Hi, I am trying to set up a GMOD chado database to read/write using Artemis. I admit not being a very experienced database user, so maybe I am missing something obvious. Anyway.
I start Artemis using art -Dchado="localhost:5432/annotation?bjorns" -Djdbc.drivers=org.postgresqlver -Dibatis and feeds my database password. This appear to work ok in the sense that there are no error messages. However, in the database list at the top left, there is only an unnamed folder, and clicking this folder nothing happens except an error appears in the terminal 'Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException ...' *GMOD The database I am using is a postgresql (v8.1.16, as I understand there was a problem with gmod and v8.3?), setup with the GMOD schema (gmod-1.0, from http://www.postgresql.org/download/): perl Makefile.PL make sudo make install make load_schema make prepdb make ontologies This appear to work as far as I can decide. * TEST DATASET A test dataset was loaded into the database by first manually setting the organism: INSERT INTO organism (abbreviation, genus, species, common_name, organism_id) VALUES ('B.bacilliformis', 'Bartonella', 'bacilliformis', 'BB', 8783); then converting a genbank file to gff and load the gff data into the database perl bp_genbank2gff3.pl NC_008783.gbk --noCDS -o . gmod_bulk_load_gff3.pl --organism 'BB' --noexon --gfffile NC_008783.gbk.gff --recreate_cache After the upload the database does contain data that makes sense as far as I can tell, and it is possible to backup the database. (There is for some reason a problem with feature types in gmod_bulk_load_gff3.pl: for now I made an ugly hardcoding to set all feature types = 1. line755) Any idea on how to get Artemis to find the data in the database is appreciated! Best Björn Nystedt -- ==================================== Björn Nystedt (Sällström) PhD Student Molecular Evolution EBC, Uppsala University Norbyv. 18C, 752 36 Uppsala Sweden phone: +46 (0)18-471 45 88 email: bjorn.nyst...@ebc.uu.se ==================================== _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
