Bundle (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.bundle.Bundle

```
public class Bundle
extends Object
```
This is a utility class that lets you manipulate a workflow bundle.

Version:

$Id: $Id

Author:

briandoconnor@gmail.com

Field Summary

Fields
Modifier and Type	Field and Description
`protected String`	`bundleDir`
`protected ArrayList<File>`	`filesArray`
`protected Metadata`	`metadata`
`protected String`	`outputDir`
`protected String`	`outputZip`
`protected String`	`permanentBundleLocation`

Constructor Summary

Constructors
Constructor and Description

Bundle()
Constructor for Bundle.

Bundle(Metadata metadata, Map<String,String> config)
Constructor for Bundle.

Constructors
Constructor and Description
`Bundle()` Constructor for Bundle.
`Bundle(Metadata metadata, Map<String,String> config)` Constructor for Bundle.

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`copyBundle(String sourceFile, String targetDir)` copyBundle.
`ReturnValue`	`copyBundleToS3(File bundle, String bundleOutputPrefix)` copyBundleToS3.
`static BundleInfo`	`findBundleInfo(File bundleDir)`
`BundleInfo`	`getBundleInfo(File bundle, File metadataFile)` getBundleInfo.
`ArrayList<File>`	`getFilesArray()` Getter for the field `filesArray`.
`Metadata`	`getMetadata()` Getter for the field `metadata`.
`String`	`getOutputDir()` Getter for the field `outputDir`.
`protected ReturnValue`	`installBundle(File bundle, File metadataFile, boolean packageIntoZip, boolean unzipIntoDir, List<String> workflows)` This method allows you to install the workflow bundle to the metadb optionally building a zip file along the way and archiving it to a safe location.
`ReturnValue`	`installBundle(File bundle, File metadataFile, List<String> workflows)` installBundle.
`ReturnValue`	`installBundleDirOnly(File bundle, File metadataFile, List<String> workflows)` installBundleDirOnly.
`ReturnValue`	`installBundleZipOnly(File bundle, File metadataFile, List<String> workflows)` installBundleZipOnly.
`ReturnValue`	`packageBundle(File bundlePath, File bundleOutput)` packageBundle.
`ReturnValue`	`packageBundleToS3(File bundlePath, String bundleOutputPrefix)` packageBundleToS3.
`static String`	`resolveWorkflowBundleDirPath(File bundleDir, String path)`
`void`	`setFilesArray(ArrayList<File> filesArray)` Setter for the field `filesArray`.
`void`	`setMetadata(Metadata metadata)` Setter for the field `metadata`.
`void`	`setOutputDir(String outputDir)` Setter for the field `outputDir`.
`ReturnValue`	`unpackageBundle(File bundle)` unpackageBundle.
`ReturnValue`	`unpackageBundleFromS3(String bundleURL)` unpackageBundleFromS3.
`ReturnValue`	`validateBundle(File bundle)` validateBundle.

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

Field Detail

permanentBundleLocation

protected String permanentBundleLocation

bundleDir
```
protected String bundleDir
```

metadata
```
protected Metadata metadata
```

outputDir
```
protected String outputDir
```

outputZip
```
protected String outputZip
```

filesArray
```
protected ArrayList<File> filesArray
```

Constructor Detail
- Bundle
```
public Bundle()
```
  Constructor for Bundle.
- Bundle
```
public Bundle(Metadata metadata,
      Map<String,String> config)
```
  Constructor for Bundle.
  
  Parameters:
  metadata - a Metadata object.
  config - a Map object.

Method Detail

findBundleInfo

public static BundleInfo findBundleInfo(File bundleDir)

resolveWorkflowBundleDirPath

public static String resolveWorkflowBundleDirPath(File bundleDir,
                                  String path)

getBundleInfo

public BundleInfo getBundleInfo(File bundle,
                       File metadataFile)

getBundleInfo.

Parameters:: bundle - a File object.; metadataFile - a File object.
Returns:: a BundleInfo object.

unpackageBundle
```
public ReturnValue unpackageBundle(File bundle)
```
unpackageBundle.

Parameters:
bundle - a File object.

