cheminee 0.1.11 → 0.1.14
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- checksums.yaml +4 -4
- data/Gemfile.lock +7 -7
- data/README.md +10 -6
- data/cheminee.gemspec +2 -1
- data/docs/BulkRequestDoc.md +2 -2
- data/docs/DefaultApi.md +91 -20
- data/docs/IndexSchema.md +20 -0
- data/docs/QueryResponseError.md +18 -0
- data/docs/QuerySearchHit.md +22 -0
- data/docs/Smiles.md +18 -0
- data/docs/StandardizedSmiles.md +20 -0
- data/lib/cheminee/api/default_api.rb +99 -25
- data/lib/cheminee/api_client.rb +21 -20
- data/lib/cheminee/api_error.rb +1 -1
- data/lib/cheminee/configuration.rb +1 -1
- data/lib/cheminee/models/bulk_request.rb +2 -2
- data/lib/cheminee/models/bulk_request_doc.rb +13 -13
- data/lib/cheminee/models/create_index_error.rb +2 -2
- data/lib/cheminee/models/get_indexes_response_error.rb +2 -2
- data/lib/cheminee/models/index_meta.rb +2 -2
- data/lib/cheminee/models/index_schema.rb +233 -0
- data/lib/cheminee/models/list_index_response_err.rb +2 -2
- data/lib/cheminee/models/post_index_bulk_response_error.rb +2 -2
- data/lib/cheminee/models/post_index_bulk_response_ok.rb +2 -2
- data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +2 -2
- data/lib/cheminee/models/query_response_error.rb +221 -0
- data/lib/cheminee/models/query_search_hit.rb +249 -0
- data/lib/cheminee/models/schema.rb +2 -2
- data/lib/cheminee/models/smiles.rb +221 -0
- data/lib/cheminee/models/standardized_smiles.rb +223 -0
- data/lib/cheminee/models/structure_response_error.rb +2 -2
- data/lib/cheminee/models/structure_search_hit.rb +2 -2
- data/lib/cheminee/version.rb +2 -2
- data/lib/cheminee.rb +6 -3
- data/pkg/cheminee-0.1.14.gem +0 -0
- data/spec/models/index_schema_spec.rb +42 -0
- data/spec/models/query_response_error_spec.rb +36 -0
- data/spec/models/query_search_hit_spec.rb +48 -0
- data/spec/models/smiles_spec.rb +36 -0
- data/spec/models/standardized_smiles_spec.rb +42 -0
- data/spec/spec_helper.rb +1 -1
- metadata +23 -3
- data/pkg/cheminee-0.1.11.gem +0 -0
@@ -6,7 +6,7 @@
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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.
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OpenAPI Generator version: 7.3.0-SNAPSHOT
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=end
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@@ -149,7 +149,7 @@ module Cheminee
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# Get extended information about an index
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# @param index [String]
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# @param [Hash] opts the optional parameters
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# @return [
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# @return [IndexSchema]
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def v1_indexes_index_get(index, opts = {})
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data, _status_code, _headers = v1_indexes_index_get_with_http_info(index, opts)
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data
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# Get extended information about an index
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# @param index [String]
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# @param [Hash] opts the optional parameters
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# @return [Array<(
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# @return [Array<(IndexSchema, Integer, Hash)>] IndexSchema data, response status code and response headers
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def v1_indexes_index_get_with_http_info(index, opts = {})
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if @api_client.config.debugging
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@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_get ...'
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post_body = opts[:debug_body]
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# return_type
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return_type = opts[:debug_return_type] || '
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return_type = opts[:debug_return_type] || 'IndexSchema'
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# auth_names
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auth_names = opts[:debug_auth_names] || []
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@@ -278,26 +278,99 @@ module Cheminee
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return data, status_code, headers
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end
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# Perform basic query search against index
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# @param index [String]
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# @param query [String]
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# @param [Hash] opts the optional parameters
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# @option opts [Integer] :limit
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# @return [Array<QuerySearchHit>]
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def v1_indexes_index_search_basic_get(index, query, opts = {})
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data, _status_code, _headers = v1_indexes_index_search_basic_get_with_http_info(index, query, opts)
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data
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end
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# Perform basic query search against index
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# @param index [String]
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# @param query [String]
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# @param [Hash] opts the optional parameters
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# @option opts [Integer] :limit
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# @return [Array<(Array<QuerySearchHit>, Integer, Hash)>] Array<QuerySearchHit> data, response status code and response headers
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def v1_indexes_index_search_basic_get_with_http_info(index, query, opts = {})
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if @api_client.config.debugging
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@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_basic_get ...'
