ADF MAGE-ML Tool Blog

Updated CVS

2005-10-30T16:42:00.000+01:00

The CVS stable module has been updated with the Release 1.0.

Release of the ADF MAGE-ML Tool version 1.0

2005-08-23T17:45:00.000+02:00

The ADF MAGE-ML Tool version 1.0 is ready. In addition of the GUI to command the tool, Users can also configure the tool through it.

Several bug fixes have been done.

Release 1.0 almost ready

2005-08-15T20:15:00.000+02:00

The ADF MAGE-ML Tool will be release soon in 1.0 version (Time to have broadband connection to updload).

Fix most of bugs about the GUI. Allow internationalisation and language change at run-time.
Includes Resources update and tool configuration.

ConfigurationFrame: change integer representation by Spinner

2005-08-12T15:23:00.000+02:00

In the configurationFrame, properties with integer type value are now displayed as Spinner.
Previously, value was displayed has TextField.

Update JLocaleChooser to display only GUI available locales

2005-08-12T15:19:00.000+02:00

The JLocaleChooser is a combobox with a list of locales. It uses to localized to GUI at run time following selected item.

In previous version, every locale with a directory in the etc/lang/i18n (contained a directory named by the locale, with the flag.gif icon)was displayed.

Now, only locales available to translate te GUI are displayed, aka English and french.

Updated Jxl api to 2.5.7

2005-08-12T14:31:00.000+02:00

The JXL api (Excel workbook reading and writing) has been updated to the last version : 2.5.7.

Version 2.5.7 (July 2005)

Handled variable arg functions which have zero parameters, such as row() and column()
Fixed WritableHyperlink so that it would handle file links (in particular file links located on a different drive letter)
Made XFRecord handle uninitialized records, and enhanced the equals() method for Font and Format to allow better copying between sheets
Detected a corrupt biff file format to throw an exception, rather than hanging in an endless loop
When writing a sheet, added to check to stop the addition of a null WorkspaceOptions object
Ignored the type object type MSOFFICDRAWING (as distinct from PICTURE) when reading/copying spreadsheets with pictures in them
Ignored, and warned, when processing charts on non biff8 workbooks
Display a warning when standard property sets aren't present in the original sheet
Display a warning about spurious block chains the small block stream
Fixed a bug when copying dates which consist of just a time - one day was subtracted from the value
Applied contributed fix for copying cell borders with colours
Added the ability to remove a comment from a cell
Applied Adam's patch to add support for horizontal/vertical centring when printing

Fix JLocale Chooser - to select GUI language

2005-08-06T19:25:00.000+02:00

The JLocaleChooser is used to select and change current locale at run time.
The JLocaleChooser did not work under MS Windows platform or if directory containing i18n data was not found.

The JLocaleChooser has been modified to handle correctly URL (change file separator to '\') and only display current, if the i18n directory is not found.

There is still a bug with de_CH flag, which do not display.
In the future, only available locale will be displayed/selecteable.

Missing internationalization resource message now displays as debug

2005-08-01T12:25:00.000+02:00

Missing internationalization resources (finishing as .label, .mnemonic, .tooltip) are not longer logged as error. These are logged as debug message, as they can be optional and can mislead the user.

Improved GUI visual presentation

2005-08-01T01:25:00.000+02:00

The button size has been fixed (in previous version, some buttons were pretty big). Improved component organization.

The project does not compile with Java 1.5

2005-07-30T22:58:00.000+02:00

The project does not compile due to generic types added in Java 1.5. But, the compile tool works with it.

The Java 1.5 will be supported in the 1.1 release.

Updated CVS

2005-07-29T01:07:00.000+02:00

The CVS server has been updated to prepare the 1.0 release.

Updated CVS

2005-07-28T00:48:00.000+02:00

The CVS server has been updated with the last development release.

Still trying to find out if cvs checkout is working.

