biolockj.util

Class MetaUtil

java.lang.Object

biolockj.util.MetaUtil

public class MetaUtil
extends Object

This utility is used to read, modify, or create a metadata file for the sequence data. The 1st row must hold the Sample ID and column names must be unique. Metadata information is cached in this class for quick access throughout the application.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	DEFAULT_COMMENT_CHAR Default comment character for any new metadata file created by a BioModule: ""
protected static String	DEFAULT_NULL_VALUE Default field value to represent null-value: "NA"
static String	META_BARCODE_COLUMN Config property "metadata.barcodeColumn"
static String	META_COLUMN_DELIM Config property: "metadata.columnDelim"
static String	META_COMMENT_CHAR Config property: "metadata.commentChar"
static String	META_FILE_PATH Config String property: "metadata.filePath"
static String	META_FILENAME_COLUMN Config property "metadata.fileNameColumn"
static String	META_NULL_VALUE Config property: "metadata.nullValue"
static String	META_REQUIRED Config Boolean property: "metadata.required"
protected static String	METADATA_COL_DELIM Default column delimiter = tab character
static String	USE_EVERY_ROW Config Boolean property: "metadata.useEveryRow"

Method Summary

Modifier and Type	Method and Description
static void	addColumn(String colName, Map<String,String> map, File fileDir, boolean removeMissingIds) Adds a column to the metadata file.
static boolean	exists() Check if metadata file exists
static boolean	fieldValuesAreUnique(String field, boolean ignoreNulls) Determine if the given field has only unique values.
static String	getColumnDelim()
static String	getField(String sampleId, String field) Get metadata field value for given sampleId.
static List<String>	getFieldNames() Get a list of all metadata fields (metadata file column names except the 1st).
static List<String>	getFieldValues(String field, boolean ignoreNulls) Get metadata column for given field name.
static String	getFileName() Get the metadata file name, if it exists, otherwise return projectName.tsv
static String	getForcedColumnName(String name) Used to generate a guaranteed to be unique column name.
static String	getID() Get the metadata file ID column name.
static String	getLatestColumnName(String name) Returns the latest version of the given column.
static File	getMetadata() Metadata file getter.
static String	getNullValue(BioModule module) Nulls left as empty cells do not process corrects in R, so a placeholder value must be defined (even if not used).
static String	getPath() Return the metadata file path
static List<String>	getRecord(String sampleId) Get metadata row for a given Sample ID.
static Set<String>	getSampleFileList()
static String	getSampleId(File file)
static List<String>	getSampleIds() Get the first column from the metadata file.
static String	getSystemMetaCol(BioModule module, String col) Return a system generated metadata column name based on the module status.
static Set<String>	getUniqueFieldValues(String field, boolean ignoreNulls) Count the number of unique values in the given field.
static boolean	hasColumn(String columnName) Check if columnName exists in the current metadata file.
static boolean	hasMetaColToSampleIdMap()
static void	initialize() Check required properties are defined and unique.
static void	refreshCache() Refresh the metadata cache.
static void	registerProps()
static void	removeColumn(String colName, File fileDir) Remove the metadata column from the metadata file
static void	setFile(File file) Set a new metadata file.
static boolean	setSampleId(File file, String sampleId)
static boolean	setSampleId(String filename, String sampleId)
static void	tapSampleAssignmentMap() A care-free wrapper for saveSampleAssignmentMap().

Methods inherited from class java.lang.Object

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

Field Detail

META_BARCODE_COLUMN

public static final String META_BARCODE_COLUMN

Config property "metadata.barcodeColumn"

See Also:

Constant Field Values

META_COLUMN_DELIM

public static final String META_COLUMN_DELIM

Config property: "metadata.columnDelim"

See Also:

Constant Field Values

META_COMMENT_CHAR

public static final String META_COMMENT_CHAR

Config property: "metadata.commentChar"

See Also:

Constant Field Values

META_FILE_PATH

public static final String META_FILE_PATH

Config String property: "metadata.filePath"

See Also:

Constant Field Values

META_FILENAME_COLUMN

public static final String META_FILENAME_COLUMN

Config property "metadata.fileNameColumn"

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Constant Field Values

META_NULL_VALUE

public static final String META_NULL_VALUE

Config property: "metadata.nullValue"

See Also:

Constant Field Values

META_REQUIRED

public static final String META_REQUIRED

Config Boolean property: "metadata.required"