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end
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# verify the required parameter 'index' is set
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if @api_client.config.client_side_validation && index.nil?
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fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_basic_get"
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end
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# verify the required parameter 'query' is set
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if @api_client.config.client_side_validation && query.nil?
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fail ArgumentError, "Missing the required parameter 'query' when calling DefaultApi.v1_indexes_index_search_basic_get"
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end
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# resource path
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local_var_path = '/v1/indexes/{index}/search/basic'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
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# query parameters
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query_params = opts[:query_params] || {}
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query_params[:'query'] = query
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query_params[:'limit'] = opts[:'limit'] if !opts[:'limit'].nil?
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# header parameters
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header_params = opts[:header_params] || {}
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# HTTP header 'Accept' (if needed)
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header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
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# form parameters
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form_params = opts[:form_params] || {}
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# http body (model)
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post_body = opts[:debug_body]
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# return_type
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return_type = opts[:debug_return_type] || 'Array<QuerySearchHit>'
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# auth_names
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auth_names = opts[:debug_auth_names] || []
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new_options = opts.merge(
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:operation => :"DefaultApi.v1_indexes_index_search_basic_get",
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:header_params => header_params,
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:query_params => query_params,
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:form_params => form_params,
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:body => post_body,
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:auth_names => auth_names,
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:return_type => return_type
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)
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data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
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if @api_client.config.debugging
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@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_basic_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
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end
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return data, status_code, headers
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end
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# Perform substructure search against index
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# @param index [String]
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# @param
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# @param smiles [String]
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# @param [Hash] opts the optional parameters
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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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# @return [Array<StructureSearchHit>]
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def v1_indexes_index_search_substructure_get(index,
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data, _status_code, _headers = v1_indexes_index_search_substructure_get_with_http_info(index,
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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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data
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end
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# Perform substructure search against index
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# @param index [String]
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# @param
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# @param smiles [String]
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# @param [Hash] opts the optional parameters
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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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# @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,
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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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@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_substructure_get ...'
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end
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@@ -305,18 +378,19 @@ module Cheminee
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if @api_client.config.client_side_validation && index.nil?
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fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_substructure_get"
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end
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# verify the required parameter '
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if @api_client.config.client_side_validation &&
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fail ArgumentError, "Missing the required parameter '
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# verify the required parameter 'smiles' is set
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if @api_client.config.client_side_validation && smiles.nil?
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fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_indexes_index_search_substructure_get"
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end
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# resource path
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local_var_path = '/v1/indexes/{index}/search/substructure'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
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# query parameters
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query_params = opts[:query_params] || {}
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query_params[:'
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query_params[:'smiles'] = smiles
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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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# header parameters
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header_params = opts[:header_params] || {}
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@@ -408,25 +482,25 @@ module Cheminee
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end
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# Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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# @param
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# @param smiles [Array<Smiles>]
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# @param [Hash] opts the optional parameters
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# @return [Array<
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def v1_standardize_post(
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data, _status_code, _headers = v1_standardize_post_with_http_info(
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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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data
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end
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# Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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# @param
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# @param smiles [Array<Smiles>]
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# @param [Hash] opts the optional parameters
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# @return [Array<(Array<
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def v1_standardize_post_with_http_info(
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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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@api_client.config.logger.debug 'Calling API: DefaultApi.v1_standardize_post ...'
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end
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# verify the required parameter '
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if @api_client.config.client_side_validation &&
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fail ArgumentError, "Missing the required parameter '
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# verify the required parameter 'smiles' is set
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if @api_client.config.client_side_validation && smiles.nil?
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fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_standardize_post"
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end
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# resource path
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local_var_path = '/v1/standardize'
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@@ -448,10 +522,10 @@ module Cheminee
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form_params = opts[:form_params] || {}
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# http body (model)
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post_body = opts[:debug_body] || @api_client.object_to_http_body(
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post_body = opts[:debug_body] || @api_client.object_to_http_body(smiles)
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# return_type
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return_type = opts[:debug_return_type] || 'Array<
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return_type = opts[:debug_return_type] || 'Array<StandardizedSmiles>'
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# auth_names
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auth_names = opts[:debug_auth_names] || []
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data/lib/cheminee/api_client.rb
CHANGED
@@ -6,7 +6,7 @@
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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.
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OpenAPI Generator version: 7.3.0-SNAPSHOT
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=end
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@@ -46,9 +46,10 @@ module Cheminee
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# Call an API with given options.
