cheminee 0.0.14 → 0.0.15

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Files changed (73) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +8 -8
  3. data/README.md +11 -33
  4. data/cheminee.gemspec +1 -2
  5. data/docs/DefaultApi.md +16 -475
  6. data/lib/cheminee/api/default_api.rb +17 -481
  7. data/lib/cheminee/api_client.rb +21 -23
  8. data/lib/cheminee/api_error.rb +1 -1
  9. data/lib/cheminee/configuration.rb +5 -6
  10. data/lib/cheminee/models/smile.rb +1 -1
  11. data/lib/cheminee/models/standardized_smile.rb +1 -1
  12. data/lib/cheminee/version.rb +2 -2
  13. data/lib/cheminee.rb +3 -18
  14. data/pkg/cheminee-0.0.15.gem +0 -0
  15. data/spec/api_client_spec.rb +1 -1
  16. data/spec/configuration_spec.rb +4 -4
  17. data/spec/spec_helper.rb +1 -1
  18. metadata +3 -75
  19. data/docs/BulkRequest.md +0 -18
  20. data/docs/BulkRequestDoc.md +0 -20
  21. data/docs/CreateIndexError.md +0 -18
  22. data/docs/GetIndexesResponseError.md +0 -18
  23. data/docs/IndexMeta.md +0 -20
  24. data/docs/IndexSchema.md +0 -20
  25. data/docs/ListIndexResponseErr.md +0 -18
  26. data/docs/PostIndexBulkResponseError.md +0 -18
  27. data/docs/PostIndexBulkResponseOk.md +0 -18
  28. data/docs/PostIndexBulkResponseOkStatus.md +0 -20
  29. data/docs/QueryResponseError.md +0 -18
  30. data/docs/QuerySearchHit.md +0 -22
  31. data/docs/Schema.md +0 -20
  32. data/docs/Smiles.md +0 -18
  33. data/docs/StandardizedSmiles.md +0 -20
  34. data/docs/StructureResponseError.md +0 -18
  35. data/docs/StructureSearchHit.md +0 -26
  36. data/docs/SubstructureSearchHit.md +0 -24
  37. data/lib/cheminee/models/bulk_request.rb +0 -223
  38. data/lib/cheminee/models/bulk_request_doc.rb +0 -232
  39. data/lib/cheminee/models/create_index_error.rb +0 -221
  40. data/lib/cheminee/models/get_indexes_response_error.rb +0 -221
  41. data/lib/cheminee/models/index_meta.rb +0 -237
  42. data/lib/cheminee/models/index_schema.rb +0 -233
  43. data/lib/cheminee/models/list_index_response_err.rb +0 -221
  44. data/lib/cheminee/models/post_index_bulk_response_error.rb +0 -221
  45. data/lib/cheminee/models/post_index_bulk_response_ok.rb +0 -223
  46. data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +0 -223
  47. data/lib/cheminee/models/query_response_error.rb +0 -221
  48. data/lib/cheminee/models/query_search_hit.rb +0 -249
  49. data/lib/cheminee/models/schema.rb +0 -233
  50. data/lib/cheminee/models/smiles.rb +0 -221
  51. data/lib/cheminee/models/standardized_smiles.rb +0 -223
  52. data/lib/cheminee/models/structure_response_error.rb +0 -221
  53. data/lib/cheminee/models/structure_search_hit.rb +0 -281
  54. data/lib/cheminee/models/substructure_search_hit.rb +0 -265
  55. data/pkg/cheminee-0.0.14.gem +0 -0
  56. data/spec/models/bulk_request_doc_spec.rb +0 -42
  57. data/spec/models/bulk_request_spec.rb +0 -36
  58. data/spec/models/create_index_error_spec.rb +0 -36
  59. data/spec/models/get_indexes_response_error_spec.rb +0 -36
  60. data/spec/models/index_meta_spec.rb +0 -42
  61. data/spec/models/index_schema_spec.rb +0 -42
  62. data/spec/models/list_index_response_err_spec.rb +0 -36
  63. data/spec/models/post_index_bulk_response_error_spec.rb +0 -36
  64. data/spec/models/post_index_bulk_response_ok_spec.rb +0 -36
  65. data/spec/models/post_index_bulk_response_ok_status_spec.rb +0 -42
  66. data/spec/models/query_response_error_spec.rb +0 -36
  67. data/spec/models/query_search_hit_spec.rb +0 -48
  68. data/spec/models/schema_spec.rb +0 -42
  69. data/spec/models/smiles_spec.rb +0 -36
  70. data/spec/models/standardized_smiles_spec.rb +0 -42
  71. data/spec/models/structure_response_error_spec.rb +0 -36
  72. data/spec/models/structure_search_hit_spec.rb +0 -60
  73. data/spec/models/substructure_search_hit_spec.rb +0 -54
@@ -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: 7.3.0-SNAPSHOT
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+ OpenAPI Generator version: 7.0.0-SNAPSHOT
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  =end
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@@ -19,491 +19,27 @@ module Cheminee
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  def initialize(api_client = ApiClient.default)
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  @api_client = api_client
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  end
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- # List indexes
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+ # @param smile [Array<Smile>]
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  # @param [Hash] opts the optional parameters
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- # @return [Array<IndexMeta>]
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- def v1_indexes_get(opts = {})
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- data, _status_code, _headers = v1_indexes_get_with_http_info(opts)
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+ # @return [Array<StandardizedSmile>]
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+ def standardize_post(smile, opts = {})
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+ data, _status_code, _headers = standardize_post_with_http_info(smile, opts)
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  data
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  end
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- # List indexes
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+ # @param smile [Array<Smile>]
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  # @param [Hash] opts the optional parameters
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- # @return [Array<(Array<IndexMeta>, Integer, Hash)>] Array<IndexMeta> data, response status code and response headers
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- def v1_indexes_get_with_http_info(opts = {})
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+ # @return [Array<(Array<StandardizedSmile>, Integer, Hash)>] Array<StandardizedSmile> data, response status code and response headers
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+ def standardize_post_with_http_info(smile, opts = {})
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  if @api_client.config.debugging
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- @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_get ...'
