aiminy

delete from stock where stock_id in (select stock_id from nd_experiment_stock where nd_experiment_id in (select nd_experiment_id from nd_experiment_project where project_id = 13));

ERROR:  update or delete on table "stock" violates foreign key constraint "stock_owner_stock_id_fkey" on table "stock_owner"
DETAIL:  Key (stock_id)=(3994) is still referenced from table "stock_owner".

aiminy

 Entry StockIDText
     1    SM-227-1
     2    SM-227-2
     3    SM-227-3
     4    SM-227-4
     5    SM-227-5
     6    SM-227-6
     7    SM-227-7
     8    SM-227-8
     9    SM-227-9

aiminy

 Account for user aiminy2013 is disabled for reason 'unconfirmed account'.

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Developer message:

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aiminy

pg_dump -h zeabase.sgn.cornell.edu -U zeabase -W zea -f zea_sgn_data_dump.sql
Password: 
pg_dump: [archiver (db)] connection to database "zea" failed: could not connect to server: Connection timed out
	Is the server running on host "zeabase.sgn.cornell.edu" (132.236.81.159) and accepting
	TCP/IP connections on port 5432?

aiminy

perl LoadScriptForTonydata.pl -H localhost -D zea -i WET10B-EVALTC-12_Plot_data_MasterStack2.csv
Use of uninitialized value in lc at /home/aiminy/cxgn/local-lib/lib/perl5/Class/DBI.pm line 196.
Use of uninitialized value in lc at /home/aiminy/cxgn/local-lib/lib/perl5/Class/DBI.pm line 196.
Use of uninitialized value in lc at /home/aiminy/cxgn/local-lib/lib/perl5/Class/DBI.pm line 196.
Use of uninitialized value in lc at /home/aiminy/cxgn/local-lib/lib/perl5/Class/DBI.pm line 196.
UNIVERSAL->import is deprecated and will be removed in a future perl at /home/aiminy/cxgn/cxgn-corelibs/lib/CXGN/Tools/Run.pm line 17.
Use of uninitialized value in lc at /home/aiminy/cxgn/local-lib/lib/perl5/Class/DBI.pm line 196.
This is test version
Database username for write access (default "postgres"): 
Password: 

aiminy

[Term]
id: CO_322:0000246
name: CIMMYT 1-5 scale
relationship: scale_of CO_322:0000245 ! Visual scoring
creation_date: 2012-01-30T05:23:26Z


[Term]
id: CO_322:0000274
name: CIMMYT 1-5 scale

aiminy

perl gmod_load_cvterms.pl -s CO -H localhost -D zea  -r postgres -p zeabase207 -d Pg -u maize_trait.obo
This script will UPDATE cvterms stored in your database from the input file! 
Default for -s: CO (specifies the database names for Dbxref objects)
Default for -F: File format set to obo
Connected to database zea on host localhost.
Parsing the ontology maize_trait.obo...
Default namespace is maize_trait 
....found namespace  'maize_trait' 
cv_id = 3
Updating an ontology in the database...

aiminy

Inserting and updating terms...
DONE UPDATING existing terms! 
**modified name for TO:0000039 - 'yield component (obsolete TO:0000039)' 
 **modified name for TO:0000380 - 'planthopper (obsolete TO:0000380)' 
 **modified name for TO:0000186 - 'environmental stress related trait (obsolete TO:0000186)' 
 **modified name for TO:0000256 - 'genetic trait (obsolete TO:0000256)' 
 **modified name for TO:0000219 - 'stem morphology (obsolete TO:0000219)' 
 **modified name for TO:0000091 - 'leafhopper (obsolete TO:0000091)' 
 **modified name for TO:0000174 - 'maturity trait (obsolete TO:0000174)' 
 **modified name for TO:0000596 - 'plant volume (sensu Poaceae) (obsolete TO:0000596)' 

aiminy

select * from cv;
<aiminy>  cv_id |                      name                      | definition 
<aiminy> -------+------------------------------------------------+------------
<aiminy>      1 | relationship                                   | 
<aiminy>      2 | cvterm_property                                | 
<aiminy>      4 | gene_ontology                                  | 
<aiminy>      7 | biological_process                             | 
<aiminy>      8 | molecular_function                             | 
<aiminy>      9 | cellular_component                             | 
<aiminy>     10 | plant_ontology                                 |