Upload via a manifest file

[tengfei]

what is a manifest file
http://docs.sevenbridges.com/docs/format-of-a-manifest-file

Supported in GUI and command line uploader, so in R API client we want to do

• interface allow you to specify which meta to keep and to ignore, by default, upload all meta with files
  p$upload(manifest_file = , manifest_metadata = TRUE, meta.keep = NULL, meta.ignore = NULL, verbal = FALSE) # with metadata = TRUE by default
• Validation: check file exists or not and stop if not all satisfied, assumption here is that user provide a manifest, it has to work and all files need to exists.
• Uploading files: print files info in verbal mode otherwise just progress bar

[tengfei]

on second thought I may use select like subset function to replace meta.keep and meta.ignore

p$upload(manifest_file = "test.csv", select = c(column1, column2))

p$upload(manifest_file = "test.csv", select = -column1)

maybe even allow users to pass filter into 'subset' arguments ?

p$upload(manifest_file = "test.csv", p-value < 0.05, select = -column1)

[tengfei]

couple example

## upload all fiels and all metadatas
p$upload(manifest_file = "~/manifest.csv")
## verbal = TRUE, print single file level progress
p$upload(manifest_file = "~/manifest.csv", overwrite = TRUE, verbal = TRUE)
## manifest_metadata = FALSE doens't attach any meta
p$upload(manifest_file = "~/manifest.csv", manifest_metadata = FALSE, overwrite = TRUE)
## filter fils first, upload only files that score < 0.5
p$upload(manifest_file = "~/manifest.csv", overwrite = TRUE, subset = score < 0.5)
## attach all meta except "bad_field" and "sample_id"
p$upload(manifest_file = "~/manifest.csv", overwrite = TRUE,
         subset = score < 0.5, select = -c(bad_field, sample_id))