| Package | Description |
|---|---|
| io.seqware.pipeline.api |
This package will store components of SeqWare that can be programmatically
called in order to manage the components of the SeqWare life-cycle.
|
| io.seqware.pipeline.engines.whitestar |
This is a simple reference implementation of a seqware engine used for development and debugging.
|
| net.sourceforge.seqware.pipeline.workflowV2 |
Back-end for the Java workflow language and Oozie engine.
|
| net.sourceforge.seqware.pipeline.workflowV2.engine.oozie |
Implementation of the Oozie workflow engine.
|
| net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object |
Implementation of workflow steps for Oozie.
|
| Modifier and Type | Method and Description |
|---|---|
static WorkflowEngine |
WorkflowTools.getWorkflowEngine(AbstractWorkflowDataModel dataModel,
Map<String,String> config,
boolean createDirectories) |
void |
WorkflowEngine.prepareWorkflow(AbstractWorkflowDataModel objectModel)
Prepare the workflow according to the info filled in the input objectModel.
|
| Modifier and Type | Method and Description |
|---|---|
void |
WhiteStarWorkflowEngine.prepareWorkflow(AbstractWorkflowDataModel objectModel) |
void |
WhiteStarWorkflowEngine.prepareWorkflow(AbstractWorkflowDataModel objectModel,
File nfsWorkDir) |
| Constructor and Description |
|---|
WhiteStarWorkflowEngine(AbstractWorkflowDataModel objectModel,
boolean useSge,
String threadsSgeParamFormat,
String maxMemorySgeParamFormat,
boolean createDirectories,
boolean parallel) |
| Modifier and Type | Method and Description |
|---|---|
AbstractWorkflowDataModel |
WorkflowDataModelFactory.getWorkflowDataModel(String bundlePath,
int workflowAccession,
int workflowRunAccession,
String workflowEngine)
load metadata.xml and load the class.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
AbstractWorkflowDataModel.prepare(AbstractWorkflowDataModel model)
Validates and potentially modifies the specified model in preparation for launching.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
OozieWorkflowXmlGenerator.generateWorkflowXml(AbstractWorkflowDataModel wfdm,
String output,
String nfsWorkDir,
org.apache.hadoop.fs.Path hdfsWorkDir,
boolean useSge,
File seqwareJar,
String threadsSgeParamFormat,
String maxMemorySgeParamFormat)
generate a dax file from the object model
|
static org.apache.hadoop.conf.Configuration |
OozieWorkflowEngine.initConf(AbstractWorkflowDataModel model) |
static org.apache.hadoop.fs.Path |
OozieWorkflowEngine.initHdfsWorkDir(AbstractWorkflowDataModel model,
org.apache.hadoop.conf.Configuration conf,
File nfsWorkDir) |
static File |
OozieWorkflowEngine.initNfsWorkDir(AbstractWorkflowDataModel model) |
void |
OozieWorkflowEngine.prepareWorkflow(AbstractWorkflowDataModel objectModel) |
| Constructor and Description |
|---|
OozieWorkflowEngine(AbstractWorkflowDataModel objectModel,
boolean useSge,
String threadsSgeParamFormat,
String maxMemorySgeParamFormat,
boolean createDirectories) |
| Constructor and Description |
|---|
WorkflowApp(AbstractWorkflowDataModel wfdm,
String nfsWorkDir,
org.apache.hadoop.fs.Path hdfsWorkDir,
boolean useSge,
File seqwareJar,
String threadsSgeParamFormat,
String maxMemorySgeParamFormat) |
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