Fixed bug with Java 1.5

2005-07-28T00:46:00.000+02:00

The source might not compile with Java 1.5. It complained about enum keyword.

Most of the enum code have been removed

Update CVS

2005-07-24T22:14:00.000+02:00

The CVS server has been updated with the last development version. It is mainly code cleaning. External api and Ms workbook have been set as binary to avoid check out error.

log4J api updated to 1.2.11

2005-07-11T17:58:00.000+02:00

The log4j api (for logging) has been updated to the version 1.2.11.
("Log4j version 1.2.11, is identical to version 1.2.9, except that the class org.apache.log4j.or.jms.MessageRenderer is now explicitly contained in the 1.2.11.jar. In previous releases of the 1.2 branch it was sometimes include and sometimes left out (bug #34491).")

Update CVS

2005-07-07T18:11:00.000+02:00

The development branch on the sourceforge cvs server has been updated.

http://sourceforge.net/cvs/?group_id=120387

Updated Jxl api to 2.5.6

2005-07-01T23:39:00.000+02:00

The jxl api has been updated to the 2.5.6 version.

New window to add configuration property

2005-06-30T18:38:00.000+02:00

A window has been added to the GUI. From the Configuration frame, the user will be able to add new property to the configuration, for exemple: update resource property....

A window to update resource will be added soon and a bug in the GUI size will be fix before 1.0 release.

SimpleGUI: Properties can be set in the GUI

2005-05-21T17:23:00.000+02:00

A Configuration Frame has been added to modify tool configuration.
Properties are ordered by module.
Some properties are unmodifiabled.

Once set, the user may only apply modification to the current instance of the tool or save configuration to file to reuse configuration next time.

Updated Jxl api to 2.5.5

2005-05-09T23:31:00.000+02:00

The jxl (Java to Excel) API has been updated to 2.5.5 version.

ADF MAGE-ML Tool available on P2P

2005-05-07T15:02:00.000+02:00

ADF MAGE-ML Tool can now be downloaded on the edonkey network.

Edonkey links:

sources:

ed2k://|file|ADF_MAGEML_Tool-1.0-RC3-source.tgz|14961363|86BBB0DCD8FC10A34051AAE01AF314F1|/

bin:
ed2k://|file|ADF_MAGEML_Tool-1.0-RC3.tgz|11787735|3666BC095AA87281EC5274D9726DBB52|/

installer:
ed2k://|file|ADF_MAGEML_Tool-1.0-RC3-installer.jar|20480630|2C71D43BFA6BB59D7CCCBFC171F52660|/

Updated Unix script

2005-05-06T12:30:00.000+02:00

For a better portability, a space has been added between "#!" and "/bin/sh".
It is mandatory for old Unix system.

Updated wiki - Added MGEDOntologyManager and ApprovedDatabaseManager

2005-05-03T00:52:00.000+02:00

MGEDOntologyManager and ApprovedDatabaseManager paged has been added to the wiki.

They describe the MGED Ontology Manager (how it works, what it provided) and the Database Manager (presents Approved Databases, how they retrieved, available information, checking,..)

Updated wiki - Added DataFileChecking

2005-05-01T01:12:00.000+02:00

The DataFileChecking page explained the checking of tabular data file (no specific to ADF).

ADFCheking page will follow,as well as MGEDOntologyManager and Approved Databases/DatabaseManager.

bug in the windows commandline script

2005-04-26T01:21:00.000+02:00

The path to the adf mage ml tool is detected as incorrect, if the path contained space. double quotes are missing.

Updated MGED Ontology file (1.2.0)

2005-04-24T00:04:00.000+02:00

The MGED Ontology 1.2.0 in Dawl+owl is finally available on the MGED Website.

The current MGED Ontology version is now 1.2.0.

Third release of the ADF MAGE-ML Tool

2005-04-18T16:07:00.000+02:00

The 1.0 RC3 version of the ADF MAGE-ML Tool has been released.

