*** S Clark wrote: |The updates to esearch, esummary, and the generic xml parser should all |be on CVS tomorrow morning (US West Coast time) along with HOPEFULLY a |functioning NCBI BLAST set of code. Hey Sean, Nico, Serge et al. Sean: I've checked out the changes to the ESearch, ESummary and generic xml parsers modules. I will hopefully have some time to test the updates to the modules in the next few days. I would also like to upgrade the pubmed module I wrote for my site (nodalpoint.org) to work with the new EUtils classes. Hopefully this should provide some more testing. Also there have been some announcements from NCBI that may effect these classes (you may have seen them): "ESummary XML will be modified the first week in June to accommodate a number of changes in PubMed" I don't know how this will effect the ESummary parser but I can investigate if you like ? "To provide more efficient processing NCBI has created a new domain for EUtilities, http://eutils.ncbi.nlm.nih.gov/entrez/eutils" I noticed the host name hasn't been updated in the latest cvs check-ins. But the test cases still seem to work with the old host name (www.ncbi.nlm.nih.gov). Further issues on testing: The ESearch interface returns various errors that are not currently handled by the ESearch classes. For example a search for "asdfg and cancer" will return the following chunk of XML in the result: <WarningList> <PhraseIgnored>and</PhraseIgnored> </WarningList> Any thoughts on how to handle these cases ? Also any thoughts on unit testing these classes ? Are there any frame works available for PHP ? Have any decisions been made about code standards for BioPHP (PEAR) ? I'd be happy to submit patches to the EUtils class to bring them up to what ever code standards are decided upon ? Further more I will be attending BOSC/ISMB [1/2] in Brisbane in June/July. I will be giving a short talk at BOSC on a few topics (My PhD research, nodalpoint.org, debian and bioinformatics). Since BOSC is *the* open-source bioinformatics conference I would be happy to mention the BioPHP project in the talk too. My question is would everyone else be happy with this ? My intention is simply to give BioPHP some publicity in the open-source bioinforamtics world. No to steal the lime light :) Lastly, does the presence of a genephp directory in cvs imply that these two code bases will be merged ? And I notice that the GenePHP website is now advertising itself as BioPHP but pointing to the GenePHP source ? My question is: Which is the official BioPHP site ? Sorry for the long email and keep up the good work :) _greg [1] http://www.iscb.org/ismb2003/index.shtml [2] http://www.open-bio.org/bosc2003/ -- Greg Tyrelle (http://www.kinglab.unsw.edu.au/~greg) "Logic only gives man what he needs, magic gives man what he wants" - Tom Robbins