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Merge branch 'development' into upstream
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syphax-bouazzouni committed Oct 10, 2024
2 parents 941eee3 + a95245b commit c0203dd
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11 changes: 7 additions & 4 deletions .github/workflows/ruby-unit-test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,14 @@ jobs:
strategy:
fail-fast: false
matrix:
ruby-version: ['3.0', '3.1']
triplestore: ['fs', 'ag']
goo-slice: [ '20', '100', '500' ]
ruby-version: [ '2.7', '3.0' ]
triplestore: [ 'fs', 'ag', 'vo', 'gb' ]

steps:
- uses: actions/checkout@v4
- name: Install Dependencies
run: sudo apt-get -y install raptor2-utils
run: sudo apt-get update && sudo apt-get -y install raptor2-utils
- name: Set up Ruby
uses: ruby/setup-ruby@v1
with:
Expand All @@ -27,8 +28,10 @@ jobs:
- name: Add config file
# tempoaray workaround for the config.rb file requirement
run: echo 'Goo.config do |config| end' > config/config.rb
- name: List directory contents
run: ls -R ./test/data
- name: Run tests
run: bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
run: GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v4
with:
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4 changes: 3 additions & 1 deletion Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ gem "activesupport"
gem "cube-ruby", require: "cube"
gem "rake"
gem "uuid"
gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
gem "request_store"


group :test do
Expand All @@ -23,3 +23,5 @@ group :profiling do
gem "thin"
end

gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
gem 'faraday', '2.7.11' #unpin if we no more support ruby 2.7
90 changes: 51 additions & 39 deletions Gemfile.lock
Original file line number Diff line number Diff line change
@@ -1,20 +1,22 @@
GIT
remote: https://github.com/ncbo/sparql-client.git
revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
branch: master
remote: https://github.com/ontoportal-lirmm/sparql-client.git
revision: c96da3ad479724a31ccd6217ab9939dddfaca40e
branch: development
specs:
sparql-client (1.0.1)
json_pure (>= 1.4)
net-http-persistent (= 2.9.4)
rdf (>= 1.0)
sparql-client (3.2.2)
net-http-persistent (~> 4.0, >= 4.0.2)
rdf (~> 3.2, >= 3.2.11)

PATH
remote: .
specs:
goo (0.0.2)
addressable (~> 2.8)
pry
rdf (= 1.0.8)
rdf (= 3.2.11)
rdf-raptor
rdf-rdfxml
rdf-vocab
redis
request_store
rest-client
Expand All @@ -31,50 +33,48 @@ GEM
multi_json (~> 1.3)
thread_safe (~> 0.1)
tzinfo (~> 0.3.37)
addressable (2.8.7)
public_suffix (>= 2.0.2, < 7.0)
addressable (2.8.6)
public_suffix (>= 2.0.2, < 6.0)
base64 (0.2.0)
builder (3.3.0)
builder (3.2.4)
coderay (1.1.3)
concurrent-ruby (1.3.4)
concurrent-ruby (1.2.3)
connection_pool (2.4.1)
cube-ruby (0.0.3)
daemons (1.4.1)
docile (1.4.1)
docile (1.4.0)
domain_name (0.6.20240107)
eventmachine (1.2.7)
faraday (2.12.0)
faraday-net_http (>= 2.0, < 3.4)
json
logger
faraday-net_http (3.3.0)
net-http
faraday (2.7.11)
base64
faraday-net_http (>= 2.0, < 3.1)
ruby2_keywords (>= 0.0.4)
faraday-net_http (3.0.2)
ffi (1.16.3)
htmlentities (4.3.4)
http-accept (1.7.0)
http-cookie (1.0.7)
domain_name (~> 0.5)
i18n (0.9.5)
concurrent-ruby (~> 1.0)
json (2.7.2)
json_pure (2.7.2)
logger (1.6.1)
link_header (0.0.8)
macaddr (1.7.2)
systemu (~> 2.6.5)
method_source (1.1.0)
mime-types (3.5.2)
mime-types-data (~> 3.2015)
mime-types-data (3.2024.0903)
mime-types-data (3.2024.0305)
minitest (4.7.5)
multi_json (1.15.0)
mustermann (3.0.3)
mustermann (3.0.0)
ruby2_keywords (~> 0.0.1)
net-http (0.4.1)
uri
net-http-persistent (2.9.4)
net-http-persistent (4.0.2)
connection_pool (~> 2.2)
netrc (0.11.0)
pry (0.14.2)
coderay (~> 1.1)
method_source (~> 1.0)
public_suffix (6.0.1)
public_suffix (5.0.5)
rack (2.2.9)
rack-accept (0.4.5)
rack (>= 0.4)
Expand All @@ -84,20 +84,33 @@ GEM
base64 (>= 0.1.0)
rack (~> 2.2, >= 2.2.4)
rake (13.2.1)
rdf (1.0.8)
addressable (>= 2.2)
redis (5.3.0)
rdf (3.2.11)
link_header (~> 0.0, >= 0.0.8)
rdf-raptor (3.2.0)
ffi (~> 1.15)
rdf (~> 3.2)
rdf-rdfxml (3.2.2)
builder (~> 3.2)
htmlentities (~> 4.3)
rdf (~> 3.2)
rdf-xsd (~> 3.2)
rdf-vocab (3.2.7)
rdf (~> 3.2, >= 3.2.4)
rdf-xsd (3.2.1)
rdf (~> 3.2)
rexml (~> 3.2)
redis (5.2.0)
redis-client (>= 0.22.0)
redis-client (0.22.2)
redis-client (0.22.1)
connection_pool
request_store (1.7.0)
request_store (1.6.0)
rack (>= 1.4)
rest-client (2.1.0)
http-accept (>= 1.7.0, < 2.0)
http-cookie (>= 1.0.2, < 2.0)
mime-types (>= 1.16, < 4.0)
netrc (~> 0.8)
rexml (3.3.7)
rexml (3.2.6)
rsolr (2.6.0)
builder (>= 2.1.2)
faraday (>= 0.9, < 3, != 2.0.0)
Expand All @@ -122,27 +135,26 @@ GEM
eventmachine (~> 1.0, >= 1.0.4)
rack (>= 1, < 3)
thread_safe (0.3.6)
tilt (2.4.0)
tilt (2.3.0)
tzinfo (0.3.62)
uri (0.13.1)
uuid (2.3.9)
macaddr (~> 1.0)

