uk.ac.ebi.adfconverter.tools.checker
Class DatabaseChecker

java.lang.Object
  uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker

public class DatabaseChecker

extends java.lang.Object

Checking for database stuff will check database tags and database accesion number In Approved db file structure, the item name are: DB tag item - DBTag database link item - URI$ database name - DBName regex - ACCRegex

Version:

1 31 July 2004 TODO test file loading each time (save memory)/ keep in memory the data TODO deal with several approved file

Author:

Pierre MARGUERITE

Constructor Summary

DatabaseChecker()
Default Constructor with a default DatabaseChecker with a default DB file path: etc/checking/public_DB_Accnos.xls

DatabaseChecker(java.lang.String DBFileStructureDescriptionFileName, java.lang.String approvedDBFile, java.lang.String nameLinkSeparator, boolean _isAccessionNumberCheckingEnable)
Constructor with a given approved DB file, approved DB file structure xml file,and the separator between DB name and web link retrieved from workbook

Method Summary

static void	addApprouvedDBFile(java.lang.String DBFile) DBFileStructureDescriptionFileName is the same of all DBfile loaded duriing execution
static boolean	checkDBAccNumber(ADFConverterLogger log, java.lang.String tag, java.lang.String AccNumber) Checks if an Accession is correct (regex matching) according to the database tag additional information will be added during MAGE object creation
static DataBuffer	checkDBTag(ADFConverterLogger log, DataBuffer tag, boolean doCuration, java.util.ArrayList userDefinedTags, boolean isStrictChecking) Checks if a DB tag is an approved Databases or a userdefined one.
static java.lang.String	getDBComment(java.lang.String dbTag) retrieves the comment for a given DBTag
static java.lang.String	getDBName(java.lang.String dbTag) retrieves the database name for a given DBTag
static java.lang.String	getDBURI(java.lang.String dbTag) retrieves the URI for a given DBTag

Methods inherited from class java.lang.Object

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

Constructor Detail

DatabaseChecker

public DatabaseChecker()
                throws IncorrectDataBaseInit

Default Constructor with a default DatabaseChecker with a default DB file path: etc/checking/public_DB_Accnos.xls

Throws:

IncorrectDataBaseInit - if an errors occurs during checker initialisation

DatabaseChecker

public DatabaseChecker(java.lang.String DBFileStructureDescriptionFileName,
                       java.lang.String approvedDBFile,
                       java.lang.String nameLinkSeparator,
                       boolean _isAccessionNumberCheckingEnable)
                throws IncorrectDataBaseInit

Constructor with a given approved DB file, approved DB file structure xml file,and the separator between DB name and web link retrieved from workbook

Parameters:

DBFileStructureDescriptionFileName - path to the file describing the approvd DB file structure

approvedDBFile - path to the approved database file

nameLinkSeparator - separator between name and link in the DB table

_isAccessionNumberCheckingEnable -

Throws:

IncorrectDataBaseInit

Method Detail

addApprouvedDBFile

public static void addApprouvedDBFile(java.lang.String DBFile)
                               throws IncorrectDataBaseInit

DBFileStructureDescriptionFileName is the same of all DBfile loaded duriing execution

Parameters:

DBFile -

Throws:

IncorrectDataBaseInit - if an error occurs during checker initialisation TODO deal with files with different data structure

checkDBAccNumber

public static boolean checkDBAccNumber(ADFConverterLogger log,
                                       java.lang.String tag,
                                       java.lang.String AccNumber)

Checks if an Accession is correct (regex matching) according to the database tag additional information will be added during MAGE object creation

Parameters:

log - logger to report comment into.

tag - the tag of the Database

AccNumber - the accession to check

Returns:

true if the Accession is corresponding to the Database tag.

checkDBTag

public static DataBuffer checkDBTag(ADFConverterLogger log,
                                    DataBuffer tag,
                                    boolean doCuration,
                                    java.util.ArrayList userDefinedTags,
                                    boolean isStrictChecking)

Checks if a DB tag is an approved Databases or a userdefined one. Two type of checking: strict : the tag must exactly match the tag in the approved Database List relax: the ckecking is case insensitive

Parameters:

log - the logger for the checked file:

tag - the tag to check

doCuration - if a curation is done on the tag

userDefinedTags - the list of databases defined by the user

isStrictChecking - if the checking is strict or relax

Returns:

the DBTag if the DBTag has been identified as known databases, if curation asked, the correct tag is return. null, otherwise

getDBComment

public static java.lang.String getDBComment(java.lang.String dbTag)

retrieves the comment for a given DBTag

Parameters:

dbTag - the given Database tag

Returns:

the corresponding comment, if the dbTag has been found. null otherwise

getDBName

public static java.lang.String getDBName(java.lang.String dbTag)

retrieves the database name for a given DBTag

Parameters:

dbTag - the given Database tag

Returns:

the corresponding db name, if the dbTag has been found. null otherwise

getDBURI

public static java.lang.String getDBURI(java.lang.String dbTag)

retrieves the URI for a given DBTag

Parameters:

dbTag - the given Database tag

Returns:

the corresponding URI, if the dbTag has been found. null otherwise