did you pass -A on mysql client cmdline to suppress loading all table names etc feature?
Sent from my iPhone On Oct 30, 2009, at 10:09 AM, Michael Zouberakis <[email protected]> wrote: > Hello, > > I'm experiencing enormous delays when attempting to query any of the > databases @ genome-mysql.cse.ucsc.edu. > > I'm using version 1.2.17 of MySQL's Query Browser and connect to > genome-mysql.cse.ucsc.edu using the information provided here > http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 > <http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29> > I can successfully connect to the server and can see a listing of all > databases in the Query Browser window. When attempting to view the > tables of > a database via Query Browser's GUI the application either hangs > completely > or takes approximately (more than) 10 minutes just to display the > tables > under a schema. I'm experiencing similar side effects when trying to > retrieve table information from a schema using a simple Java class > (MySQL > JDBC version 5.1.2). > > Any suggestions/hints on how to overcome this issue are welcome. > Thanks in > advance. > > Kind Regards, > Michael > > On Fri, Oct 30, 2009 at 12:25 AM, Brooke Rhead <[email protected]> > wrote: > >> Hello Michael, >> >> I cannot tell you why your tools are not working for all databases, >> but I >> can point out a few things that may be helpful to you: >> >> 1. You should be able to access genome-mysql.cse.ucsc.edu without a >> password. Instructions are here: >> http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 >> >> 2. The only mouse databases that are available in full on the >> public server >> are mm7, mm8 and mm9. Earlier mouse browsers have been archived ( >> http://genome-archive.cse.ucsc.edu/) and are no longer available on >> the >> public mysql server, except for a single "chromInfo" table in the >> mm5 and >> mm6 databases. >> >> >>> Are schemas mm8 and mm9 not public? >> >> All of the data on genome-mysql.cse.ucsc.edu should be publicly >> accessible. >> >> I hope this information is helpful. If you have further questions, >> please >> feel free to write back to the mailing list at [email protected]. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 10/29/09 01:06, Michael Zouberakis wrote: >> >>> Hello, >>> >>> I'm writing on behalf of BSRC Al. Fleming Institute's BioIT Unit. >>> >>> We have developed an online database containing mouse related web >>> resources >>> called the Mouse Resource Browser a.k.a. MRB (http://bioit.fleming.gr/mrb >>> ). >>> >>> One of the recorded resources is UCSC's Genome Browser ( >>> http://bioit.fleming.gr/mrb/Controller?workflow=ViewModel&eid=238). >>> >>> On the "Technical Tab" of your resource's view you'll notice a >>> section >>> entitled "Direct Database Access". >>> >>> Under that section MRB provides a tool called "wsGenerator" which >>> parses a >>> database's schema and generates Java SOAP API classes and schema >>> descriptive >>> XML and PNG files. >>> >>> In Genome Browser's case we provide links to mm5 and mm8 databases >>> located >>> @ >>> genome-mysql.cse.ucsc.edu using genomep as username and password as >>> password. >>> >>> wsGenerator can successfully parse the mm5 schema but fails to >>> parse your >>> mm8 schema. Even with various MySQL clients schema mm8 and mm9 >>> seem not to >>> be accessible. Is there a reason for that? Are schemas mm8 and mm9 >>> not >>> public? >>> >>> Also could you point out other databases on your publicly >>> available server >>> that might be of interest to bench scientists working with mice? >>> >>> Thank you in advance. >>> >>> Kind regards, >>> Michael Zouberakis >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
