cheminee 0.1.18 → 0.1.21

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Files changed (36) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +9 -9
  3. data/README.md +5 -4
  4. data/cheminee.gemspec +1 -1
  5. data/docs/DefaultApi.md +11 -5
  6. data/docs/QuerySearchHit.md +1 -1
  7. data/docs/StructureSearchHit.md +1 -1
  8. data/lib/cheminee/api/default_api.rb +7 -1
  9. data/lib/cheminee/api_client.rb +3 -3
  10. data/lib/cheminee/api_error.rb +1 -1
  11. data/lib/cheminee/configuration.rb +11 -1
  12. data/lib/cheminee/models/bulk_request.rb +1 -1
  13. data/lib/cheminee/models/bulk_request_doc.rb +1 -1
  14. data/lib/cheminee/models/converted_smiles.rb +1 -1
  15. data/lib/cheminee/models/create_index_error.rb +1 -1
  16. data/lib/cheminee/models/get_indexes_response_error.rb +1 -1
  17. data/lib/cheminee/models/index_meta.rb +1 -1
  18. data/lib/cheminee/models/index_schema.rb +1 -1
  19. data/lib/cheminee/models/list_index_response_err.rb +1 -1
  20. data/lib/cheminee/models/mol_block.rb +1 -1
  21. data/lib/cheminee/models/post_index_bulk_response_error.rb +1 -1
  22. data/lib/cheminee/models/post_index_bulk_response_ok.rb +1 -1
  23. data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +1 -1
  24. data/lib/cheminee/models/query_response_error.rb +1 -1
  25. data/lib/cheminee/models/query_search_hit.rb +7 -3
  26. data/lib/cheminee/models/schema.rb +1 -1
  27. data/lib/cheminee/models/smiles.rb +1 -1
  28. data/lib/cheminee/models/standardized_smiles.rb +1 -1
  29. data/lib/cheminee/models/structure_response_error.rb +1 -1
  30. data/lib/cheminee/models/structure_search_hit.rb +7 -3
  31. data/lib/cheminee/version.rb +2 -2
  32. data/lib/cheminee.rb +1 -1
  33. data/pkg/cheminee-0.1.21.gem +0 -0
  34. data/spec/spec_helper.rb +1 -1
  35. metadata +17 -17
  36. data/pkg/cheminee-0.1.18.gem +0 -0
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/Gemfile.lock CHANGED
@@ -1,7 +1,7 @@
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  PATH
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  remote: .
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  specs:
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- cheminee (0.1.18)
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+ cheminee (0.1.21)
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  typhoeus (~> 1.0, >= 1.0.1)
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  GEM
@@ -13,11 +13,11 @@ GEM
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  diff-lcs (1.5.1)
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  ethon (0.16.0)
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  ffi (>= 1.15.0)
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- ffi (1.16.3)
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+ ffi (1.17.0-x86_64-linux-gnu)
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  jaro_winkler (1.5.6)
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- method_source (1.0.0)
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- parallel (1.24.0)
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- parser (3.3.0.5)
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+ method_source (1.1.0)
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+ parallel (1.25.1)
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+ parser (3.3.3.0)
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  ast (~> 2.4.1)
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  racc
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  pry (0.14.2)
@@ -28,7 +28,7 @@ GEM
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  pry (>= 0.13, < 0.15)
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  psych (5.1.2)
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  stringio
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- racc (1.7.3)
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+ racc (1.8.0)
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  rainbow (3.1.1)
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  rake (13.0.6)
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  rspec (3.13.0)
@@ -37,10 +37,10 @@ GEM
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  rspec-mocks (~> 3.13.0)
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  rspec-core (3.13.0)
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  rspec-support (~> 3.13.0)
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- rspec-expectations (3.13.0)
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+ rspec-expectations (3.13.1)
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  diff-lcs (>= 1.2.0, < 2.0)
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  rspec-support (~> 3.13.0)
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- rspec-mocks (3.13.0)
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+ rspec-mocks (3.13.1)
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  diff-lcs (>= 1.2.0, < 2.0)
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  rspec-support (~> 3.13.0)
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  rspec-support (3.13.1)
@@ -53,7 +53,7 @@ GEM
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  ruby-progressbar (~> 1.7)
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  unicode-display_width (>= 1.4.0, < 1.6)
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  ruby-progressbar (1.13.0)
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- stringio (3.1.0)
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+ stringio (3.1.1)
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  typhoeus (1.4.1)
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  ethon (>= 0.9.0)
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  unicode-display_width (1.5.0)
data/README.md CHANGED
@@ -7,7 +7,8 @@ Cheminée: The Chemical Structure Search Engine
