Deprecate Culex quinquefasciatus from Apollo

[mpoelchau]

We hosted Culex quinquefasciatus on Apollo for a brief spell in collaboration with VectorBase. Now VB is ready to take over this organism completely. We'll need to deprecate it from Apollo. @childers can you take this on/work on this with me?

• I've already made the organism private
• back up annotations and tracks
• We'll need to remove manual annotations before removing the org from Apollo completely - I believe there's a groovy script for that

[childers]

@mpoelchau I'm on it, Thanks!

[childers]

@mpoelchau It took some work because my groovy installation was not working but I was able to delete the annotations via the groovy script:

$ groovy ./delete_annotations_from_organism.groovy  -organismname Culex_quinquefasciatus -destinationurl https://apollo.nal.usda.gov/apollo-2.6.5/
Enter admin username: web_apollo_admin
Enter admin password: 

Then I was able to delete the organism through the admin interface.

[childers]

Also need to remove it from the genomics workspace

• [x] make it not shown
• [ ] remove the blastDBs and remove organism from the DB

$ python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa  --shown false 
1 species finished 
all done

$ python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna   --shown false 
1 species finished 
all done

$ python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna  --shown false 
1 species finished 
all done

$ python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa  --shown false 
1 species finished 
all done

$ python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna --shown false 
1 species finished 
all done

[childers]

finished removing this organism from the genomics workspace:

python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna   --shown false 
python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna  --shown false 
python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa  --shown false 
python manage.py blast_shown GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna --shown false 

  90 | Culex quinquefasciatus
django=> delete from hmmer_hmmerdb where organism_id =90;

django=> delete from blast_jbrowsesetting where blast_db_id = 490;

delete from blast_sequence where blast_db_id = 490;
delete from blast_sequence where blast_db_id = 491;
delete from blast_sequence where blast_db_id = 492;
delete from blast_sequence where blast_db_id = 493;

 django=> delete from blast_sequence where blast_db_id = 490;
DELETE 57
django=> delete from blast_sequence where blast_db_id = 491;
DELETE 27900
django=> delete from blast_sequence where blast_db_id = 492;
DELETE 24531
django=> delete from blast_sequence where blast_db_id = 493;
DELETE 24531

delete from blast_blastdb where organism_id =90;
DELETE 4

django=> delete from app_organism where id =90;
DELETE 1