See Also:

Constant Field Values

USE_EVERY_ROW

public static final String USE_EVERY_ROW

Config Boolean property: "metadata.useEveryRow"

See Also:

Constant Field Values

METADATA_COL_DELIM

protected static final String METADATA_COL_DELIM

Default column delimiter = tab character

See Also:

Constant Field Values

DEFAULT_COMMENT_CHAR

protected static final String DEFAULT_COMMENT_CHAR

Default comment character for any new metadata file created by a BioModule: ""

See Also:

Constant Field Values

DEFAULT_NULL_VALUE

protected static final String DEFAULT_NULL_VALUE

Default field value to represent null-value: "NA"

See Also:

Constant Field Values

Method Detail

addColumn

public static void addColumn(String colName,
                             Map<String,String> map,
                             File fileDir,
                             boolean removeMissingIds)
                      throws MetadataException,
                             IOException,
                             DockerVolCreationException

Adds a column to the metadata file. The updated metadata file is output to the fileDir. Once the new file is created, the new file is cached in memory and used as the new metadata.

Parameters:

colName - Name of new column

map - Map relates Sample ID to a field value

fileDir - File representing output directory for new metadata file

removeMissingIds - if TRUE, sampleIds not include in the map arg will be removed from the metadata

Throws:

MetadataException - if errors occur attemptingto get/put metadata into cache

IOException - if errors occur attempting to read metadata file

DockerVolCreationException

FileNotFoundException - if metadata file not found

exists

public static boolean exists()

Check if metadata file exists

Returns:

TRUE if metadata exists

fieldValuesAreUnique

public static boolean fieldValuesAreUnique(String field,
                                           boolean ignoreNulls)
                                    throws MetadataException

Determine if the given field has only unique values.

Parameters:

field - Metadata column

ignoreNulls - if TRUE ignore duplicate "metadata.nullValue" values

Returns:

boolean if field values are unique

Throws:

MetadataException - if field not found in metadata file

getColumnDelim

public static String getColumnDelim()

getField

public static String getField(String sampleId,
                              String field)
                       throws MetadataException

Get metadata field value for given sampleId.

Parameters:

sampleId - Sample ID

field - Field Name (column name in metadata file)

Returns:

Metadata field value

Throws:

MetadataException - if field not found in the metadata for the given sample Id.

getFieldNames

public static List<String> getFieldNames()

Get a list of all metadata fields (metadata file column names except the 1st).

Returns:

List of metadata column names, excluding the 1st column

getFieldValues

public static List<String> getFieldValues(String field,
                                          boolean ignoreNulls)
                                   throws MetadataException

Get metadata column for given field name.

Parameters:

field - Column name

ignoreNulls - if TRUE ignore duplicate "metadata.nullValue" values

Returns:

List of Column values for sample ID

Throws:

MetadataException - if unable to find metadata filed values

getFileName

public static String getFileName()

Get the metadata file name, if it exists, otherwise return projectName.tsv

Returns:

Name of metadata file, or a default name if no metadata file exists #throws Exception if errors occur

getForcedColumnName

public static String getForcedColumnName(String name)
                                  throws MetadataException,
                                         FileNotFoundException,
                                         IOException,
                                         DockerVolCreationException

Used to generate a guaranteed to be unique column name. If parameter "name" already exists, this will return name_1, or name_2, etc until an unused column name is found. If a column already exists, but contains only Config."metadata.nullValue" values, return the name of that empty column to overwrite.

Parameters:

name - Base column name

Returns:

Column name

Throws:

MetadataException - if metadata file not found and cannot be assigned

IOException - If unable to modify the system file

FileNotFoundException - if metadata file path not found

DockerVolCreationException

getID

public static String getID()

Get the metadata file ID column name. This value may change as updates are made by BioModules.

Returns:

Metadata ID column name

getLatestColumnName

public static String getLatestColumnName(String name)

Returns the latest version of the given column.

Parameters:

name - Base column name

Returns:

column name

getMetadata

public static File getMetadata()
                        throws MetadataException

Metadata file getter. This path changes as new versions are created by the BioModules.

