| 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.plugins |
Newly written SeqWare plugins
|
| io.seqware.pipeline.plugins.sanity |
Base classes for the sanity check tool.
|
| io.seqware.pipeline.plugins.sanity.checks |
Various state checks.
|
| net.sourceforge.seqware.common.metadata |
Critical classes that effectively convert API calls into actions against the DB and web service.
|
| 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.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.batchmetadatainjection |
PDE's batch metadata injection utility
|
| net.sourceforge.seqware.pipeline.plugins.fileprovenance |
Dump out the file provenance report to the user.
|
| net.sourceforge.seqware.pipeline.workflowV2 |
Back-end for the Java workflow language and Oozie engine.
|
| Modifier and Type | Field and Description |
|---|---|
protected Metadata |
Scheduler.metadata |
| Constructor and Description |
|---|
Scheduler(Metadata metadata,
Map<String,String> config)
Constructor for BasicWorkflow.
|
| Modifier and Type | Method and Description |
|---|---|
void |
UserSettingsPlugin.setMetadata(Metadata metadata)
Lets you set the metadata object
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
SanityCheckPluginInterface.check(QueryRunner qRunner,
Metadata metadataWS) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
DB_WS_ConsistencyCheck.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
WS_Check.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
Oozie_Check.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
Script_Check.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
HDFS_Check.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
BundleDir_Check.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
DB_Check.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
CLICheck.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
TutorialCheck.check(QueryRunner qRunner,
Metadata metadataWS) |
boolean |
ClientServerConsistencyCheck.check(QueryRunner qRunner,
Metadata metadataWS) |
| Modifier and Type | Class and Description |
|---|---|
class |
MetadataDB
MetadataDB class.
|
class |
MetadataInMemory
This stores some metadata in memory as an exploration of running workflows without a running database or web service.
|
class |
MetadataNoConnection
MetadataNoConnection class.
|
class |
MetadataWS |
| Modifier and Type | Method and Description |
|---|---|
static Metadata |
MetadataFactory.get(Map<String,String> settings) |
| Modifier and Type | Field and Description |
|---|---|
protected Metadata |
Bundle.metadata |
| Modifier and Type | Method and Description |
|---|---|
Metadata |
Bundle.getMetadata()
Getter for the field
metadata. |
| Modifier and Type | Method and Description |
|---|---|
void |
Bundle.setMetadata(Metadata metadata)
Setter for the field
metadata. |
| Constructor and Description |
|---|
Bundle(Metadata metadata,
Map<String,String> config)
Constructor for Bundle.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DeciderInterface.setMetadata(Metadata metadata)
Lets you set the metadata object
|
| Modifier and Type | Method and Description |
|---|---|
void |
BasicDecider.setMetaws(Metadata metaws) |
| Modifier and Type | Method and Description |
|---|---|
Metadata |
Module.getMetadata()
Getter for the field
metadata. |
| Modifier and Type | Method and Description |
|---|---|
void |
Module.setMetadata(Metadata metadata)
Setter for the field
metadata. |
| Modifier and Type | Field and Description |
|---|---|
protected Metadata |
Plugin.metadata |
| Modifier and Type | Method and Description |
|---|---|
void |
PluginInterface.setMetadata(Metadata metadata)
Lets you set the metadata object
|
void |
Plugin.setMetadata(Metadata metadata)
Lets you set the metadata object
|
| Modifier and Type | Method and Description |
|---|---|
protected Metadata |
WorkflowStatusChecker.getMetadata() |
| Modifier and Type | Method and Description |
|---|---|
void |
HelloWorld.setMetadata(Metadata metadata)
Lets you set the metadata object
|
void |
WorkflowRunFilesInitialPopulationPlugin.setMetadata(Metadata metadata)
Lets you set the metadata object
|
void |
MarkdownPlugin.setMetadata(Metadata metadata)
Lets you set the metadata object
|
| Modifier and Type | Method and Description |
|---|---|
void |
SampleInfo.print(Appendable writer,
Metadata metadata) |
void |
RunInfo.print(Appendable writer,
Metadata metadata) |
void |
LaneInfo.print(Appendable writer,
Metadata metadata) |
| Constructor and Description |
|---|
BatchMetadataParser(Metadata metadata,
Map<String,String> fields,
boolean interactive) |
CreateFromScratch(Metadata metadata,
Map<String,String> fields,
boolean interactive) |
ParseMiseqFile(Metadata metadata,
Map<String,String> fields,
boolean interactive) |
| Modifier and Type | Method and Description |
|---|---|
static Map<FileProvenanceParam,List<String>> |
ProvenanceUtility.convertOptionsToMap(joptsimple.OptionSet options,
Metadata metadata) |
| Constructor and Description |
|---|
WorkflowDataModelFactory(Map<String,String> config,
Metadata metadata)
This constructs the factory with only the parameters which shouldn't change from workflow to workflow.
|
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