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  This SDK is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
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  - API version: 1.0
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- - Package version: 0.1.18
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+ - Package version: 0.1.21
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+ - Generator version: 7.8.0-SNAPSHOT
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  - Build package: org.openapitools.codegen.languages.RubyClientCodegen
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  For more information, please visit [https://github.com/rdkit-rs/cheminee](https://github.com/rdkit-rs/cheminee)
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@@ -24,16 +25,16 @@ gem build cheminee.gemspec
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  Then either install the gem locally:
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  ```shell
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- gem install ./cheminee-0.1.18.gem
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+ gem install ./cheminee-0.1.21.gem
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  ```
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- (for development, run `gem install --dev ./cheminee-0.1.18.gem` to install the development dependencies)
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+ (for development, run `gem install --dev ./cheminee-0.1.21.gem` to install the development dependencies)
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  or publish the gem to a gem hosting service, e.g. [RubyGems](https://rubygems.org/).
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  Finally add this to the Gemfile:
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- gem 'cheminee', '~> 0.1.18'
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+ gem 'cheminee', '~> 0.1.21'
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  ### Install from Git
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data/cheminee.gemspec CHANGED
@@ -8,7 +8,7 @@
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  The version of the OpenAPI document: 1.0
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  Generated by: https://openapi-generator.tech
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- OpenAPI Generator version: 7.4.0-SNAPSHOT
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+ Generator version: 7.8.0-SNAPSHOT
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  =end
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data/docs/DefaultApi.md CHANGED
@@ -418,7 +418,8 @@ smiles = 'smiles_example' # String |
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  opts = {
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  result_limit: 56, # Integer |
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  tautomer_limit: 56, # Integer |
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- extra_query: 'extra_query_example' # String |
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+ extra_query: 'extra_query_example', # String |
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+ use_scaffolds: 'use_scaffolds_example' # String |
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  }
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  begin
@@ -457,6 +458,7 @@ end
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  | **result_limit** | **Integer** | | [optional] |
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  | **tautomer_limit** | **Integer** | | [optional] |
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  | **extra_query** | **String** | | [optional] |
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+ | **use_scaffolds** | **String** | | [optional] |
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  ### Return type
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@@ -533,7 +535,7 @@ No authorization required
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  ## v1_standardize_post
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- > <Array<StandardizedSmiles>> v1_standardize_post(smiles)
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+ > <Array<StandardizedSmiles>> v1_standardize_post(smiles, opts)
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  Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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@@ -545,10 +547,13 @@ require 'cheminee'
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  api_instance = Cheminee::DefaultApi.new
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  smiles = [Cheminee::Smiles.new({smiles: 'smiles_example'})] # Array<Smiles> |
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+ opts = {
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+ attempt_fix: 'attempt_fix_example' # String |
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+ }
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  begin
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  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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- result = api_instance.v1_standardize_post(smiles)
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+ result = api_instance.v1_standardize_post(smiles, opts)
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  p result
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  rescue Cheminee::ApiError => e
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  puts "Error when calling DefaultApi->v1_standardize_post: #{e}"
@@ -559,12 +564,12 @@ end
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  This returns an Array which contains the response data, status code and headers.
