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

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

Direct Known Subclasses:

OptimizedADFChecker

public class OptimizedFileChecker

extends java.lang.Object

Checks data tables in an optimized way ( memory, CPU) Data tables are checked row by row.

Since:

6 févr. 2005

Version:

1

Author:

Pierre MARGUERITE

Constructor Summary

OptimizedFileChecker()
Constructor

Method Summary

boolean	checkCurrentRowFieldDependance(java.util.Hashtable itemTable) Checks dependances between fields of a row.
java.util.ArrayList	checkDocument(java.io.File file, java.lang.String structureFile, boolean strictMode, boolean stepByStepMode, boolean doCuration) Checks a file against a document structure (contains in a XML file)
boolean	checkFile(java.io.File file, java.lang.String structureFile, boolean strictMode, boolean stepByStepMode, boolean doCuration)
boolean	checkFile(java.io.File file, java.lang.String structureFile, java.lang.String structureName, boolean strictMode, boolean stepByStepMode, boolean doCuration)
CorrectableDataTable	checkFileAndCurate(java.io.File checkFile, java.lang.String fileStructure, boolean strictMode, boolean stepByStepMode) Checks and curates a data file.
CorrectableDataTable	checkFileAndCurate(java.io.File checkFile, java.lang.String fileStructure, java.lang.String structureName, boolean strictMode, boolean stepByStepMode) Checks and curates a data file.
boolean	checkFileData(java.io.File file, java.lang.String structureFile, java.lang.String structureName, boolean strictMode, boolean stepByStepMode, boolean doCuration)
boolean	checkVerticalDataTable(DataTable dataTable, HeaderType header, boolean strictMode, boolean doCuration, boolean stepByStepMode) checks a vertical data table against a structure file The whole table is checked ( not row by row)
static java.lang.String	convert2Regex(java.lang.String regex) Characters // x The character x // \\ The backslash character // \0n The character with octal value 0n (0 <= n <= 7) // \0nn The character with octal value 0nn (0 <= n <= 7) // \0mnn The character with octal value 0mnn (0 <= m <= 3, 0 <= n <= 7) // \xhh The character with hexadecimal value 0xhh //// \ uhhhh The character with hexadecimal value 0xhhhh // \t The tab character (' ') // \n The newline (line feed) character (' ') // \r The carriage-return character (' ') // \f The form-feed character (' ') // \a The alert (bell) character ('') // \e The escape character ('') // \cx The control character corresponding to x // Character classes // [abc] a, b, or c (simple class) // [^abc] Any character except a, b, or c (negation) // [a-zA-Z] a through z or A through Z, inclusive (range) // [a-d[m-p]] a through d, or m through p: [a-dm-p] (union) // [a-z&&[def]] d, e, or f (intersection) // [a-z&&[^bc]] a through z, except for b and c: [ad-z] (subtraction) // [a-z&&[^m-p]] a through z, and not m through p: [a-lq-z](subtraction) // Predefined character classes // .
CorrectableDataTable	getCuratedTable() Retrieves the curated data table for the current data file
static void	main(java.lang.String[] argv)

Methods inherited from class java.lang.Object

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

Constructor Detail

OptimizedFileChecker

public OptimizedFileChecker()

Constructor

Method Detail

checkCurrentRowFieldDependance

public boolean checkCurrentRowFieldDependance(java.util.Hashtable itemTable)

Checks dependances between fields of a row. A value in a field can be mandatory in a field, if a value is present in another field?

Parameters:

itemTable - list of none empty fields in a row

Returns:

true, if dependances are verified/correct. null, otherwise

checkDocument

public java.util.ArrayList checkDocument(java.io.File file,
                                         java.lang.String structureFile,
                                         boolean strictMode,
                                         boolean stepByStepMode,
                                         boolean doCuration)

Checks a file against a document structure (contains in a XML file)

Parameters:

file - data file to check

structureFile - the structure file containing the structure definition

strictMode - true, if the strict checking mode is enabled. false, otherwise

stepByStepMode - true, if the strict checking mode is enabled. false, otherwise

Returns:

checkFile

public boolean checkFile(java.io.File file,
                         java.lang.String structureFile,
                         boolean strictMode,
                         boolean stepByStepMode,
                         boolean doCuration)

checkFile

public boolean checkFile(java.io.File file,
                         java.lang.String structureFile,
                         java.lang.String structureName,
                         boolean strictMode,
                         boolean stepByStepMode,
                         boolean doCuration)

checkFileAndCurate

public CorrectableDataTable checkFileAndCurate(java.io.File checkFile,
                                               java.lang.String fileStructure,
                                               boolean strictMode,
                                               boolean stepByStepMode)
                                        throws ErrorInitLog,
                                               IncorrectFile,
                                               IncorrectFileStructure,
                                               java.io.IOException,
                                               IncorrectDataTableException,
                                               IncorrectDataFile

Checks and curates a data file.

Parameters:

checkFile - path to the data file

fileStructure - file describing the structure of the data file

strictMode - if the checking is strict

stepByStepMode - if checking is done step by step

Returns:

the curated data table corresponding to the data file

Throws:

ErrorInitLog - if an error occurs during logger initialisation

IncorrectFile - if the data file is incorrect

IncorrectFileStructure - if the structure file is incorrect

java.io.IOException - if an error occurs during file access

IncorrectDataTableException - if an error occurs

IncorrectDataFile - if the data file is incorrect

checkFileAndCurate

public CorrectableDataTable checkFileAndCurate(java.io.File checkFile,
                                               java.lang.String fileStructure,
                                               java.lang.String structureName,
                                               boolean strictMode,
                                               boolean stepByStepMode)
                                        throws ErrorInitLog,
                                               IncorrectFile,
                                               IncorrectFileStructure,
                                               java.io.IOException,
                                               IncorrectDataTableException,
                                               IncorrectDataFile

Checks and curates a data file.

Parameters:

checkFile - path to the data file

fileStructure - file describing the structure of the data file

strictMode - if the checking is strict

stepByStepMode - if checking is done step by step

Returns:

the curated data table corresponding to the data file

Throws:

ErrorInitLog - if an error occurs during logger initialisation

IncorrectFile - if the data file is incorrect

IncorrectFileStructure - if the structure file is incorrect

java.io.IOException - if an error occurs during file access

IncorrectDataTableException - if an error occurs

IncorrectDataFile - if the data file is incorrect

checkFileData

public boolean checkFileData(java.io.File file,
                             java.lang.String structureFile,
                             java.lang.String structureName,
                             boolean strictMode,
                             boolean stepByStepMode,
                             boolean doCuration)

checkVerticalDataTable

public boolean checkVerticalDataTable(DataTable dataTable,
                                      HeaderType header,
                                      boolean strictMode,
                                      boolean doCuration,
                                      boolean stepByStepMode)
                               throws IncorrectFileStructure,
                                      IncorrectDataTableException

checks a vertical data table against a structure file The whole table is checked ( not row by row)

Parameters:

dataTable - the data table to check

header - the structure definition of the table header (header information)

doCuration - true, if data are curated and export in a file

strictMode - checking in strictmode

stepByStepMode - define step by step mode. null, otherwise.

Returns:

true if the datatable is correct. false, otherwise.

Throws:

ErrorInitLog - if an error occurs during the logger initialisation

IncorrectFile - if a file is incorrect.

IncorrectFileStructure - if the structure definition file is incorrect

java.io.IOException - if an error occurs during file access.

IncorrectDataTableException - if the data table is incorrect

convert2Regex

public static java.lang.String convert2Regex(java.lang.String regex)

