| 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.
|
| io.seqware.pipeline.plugins |
Newly written SeqWare plugins
|
| io.seqware.pipeline.plugins.sanity |
Base classes for the sanity check tool.
|
| net.sourceforge.seqware.common.hibernate |
Looks like utility classes for navigating the metadb.
|
| net.sourceforge.seqware.common.metadata |
Critical classes that effectively convert API calls into actions against the DB and web service.
|
| net.sourceforge.seqware.common.model |
Hibernate model classes for the metadb.
|
| net.sourceforge.seqware.common.model.lists |
Looks like various container classes for XML serialization.
|
| net.sourceforge.seqware.common.module |
Utility classes really.
|
| net.sourceforge.seqware.common.util.filetools |
Tools for dealing with files.
|
| net.sourceforge.seqware.common.util.runtools |
Tools for running commands.
|
| net.sourceforge.seqware.pipeline.bundle |
Utility classes for interacting with workflow bundles.
|
| net.sourceforge.seqware.pipeline.decider |
Interface for deciders.
|
| net.sourceforge.seqware.pipeline.deciders |
BasicDecider.
|
| net.sourceforge.seqware.pipeline.module |
This package provides the SeqWare module interface and API, including
common code and classes.
|
| net.sourceforge.seqware.pipeline.modules |
Executables that can be called by workflows and users.
|
| net.sourceforge.seqware.pipeline.modules.utilities |
Modules that are used by workflows.
|
| net.sourceforge.seqware.pipeline.plugin |
Interface for plugins and the workflow launcher for some reason.
|
| net.sourceforge.seqware.pipeline.plugins |
Create and manipulate databases for extended testing.
|
| net.sourceforge.seqware.pipeline.plugins.checkdb |
Check the metadb for errors in convention and structure.
|
| net.sourceforge.seqware.pipeline.plugins.deletion |
Implementation for the deletion tool that can delete workflow runs.
|
| net.sourceforge.seqware.pipeline.plugins.fileprovenance |
Dump out the file provenance report to the user.
|
| net.sourceforge.seqware.pipeline.workflowV2.engine.oozie |
Implementation of the Oozie workflow engine.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
WorkflowEngine.runWorkflow()
Run the prepared workflow.
|
ReturnValue |
Scheduler.scheduleInstalledBundle(String workflowAccession,
List<String> iniFiles,
boolean metadataWriteback,
List<String> parentAccessions,
List<String> parentsLinkedToWR,
List<String> cmdLineOptions,
String scheduledHost,
String workflowEngine,
Set<Integer> inputFiles)
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.
|
ReturnValue |
Scheduler.scheduleInstalledBundle(String workflowAccession,
List<String> iniFiles,
boolean metadataWriteback,
List<String> parentAccessions,
List<String> parentsLinkedToWR,
List<String> cmdLineOptions,
String scheduledHost,
String workflowEngine,
Set<Integer> inputFiles,
boolean allowMissingVars)
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.All needed
info is pulled from the workflow table which was populated when the workflow was installed.
|
ReturnValue |
WorkflowEngine.watchWorkflow(String jobToken)
Watch a workflow and return running information until it completes.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
WhiteStarWorkflowEngine.runWorkflow() |
ReturnValue |
WhiteStarWorkflowEngine.runWorkflow(SortedSet<String> set)
Run a workflow, steps contained within set are skipped.
|
ReturnValue |
WhiteStarWorkflowEngine.watchWorkflow(String jobToken) |
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
WorkflowRescheduler.clean_up() |
ReturnValue |
WorkflowRelauncher.clean_up() |
ReturnValue |
WorkflowWatcher.clean_up() |
ReturnValue |
UserSettingsPlugin.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
FileProvenanceQueryTool.clean_up() |
ReturnValue |
WorkflowScheduler.clean_up() |
ReturnValue |
WorkflowLauncher.clean_up() |
ReturnValue |
WorkflowLifecycle.clean_up() |
ReturnValue |
WorkflowRescheduler.do_run() |
ReturnValue |
WorkflowRelauncher.do_run() |
ReturnValue |
WorkflowWatcher.do_run() |
ReturnValue |
UserSettingsPlugin.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
FileProvenanceQueryTool.do_run() |
ReturnValue |
WorkflowScheduler.do_run() |
ReturnValue |
WorkflowLauncher.do_run() |
ReturnValue |
WorkflowLifecycle.do_run() |
ReturnValue |
WorkflowRescheduler.do_test() |
ReturnValue |
WorkflowRelauncher.do_test() |
ReturnValue |
WorkflowWatcher.do_test() |
ReturnValue |
UserSettingsPlugin.do_test()
Perform any active system testing here.
