Package ubic.gemma.cli.options

Class DataFileOptionsUtils

java.lang.Object

ubic.gemma.cli.options.DataFileOptionsUtils

public class DataFileOptionsUtils
extends Object

Utilities to add and process options for data files (raw data, processed data, designs, etc.).

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXCLUDE_SAMPLE_IDENTIFIERS_OPTION
static final String	OUTPUT_DIR_OPTION
static final String	OUTPUT_FILE_OPTION
static final String	SCALE_TYPE_OPTION
static final String	SEPARATE_SAMPLE_FROM_ASSAYS_IDENTIFIERS_OPTION
static final String	STANDARD_LOCATION_OPTION
static final String	STANDARD_OUTPUT_OPTION
static final String	USE_BIO_ASSAY_IDS_OPTION
static final String	USE_ENSEMBL_IDS_OPTION
static final String	USE_MULTIPLE_ROWS_FOR_ASSAYS_OPTION
static final String	USE_RAW_COLUMN_NAMES_OPTION

Constructor Summary

Constructors

Constructor	Description
DataFileOptionsUtils()

Method Summary

Modifier and Type	Method	Description
static void	addCellMetadataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)
static void	addDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, boolean allowFile, boolean allowDirectory, boolean allowCurrentDirectory, boolean allowStdout, BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)	Add options for writing data files, such as raw or processed data files.
static void	addDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)
static void	addDesignFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)
static void	addExpressionDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)
static void	addSingleCellExpressionDataFileOptions(org.apache.commons.cli.Options options, String what, boolean allowStandardLocation, BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)
static CellMetadataFileOptionValue	getCellMetadataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, String forceOption, boolean force)
static DataFileOptionValue	getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, boolean allowStdout, boolean allowCurrentDirectory, String forceOption, boolean force)	Obtain the result of the data file options added by addDataFileOptions(Options, String, boolean, boolean, boolean, boolean, boolean, BiConsumer)
static DataFileOptionValue	getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, String forceOption, boolean force)
static DesignFileOptionValue	getDesignFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, String forceOption, boolean force)
static ExpressionDataFileOptionValue	getExpressionDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, String forceOption, boolean force)
static SingleCellExpressionDataFileOptionValue	getSingleCellExpressionDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, String forceOption, boolean force)

Methods inherited from class java.lang.Object

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

Field Details

OUTPUT_FILE_OPTION

public static final String OUTPUT_FILE_OPTION

See Also:

• Constant Field Values

OUTPUT_DIR_OPTION

public static final String OUTPUT_DIR_OPTION

See Also:

• Constant Field Values

STANDARD_LOCATION_OPTION

public static final String STANDARD_LOCATION_OPTION

See Also:

• Constant Field Values

STANDARD_OUTPUT_OPTION

public static final String STANDARD_OUTPUT_OPTION

See Also:

• Constant Field Values

EXCLUDE_SAMPLE_IDENTIFIERS_OPTION

public static final String EXCLUDE_SAMPLE_IDENTIFIERS_OPTION

See Also:

• Constant Field Values

USE_BIO_ASSAY_IDS_OPTION

public static final String USE_BIO_ASSAY_IDS_OPTION

See Also:

• Constant Field Values

USE_RAW_COLUMN_NAMES_OPTION

public static final String USE_RAW_COLUMN_NAMES_OPTION

See Also:

• Constant Field Values

SCALE_TYPE_OPTION

public static final String SCALE_TYPE_OPTION

See Also:

• Constant Field Values

USE_MULTIPLE_ROWS_FOR_ASSAYS_OPTION

public static final String USE_MULTIPLE_ROWS_FOR_ASSAYS_OPTION

See Also:

• Constant Field Values

SEPARATE_SAMPLE_FROM_ASSAYS_IDENTIFIERS_OPTION

public static final String SEPARATE_SAMPLE_FROM_ASSAYS_IDENTIFIERS_OPTION

See Also:

• Constant Field Values

USE_ENSEMBL_IDS_OPTION

public static final String USE_ENSEMBL_IDS_OPTION

See Also:

• Constant Field Values

Constructor Details

DataFileOptionsUtils

public DataFileOptionsUtils()

Method Details

addDataFileOptions

public static void addDataFileOptions(org.apache.commons.cli.Options options,
 String what,
 boolean allowStandardLocation,
 BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)

addDataFileOptions

public static void addDataFileOptions(org.apache.commons.cli.Options options,
 String what,
 boolean allowStandardLocation,
 boolean allowFile,
 boolean allowDirectory,
 boolean allowCurrentDirectory,
 boolean allowStdout,
 BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)

Add options for writing data files, such as raw or processed data files.

