From 6b85d0377bbcc8447765e651d03bd475dca5d0f8 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 21 Jul 2022 11:10:09 +0200
Subject: [PATCH 1/2] add a script to import an ontology and its latest_sub
 from other portal

---
 bin/ncbo_ontology_import | 171 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 171 insertions(+)
 create mode 100755 bin/ncbo_ontology_import

diff --git a/bin/ncbo_ontology_import b/bin/ncbo_ontology_import
new file mode 100755
index 00000000..f28ba255
--- /dev/null
+++ b/bin/ncbo_ontology_import
@@ -0,0 +1,171 @@
+#!/usr/bin/env ruby
+
+$0 = 'ncbo_cron'
+
+# Exit cleanly from an early interrupt
+Signal.trap('INT') { exit 1 }
+
+# Setup the bundled gems in our environment
+require 'bundler/setup'
+# redis store for looking up queued jobs
+require 'redis'
+
+require_relative '../lib/ncbo_cron'
+require_relative '../config/config'
+require 'net/http'
+
+# Script for importing ontologies + latest_submission into ontoportal appliance
+
+
+require 'optparse'
+ontologies_acronyms = ''
+ontology_source = ''
+source_api = ''
+username = ''
+opt_parser = OptionParser.new do |opts|
+  opts.banner = 'Usage: ncbo_ontology_import [options]'
+  opts.on('-o', '--ontology ACRONYM', 'Ontologies acronyms which we want to import (separated by comma)') do |acronym|
+    ontologies_acronyms = acronym
+  end
+
+  opts.on('--from url', 'The ontoportal api url source of the ontology') do |url|
+    ontology_source = url.to_s
+  end
+
+  opts.on('--from-api api', 'An apikey to acces the ontoportal api') do |api|
+    source_api = api.to_s
+  end
+
+  opts.on('--admin-user username', 'The target admin user that will submit the ontology') do |user|
+    username = user.to_s
+  end
+  # Display the help screen, all programs are assumed to have this option.
+  opts.on( '-h', '--help', 'Display this screen') do
+    puts opts
+    exit
+  end
+end
+opt_parser.parse!
+
+# URL of the API and APIKEY of the Otoportal  we want to import data FROM
+SOURCE_API =  ontology_source || 'http://data.bioontology.org'
+SOURCE_APIKEY =  source_api ||  '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'
+
+
+# The username of the user that will have the administration rights on the ontology on the target portal
+TARGETED_PORTAL_USER = username
+
+# The list of acronyms of ontologies to import
+ONTOLOGIES_TO_IMPORT = ontologies_acronyms.split(',') || []
+
+
+def get_user(username)
+  user = LinkedData::Models::User.find(username).first
+  raise "The user #{username} does not exist" if user.nil?
+  user.bring_remaining
+end
+
+
+# A function to create a new ontology (if already Acronym already existing on the portal it will return HTTPConflict)
+def create_ontology(ont_info)
+
+  new_ontology = LinkedData::Models::Ontology.new
+
+  new_ontology.acronym = ont_info['acronym']
+  new_ontology.name = ont_info['name']
+  new_ontology.administeredBy = [USER]
+  if ont_info['viewingRestriction'] == 'private'
+    # In case of private ontology (acl: list of user that have the right to see the ontology)
+    new_ontology.viewingRestriction = 'private'
+    new_ontology.acl = [USER]
+  end
+  new_ontology
+end
+
+# A function that take the submission informations from the source Ontoportal to create a new submission
+# 2 possibilities:
+# - the source Ontoportal 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, ontology)
+  new_submission = LinkedData::Models::OntologySubmission.new
+  # 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?
+    sub_info['pullLocation'] = "#{sub_info['ontology']['links']['download']}?apikey=#{SOURCE_APIKEY}"
+  end
+
+  # Build the json body
+  # hasOntologyLanguage options: OWL, UMLS, SKOS, OBO
+  # status: alpha, beta, production, retired
+  attr_to_reject = %w[id submissionStatus hasOntologyLanguage metrics ontology @id @type contact]
+  to_copy = sub_info.select do |k,v|
+    !v.nil? && !v.is_a?(Hash) && !v.to_s.empty? && !attr_to_reject.include?(k)
+  end
+  to_copy["ontology"] = ontology
+  to_copy["contact"] =  [LinkedData::Models::Contact.where(email: USER.email).first]
+  to_copy["hasOntologyLanguage"] =  LinkedData::Models::OntologyFormat.where(acronym: sub_info["hasOntologyLanguage"]).first
+
+  to_copy.each do |key, value|
+    attribute_settings = new_submission.class.attribute_settings(key.to_sym)
+
+    if attribute_settings
+      if  attribute_settings[:enforce]&.include?(:date_time)
+        value = DateTime.parse(value)
+      elsif attribute_settings[:enforce]&.include?(:uri) && attribute_settings[:enforce]&.include?(:list)
+        value = value.map { |v| RDF::IRI.new(v) }
+      elsif  attribute_settings[:enforce]&.include?(:uri)
+        value = RDF::IRI.new(value)
+      end
+    end
+
+    new_submission.send("#{key}=", value)
+  end
+
+  new_submission
+end
+
+
+USER = get_user username
+#get apikey for admin user
+TARGET_APIKEY = USER.apikey
+
+SOURCE_APIKEY == '' && abort('SOURCE_APIKEY has to be set')
+
+def result_log(ressource, errors)
+  if !errors
+    puts "#{ressource} imported successfully"
+  else
+    puts errors
+  end
+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")))
+  puts "Import #{ont} " ,
+       "From #{SOURCE_API}"
+  # if the ontology is already created then it will return HTTPConflict, no consequences
+  raise "The ontology #{ont} does not exist" if sub_info['ontology'].nil?
+  new_ontology = create_ontology(sub_info['ontology'])
+  errors = nil
+  if new_ontology.valid?
+    new_ontology.save
+  else
+    errors = new_ontology.errors
+    new_ontology = nil
+  end
+  result_log ont, errors
+
+  new_ontology ||= LinkedData::Models::Ontology.where(acronym: ont).first
+  new_submission = upload_submission(sub_info, new_ontology)
+  if new_submission.valid?
+    new_submission.save
+    errors = nil
+  else
+    errors = new_submission.errors
+  end
+  result_log(sub_info["id"], errors)
+end
+
+
+