|
ReturnValue |
FileProvenanceQueryTool.do_test() |
ReturnValue |
WorkflowScheduler.do_test() |
ReturnValue |
WorkflowLauncher.do_test() |
ReturnValue |
WorkflowLifecycle.do_test() |
ReturnValue |
WorkflowRescheduler.init() |
ReturnValue |
WorkflowRelauncher.init() |
ReturnValue |
WorkflowWatcher.init() |
ReturnValue |
UserSettingsPlugin.init()
Plugin initialization code goes here.
|
ReturnValue |
FileProvenanceQueryTool.init() |
ReturnValue |
WorkflowScheduler.init() |
ReturnValue |
WorkflowLauncher.init() |
ReturnValue |
WorkflowLifecycle.init() |
ReturnValue |
UserSettingsPlugin.parse_parameters()
Parameter validation code goes here.
|
static ReturnValue |
WorkflowRescheduler.validateEngineString(String engine) |
static ReturnValue |
WorkflowScheduler.validateEngineString(String engine) |
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
SanityCheck.clean_up() |
ReturnValue |
SanityCheck.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
SanityCheck.do_test()
Perform any active system testing here.
|
ReturnValue |
SanityCheck.init()
Plugin initialization code goes here.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
FindAllTheFiles.addAttributeToReturnValue(ReturnValue ret,
String key,
String value) |
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 | Method and Description |
|---|---|
ReturnValue |
MetadataWS.add_empty_processing_event_by_parent_accession(int[] parentAccessions)
add_empty_processing_event_by_parent_accession.
|
ReturnValue |
Metadata.add_empty_processing_event_by_parent_accession(int[] parentAccessions)
add_empty_processing_event_by_parent_accession.
|
ReturnValue |
MetadataNoConnection.add_empty_processing_event_by_parent_accession(int[] parentAccessions)
add_empty_processing_event_by_parent_accession.
|
ReturnValue |
MetadataDB.add_empty_processing_event_by_parent_accession(int[] parentAccessions)
add_empty_processing_event_by_parent_accession.
|
ReturnValue |
MetadataInMemory.add_empty_processing_event_by_parent_accession(int[] parentAccessions) |
ReturnValue |
MetadataWS.add_empty_processing_event(int[] parentIDs)
add_empty_processing_event.
|
ReturnValue |
Metadata.add_empty_processing_event(int[] parentIDs)
add_empty_processing_event.
|
ReturnValue |
MetadataNoConnection.add_empty_processing_event(int[] parentIDs)
add_empty_processing_event.
|
ReturnValue |
MetadataDB.add_empty_processing_event(int[] parentIDs)
add_empty_processing_event.
|
ReturnValue |
MetadataInMemory.add_empty_processing_event(int[] parentIDs) |
ReturnValue |
MetadataWS.add_task_group(int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
add_task_group.
|
ReturnValue |
Metadata.add_task_group(int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
add_task_group.
|
ReturnValue |
MetadataNoConnection.add_task_group(int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
add_task_group.
|
ReturnValue |
MetadataDB.add_task_group(int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
add_task_group.
|
ReturnValue |
MetadataInMemory.add_task_group(int[] parentIDs,
int[] childIDs,
String algorithm,
String description) |
ReturnValue |
MetadataWS.addExperiment(Integer studySwAccession,
Integer platformId,
String description,
String title,
Integer experimentLibraryDesignId,
Integer experimentSpotDesignId)
addExperiment.
|
ReturnValue |
Metadata.addExperiment(Integer studySwAccession,
Integer platformId,
String description,
String title,
Integer experimentLibraryDesignId,
Integer experimentSpotDesignId)
addExperiment.
|
ReturnValue |
MetadataNoConnection.addExperiment(Integer studySwAccession,
Integer platformId,
String description,
String title,
Integer experimentLibraryDesignId,
Integer experimentSpotDesignId)
addExperiment.
|
ReturnValue |
MetadataDB.addExperiment(Integer studySwAccession,
Integer platformId,
String description,
String title,
Integer experiment_library_design_id,
Integer experiment_spot_design_id)
addExperiment.
|
ReturnValue |
MetadataInMemory.addExperiment(Integer studySwAccession,
Integer platformId,
String description,
String title,
Integer experimentLibraryDesignId,
Integer experimentSpotDesignId) |
ReturnValue |
MetadataWS.addIUS(Integer laneAccession,
Integer sampleAccession,
String name,
String description,
String barcode,
boolean skip) |
ReturnValue |
Metadata.addIUS(Integer laneAccession,
Integer sampleAccession,
String name,
String description,
String barcode,
boolean skip)
addSample.