Parameters:

allowStandardLocation - if true, the standard location option will be added

allowFile - if true, the output file option will be added, otherwise only the output directory will be added

allowDirectory - if true, the output directory option will be added

allowCurrentDirectory - if true, writing to the current directory will be allowed

allowStdout - if true, the standard output option will be added

addSingleOption - a function that adds a single option to the given option group; this is needed because a CLI might want to track which options apply to individual entities separately.

See Also:

• ExpressionDataFileService
• ExpressionDataFileUtils

addExpressionDataFileOptions

public static void addExpressionDataFileOptions(org.apache.commons.cli.Options options,
 String what,
 boolean allowStandardLocation,
 BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)

addSingleCellExpressionDataFileOptions

public static void addSingleCellExpressionDataFileOptions(org.apache.commons.cli.Options options,
 String what,
 boolean allowStandardLocation,
 BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)

addDesignFileOptions

public static void addDesignFileOptions(org.apache.commons.cli.Options options,
 String what,
 boolean allowStandardLocation,
 BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)

addCellMetadataFileOptions

public static void addCellMetadataFileOptions(org.apache.commons.cli.Options options,
 String what,
 boolean allowStandardLocation,
 BiConsumer<org.apache.commons.cli.OptionGroup,org.apache.commons.cli.Option> addSingleOption)

getDataFileOptionValue

public static DataFileOptionValue getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine,
 boolean allowStandardLocation,
 String forceOption,
 boolean force)
                                                  throws org.apache.commons.cli.ParseException

Throws:

org.apache.commons.cli.ParseException

getDataFileOptionValue

public static DataFileOptionValue getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine,
 boolean allowStandardLocation,
 boolean allowStdout,
 boolean allowCurrentDirectory,
 String forceOption,
 boolean force)
                                                  throws org.apache.commons.cli.ParseException

Obtain the result of the data file options added by addDataFileOptions(Options, String, boolean, boolean, boolean, boolean, boolean, BiConsumer)

Parameters:

allowStandardLocation - if true, the standard location option will be considered and used as a default if no other destination is selected. Otherwise, standard output will be used as a default.

allowStdout - if true, the standard output option will be considered and used as a default if no other destination is selected. Otherwise, the current directory will be used as a default.

allowCurrentDirectory - if true, the current directory will be used as a default if no other destination is selected. Note that a file can be written to inside that directory via DataFileOptionValue.getOutputFile(String)

Throws:

org.apache.commons.cli.MissingOptionException - if no destination is selected and no default location is allowed.

org.apache.commons.cli.ParseException

getExpressionDataFileOptionValue

public static ExpressionDataFileOptionValue getExpressionDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine,
 boolean allowStandardLocation,
 String forceOption,
 boolean force)
                                                                      throws org.apache.commons.cli.ParseException

Throws:

org.apache.commons.cli.ParseException

getSingleCellExpressionDataFileOptionValue

public static SingleCellExpressionDataFileOptionValue getSingleCellExpressionDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine,
 boolean allowStandardLocation,
 String forceOption,
 boolean force)
                                                                                          throws org.apache.commons.cli.ParseException

Throws:

org.apache.commons.cli.ParseException

getDesignFileOptionValue

public static DesignFileOptionValue getDesignFileOptionValue(org.apache.commons.cli.CommandLine commandLine,
 boolean allowStandardLocation,
 String forceOption,
 boolean force)
                                                      throws org.apache.commons.cli.ParseException

Throws:

org.apache.commons.cli.ParseException

getCellMetadataFileOptionValue

public static CellMetadataFileOptionValue getCellMetadataFileOptionValue(org.apache.commons.cli.CommandLine commandLine,
 boolean allowStandardLocation,
 String forceOption,
 boolean force)
                                                                  throws org.apache.commons.cli.ParseException

Throws:

org.apache.commons.cli.ParseException