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Develop to Master merge, release v5.33.0 #167

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6 changes: 6 additions & 0 deletions .env
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
API_URL=http://localhost:9393
ONTOLOGIES_LINKED_DATA_PATH=
GOO_PATH=
SPARQL_CLIENT_PATH=
ONTOPORTAL_KB=ontoportal_kb
REDIS_HOST=redis-ut
14 changes: 8 additions & 6 deletions Gemfile
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
source 'https://rubygems.org'

gem 'activesupport', '~> 3.2'
gem 'activesupport', '~> 5'
# see https://github.com/ncbo/ontologies_api/issues/69
gem 'bigdecimal', '1.4.2'
gem 'bigdecimal'
# gem 'faraday', '~> 1.9'
gem 'json-schema', '~> 2.0'
gem 'multi_json', '~> 1.0'
gem 'oj', '~> 3.0'
gem 'multi_json'
gem 'oj'
gem 'parseconfig'
gem 'rack'
gem 'rake', '~> 10.0'
@@ -72,7 +72,9 @@ group :profiling do
end

group :test do
gem 'minitest', '~> 4.0'
gem 'crack', '0.4.5'
gem 'minitest', '~> 5.0'
gem 'minitest-hooks', "~> 1.5"
gem 'minitest-stub_any_instance'
gem 'rack-test'
gem 'simplecov', require: false
59 changes: 37 additions & 22 deletions Gemfile.lock
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
GIT
remote: https://github.com/ncbo/goo.git
revision: 70007faf43d0d96292809f89f15a27a757ccaa25
revision: aaa3941b48edbc317ec42ba4ecb44c0defeccef6
branch: develop
specs:
goo (0.0.2)
@@ -16,7 +16,7 @@ GIT

GIT
remote: https://github.com/ncbo/ncbo_annotator.git
revision: 2fb892f92f66b876b9793944124f72821f3b3eb8
revision: b2731c98bfef0958fecb440c8648b7755a670895
branch: develop
specs:
ncbo_annotator (0.0.1)
@@ -27,7 +27,7 @@ GIT

GIT
remote: https://github.com/ncbo/ncbo_cron.git
revision: 3bb491139267efc37d3b752888824ca3dd976e85
revision: cf66e7d076a94e6d669ffeb09c6bcd988226ece3
branch: develop
specs:
ncbo_cron (0.0.1)
@@ -56,7 +56,7 @@ GIT