|
ReturnValue |
MetadataNoConnection.addIUS(Integer laneAccession,
Integer sampleAccession,
String name,
String description,
String barcode,
boolean skip) |
ReturnValue |
MetadataDB.addIUS(Integer laneAccession,
Integer sampleAccession,
String name,
String description,
String barcode,
boolean skip) |
ReturnValue |
MetadataInMemory.addIUS(Integer laneAccession,
Integer sampleAccession,
String name,
String description,
String barcode,
boolean skip) |
ReturnValue |
MetadataWS.addLane(Integer sequencerRunAccession,
Integer studyTypeId,
Integer libraryStrategyId,
Integer librarySelectionId,
Integer librarySourceId,
String name,
String description,
String cycleDescriptor,
boolean skip,
Integer laneNumber) |
ReturnValue |
Metadata.addLane(Integer sequencerRunAccession,
Integer studyTypeId,
Integer libraryStrategyId,
Integer librarySelectionId,
Integer librarySourceId,
String name,
String description,
String cycleDescriptor,
boolean skip,
Integer laneNumber)
addSample.
|
ReturnValue |
MetadataNoConnection.addLane(Integer sequencerRunAccession,
Integer studyTypeId,
Integer libraryStrategyId,
Integer librarySelectionId,
Integer librarySourceId,
String name,
String description,
String cycleDescriptor,
boolean skip,
Integer laneNumber) |
ReturnValue |
MetadataDB.addLane(Integer sequencerRunAccession,
Integer studyTypeId,
Integer libraryStrategyId,
Integer librarySelectionId,
Integer librarySourceId,
String name,
String description,
String cycleDescriptor,
boolean skip,
Integer laneNumber) |
ReturnValue |
MetadataInMemory.addLane(Integer sequencerRunAccession,
Integer studyTypeId,
Integer libraryStrategyId,
Integer librarySelectionId,
Integer librarySourceId,
String name,
String description,
String cycleDescriptor,
boolean skip,
Integer laneNumber) |
ReturnValue |
MetadataWS.addSample(Integer experimentAccession,
Integer parentSampleAccession,
Integer organismId,
String description,
String title)
addSample.
|
ReturnValue |
Metadata.addSample(Integer experimentAccession,
Integer parentSampleAccession,
Integer organismId,
String description,
String title)
addSample.
|
ReturnValue |
MetadataNoConnection.addSample(Integer experimentAccession,
Integer parentSampleAccession,
Integer organismId,
String description,
String title)
addSample.
|
ReturnValue |
MetadataDB.addSample(Integer experimentAccession,
Integer parentSampleAccession,
Integer organismId,
String description,
String title)
addSample.
|
ReturnValue |
MetadataInMemory.addSample(Integer experimentAccession,
Integer parentSampleAccession,
Integer organismId,
String description,
String title) |
ReturnValue |
MetadataWS.addSequencerRun(Integer platformAccession,
String name,
String description,
boolean pairdEnd,
boolean skip,
String filePath,
SequencerRunStatus status)
FIXME: there are problems with setting accession when I should set ID
|
ReturnValue |
Metadata.addSequencerRun(Integer platformAccession,
String name,
String description,
boolean pairdEnd,
boolean skip,
String filePath,
SequencerRunStatus status)
addSample.
|
ReturnValue |
MetadataNoConnection.addSequencerRun(Integer platformAccession,
String name,
String description,
boolean pairdEnd,
boolean skip,
String filePath,
SequencerRunStatus status) |
ReturnValue |
MetadataDB.addSequencerRun(Integer platformAccession,
String name,
String description,
boolean pairdEnd,
boolean skip,
String filePath,
SequencerRunStatus status) |
ReturnValue |
MetadataInMemory.addSequencerRun(Integer platformAccession,
String name,
String description,
boolean pairdEnd,
boolean skip,
String filePath,
SequencerRunStatus status) |
ReturnValue |
MetadataWS.addStudy(String title,
String description,
String centerName,
String centerProjectName,
Integer studyTypeId)
addStudy.
|
ReturnValue |
Metadata.addStudy(String title,
String description,
String centerName,
String centerProjectName,
Integer studyTypeId)
addStudy.
|
ReturnValue |
MetadataNoConnection.addStudy(String title,
String description,
String centerName,
String centerProjectName,
Integer studyTypeId)
addStudy.
|
ReturnValue |
MetadataDB.addStudy(String title,
String description,
String centerName,
String centerProjectName,
Integer studyTypeId)
addStudy.
|
ReturnValue |
MetadataInMemory.addStudy(String title,
String description,
String centerName,
String centerProjectName,
Integer studyTypeId) |
ReturnValue |
MetadataWS.addWorkflow(String name,
String version,
String description,
String baseCommand,
String configFile,
String templateFile,
String provisionDir,
boolean storeProvisionDir,
String archiveZip,
boolean storeArchiveZip,
String workflowClass,
String workflowType,
String workflowEngine,
String seqwareVersion)
addWorkflow.
