Java Web Services Developer Pack 1.5 FCS

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

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

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

The jxl API has been updated to version 2.5.3.

Tool installers created

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

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.

Installation script creation

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

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

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

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

log file size has been reduced.

New wiki page

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

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

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

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

start to implements OptimizedADFChecker

New class

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

The adfconverter-general mailing list has been created:

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