GIT
remote: https://github.com/ncbo/ontologies_linked_data.git
revision: c30887ee907acd39500cae6c12f45edb06fe0802
revision: a22fae3150d8e84e3b6fd19223a5ce2111e8ce94
branch: develop
specs:
ontologies_linked_data (0.0.1)
@@ -103,9 +103,11 @@ GIT
GEM
remote: https://rubygems.org/
specs:
activesupport (3.2.22.5)
i18n (~> 0.6, >= 0.6.4)
multi_json (~> 1.0)
activesupport (5.2.8.1)
concurrent-ruby (~> 1.0, >= 1.0.2)
i18n (>= 0.7, < 2)
minitest (~> 5.1)
tzinfo (~> 1.1)
addressable (2.8.7)
public_suffix (>= 2.0.2, < 7.0)
airbrussh (1.5.3)
@@ -116,7 +118,8 @@ GEM
bcrypt (3.1.20)
bcrypt_pbkdf (1.1.1)
bcrypt_pbkdf (1.1.1-arm64-darwin)
bigdecimal (1.4.2)
bcrypt_pbkdf (1.1.1-x86_64-darwin)
bigdecimal (3.1.8)
builder (3.3.0)
capistrano (3.19.1)
airbrussh (>= 1.0.0)
@@ -133,8 +136,7 @@ GEM
coderay (1.1.3)
concurrent-ruby (1.3.4)
connection_pool (2.4.1)
crack (1.0.0)
bigdecimal
crack (0.4.5)
rexml
cube-ruby (0.0.3)
dante (0.2.0)
@@ -154,6 +156,7 @@ GEM
faraday (~> 2.0)
ffi (1.17.0-aarch64-linux-gnu)
ffi (1.17.0-arm64-darwin)
ffi (1.17.0-x86_64-darwin)
ffi (1.17.0-x86_64-linux-gnu)
gapic-common (0.22.0)
faraday (>= 1.9, < 3.a)
@@ -179,6 +182,7 @@ GEM
google-cloud-errors (1.4.0)
google-protobuf (3.25.5-aarch64-linux)
google-protobuf (3.25.5-arm64-darwin)
google-protobuf (3.25.5-x86_64-darwin)
google-protobuf (3.25.5-x86_64-linux)
googleapis-common-protos (1.6.0)
google-protobuf (>= 3.18, < 5.a)
@@ -199,6 +203,9 @@ GEM
grpc (1.66.0-arm64-darwin)
google-protobuf (>= 3.25, < 5.0)
googleapis-common-protos-types (~> 1.0)
grpc (1.66.0-x86_64-darwin)
google-protobuf (>= 3.25, < 5.0)
googleapis-common-protos-types (~> 1.0)
grpc (1.66.0-x86_64-linux)
google-protobuf (>= 3.25, < 5.0)
googleapis-common-protos-types (~> 1.0)
@@ -209,13 +216,13 @@ GEM
http-accept (1.7.0)
http-cookie (1.0.7)
domain_name (~> 0.5)
i18n (0.9.5)
i18n (1.14.6)
concurrent-ruby (~> 1.0)
json (2.7.2)
json-schema (2.8.1)
addressable (>= 2.4)
json_pure (2.7.2)
jwt (2.9.0)
jwt (2.9.1)
base64
kgio (2.11.4)
language_server-protocol (3.17.0.3)
@@ -233,7 +240,9 @@ GEM
mime-types-data (~> 3.2015)
mime-types-data (3.2024.0903)
mini_mime (1.1.5)
minitest (4.7.5)
minitest (5.25.1)
minitest-hooks (1.5.2)
minitest (> 5.3)
minitest-stub_any_instance (1.0.3)
mlanett-redis-lock (0.2.7)
redis
@@ -257,7 +266,9 @@ GEM
net-ssh (7.2.3)
netrc (0.11.0)
newrelic_rpm (9.13.0)
oj (3.16.1)
oj (3.16.6)
bigdecimal (>= 3.0)
ostruct (>= 0.2)
omni_logger (0.1.4)
logger
os (1.1.4)
@@ -369,10 +380,11 @@ GEM
ostruct
systemu (2.6.5)
temple (0.10.3)
thread_safe (0.3.6)
tilt (2.4.0)
timeout (0.4.1)
tzinfo (2.0.6)
concurrent-ruby (~> 1.0)
tzinfo (1.2.11)
thread_safe (~> 0.1)
unicode-display_width (2.6.0)
unicorn (6.1.0)
kgio (~> 2.6)
@@ -387,35 +399,38 @@ GEM
addressable (>= 2.8.0)
crack (>= 0.3.2)
hashdiff (>= 0.4.0, < 2.0.0)
webrick (1.8.1)
webrick (1.8.2)

PLATFORMS
aarch64-linux
arm64-darwin-22
x86_64-darwin-23
x86_64-linux

DEPENDENCIES
activesupport (~> 3.2)
activesupport (~> 5)
bcrypt_pbkdf (>= 1.0, < 2.0)
bigdecimal (= 1.4.2)
bigdecimal
capistrano (~> 3)
capistrano-bundler
capistrano-locally
capistrano-rbenv
crack (= 0.4.5)
cube-ruby
ed25519 (>= 1.2, < 2.0)
ffi
goo!
haml (~> 5.2.2)
json-schema (~> 2.0)
minitest (~> 4.0)
minitest (~> 5.0)
minitest-hooks (~> 1.5)
minitest-stub_any_instance
multi_json (~> 1.0)
multi_json
ncbo_annotator!
ncbo_cron!
ncbo_ontology_recommender!
newrelic_rpm
oj (~> 3.0)
oj
ontologies_linked_data!
parseconfig
rack
4 changes: 2 additions & 2 deletions test/controllers/test_annotator_controller.rb
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@