|
ReturnValue |
Metadata.addWorkflow(String name,
String version,
String description,
String baseCommand,
String configFile,
String templateFile,
String provisionDir,
boolean storeProvisionDir,
String archiveZip,
boolean storeArchiveZip,
String workflowClass,
String workflowType,
String workflowEngine,
String seqwareVersion)
addWorkflow.
|
ReturnValue |
MetadataNoConnection.addWorkflow(String name,
String version,
String description,
String baseCommand,
String configFile,
String templateFile,
String provisionDir,
boolean storeProvisionDir,
String archiveZip,
boolean storeArchiveZip,
String workflowClass,
String workflowType,
String workflowEngine,
String seqwareVersion)
addWorkflow.
|
ReturnValue |
MetadataDB.addWorkflow(String name,
String version,
String description,
String baseCommand,
String configFile,
String templateFile,
String provisionDir,
boolean storeProvisionDir,
String archiveZip,
boolean storeArchiveZip,
String workflowClass,
String workflowType,
String workflowEngine,
String seqwareVersion) |
ReturnValue |
MetadataInMemory.addWorkflow(String name,
String version,
String description,
String baseCommand,
String configFile,
String templateFile,
String provisionDir,
boolean storeProvisionDir,
String archiveZip,
boolean storeArchiveZip,
String workflowClass,
String workflowType,
String workflowEngine,
String seqwareVersion) |
protected ReturnValue |
MetadataWS.addWorkflowParam(HashMap<String,Map<String,String>> hm,
String key,
Workflow workflow) |
ReturnValue |
MetadataWS.associate_processing_event_with_parents_and_child(int processingID,
int[] parentIDs,
int[] childIDs)
associate_processing_event_with_parents_and_child.
|
ReturnValue |
Metadata.associate_processing_event_with_parents_and_child(int processingID,
int[] parentIDs,
int[] childIDs)
associate_processing_event_with_parents_and_child.
|
ReturnValue |
MetadataNoConnection.associate_processing_event_with_parents_and_child(int processingID,
int[] parentIDs,
int[] childIDs)
associate_processing_event_with_parents_and_child.
|
ReturnValue |
MetadataDB.associate_processing_event_with_parents_and_child(int processingID,
int[] parentIDs,
int[] childIDs)
associate_processing_event_with_parents_and_child.
|
ReturnValue |
MetadataInMemory.associate_processing_event_with_parents_and_child(int processingID,
int[] parentIDs,
int[] childIDs) |
ReturnValue |
MetadataWS.clean_up()
clean_up.
|
ReturnValue |
Metadata.clean_up()
clean_up.
|
ReturnValue |
MetadataNoConnection.clean_up()
clean_up.
|
ReturnValue |
MetadataDB.clean_up()
clean_up.
|
ReturnValue |
MetadataInMemory.clean_up() |
ReturnValue |
MetadataWS.processing_event_to_task_group(int processingID,
int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
processing_event_to_task_group.
|
ReturnValue |
Metadata.processing_event_to_task_group(int processingID,
int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
processing_event_to_task_group.
|
ReturnValue |
MetadataNoConnection.processing_event_to_task_group(int processingID,
int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
processing_event_to_task_group.
|
ReturnValue |
MetadataDB.processing_event_to_task_group(int processingID,
int[] parentIDs,
int[] childIDs,
String algorithm,
String description)
processing_event_to_task_group.
|
ReturnValue |
MetadataInMemory.processing_event_to_task_group(int processingID,
int[] parentIDs,
int[] childIDs,
String algorithm,
String description) |
ReturnValue |
MetadataDB.set_processing_update_tstmp_if_null(int processingID) |
ReturnValue |
MetadataWS.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
Metadata.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
MetadataNoConnection.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
MetadataDB.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
MetadataInMemory.update_processing_event(int processingID,
ReturnValue retval) |
ReturnValue |
MetadataWS.update_processing_status(int processingID,
ProcessingStatus status)
update_processing_status.
|
ReturnValue |
Metadata.update_processing_status(int processingID,
ProcessingStatus status)
update_processing_status.
|
ReturnValue |
MetadataNoConnection.update_processing_status(int processingID,
ProcessingStatus status)
update_processing_status.
|
ReturnValue |
MetadataDB.update_processing_status(int processingID,
ProcessingStatus status)
update_processing_status.
|
ReturnValue |
MetadataInMemory.update_processing_status(int processingID,
ProcessingStatus status) |
ReturnValue |
MetadataWS.update_processing_workflow_run(int processingID,
int workflowRunAccession)
update_processing_workflow_run.
|
ReturnValue |
Metadata.update_processing_workflow_run(int processingID,
int workflowRunID)
update_processing_workflow_run.
|
ReturnValue |
MetadataNoConnection.update_processing_workflow_run(int processingID,
int workflowRunAccession)
update_processing_workflow_run.
