Opencga-export minor refactor
antonioaltamura opened this issue · 2 comments
antonioaltamura commented
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 thelimit
param. When you change it in the table that is not being reflected in the tabs "Link" and "Opencga Script Code". See screenshot.
- Improve JS client code.
username
andpassword
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
antonioaltamura commented
pamag commented
Review
Reviewed
OpenCGA commit:
4947bd62b3bed373d7adac94c45d365bdce59c56
IVA commit:
7e2958f01bf37ba12d53de307abdb57511040533
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