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- > <Array(<Array<StandardizedSmiles>>, Integer, Hash)> v1_standardize_post_with_http_info(smiles)
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+ > <Array(<Array<StandardizedSmiles>>, Integer, Hash)> v1_standardize_post_with_http_info(smiles, opts)
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  ```ruby
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  begin
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  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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- data, status_code, headers = api_instance.v1_standardize_post_with_http_info(smiles)
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+ data, status_code, headers = api_instance.v1_standardize_post_with_http_info(smiles, opts)
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  p status_code # => 2xx
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  p headers # => { ... }
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  p data # => <Array<StandardizedSmiles>>
@@ -578,6 +583,7 @@ end
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  | Name | Type | Description | Notes |
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  | ---- | ---- | ----------- | ----- |
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  | **smiles** | [**Array&lt;Smiles&gt;**](Smiles.md) | | |
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+ | **attempt_fix** | **String** | | [optional] |
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  ### Return type
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@@ -4,7 +4,7 @@
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  | Name | Type | Description | Notes |
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- | **extra_data** | **Object** | | |
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+ | **extra_data** | **String** | | |
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  | **smiles** | **String** | | |
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  | **query** | **String** | | |
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  | Name | Type | Description | Notes |
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- | **extra_data** | **Object** | | |
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  | **smiles** | **String** | | |
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  | **score** | **Float** | | |
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  | **query** | **String** | | |
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  The version of the OpenAPI document: 1.0
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  Generated by: https://openapi-generator.tech
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- OpenAPI Generator version: 7.4.0-SNAPSHOT
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+ Generator version: 7.8.0-SNAPSHOT
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@@ -429,6 +429,7 @@ module Cheminee
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  # @option opts [Integer] :result_limit
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  # @option opts [Integer] :tautomer_limit
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  # @option opts [String] :extra_query
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+ # @option opts [String] :use_scaffolds
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  # @return [Array<StructureSearchHit>]
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  def v1_indexes_index_search_substructure_get(index, smiles, opts = {})
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  data, _status_code, _headers = v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts)
@@ -442,6 +443,7 @@ module Cheminee
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  # @option opts [Integer] :result_limit
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  # @option opts [Integer] :tautomer_limit
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  # @option opts [String] :extra_query
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+ # @option opts [String] :use_scaffolds
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  # @return [Array<(Array<StructureSearchHit>, Integer, Hash)>] Array<StructureSearchHit> data, response status code and response headers
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  def v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts = {})
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  if @api_client.config.debugging
@@ -464,6 +466,7 @@ module Cheminee
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  query_params[:'result_limit'] = opts[:'result_limit'] if !opts[:'result_limit'].nil?
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  query_params[:'tautomer_limit'] = opts[:'tautomer_limit'] if !opts[:'tautomer_limit'].nil?
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  query_params[:'extra_query'] = opts[:'extra_query'] if !opts[:'extra_query'].nil?
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+ query_params[:'use_scaffolds'] = opts[:'use_scaffolds'] if !opts[:'use_scaffolds'].nil?
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  # header parameters
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@@ -557,6 +560,7 @@ module Cheminee
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  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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  # @param [Hash] opts the optional parameters
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+ # @option opts [String] :attempt_fix
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  # @return [Array<StandardizedSmiles>]
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  def v1_standardize_post(smiles, opts = {})
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  data, _status_code, _headers = v1_standardize_post_with_http_info(smiles, opts)
@@ -566,6 +570,7 @@ module Cheminee
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  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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  # @param smiles [Array<Smiles>]
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  # @param [Hash] opts the optional parameters
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+ # @option opts [String] :attempt_fix
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  # @return [Array<(Array<StandardizedSmiles>, Integer, Hash)>] Array<StandardizedSmiles> data, response status code and response headers
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  def v1_standardize_post_with_http_info(smiles, opts = {})
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  if @api_client.config.debugging
@@ -580,6 +585,7 @@ module Cheminee
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  # query parameters
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+ query_params[:'attempt_fix'] = opts[:'attempt_fix'] if !opts[:'attempt_fix'].nil?
