Package fr.ens.biologie.genomique.eoulsan.galaxytools

Class GalaxyToolXMLParserUtils

java.lang.Object

fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils

public final class GalaxyToolXMLParserUtils
extends Object

This class define static utils methods to extract data in Galaxy tool XML file.

Since:

2.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
GalaxyToolXMLParserUtils()

Method Summary

Modifier and Type	Method	Description
static String	extractCheetahScript(Document doc)	Extract command tag in string.
static List<Element>	extractChildElementsByTagName(Element parentElement, String elementName)	Extract child elements by tag name.
static Map<String,ToolElement>	extractConditionalParamElement(ToolInfo toolInfo, Element parent)	Extract conditional param element.
static Map<String,ToolElement>	extractConditionalParamElement(ToolInfo toolInfo, Element parent, Map<String,Parameter> stepParameters)	Extract conditional param element.
static String	extractDescription(Document doc)	Extract description tag in string.
static String	extractDockerImage(Document doc)	Extract docker image attribute in string.
static List<Element>	extractElementsByTagName(ToolInfo toolInfo, Document doc, String tagName)	Extract elements by tag name.
static List<Element>	extractElementsByTagName(ToolInfo toolInfo, Document doc, String tagName, int expectedCount)	Extract elements by tag name.
static List<Element>	extractElementsByTagName(Element parent, String tagName)	Extract elements by tag name.
static List<Element>	extractElementsByTagName(Element parent, String tagName, int expectedCount)	Extract elements by tag name.
static Map<String,ToolElement>	extractInputs(ToolInfo toolInfo, Document doc, Map<String,Parameter> stepParameters)	Extract all input parameters define in document.
static List<String>	extractInterpreters(Document doc)	Extract interpreter attribute in string.
static Map<String,ToolElement>	extractOutputs(ToolInfo toolInfo, Document doc, Map<String,Parameter> stepParameters)	Extract all output parameters define in document.
static Map<String,ToolElement>	extractParamElement(ToolInfo toolInfo, Element parent, String elementName)	Extract parameter elements.
static Map<String,ToolElement>	extractParamElement(ToolInfo toolInfo, Element parent, String elementName, Map<String,Parameter> stepParameters)	Extract parameter elements.
static String	extractToolID(Document doc)	Extract tool id tag in string.
static String	extractToolName(Document doc)	Extract tool name tag in string.
static String	extractToolVersion(Document doc)	Extract tool version attribute in string.
static String	extractValueFromElement(Document doc, String elementName, int index, String attributeName)	Extract text from DOM from tag name, at the index place.
static EoulsanException	newEoulsanException(ToolInfo toolInfo, String message)	Create an EoulsanException.
static EoulsanException	newEoulsanException(ToolInfo toolInfo, String parameterName, String message)	Create an EoulsanException.
static void	setElementValue(ToolElement toolElement, Map<String,Parameter> stepParameters)	Set the tool element value.

Methods inherited from class java.lang.Object

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

Constructor Detail

GalaxyToolXMLParserUtils

public GalaxyToolXMLParserUtils()

Method Detail

extractParamElement

public static Map<String,ToolElement> extractParamElement(ToolInfo toolInfo,
                                                                Element parent,
                                                                String elementName)
                                                         throws EoulsanException

Extract parameter elements.

Parameters:

toolInfo - the ToolInfo object

parent - the parent

elementName - the element name

Returns:

a map with the Galaxy tool elements

Throws:

EoulsanException - the Eoulsan exception

extractParamElement

public static Map<String,ToolElement> extractParamElement(ToolInfo toolInfo,
                                                                Element parent,
                                                                String elementName,
                                                                Map<String,Parameter> stepParameters)
                                                         throws EoulsanException

Extract parameter elements.

Parameters:

toolInfo - the ToolInfo object

parent - the parent

elementName - the element name

stepParameters - step parameters

Returns:

a map with the Galaxy tool elements

Throws:

EoulsanException - the Eoulsan exception

setElementValue

public static void setElementValue(ToolElement toolElement,
                                   Map<String,Parameter> stepParameters)
                            throws EoulsanException

Set the tool element value.

Parameters:

toolElement - tool element

stepParameters - step parameters

Throws:

EoulsanException - if an error occurs while setting the value

extractConditionalParamElement

public static Map<String,ToolElement> extractConditionalParamElement(ToolInfo toolInfo,
                                                                           Element parent)
                                                                    throws EoulsanException

Extract conditional param element.

Parameters:

parent - the parent

Returns:

the map

Throws:

EoulsanException - the Eoulsan exception

extractConditionalParamElement

public static Map<String,ToolElement> extractConditionalParamElement(ToolInfo toolInfo,
                                                                           Element parent,
                                                                           Map<String,Parameter> stepParameters)
                                                                    throws EoulsanException

Extract conditional param element.