|
ReturnValue |
MetadataDB.update_processing_workflow_run(int processingID,
int workflowRunAccession)
update_processing_workflow_run.
|
ReturnValue |
MetadataInMemory.update_processing_workflow_run(int processingID,
int workflowRunID) |
ReturnValue |
MetadataWS.update_workflow_run(int workflowRunId,
String pegasusCmd,
String workflowTemplate,
WorkflowRunStatus status,
String statusCmd,
String workingDirectory,
String dax,
String ini,
String host,
String stdErr,
String stdOut,
String workflowEngine,
Set<Integer> inputFiles)
update_workflow_run.
|
ReturnValue |
Metadata.update_workflow_run(int workflowRunId,
String pegasusCmd,
String workflowTemplate,
WorkflowRunStatus status,
String statusCmd,
String workingDirectory,
String dax,
String ini,
String host,
String stdErr,
String stdOut,
String workflowEngine,
Set<Integer> inputFiles)
update_workflow_run.
|
ReturnValue |
MetadataNoConnection.update_workflow_run(int workflowRunId,
String pegasusCmd,
String workflowTemplate,
WorkflowRunStatus status,
String statusCmd,
String workingDirectory,
String dax,
String ini,
String host,
String stdErr,
String stdOut,
String workflowEngine,
Set<Integer> inputFiles)
update_workflow_run.
|
ReturnValue |
MetadataDB.update_workflow_run(int workflowRunId,
String pegasusCmd,
String workflowTemplate,
WorkflowRunStatus status,
String statusCmd,
String workingDirectory,
String dax,
String ini,
String host,
String stdErr,
String stdOut,
String workflowengine,
Set<Integer> inputFiles)
update_workflow_run.
|
ReturnValue |
MetadataInMemory.update_workflow_run(int workflowRunId,
String pegasusCmd,
String workflowTemplate,
WorkflowRunStatus status,
String statusCmd,
String workingDirectory,
String dax,
String ini,
String host,
String stdErr,
String stdOut,
String workflowEngine,
Set<Integer> inputFiles) |
ReturnValue |
MetadataWS.updateWorkflow(int workflowId,
String permanentBundleLocation)
updateWorkflow.
|
ReturnValue |
Metadata.updateWorkflow(int workflowId,
String permanentBundleLocation)
updateWorkflow.
|
ReturnValue |
MetadataNoConnection.updateWorkflow(int workflowId,
String permanentBundleLocation)
updateWorkflow.
|
ReturnValue |
MetadataDB.updateWorkflow(int workflowId,
String permanentBundleLocation)
updateWorkflow.
|
ReturnValue |
MetadataInMemory.updateWorkflow(int workflowId,
String permanentBundleLocation) |
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
MetadataWS.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
Metadata.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
MetadataNoConnection.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
MetadataDB.update_processing_event(int processingID,
ReturnValue retval)
update_processing_event.
|
ReturnValue |
MetadataInMemory.update_processing_event(int processingID,
ReturnValue retval) |
| Modifier and Type | Method and Description |
|---|---|
static ReturnValue |
Processing.clone(Processing newP)
clone.
|
| Modifier and Type | Field and Description |
|---|---|
protected List<ReturnValue> |
ReturnValueList.tList |
| Modifier and Type | Method and Description |
|---|---|
List<ReturnValue> |
ReturnValueList.getList()
getList.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ReturnValueList.add(ReturnValue ex)
add.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ReturnValueList.setList(List<ReturnValue> list)
setList.
|
| Modifier and Type | Method and Description |
|---|---|
static ReturnValue |
ReturnValue.featureNotImplemented()
featureNotImplemented.
|
| Modifier and Type | Field and Description |
|---|---|
ReturnValue |
FileTools.LocalhostPair.returnValue |
| Modifier and Type | Method and Description |
|---|---|
static ReturnValue |
FileTools.dirPathExistsAndReadable(File file)
dirPathExistsAndReadable.
|
static ReturnValue |
FileTools.dirPathExistsAndWritable(File file)
dirPathExistsAndWritable.
|
static ReturnValue |
FileTools.fileExistsAndNotEmpty(File file)
fileExistsAndNotEmpty.
|
static ReturnValue |
FileTools.fileExistsAndReadable(File file)
fileExistsAndReadable.
|
static ReturnValue |
FileTools.verifyFile(File file)
verifyFile.
|
| Constructor and Description |
|---|
FileTools.LocalhostPair(String hostname,
ReturnValue returnValue) |
| Modifier and Type | Method and Description |
|---|---|
static ReturnValue |
RunTools.runCommand(Map<String,String> env,
String[] command) |
static ReturnValue |
RunTools.runCommand(Map<String,String> env,
String[] command,
int stdoutCapacity,
int stderrCapacity) |
static ReturnValue |
RunTools.runCommand(Map<String,String> env,
String[] command,
int stdoutCapacity,
int stderrCapacity,
String permanentStoragePrefix)
A simple command runner that captures the return value of the program.
