Merge branch 'GPML_conversion' into 'master'

examples of GPML conversion in MINERVA v15.beta.2

See merge request !9

WikiPathways/GPML_conversion/MINERVA_converter.R

+##################################################
+## Project: COVID-19 Disease Map
+## Script purpose: Convert WikiPathways (GPML) using MINERVA API calls (v15.beta.2)
+##                 see documentation at https://minerva.pages.uni.lu/doc/api/
+##                 Warning: v15.beta.2 is still being tested, GPML not among handled formats in the documentation
+## Date: 31.03.2020
+## Author: Marek Ostaszewski
+##################################################
+
+library(httr)
+
+### An example file will be a WikiPathways file set up 
+### by Egon Wilighagen at https://github.com/wikipathways/SARS-CoV-2-WikiPathways
+infile <- "https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4846.gpml"
+
+### Create a character vector of the xml file, read line by line, close connection
+con <- url(infile)
+rls <- paste(readLines(con), collapse = "\n")
+close(con)
+
+### Scenario A
+### Convert the WikiPathways GPML file to a CellDesigner file
+### an example curl call for this would be:
+### curl -X POST --data-binary @infile -H 'Content-Type: text/plain' https://minerva-covid19-curation.lcsb.uni.lu/minerva/api/convert/GPML:CellDesigner_SBML > outfile
+
+### We use httr::POST to execute the API call, and then write down the response
+res <- httr::POST(url = "https://minerva-covid19-curation.lcsb.uni.lu/minerva/api/convert/GPML:CellDesigner_SBML",
+                  body = rls,
+                  content_type("text/plain"))
+### Get resulting XML content as text
+cont <- content(res, as = "text")
+### Write the result to a file
+cat(cont, file = "out.xml")
+
+### Scenario B
+### Convert the WikiPathways GPML file to a PNG preview, useful for a quick check if conversion was acceptable 
+### an example curl call for this would be:
+### curl -X POST --data-binary @infile -H 'Content-Type: text/plain' https://minerva-covid19-curation.lcsb.uni.lu/minerva/api/convert/image/GPML:png > outfile
+
+### Similarly, we use httr::POST to execute the API call, and then write down the response
+res <- httr::POST(url = "https://minerva-covid19-curation.lcsb.uni.lu/minerva/api/convert/image/GPML:png",
+                  body = rls,
+                  content_type("text/plain"))
+### Here, the content is binary (PNG image)
+cont <- content(res, as = "raw", type = "image/png")
+### We use the "write binary" routine of R (open connection, writeBin, close connection)
+write.filename = file("out.png", "wb")
+writeBin(cont, write.filename)
+close(write.filename)