Characters // x The character x // \\ The backslash character // \0n The character with octal value 0n (0 <= n <= 7) // \0nn The character with octal value 0nn (0 <= n <= 7) // \0mnn The character with octal value 0mnn (0 <= m <= 3, 0 <= n <= 7) // \xhh The character with hexadecimal value 0xhh //// \ uhhhh The character with hexadecimal value 0xhhhh // \t The tab character (' ') // \n The newline (line feed) character (' ') // \r The carriage-return character (' ') // \f The form-feed character (' ') // \a The alert (bell) character ('') // \e The escape character ('') // \cx The control character corresponding to x // Character classes // [abc] a, b, or c (simple class) // [^abc] Any character except a, b, or c (negation) // [a-zA-Z] a through z or A through Z, inclusive (range) // [a-d[m-p]] a through d, or m through p: [a-dm-p] (union) // [a-z&&[def]] d, e, or f (intersection) // [a-z&&[^bc]] a through z, except for b and c: [ad-z] (subtraction) // [a-z&&[^m-p]] a through z, and not m through p: [a-lq-z](subtraction) // Predefined character classes // . Any character (may or may not match line terminators) // \d A digit: [0-9] // \D A non-digit: [^0-9] // \s A whitespace character: [ \t\n\x0B\f\r] // \S A non-whitespace character: [^\s] // \w A word character: [a-zA-Z_0-9] // \W A non-word character: [^\w] // // POSIX character classes (US-ASCII only) // \p{Lower} A lower-case alphabetic character: [a-z] // \p{Upper} An upper-case alphabetic character:[A-Z] // \p{ASCII} All ASCII:[\x00-\x7F] // \p{Alpha} An alphabetic character:[\p{Lower}\p{Upper}] // \p{Digit} A decimal digit: [0-9] // \p{Alnum} An alphanumeric character:[\p{Alpha}\p{Digit}] // \p{Punct} Punctuation: One of !"#$%&'()*+,-./:;<=>?@[\]^_`{|}~ // \p{Graph} A visible character: [\p{Alnum}\p{Punct}] // \p{Print} A printable character: [\p{Graph}] // \p{Blank} A space or a tab: [ \t] // \p{Cntrl} A control character: [\x00-\x1F\x7F] // \p{XDigit} A hexadecimal digit: [0-9a-fA-F] // \p{Space} A whitespace character: [ \t\n\x0B\f\r] // Classes for Unicode blocks and categories // \p{InGreek} A character in the Greek block (simple block) // \p{Lu} An uppercase letter (simple category) // \p{Sc} A currency symbol // \P{InGreek} Any character except one in the Greek block (negation) // [\p{L}&&[^\p{Lu}]] Any letter except an uppercase letter (subtraction) // Boundary matchers // ^ The beginning of a line // $ The end of a line // \b A word boundary // \B A non-word boundary // \A The beginning of the input // \G The end of the previous match // \Z The end of the input but for the final terminator, if any // \z The end of the input // Greedy quantifiers // X? X, once or not at all // X* X, zero or more times // X+ X, one or more times // X{n} X, exactly n times // X{n,} X, at least n times // X{n,m} X, at least n but not more than m times // Reluctant quantifiers // X?? X, once or not at all // X*? X, zero or more times // X+? X, one or more times // X{n}? X, exactly n times // X{n,}? X, at least n times // X{n,m}? X, at least n but not more than m times // Possessive quantifiers // X?+ X, once or not at all // X*+ X, zero or more times // X++ X, one or more times // X{n}+ X, exactly n times // X{n,}+ X, at least n times // X{n,m}+ X, at least n but not more than m times // // this.logical operators // XY X followed by Y // X|Y Either X or Y // (X) X, as a capturing group // Back references // \n Whatever the nth capturing group matched // Quotation // \ Nothing, but quotes the following character // \Q Nothing, but quotes all characters until \E // \E Nothing, but ends quoting started by \Q // Special constructs (non-capturing) // (?:X) X, as a non-capturing group // (?idmsux-idmsux) Nothing, but turns match flags on - off // (?idmsux-idmsux:X) X, as a non-capturing group with the given flags on - off // (?=X) X, via zero-width positive lookahead // (?!X) X, via zero-width negative lookahead // (?<=X) X, via zero-width positive lookbehind // (?X) X, as an independent, non-capturing group // TODO convertString 2 Regex dont deal with every charachter Convert a String in a Java regex: special charaters are not recognised in that String.

Parameters:

regex - the regex to convert

Returns:

the String corresponding to the provided regex String , modified to be recognized as a Java regex

getCuratedTable

public CorrectableDataTable getCuratedTable()

Retrieves the curated data table for the current data file

Returns:

the curated table

main

public static void main(java.lang.String[] argv)