Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix remote pull ontology process for zipped submissions #55

Open
wants to merge 12 commits into
base: develop
Choose a base branch
from
Open
Prev Previous commit
Next Next commit
use the pl/enhance-zipped-submissions-support branch to pass tests
syphax-bouazzouni committed Sep 21, 2023
commit 2f3f4cbf71c09728c21198d184b42f0f56582d98
3 changes: 1 addition & 2 deletions Gemfile
Original file line number Diff line number Diff line change
@@ -24,8 +24,7 @@ gem 'cube-ruby', require: 'cube'

gem 'goo', github: 'ncbo/goo', branch: 'master'
gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
gem 'ncbo_resource_index', github: 'ncbo/resource_index'
gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pl/enhance-zipped-submissions-support'
gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'

# Testing
157 changes: 65 additions & 92 deletions Gemfile.lock
Original file line number Diff line number Diff line change
@@ -1,22 +1,21 @@
GIT
remote: https://github.com/ncbo/goo.git
revision: a66e3e2b61e9caeed7cd05d3047d2df7c1254f4c
revision: daea7822af9e5ca1961d6873a758735133a1b2db
branch: master
specs:
goo (0.0.2)
addressable (= 2.3.5)
addressable (~> 2.8)
pry
rdf (= 1.0.8)
redis
rest-client
rsolr
sparql-client
systemu
uuid

GIT
remote: https://github.com/ncbo/ncbo_annotator.git
revision: f2e5d3d39caefee65078d808872ef5f785808bda
revision: 04226ac5840a328e6f906f15c769ee6ee5723102
branch: master
specs:
ncbo_annotator (0.0.1)
@@ -26,9 +25,19 @@ GIT
ruby-xxHash

GIT
remote: https://github.com/ncbo/ontologies_linked_data.git
revision: f3532d2c8bab45887b5d20f80d5e892487e78cdd
remote: https://github.com/ncbo/sparql-client.git
revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
branch: master
specs:
sparql-client (1.0.1)
json_pure (>= 1.4)
net-http-persistent (= 2.9.4)
rdf (>= 1.0)

GIT
remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
revision: 299a01cf90d7588292255d240899e9716ef7be30
branch: pl/enhance-zipped-submissions-support
specs:
ontologies_linked_data (0.0.1)
activesupport
@@ -37,7 +46,6 @@ GIT
json
libxml-ruby
multi_json
ncbo_resource_index
oj
omni_logger
pony
@@ -46,29 +54,6 @@ GIT
rsolr
rubyzip

GIT
remote: https://github.com/ncbo/resource_index.git
revision: 24a7f14a6da4f4a0eaba1016ca5a378dfccd7441
specs:
ncbo_resource_index (0.0.1)
elasticsearch (= 2.0.0)
mysql2 (= 0.5.2)
pony
ref
ruby-xxHash
sequel
typhoeus

GIT
remote: https://github.com/ncbo/sparql-client.git
revision: fb4a89b420f8eb6dda5190a126b6c62e32c4c0c9
branch: master
specs:
sparql-client (1.0.1)
json_pure (>= 1.4)
net-http-persistent (= 2.9.4)
rdf (>= 1.0)

