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Merge branch 'development' into fix/redis-warining
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@syphax-bouazzouni
syphax-bouazzouni committed May 1, 2024
2 parents 98861fd + 73309f6 commit 5795904
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2 changes: 1 addition & 1 deletion Gemfile.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ GIT

GIT
remote: https://github.com/ontoportal-lirmm/goo.git
revision: 8f0a9a5bddba03d9d660a363c4e6618da479db9f
revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
branch: development
specs:
goo (0.0.2)
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32 changes: 28 additions & 4 deletions controllers/search_controller.rb
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Expand Up @@ -22,20 +22,20 @@ class SearchController < ApplicationController
format = params.fetch("hasOntologyLanguage", "").split(',')
is_of_type = params.fetch("isOfType", "").split(',')
has_format = params.fetch("hasFormat", "").split(',')
visibility = params["visibility"]&.presence || "public"
visibility = params["visibility"]
show_views = params["show_views"] == 'true'
sort = params.fetch("sort", "score desc, ontology_name_sort asc, ontology_acronym_sort asc")
page, page_size = page_params

fq = [
'resource_model:"ontology_submission"',
'submissionStatus_txt:ERROR_* OR submissionStatus_txt:"RDF" OR submissionStatus_txt:"UPLOADED"',
"ontology_viewingRestriction_t:#{visibility}",
groups.map { |x| "ontology_group_txt:\"http://data.bioontology.org/groups/#{x.upcase}\"" }.join(' OR '),
categories.map { |x| "ontology_hasDomain_txt:\"http://data.bioontology.org/categories/#{x.upcase}\"" }.join(' OR '),
languages.map { |x| "naturalLanguage_txt:\"#{x.downcase}\"" }.join(' OR '),
]

fq << "ontology_viewingRestriction_t:#{visibility}" unless visibility.blank?
fq << "!ontology_viewOf_t:*" unless show_views

fq << format.map { |x| "hasOntologyLanguage_t:\"http://data.bioontology.org/ontology_formats/#{x}\"" }.join(' OR ') unless format.blank?
Expand Down Expand Up @@ -75,7 +75,15 @@ class SearchController < ApplicationController
old_resource_id = acronyms_ids[acronym]
old_id = old_resource_id.split('/').last.to_i rescue 0

if acronym.blank? || old_id && id && (id <= old_id)
already_found = (old_id && id && (id <= old_id))
not_restricted = (doc["ontology_viewingRestriction_t"]&.eql?('public') || current_user&.admin?)
user_not_restricted = not_restricted ||
Array(doc["ontology_viewingRestriction_txt"]).any? {|u| u.split(' ').last == current_user&.username} ||
Array(doc["ontology_acl_txt"]).any? {|u| u.split(' ').last == current_user&.username}

user_restricted = !user_not_restricted

if acronym.blank? || already_found || user_restricted
total_found -= 1
next
end
Expand All @@ -99,10 +107,26 @@ class SearchController < ApplicationController
get '/content' do
query = params[:query] || params[:q]
page, page_size = page_params

ontologies = params.fetch("ontologies", "").split(',')

unless current_user&.admin?
restricted_acronyms = restricted_ontologies_to_acronyms(params)
ontologies = ontologies.empty? ? restricted_acronyms : ontologies & restricted_acronyms
end


types = params.fetch("types", "").split(',')
qf = params.fetch("qf", "")

qf = [
"ontology_t^100 resource_id^10",
"http___www.w3.org_2004_02_skos_core_prefLabel_txt^30",
"http___www.w3.org_2004_02_skos_core_prefLabel_t^30",
"http___www.w3.org_2000_01_rdf-schema_label_txt^30",
"http___www.w3.org_2000_01_rdf-schema_label_t^30",
].join(' ') if qf.blank?

fq = []

fq << ontologies.map { |x| "ontology_t:\"#{x}\"" }.join(' OR ') unless ontologies.blank?
Expand All @@ -117,7 +141,7 @@ class SearchController < ApplicationController
docs = resp["response"]["docs"]


reply 200,page_object(docs, total_found)
reply 200, page_object(docs, total_found)
end
end