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  # @param [String] mime MIME
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  end
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  # @return [String] the sanitized filename
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293
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  end
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  # @return [true, false]
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  attr_accessor :debugging
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+ # Set this to ignore operation servers for the API client. This is useful when you need to
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+ # send requests to a different server than the one specified in the OpenAPI document.
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+ # Will default to the base url defined in the spec but can be overridden by setting
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+ # `scheme`, `host`, `base_path` directly.
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+ # Default to false.
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+ # @return [true, false]
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+ attr_accessor :ignore_operation_servers
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@@ -166,6 +174,7 @@ module Cheminee
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  @timeout = 0
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  @debugging = false
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+ @ignore_operation_servers = false
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  @inject_format = false
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  @force_ending_format = false
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  @logger = defined?(Rails) ? Rails.logger : Logger.new(STDOUT)
@@ -200,6 +209,7 @@ module Cheminee
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  # Returns base URL for specified operation based on server settings
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  def base_url(operation = nil)
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+ return "#{scheme}://#{[host, base_path].join('/').gsub(/\/+/, '/')}".sub(/\/+\z/, '') if ignore_operation_servers
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  if operation_server_settings.key?(operation) then
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  index = server_operation_index.fetch(operation, server_index)
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  server_url(index.nil? ? 0 : index, server_operation_variables.fetch(operation, server_variables), operation_server_settings[operation])
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  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -38,7 +38,7 @@ module Cheminee
38
38
  # Attribute type mapping.
39
39
  def self.openapi_types
40
40
  {
41
- :'extra_data' => :'Object',
41
+ :'extra_data' => :'String',
42
42
  :'smiles' => :'String',
43
43
  :'query' => :'String'
44
44
  }
@@ -47,7 +47,6 @@ module Cheminee
47
47
  # List of attributes with nullable: true
48
48
  def self.openapi_nullable
49
49
  Set.new([
50
- :'extra_data',
51
50
  ])
52
51
  end
53
52
 
@@ -90,6 +89,10 @@ module Cheminee
90
89
  def list_invalid_properties
91
90
  warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
92
91
  invalid_properties = Array.new
92
+ if @extra_data.nil?
93
+ invalid_properties.push('invalid value for "extra_data", extra_data cannot be nil.')
94
+ end
95
+
93
96
  if @smiles.nil?
94
97
  invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
95
98
  end
@@ -105,6 +108,7 @@ module Cheminee
105
108
  # @return true if the model is valid
106
109
  def valid?
107
110
  warn '[DEPRECATED] the `valid?` method is obsolete'
111
+ return false if @extra_data.nil?
108
112
  return false if @smiles.nil?
109
113
  return false if @query.nil?
110
114
  true
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -44,7 +44,7 @@ module Cheminee
44
44
  # Attribute type mapping.
45
45
  def self.openapi_types
46
46
  {
47
- :'extra_data' => :'Object',
47
+ :'extra_data' => :'String',
48
48
  :'smiles' => :'String',
49
49
  :'score' => :'Float',
50
50
  :'query' => :'String',
@@ -55,7 +55,6 @@ module Cheminee
55
55
  # List of attributes with nullable: true
56
56
  def self.openapi_nullable
57
57
  Set.new([
58
- :'extra_data',
59
58
  ])
60
59
  end
61
60
 
@@ -110,6 +109,10 @@ module Cheminee
110
109
  def list_invalid_properties
111
110
  warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
112
111
  invalid_properties = Array.new
112
+ if @extra_data.nil?
113
+ invalid_properties.push('invalid value for "extra_data", extra_data cannot be nil.')
114
+ end
115
+
113
116
  if @smiles.nil?
114
117
  invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
115
118
  end
@@ -133,6 +136,7 @@ module Cheminee
133
136
  # @return true if the model is valid
134
137
  def valid?
135
138
  warn '[DEPRECATED] the `valid?` method is obsolete'
139
+ return false if @extra_data.nil?
136
140
  return false if @smiles.nil?
137
141
  return false if @score.nil?
138
142
  return false if @query.nil?
@@ -6,10 +6,10 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
13
13
  module Cheminee
14
- VERSION = '0.1.18'
14
+ VERSION = '0.1.21'
15
15
  end
data/lib/cheminee.rb CHANGED
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
Binary file
data/spec/spec_helper.rb CHANGED
@@ -6,7 +6,7 @@
6
6
  The version of the OpenAPI document: 1.0
7
7
 
8
8
  Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.4.0-SNAPSHOT
9
+ Generator version: 7.8.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: cheminee
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.1.18
4
+ version: 0.1.21
5
5
  platform: ruby
6
6
  authors:
7
7
  - Xavier Lange
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2024-02-28 00:00:00.000000000 Z
11
+ date: 2024-07-08 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: typhoeus
@@ -116,7 +116,7 @@ files:
116
116
  - lib/cheminee/version.rb
117
117
  - openapi-generator-config.json
118
118
  - openapi.json
119
- - pkg/cheminee-0.1.18.gem
119
+ - pkg/cheminee-0.1.21.gem
120
120
  - spec/api/default_api_spec.rb
121
121
  - spec/api_client_spec.rb
122
122
  - spec/configuration_spec.rb
@@ -170,26 +170,26 @@ test_files:
170
170
  - spec/api/default_api_spec.rb
171
171
  - spec/api_client_spec.rb
172
172
  - spec/configuration_spec.rb
173
+ - spec/models/bulk_request_spec.rb
174
+ - spec/models/query_search_hit_spec.rb
175
+ - spec/models/index_schema_spec.rb
176
+ - spec/models/index_meta_spec.rb
177
+ - spec/models/post_index_bulk_response_ok_status_spec.rb
178
+ - spec/models/get_indexes_response_error_spec.rb
173
179
  - spec/models/post_index_bulk_response_ok_spec.rb
180
+ - spec/models/query_response_error_spec.rb
174
181
  - spec/models/post_index_bulk_response_error_spec.rb
182
+ - spec/models/smiles_spec.rb
175
183
  - spec/models/standardized_smile_spec.rb
176
- - spec/models/smile_spec.rb
177
- - spec/models/structure_response_error_spec.rb
184
+ - spec/models/bulk_request_doc_spec.rb
178
185
  - spec/models/converted_smiles_spec.rb
179
- - spec/models/index_schema_spec.rb
180
- - spec/models/get_indexes_response_error_spec.rb
181
- - spec/models/query_search_hit_spec.rb
182
- - spec/models/bulk_request_spec.rb
183
- - spec/models/query_response_error_spec.rb
186
+ - spec/models/standardized_smiles_spec.rb
187
+ - spec/models/schema_spec.rb
188
+ - spec/models/smile_spec.rb
189
+ - spec/models/create_index_error_spec.rb
184
190
  - spec/models/substructure_search_hit_spec.rb
185
191
  - spec/models/mol_block_spec.rb
186
- - spec/models/bulk_request_doc_spec.rb
187
- - spec/models/post_index_bulk_response_ok_status_spec.rb
188
- - spec/models/smiles_spec.rb
189
- - spec/models/schema_spec.rb
190
192
  - spec/models/structure_search_hit_spec.rb
191
- - spec/models/standardized_smiles_spec.rb
193
+ - spec/models/structure_response_error_spec.rb
192
194
  - spec/models/list_index_response_err_spec.rb
193
- - spec/models/index_meta_spec.rb
194
- - spec/models/create_index_error_spec.rb
195
195
  - spec/spec_helper.rb
Binary file