Hi Rohit
The first error suggests a strange character in your cvterm table in the
column is_relationshiptype. There appears to be a charcter (t?) when the
mapping is expecting an integer. You should find that and change it to an
integer.
The second exception looks like it has failed to find the sequences. To
find the organisms with top level features with residues it runs this
query which you can try :
SELECT DISTINCT ON( feature.organism_id )
organism.organism_id AS organismId,
abbreviation, genus, species, common_name AS commonName, comment
FROM feature
join organism using (organism_id)
join cvterm on feature.type_id = cvterm.cvterm_id
WHERE residues notnull AND residues != ''
AND (cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
cvterm.name IN ('supercontig', 'ultra_scaffold', 'golden_path_region',
'contig'));
This assumes that the sequence features have type_id *chromosome*,
*sequence*, supercontig, ultra_scaffold, golden_path_region or contig. If
your sequence features do not belong to that list you can modify it in
artemis_sqlmap/Feature.xml. Please let me know if you think something
needs adding to this list.
Regards
Tim
On Thu, 22 Oct 2009, parimi rohit wrote:
Hi All,
I am following the wiki page that has the tutorial to integrate Artemis with
Chado schema. I have
postgres as well as chado schema installed. I used Apollo to annotate data from
one of the
databases that we created. Now, I am trying to use Artemis on the same data.
However I am having
problems in running Artemis over the database. I started Artemis with the
following command as
given in the wiki page:
$: ./art -Dchado="localhost:5432/rohit_chado_01?rohit" -Dibatis
I entered my credentials in the login window and the Database and File Manager
window opened.
However I am able to view nothing in the Database part of the window even
though there exist
many. Also double clicking the folder in the database window is giving an
exception in the
terminal.
I copied the terminal errors in a text file and I am attaching it in this mail.
The attachment
contains error information for 2 different databases. Please let me know the
problem and the way
to solve this so that it will work with the data that we have.
Regards,
Rohit
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