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 Details

    • GalaxyToolXMLParserUtils

      public GalaxyToolXMLParserUtils()

  • Method Details

    • 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:
      toolInfo - tool info object
      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:
      toolInfo - tool info object
      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:
      toolInfo - tool info object
      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
      Returns:
      a new EoulsanException
      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
      Returns:
      a new EoulsanException
      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.