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ebi-gene-expression-group / atlas-annotations

The pipeline producing bioentity annotations used in Expression Atlas searches
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The species-properties.json file generated by atlas_species.sh is not right #16

Open alfonsomunozpomer opened 5 years ago

alfonsomunozpomer commented 5 years ago

Error introduced in https://github.com/ebi-gene-expression-group/atlas-annotations/commit/8f0da818153dfb04139e896638b934c87a08767c

The following println statement in src/Directories.sc:

println("Using the following paths for sources of experiments:")

Makes that running the script to generate the species file, ./sh/atlas_species.sh, produces the following (badly-formatted) JSON file:

Using the following paths for sources of experiments:
[{
  "name":"Aegilops_tauschii",
  "defaultQueryFactorType":"ORGANISM_PART",
  "kingdom":"plants",
  "resources":[{
    "type":"genome_browser",
...
pcm32 commented 5 years ago

Thanks for flagging up, probably safest thing would be to set:

https://github.com/ebi-gene-expression-group/atlas-annotations/blob/5abd2291944f7aaa3354424d60edf0d0cae568b3/src/atlas/AtlasSpecies.sc#L98

to write to a file instead of stdout.