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LegumeFederation / cmap-js

Display and compare biological maps (genetic, physical, cytogenetic, genomic, linkage groups, chromosomes, scaffolds).
GNU General Public License v3.0
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Obsolete LIS URL for aliases #149

Open That-Thing opened 2 weeks ago

That-Thing commented 2 weeks ago

The _buttonTest function in Popover.js makes a request to various LIS in order to retrieve aliases. The request falls through because the url which is being requested returns a 404 on LIS Example url: https://www.legumeinfo.org/gene_links/glyma.Glyma.01G163900/json

image

adf-ncgr commented 2 weeks ago

@That-Thing that is an obsolete URL for the gene "linkouts" service. The current implementation lives at: https://services.lis.ncgr.org/gene_linkouts?genes=glyma.Wm82.gnm4.ann1.Glyma.01G163900 probably the payload structure has changed somewhat too. Let me know if you need any further details. Notice that the service requires that the gene ids have their "full yuck" prefixing, ie glyma.Wm82.gnm4.ann1.Glyma.01G163900 not just glyma.Glyma.01G163900 or Glyma.01G163900

That-Thing commented 2 weeks ago

The full prefix does not seem to be present anywhere in the data used by cmap-js which poses an issue.

That-Thing commented 2 weeks ago

Data in glyma.collinearity+genes+markers.cmap doesn't have information needed to fill out the new url, so it will have to be updated