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Convert colData to JSON

Source: R/json_convert.R
convert_colData_to_json.Rd

Convert colData to JSON format for elasticsearch indexing.

Usage

convert_colData_to_json(
  cdata,
  identifiers,
  req_cols = c("cellline", "cellline_name", "cellline_tissue", "cellline_ref_div_time")
)

Arguments

cdata

data.table of colData.

identifiers

charvec with identifiers

req_cols

charvec required columns

Value

JSON string capturing the cdata.

Details

Standardizes the cdata to common schema fields and tidies formatting to be condusive to joining with other JSON responses.

Examples

cdata <- data.table::data.table(
  mycellline = letters, 
  mycelllinename = letters, 
  mycelllinetissue = letters,
  cellline_ref_div_time = "cellline_ref_div_time")
identifiers <- list(cellline = "mycellline",
                    cellline_name = "mycelllinename",
                    cellline_ref_div_time = "cellline_ref_div_time",
                    cellline_tissue = "mycelllinetissue")
convert_colData_to_json(cdata, identifiers)
#> [1] "\"cellline\":[\"a\",\"b\",\"c\",\"d\",\"e\",\"f\",\"g\",\"h\",\"i\",\"j\",\"k\",\"l\",\"m\",\"n\",\"o\",\"p\",\"q\",\"r\",\"s\",\"t\",\"u\",\"v\",\"w\",\"x\",\"y\",\"z\"],\"cellline_name\":[\"a\",\"b\",\"c\",\"d\",\"e\",\"f\",\"g\",\"h\",\"i\",\"j\",\"k\",\"l\",\"m\",\"n\",\"o\",\"p\",\"q\",\"r\",\"s\",\"t\",\"u\",\"v\",\"w\",\"x\",\"y\",\"z\"],\"cellline_tissue\":[\"a\",\"b\",\"c\",\"d\",\"e\",\"f\",\"g\",\"h\",\"i\",\"j\",\"k\",\"l\",\"m\",\"n\",\"o\",\"p\",\"q\",\"r\",\"s\",\"t\",\"u\",\"v\",\"w\",\"x\",\"y\",\"z\"],\"cellline_ref_div_time\":[\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\",\"cellline_ref_div_time\"], \"misc_coldata\": {}"