FindAllTheFiles (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.common.hibernate.FindAllTheFiles

```
public class FindAllTheFiles
extends Object
```
Static methods that provide a bridge between BasicDecider and the old SymlinkFileReporter. The history behind this is that the BasicDecider used to rely upon the code shared with SymlinkFileReporter. Deciders that are based on BasicDecider thus code directly against these headers. This class also used to handle all of the actual traversal of the database hierarchy to find files, hence the name.

Version:

$Id: $Id

Author:

mtaschuk

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class FindAllTheFiles.Header

Nested Classes
Modifier and Type	Class and Description
`static class`	`FindAllTheFiles.Header`

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`EXPERIMENT_ATTRIBUTES` Constant `EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"`
`static String`	`EXPERIMENT_NAME` Constant `EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"`
`static String`	`EXPERIMENT_SWA` Constant `EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"`
`static String`	`EXPERIMENT_TAG_PREFIX` Constant `EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"`
`static String`	`FILE_ATTRIBUTES`
`static String`	`FILE_DESCRIPTION`
`static String`	`FILE_MD5SUM`
`static String`	`FILE_PATH`
`static String`	`FILE_SIZE`
`static String`	`FILE_SWA` Constant `FILE_SWA="Header.FILE_SWA.getTitle()"`
`static String`	`FILE_TAG_PREFIX`
`static String`	`INPUT_FILE_FILE_PATHS`
`static String`	`INPUT_FILE_META_TYPES`
`static String`	`INPUT_FILE_SWIDS`
`static String`	`IUS_ATTRIBUTES` Constant `IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"`
`static String`	`IUS_SWA` Constant `IUS_SWA="Header.IUS_SWA.getTitle()"`
`static String`	`IUS_TAG` Constant `IUS_TAG="Header.IUS_TAG.getTitle()"`
`static String`	`IUS_TAG_PREFIX` Constant `IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"`
`static String`	`LANE_ATTRIBUTES` Constant `LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"`
`static String`	`LANE_NAME` Constant `LANE_NAME="Header.LANE_NAME.getTitle()"`
`static String`	`LANE_NUM` Constant `LANE_NUM="Header.LANE_NUM.getTitle()"`
`static String`	`LANE_SWA` Constant `LANE_SWA="Header.LANE_SWA.getTitle()"`
`static String`	`LANE_TAG_PREFIX` Constant `LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"`
`static String`	`PARENT_SAMPLE_ATTRIBUTES` Constant `PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}`
`static String`	`PARENT_SAMPLE_NAME` Constant `PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"`
`static String`	`PARENT_SAMPLE_SWA` Constant `PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"`
`static String`	`PARENT_SAMPLE_TAG_PREFIX` Constant `PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}`
`static String`	`PROCESSING_ALGO` Constant `PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"`
`static String`	`PROCESSING_ATTRIBUTES` Constant `PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"`
`static String`	`PROCESSING_DATE` Constant `PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"`
`static String`	`PROCESSING_SWID` Constant `PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"`
`static String`	`PROCESSING_TAG_PREFIX` Constant `PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"`
`static String`	`SAMPLE_ATTRIBUTES` Constant `SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"`
`static String`	`SAMPLE_NAME` Constant `SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"`
`static String`	`SAMPLE_SWA` Constant `SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"`
`static String`	`SAMPLE_TAG_PREFIX` Constant `SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"`
`static String`	`SEQUENCER_RUN_ATTRIBUTES` Constant `SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}`
`static String`	`SEQUENCER_RUN_NAME` Constant `SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"`
`static String`	`SEQUENCER_RUN_SWA` Constant `SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"`
`static String`	`SEQUENCER_RUN_TAG_PREFIX` Constant `SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}`
`static String`	`STUDY_ATTRIBUTES` Constant `STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"`
`static String`	`STUDY_SWA` Constant `STUDY_SWA="Header.STUDY_SWA.getTitle()"`
`static String`	`STUDY_TAG_PREFIX` Constant `STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"`
`static String`	`STUDY_TITLE` Constant `STUDY_TITLE="Header.STUDY_TITLE.getTitle()"`
`static String`	`WORKFLOW_NAME` Constant `WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"`
`static String`	`WORKFLOW_RUN_NAME` Constant `WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"`
`static String`	`WORKFLOW_RUN_STATUS` Constant `WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"`
`static String`	`WORKFLOW_RUN_SWA` Constant `WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"`
`static String`	`WORKFLOW_SWA` Constant `WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"`
`static String`	`WORKFLOW_VERSION` Constant `WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"`

Constructor Summary

Constructors
Constructor and Description

FindAllTheFiles()

Constructors
Constructor and Description
`FindAllTheFiles()`

Method Summary

Methods
Modifier and Type	Method and Description
`static void`	`addAttributeToReturnValue(ReturnValue ret, String key, String value)`
`static void`	`print(Writer writer, ReturnValue ret, String studyName, boolean showStatus, FileMetadata fm)`
`static void`	`print(Writer writer, ReturnValue ret, String studyName, boolean showStatus, FileMetadata fm, boolean reportInputFiles)` Prints a line to the Excel spreadsheet.
`static void`	`printHeader(Writer writer, boolean showStatus)`
`static void`	`printHeader(Writer writer, boolean showStatus, boolean reportInputFiles)` Print the header of the Excel spreadsheet to file.

