EMBOSS: Project Meeting (Mon 2nd March 09)
Peter has updated the protein feature internals to improve the display of non-standard features in DASGFF output. Updated code and QA tests have been committed.
Mahmut has updated the EMBRACE wiki with EMBOSS 6.0 SoapLab typed services. There have been issues with the typed service WSDL files as they import XSD definitions. Perl clients do not recognize the import definition. Other clients (e.g. taverna) do understand imports but have other problems. The WSDL style will change to include the XSD. This will also make it easier to generate the WSDL with acdxsd.
Results types are extended in WSDL for the Run and RunAndWaitFor methods. Extensions will be avoided so that Taverna can use typed service WSDL files.
Alan suggested checking the EMBRACE technology recommendations for standard service names. Alternative names may be needed to make SoapLab fully compliant.
The SoapLab server was restarted 4 weeks ago (to implement typed services) and has served over 1 million HTTP requests (including Taverna client startups). No hanging threads were seen.
Mahmut has added DAS services for nucleotide sequences. There is now a total of 14 EMBOSS DAS services. Dasty was used for testing. The services have now been run under the Ensembl client, using DbFetch to retrieve data from Ensembl Gene and Ensembl Transcript to retain Ensembl identifiers in the DAS output. Some display issues remain to be resolved.
Mahmut and Peter will attend a DAS workshop next week.
Alan noted that when making changes anything that affects the revised book text needs to be noted and checked.
Mahmut has been in contact with the EMBRACE registry team with regard to a programmatic API for service registration.
A printed copy will be needed to make decisions on content, appendices and sections to be excluded from the final versions.
Peter has located the original TeX file for the tutorial and will update the examples to use accession numbers and check for changes to outputs.