Problem with the function "create_point" when I try to restore a new database

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Problem with the function "create_point" when I try to restore a new database

Lavigne, Patricia
Problem with the function "create_point" when I try to restore a new database

Hi,

I have a problem to restore a chado database. I didn't have an error message when I made the back up of the database. And now, when I try to restore it in a new database, I have a problem with the function "create_point".

I find some conversations (see below) about the function "create_point". But I don't anderstand how to resolve the problem. I need your help.

http://comments.gmane.org/gmane.science.biology.gmod.schema/1055
http://generic-model-organism-system-database.450254.n5.nabble.com/Error-at-the-time-of-chado-database-import-on-frange-featuregoup-foreign-keys-td460184.html

I use the command (see the attached file named load_out.txt):
psql      chado_3       <      chado_dump_25-05-2010.sql      > load_out.txt



And the error message is:

ERREUR:  le langage « plpgsql » existe déjà
ERREUR:  la fonction create_point(integer, integer) n'existe pas
LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
                      ^
ASTUCE : Aucune fonction ne correspond au nom donné et aux types d'arguments.
Vous devez ajouter des conversions explicites de type.
REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXTE : fonction SQL « boxrange » durant « inlining »
instruction SQL « SELECT fk."group_id" FROM ONLY "frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."feature
" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."group_id") WHERE pk."feature_id" IS NULL AND (fk."group_id" I
S NOT NULL) »
ERREUR:  la fonction create_point(integer, integer) n'existe pas
LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
                      ^
ASTUCE : Aucune fonction ne correspond au nom donné et aux types d'arguments.
Vous devez ajouter des conversions explicites de type.
REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXTE : fonction SQL « boxrange » durant « inlining »
instruction SQL « SELECT fk."object_id" FROM ONLY "frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."featur
e" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."object_id") WHERE pk."feature_id" IS NULL AND (fk."object_id
" IS NOT NULL) »
ERREUR:  la fonction create_point(integer, integer) n'existe pas
LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
                      ^
ASTUCE : Aucune fonction ne correspond au nom donné et aux types d'arguments.
Vous devez ajouter des conversions explicites de type.
REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXTE : fonction SQL « boxrange » durant « inlining »
instruction SQL « SELECT fk."srcfeature_id" FROM ONLY "frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."fe
ature" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."srcfeature_id") WHERE pk."feature_id" IS NULL AND (fk."s
rcfeature_id" IS NOT NULL) »
ERREUR:  la fonction create_point(integer, integer) n'existe pas
LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
                      ^
ASTUCE : Aucune fonction ne correspond au nom donné et aux types d'arguments.
Vous devez ajouter des conversions explicites de type.
REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXTE : fonction SQL « boxrange » durant « inlining »
instruction SQL « SELECT fk."subject_id" FROM ONLY "frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."featu
re" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."subject_id") WHERE pk."feature_id" IS NULL AND


Chado:          1.14
PostgreSQL:  8.4.4


Thank you in advance.
Patricia.


<<load_out.txt>>

........................................................................................
Patricia LAVIGNE
Biologiste bioinformaticienne / Biologist bioinformatician


Ressources naturelles Canada, Service canadien des forêts, Centre de foresterie des Laurentides / Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre
1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada G1V 4C7


Téléphone : (418) 648-4947
Télécopieur : (418) 648-5849
Courriel /Email : [hidden email]
........................................................................................



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Re: Problem with the function "create_point" when I try to restore a new database

Scott Cain
Hi Patricia,

I've seen that before too, but have yet to spend much time figuring
out what is going on.  I assume that when this happens, some
range-based queries for GBrowse might be slower, but otherwise it
won't cause a problem.  I think the ultimate fix is to rewrite the
range queries to us GiST, but that means I (or somebody) will have to
take the time to learn how to use them appropriately.