|
static ReturnValue |
RunTools.runCommand(String command)
runCommand.
|
static ReturnValue |
RunTools.runCommand(String[] command)
runCommand.
|
static ReturnValue |
RunTools.waitAndGetReturn(Process p,
int stdoutLineCapacity,
int stderrLineCapacity,
String permanentStoragePrefix)
Wait on a process to finish, then parse information into return value
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
Bundle.copyBundle(String sourceFile,
String targetDir)
copyBundle.
|
ReturnValue |
Bundle.copyBundleToS3(File bundle,
String bundleOutputPrefix)
copyBundleToS3.
|
protected ReturnValue |
Bundle.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 |
Bundle.installBundle(File bundle,
File metadataFile,
List<String> workflows)
installBundle.
|
ReturnValue |
Bundle.installBundleDirOnly(File bundle,
File metadataFile,
List<String> workflows)
installBundleDirOnly.
|
ReturnValue |
Bundle.installBundleZipOnly(File bundle,
File metadataFile,
List<String> workflows)
installBundleZipOnly.
|
ReturnValue |
Bundle.packageBundle(File bundlePath,
File bundleOutput)
packageBundle.
|
ReturnValue |
Bundle.packageBundleToS3(File bundlePath,
String bundleOutputPrefix)
packageBundleToS3.
|
ReturnValue |
Bundle.unpackageBundle(File bundle)
unpackageBundle.
|
ReturnValue |
Bundle.unpackageBundleFromS3(String bundleURL)
unpackageBundleFromS3.
|
ReturnValue |
Bundle.validateBundle(File bundle)
validateBundle.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
DeciderInterface.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
DeciderInterface.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
DeciderInterface.do_summary()
Just returns a summary of what would be run.
|
ReturnValue |
DeciderInterface.do_test()
Perform any active system testing here.
|
ReturnValue |
DeciderInterface.init()
Plugin initialization code goes here.
|
ReturnValue |
DeciderInterface.parse_parameters()
Parameter validation code goes here.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
BasicDecider.clean_up() |
ReturnValue |
BasicDecider.do_run() |
ReturnValue |
BasicDecider.do_summary() |
ReturnValue |
BasicDecider.do_test() |
protected ReturnValue |
BasicDecider.doFinalCheck(String commaSeparatedFilePaths,
String commaSeparatedParentAccessions)
allow to user to do the final check and decide to run or cancel the decider e.g.
|
ReturnValue |
BasicDecider.init() |
| Modifier and Type | Method and Description |
|---|---|
Map<String,List<ReturnValue>> |
BasicDecider.separateFiles(List<ReturnValue> vals,
String groupBy) |
| 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 |
|---|---|
Map<String,List<ReturnValue>> |
BasicDecider.separateFiles(List<ReturnValue> vals,
String groupBy) |
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
ModuleInterface.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
Module.clean_up()
clean_up.
|
ReturnValue |
ModuleInterface.do_run()
Performs the main tasks for the module.
|
abstract ReturnValue |
Module.do_run()
do_run.
|
ReturnValue |
TestModule.do_run()
do_run.
|
ReturnValue |
ModuleInterface.do_test()
Perform any active system testing here.
|
abstract ReturnValue |
Module.do_test()
do_test.
|
ReturnValue |
TestModule.do_test()
do_test.
|
ReturnValue |
ModuleInterface.do_verify_input()
Input data validation code goes here.
|
abstract ReturnValue |
Module.do_verify_input()
do_verify_input.
|
ReturnValue |
TestModule.do_verify_input()
do_verify_input.
|
ReturnValue |
ModuleInterface.do_verify_output()
Perform post-task tests here.
|
abstract ReturnValue |
Module.do_verify_output()
do_verify_output.
|
ReturnValue |
TestModule.do_verify_output()
do_verify_output.
|
ReturnValue |
ModuleInterface.do_verify_parameters()
Parameter validation code goes here.
|
abstract ReturnValue |
Module.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
TestModule.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
ModuleInterface.init()
Module initialization code goes here.
|
ReturnValue |
Module.init()
init.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
GenericCommandRunner.clean_up()
clean_up.
|
ReturnValue |
GenericMetadataSaver.clean_up()
Deprecated.
clean_up.
|
ReturnValue |
GenericCommandRunner.do_run()
do_run.
|
ReturnValue |
GenericMetadataSaver.do_run()
Deprecated.
do_run.
|
ReturnValue |
GenericCommandRunner.do_test()
do_test.
|
ReturnValue |
GenericMetadataSaver.do_test()
Deprecated.
do_test.
