From 7e04c510f44f8ced9fdc5bd21438ec4fc16caed2 Mon Sep 17 00:00:00 2001 From: gebele Date: Fri, 30 Jun 2017 14:18:04 +0000 Subject: consistend use of RestClientWrapper to import datasets --- lib/import.rb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/lib/import.rb b/lib/import.rb index 96e7ad1..0857717 100644 --- a/lib/import.rb +++ b/lib/import.rb @@ -10,18 +10,17 @@ module OpenTox def self.import # time critical step: JSON parsing (>99%), Oj brings only minor speed gains (~1%) datasets = {} - bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"] + bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle', {}, {accept: :json}))["dataset"] bundles.each do |bundle| datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"].strip) $logger.debug bundle["title"].strip - nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"] + nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"], {}, {accept: :json}))["dataEntry"] nanoparticles.each_with_index do |np,n| 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}") + data = JSON.parse(RestClientWrapper.get("https://data.enanomapper.net/query/compound/url/all?search=#{uri}", {}, {accept: :json})) source = data["dataEntry"][0]["compound"]["URI"] smiles = data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23SMILESDefault"] names = [] @@ -52,7 +51,7 @@ module OpenTox nanoparticle.dataset_ids << datasets[bundle_uri].id end - studies = JSON.parse(RestClientWrapper.get(File.join(np["compound"]["URI"],"study")))["study"] + studies = JSON.parse(RestClientWrapper.get(File.join(np["compound"]["URI"],"study"), {}, {accept: :json}))["study"] studies.each do |study| dataset = datasets[np["bundles"].keys.first] proteomics_features = {} -- cgit v1.2.3