PATH
remote: .
specs:
@@ -86,37 +71,26 @@ PATH
GEM
remote: https://rubygems.org/
specs:
activesupport (4.0.13)
i18n (~> 0.6, >= 0.6.9)
minitest (~> 4.2)
multi_json (~> 1.3)
thread_safe (~> 0.1)
tzinfo (~> 0.3.37)
addressable (2.3.5)
bcrypt (3.1.16)
activesupport (3.2.22.5)
i18n (~> 0.6, >= 0.6.4)
multi_json (~> 1.0)
addressable (2.8.5)
public_suffix (>= 2.0.2, < 6.0)
bcrypt (3.1.19)
builder (3.2.4)
coderay (1.1.3)
concurrent-ruby (1.1.9)
concurrent-ruby (1.2.2)
connection_pool (2.4.1)
cube-ruby (0.0.3)
dante (0.2.0)
declarative (0.0.20)
domain_name (0.5.20190701)
unf (>= 0.0.5, < 1.0.0)
elasticsearch (2.0.0)
elasticsearch-api (= 2.0.0)
elasticsearch-transport (= 2.0.0)
elasticsearch-api (2.0.0)
multi_json
elasticsearch-transport (2.0.0)
faraday
multi_json
email_spec (2.1.1)
htmlentities (~> 4.3.3)
launchy (~> 2.1)
mail (~> 2.6)
ethon (0.15.0)
ffi (>= 1.15.0)
faraday (1.10.0)
faraday (1.10.3)
faraday-em_http (~> 1.0)
faraday-em_synchrony (~> 1.0)
faraday-excon (~> 1.1)
@@ -132,23 +106,23 @@ GEM
faraday-em_synchrony (1.0.0)
faraday-excon (1.1.0)
faraday-httpclient (1.0.1)
faraday-multipart (1.0.3)
multipart-post (>= 1.2, < 3)
faraday-multipart (1.0.4)
multipart-post (~> 2)
faraday-net_http (1.0.1)
faraday-net_http_persistent (1.2.0)
faraday-patron (1.0.0)
faraday-rack (1.0.0)
faraday-retry (1.0.3)
ffi (1.15.5)
google-api-client (0.10.3)
addressable (~> 2.3)
googleauth (~> 0.5)
httpclient (~> 2.7)
hurley (~> 0.1)
memoist (~> 0.11)
mime-types (>= 1.6)
google-api-client (0.52.0)
addressable (~> 2.5, >= 2.5.1)
googleauth (~> 0.9)
httpclient (>= 2.8.1, < 3.0)
mini_mime (~> 1.0)
representable (~> 3.0)
retriable (>= 2.0, < 4.0)
rexml
signet (~> 0.12)
googleauth (0.17.1)
faraday (>= 0.17.3, < 2.0)
jwt (>= 1.4, < 3.0)
@@ -158,34 +132,33 @@ GEM
signet (~> 0.15)
htmlentities (4.3.4)
http-accept (1.7.0)
http-cookie (1.0.4)
http-cookie (1.0.5)
domain_name (~> 0.5)
httpclient (2.8.3)
hurley (0.2)
i18n (0.9.5)
concurrent-ruby (~> 1.0)
json (2.6.1)
json_pure (2.6.1)
jwt (2.3.0)
launchy (2.4.3)
addressable (~> 2.3)
libxml-ruby (3.2.2)
logger (1.5.0)
json (2.6.3)
json_pure (2.6.3)
jwt (2.7.1)
launchy (2.5.2)
addressable (~> 2.8)
libxml-ruby (4.1.1)
logger (1.5.3)
macaddr (1.7.2)
systemu (~> 2.6.5)
mail (2.6.6)
mime-types (>= 1.16, < 4)
memoist (0.16.2)
method_source (1.0.0)
mime-types (3.4.1)
mime-types (3.5.1)
mime-types-data (~> 3.2015)
mime-types-data (3.2022.0105)
mime-types-data (3.2023.0808)
mini_mime (1.1.5)
minitest (4.7.5)
mlanett-redis-lock (0.2.7)
redis
multi_json (1.15.0)
multipart-post (2.1.1)
mysql2 (0.5.2)
multipart-post (2.3.0)
net-http-persistent (2.9.4)
netrc (0.11.0)
oj (2.18.5)
@@ -195,18 +168,21 @@ GEM
parseconfig (1.1.2)
pony (1.13.1)
mail (>= 2.0)
pry (0.14.1)
pry (0.14.2)
coderay (~> 1.1)
method_source (~> 1.0)
rack (2.2.3)
rack-test (1.1.0)
rack (>= 1.0, < 3)
public_suffix (5.0.3)
rack (3.0.8)
rack-test (2.1.0)
rack (>= 1.3)
rake (13.0.6)
rdf (1.0.8)
addressable (>= 2.2)
redis (4.6.0)
ref (2.0.0)
representable (3.1.1)
redis (5.0.7)
redis-client (>= 0.9.0)
redis-client (0.17.0)
connection_pool
representable (3.2.0)
declarative (< 0.1.0)
trailblazer-option (>= 0.1.1, < 0.2.0)
uber (< 0.2.0)
@@ -216,6 +192,7 @@ GEM
mime-types (>= 1.16, < 4.0)
netrc (~> 0.8)
retriable (3.1.2)
rexml (3.2.6)
rsolr (2.5.0)
builder (>= 2.1.2)
faraday (>= 0.9, < 3, != 2.0.0)
@@ -224,26 +201,23 @@ GEM
rubyzip (2.3.2)
rufus-scheduler (2.0.24)
tzinfo (>= 0.3.22)
sequel (5.54.0)
signet (0.15.0)
addressable (~> 2.3)
faraday (>= 0.17.3, < 2.0)
signet (0.18.0)
addressable (~> 2.8)
faraday (>= 0.17.5, < 3.a)
jwt (>= 1.5, < 3.0)
multi_json (~> 1.10)
sys-proctable (1.2.6)
ffi
sys-proctable (1.3.0)
ffi (~> 1.1)
systemu (2.6.5)
test-unit-minitest (0.9.1)
minitest (~> 4.7)
thread_safe (0.3.6)
trailblazer-option (0.1.2)
typhoeus (1.4.0)
ethon (>= 0.9.0)
tzinfo (0.3.60)
tzinfo (2.0.6)
concurrent-ruby (~> 1.0)
uber (0.1.0)
unf (0.1.4)
unf_ext
unf_ext (0.0.8)
unf_ext (0.0.8.2)
uuid (2.3.9)
macaddr (~> 1.0)

@@ -263,7 +237,6 @@ DEPENDENCIES
multi_json
ncbo_annotator!
ncbo_cron!
ncbo_resource_index!
oj (~> 2.0)
ontologies_linked_data!
parseconfig
@@ -277,4 +250,4 @@ DEPENDENCIES
test-unit-minitest

BUNDLED WITH
2.1.4
2.3.15