cheminee 0.1.18 → 0.1.21
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- checksums.yaml +4 -4
- data/Gemfile.lock +9 -9
- data/README.md +5 -4
- data/cheminee.gemspec +1 -1
- data/docs/DefaultApi.md +11 -5
- data/docs/QuerySearchHit.md +1 -1
- data/docs/StructureSearchHit.md +1 -1
- data/lib/cheminee/api/default_api.rb +7 -1
- data/lib/cheminee/api_client.rb +3 -3
- data/lib/cheminee/api_error.rb +1 -1
- data/lib/cheminee/configuration.rb +11 -1
- data/lib/cheminee/models/bulk_request.rb +1 -1
- data/lib/cheminee/models/bulk_request_doc.rb +1 -1
- data/lib/cheminee/models/converted_smiles.rb +1 -1
- data/lib/cheminee/models/create_index_error.rb +1 -1
- data/lib/cheminee/models/get_indexes_response_error.rb +1 -1
- data/lib/cheminee/models/index_meta.rb +1 -1
- data/lib/cheminee/models/index_schema.rb +1 -1
- data/lib/cheminee/models/list_index_response_err.rb +1 -1
- data/lib/cheminee/models/mol_block.rb +1 -1
- data/lib/cheminee/models/post_index_bulk_response_error.rb +1 -1
- data/lib/cheminee/models/post_index_bulk_response_ok.rb +1 -1
- data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +1 -1
- data/lib/cheminee/models/query_response_error.rb +1 -1
- data/lib/cheminee/models/query_search_hit.rb +7 -3
- data/lib/cheminee/models/schema.rb +1 -1
- data/lib/cheminee/models/smiles.rb +1 -1
- data/lib/cheminee/models/standardized_smiles.rb +1 -1
- data/lib/cheminee/models/structure_response_error.rb +1 -1
- data/lib/cheminee/models/structure_search_hit.rb +7 -3
- data/lib/cheminee/version.rb +2 -2
- data/lib/cheminee.rb +1 -1
- data/pkg/cheminee-0.1.21.gem +0 -0
- data/spec/spec_helper.rb +1 -1
- metadata +17 -17
- data/pkg/cheminee-0.1.18.gem +0 -0
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 94540570dc590389820fe841bb3d558f78e6c9af38b3e7cf0fce6ff15feb4341
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data.tar.gz: dcca2f608d6482fd53e0a6945033027c0c45e6aecb8a39b7e560080abe7d5be0
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 89a4957b0f810d2013e6b99d07ccf8b9325b829490c3ea9abafc1017e315e89848c5acb8dde935e764200ea50f30e6f5f10f3420f2d583b94aa1ea217d059b6b
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data.tar.gz: 960a8638b55c76baa9396a1e1d01d1f88f51a34c1460131ba4178d4a13249fff4bd565397f0cb51cde2fab7dd4f819de1b115e5d621d9c8f947a134c4cdd81a7
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data/Gemfile.lock
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PATH
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remote: .
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specs:
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cheminee (0.1.
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cheminee (0.1.21)
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typhoeus (~> 1.0, >= 1.0.1)
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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.
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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.
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parallel (1.
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parser (3.3.0
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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)
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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.
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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)
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rspec-mocks (~> 3.13.0)
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rspec-core (3.13.0)
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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.
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typhoeus (1.4.1)
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unicode-display_width (1.5.0)
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data/README.md
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@@ -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.
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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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Then either install the gem locally:
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```shell
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gem install ./cheminee-0.1.
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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.
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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.
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gem 'cheminee', '~> 0.1.21'
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### Install from Git
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data/cheminee.gemspec
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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
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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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## 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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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}"
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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>>
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **smiles** | [**Array<Smiles>**](Smiles.md) | | |
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| **attempt_fix** | **String** | | [optional] |
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### Return type
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data/docs/QuerySearchHit.md
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data/docs/StructureSearchHit.md
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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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=end
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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)
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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
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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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header_params = opts[:header_params] || {}
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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<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)
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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
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# query parameters
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query_params = opts[:query_params] || {}
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query_params[:'attempt_fix'] = opts[:'attempt_fix'] if !opts[:'attempt_fix'].nil?
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# header parameters
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header_params = opts[:header_params] || {}
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data/lib/cheminee/api_client.rb
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=end
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# @param [String] mime MIME
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# @return [Boolean] True if the MIME is application/json
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def json_mime?(mime)
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(mime == '*/*') || !(mime =~
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end
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# Deserialize the response to the given return type.
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# @param [String] filename the filename to be sanitized
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# @return [String] the sanitized filename
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def sanitize_filename(filename)
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filename.
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filename.split(/[\/\\]/).last
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end
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def build_request_url(path, opts = {})
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data/lib/cheminee/api_error.rb
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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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# Defines the logger used for debugging.
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# Default to `Rails.logger` (when in Rails) or logging to STDOUT.
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#
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@timeout = 0
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@params_encoding = nil
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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)
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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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# Attribute type mapping.
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def self.openapi_types
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{
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:'extra_data' => :'
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:'extra_data' => :'String',
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:'smiles' => :'String',
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:'query' => :'String'
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}
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@@ -47,7 +47,6 @@ module Cheminee
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# List of attributes with nullable: true
|
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def self.openapi_nullable
|
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Set.new([
|
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-
:'extra_data',
|
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50
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])
|
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51
|
end
|
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|
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@@ -90,6 +89,10 @@ module Cheminee
|
|
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|
def list_invalid_properties
|
91
90
|
warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
|
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|
invalid_properties = Array.new
|
92
|
+
if @extra_data.nil?
|
93
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+
invalid_properties.push('invalid value for "extra_data", extra_data cannot be nil.')
|
94
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+
end
|
95
|
+
|
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if @smiles.nil?
|
94
97
|
invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
|
95
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|
end
|
@@ -105,6 +108,7 @@ module Cheminee
|
|
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|
# @return true if the model is valid
|
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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 @@
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6
6
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The version of the OpenAPI document: 1.0
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7
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8
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Generated by: https://openapi-generator.tech
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9
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-
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9
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+
Generator version: 7.8.0-SNAPSHOT
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|
=end
|
12
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|
|
@@ -44,7 +44,7 @@ module Cheminee
|
|
44
44
|
# Attribute type mapping.
|
45
45
|
def self.openapi_types
|
46
46
|
{
|
47
|
-
:'extra_data' => :'
|
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?
|
data/lib/cheminee/version.rb
CHANGED
@@ -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
|
-
|
9
|
+
Generator version: 7.8.0-SNAPSHOT
|
10
10
|
|
11
11
|
=end
|
12
12
|
|
13
13
|
module Cheminee
|
14
|
-
VERSION = '0.1.
|
14
|
+
VERSION = '0.1.21'
|
15
15
|
end
|
data/lib/cheminee.rb
CHANGED
Binary file
|
data/spec/spec_helper.rb
CHANGED
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.
|
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-
|
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.
|
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/
|
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/
|
180
|
-
- spec/models/
|
181
|
-
- spec/models/
|
182
|
-
- spec/models/
|
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/
|
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
|
data/pkg/cheminee-0.1.18.gem
DELETED
Binary file
|