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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Ontology no longer builds with error in taxon constraints only_in_taxon #27470

Closed kltm closed 6 months ago

kltm commented 6 months ago

go-ontology now failing with:

16:35:26  JAVA_OPTS=-Xmx6G ./dosdp-tools-0.19.3/bin/dosdp-tools generate --infile=../taxon_constraints/only_in_taxon.tsv --obo-prefixes=true --template=../taxon_constraints/only_in_taxon.yaml --outfile=../taxon_constraints/only_in_taxon.ofn
16:35:29  [34m2024-03-27 23:35:28.823Z[0m [31merror[0m [[37m[0m] [31m[context: command=generate;pattern=../taxon_constraints/only_in_taxon.yaml;input=../taxon_constraints/only_in_taxon.tsv;output=../taxon_constraints/only_in_taxon.ofn] Failed to parse class expression: only_in_taxon some 'Viridiplantae':
16:35:29  Encountered 'Viridiplantae' at line 1 column 20. Expected one of:
16:35:29    Class name
16:35:29    (
16:35:29    {
16:35:29    Self
16:35:29  [0m
16:35:29  [34m2024-03-27 23:35:28.870Z[0m [31merror[0m [[37m[0m] [31m[context: ] Failed to parse class expression: only_in_taxon some 'Viridiplantae'[0m
16:35:29  
16:35:29  real  0m4.897s
16:35:29  user  0m16.940s
16:35:29  sys   0m1.442s
16:35:29  make: *** [Makefile:354: ../taxon_constraints/only_in_taxon.ofn] Error 1
kltm commented 6 months ago

Looking at recent changes in https://github.com/geneontology/go-ontology/commits/master/src/taxon_constraints/only_in_taxon.tsv

kltm commented 6 months ago

Note from @balhoff 

Probably a tab mishap in that TSV. Could someone take a look at that? Once it is correct then GitHub will show it as a nice table
This is happening a lot. I guess we need to add a format check for those
ValWood commented 6 months ago

Sorry! I'm going to start doing the taxon restrictions in VS code. Its easier to spot errors that in the Git editor

cmungall commented 6 months ago

@kltm did your PR fix it?

kltm commented 6 months ago

We seem to be clear now.

kltm commented 6 months ago

The error is back.

kltm commented 6 months ago

After two passes, error returned on midnight March 30th run.

kltm commented 6 months ago

The following stanzas seem to have been created with spaces, not tabs:

GO:0016120  carotene biosynthetic process  NCBITaxon:33090  Viridiplantae
GO:1990220  GroEL-GroES     NCBITaxon:Union_0000004 Prokaryota
GO:0010736  serum response element binding      NCBITaxon:6072  Eumetazoa
GO:0009887  animal organ morphogenesis  NCBITaxon:6072  Eumetazoa
GO:0010236  plastoquinone biosynthetic process  NCBITaxon:33090  Viridiplantae
GO:0051960  regulation of nervous system development   NCBITaxon:6072   Eumetazoa

@pgaudet @ValWood It looks like these got in with this commit: https://github.com/geneontology/go-ontology/commit/e88dc02a21eee07bb496b1440b5d6c81a637e2da .

balhoff commented 6 months ago

I think #27482 and #27483 have cleared this up.