class TestAnnotatorController < TestCase

def self.before_suite
def before_suite
@@redis = Redis.new(:host => Annotator.settings.annotator_redis_host, :port => Annotator.settings.annotator_redis_port)
db_size = @@redis.dbsize
if db_size > MAX_TEST_REDIS_SIZE
@@ -25,7 +25,7 @@ def self.before_suite
annotator = Annotator::Models::NcboAnnotator.new
annotator.init_redis_for_tests()
annotator.create_term_cache_from_ontologies(@@ontologies, false)
mapping_test_set
self.class.mapping_test_set
end

def test_annotate
15 changes: 9 additions & 6 deletions test/controllers/test_batch_controller.rb
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
require_relative '../test_case'

class TestBatchController < TestCase
def self.before_suite
def before_suite
LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
@@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true)
end

@@ -25,7 +26,7 @@ def test_class_batch_one_ontology
assert last_response.ok?
data = MultiJson.load(last_response.body)
classes = data["http://www.w3.org/2002/07/owl#Class"]
assert classes.length == 4
assert_equal 4, classes.length
classes.each do |klass|
assert_instance_of String, klass["prefLabel"]
assert_instance_of Array, klass["synonym"]
@@ -75,18 +76,19 @@ def test_class_batch_multiple
assert last_response.ok?
data = MultiJson.load(last_response.body)
classes = data["http://www.w3.org/2002/07/owl#Class"]
assert classes.length == 6
assert_equal 6, classes.length
classes.each do |klass|
assert_instance_of String, klass["prefLabel"]
assert !klass["synonym"]
assert klass["prefLabel"] == class_ids[klass["@id"]]
refute klass["synonym"]
assert_equal klass["prefLabel"], class_ids[klass["@id"]]
end
end


def test_class_all_bro
mccl = @@ontologies.select { |y| y.id.to_s.include? "MCCL"}.first
assert mccl, "mccl is not found to execute batch test."
# binding.pry
classes = LinkedData::Models::Class.in(mccl.latest_submission).include(:prefLabel).page(1,500).read_only.all
class_ids = {}
classes.each do |klass|
@@ -101,9 +103,10 @@ def test_class_all_bro
}
post "/batch/", call_params
assert last_response.ok?
# refute last_response.ok?
data = MultiJson.load(last_response.body)
classes_response = data["http://www.w3.org/2002/07/owl#Class"]
assert classes_response.length == classes.length
assert_equal classes.length, classes_response.length
classes_response.each do |klass|
assert_instance_of String, klass["prefLabel"]
assert klass["prefLabel"] == class_ids[klass["@id"]]
2 changes: 1 addition & 1 deletion test/controllers/test_classes_controller.rb
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@

class TestClassesController < TestCase

def self.before_suite
def before_suite
options = {ont_count: 1,
submission_count: 3,
submissions_to_process: [1, 2],
2 changes: 1 addition & 1 deletion test/controllers/test_instances_controller.rb
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@

class TestInstancesController < TestCase

def self.before_suite
def before_suite
LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
process_submission: true,
acronym: 'XCT-TEST-INST',
4 changes: 2 additions & 2 deletions test/controllers/test_mappings_controller.rb
Original file line number Diff line number Diff line change
@@ -2,8 +2,8 @@

class TestMappingsController < TestCase

def self.before_suite

def before_suite
self.backend_4s_delete
["BRO-TEST-MAP-0","CNO-TEST-MAP-0","FAKE-TEST-MAP-0"].each do |acr|
LinkedData::Models::OntologySubmission.where(ontology: [acronym: acr]).to_a.each do |s|
s.delete
2 changes: 1 addition & 1 deletion test/controllers/test_metrics_controller.rb
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@

class TestMetricsController < TestCase

def self.before_suite
def before_suite
if OntologySubmission.all.count > 100
puts "this test is going to wipe out all submission and ontologies. probably this is not a test env."
return
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