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

- Field Detail
  - STUDY_TITLE
```
public static final String STUDY_TITLE
```
    Constant STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
  - STUDY_SWA
```
public static final String STUDY_SWA
```
    Constant STUDY_SWA="Header.STUDY_SWA.getTitle()"
  - STUDY_TAG_PREFIX
```
public static final String STUDY_TAG_PREFIX
```
    Constant STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
  - STUDY_ATTRIBUTES
```
public static final String STUDY_ATTRIBUTES
```
    Constant STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
  - EXPERIMENT_NAME
```
public static final String EXPERIMENT_NAME
```
    Constant EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"
  - EXPERIMENT_SWA
```
public static final String EXPERIMENT_SWA
```
    Constant EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"
  - EXPERIMENT_TAG_PREFIX
```
public static final String EXPERIMENT_TAG_PREFIX
```
    Constant EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"
  - EXPERIMENT_ATTRIBUTES
```
public static final String EXPERIMENT_ATTRIBUTES
```
    Constant EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"
  - PARENT_SAMPLE_NAME
```
public static final String PARENT_SAMPLE_NAME
```
    Constant PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"
  - PARENT_SAMPLE_SWA
```
public static final String PARENT_SAMPLE_SWA
```
    Constant PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"
  - PARENT_SAMPLE_TAG_PREFIX
```
public static final String PARENT_SAMPLE_TAG_PREFIX
```
    Constant PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}
  - PARENT_SAMPLE_ATTRIBUTES
```
public static final String PARENT_SAMPLE_ATTRIBUTES
```
    Constant PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}
  - SAMPLE_NAME
```
public static final String SAMPLE_NAME
```
    Constant SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
  - SAMPLE_SWA
```
public static final String SAMPLE_SWA
```
    Constant SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
  - SAMPLE_TAG_PREFIX
```
public static final String SAMPLE_TAG_PREFIX
```
    Constant SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
  - SAMPLE_ATTRIBUTES
```
public static final String SAMPLE_ATTRIBUTES
```
    Constant SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
  - IUS_SWA
```
public static final String IUS_SWA
```
    Constant IUS_SWA="Header.IUS_SWA.getTitle()"
  - IUS_TAG
```
public static final String IUS_TAG
```
    Constant IUS_TAG="Header.IUS_TAG.getTitle()"
  - IUS_TAG_PREFIX
```
public static final String IUS_TAG_PREFIX
```
    Constant IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"
  - IUS_ATTRIBUTES
```
public static final String IUS_ATTRIBUTES
```
    Constant IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"
  - LANE_NAME
```
public static final String LANE_NAME
```
    Constant LANE_NAME="Header.LANE_NAME.getTitle()"
  - LANE_SWA
```
public static final String LANE_SWA
```
    Constant LANE_SWA="Header.LANE_SWA.getTitle()"
  - LANE_NUM
```
public static final String LANE_NUM
```
    Constant LANE_NUM="Header.LANE_NUM.getTitle()"
  - LANE_TAG_PREFIX
```
public static final String LANE_TAG_PREFIX
```
    Constant LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"
  - LANE_ATTRIBUTES
```
public static final String LANE_ATTRIBUTES
```
    Constant LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"
  - SEQUENCER_RUN_NAME
```
public static final String SEQUENCER_RUN_NAME
```
    Constant SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
  - SEQUENCER_RUN_SWA
```
public static final String SEQUENCER_RUN_SWA
```
    Constant SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
  - SEQUENCER_RUN_TAG_PREFIX
```
public static final String SEQUENCER_RUN_TAG_PREFIX
```
    Constant SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
  - SEQUENCER_RUN_ATTRIBUTES
```
public static final String SEQUENCER_RUN_ATTRIBUTES
```
    Constant SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
  - WORKFLOW_RUN_NAME
```
public static final String WORKFLOW_RUN_NAME
```
    Constant WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"
  - WORKFLOW_RUN_SWA
```
public static final String WORKFLOW_RUN_SWA
```
    Constant WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"
  - WORKFLOW_RUN_STATUS
```
public static final String WORKFLOW_RUN_STATUS
```
    Constant WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"
  - WORKFLOW_NAME
```
public static final String WORKFLOW_NAME
```
    Constant WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"
  - WORKFLOW_SWA
```
public static final String WORKFLOW_SWA
```
    Constant WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"
  - WORKFLOW_VERSION
```
public static final String WORKFLOW_VERSION
```
    Constant WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"
  - FILE_SWA
```
public static final String FILE_SWA
```
    Constant FILE_SWA="Header.FILE_SWA.getTitle()"
  - FILE_TAG_PREFIX
```
public static final String FILE_TAG_PREFIX
```
  - FILE_ATTRIBUTES
```
public static final String FILE_ATTRIBUTES
```
  - FILE_DESCRIPTION
```
public static final String FILE_DESCRIPTION
```
  - FILE_SIZE
```
public static final String FILE_SIZE
```
  - FILE_MD5SUM
```
public static final String FILE_MD5SUM
```
  - FILE_PATH
```
public static final String FILE_PATH
```
  - PROCESSING_DATE
```
public static final String PROCESSING_DATE
```
    Constant PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"
  - PROCESSING_SWID
```
public static final String PROCESSING_SWID
```
    Constant PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"
  - PROCESSING_ALGO
```
public static final String PROCESSING_ALGO
```
    Constant PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"
  - PROCESSING_TAG_PREFIX
```
public static final String PROCESSING_TAG_PREFIX
```
    Constant PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"
  - PROCESSING_ATTRIBUTES
```
public static final String PROCESSING_ATTRIBUTES
```
    Constant PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"
  - INPUT_FILE_META_TYPES
```
public static final String INPUT_FILE_META_TYPES
```
  - INPUT_FILE_FILE_PATHS
```
public static final String INPUT_FILE_FILE_PATHS
```
  - INPUT_FILE_SWIDS
```
public static final String INPUT_FILE_SWIDS
```
- Constructor Detail
  - FindAllTheFiles
```
public FindAllTheFiles()
```
- Method Detail
  - addAttributeToReturnValue
```
public static void addAttributeToReturnValue(ReturnValue ret,
                             String key,
                             String value)
```
  - print
```
public static void print(Writer writer,
         ReturnValue ret,
         String studyName,
         boolean showStatus,
         FileMetadata fm)
                  throws IOException
```
    Throws:
    