|
ReturnValue |
GenericCommandRunner.do_verify_input()
do_verify_input.
|
ReturnValue |
GenericMetadataSaver.do_verify_input()
Deprecated.
do_verify_input.
|
ReturnValue |
GenericCommandRunner.do_verify_output()
do_verify_output.
|
ReturnValue |
GenericMetadataSaver.do_verify_output()
Deprecated.
do_verify_output.
|
ReturnValue |
GenericCommandRunner.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
GenericMetadataSaver.do_verify_parameters()
Deprecated.
do_verify_parameters.
|
ReturnValue |
GenericCommandRunner.init()
init.
|
ReturnValue |
GenericMetadataSaver.init()
Deprecated.
init.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
S3ListFiles.clean_up()
clean_up.
|
ReturnValue |
S3DeleteFiles.clean_up()
clean_up.
|
ReturnValue |
S3CreateFileURLs.clean_up()
clean_up.
|
ReturnValue |
S3UploadDirectory.do_run() |
ReturnValue |
S3ListFiles.do_run()
do_run.
|
ReturnValue |
ProvisionDependenciesBundle.do_run()
do_run.
|
ReturnValue |
S3DeleteFiles.do_run()
do_run.
|
ReturnValue |
ProvisionFiles.do_run()
do_run.
|
ReturnValue |
S3CreateFileURLs.do_run()
do_run.
|
ReturnValue |
S3UploadDirectory.do_test()
Things to check: * FIXME
|
ReturnValue |
S3ListFiles.do_test()
do_test.
|
ReturnValue |
ProvisionDependenciesBundle.do_test()
do_test.
|
ReturnValue |
S3DeleteFiles.do_test()
do_test.
|
ReturnValue |
ProvisionFiles.do_test()
do_test.
|
ReturnValue |
S3CreateFileURLs.do_test()
do_test.
|
ReturnValue |
S3UploadDirectory.do_verify_input() |
ReturnValue |
S3ListFiles.do_verify_input()
do_verify_input.
|
ReturnValue |
ProvisionDependenciesBundle.do_verify_input()
do_verify_input.
|
ReturnValue |
S3DeleteFiles.do_verify_input()
do_verify_input.
|
ReturnValue |
ProvisionFiles.do_verify_input()
do_verify_input.
|
ReturnValue |
S3CreateFileURLs.do_verify_input()
do_verify_input.
|
ReturnValue |
S3UploadDirectory.do_verify_output() |
ReturnValue |
S3ListFiles.do_verify_output()
do_verify_output.
|
ReturnValue |
ProvisionDependenciesBundle.do_verify_output()
do_verify_output.
|
ReturnValue |
S3DeleteFiles.do_verify_output()
do_verify_output.
|
ReturnValue |
ProvisionFiles.do_verify_output()
do_verify_output.
|
ReturnValue |
S3CreateFileURLs.do_verify_output()
do_verify_output.
|
ReturnValue |
S3UploadDirectory.do_verify_parameters() |
ReturnValue |
S3ListFiles.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
ProvisionDependenciesBundle.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
S3DeleteFiles.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
ProvisionFiles.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
S3CreateFileURLs.do_verify_parameters()
do_verify_parameters.
|
ReturnValue |
S3ListFiles.init()
init.
|
ReturnValue |
S3DeleteFiles.init()
init.
|
ReturnValue |
S3CreateFileURLs.init()
init.
|
protected ReturnValue |
S3UploadDirectory.recursivelyUploadDir(String inputDir,
String outputBucket,
String outputPrefix,
com.amazonaws.services.s3.transfer.TransferManager tx) |
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
PluginInterface.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
PluginInterface.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
PluginInterface.do_test()
Perform any active system testing here.
|
ReturnValue |
PluginInterface.init()
Plugin initialization code goes here.
|
ReturnValue |
PluginInterface.parse_parameters()
Parameter validation code goes here.
|
ReturnValue |
Plugin.parse_parameters()
Parameter validation code goes here.
|
| Modifier and Type | Method and Description |
|---|---|
protected ReturnValue |
Metadata.addExperiment() |
protected ReturnValue |
Metadata.addFile() |
protected ReturnValue |
Metadata.addIUS() |
protected ReturnValue |
Metadata.addLane() |
protected ReturnValue |
Metadata.addSample() |
protected ReturnValue |
Metadata.addSequencerRun() |
protected ReturnValue |
Metadata.addStudy() |
protected ReturnValue |
Metadata.addWorkflow() |
protected ReturnValue |
Metadata.addWorkflowRun() |
ReturnValue |
ProcessingDataStructure2Dot.clean_up() |
ReturnValue |
ModuleRunner.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
BundleManager.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
HelloWorld.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
WorkflowRunFilesInitialPopulationPlugin.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
Metadata.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
AttributeAnnotator.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
WorkflowStatusChecker.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
MarkdownPlugin.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
OozieXML2Dot.clean_up() |
ReturnValue |
CycleChecker.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
BatchMetadataInjection.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
WorkflowRunReporter.clean_up()
Perform post-task clean-up here.