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#
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# @return [Array<(Object, Integer, Hash)>] an array of 3 elements:
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# the data deserialized from response body (
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# the data deserialized from response body (may be a Tempfile or nil), response status code and response headers.
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def call_api(http_method, path, opts = {})
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request = build_request(http_method, path, opts)
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tempfile = download_file(request) if opts[:return_type] == 'File'
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response = request.run
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if @config.debugging
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@@ -70,7 +71,9 @@ module Cheminee
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end
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end
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if opts[:return_type]
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if opts[:return_type] == 'File'
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data = tempfile
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elsif opts[:return_type]
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data = deserialize(response, opts[:return_type])
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else
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data = nil
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@@ -125,9 +128,7 @@ module Cheminee
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end
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end
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download_file(request) if opts[:return_type] == 'File'
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request
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Typhoeus::Request.new(url, req_opts)
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end
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# Builds the HTTP request body
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@@ -165,6 +166,8 @@ module Cheminee
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# process can use.
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#
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# @see Configuration#temp_folder_path
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#
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# @return [Tempfile] the tempfile generated
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def download_file(request)
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tempfile = nil
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encoding = nil
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@@ -179,21 +182,24 @@ module Cheminee
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prefix = prefix + '-' unless prefix.end_with?('-')
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encoding = response.body.encoding
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tempfile = Tempfile.open(prefix, @config.temp_folder_path, encoding: encoding)
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@tempfile = tempfile
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end
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request.on_body do |chunk|
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chunk.force_encoding(encoding)
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tempfile.write(chunk)
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end
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request
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# run the request to ensure the tempfile is created successfully before returning it
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request.run
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if tempfile
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tempfile.close
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@config.logger.info "Temp file written to #{tempfile.path}, please copy the file to a proper folder "\
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"with e.g. `FileUtils.cp(tempfile.path, '/new/file/path')` otherwise the temp file "\
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"will be deleted automatically with GC. It's also recommended to delete the temp file "\
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"explicitly with `tempfile.delete`"
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else
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fail ApiError.new("Failed to create the tempfile based on the HTTP response from the server: #{request.inspect}")
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end
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tempfile
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end
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# Check if the given MIME is a JSON MIME.
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@@ -214,11 +220,6 @@ module Cheminee
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# @param [String] return_type some examples: "User", "Array<User>", "Hash<String, Integer>"
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def deserialize(response, return_type)
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body = response.body
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-
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# handle file downloading - return the File instance processed in request callbacks
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# note that response body is empty when the file is written in chunks in request on_body callback
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-
return @tempfile if return_type == 'File'
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-
|
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|
return nil if body.nil? || body.empty?
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# return response body directly for String return type
|
data/lib/cheminee/api_error.rb
CHANGED
@@ -6,7 +6,7 @@
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|
6
6
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The version of the OpenAPI document: 1.0
|
7
7
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8
8
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Generated by: https://openapi-generator.tech
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9
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-
OpenAPI Generator version: 7.
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9
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+
OpenAPI Generator version: 7.3.0-SNAPSHOT
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10
10
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11
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=end
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12
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@@ -168,7 +168,7 @@ module Cheminee
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168
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else # model
|
169
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# models (e.g. Pet) or oneOf
|
170
170
|
klass = Cheminee.const_get(type)
|
171
|
-
klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
171
|
+
klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
172
172
|
end
|
173
173
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end
|
174
174
|
|
@@ -6,7 +6,7 @@
|
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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.
|
9
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+
OpenAPI Generator version: 7.3.0-SNAPSHOT
|
10
10
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11
11
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=end
|
12
12
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|
@@ -15,7 +15,7 @@ require 'time'
|
|
15
15
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16
16
|
module Cheminee
|
17
17
|
class BulkRequestDoc
|
18
|
-
attr_accessor :
|
18
|
+
attr_accessor :smiles
|
19
19
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20
20
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# This value can store an arbitrary JSON object like '{}'
|
21
21
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attr_accessor :extra_data
|
@@ -23,7 +23,7 @@ module Cheminee
|
|
23
23
|
# Attribute mapping from ruby-style variable name to JSON key.
|
24
24
|
def self.attribute_map
|
25
25
|
{
|
26
|
-
:'
|
26
|
+
:'smiles' => :'smiles',
|
27
27
|
:'extra_data' => :'extra_data'
|
28
28
|
}
|
29
29
|
end
|
@@ -36,7 +36,7 @@ module Cheminee
|
|
36
36
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# Attribute type mapping.
