Commit 46624171 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

updated integration script

parent 670ebdda
......@@ -9,6 +9,9 @@ options(stringsAsFactors = F)
library(httr)
library(xml2)
library(here)
setwd(paste0(here(),"/Integration/"))
### An 'xml2' namespace structure for parsing CellDesigner xml
ns_cd <- xml_ns_rename(xml_ns(read_xml("<root>
......@@ -130,12 +133,18 @@ for(r in 1:nrow(res)) {
}
### If the overview map and the mapping are to be constructed de novo
reconstruct_overview = F
reconstruct_mapping = F
reconstruct_overview = T
reconstruct_mapping = T
if(reconstruct_overview) {
### Create a sinple SBML file and convert it to CellDesigner, gives circular layout
ovw <- construct_overview(res$Name)
ovw <- gsub("w=\"90.0\" h=\"30.0\"", "w=\"190.0\" h=\"40.0\"", ovw)
ovw <- gsub("width=\"90.0\" height=\"30.0\"", "width=\"190.0\" height=\"40.0\"", ovw)
ovw <- gsub("width=\"90.0\" height=\"30.0\"", "width=\"190.0\" height=\"40.0\"", ovw)
ovw <- gsub("color=\"FFCC99FF\"", "color=\"FFCCFFFF\"", ovw)
cat(ovw, file = paste0("output/overview.xml"))
}
......
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