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Merged
alexskr merged 4 commits into from
Oct 28, 2025
Merged

Sync: ncbo v6.7.0 release #28

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a406952
add url datatype for attributes that should be restricted to HTTP/HTTPS
alexskr Aug 29, 2025
9cae83d
Merge pull request #258 from ncbo/chore/set_url_type
alexskr Aug 29, 2025
0bc976c
Merge pull request #259 from ncbo/develop
alexskr Oct 27, 2025
1a6d426
reset branch specifier to master
alexskr Oct 27, 2025
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2 changes: 1 addition & 1 deletion Gemfile
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Expand Up @@ -18,7 +18,7 @@ gem 'request_store'
gem 'rest-client'
gem 'rsolr'
gem 'thin', '~> 1.0' # compatibility version pin. thin should be replaced with webmoc

gem "down", "~> 5.0"

# Testing
group :test do
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23 changes: 13 additions & 10 deletions Gemfile.lock
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@@ -1,6 +1,6 @@
GIT
remote: https://github.com/ncbo/goo.git
revision: 26c0a69e67ac59778a46caf51202ebd38ccac767
revision: 5cac44e06a6bf0c093563dad66240ab07fec4d9c
branch: master
specs:
goo (0.0.2)
Expand Down Expand Up @@ -63,18 +63,20 @@ GEM
logger (~> 1.5)
coderay (1.1.3)
concurrent-ruby (1.3.5)
connection_pool (2.5.3)
connection_pool (2.5.4)
cube-ruby (0.0.3)
daemons (1.4.1)
date (3.4.1)
docile (1.4.1)
domain_name (0.6.20240107)
down (5.4.2)
addressable (~> 2.8)
email_spec (2.3.0)
htmlentities (~> 4.3.3)
launchy (>= 2.1, < 4.0)
mail (~> 2.7)
eventmachine (1.2.7)
faraday (2.13.4)
faraday (2.14.0)
faraday-net_http (>= 2.0, < 3.5)
json
logger
Expand All @@ -86,11 +88,11 @@ GEM
hashie (5.0.0)
htmlentities (4.3.4)
http-accept (1.7.0)
http-cookie (1.0.8)
http-cookie (1.1.0)
domain_name (~> 0.5)
i18n (0.9.5)
concurrent-ruby (~> 1.0)
json (2.13.2)
json (2.15.2)
json_pure (2.8.1)
language_server-protocol (3.17.0.5)
launchy (3.1.1)
Expand All @@ -111,7 +113,7 @@ GEM
mime-types (3.7.0)
logger
mime-types-data (~> 3.2025, >= 3.2025.0507)
mime-types-data (3.2025.0819)
mime-types-data (3.2025.0924)
mini_mime (1.1.5)
minitest (4.7.5)
minitest-reporters (0.14.24)
Expand Down Expand Up @@ -160,7 +162,7 @@ GEM
method_source (~> 1.0)
public_suffix (5.1.1)
racc (1.8.1)
rack (2.2.17)
rack (2.2.20)
rack-test (0.8.3)
rack (>= 1.0, < 3)
rainbow (3.1.1)
Expand All @@ -169,7 +171,7 @@ GEM
addressable (>= 2.2)
redis (5.4.1)
redis-client (>= 0.22.0)
redis-client (0.25.2)
redis-client (0.26.1)
connection_pool
regexp_parser (2.11.2)
request_store (1.7.0)
Expand Down Expand Up @@ -199,7 +201,7 @@ GEM
prism (~> 1.4)
ruby-progressbar (1.13.0)
ruby2_keywords (0.0.5)
rubyzip (3.0.1)
rubyzip (3.0.2)
simplecov (0.22.0)
docile (~> 1.1)
simplecov-html (~> 0.11)
Expand All @@ -222,7 +224,7 @@ GEM
unicode-display_width (3.1.5)
unicode-emoji (~> 4.0, >= 4.0.4)
unicode-emoji (4.0.4)
uri (1.0.3)
uri (1.0.4)
uuid (2.3.9)
macaddr (~> 1.0)

Expand All @@ -238,6 +240,7 @@ DEPENDENCIES
addressable (~> 2.8)
bcrypt (~> 3.0)
cube-ruby
down (~> 5.0)
email_spec
ffi
goo!
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12 changes: 4 additions & 8 deletions lib/ontologies_linked_data/models/ontology_submission.rb
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Expand Up @@ -3,7 +3,7 @@
require 'uri'
require 'open-uri'
require 'cgi'
require 'benchmark'
# require 'benchmark'
require 'csv'
require 'fileutils'

Expand Down Expand Up @@ -59,12 +59,8 @@ class OntologySubmission < LinkedData::Models::Base
# Description metadata
attribute :description, namespace: :omv, enforce: %i[concatenate], fuzzy_search: true

# attribute :homepage
# attribute :documentation, namespace: :omv
# attribute :publication
# attribute :uri, namespace: :omv
attribute :homepage, namespace: :foaf, type: :uri
attribute :documentation, namespace: :omv, type: :uri
attribute :homepage, namespace: :foaf, type: :url
attribute :documentation, namespace: :omv, type: :url
attribute :publication, type: %i[uri list]
attribute :uri, namespace: :omv, type: :uri, enforce: %i[distinct_of_identifier], fuzzy_search: true

Expand Down Expand Up @@ -124,7 +120,7 @@ class OntologySubmission < LinkedData::Models::Base
attribute :wasInvalidatedBy, namespace: :prov, type: :list

# Links
attribute :pullLocation, type: :uri # URI for pulling ontology
attribute :pullLocation, type: :url # URL for pulling ontology
attribute :isFormatOf, namespace: :dct, type: :uri
attribute :hasFormat, namespace: :dct, type: %i[uri list]
attribute :dataDump, namespace: :void, type: :uri, default: -> (s) { data_dump_default(s) }
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2 changes: 1 addition & 1 deletion lib/ontologies_linked_data/models/project.rb
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Expand Up @@ -7,7 +7,7 @@ class Project < LinkedData::Models::Base
attribute :created, enforce: [:date_time], :default => lambda {|x| DateTime.now }
attribute :updated, enforce: [:date_time], :default => lambda {|x| DateTime.now }
attribute :name, enforce: [:existence, :safe_text_256]
attribute :homePage, enforce: [:uri, :existence]
attribute :homePage, enforce: [:url, :existence]
attribute :description, enforce: [:existence, :safe_text]
attribute :contacts, enforce: [:safe_text_256]
attribute :institution, enforce: [:safe_text_256]
Expand Down