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+ @api_client.config.logger.debug 'Calling API: DefaultApi.standardize_post ...'
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  end
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- # resource path
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- local_var_path = '/v1/indexes'
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-
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- # query parameters
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- query_params = opts[:query_params] || {}
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-
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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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-
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- # form parameters
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- form_params = opts[:form_params] || {}
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-
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- # http body (model)
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- post_body = opts[:debug_body]
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-
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- # return_type
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- return_type = opts[:debug_return_type] || 'Array<IndexMeta>'
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-
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- # auth_names
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- auth_names = opts[:debug_auth_names] || []
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-
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- new_options = opts.merge(
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- :operation => :"DefaultApi.v1_indexes_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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-
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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_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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-
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- # Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
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- # @param index [String]
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- # @param bulk_request [BulkRequest]
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- # @param [Hash] opts the optional parameters
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- # @return [PostIndexBulkResponseOk]
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- def v1_indexes_index_bulk_index_post(index, bulk_request, opts = {})
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- data, _status_code, _headers = v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request, opts)
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- data
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- end
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-
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- # Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
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- # @param index [String]
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- # @param bulk_request [BulkRequest]
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- # @param [Hash] opts the optional parameters
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- # @return [Array<(PostIndexBulkResponseOk, Integer, Hash)>] PostIndexBulkResponseOk data, response status code and response headers
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- def v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request, 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_bulk_index_post ...'
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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_bulk_index_post"
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- end
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- # verify the required parameter 'bulk_request' is set
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- if @api_client.config.client_side_validation && bulk_request.nil?
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- fail ArgumentError, "Missing the required parameter 'bulk_request' when calling DefaultApi.v1_indexes_index_bulk_index_post"
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- end
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- # resource path
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- local_var_path = '/v1/indexes/{index}/bulk_index'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
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-
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- # query parameters
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- query_params = opts[:query_params] || {}
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-
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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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- # HTTP header 'Content-Type'
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- content_type = @api_client.select_header_content_type(['application/json; charset=utf-8'])
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- if !content_type.nil?
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- header_params['Content-Type'] = content_type
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- end
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-
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- # form parameters
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- form_params = opts[:form_params] || {}
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-
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- # http body (model)
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- post_body = opts[:debug_body] || @api_client.object_to_http_body(bulk_request)
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-
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- # return_type
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- return_type = opts[:debug_return_type] || 'PostIndexBulkResponseOk'
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-
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- # auth_names
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- auth_names = opts[:debug_auth_names] || []
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-
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- new_options = opts.merge(
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- :operation => :"DefaultApi.v1_indexes_index_bulk_index_post",
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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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-
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- data, status_code, headers = @api_client.call_api(:POST, 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_bulk_index_post\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
148
-
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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 [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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- end
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-
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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<(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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- end
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- # verify the required parameter 'index' is set
167
- if @api_client.config.client_side_validation && index.nil?
168
- fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_get"
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- end
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- # resource path
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- local_var_path = '/v1/indexes/{index}'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
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-
173
- # query parameters
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- query_params = opts[:query_params] || {}
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-
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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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-
181
- # form parameters
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- form_params = opts[:form_params] || {}
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-
184
- # http body (model)
185
- post_body = opts[:debug_body]
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-
187
- # return_type
188
- return_type = opts[:debug_return_type] || 'IndexSchema'
189
-
190
- # auth_names
191
- auth_names = opts[:debug_auth_names] || []
192
-
193
- new_options = opts.merge(
194
- :operation => :"DefaultApi.v1_indexes_index_get",
195
- :header_params => header_params,
196
- :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,
200
- :return_type => return_type
201
- )
202
-
203
- data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
204
- if @api_client.config.debugging
205
- @api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
206
- end
207
- return data, status_code, headers
208
- end
209
-
210
- # Create an index
211
- # @param index [String]
212
- # @param schema [String]
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- # @param [Hash] opts the optional parameters
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- # @option opts [String] :sort_by
215
- # @return [IndexMeta]
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- def v1_indexes_index_post(index, schema, opts = {})
217
- data, _status_code, _headers = v1_indexes_index_post_with_http_info(index, schema, opts)
218
- data
219
- end
220
-
221
- # Create an index
222
- # @param index [String]
223
- # @param schema [String]
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- # @param [Hash] opts the optional parameters
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- # @option opts [String] :sort_by
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- # @return [Array<(IndexMeta, Integer, Hash)>] IndexMeta data, response status code and response headers
227
- def v1_indexes_index_post_with_http_info(index, schema, opts = {})
228
- if @api_client.config.debugging
229
- @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_post ...'
