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Bioconductor / AnVIL

Interact with AnVIL and Leonardo projects
https://bioconductor.org/packages/AnVIL
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Url encoding paths #4

Open bjstubbs opened 5 years ago

bjstubbs commented 5 years ago

Do we want to auto-encode paths/char inputs to the apis?

example:

library(AnVIL) library(httr) library(jsonlite)

mypath="github.com/vjcitn/vardemo/AnnotatingWGSVariantsWithBioc" mypath [1] "github.com/vjcitn/vardemo/AnnotatingWGSVariantsWithBioc"

this fails because of the "/"'s

fromJSON(content(dockstore$getPublishedWorkflowByPath(mypath),"text")) $code [1] 404

$message [1] "HTTP 404 Not Found"

mypath2=URLencode(mypath,reserve=TRUE) mypath2 [1] "github.com%2Fvjcitn%2Fvardemo%2FAnnotatingWGSVariantsWithBioc" fromJSON(content(dockstore$getPublishedWorkflowByPath(mypath2),"text")) $aliases NULL

$author [1] ""

$checker_id NULL

$dbCreateDate [1] 1.549286e+12

$dbUpdateDate [1] 1.549296e+12

$defaultTestParameterFilePath NULL

$defaultVersion NULL

$description NULL

$descriptorType [1] "wdl"

$email [1] ""

$full_workflow_path [1] "github.com/vjcitn/vardemo/AnnotatingWGSVariantsWithBioc"

mtmorgan commented 5 years ago

This is a good idea but I don't know how to implement this cleanly / generally. Is it helpful (or only confusing?) to provide an encode() function to wrap URLencode(reserved=TRUE) ?