Bonjour Fabrice,
it looks like my Chado DB is the same as yours, i.e. 'synonym' belongs to the
feature_property cv.
However, my chado adapter inherits from riceInstance, which has
<propertyTypeCV>feature_property</propertyTypeCV>
already set.
I've nonetheless tried your suggestion and added that property directly to my
<chadodb> configuration, and I am still getting the same error as before.
Perhaps I am seeing a different issue than the one you describe?
In any case, many thanks for your suggestions,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
-----Original Message-----
From: Fabrice Legeai [mailto:[EMAIL PROTECTED]
Sent: Fri 10/3/2008 12:24 AM
To: Isabelle Phan
Cc: Ed Lee; [email protected]; Scott Cain; Gowthaman Ramasamy
Subject: Re: [apollo] saving to chado DB
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
>>>>>>> _______________________________________________
>>>>>>> apollo mailing list
>>>>>>> [email protected]
>>>>>>> http://mail.fruitfly.org/mailman/listinfo/apollo
>>>>>>>
>>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> apollo mailing list
>>>>> [email protected]
>>>>> http://mail.fruitfly.org/mailman/listinfo/apollo
>>>>>
>>>>>
>>>>
>>>> --
>>>> --------------------------------------------------------------
>>>> ----------
>>>> Scott Cain, Ph. D.
>>>> [EMAIL PROTECTED]
>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>>
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>>>
>>>
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>>
>
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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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