|
37
37
|
def self.openapi_types
|
38
38
|
{
|
39
|
-
:'
|
39
|
+
:'smiles' => :'String',
|
40
40
|
:'extra_data' => :'Object'
|
41
41
|
}
|
42
42
|
end
|
@@ -63,10 +63,10 @@ module Cheminee
|
|
63
63
|
h[k.to_sym] = v
|
64
64
|
}
|
65
65
|
|
66
|
-
if attributes.key?(:'
|
67
|
-
self.
|
66
|
+
if attributes.key?(:'smiles')
|
67
|
+
self.smiles = attributes[:'smiles']
|
68
68
|
else
|
69
|
-
self.
|
69
|
+
self.smiles = nil
|
70
70
|
end
|
71
71
|
|
72
72
|
if attributes.key?(:'extra_data')
|
@@ -79,8 +79,8 @@ module Cheminee
|
|
79
79
|
def list_invalid_properties
|
80
80
|
warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
|
81
81
|
invalid_properties = Array.new
|
82
|
-
if @
|
83
|
-
invalid_properties.push('invalid value for "
|
82
|
+
if @smiles.nil?
|
83
|
+
invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
|
84
84
|
end
|
85
85
|
|
86
86
|
invalid_properties
|
@@ -90,7 +90,7 @@ module Cheminee
|
|
90
90
|
# @return true if the model is valid
|
91
91
|
def valid?
|
92
92
|
warn '[DEPRECATED] the `valid?` method is obsolete'
|
93
|
-
return false if @
|
93
|
+
return false if @smiles.nil?
|
94
94
|
true
|
95
95
|
end
|
96
96
|
|
@@ -99,7 +99,7 @@ module Cheminee
|
|
99
99
|
def ==(o)
|
100
100
|
return true if self.equal?(o)
|
101
101
|
self.class == o.class &&
|
102
|
-
|
102
|
+
smiles == o.smiles &&
|
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103
|
extra_data == o.extra_data
|
104
104
|
end
|
105
105
|
|
@@ -112,7 +112,7 @@ module Cheminee
|
|
112
112
|
# Calculates hash code according to all attributes.
|
113
113
|
# @return [Integer] Hash code
|
114
114
|
def hash
|
115
|
-
[
|
115
|
+
[smiles, extra_data].hash
|
116
116
|
end
|
117
117
|
|
118
118
|
# Builds the object from hash
|
@@ -177,7 +177,7 @@ module Cheminee
|
|
177
177
|
else # model
|
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178
|
# models (e.g. Pet) or oneOf
|
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179
|
klass = Cheminee.const_get(type)
|
180
|
-
klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
180
|
+
klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
181
181
|
end
|
182
182
|
end
|
183
183
|
|
@@ -6,7 +6,7 @@
|
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6
6
|
The version of the OpenAPI document: 1.0
|
7
7
|
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8
8
|
Generated by: https://openapi-generator.tech
|
9
|
-
OpenAPI Generator version: 7.
|
9
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+
OpenAPI Generator version: 7.3.0-SNAPSHOT
|
10
10
|
|
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11
|
=end
|
12
12
|
|
@@ -166,7 +166,7 @@ module Cheminee
|
|
166
166
|
else # model
|
167
167
|
# models (e.g. Pet) or oneOf
|
168
168
|
klass = Cheminee.const_get(type)
|
169
|
-
klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
169
|
+
klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
170
170
|
end
|
171
171
|
end
|
172
172
|
|
@@ -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.
|
9
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+
OpenAPI Generator version: 7.3.0-SNAPSHOT
|
10
10
|
|
11
11
|
=end
|
12
12
|
|
@@ -166,7 +166,7 @@ module Cheminee
|
|
166
166
|
else # model
|
167
167
|
# models (e.g. Pet) or oneOf
|
168
168
|
klass = Cheminee.const_get(type)
|
169
|
-
klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
169
|
+
klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
170
170
|
end
|
171
171
|
end
|
172
172
|
|
@@ -6,7 +6,7 @@
|
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6
6
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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.
|
9
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+
OpenAPI Generator version: 7.3.0-SNAPSHOT
|
10
10
|
|
11
11
|
=end
|
12
12
|
|
@@ -182,7 +182,7 @@ module Cheminee
|
|
182
182
|
else # model
|
183
183
|
# models (e.g. Pet) or oneOf
|
184
184
|
klass = Cheminee.const_get(type)
|
185
|
-
klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
185
|
+
klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
|
186
186
|
end
|
187
187
|
end
|
188
188
|
|