From 30f702e557d21877296143c3c428fb8569326c7e Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Fri, 29 Jul 2022 17:32:22 +0200
Subject: [PATCH 2/2] make the SOURCE_APIKEY and SOURCE_API arguments mandatory

---
 bin/ncbo_ontology_import | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/bin/ncbo_ontology_import b/bin/ncbo_ontology_import
index f28ba255..db2e90c5 100755
--- a/bin/ncbo_ontology_import
+++ b/bin/ncbo_ontology_import
@@ -47,9 +47,9 @@ opt_parser = OptionParser.new do |opts|
 end
 opt_parser.parse!
 
-# URL of the API and APIKEY of the Otoportal  we want to import data FROM
-SOURCE_API =  ontology_source || 'http://data.bioontology.org'
-SOURCE_APIKEY =  source_api ||  '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'
+# URL of the API and APIKEY of the Ontoportal  we want to import data FROM
+SOURCE_API =  ontology_source
+SOURCE_APIKEY =  source_api
 
 
 # The username of the user that will have the administration rights on the ontology on the target portal
@@ -129,7 +129,8 @@ USER = get_user username
 #get apikey for admin user
 TARGET_APIKEY = USER.apikey
 
-SOURCE_APIKEY == '' && abort('SOURCE_APIKEY has to be set')
+SOURCE_APIKEY == '' && abort('--from-api has to be set')
+SOURCE_API == '' && abort('--from has to be set')
 
 def result_log(ressource, errors)
   if !errors