| Package | Description |
|---|---|
| net.sourceforge.seqware.common.hibernate |
Looks like utility classes for navigating the metadb.
|
| net.sourceforge.seqware.common.module |
Utility classes really.
|
| net.sourceforge.seqware.common.util.filetools |
Tools for dealing with files.
|
| net.sourceforge.seqware.pipeline.deciders |
BasicDecider.
|
| net.sourceforge.seqware.pipeline.modules.utilities |
Modules that are used by workflows.
|
| net.sourceforge.seqware.pipeline.plugins |
Create and manipulate databases for extended testing.
|
| net.sourceforge.seqware.pipeline.plugins.filelinker |
Import files into the metadb.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
FindAllTheFiles.print(Writer writer,
ReturnValue ret,
String studyName,
boolean showStatus,
FileMetadata fm) |
static void |
FindAllTheFiles.print(Writer writer,
ReturnValue ret,
String studyName,
boolean showStatus,
FileMetadata fm,
boolean reportInputFiles)
Prints a line to the Excel spreadsheet.
|
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<FileMetadata> |
ReturnValue.files |
| Modifier and Type | Method and Description |
|---|---|
ArrayList<FileMetadata> |
ReturnValue.getFiles()
Getter for the field
files. |
| Modifier and Type | Method and Description |
|---|---|
void |
ReturnValue.setFiles(ArrayList<FileMetadata> files)
Setter for the field
files. |
| Modifier and Type | Method and Description |
|---|---|
static void |
ProvisionFilesUtil.calculateInputMetadata(String input,
FileMetadata metadata) |
File |
ProvisionFilesUtil.copyToFile(BufferedInputStream reader,
String output,
boolean fullOutputPath,
int bufLen,
String input,
Cipher decryptCipher,
Cipher encryptCipher,
FileMetadata metadata)
Copy reader into output using Cipher.
|
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
BasicDecider.checkFileDetails(ReturnValue returnValue,
FileMetadata fm)
Performs any additional checks on the file before adding it to the list of files to incorporate.
|
protected void |
BasicDecider.printFileMetadata(ReturnValue file,
FileMetadata fm) |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
ProvisionFiles.provisionFile(String input,
String output,
boolean skipIfMissing,
ArrayList<FileMetadata> fileArray,
boolean fullOutputPath,
FileMetadata metadata)
provisionFile.
|
protected boolean |
ProvisionFiles.putDestination(BufferedInputStream reader,
String output,
int bufLen,
String input,
ArrayList<FileMetadata> fileArray,
boolean fullOutputPath,
FileMetadata metadata)
HTTP writeback currently not supported S3 uses multi-part upload which should deal with failed uploads (maybe) I'm not really dealing
with failed upload recovery here...
|
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
ProvisionFiles.provisionFile(String input,
String output,
boolean skipIfMissing,
ArrayList<FileMetadata> fileArray,
boolean fullOutputPath,
FileMetadata metadata)
provisionFile.
|
protected boolean |
ProvisionFiles.putDestination(BufferedInputStream reader,
String output,
int bufLen,
String input,
ArrayList<FileMetadata> fileArray,
boolean fullOutputPath,
FileMetadata metadata)
HTTP writeback currently not supported S3 uses multi-part upload which should deal with failed uploads (maybe) I'm not really dealing
with failed upload recovery here...
|
| Modifier and Type | Method and Description |
|---|---|
static FileMetadata |
Metadata.fileString2FileMetadata(String fileString) |
| Modifier and Type | Method and Description |
|---|---|
static Map<Integer,List<FileMetadata>> |
FileLinkerParser.parse(String filename,
char separator) |
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