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4 changes: 2 additions & 2 deletions controllers/users_controller.rb
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Expand Up @@ -99,14 +99,14 @@ class UsersController < ApplicationController
private


def create_user
def create_user(send_notifications: true)
params ||= @params
user = User.find(params["username"]).first
error 409, "User with username `#{params["username"]}` already exists" unless user.nil?
params.delete("role") unless current_user.admin?
user = instance_from_params(User, params)
if user.valid?
user.save(send_notifications: false)
user.save(send_notifications: send_notifications)
else
error 422, user.errors
end
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80 changes: 75 additions & 5 deletions test/controllers/test_search_models_controller.rb
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Expand Up @@ -18,7 +18,8 @@ def test_show_all_collection
get '/admin/search/collections'
assert last_response.ok?
res = MultiJson.load(last_response.body)
assert_equal res["collections"].sort, Goo.search_connections.keys.map(&:to_s).sort
array = %w[agents_metadata ontology_data ontology_metadata prop_search_core1 term_search_core1]
assert_equal res["collections"].sort , array.sort
end

def test_collection_schema
Expand Down Expand Up @@ -55,6 +56,77 @@ def test_collection_search
assert_equal 2, res['response']['numFound']
end

def test_search_security
count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
process_submission: true,
process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
acronym: "BROSEARCHTEST",
name: "BRO Search Test",
file_path: "./test/data/ontology_files/BRO_v3.2.owl",
ont_count: 1,
submission_count: 1,
ontology_type: "VALUE_SET_COLLECTION"
})

count, acronyms, mccl = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
process_submission: true,
process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
acronym: "MCCLSEARCHTEST",
name: "MCCL Search Test",
file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl",
ont_count: 1,
submission_count: 1
})


subs = LinkedData::Models::OntologySubmission.all
subs.each do |s|
s.bring_remaining
s.index_all(Logger.new($stdout))
end


allowed_user = User.new({
username: "allowed",
email: "test1@example.org",
password: "12345"
})
allowed_user.save

blocked_user = User.new({
username: "blocked",
email: "test2@example.org",
password: "12345"
})
blocked_user.save

bro = bro.first
bro.bring_remaining
bro.acl = [allowed_user]
bro.viewingRestriction = "private"
bro.save

self.class.enable_security
get "/search/ontologies?query=#{bro.acronym}&apikey=#{blocked_user.apikey}"
response = MultiJson.load(last_response.body)["collection"]
assert_empty response.select{|x| x["ontology_acronym_text"].eql?(bro.acronym)}

get "/search/ontologies/content?q=*Research_Lab_Management*&apikey=#{blocked_user.apikey}"
assert last_response.ok?
res = MultiJson.load(last_response.body)
assert_equal 0, res['totalCount']

get "/search/ontologies?query=#{bro.acronym}&apikey=#{allowed_user.apikey}"
response = MultiJson.load(last_response.body)["collection"]
refute_empty response.select{|x| x["ontology_acronym_text"].eql?(bro.acronym)}

get "/search/ontologies/content?q=*Research_Lab_Management*&apikey=#{allowed_user.apikey}"
assert last_response.ok?
res = MultiJson.load(last_response.body)
assert_equal 1, res['totalCount']

self.class.reset_security(false)
end

def test_ontology_metadata_search
count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
Expand Down Expand Up @@ -345,7 +417,7 @@ def test_agents_search
def test_search_data
count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
process_submission: true,
process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
process_options: { process_rdf: true, extract_metadata: false, index_all_data: true, generate_missing_labels: false},
acronym: "BROSEARCHTEST",
name: "BRO Search Test",
file_path: "./test/data/ontology_files/BRO_v3.2.owl",
Expand All @@ -356,7 +428,7 @@ def test_search_data

count, acronyms, mccl = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
process_submission: true,
process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
process_options: { process_rdf: true, extract_metadata: false, index_all_data: true, generate_missing_labels: false},
acronym: "MCCLSEARCHTEST",
name: "MCCL Search Test",
file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl",
Expand All @@ -368,8 +440,6 @@ def test_search_data
subs = LinkedData::Models::OntologySubmission.all
count = []
subs.each do |s|
s.bring_remaining
s.index_all_data(Logger.new($stdout))
count << Goo.sparql_query_client.query("SELECT (COUNT( DISTINCT ?id) as ?c) FROM <#{s.id}> WHERE {?id ?p ?v}")
.first[:c]
.to_i
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