colrapi 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 9159517b23fc36d214d6e0c1fc611c15d027c2dc58409c859f8c3486728305526d2ec1508c564ebc7ad6bc1bf21e047d989ea08dce8346bdecbee15c05b34ca9

data/.github/workflows/main.yml

@@ -10,7 +10,7 @@ jobs:
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:
-        ruby-version: 3.1.3
+        ruby-version: 3.3.4
         bundler-cache: true
     - name: Run the default task
       run: bundle exec rake

data/.gitignore

@@ -8,4 +8,5 @@
 /pkg/
 /spec/reports/
 /tmp/
-*.gem
+*.gem
+Gemfile.lock

data/CHANGELOG.md

@@ -1,5 +1,10 @@
 ## [Unreleased]
 
+## [0.1.2] - 2024-09-11
+ - Removed Gemfile.lock
+ - Bumped development depency versions to avoid CVE-2024-43398
+ - Added attempt param to archive endpoint
+
 ## [0.1.1] - 2023-04-17
 - Updated Faraday version
 

data/README.md

@@ -29,7 +29,7 @@ In development, this is it for now:
 
 After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
 
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, update the `CHANGELOG.md`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
 
 ## Contributing
 

data/colrapi.gemspec

@@ -12,7 +12,7 @@ Gem::Specification.new do |s|
   s.description   = "colrapi (a play on Kholrabi) is a low-level wrapper around the Catalog of Life API."
   s.homepage      = "https://github.com/SpeciesFileGroup/colrapi"
   s.license       = "NCSA"
-  s.required_ruby_version = ">= 2.4.0"
+  s.required_ruby_version = ">= 2.5.0"
 
  # s.metadata["allowed_push_host"] = "TODO: Set to 'https://mygemserver.com'"
 
@@ -33,22 +33,16 @@ Gem::Specification.new do |s|
   # s.add_dependency "example-gem", "~> 1.0"
 
   s.add_development_dependency "bundler", "~> 2.1", ">= 2.1.4"
-  # s.add_development_dependency "codecov", "~> 0.5.0"
-  # s.add_development_dependency "json", "~> 2.3", ">= 2.3.1"
   s.add_development_dependency "rake", "~> 13.0", ">= 13.0.1"
-  # s.add_development_dependency "standard", "~> 1.0"
-  # s.add_development_dependency "simplecov", "~> 0.21.2"
   s.add_development_dependency "test-unit", "~> 3.3", ">= 3.3.6"
   s.add_development_dependency "vcr", "~> 6.0"
   s.add_development_dependency "webmock", "~> 3.18"
+  s.add_development_dependency "rexml", "~> 3.3", ">= 3.3.6"
 
   s.add_runtime_dependency "faraday", "~> 2.2"
   s.add_runtime_dependency "faraday-follow_redirects", ">= 0.1", "< 0.4"
   s.add_runtime_dependency "multi_json", "~> 1.15"
 
-  # TODO: comment out
-  s.add_development_dependency "byebug"
-
   #  s.add_runtime_dependency "thor", "~> 1.0", ">= 1.0.1"
 
   # For more information and examples about making a new gem, checkout our

data/lib/colrapi/request.rb

@@ -17,6 +17,7 @@ module Colrapi
       @url = args[:url]
       @q = Array(args[:q]) if args[:q]
       @id = args[:id]
+      @attempt = args[:attempt]
       @format = args[:format]
       @regexp = args[:regexp]
       @content = Array(args[:content]) if args[:content]
@@ -108,7 +109,7 @@ module Colrapi
 
     def perform
 
-      args = { q: @q, regex: @regexp, content: @content, name: @name, authorship: @authorship, code: @code, type: @type,
+      args = { q: @q, regex: @regexp, attempt: @attempt, content: @content, name: @name, authorship: @authorship, code: @code, type: @type,
                rank: @rank, minRank: @min_rank, maxRank: @max_rank, parentRank: @parent_rank, projectKey: @project_id,
                term: @term, termOp: @term_operator, status: @status, decisionMode: @decision_mode,
                alias: @short_title, private: @private, releasedFrom: @released_from, contributesTo: @contributes_to,

