Re: [mart-dev] marteditor hangs on bad db design

[Alexandre Gattiker]

Hi Damian,

Here is an example schema that is sufficient to hang marteditor.

CREATE TABLE Sc__main__main (
    id_key int auto_increment primary key,

     gene varchar(10),
     col1 int
);

CREATE TABLE Sc__bbb__main (
    id_key int auto_increment primary key,

     gene varchar(10),
     col2 int
);

Making all column names unique didn't seem to solve it.

CREATE TABLE Sc__main__main (
    id_key int auto_increment primary key,

     gene varchar(10),
     col1 int
);

CREATE TABLE Sc__bbb__main (
    id_key2 int auto_increment primary key,

     gene2 varchar(10),
     col2 int
);


Best
Alexandre





Damian Smedley wrote:

On Thu, 20 Jul 2006, Alexandre Gattiker wrote:

Damian Smedley wrote:

On Thu, 20 Jul 2006, Alexandre Gattiker wrote:

Hello,

If a mart database accidentally contains two __main tables for the same dataset, marteditor in "Naive" mode hangs in the following loop at DatabaseDatasetConfigUtils.java line 3342.

do you mean two tables with exactly the same name? All our ensembl
datasets have two __main tables per dataset so that shouldn't be a
problem. What are the names of your main tables out of interest - we will
investigate

my tables were named something like:

Scerevisiae__aaa__main
Scerevisiae__bbb__main

According to the doc the part in the middle is irrelevant, and there should only be one __main table with a given prefix part, if I understand correctly.

guess our docs are a bit misleading on this - we will improve it for the
0_5 release :) Your table names should be fine (eg) in
hsapiens_gene_ensembl we have:

hsapiens_gene_ensembl__gene__main with gene_id_key
hsapiens_gene_ensembl__transcript__main with gene_id_key,
transcript_id_key

suspect it is the combination of your main tables and keys that is causing
the hang rather than the table names - what are your keys?

cheers
Damian

Cheers
Alexandre


--
Alexandre Gattiker
Swiss Institute of Bioinformatics, Genome Bioinformatics Group
Biozentrum                                Tel. +41 61 267 1579
Klingelbergstrasse 50                     Fax  +41 61 267 1585
4056 Basel                                 [EMAIL PROTECTED]
Switzerland             http://www.biozentrum.unibas.ch/primig

--
Alexandre Gattiker
Swiss Institute of Bioinformatics, Genome Bioinformatics Group
Biozentrum                                Tel. +41 61 267 1579
Klingelbergstrasse 50                     Fax  +41 61 267 1585
4056 Basel                                 [EMAIL PROTECTED]
Switzerland             http://www.biozentrum.unibas.ch/primig