Parameters:

parent - the parent

stepParameters - the step parameters

Returns:

the map

Throws:

EoulsanException - the Eoulsan exception

extractElementsByTagName

public static List<Element> extractElementsByTagName(ToolInfo toolInfo,
                                                     Document doc,
                                                     String tagName)
                                              throws EoulsanException

Extract elements by tag name.

Parameters:

doc - the doc

tagName - the tag name

Returns:

the list

Throws:

EoulsanException - the Eoulsan exception

extractElementsByTagName

public static List<Element> extractElementsByTagName(ToolInfo toolInfo,
                                                     Document doc,
                                                     String tagName,
                                                     int expectedCount)
                                              throws EoulsanException

Extract elements by tag name.

Parameters:

toolInfo - ToolInfo object

doc - the doc

tagName - the tag name

expectedCount - the expected count

Returns:

the list

Throws:

EoulsanException - the Eoulsan exception

newEoulsanException

public static EoulsanException newEoulsanException(ToolInfo toolInfo,
                                                   String message)
                                            throws EoulsanException

Create an EoulsanException.

Parameters:

toolInfo - toolInfo object

message - error message

Throws:

EoulsanException - in any case

newEoulsanException

public static EoulsanException newEoulsanException(ToolInfo toolInfo,
                                                   String parameterName,
                                                   String message)
                                            throws EoulsanException

Create an EoulsanException.

Parameters:

toolInfo - toolInfo object

parameterName - parameter name

message - error message

Throws:

EoulsanException - in any case

extractElementsByTagName

public static List<Element> extractElementsByTagName(Element parent,
                                                     String tagName)
                                              throws EoulsanException

Extract elements by tag name.

Parameters:

parent - the parent

tagName - the tag name

Returns:

the list

Throws:

EoulsanException - the Eoulsan exception

extractElementsByTagName

public static List<Element> extractElementsByTagName(Element parent,
                                                     String tagName,
                                                     int expectedCount)
                                              throws EoulsanException

Extract elements by tag name.

Parameters:

parent - the parent

tagName - the tag name

expectedCount - the expected count

Returns:

the list

Throws:

EoulsanException - the Eoulsan exception

extractChildElementsByTagName

public static List<Element> extractChildElementsByTagName(Element parentElement,
                                                          String elementName)

Extract child elements by tag name.

Parameters:

parentElement - the parent element

elementName - the element name

Returns:

the list

extractOutputs

public static Map<String,ToolElement> extractOutputs(ToolInfo toolInfo,
                                                           Document doc,
                                                           Map<String,Parameter> stepParameters)
                                                    throws EoulsanException

Extract all output parameters define in document.

Parameters:

toolInfo - the tool information

doc - document represented tool xml

stepParameters - parameters for analysis

Returns:

all output parameters

Throws:

EoulsanException - if none output parameter found

extractInputs

public static Map<String,ToolElement> extractInputs(ToolInfo toolInfo,
                                                          Document doc,
                                                          Map<String,Parameter> stepParameters)
                                                   throws EoulsanException

Extract all input parameters define in document.

Parameters:

toolInfo - the tool information

doc - document represented tool xml

stepParameters - parameters for analysis

Returns:

all input parameters

Throws:

EoulsanException - if none input parameter found

extractCheetahScript

public static String extractCheetahScript(Document doc)

Extract command tag in string.

Parameters:

doc - document represented tool xml

Returns:

command string

extractInterpreters

public static List<String> extractInterpreters(Document doc)

Extract interpreter attribute in string.

Parameters:

doc - document represented tool xml

Returns:

interpreter names

extractDockerImage

public static String extractDockerImage(Document doc)

Extract docker image attribute in string.

Parameters:

doc - document represented tool xml

Returns:

the docker image name

extractDescription

public static String extractDescription(Document doc)

Extract description tag in string.

Parameters:

doc - document represented tool xml

Returns:

description

extractToolVersion

public static String extractToolVersion(Document doc)

Extract tool version attribute in string.

Parameters:

doc - document represented tool xml

Returns:

tool version string

extractToolName

public static String extractToolName(Document doc)

Extract tool name tag in string.

Parameters:

doc - document represented tool xml

Returns:

tool name string

extractToolID

public static String extractToolID(Document doc)

Extract tool id tag in string.

Parameters:

doc - document represented tool xml

Returns:

tool id string

extractValueFromElement

public static String extractValueFromElement(Document doc,
                                             String elementName,
                                             int index,
                                             String attributeName)

Extract text from DOM from tag name, at the index place. If attribute name defined return value attribute, otherwise return content text of element.

Parameters:

doc - document represented tool xml

elementName - element name to extract

index - index of element name to extract

attributeName - attribute name from element name to extract

Returns:

value corresponding to element name content or attribute of element name. Return null, if none corresponding element or attribute found.