data/lib/colrapi/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Colrapi
-  VERSION = "0.1.1"
+  VERSION = "0.1.2"
 end

data/lib/colrapi.rb

@@ -25,11 +25,12 @@ module Colrapi
   # Get a dataset's original archive
   #
   # @param dataset_id [String] The dataset id
+  # @param attempt [Integer] Returns archive for a past import attempt number
   #
   # @return [Binary] An archive of the original dataset
-  def self.archive(dataset_id, verbose: false)
+  def self.archive(dataset_id, attempt: nil, verbose: false)
     endpoint = "dataset/#{dataset_id}/archive"
-    Request.new(endpoint: endpoint, verbose: verbose).perform
+    Request.new(endpoint: endpoint, attempt: attempt, verbose: verbose).perform
   end
 
   # Get dataset metadata

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: colrapi
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - Matt Yoder, Geoff Ower
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2023-04-17 00:00:00.000000000 Z
+date: 2024-10-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -98,6 +98,26 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.18'
+- !ruby/object:Gem::Dependency
+  name: rexml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.3.6
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.3.6
 - !ruby/object:Gem::Dependency
   name: faraday
   requirement: !ruby/object:Gem::Requirement
@@ -146,20 +166,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.15'
-- !ruby/object:Gem::Dependency
-  name: byebug
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
 description: colrapi (a play on Kholrabi) is a low-level wrapper around the Catalog
   of Life API.
 email:
@@ -173,7 +179,6 @@ files:
 - CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
-- Gemfile.lock
 - LICENSE.txt
 - README.md
 - Rakefile
@@ -193,7 +198,7 @@ licenses:
 metadata:
   homepage_uri: https://github.com/SpeciesFileGroup/colrapi
   source_code_uri: https://github.com/SpeciesFileGroup/colrapi
-  changelog_uri: https://github.com/SpeciesFileGroup/colrapi/releases/tag/v0.1.1
+  changelog_uri: https://github.com/SpeciesFileGroup/colrapi/releases/tag/v0.1.2
 post_install_message:
 rdoc_options: []
 require_paths:
@@ -202,14 +207,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.4.0
+      version: 2.5.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.10
+rubygems_version: 3.5.11
 signing_key:
 specification_version: 4
 summary: Catalog of Life Client

data/Gemfile.lock

@@ -1,55 +0,0 @@
-PATH
-  remote: .
-  specs:
-    colrapi (0.1.1)
-      faraday (~> 2.2)
-      faraday-follow_redirects (>= 0.1, < 0.4)
-      multi_json (~> 1.15)
-
-GEM
-  remote: https://rubygems.org/
-  specs:
-    addressable (2.8.1)
-      public_suffix (>= 2.0.2, < 6.0)
-    byebug (11.1.3)
-    crack (0.4.5)
-      rexml
-    faraday (2.7.4)
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
-    faraday-follow_redirects (0.3.0)
-      faraday (>= 1, < 3)
-    faraday-net_http (3.0.2)
-    hashdiff (1.0.1)
-    minitest (5.15.0)
-    multi_json (1.15.0)
-    power_assert (2.0.1)
-    public_suffix (5.0.1)
-    rake (13.0.6)
-    rexml (3.2.5)
-    ruby2_keywords (0.0.5)
-    rubyzip (2.3.2)
-    test-unit (3.5.3)
-      power_assert
-    vcr (6.0.0)
-    webmock (3.18.1)
-      addressable (>= 2.8.0)
-      crack (>= 0.3.2)
-      hashdiff (>= 0.4.0, < 2.0.0)
-
-PLATFORMS
-  x86_64-linux
-
-DEPENDENCIES
-  bundler (~> 2.1, >= 2.1.4)
-  byebug
-  colrapi!
-  minitest (~> 5.0)
-  rake (~> 13.0)
-  rubyzip
-  test-unit (~> 3.3, >= 3.3.6)
-  vcr (~> 6.0)
-  webmock (~> 3.18)
-
-BUNDLED WITH
-   2.3.24