It adds a SimpleGUI with minimal options, multilanguage support, drag and drop (tested under Ms Windows), and look and feels.

MAGE-stk has also been updated

Updated Jxl Api to 2.5.4

2005-04-11T19:26:00.000+02:00

Made SimpleGUI multilanguage

2005-04-10T12:40:00.000+02:00

The internationalisation of the SimpleGUI is done.
The default language is english. Currently, only french is supported.

Texts are contained in files in the etc/lang directory.

It used the ResourceBundle class.

Using JFlex API to open url

2005-04-09T00:23:00.000+02:00

THe JFlex is used as ANt task to create class from lex file.

Available there: http://jflex.de

Added options to launch the SimpleGUI

2005-04-08T22:52:00.000+02:00

Possibility to set the UI LookAndFeel.

SimpleGUI - added Drag and Drop to main window

2005-04-07T23:04:00.000+02:00

File to treat can now be added by drag and drop from file explorer.

Simply drag it from the native file explorer and drop it in the text field.

The GUI should be release soon.

SimpleGUI - added About frame

2005-04-07T23:00:00.000+02:00

Added a About frame, with general information about the tool and the license under the tool is release.

For general information, an HTML file is used. Links open the default browser or mail reader.
As Java does not handle relative path to image, it has been modified to allow this, but it is really slow.

Passed MAGE-ML Test : A-WMIT-1

2005-04-05T19:54:00.000+02:00

The tool converts correctly the A-WMIT-1 experiment MAGE-ML file.
About 4992 Features

Need to improve exporter.
Create CompositeSequence if missing in MAGE-ML file.

2005-04-05T02:30:00.000+02:00

ADF MAGE-ML Tool Simple GUI with minimal options

2005-04-05T02:28:00.000+02:00

Simple GUI - with Windows Look and feel

Updated Changelog

2005-04-05T01:56:00.000+02:00

The changelog has been updated on the Sourceforge site for release 1.0 RC2.

fixed bug if adr file is missing

2005-03-26T23:54:00.000+01:00

The tool now displays a message if the adr file is missing.

Creation of a simple GUI for the tool;

2005-03-26T16:59:00.000+01:00

I am currently working a very simple GUI, offering to the user to check or check and convert a array design file (adh or MAGE-ML). The user could also ask for a curation of data.

Script to convert ADF from previous format to new one

2005-03-26T16:50:00.000+01:00

The previous ADF format was composed of one file containing Feature, Reporter and CompositeSequence data.
The new format is composed of three parts : meta-data (adh), Feature/Reporter and CompositeSequence.

This script is supposed to create the three parts.
Currently, the script, written in Perl split feature/Reporter and CompositeSequence data in two files (adr and adc) following header Items. Now checking is done.

So, the script only support ADF text file and is only useful if there are also CompositeSequence data.
In the future, the script will propose to create interactively the adh part/file.

Added Updater

2005-03-19T16:10:00.000+01:00

The tool now includes an updater. For a given resource, the updater is looking for a new version on a list of mirror servers.

requires Internet connection.

Unix script updated

2005-03-15T19:26:00.000+01:00

The Unix shell script to launch the ADF MAGE-ML tool has been updated It now checks the variables (JAVA_HOME and ADFCONVERTERHOME) and if the ADFCONVERTERHOME is really the directory containing the ADF MAGE-ML Tool files. For this, it is checked if the adfconverter.properties file is contained in the etc subdirectory.

Updated MGEDOntologyClassEntry

2005-03-15T19:22:00.000+01:00

Updated MGEDOntologyClassEntry to match new version of the MGED Ontology manager from MAGE working group.
http://mged.sourceforge.net/software/index.php

Updated windows script to launch the tool.

2005-03-14T10:04:00.000+01:00

THe .bat script called to launch the application has been modified to check variables (ADFCONVERTERHOME,path to the java exec ) before calling the tool.

