EMBOSS: Project Meeting (Mon 13th October 08)
Peter is running a full test of the profiled dbx code. The test run completed, but hit an error when closing the huge descriptions index. It is not clear whether this was a code or a disk problem. We will order a large local disk to repeat the test.
Peter has added a new application dbxreport to analyse the dbx index files and report total keys and free space. The output indicates possible index problems where the key numbers fail to add up. To support dbxreport, a new page type NumBucket was needed. The index reading code tests for both NumBucket and Bucket page type to provide back compatibility, but dbxreport will give incorrect results on index files with Bucket page type used for NumBucket pages.
Peter has fixed a problem in einverted which expected all ambiguity codes to be 'N'.
Creating jobs but not starting the job caused some issues in the removal of old jobs.
Problems for a frequent user creating jobs through a python client have been resolved. This was related to SoapLab2 exceptions. These did not obey JavaBean rules and so cannot be used by Axis. They were replaced by the SoapLab 1.0 exception class.
The EBI wrapper services (WsBlast, etc.) are not included in SoapLab 2.0. These services can now be run from their own native web service interfaces.
Log message density has been reduced.
MIRA services are currently disabled. Work is needed to pass the directory and return filename. The output definition depends on the options. Input files have a prefix in the commandline. Some fixes to the ACD file and C source are needed. QA tests are complicated by the need to copy files and create a directory.
Job directories need to be restructured to reduce their size, possibly once per hour.
Comments on the admin guide are completed.
Further comments are added to the "to do" and remarks sections.
The chapters in the developer's guide have been rearranged. Jon will work on the text next month.
Book content needs to be put on the website to test the stylesheets.
The Fuse update is done. Mahmut noted that eclipse metadata has grown to 1GB so this is now not copied. Netbeans use has been reduced.