCommandName
in interfaceCLI
- Overrides:
getCommandName
in classAbstractCLI
- Returns:
- name; if null or blank, this will not be available as a shortcut command.
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getShortDesc
public String getShortDesc()
Description copied from interface:CLI
Obtain a short description for this command explaining what it does.- Specified by:
getShortDesc
in interfaceCLI
- Overrides:
getShortDesc
in classAbstractCLI
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getCommandGroup
public CLI.CommandGroup getCommandGroup()
Description copied from interface:CLI
Obtain the command group for this CLI.- Specified by:
getCommandGroup
in interfaceCLI
- Overrides:
getCommandGroup
in classAbstractCLI
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buildOptions
protected void buildOptions(org.apache.commons.cli.Options options)
Description copied from class:AbstractCLI
Build option implementation.Implement this method to add options to your command line, using the OptionBuilder.
This is called right after
AbstractCLI.buildStandardOptions(Options)
so the options will be added after standard options.- Overrides:
buildOptions
in classAbstractCLI
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doAuthenticatedWork
protected void doAuthenticatedWork()
- Specified by:
doAuthenticatedWork
in classAbstractAuthenticatedCLI
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processOptions
protected void processOptions(org.apache.commons.cli.CommandLine commandLine)
Description copied from class:AbstractCLI
Process command line options.Implement this to provide processing of options. It is called after
AbstractCLI.buildOptions(Options)
and right beforeAbstractCLI.doWork()
.- Overrides:
processOptions
in classAbstractCLI
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