No, I haven't used the -A switch. Actually retrieving all table names and fields is exactly what I need for my application.
On Fri, Oct 30, 2009 at 7:02 PM, Galt Barber <[email protected]> wrote: > 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
