Commit 1dd5f8a6 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

Merge branch 'repo_update' into 'master'

Hipathia translation script updated, zip handled

See merge request !244
parents 87df75a5 d9c82e40
......@@ -11,21 +11,32 @@ library(jsonlite)
### A convenience function to handle API queries
ask_GET <- function(furl, fask) {
print(URLencode(paste0(furl, fask)))
resp <- httr::GET(url = URLencode(paste0(furl, fask)),
resp <- httr::GET(url = URLencode(paste0(furl, fask)), write_memory(),
httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
### Currently ignoring SSL!
httr::set_config(config(ssl_verifypeer = 0L)))
if(httr::status_code(resp) == 200) {
### when the content is sent as a zip file, it needs to be handled differently,
### i.e. saved to a tmp file and unzipped
if(headers(resp)$`content-type` == "application/zip") {
tmp <- tempfile()
tmpc <- file(tmp, "wb")
writeBin(httr::content(resp, as = "raw"), con = tmpc)
close(tmpc)
unzipped <- unzip(tmp)
file.remove(tmp)
return(unzipped)
}
return(httr::content(resp, as = "text"))
}
return(NULL)
}
### Define the source file (GitLab, raw link)
diagram <- "https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/Pyrimidine%20deprivation/Pyrimidine_deprivation_stable.xml"
diagram <- "https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/ER%20Stress/ER_Stress_stable.xml"
### Read in the raw SIF version (here straight from the github of Aurelien)
raw_sif <- read.table(url("https://git-r3lab.uni.lu/covid/models/-/raw/master/Executable%20Modules/SBML_qual_build/sif/Pyrimidine_deprivation_stable_raw.sif"),
raw_sif <- read.table(url("https://git-r3lab.uni.lu/covid/models/-/raw/master/Executable%20Modules/SBML_qual_build/sif/ER_Stress_stable_raw.sif"),
sep = " ", header = F, stringsAsFactors = F)
### Read the list of resources to be integrated, from the MINERVA build scripts
......@@ -86,13 +97,11 @@ group_elements <- function(feid, felements, fentrez) {
get_groups <- function(fname) {
message(paste0("Getting groups for ", fname, "..."))
library(xml2)
### Currently comment out the MINERVA download, some content dlded as binary!
# cd_map <- read_xml(ask_GET(mnv_base,
# paste0("models/",
# models$idObject[models$name == fname],
# ":downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser")))
cd_map <- read_xml(diagram)
print(cd_map)
## Currently comment out the MINERVA download, some content dlded as binary!
cd_map <- read_xml(ask_GET(mnv_base,
paste0("models/",
models$idObject[models$name == fname],
":downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser")))
### CellDesigner namespace
ns_cd <- xml_ns_rename(xml_ns(read_xml("<root>
<sbml xmlns = \"http://www.sbml.org/sbml/level2/version4\"/>
......@@ -101,7 +110,6 @@ get_groups <- function(fname) {
d1 = "sbml", d2 = "cd")
### Get complex ids
cids <- xml_attr(xml_find_all(cd_map, "//cd:complexSpeciesAlias", ns_cd), "species")
print(cids)
### For each check, which is hypothetical
hypocs <- sapply(cids,
function(x) {
......
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