updated conversion: handle non-graphical nodes and use recent header specification

xgmml/xgmml_to_gpml.R

@@ -90,6 +90,9 @@ write_Pathway <- function(gpml_pathway, filename) {
 cys_nodedata <- function(cys_node_xgmml) {
   nd_attrs <- xml_attrs(cys_node_xgmml)
   gr_attrs <- xml_attrs(xml_find_first(cys_node_xgmml, "./xgmml:graphics", ns = ns_xgmml))
+  if(is.na(gr_attrs[1])) {
+    return(NULL)
+  } 
   return(data.frame(id = nd_attrs["id"], label = nd_attrs["label"],
                     type = xml_attrs(xml_find_first(cys_node_xgmml, "./xgmml:att[@name='mol_type']", ns = ns_xgmml))["value"],
                     x = as.numeric(gr_attrs["x"]), y = as.numeric(gr_attrs["y"]),
@@ -100,6 +103,9 @@ cys_nodedata <- function(cys_node_xgmml) {
 cys_edgedata <- function(cys_edge_xgmml) {
   eg_attrs <- xml_attrs(cys_edge_xgmml)
   gr_attrs <- xml_attrs(xml_find_first(cys_edge_xgmml, "./xgmml:graphics", ns = ns_xgmml))
+  if(is.na(gr_attrs[1])) {
+    return(NULL)
+  } 
   return(data.frame(id = eg_attrs["id"], label = eg_attrs["label"],
                     source = eg_attrs["source"], target = eg_attrs["target"], color = gr_attrs["fill"], thickness = gr_attrs["width"]))
 }
@@ -142,14 +148,14 @@ xgmml_gpml <- function(xgmml_file, output,
   
   if(curl_image) {
     message("Creating image ...")
-    system(paste0("curl -X POST --data-binary @", output," -H 'Content-Type: text/plain'",
+    system(paste0("curl -X POST --data-binary @", output," -H 'Content-Type: application/octet-stream'",
                   " https://minerva-dev.lcsb.uni.lu/minerva/api/convert/image/GPML:png > ",
                   paste0(output,".png")))
   }
   
   if(target_output != "") {
     message("Translating  to ...")
-    system(paste0("curl -X POST --data-binary @", output," -H 'Content-Type: text/plain'",
+    system(paste0("curl -X POST --data-binary @", output," -H 'Content-Type: application/octet-stream'",
                   " https://minerva-dev.lcsb.uni.lu/minerva/api/convert/GPML:", target_output," > ",
                   paste0(output,target_output,".xml")))
   }