Updated shortcut installer

2005-03-14T09:58:00.000+01:00

Added shortcut to documentation files, to tool website.
Fixed problem to open window in normal size (not minimized)

Fixed/clean Unix shortcut file.

Added DBVersion for MAGE identifier generation

2005-03-12T00:42:00.000+01:00

The DBVersion variable can be added to the database identifier rule.
It will be replaced by the version of th DB. Currently, only the MGED ontology is supported.

Updated MAGE-stk API

2005-03-12T00:10:00.000+01:00

The MAGE-stk API has been updated to MAGEstk-2004-11-29-src-v1.1-compatible.jar. The API has been compiled from source (binaries don't seem to work).

Updated MAGE identifier export during ADF conversion

2005-03-09T20:57:00.000+01:00

The MAGE identifier export during ADF conversion to MAGE-ML has been modified to export identifier during conversion.

Previously, the export was done after the conversion (and also using more memory).

Performance should be improved.

updated file XML Schema and jaxb

2005-03-09T16:30:00.000+01:00

Updated XML Schema to allow to skip file first line, due to the new format of the approved databases file.

Updated as well JaxB api

Compilation wiki page created

2005-03-08T23:36:00.000+01:00

Added a wiki page on the compilation of the Tool source code.

Currently, only explains compilation with Ant from Apache software.

Updated ADFConverterLoggerImpl for updated Log4j api

2005-03-08T23:05:00.000+01:00

the ADFConverterLoggerImpl has been updated due to the deprecation of the Priority class. Changed it to Level class.

tgz, zip, bz2 project released

2005-03-08T18:14:00.000+01:00

The ADF MAGE-ML Tool has been released as tgz, zip, bz2 files. This is the same version than for the installer.

Available here:
http://sourceforge.net/project/showfiles.php?group_id=120387&package_id=145516

This version is the preview version 1.0 RC1.

Added Examples file to sourceforge

2005-03-08T13:36:00.000+01:00

Uploaded an archive file (zip, tgz, tar.bz2) containing several ADF and MAGE-ML files to test the Tool.

Files are in the examples directory.

New Test Results wiki Page

2005-03-07T18:13:00.000+01:00

The TestS page has been added to the tool development wiki.

This page contains results from test files.

Currently, there is the study of the 60000 features ADF tests.

60000 features/Reporters test passed

2005-03-07T11:30:00.000+01:00

The Tool has been tested with an ADF containing 60000 features (same number of Reporters - to stress the application).

The checking/conversion has been made in 30 hours (can still be improved).

See new Tests wiki page.

AdfConversion wiki page created

2005-03-05T00:01:00.000+01:00

The AdfConversion page has been created about the conversion of ADF to MAGE-ML (data to MAGE object).

Created objects

MAGE identifieer generation

Installation wiki page updated

2005-03-04T21:55:00.000+01:00

The installation page has been updated to match information contained in the INSTALL.txt file.

Information for archive file.

INSTALL.txt file created

2005-03-04T15:56:00.000+01:00

The INSTALL.txt file explains how to install the tool without using the installer.

New version of the approved databases file

2005-03-04T10:21:00.000+01:00

THere is a new version of the approved databases file maintaint by the EBI. But, due to a sligthly format modification. The tool can not handle it without modification.

A version number is added on the first line

Question: shall we add the MGED ontology version to the MAGE identifier?

2005-03-02T16:02:00.000+01:00

From information for submitter: (http://www.ebi.ac.uk/~ele/ext/submitter.html#db)
The database codes are prefixed with ebi.ac.uk:Database:, e.g. ebi.ac.uk:Database:embl. In the cases of databases where a version/build is known, you can provide this information within the code, e.g. ebi.ac.uk:Database:unigene:129 (or unigene:129 in the case of ADF submissions via MIAMExpress).

Should add it as the version number is retrieved from MGED Ontology file?

and do the same for others databases with the current database number?
Or shall we add databases version in the configuration file or in a txt file?

XML characters translations

2005-03-01T19:35:00.000+01:00

Lists for character corrections for XML - have to be done in the Tool:

Journal du net

Quelques caractères spéciaux et entités correspondantes
Caractère	Entité correspondante
é	é
è	è
à	à
ù	ù
ê	ê
ï	ï
ë	ë
Ê	Ê
ç	ç
oe	&oelig;

Java Web Services Developer Pack 1.5 FCS

2005-02-28T23:26:00.000+01:00

The Java Web Services Developer Pack 1.5 FCS is available, with JaxB 1.0.4.

The ADF MAGE-ML Tool should be updated soon.

http://java.sun.com/webservices/jwsdp/index.jsp

Log4j updated - 1.2.9

2005-02-28T22:48:00.000+01:00

The Log4J api has been udpated to the version 1.2.9 (from 1.2.8).

http://logging.apache.org/log4j/docs/index.html

First public release

2005-02-28T21:41:00.000+01:00

The first public release is available on the sourceforge website:

http://sourceforge.net/project/showfiles.php?group_id=120387&package_id=145516

This is a preview version : 1.0 RC1 for bug hunting.

This page provided two installers for the ADF MAGE-ML Tool (standard/off line and web/online).

jxl api updated -2.5.3

2005-02-28T08:49:00.000+01:00

The jxl API has been updated to version 2.5.3.

Tool installers created

2005-02-28T00:47:00.001+01:00

Installers (standard and web) have been created for the ADF MAGE-ML Tool.

The full installer is about 19 Mb and the web 1mb.

They will be available by tomorrow (version 1.0 RC1), time to fix a bug with java exec in the tool script.

Tool installers created

2005-02-28T00:47:00.000+01:00

Installation script creation

2005-02-27T00:13:00.000+01:00

Starts to create script to install the application.

After project archive file uncompressed, a script (configure.bat / configure.sh following operating system) creates the script used to launch the application. Scripts should be improved to fill in the tool configuration file.

Starts to work on the installer. The installer used izpack, a java X installer (windows, mac and unix support). The configuration file creation is missing.

Tool now handles ADF XLS file

2005-02-27T00:10:00.000+01:00

The tool can check and convert ADF in Microsoft Excel format.

Additionaly, Most of bugs seems fixed. A preview version will be released soon.

4000 features test

2005-02-21T15:23:00.000+01:00

A test with an ADF containing 4000 features has been done.
The test does not fail.

Output MAGE-ML file size : 23,3 Mb

Total execution time: 3 minutes

Tool initialisation duration: 4 seconds

File checking duration: 1 min 46

Conversion duration: 30 secondes

identifier export duration (8000 identifiers): 3 s

MAGE-ML export duration: 4s (temp files/raw data) + (reading and pretty writinhg + validation) 10 s

New option

2005-02-19T16:26:00.000+01:00

For ADF checking, the duplicate detection can now be disabled, to improve execution time.

log file size has been reduced.

New wiki page

2005-02-19T12:32:00.000+01:00

The Tool configuration page has been added into the wiki.

http://marguerpie.free.fr/wikini/wakka.php?wiki=TheConfiguration

60000 features test failed due to an incorrect file

2005-02-18T16:47:00.000+01:00

But, we can notice:

need 16 hours to deal with the ADF file

Use a lot of memory (about 150 mb- maybe more)

(there is certainly a memory leak) / memory doesn't seem to be freed correcly.

Application specific file structure definition

2005-02-17T23:53:00.000+01:00

Following the ADF specification, there are four allowed applications:

gene_expression

snp_detection

comparative_genomic_hybridization

binding_site_identification

Any other application is compulsed as default case (containing all possible cases)

There is one xml file per file format. (text, workbook)

each file are named as follow:
ADF-fileformat-application.xml

definition files have created or checked/completed.

