de.jstacs.utils.galaxy
Class GalaxyAdaptor

java.lang.Object
  de.jstacs.utils.galaxy.GalaxyAdaptor

public class GalaxyAdaptor
extends Object

Adaptor class between the parameter representation of Jstacs in Parameters and ParameterSets and the parameter representation in Galaxy. A GalaxyAdaptor can be created from a ParameterSet containing all parameters that are necessary for the execution of some program that shall be included in a Galaxy installation. The conversion is done by the method parse(String[]). If this method is called with first argument equal to "--create" and second argument a filename, then the Galaxy-representation of the current ParameterSet is stored to that file. Afterwards, the application and this file must be added to tool_conf.xml (see Galaxy tutorial for details). During the execution of the main program, addResult(Result, boolean, boolean) and addResultSet(ResultSet, boolean, boolean) can be used to add results of the computation to the results displayed in Galaxy, to export these and to add these to a summary page. If a protocol of the program run shall be written, a GalaxyAdaptor.Protocol object can be obtained by the getProtocol(boolean) method. After all results have been added and the protocol has been written, the method writeOutput() must be called to create the appropriate output files within Galaxy.

Author:

Jan Grau

Nested Class Summary

static class	GalaxyAdaptor.FileResult Result for files that are results of some computation.
static class	GalaxyAdaptor.LinkedImageResult Class for an ImageResult that is linked to a file that can be downloaded.
static class	GalaxyAdaptor.Protocol Class for a Protocol writer.

Constructor Summary

GalaxyAdaptor(ParameterSet parameters, String toolname, String description, String version, String command)
Creates a new GalaxyAdaptor from a given ParameterSet containing all parameters that are necessary for a program is shall be included in a Galaxy installation.

Method Summary

void	addResult(Result res, boolean export, boolean includeInSummary) Adds a result to the results of a program run.
void	addResultSet(ResultSet res, boolean exportAll, boolean includeInSummary) Adds a set of results to the results of a program run.
String	export(String filename, Result res) Exports a specified GalaxyAdaptor.LinkedImageResult of a program execution to a file provided by filename and returns the corresponding Galaxy data type.
void	fromGalaxyConfig(String filename) Parses the values of the parameters from a galaxy script file
static String	getColor(int depth) Returns the color for a specified depth within the parameter hierarchy.
String	getHtmlFilesPath() Returns the path where files, e.g. images, that shall be linked from the HTML summary shall be stored in.
static int	getHtmlId() Gets a unique id that can be used, e.g. to create unique filenames.
static String	getLegalName(String name) Returns a legal variable name in Galaxy
GalaxyAdaptor.Protocol	getProtocol(boolean exportProtocol) Returns an object for writing a protocol of a program run
boolean	parse(String[] args) Parses the command line.
void	setHelp(File helpfile) Sets the help, i.e., a more detailed description of the program to the contents of helpfile.
void	setHelp(String help) Sets the help, i.e., a more detailed description of the program to help.
String	toGalaxyConfig() Creates the contents of a Galaxy configuration file from all the information provided to this GalaxyAdaptor.
void	writeOutput() Writes all output files of one program execution.

Methods inherited from class java.lang.Object

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

Constructor Detail

GalaxyAdaptor

public GalaxyAdaptor(ParameterSet parameters,
                     String toolname,
                     String description,
                     String version,
                     String command)

Creates a new GalaxyAdaptor from a given ParameterSet containing all parameters that are necessary for a program is shall be included in a Galaxy installation. Besides the parameters, a name, a description, and a version number of the program must be provided. Additionally, the user must provide the command to run this program. For instance, if the program is bundled into a jar MyJar.jar, this command could be java -jar MyJar.jar.

Parameters:

parameters - the parameters of the program

toolname - the name of the program

description - a description of the program, may be supplemented by additional help provided by setHelp(File) or setHelp(String)

version - the version of the program

command - the command to run the program

Method Detail

getColor

public static String getColor(int depth)

Returns the color for a specified depth within the parameter hierarchy.

Parameters:

depth - the depth

Returns:

the color

getHtmlId

public static int getHtmlId()

Gets a unique id that can be used, e.g. to create unique filenames.

Returns:

the id

setHelp

public void setHelp(String help)

Sets the help, i.e., a more detailed description of the program to help.

Parameters:

help - the help text

setHelp

public void setHelp(File helpfile)
             throws IOException

Sets the help, i.e., a more detailed description of the program to the contents of helpfile.

Parameters:

helpfile - the file containing the help text

Throws:

IOException - if helpfile could not be read

getProtocol

public GalaxyAdaptor.Protocol getProtocol(boolean exportProtocol)

Returns an object for writing a protocol of a program run

Parameters:

exportProtocol - if true the protocol will be exported and accessible as extra result within Galaxy

Returns:

the protocol object

toGalaxyConfig

public String toGalaxyConfig()
                      throws Exception

Creates the contents of a Galaxy configuration file from all the information provided to this GalaxyAdaptor.

Returns:

the configuration

Throws:

Exception - if any of the parameters could not be converted

fromGalaxyConfig

public void fromGalaxyConfig(String filename)
                      throws Exception

Parses the values of the parameters from a galaxy script file

Parameters:

filename - the name of the script file

Throws:

Exception - if the parameter values could not be parsed

export

public String export(String filename,
                     Result res)
              throws IOException

Exports a specified GalaxyAdaptor.LinkedImageResult of a program execution to a file provided by filename and returns the corresponding Galaxy data type.

Parameters:

filename - the filename

res - the result

Returns:

the data type

Throws:

IOException - if the contents of res could not be written to the file

writeOutput

public void writeOutput()
                 throws IOException

Writes all output files of one program execution. This includes the summary of the execution, exported results and protocols, and images.

Throws:

IOException - if any of the files could not be created or written

parse

public boolean parse(String[] args)
              throws Exception

Parses the command line. If the first argument is equal to "--create", then the configuration file is written to the file with filename provided in the second argument. Otherwise the first argument must be "--run" to parse the parameters of a program run within Galaxy.

Parameters:

args - the arguments

Returns:

true if this execution should be a program run (as opposed to writing a configuration file)

Throws:

Exception - if the arguments could not be parsed or the Galaxy configuration file could not be created

addResult

public void addResult(Result res,
                      boolean export,
                      boolean includeInSummary)

Adds a result to the results of a program run.

Parameters:

res - the result

export - if true the result is exported to its own Galaxy result, e.g. for evaluation in other application within Galaxy

includeInSummary - if true the result is shown on the summary page

addResultSet

public void addResultSet(ResultSet res,
                         boolean exportAll,
                         boolean includeInSummary)

Adds a set of results to the results of a program run.

Parameters:

res - the results

exportAll - if true all results in this set are exported to their own Galaxy result, e.g. for evaluation in other application within Galaxy

includeInSummary - if true the results are shown on the summary page

getLegalName

public static String getLegalName(String name)

Returns a legal variable name in Galaxy

Parameters:

name - the original name

Returns:

the legalized name

getHtmlFilesPath

public String getHtmlFilesPath()

Returns the path where files, e.g. images, that shall be linked from the HTML summary shall be stored in.

Returns:

the path