Commit 216912a9 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

an improvement in the access script and a small diagram correction

parent f4a55078
Pipeline #38124 passed with stages
in 4 minutes and 55 seconds
......@@ -7401,27 +7401,27 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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<celldesigner:linkAnchor position="ESE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfReactantLinks>
<celldesigner:reactantLink reactant="s31" alias="sa410" targetLineIndex="-1,0">
<celldesigner:linkAnchor position="INACTIVE"/>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="vertical"/>
<celldesigner:lineDirection index="1" value="horizontal"/>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.05136454053978312,-0.22074017422055014</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
</celldesigner:reactantLink>
</celldesigner:listOfReactantLinks>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
<celldesigner:lineDirection index="2" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.6369865784088766,-0.0018477757758113 0.8712856170364986,-0.08661146647953544</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#re109">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:doi:10.1016%2Fj.cell.2009.02.026"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00501" species="s83">
<speciesReference metaid="CDMT00485" species="s129">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa403</celldesigner:alias>
<celldesigner:alias>sa209</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference metaid="CDMT00486" species="s31">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa410</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00502" species="s219">
<speciesReference metaid="CDMT00487" species="s215">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa412</celldesigner:alias>
<celldesigner:alias>csa8</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
......
......@@ -7,66 +7,33 @@
options(stringsAsFactors = F)
library(httr)
library(jsonlite)
library(here)
setwd(paste0(here(),"/Integration/MINERVA_build/"))
### Map and pathway enrichment analysis.
### Requires commandline input or file "input.txt" to be present in the script directory.
### A convenience function to handle API queries
ask_GET <- function(furl, fask) {
resp <- httr::GET(url = paste0(furl, fask),
httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
if(httr::status_code(resp) == 200) {
return(httr::content(resp, as = "text"))
}
return(NULL)
}
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/minerva_access_functions.R")
### The address of the COVID-19 Disease Map in MINERVA
map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
### Get configuration of the COVID-19 Disease Map, to obtain the latest (default) version
cfg <- ask_GET(map, "configuration/")
cfg <- fromJSON(cfg)
project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
### The address of the latest (default) build
mnv_base <- paste0(map,"projects/",project_id,"/")
message(paste0("Asking for diagrams in: ", mnv_base, "models/"))
### Get diagrams
models <- ask_GET(mnv_base, "models/")
models <- fromJSON(models, flatten = F)
components <- get_map_components(map)
### Get elements of diagrams
model_elements <- lapply(models$idObject,
function(x) fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/"),
"bioEntities/elements/?columns=id,name,type,references"),
flatten = F))
### You may want to save components to JSON if you want to explore the structure of MINERVA's output
all_hgncs <- c()
### Go through all diagram elements and:
for(me in model_elements) {
get_annotations <- function(model_elements, annotation_type) {
### For erroneous response, skip to next diagram
if(is.null(me)) { next }
if(is.null(model_elements)) { return(NULL) }
### Only elements that have annotations
these_refs <- me$references[sapply(me$references, length) > 0]
these_refs <- model_elements$references[sapply(model_elements$references, length) > 0]
### For empty list, skip to next diagram
if(length(these_refs) == 0) { next }
### Get all HGNC symbols, for elements that have annotations
all_hgncs <- c(all_hgncs, sapply(these_refs,
function(x) x[x$type == "HGNC_SYMBOL", "resource"]))
all_hgncs <- all_hgncs[sapply(all_hgncs,
function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
if(length(these_refs) == 0) { return(NULL) }
### Get all identifiers, for elements that have the requested annotation
identifiers <- sapply(these_refs,
function(x) x[x$type == annotation_type, "resource"])
identifiers <- identifiers[sapply(identifiers,
function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
return(identifiers)
}
### Get unique HGNC symbols
all_hgncs <- unique(all_hgncs)
### Get all HGNC symbols
all_hgncs <- sapply(components$map_elements, get_annotations, "HGNC_SYMBOL")
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