Returns:
a ReturnValue object.

unpackageBundleFromS3
```
public ReturnValue unpackageBundleFromS3(String bundleURL)
```
unpackageBundleFromS3.

Parameters:
bundleURL - a String object.

Returns:
a ReturnValue object.

packageBundle

public ReturnValue packageBundle(File bundlePath,
                        File bundleOutput)

packageBundle.

Parameters:: bundlePath - a File object.; bundleOutput - a File object.
Returns:: a ReturnValue object.

packageBundleToS3

public ReturnValue packageBundleToS3(File bundlePath,
                            String bundleOutputPrefix)

packageBundleToS3.

Parameters:: bundlePath - a File object.; bundleOutputPrefix - a String object.
Returns:: a ReturnValue object.

copyBundleToS3

public ReturnValue copyBundleToS3(File bundle,
                         String bundleOutputPrefix)

copyBundleToS3.

Parameters:: bundle - a File object.; bundleOutputPrefix - a String object.
Returns:: a ReturnValue object.

copyBundle

public ReturnValue copyBundle(String sourceFile,
                     String targetDir)

copyBundle.

Parameters:: sourceFile - a String object.; targetDir - a String object.
Returns:: a ReturnValue object.

validateBundle
```
public ReturnValue validateBundle(File bundle)
```
validateBundle.

Parameters:
bundle - a File object.

Returns:
a ReturnValue object.

installBundleZipOnly

public ReturnValue installBundleZipOnly(File bundle,
                               File metadataFile,
                               List<String> workflows)

installBundleZipOnly.

Parameters:: bundle - a File object.; metadataFile - a File object.; workflows -
Returns:: a ReturnValue object.

installBundleDirOnly

public ReturnValue installBundleDirOnly(File bundle,
                               File metadataFile,
                               List<String> workflows)

installBundleDirOnly.

Parameters:: bundle - a File object.; metadataFile - a File object.; workflows -
Returns:: a ReturnValue object.

installBundle

public ReturnValue installBundle(File bundle,
                        File metadataFile,
                        List<String> workflows)

installBundle.

Parameters:: bundle - a File object.; metadataFile - a File object.; workflows -
Returns:: a ReturnValue object.

installBundle
```
protected ReturnValue installBundle(File bundle,
                        File metadataFile,
                        boolean packageIntoZip,
                        boolean unzipIntoDir,
                        List<String> workflows)
```
This method allows you to install the workflow bundle to the metadb optionally building a zip file along the way and archiving it to a safe location.

Parameters:
bundle - a File object.
metadataFile - a File object.
packageIntoZip - a boolean.
unzipIntoDir - a boolean.
workflows - a list to store installed workflows for output

Returns:
a ReturnValue object.

getMetadata
```
public Metadata getMetadata()
```
Getter for the field metadata.

Returns:
a Metadata object.

setMetadata
```
public void setMetadata(Metadata metadata)
```
Setter for the field metadata.

Parameters:
metadata - a Metadata object.

getOutputDir
```
public String getOutputDir()
```
Getter for the field outputDir.

Returns:
a String object.

setOutputDir
```
public void setOutputDir(String outputDir)
```
Setter for the field outputDir.

Parameters:
outputDir - a String object.

getFilesArray
```
public ArrayList<File> getFilesArray()
```
Getter for the field filesArray.

Returns:
a ArrayList object.

setFilesArray
```
public void setFilesArray(ArrayList<File> filesArray)
```
Setter for the field filesArray.

Parameters:
filesArray - a ArrayList object.

Class Bundle

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

permanentBundleLocation

bundleDir

metadata

outputDir

outputZip

filesArray

Constructor Detail

Bundle

Bundle

Method Detail

findBundleInfo

resolveWorkflowBundleDirPath

getBundleInfo

unpackageBundle

unpackageBundleFromS3

packageBundle

packageBundleToS3

copyBundleToS3

copyBundle

validateBundle

installBundleZipOnly

installBundleDirOnly

installBundle

installBundle

getMetadata

setMetadata

getOutputDir

setOutputDir

getFilesArray

setFilesArray