ExternalDatabaseEvidenceImporterAbstractCLI (Gemma 1.31.4 API)

java.lang.Object
- ubic.gemma.core.util.AbstractCLI
- - ubic.gemma.core.util.AbstractAuthenticatedCLI
  - - ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI

All Implemented Interfaces:

CLI

Direct Known Subclasses:

CtdDatabaseImporterCli, DgaDatabaseImporterCli, GwasDatabaseImporterCli, OmimDatabaseImporterCli, RgdDatabaseImporterCli, SfariDatabaseImporterCli
```
@Deprecated
public abstract class ExternalDatabaseEvidenceImporterAbstractCLI
extends AbstractAuthenticatedCLI
```
Deprecated.

Author:

nicolas

Field Summary

Fields
Modifier and Type	Field	Description
`protected GeneService`	`geneService`	Deprecated.
`protected ubic.gemma.core.loader.association.phenotype.PhenotypeProcessingUtil`	`ppUtil`	Deprecated.
`protected TaxonService`	`taxonService`	Deprecated.
`protected String`	`writeFolder`	Deprecated.

Fields inherited from class ubic.gemma.core.util.AbstractCLI
ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, log, SUCCESS

Constructor Summary

Constructors
Constructor Description

ExternalDatabaseEvidenceImporterAbstractCLI()
Deprecated.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`GemmaCLI.CommandGroup`	`getCommandGroup()`	Deprecated. Obtain the command group for this CLI.
`protected void`	`init()`	Deprecated. load all needed services and initialize data structures

Methods inherited from class ubic.gemma.core.util.AbstractAuthenticatedCLI
executeBatchTasks, processStandardOptions, requireLogin

Methods inherited from class ubic.gemma.core.util.AbstractCLI
addAutoOption, addAutoOption, addBatchOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, buildOptions, buildStandardOptions, doWork, executeCommand, getAutoSeekEventType, getBean, getBean, getLimitingDate, getNumThreads, getOptions, isAutoSeek, processOptions, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.core.util.CLI
getCommandName, getShortDesc

- Field Detail
  - writeFolder
```
protected String writeFolder
```
    Deprecated.
  - ppUtil
```
protected ubic.gemma.core.loader.association.phenotype.PhenotypeProcessingUtil ppUtil
```
    Deprecated.
  - taxonService
```
protected TaxonService taxonService
```
    Deprecated.
  - geneService
```
protected GeneService geneService
```
    Deprecated.
- Constructor Detail
  - ExternalDatabaseEvidenceImporterAbstractCLI
```
public ExternalDatabaseEvidenceImporterAbstractCLI()
```
    Deprecated.
- Method Detail
  - getCommandGroup
```
public GemmaCLI.CommandGroup getCommandGroup()
```
    Deprecated.
    
    Description copied from interface: CLI
    
    Obtain the command group for this CLI.
  - init
```
protected void init()
             throws Exception
```
    Deprecated.
    
    load all needed services and initialize data structures
    
    Throws:
    
    Exception