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authorChristoph Helma <helma@in-silico.ch>2016-11-10 12:23:46 +0100
committerChristoph Helma <helma@in-silico.ch>2016-11-10 12:23:46 +0100
commit9e7b36613e98601de7b2ceb2d4442e11f1ae868a (patch)
treecbb3148fb82e451505d4d864bb4547b5c2c3b33d /lib/import.rb
parenta90047977da5a635072f2833816726eaf721aa88 (diff)
intermediate commit, may be defunct
Diffstat (limited to 'lib/import.rb')
-rw-r--r--lib/import.rb44
1 files changed, 31 insertions, 13 deletions
diff --git a/lib/import.rb b/lib/import.rb
index 8e57401..541c9b5 100644
--- a/lib/import.rb
+++ b/lib/import.rb
@@ -9,6 +9,12 @@ module OpenTox
#get list of bundle URIs
bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
File.open(File.join(dir,"bundles.json"),"w+"){|f| f.puts JSON.pretty_generate(bundles)}
+ # bundles
+ # id/summary
+ # id/compound
+ # id/substance
+ # id/property
+
bundles.each do |bundle|
$logger.debug bundle["title"]
nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"]
@@ -32,32 +38,43 @@ module OpenTox
t2 = 0
datasets = {}
JSON.parse(File.read(File.join(dir,"bundles.json"))).each do |bundle|
+ if bundle["id"] == 3
datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"])
+ end
end
- Dir[File.join(dir,"study*.json")].each do |s|
+ # TODO this is only for protein corona
+ Dir[File.join(dir,"study-F*.json")].each do |s|
t = Time.now
study = JSON.parse(File.read(s))
np = JSON.parse(File.read(File.join(dir,"nanoparticle-#{study['owner']['substance']['uuid']}.json")))
- core = {}
- coating = []
+ core_id = nil
+ coating_ids = []
np["composition"].each do |c|
+ uri = c["component"]["compound"]["URI"]
+ uri = CGI.escape File.join(uri,"&media=application/json")
+ data = JSON.parse(RestClientWrapper.get "https://data.enanomapper.net/query/compound/url/all?media=application/json&search=#{uri}")
+ smiles = data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23SMILESDefault"]
+ names = []
+ names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
+ names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23IUPACNameDefault"]
+ if smiles
+ compound = Compound.find_or_create_by(:smiles => smiles)
+ compound.names = names.compact
+ else
+ compound = Compound.find_or_create_by(:names => names)
+ end
+ compound.save
if c["relation"] == "HAS_CORE"
- core = {
- :uri => c["component"]["compound"]["URI"],
- :name => c["component"]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
- }
+ core_id = compound.id.to_s
elsif c["relation"] == "HAS_COATING"
- coating << {
- :uri => c["component"]["compound"]["URI"],
- :name => c["component"]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
- }
+ coating_ids << compound.id.to_s
end
end if np["composition"]
nanoparticle = Nanoparticle.find_or_create_by(
:name => np["values"]["https://data.enanomapper.net/identifier/name"],
:source => np["compound"]["URI"],
- :core => core,
- :coating => coating
+ :core_id => core_id,
+ :coating_ids => coating_ids
)
np["bundles"].keys.each do |bundle_uri|
nanoparticle.dataset_ids << datasets[bundle_uri].id
@@ -104,6 +121,7 @@ module OpenTox
nanoparticle.parse_ambit_value feature, effect["result"], dataset
end
end
+ p nanoparticle
nanoparticle.save
end
datasets.each { |u,d| d.save }