R script to parse json into tsv (species coordnates)

scripts/GFS_IndicatorsTool/read_csv.R

@@ -0,0 +1,47 @@
+library("rjson")
+
+
+input <- fromJSON(file=file.path(outputFolder, "input.json"))
+
+print(input)
+
+tsv_json <-input$csv
+
+##### Parse json text
+
+### remove square brackets
+tsv_json = substr(tsv_json, 3, nchar(tsv_json)-2)
+
+### split lines
+tsv_lines = strsplit(tsv_json, '\\), \\(')[[1]]
+
+### convet to table
+tsv_tab = do.call(rbind, strsplit(tsv_lines, ', '))
+
+### convert to data.frame, set header
+tsv_df = data.frame(tsv_tab[-1,])
+colnames(tsv_df) = tsv_tab[1,]
+
+colnames(tsv_df)[colnames(tsv_df)=="'decimal_latitude'"] = 'decimal_latitude'
+colnames(tsv_df)[colnames(tsv_df)=="'decimal_longitude'"] = 'decimal_longitude'
+
+### set coordinates as numeric
+tsv_df$decimal_latitude = as.numeric(tsv_df$decimal_latitude)
+tsv_df$decimal_longitude = as.numeric(tsv_df$decimal_longitude)
+
+### set output path
+tsv_out<-file.path(outputFolder, "species_obs.tsv")
+
+
+### save output
+write.table(tsv_df, file=tsv_out, sep='\t', quote=F, row.names = F, col.names = T)
+
+
+
+
+### return output
+output <- list("csv_out"=tsv_out)
+print(output)
+
+jsonData <- toJSON(output, indent=2)
+write(jsonData, file.path(outputFolder,"output.json"))

scripts/GFS_IndicatorsTool/read_csv.yml

@@ -1,10 +1,9 @@
-script: read_csv.py
-name: Read CSV
+script: read_csv.R
+name: JSON to TSV
 author: 
-  - name: Jean-Michel Lord
-    identifier: https://orcid.org/0009-0007-3826-1125
+  - name: Oliver Selmoni
 license: CC0
-description: "Sample python script that increments a number."
+description: "Parse json string to tsv"
 timeout: 1
 inputs:
   csv: