new script to import ontologies

Vincent Emonet said in 2015 (thank you!):

Here is a little and easy Ruby script to load ontologies from a BioPortal Appliance to another (using pullLocation when it can so the ontology will be automatically updated)

All the variables used for the configuration are at the top of the script (APIs URL and keys, list of ontologies to import)

ruby/bioportal_ontologies_import.rb

@@ -0,0 +1,112 @@
+#!/usr/bin/ruby
+
+# A script by Vincent Emonet to auto import ontologies from a BioPortal appliance to another
+# It will import the metadata too
+# Fill the following variables with
+
+# URL of the API and APIKEY of the BioPortal we want to import data FROM
+SOURCE_API = "http://data.bioontology.org"
+SOURCE_APIKEY = ""
+
+# URL of the API and APIKEY of the BioPortal we want to import data TO
+TARGET_API = "http://agroportal.lirmm.fr"
+TARGET_APIKEY = ""
+
+# The username of the user that will have the administration rights on the ontology on the target portal
+TARGETED_PORTAL_USER = "admin"
+
+# The list of acronyms of ontologies to import
+ONTOLOGIES_TO_IMPORT = ["STY"]
+
+
+
+require 'json'
+require 'net/http'
+
+# A function to create a new ontology (if already Acronym already existing on the portal it will return HTTPConflict)
+def create_ontology(ont_info)
+  uri = URI.parse(TARGET_API)
+  http = Net::HTTP.new(uri.host, uri.port)
+
+  req = Net::HTTP::Put.new("/ontologies/#{ont_info["acronym"]}")
+  req['Content-Type'] = "application/json"
+  req['Authorization'] = "apikey token=#{TARGET_APIKEY}"
+
+  if (ont_info["viewingRestriction"] == "private")
+    # In case of private ontology (acl: list of user that have the right to see the ontology)
+    req.body = { "acronym": ont_info["acronym"], "name": ont_info["name"], "group": ont_info["group"], "hasDomain": ont_info["hasDomain"], "administeredBy": [TARGETED_PORTAL_USER], "viewingRestriction": "private", "acl": [TARGETED_PORTAL_USER]}.to_json
+  else
+    req.body = { "acronym": ont_info["acronym"], "name": ont_info["name"], "group": ont_info["group"], "hasDomain": ont_info["hasDomain"], "administeredBy": [TARGETED_PORTAL_USER]}.to_json
+  end
+
+  response = http.start do |http|
+    http.request(req)
+  end
+
+  return response
+end
+
+# A function that take the submission informations from the source BioPortal to create a new submission
+# 2 possibilities:
+# - the source BioPortal pulls the ontology from an URL (pullLocation is filled), in this case we directly pull from this URL
+# - Or it stores it directly in the portal, in this case we pull it from the portal download link
+def upload_submission(sub_info)
+  uri = URI.parse(TARGET_API)
+  http = Net::HTTP.new(uri.host, uri.port)
+
+  req = Net::HTTP::Post.new("/ontologies/#{sub_info["ontology"]["acronym"]}/submissions")
+  req['Content-Type'] = "application/json"
+  req['Authorization'] = "apikey token=#{TARGET_APIKEY}"
+
+  # Check if the source BioPortal is pulling the ontology from an URL
+  # If yes then we will pull the ontology from this place (allow auto update of the ontology when the ontology is changed in its source URL)
+  if sub_info["pullLocation"].nil?
+    pull_location = "#{sub_info["ontology"]["links"]["download"]}?apikey=#{SOURCE_APIKEY}"
+  else
+    pull_location = sub_info["pullLocation"]
+  end
+
+  # Extract contacts
+  contacts = []
+  sub_info["contact"].each do |contact|
+    contacts.push({"name": contact["name"],"email": contact["email"]})
+  end
+
+  # Build the json body
+  # hasOntologyLanguage options: OWL, UMLS, SKOS, OBO
+  # status: alpha, beta, production, retired
+  req.body = {
+      "contact": contacts,
+      "hasOntologyLanguage": sub_info["hasOntologyLanguage"],
+      "released": sub_info["released"],
+      "ontology": "#{TARGET_API}/ontologies/#{sub_info["ontology"]["acronym"]}",
+      "description": sub_info["description"],
+      "status": sub_info["status"],
+      "version": sub_info["version"],
+      "homepage": sub_info["homepage"],
+      "documentation": sub_info["documentation"],
+      "publication": sub_info["publication"],
+      "naturalLanguage": sub_info["naturalLanguage"],
+      "pullLocation": pull_location
+  }.to_json
+
+  #puts req.body.to_s
+  response = http.start do |http|
+    http.request(req)
+  end
+
+  return response
+end
+
+
+# Go through all ontologies acronym and get their latest_submission informations
+ONTOLOGIES_TO_IMPORT.each do |ont|
+  sub_info = JSON.parse(Net::HTTP.get(URI.parse("#{SOURCE_API}/ontologies/#{ont}/latest_submission?apikey=#{SOURCE_APIKEY}&display=all")))
+
+  # if the ontology is already created then it will return HTTPConflict, no consequences
+  puts create_ontology(sub_info["ontology"])
+
+  puts upload_submission(sub_info)
+end
+
+