Returns:

Metadata file

Throws:

MetadataException - if attempt to assign new metadata file fails

getNullValue

public static String getNullValue(BioModule module)

Nulls left as empty cells do not process corrects in R, so a placeholder value must be defined (even if not used). This value is read from the property $Config?"metadata.nullValue". If undefined, use "NA"

Parameters:

module - BioModule calling MetaUtil

Returns:

Null value string

getPath

public static String getPath()

Return the metadata file path

Returns:

String the metadata file path

getRecord

public static List<String> getRecord(String sampleId)
                              throws MetadataException

Get metadata row for a given Sample ID.

Parameters:

sampleId - Sample ID

Returns:

Metadata row values for sample ID

Throws:

MetadataException - if Sample ID not found or metadata file doesn't exist

getSampleIds

public static List<String> getSampleIds()

Get the first column from the metadata file.

Returns:

Sample IDs found in metadata file

getSystemMetaCol

public static String getSystemMetaCol(BioModule module,
                                      String col)
                               throws MetadataException,
                                      FileNotFoundException,
                                      IOException,
                                      DockerVolCreationException

Return a system generated metadata column name based on the module status.

Parameters:

module - BioModule

col - Column name

Returns:

Metadata column name

Throws:

MetadataException - if metadata file not found and cannot be assigned

IOException - If unable to modify the system file

FileNotFoundException - if metadata file path not found

DockerVolCreationException

getUniqueFieldValues

public static Set<String> getUniqueFieldValues(String field,
                                               boolean ignoreNulls)
                                        throws MetadataException

Count the number of unique values in the given field.

Parameters:

field - Column header

ignoreNulls - if TRUE ignore duplicate "metadata.nullValue" values

Returns:

Number of unique values

Throws:

MetadataException - if field not found

hasColumn

public static boolean hasColumn(String columnName)

Check if columnName exists in the current metadata file.

Parameters:

columnName - Column name

Returns:

TRUE if columnName exists in hearder row of metadata file

initialize

public static void initialize()
                       throws Exception

Check required properties are defined and unique. Some undefined properties will use a default values as per the R{utils} read.table() function.

• "metadata.columnDelim" column separator
• "metadata.commentChar" indicates start of comment in a cell, Requires length == 1
• "metadata.nullValue" indicates null cell

Throws:

Exception

hasMetaColToSampleIdMap

public static boolean hasMetaColToSampleIdMap()
                                       throws ConfigFormatException,
                                              ConfigViolationException,
                                              MetadataException

Throws:

ConfigFormatException

ConfigViolationException

MetadataException

getSampleId

public static String getSampleId(File file)
                          throws Exception

Throws:

Exception

getSampleFileList

public static Set<String> getSampleFileList()
                                     throws Exception

Throws:

Exception

setSampleId

public static boolean setSampleId(String filename,
                                  String sampleId)
                           throws ConfigViolationException,
                                  ConfigFormatException,
                                  MetadataException,
                                  IOException

Parameters:

filename -

sampleId -

Returns:

true if that filename is associated with that sample when method completes; otherwise false.

Throws:

ConfigViolationException

ConfigFormatException

MetadataException - if methods attempts to assign an existing file name to a different sample

IOException

setSampleId

public static boolean setSampleId(File file,
                                  String sampleId)
                           throws ConfigViolationException,
                                  ConfigFormatException,
                                  MetadataException,
                                  IOException

Throws:

ConfigViolationException

ConfigFormatException

MetadataException

IOException

refreshCache

public static void refreshCache()
                         throws MetadataException

Refresh the metadata cache.

Throws:

MetadataException - if unable to refresh cache

removeColumn

public static void removeColumn(String colName,
                                File fileDir)
                         throws FileNotFoundException,
                                IOException,
                                MetadataException,
                                DockerVolCreationException

Remove the metadata column from the metadata file

Parameters:

colName - Name of column to remove

fileDir - File representing output directory for new metadata file

Throws:

MetadataException - if metadata file not found and cannot be assigned

IOException - If unable to modify the system file

FileNotFoundException - if metadata file path not found

DockerVolCreationException

setFile

public static void setFile(File file)
                    throws MetadataException,
                           DockerVolCreationException

Set a new metadata file.

Parameters:

file - New metadata file

Throws:

MetadataException - if null parameter is passed

DockerVolCreationException

tapSampleAssignmentMap

public static void tapSampleAssignmentMap()

A care-free wrapper for saveSampleAssignmentMap(). Save a table of the filenames that link to a given sample id. If any exceptions are thrown, do nothing.

registerProps

public static void registerProps()
                          throws API_Exception

Throws:

API_Exception