OptimizedFileChecker class is working

2005-02-14T13:25:00.000+01:00

OptimizedFileChecker class needs testing, treaking to allow File Checker replacement.

start to implements OptimizedADFChecker

New class

2005-02-12T13:51:00.000+01:00

A new class has been created: OptimizedFileChecker (OptimizedADFchecker will follow).
in uk.ac.ebi.adfconverter.tools.checker package.

They will replace FileChecker and ADFChecker classes.

Allow to check horizontal table as "independant" row, row by row to save memory during checking.

New ADF MAGE Tool Mailing list

2005-02-06T11:43:00.000+01:00

The adfconverter-general mailing list has been created:

http://lists.sourceforge.net/mailman/listinfo/adfconverter-general to subscribe.

step by step File checking bug fix

2005-01-31T14:40:00.000+01:00

Bug due to '&&' rule.

Optimisation can be started.

Wiki page

2005-01-26T20:45:00.000+01:00

A wiki page has been created for developer and/or as Howto:

http://marguerpie.free.fr/wikini/wakka.php?wiki=AdfMage

source code cleaning done

2005-01-26T13:05:00.000+01:00

The code cleaning is done:

Add ArrayExpress license
Add comments
remove unnecessary elements.

TODO:

fix bug with ADF workbook
optimize file/ ADF reading (mainly for memory).

Sourceforge Web page update

2005-01-21T22:30:00.000+01:00

add meta tag for referencing
update schema documentation
no yet reference in google

Microsoft Excel Workbook limitation

2005-01-12T15:47:00.000+01:00

The maximum number of rows in a Microsoft Excel 5.0 or 7.0 worksheet is 16,384

The maximum number of rows in a Microsoft Excel 97 worksheet is 65,536.

It is supposed that Microsoft Excel 97 is used.

If row numbers are upper to 65,535 (one row for header), the output file format is switch to text file.

API Update

2005-01-10T22:42:00.000+01:00

Jxl updated to version 2.5.1

Technical Documentation

2004-12-14T13:29:00.000+01:00

I start to write the project technical documentation. This documentation will explain the project and technical information about the tool for facilitating rework on the project.

Zip archive file support

2004-11-30T23:59:00.000+01:00

Added support for zip file. (sub-directories supported)
contents is extracted in a sub directory called by the name of the zip file (without ".zip")

Tar file

2004-11-30T23:33:00.000+01:00

Add tar archive file support.
contents is uncompressed in a subdirectory called by the name if the archive file name.

[Mged-mage] New Java MAGEstk release

2004-11-30T14:10:00.000+01:00

A new version of the Java MAGEstk has been released on the MGED sourceforge site :
http://sourceforge.net/project/showfiles.php?group_id=16076&package_id=27724

Classes for MGED Ontology management releases as separe jar file.

They have not yet been included in the ADF MAGE-ML Tool.

TODO List

2004-11-29T23:42:00.000+01:00

Add default file encoding for reading and writing (set to UTF-8)
Add support to ~~zip~~, gz and tgz files
Change XML Schema namespace from http://www.ebi.ac.uk/adfconverter to http://www.ebi.ac.uk/adf ?

The first post

2004-11-13T14:34:00.000+01:00

This blog is starting to present progress of the ADF MAGE-ML Tool, from the Microarray Informatics Team at the European Bioinformatics Institute in Cambridge, UK.

This project starts by a 6 months master project in bioinformatics in the MicroArray Informatics Team..

Sourceforge web page

2004-11-13T13:50:00.000+01:00

The sourceforfe web page is now up.
Not so different from the EBI page.

13th November 2004

2004-11-13T11:12:00.000+01:00

The project is now on sourceforge: http://adfconverter.sourceforge.net.
I restarted to work on it after the end of my master (end of october).

Adding license to each source file
add checking of configuration properties (it's always better to check every parameter).