opencb/jsorolla

Opencga-export minor refactor

antonioaltamura opened this issue · 2 comments

opencga-export needs a couple of improvements:

  • Improve customisation
    the component lacks customisability. For instance, for the tabs to show: one client may want to keep "Download" and "Export" button separated, in that case "Download table" tab should be hidden in the Export modal, or maybe someone may want to hide "Export Query".
  • Minor bug
    it seems there is a problem with the limit param. When you change it in the table that is not being reflected in the tabs "Link" and "Opencga Script Code". See screenshot.
    Screenshot from 2022-02-22 16-47-46
  • Improve JS client code. username and password are undefined, it needs a bit of in-code documentation.
  • Add support to clinical variants (Sample Variant Browser) in Code and Script tabs
  • Enable Export in all browsers (including the new Disease Panel Browser) and review the generation of the CLI command for all the entities

About the limit params, there are 3 options:

  • add a dropdown to set the limit (see screenshot)
    Screenshot from 2022-02-23 16-32-36
  • hardcode a limit of 1000
  • make the code editable (see gif)
    export
pamag commented

Review

Reviewed

OpenCGA commit:
    4947bd62b3bed373d7adac94c45d365bdce59c56
IVA commit:
    7e2958f01bf37ba12d53de307abdb57511040533

image

ISSUES with tsv export

The id and SNP_ID column:

[0] id = 17:41201702 C/T
[1] SNP ID = -
[2] gene = BRCA1,
  • 'SNP ID' better to be 'SNP_ID' (no spaces)
  • Column SNP_ID is always '-' the id is missing
  • 'id' column -> if this is a pretty print of the snp_id, better to make two columns chr_pos, alleles
  • 'gene' column ends with ',' always
  • Indels => need a '-' in the missing allele: "17:41268209 /T" -> "17:41268209 -/T"
  • The file needs a return at the end -> end the file with an empty line