biolockj.util

Class RMetaUtil

java.lang.Object

biolockj.util.RMetaUtil

public final class RMetaUtil
extends Object

This utility is used to validate the metadata to help ensure the format is valid R script input.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	BINARY_FIELDS Config Internal List property: "R_internal.binaryFields" Binary fields contain only 2 unique non-NA options
protected static String	NUM_META_COLS Name of R script variable with metadata column count
protected static String	R_EXCLUDE_FIELDS Config List property: "r.excludeFields" R reports must contain at least one valid nominal or numeric metadata field.
protected static String	R_MDS_REPORT_FIELDS Config List property: "r_PlotMds.reportFields" Fields listed here must exist in the metadata file.
protected static String	R_NOMINAL_FIELDS Config List property: "r.nominalFields" Override default property type by explicitly listing it as nominal.
protected static String	R_NUMERIC_FIELDS Config List property: "r.numericFields" Override default property type by explicitly listing it as numeric.
protected static String	R_REPORT_FIELDS Config List property: "r.reportFields" R reports must contain at least one valid field.

Method Summary

Modifier and Type	Method and Description
static void	classifyReportableMetadata(BioModule module) Classify and verify the R filter and reportable metadata fields listed in the Config file. All metadata fields are reported unless specific fields are listed in: Config."r.reportFields".
static Set<String>	getBinaryFields(BioModule module) Get the Config."R_internal.binaryFields" fields containing only 2 non-numeric values.
static boolean	isMetaMergeTable(File file) Method analyzes the file name to determine if the file could be output from the BioModule AddMetadataToTaxaTables
static boolean	reportAllFields(BioModule module) The override property: Config."r.reportFields" can be used to list the metadata reportable fields for use in the R modules.
static boolean	updateRConfig(BioModule module) Get updated R config props
static void	verifyMetadataFieldsExist(BioModule module, String prop, Collection<String> fields) This method verifies the fields given exist in the metadata file.

Methods inherited from class java.lang.Object

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

Field Detail

BINARY_FIELDS

protected static final String BINARY_FIELDS

Config Internal List property: "R_internal.binaryFields"
Binary fields contain only 2 unique non-NA options

See Also:

Constant Field Values

NUM_META_COLS

protected static final String NUM_META_COLS

Name of R script variable with metadata column count

See Also:

Constant Field Values

R_EXCLUDE_FIELDS

protected static final String R_EXCLUDE_FIELDS

Config List property: "r.excludeFields"
R reports must contain at least one valid nominal or numeric metadata field.

See Also:

Constant Field Values

R_MDS_REPORT_FIELDS

protected static final String R_MDS_REPORT_FIELDS

Config List property: "r_PlotMds.reportFields"
Fields listed here must exist in the metadata file.

See Also:

Constant Field Values

R_NOMINAL_FIELDS

protected static final String R_NOMINAL_FIELDS

Config List property: "r.nominalFields"
Override default property type by explicitly listing it as nominal.

See Also:

Constant Field Values

R_NUMERIC_FIELDS

protected static final String R_NUMERIC_FIELDS

Config List property: "r.numericFields"
Override default property type by explicitly listing it as numeric.

See Also:

Constant Field Values

R_REPORT_FIELDS

protected static final String R_REPORT_FIELDS

Config List property: "r.reportFields"
R reports must contain at least one valid field.

See Also:

Constant Field Values

Method Detail

classifyReportableMetadata

public static void classifyReportableMetadata(BioModule module)
                                       throws Exception

Classify and verify the R filter and reportable metadata fields listed in the Config file.
All metadata fields are reported unless specific fields are listed in: Config."r.reportFields". Each field is classified as binary, nominal, or numeric which determines the R statistical test used and the type of plot generated.

• Fields with exactly 2 unique non-null values are classified as binary data unless specified in: Config."r.numericFields"
• Fields with numeric data are classified as numeric data unless specified in: Config."r.nominalFields"
• Fields with nominal or mixed nominal/numeric data are classified as nominal data.

If Config."report.numReads" = "Y", add the last read count field in the metadata file as a numeric field store in {link biolockj.module.implicit.RegisterNumReads#getNumReadFieldName()}

If Config."report.numHits" = "Y", add the ParserModuleImpl.getOtuCountField() field as a numeric field.

Perform validations:

• Verify reportable metadata fields exist and contain at least 2 unique values
• Verify numeric fields contain all numeric data

Save MASTER Config properties to store lists of binary, nominal, and numeric fields

Parameters:

module - BioModule

Throws:

Exception - if Config lists invalid metadata fields or metadata filed has less than 2 unique values

getBinaryFields

public static Set<String> getBinaryFields(BioModule module)
                                   throws Exception

Get the Config."R_internal.binaryFields" fields containing only 2 non-numeric values.

Parameters:

module - is the Calling BioModule

Returns:

Set of column names with only 2 non-numeric values

Throws:

Exception - if unable to assing binary fields

isMetaMergeTable

public static boolean isMetaMergeTable(File file)

Method analyzes the file name to determine if the file could be output from the BioModule AddMetadataToTaxaTables

Parameters:

file - Ambiguous file

Returns:

TRUE if named like a meta merged file

reportAllFields

public static boolean reportAllFields(BioModule module)

The override property: Config."r.reportFields" can be used to list the metadata reportable fields for use in the R modules. If undefined, report all fields.

Parameters:

module - BioModule

Returns:

true if "r.reportFields" is empty

updateRConfig

public static boolean updateRConfig(BioModule module)
                             throws Exception

Get updated R config props

Parameters:

module - BioModule

Returns:

map of R props by data type

Throws:

Exception - if errors occur

verifyMetadataFieldsExist

public static void verifyMetadataFieldsExist(BioModule module,
                                             String prop,
                                             Collection<String> fields)
                                      throws Exception

This method verifies the fields given exist in the metadata file.

Parameters:

module - Source BioModule calling this utility

prop - Config property name

fields - Set of metadata fields

Throws:

Exception - if the metadata column does not exist