Package org.galaxyproject.dockstore_galaxy_interface.language

Class GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl

java.lang.Object

org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl

All Implemented Interfaces:

io.dockstore.language.CompleteLanguageInterface, io.dockstore.language.MinimalLanguageInterface, io.dockstore.language.RecommendedLanguageInterface, org.pf4j.ExtensionPoint

Enclosing class:

GalaxyWorkflowPlugin

@Extension
public static class GalaxyWorkflowPlugin.GalaxyWorkflowPluginImpl
extends Object
implements io.dockstore.language.CompleteLanguageInterface

Nested Class Summary

Nested classes/interfaces inherited from interface io.dockstore.language.CompleteLanguageInterface

io.dockstore.language.CompleteLanguageInterface.RowData, io.dockstore.language.CompleteLanguageInterface.RowType

Nested classes/interfaces inherited from interface io.dockstore.language.MinimalLanguageInterface

io.dockstore.language.MinimalLanguageInterface.FileMetadata, io.dockstore.language.MinimalLanguageInterface.FileReader, io.dockstore.language.MinimalLanguageInterface.GenericFileType, io.dockstore.language.MinimalLanguageInterface.WorkflowMetadata

Constructor Summary

Constructors

Constructor	Description
GalaxyWorkflowPluginImpl()

Method Summary

Modifier and Type	Method	Description
protected Optional<String>	findTestParameterFile(String initialPath, io.dockstore.language.MinimalLanguageInterface.FileReader reader)
List<io.dockstore.language.CompleteLanguageInterface.RowData>	generateToolsTable(String initialPath, String contents, Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)
io.dockstore.common.DescriptorLanguage	getDescriptorLanguage()
Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata>	indexWorkflowFiles(String initialPath, String contents, io.dockstore.language.MinimalLanguageInterface.FileReader reader)
Pattern	initialPathPattern()
static boolean	isGXFormat2Workflow(Map<String,Object> workflow)	This is basically stolen from org.galaxyproject.gxformat2.Lint.
String	launchInstructions(String trsID)
Map<String,Object>	loadCytoscapeElements(String initialPath, String contents, Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)
io.dockstore.language.MinimalLanguageInterface.WorkflowMetadata	parseWorkflowForMetadata(String initialPath, String content, Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)
protected Boolean	pathExistsFromReader(io.dockstore.language.MinimalLanguageInterface.FileReader reader, String path)
io.dockstore.common.VersionTypeValidation	validateTestParameterSet(Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)
io.dockstore.common.VersionTypeValidation	validateWorkflowSet(String initialPath, String contents, Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GalaxyWorkflowPluginImpl

public GalaxyWorkflowPluginImpl()

Method Details

isGXFormat2Workflow

public static boolean isGXFormat2Workflow(Map<String,Object> workflow)

This is basically stolen from org.galaxyproject.gxformat2.Lint. However, that is generated code and cannot be modified so putting it here along with this warning that the two should probably be in sync.

Parameters:

workflow -

Returns:

launchInstructions

public String launchInstructions(String trsID)

Specified by:

launchInstructions in interface io.dockstore.language.RecommendedLanguageInterface

loadCytoscapeElements

public Map<String,Object> loadCytoscapeElements(String initialPath,
 String contents,
 Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)

Specified by:

loadCytoscapeElements in interface io.dockstore.language.CompleteLanguageInterface

generateToolsTable

public List<io.dockstore.language.CompleteLanguageInterface.RowData> generateToolsTable(String initialPath,
 String contents,
 Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)

Specified by:

generateToolsTable in interface io.dockstore.language.CompleteLanguageInterface

validateWorkflowSet

public io.dockstore.common.VersionTypeValidation validateWorkflowSet(String initialPath,
 String contents,
 Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)

Specified by:

validateWorkflowSet in interface io.dockstore.language.RecommendedLanguageInterface

validateTestParameterSet

public io.dockstore.common.VersionTypeValidation validateTestParameterSet(Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)

Specified by:

validateTestParameterSet in interface io.dockstore.language.RecommendedLanguageInterface

getDescriptorLanguage

public io.dockstore.common.DescriptorLanguage getDescriptorLanguage()

Specified by:

getDescriptorLanguage in interface io.dockstore.language.MinimalLanguageInterface

initialPathPattern

public Pattern initialPathPattern()

Specified by:

initialPathPattern in interface io.dockstore.language.MinimalLanguageInterface

indexWorkflowFiles

public Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexWorkflowFiles(String initialPath,
 String contents,
 io.dockstore.language.MinimalLanguageInterface.FileReader reader)

Specified by:

indexWorkflowFiles in interface io.dockstore.language.MinimalLanguageInterface

findTestParameterFile

protected Optional<String> findTestParameterFile(String initialPath,
 io.dockstore.language.MinimalLanguageInterface.FileReader reader)

pathExistsFromReader

protected Boolean pathExistsFromReader(io.dockstore.language.MinimalLanguageInterface.FileReader reader,
 String path)

parseWorkflowForMetadata

public io.dockstore.language.MinimalLanguageInterface.WorkflowMetadata parseWorkflowForMetadata(String initialPath,
 String content,
 Map<String,io.dockstore.language.MinimalLanguageInterface.FileMetadata> indexedFiles)

Specified by:

parseWorkflowForMetadata in interface io.dockstore.language.MinimalLanguageInterface