Saturday, March 26, 2005

fixed bug if adr file is missing

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

Creation of a simple GUI for the tool;

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

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.

Saturday, March 19, 2005

Added Updater

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.

Tuesday, March 15, 2005

Unix script updated

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 file is contained in the etc subdirectory.

Updated MGEDOntologyClassEntry

Updated MGEDOntologyClassEntry to match new version of the MGED Ontology manager from MAGE working group.

Monday, March 14, 2005

Updated windows script to launch the tool.

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

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

Fixed/clean Unix shortcut file.

Saturday, March 12, 2005

Added DBVersion for MAGE identifier generation

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

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).

Wednesday, March 09, 2005

Updated MAGE identifier export during ADF conversion

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

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

Tuesday, March 08, 2005

Compilation wiki page created

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

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

tgz, zip, bz2 project released

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

Available here:

This version is the preview version 1.0 RC1.

Added Examples file to sourceforge

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.

Monday, March 07, 2005

New Test Results wiki Page

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

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.

Saturday, March 05, 2005

AdfConversion wiki page created

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

  • Created objects

  • MAGE identifieer generation

Friday, March 04, 2005

Installation wiki page updated

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

Information for archive file.

INSTALL.txt file created

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

New version of the approved databases file

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

Wednesday, March 02, 2005

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

From information for submitter: (
The database codes are prefixed with, e.g. In the cases of databases where a version/build is known, you can provide this information within the code, e.g. (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?

Tuesday, March 01, 2005

XML characters translations

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

Quelques caractères spéciaux et entités correspondantes