Scott


On Fri, Sep 3, 2010 at 3:36 PM, Lavigne, Patricia
<[hidden email]> wrote:

> Hi,
>
> I have a problem to restore a chado database. I didn't have an error message
> when I made the back up of the database. And now, when I try to restore it
> in a new database, I have a problem with the function "create_point".
>
> I find some conversations (see below) about the function "create_point". But
> I don't anderstand how to resolve the problem. I need your help.
>
> http://comments.gmane.org/gmane.science.biology.gmod.schema/1055
> http://generic-model-organism-system-database.450254.n5.nabble.com/Error-at-the-time-of-chado-database-import-on-frange-featuregoup-foreign-keys-td460184.html
>
> I use the command (see the attached file named load_out.txt):
> psql      chado_3       <      chado_dump_25-05-2010.sql      > load_out.txt
>
> And the error message is:
>
> ERREUR:  le langage « plpgsql » existe déjà
> ERREUR:  la fonction create_point(integer, integer) n'existe pas
> LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
>                       ^
> ASTUCE : Aucune fonction ne correspond au nom donné et aux types
> d'arguments.
> Vous devez ajouter des conversions explicites de type.
> REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
> CONTEXTE : fonction SQL « boxrange » durant « inlining »
> instruction SQL « SELECT fk."group_id" FROM ONLY "frange"."featuregroup" fk
> LEFT OUTER JOIN ONLY "public"."feature
> " pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."group_id") WHERE
> pk."feature_id" IS NULL AND (fk."group_id" I
> S NOT NULL) »
> ERREUR:  la fonction create_point(integer, integer) n'existe pas
> LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
>                       ^
> ASTUCE : Aucune fonction ne correspond au nom donné et aux types
> d'arguments.
> Vous devez ajouter des conversions explicites de type.
> REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
> CONTEXTE : fonction SQL « boxrange » durant « inlining »
> instruction SQL « SELECT fk."object_id" FROM ONLY "frange"."featuregroup" fk
> LEFT OUTER JOIN ONLY "public"."featur
> e" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."object_id") WHERE
> pk."feature_id" IS NULL AND (fk."object_id
> " IS NOT NULL) »
> ERREUR:  la fonction create_point(integer, integer) n'existe pas
> LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
>                       ^
> ASTUCE : Aucune fonction ne correspond au nom donné et aux types
> d'arguments.
> Vous devez ajouter des conversions explicites de type.
> REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
> CONTEXTE : fonction SQL « boxrange » durant « inlining »
> instruction SQL « SELECT fk."srcfeature_id" FROM ONLY
> "frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."fe
> ature" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."srcfeature_id")
> WHERE pk."feature_id" IS NULL AND (fk."s
> rcfeature_id" IS NOT NULL) »
> ERREUR:  la fonction create_point(integer, integer) n'existe pas
> LIGNE 1 : SELECT box (create_point(0, $1), create_point($2,500000000))
>                       ^
> ASTUCE : Aucune fonction ne correspond au nom donné et aux types
> d'arguments.
> Vous devez ajouter des conversions explicites de type.
> REQUÊTE : SELECT box (create_point(0, $1), create_point($2,500000000))
> CONTEXTE : fonction SQL « boxrange » durant « inlining »
> instruction SQL « SELECT fk."subject_id" FROM ONLY "frange"."featuregroup"
> fk LEFT OUTER JOIN ONLY "public"."featu
> re" pk ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."subject_id") WHERE
> pk."feature_id" IS NULL AND
>
> Chado:          1.14
> PostgreSQL:  8.4.4
>
> Thank you in advance.
> Patricia.
>
> <<load_out.txt>>
>
> ........................................................................................
> Patricia LAVIGNE
> Biologiste bioinformaticienne / Biologist bioinformatician
>
> Ressources naturelles Canada, Service canadien des forêts, Centre de
> foresterie des Laurentides / Natural Resources Canada, Canadian Forest
> Service, Laurentian Forestry Centre
> 1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada
> G1V 4C7
>
> Téléphone : (418) 648-4947
> Télécopieur : (418) 648-5849
> Courriel /Email : [hidden email]
> ........................................................................................
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
This SF.net Dev2Dev email is sponsored by:

Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
_______________________________________________
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[hidden email]
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