|
ReturnValue |
FileLinker.clean_up() |
ReturnValue |
ProcessingDataStructure2Dot.do_run() |
ReturnValue |
ModuleRunner.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
BundleManager.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
HelloWorld.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
WorkflowRunFilesInitialPopulationPlugin.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
Metadata.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
AttributeAnnotator.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
WorkflowStatusChecker.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
MarkdownPlugin.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
OozieXML2Dot.do_run() |
ReturnValue |
CycleChecker.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
BatchMetadataInjection.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
WorkflowRunReporter.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
FileLinker.do_run() |
ReturnValue |
ProcessingDataStructure2Dot.do_test() |
ReturnValue |
ModuleRunner.do_test()
Perform any active system testing here.
|
ReturnValue |
BundleManager.do_test()
Perform any active system testing here.
|
ReturnValue |
HelloWorld.do_test()
Perform any active system testing here.
|
ReturnValue |
WorkflowRunFilesInitialPopulationPlugin.do_test()
Perform any active system testing here.
|
ReturnValue |
Metadata.do_test()
Perform any active system testing here.
|
ReturnValue |
AttributeAnnotator.do_test()
Perform any active system testing here.
|
ReturnValue |
WorkflowStatusChecker.do_test()
Perform any active system testing here.
|
ReturnValue |
MarkdownPlugin.do_test()
Perform any active system testing here.
|
ReturnValue |
OozieXML2Dot.do_test() |
ReturnValue |
CycleChecker.do_test()
Perform any active system testing here.
|
ReturnValue |
BatchMetadataInjection.do_test()
Perform any active system testing here.
|
ReturnValue |
WorkflowRunReporter.do_test()
Perform any active system testing here.
|
ReturnValue |
FileLinker.do_test() |
ReturnValue |
ProcessingDataStructure2Dot.init() |
ReturnValue |
ModuleRunner.init()
Plugin initialization code goes here.
|
ReturnValue |
BundleManager.init()
Plugin initialization code goes here.
|
ReturnValue |
HelloWorld.init()
Plugin initialization code goes here.
|
ReturnValue |
WorkflowRunFilesInitialPopulationPlugin.init()
Plugin initialization code goes here.
|
ReturnValue |
Metadata.init()
Plugin initialization code goes here.
|
ReturnValue |
AttributeAnnotator.init()
Plugin initialization code goes here.
|
ReturnValue |
WorkflowStatusChecker.init()
Plugin initialization code goes here.
|
ReturnValue |
MarkdownPlugin.init()
Plugin initialization code goes here.
|
ReturnValue |
OozieXML2Dot.init() |
ReturnValue |
CycleChecker.init()
Plugin initialization code goes here.
|
ReturnValue |
BatchMetadataInjection.init()
Plugin initialization code goes here.
|
ReturnValue |
WorkflowRunReporter.init()
Plugin initialization code goes here.
|
ReturnValue |
FileLinker.init() |
protected ReturnValue |
Metadata.listFields(String table)
list the fields available to set
|
ReturnValue |
ModuleRunner.parse_parameters()
parse_parameters.
|
ReturnValue |
HelloWorld.parse_parameters()
Parameter validation code goes here.
|
ReturnValue |
WorkflowRunFilesInitialPopulationPlugin.parse_parameters()
Parameter validation code goes here.
|
ReturnValue |
MarkdownPlugin.parse_parameters()
Parameter validation code goes here.
|
protected ReturnValue |
Metadata.parseFields() |
protected ReturnValue |
Metadata.parseFiles() |
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
CheckDB.clean_up() |
ReturnValue |
CheckDB.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
CheckDB.do_test()
Perform any active system testing here.
|
ReturnValue |
CheckDB.init()
Plugin initialization code goes here.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
DeletionDB.clean_up() |
ReturnValue |
DeletionDB.do_run()
Performs the main tasks for the plugin.
|
ReturnValue |
DeletionDB.do_test()
Perform any active system testing here.
|
ReturnValue |
DeletionDB.init()
Plugin initialization code goes here.
|
| Modifier and Type | Method and Description |
|---|---|
ReturnValue |
FileProvenanceReporter.clean_up() |
ReturnValue |
FileProvenanceReporter.do_run() |
ReturnValue |
FileProvenanceReporter.do_test() |
ReturnValue |
FileProvenanceReporter.init() |
| 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
|
ReturnValue |
OozieWorkflowEngine.runWorkflow() |
ReturnValue |
OozieWorkflowEngine.watchWorkflow(String jobToken) |
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