Removed functionality to get INSDC xrefs from FlyBase; these are better determined with the xref pipeline, which attaches them to translations rather than genes.
Minor updates to xref config for some metazoans
[ENSCORESW-543]. Version is left undef to match the healthchecks expected behaviour (null instead of empty).
The getter method returns the empty string in case version is undef (matching the method signature of the
documentation).
The equals method use the getter method instead of accessing the attribute directly.
ENSCORESW-866: allow NULL as default value for karyotype and stain
updated to release 76
update test databases to release 76
patch ontology databases to release 76
update to gff3 output format:
- for ID field, concatenate object type before the stable id
- if gene biotype is protein_coding, the so term is replaced by gene
more sanity checks for the GFFSerializer
updated test module
ENSCORESW-855: exons are shared across several transcripts, cannot be unique
as ID has to be unique, exons have no ID field, only Name
ENSCORESW-861: initialize driver before testing it
[ENSCORESW-836]. Support for automatically loading the species_id.
[ENSCORESW-836]. Add species id based on constructor flag and on whether species is provided.
[ENSCORESW-836]. Completed method to find and add species_id attribute.
ENSCORESW-852 & ENSCORESW-373:
Xenopus_Jamboree/Jamboree replaced with more meaningful Xenbase name
needs to be ignored in Uniprot file
treated like other official naming sources, transcripts get gene display label with -201 extension
ENSCORESW-873: for uniprot, label should be the same as accession
ENSCORESW-875: include HGNC prefix in HGNC download, downstream updates to match the new ids
FlyBase priority descriptions were too long for xref source table. Must always have been truncated, but now shortened in case your mysql server doesn't do automatic truncation.
when checking a boolean, checkif true, not if defined
homo_sapiens/patch/transcript.txt: SQLite does not like header.
exon.t: ignore 'datatype mismatch' bind errors on floating point for SQLite.