sequence service unable to retrieve remote sequences

[nathandunn]

This works here:

http://localhost:8080/apollo/sequence/bee/Group9.10:3995589..3999237

but using a remote sequence does not:

http://localhost:8080/apollo/sequence/Remotefly/2L:1..235

getting:

File not found on server: /Users/nathandunn/repositories/jbrowse-config/jbrowse/data/Drosophila melanogaster/seq/d3c/34b/35/2L-0.txtz

[nathandunn]

Around line 266 of grails-app/services/org/bbop/apollo/SequenceService.groovy 263: return uncompressedStr.toUpperCase() 264: } 265: 266: throw new RuntimeException("File not found on server: " + filePath) 267: 268: } 269: Around line 266 of grails-app/services/org/bbop/apollo/SequenceService.groovy 263: return uncompressedStr.toUpperCase() 264: } 265: 266: throw new RuntimeException("File not found on server: " + filePath) 267: 268: } 269: `

[nathandunn]

URL Template is: http://agrjbrowse2.s3-website-us-east-1.amazonaws.com/FlyBase/fruitfly/seq/{refseq_dirpath}/{refseq}-

The problem is the sequence directory is just the path to the organism . . . which obiviously incorrect:

/Users/nathandunn/repositories/jbrowse-config/jbrowse/data/Drosophila melanogaster/seq/d3c/34b/35

[nathandunn]

The problme is that it should load the trackList here, instead of pulling off the directory:

 String seqDir = String.format("%s/seq/%s/%s/%s", sequence.organism.directory, dirs[0], dirs[1], dirs[2]);