Hi Marek, Here are a few answers that I can give you right now. Please let me know if you have more questions.
All the scripts I used for creating and registering pygr.Data is saved in /result/pygr_project in leelab2. See README_RESTART_PROCEDURE.txt for some details. If you want to see what is going on in biodb2:5000, you can login biodb2 (root passwd same as leelab2) and check /data/server directory. There are scripts starting with 1_, 2_, 3_, and 4_ according to their steps. And simple_5000.py is the script I used for starting pygr.Data resources in biodb2:5000. Latest version of pygr is /data/server/pygr and I set PYTHONPATH to build directory of /data/server/pygr. Yours, Namshin Kim On Tue, Jan 27, 2009 at 4:22 AM, Christopher Lee <[email protected]> wrote: > > Hi Marek, > yes, Namshin set up a pygr.Data mysql resource database for all our > leelab internal resources. The database name is PYGRDB_JAN06, and the > table name is pygrdata, so you would add mysql:PYGRDB_JAN06.pygrdata > to your PYGRDATAPATH, assuming that you have configured your ~/.my.cnf > config file with the mysql server, username, and password info. I'll > give you that separately. > > More responses below. > > -- Chris > > On Jan 23, 2009, at 8:50 AM, Marek Szuba wrote: > > > Hello Chris, > > > > Attached you will find a patch which attempts to address Pygr issue > > 14. > > It does the following: > > - allows specifying the type of matching to be performed. Types > > supported at present are 'p', which engages old > > exact-match-on-beginning behaviour (default), and 'r', which enables > > regex support via Python's standard re module; > > - gives pattern a default value of '' so that pygr.Data.dir() can be > > called instead of pygr.Data.dir('') to get all IDs; > > - adds missing description string to ResourceDBMySQL.dir(). > > I'll take a look. I'll be back in LA on the 28th. > > > > > > > The main part of this patch is of course adding support for regular > > expressions. I have confirmed that regex search patterns work when > > querying ResourceDBShelve, they also appear to work in client-server > > mode (I launched my own server and could see the method being called > > correctly in its logs, however it seems I didn't configure data > > sources > > correctly because dir() returns an empty list regardless of its > > arguments). As for SQL support, it SHOULD in principle work but I > > haven't tested it yet - is there a pygr.Data MySQL database around > > that > > I could use for this purpose? > > Namshin can answer any questions you may have about creating and > starting an XMLRPC pygr.Data server. He can probably just point you > at the scripts that he uses. > > > > > > > > Please let me know what you think. Myself, I am not entirely happy > > with > > two things and will appreciate any suggestions on how to improve them: > > - the way matching type is selected - I can't quite put my finger on > > it but doing it the way it's done now feels clumsy, normally I would > > use an enumeration type for this but Python doesn't seem to provide > > them yet; > > > > - the fact re.compile is called in each backend's dir() rather than > > just once in the frontend, as it's inefficient if multiple backends > > are queried. The problem with the latter is that xmlrpclib doesn't > > know how to marshal compiled patterns. > > I don't see this as a problem. XMLRPC only marshals a few primitive > data types, in keeping with its usage as a broad standard. You could > even argue that in our specific case this helps preserve modularity. > That is, the client shouldn't know the details of *how* the server is > going to implement the search. For example, someone could implement a > pygr.Data XMLRPC server in Java and have a completely different > internal data structure for compiled regexps. Or for that matter, the > python standard lib might someday make a change in that internal data > structure for compiled regexps, such that it would be incompatible > with a pattern compiled using an earlier version of Python... > > > > > > Cheers, > > -- > > MS > > <pygrData-searchImprovements.patch> > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