PLATFORMS
arm64-darwin-22
x86_64-darwin-21
x86_64-darwin-23
x86_64-linux

DEPENDENCIES
activesupport
cube-ruby
faraday (= 2.7.11)
goo!
minitest (< 5.0)
pry
rack-accept
rack-post-body-to-params
rake
request_store
simplecov
simplecov-cobertura
sinatra
Expand All @@ -151,4 +163,4 @@ DEPENDENCIES
uuid

BUNDLED WITH
2.5.20
2.4.22
6 changes: 0 additions & 6 deletions Rakefile
Original file line number Diff line number Diff line change
Expand Up @@ -50,12 +50,6 @@ Rake::TestTask.new do |t|
t.warning = false
end

Rake::TestTask.new do |t|
t.name = "test:inmutable"
t.test_files = FileList['test/test_inmutable.rb']
t.warning = false
end

Rake::TestTask.new do |t|
t.name = "test:inverse"
t.test_files = FileList['test/test_inverse.rb']
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70 changes: 51 additions & 19 deletions docker-compose.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,40 +10,36 @@ services:
retries: 30

solr-ut:
image: ontoportal/solr-ut:0.1.0
image: solr:8.11.2
ports:
- 8983:8983
healthcheck:
test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"]
start_period: 10s
interval: 10s
timeout: 5s
retries: 5
command: bin/solr start -cloud -f

agraph-ut:
image: franzinc/agraph:v8.2.1
image: franzinc/agraph:v8.1.0
platform: linux/amd64
environment:
- AGRAPH_SUPER_USER=test
- AGRAPH_SUPER_PASSWORD=xyzzy
shm_size: 1g
ports:
# - 10035:10035
- 10000-10035:10000-10035
volumes:
- agdata:/agraph/data
# - ./agraph/etc:/agraph/etc
command: >
bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start
; agtool repos create ontoportal_test --supersede
; agtool users add anonymous
; agtool users grant anonymous root:ontoportal_test:rw
; tail -f /agraph/data/agraph.log"
healthcheck:
test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"]
start_period: 30s
interval: 10s
timeout: 10s
retries: 10
bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start
; agtool repos create ontoportal_test --supersede
; agtool users add anonymous
; agtool users grant anonymous root:ontoportal_test:rw
; tail -f /agraph/data/agraph.log"
# healthcheck:
# test: ["CMD-SHELL", "curl -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1"]
# start_period: 10s
# interval: 10s
# timeout: 5s
# retries: 5
profiles:
- ag

Expand All @@ -58,5 +54,41 @@ services:
&& 4s-httpd -D -s-1 -p 9000 ontoportal_kb"
profiles:
- fs
virtuoso-ut:
image: tenforce/virtuoso:virtuoso7.2.5
platform: linux/amd64
environment:
- SPARQL_UPDATE=true
ports:
- 1111:1111
- 8890:8890

profiles:
- vo

graphdb:
image: ontotext/graphdb:10.3.3
platform: linux/amd64
privileged: true
environment:
GDB_HEAP_SIZE: 5G
GDB_JAVA_OPTS: >-
-Xms5g -Xmx5g
ports:
- 7200:7200
- 7300:7300
volumes:
- ./test/data/graphdb-repo-config.ttl:/opt/graphdb/dist/configs/templates/data/graphdb-repo-config.ttl
- ./test/data/graphdb-test-load.nt:/opt/graphdb/dist/configs/templates/data/graphdb-test-load.nt

entrypoint: >
bash -c " importrdf load -f -c /opt/graphdb/dist/configs/templates/data/graphdb-repo-config.ttl -m parallel /opt/graphdb/dist/configs/templates/data/graphdb-test-load.nt ; graphdb -Ddefault.min.distinct.threshold=3000 "
profiles:
- gb

volumes:
agdata:




6 changes: 4 additions & 2 deletions goo.gemspec
Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,12 @@ Gem::Specification.new do |s|
s.email = "[email protected]"
s.files = Dir["lib/**/*.rb"]
s.homepage = "http://github.com/ncbo/goo"

s.add_dependency("addressable", "~> 2.8")
s.add_dependency("pry")
s.add_dependency("rdf", "= 1.0.8")
s.add_dependency("rdf", "3.2.11") #unpin when we support only Ruby >= 3.0
s.add_dependency("rdf-vocab")
s.add_dependency("rdf-rdfxml")
s.add_dependency("rdf-raptor")
s.add_dependency("redis")
s.add_dependency("rest-client")
s.add_dependency("rsolr")
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