    IOException
  - print
```
public static void print(Writer writer,
         ReturnValue ret,
         String studyName,
         boolean showStatus,
         FileMetadata fm,
         boolean reportInputFiles)
                  throws IOException
```
    Prints a line to the Excel spreadsheet.
    
    Parameters:
    reportInputFiles -
    writer - a Writer object.
    ret - a ReturnValue object.
    studyName - a String object.
    showStatus - a boolean.
    fm - a FileMetadata object.
    
    Throws:
    
    IOException - if any.
  - printHeader
```
public static void printHeader(Writer writer,
               boolean showStatus)
                        throws IOException
```
    Throws:
    
    IOException
  - printHeader
```
public static void printHeader(Writer writer,
               boolean showStatus,
               boolean reportInputFiles)
                        throws IOException
```
    Print the header of the Excel spreadsheet to file.
    
    Parameters:
    reportInputFiles -
    writer - a Writer object.
    showStatus - a boolean.
    
    Throws:
    
    IOException - if any.

Class FindAllTheFiles

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

STUDY_TITLE

STUDY_SWA

STUDY_TAG_PREFIX

STUDY_ATTRIBUTES

EXPERIMENT_NAME

EXPERIMENT_SWA

EXPERIMENT_TAG_PREFIX

EXPERIMENT_ATTRIBUTES

PARENT_SAMPLE_NAME

PARENT_SAMPLE_SWA

PARENT_SAMPLE_TAG_PREFIX

PARENT_SAMPLE_ATTRIBUTES

SAMPLE_NAME

SAMPLE_SWA

SAMPLE_TAG_PREFIX

SAMPLE_ATTRIBUTES

IUS_SWA

IUS_TAG

IUS_TAG_PREFIX

IUS_ATTRIBUTES

LANE_NAME

LANE_SWA

LANE_NUM

LANE_TAG_PREFIX

LANE_ATTRIBUTES

SEQUENCER_RUN_NAME

SEQUENCER_RUN_SWA

SEQUENCER_RUN_TAG_PREFIX

SEQUENCER_RUN_ATTRIBUTES

WORKFLOW_RUN_NAME

WORKFLOW_RUN_SWA

WORKFLOW_RUN_STATUS

WORKFLOW_NAME

WORKFLOW_SWA

WORKFLOW_VERSION

FILE_SWA

FILE_TAG_PREFIX

FILE_ATTRIBUTES

FILE_DESCRIPTION

FILE_SIZE

FILE_MD5SUM

FILE_PATH

PROCESSING_DATE

PROCESSING_SWID

PROCESSING_ALGO

PROCESSING_TAG_PREFIX

PROCESSING_ATTRIBUTES

INPUT_FILE_META_TYPES

INPUT_FILE_FILE_PATHS

INPUT_FILE_SWIDS

Constructor Detail

FindAllTheFiles

Method Detail

addAttributeToReturnValue

print

print

printHeader

printHeader