Hi,
I got the same kind of troubles with comments and author. But everything
went great as soon as I modified the chado-adapter.xml.
I mentionned to extract the property (e.g. synonym, comment, author)
from the feature_property cv where they are stored in my database (I
think this cv have created when I loaded Chado)..
So try to figure out what cv the synonym term belong to in your
database, and modify the propertyTypeCV of your Chado-adapter like that :
<propertyTypeCV>feature_property</propertyTypeCV>
It might be helpful.
cheers,
Fabrice
Ed Lee wrote:
Hi Isabelle,
Scott's gut feeling is probably right about Apollo needing the 'synonym'
cvterm to belong to a specific cv. For some reason, Apollo expects it
to belong to the 'null' cv (not an empty cv, but a cv called 'null').
I'm not sure the historic reason for this decision and I'm guessing your
Chado instance has the 'synonym' cvterm that belongs to another cv.
Anyway, I've made modifications to the code to try to use the 'null' cv
first (as to not break expected behavior) but to fall back to whatever
other cv if it's not found.
I'll cut a new release of Apollo with this bug fix tomorrow and you can
give it a try and let me know how it works.
Out of curiosity, could you run the SQL query that Scott mentioned and
send the results?
Cheers,
Ed
On Thu, 2008-10-02 at 15:09 -0700, Isabelle Phan wrote:
forgot to say I am still getting the error upon saving and I am unable
to delete a synonym.
What can I try next?
Isabelle
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Isabelle Phan
Sent: Thursday, October 02, 2008 3:04 PM
To: Scott Cain
Cc: [email protected]; Gowthaman Ramasamy
Subject: RE: [apollo] saving to chado DB
I am using
apollo.dataadapter.chado.jdbc.PostgresChadoAdapter
Isabelle
-----Original Message-----
From: Scott Cain [mailto:[EMAIL PROTECTED]
Sent: Thursday, October 02, 2008 3:01 PM
To: Isabelle Phan
Cc: Ed Lee; [email protected]; Gowthaman Ramasamy
Subject: Re: [apollo] saving to chado DB
Hi Isabelle,
It could be that these additions are no longer required,
depending on
which adapter you are using to talk to Chado (which Ed or I should
have asked in the first place). Honestly, I'm not sure how you tell
--but there are two and the older one is what needed much of that
"stuff" in the apollo-inserts file. Most people would probably want
to be using the newer one.
Scott
On Thu, Oct 2, 2008 at 5:51 PM, Isabelle Phan
<[EMAIL PROTECTED]> wrote:
Hello Ed and Scott,
first I discovered:
http://gmod.org/wiki/Apollo-Chado
perhaps this link could be added to the Apollo documentation?
So I added the cv terms, but apollo-inserts (.sql??) fails:
ERROR: null value in column "cv_id" violates not-null constraint
-> this is caused by bug in SQL statement:
insert into cvterm (name, cv_id, dbxref_id,
is_relationshiptype) values
('producedby',(select cv_id from cv where name='Relationship
Ontology'),(select dbxref_id from dbxref where accession =
'Relationship
Ontology:producedby'),1);
I kind of guess it should be:
....select cv_id from cv where name='relationship'...
NOTICE: CREATE TABLE will create implicit sequence
"feature_namegenerator_feature_namegenerator_id_seq" for
serial column
"feature_namegenerator.feature_namegenerator_id"
NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index
"feature_namegenerator_pkey" for table "feature_namegenerator"
CREATE TABLE
INSERT 0 0
INSERT 0 0
ERROR: aggregates not allowed in WHERE clause
These statements are invalid:
INSERT INTO feature_namegenerator (name,type_id,count)
SELECT substr(name, 0 , (position('-' in name))),
(select cvterm_id from cvterm where cv_id=7 and
name='transcript'),
to_number(max(substring(name from 21)), '99999')
FROM feature WHERE name like 'RICE%-transcript%' group by name;
INSERT INTO feature_namegenerator (name,type_id,count)
SELECT substr(name, 0 , (position('-' in name))),
(select cvterm_id from cvterm where cv_id=14 and
name='protein'),
to_number(max(substring(name from 19)), '99999')
FROM feature WHERE name like 'RICE%-protein%' group by name;
I am not sure what the correct statements should be,
apart that the
cvterm_id is null and so even if the SQL syntax was
correct, the inserts
would fail.
any hints?
Isabelle
-----Original Message-----
From: Ed Lee [mailto:[EMAIL PROTECTED]
Sent: Thursday, October 02, 2008 1:25 PM
To: Isabelle Phan
Cc: [email protected]; Gowthaman Ramasamy
Subject: Re: [apollo] saving to chado DB
Hi Isabelle,
I'll take a look at the mentioned issues. Unfortunately
SourceForge's
CVS is down (again...) so I'll need for it to come back up
before I can
commit any changes. I'll let you know what I find.
Cheers,
Ed
On Thu, 2008-10-02 at 12:29 -0700, Isabelle Phan wrote:
Hello
I am running Apollo 1.9.5 on a chado database and having
trouble editing
data with the Annotation editor:
1) add synonym to gene name seems to work, data is saved
in tables
feature_synonym and synonym in but error logs returns:
lookup failed for cvterm_id for cvterm with name ='synonym'
database has no 'synonym' cvterm;
I checked that an entry exists in table cvterm with name
= 'synonym'
(cvterm_id=28874), so I don't quite understand that message.
2) delete synonym from gene name fails. The interface
shows no error
upon saving, but the records are still there in
feature_synonym and
synonym, and the error logs show the same messages as above
after the
DELETE statement.
Isabelle
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--
--------------------------------------------------------------
----------
Scott Cain, Ph. D.
[EMAIL PROTECTED]
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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--
Fabrice Legeai
INRA UMR Bio3P IRISA Equipe Symbiose
IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 71 18
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