230
- end
231
- # verify the required parameter 'index' is set
232
- if @api_client.config.client_side_validation && index.nil?
233
- fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_post"
234
- end
235
- # verify the required parameter 'schema' is set
236
- if @api_client.config.client_side_validation && schema.nil?
237
- fail ArgumentError, "Missing the required parameter 'schema' when calling DefaultApi.v1_indexes_index_post"
238
- end
239
- # resource path
240
- local_var_path = '/v1/indexes/{index}'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
241
-
242
- # query parameters
243
- query_params = opts[:query_params] || {}
244
- query_params[:'schema'] = schema
245
- query_params[:'sort_by'] = opts[:'sort_by'] if !opts[:'sort_by'].nil?
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-
247
- # header parameters
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- header_params = opts[:header_params] || {}
249
- # HTTP header 'Accept' (if needed)
250
- header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
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-
252
- # form parameters
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- form_params = opts[:form_params] || {}
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-
255
- # http body (model)
256
- post_body = opts[:debug_body]
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-
258
- # return_type
259
- return_type = opts[:debug_return_type] || 'IndexMeta'
260
-
261
- # auth_names
262
- auth_names = opts[:debug_auth_names] || []
263
-
264
- new_options = opts.merge(
265
- :operation => :"DefaultApi.v1_indexes_index_post",
266
- :header_params => header_params,
267
- :query_params => query_params,
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- :form_params => form_params,
269
- :body => post_body,
270
- :auth_names => auth_names,
271
- :return_type => return_type
272
- )
273
-
274
- data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
275
- if @api_client.config.debugging
276
- @api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
277
- end
278
- return data, status_code, headers
279
- end
280
-
281
- # Perform basic query search against index
282
- # @param index [String]
283
- # @param query [String]
284
- # @param [Hash] opts the optional parameters
285
- # @option opts [Integer] :limit
286
- # @return [Array<QuerySearchHit>]
287
- def v1_indexes_index_search_basic_get(index, query, opts = {})
288
- data, _status_code, _headers = v1_indexes_index_search_basic_get_with_http_info(index, query, opts)
289
- data
290
- end
291
-
292
- # Perform basic query search against index
293
- # @param index [String]
294
- # @param query [String]
295
- # @param [Hash] opts the optional parameters
296
- # @option opts [Integer] :limit
297
- # @return [Array<(Array<QuerySearchHit>, Integer, Hash)>] Array<QuerySearchHit> data, response status code and response headers
298
- def v1_indexes_index_search_basic_get_with_http_info(index, query, opts = {})
299
- if @api_client.config.debugging
300
- @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_basic_get ...'
301
- end
302
- # verify the required parameter 'index' is set
303
- if @api_client.config.client_side_validation && index.nil?
304
- fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_basic_get"
305
- end
306
- # verify the required parameter 'query' is set
307
- if @api_client.config.client_side_validation && query.nil?
308
- fail ArgumentError, "Missing the required parameter 'query' when calling DefaultApi.v1_indexes_index_search_basic_get"
309
- end
310
- # resource path
311
- local_var_path = '/v1/indexes/{index}/search/basic'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
312
-
313
- # query parameters
314
- query_params = opts[:query_params] || {}
315
- query_params[:'query'] = query
316
- query_params[:'limit'] = opts[:'limit'] if !opts[:'limit'].nil?
317
-
318
- # header parameters
319
- header_params = opts[:header_params] || {}
320
- # HTTP header 'Accept' (if needed)
321
- header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
322
-
323
- # form parameters
324
- form_params = opts[:form_params] || {}
325
-
326
- # http body (model)
327
- post_body = opts[:debug_body]
328
-
329
- # return_type
330
- return_type = opts[:debug_return_type] || 'Array<QuerySearchHit>'
331
-
332
- # auth_names
333
- auth_names = opts[:debug_auth_names] || []
334
-
335
- new_options = opts.merge(
336
- :operation => :"DefaultApi.v1_indexes_index_search_basic_get",
337
- :header_params => header_params,
338
- :query_params => query_params,
339
- :form_params => form_params,
340
- :body => post_body,
341
- :auth_names => auth_names,
342
- :return_type => return_type
343
- )
344
-
345
- data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
346
- if @api_client.config.debugging
347
- @api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_basic_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
348
- end
349
- return data, status_code, headers
350
- end
351
-
352
- # Perform substructure search against index
353
- # @param index [String]
354
- # @param smiles [String]
355
- # @param [Hash] opts the optional parameters
356
- # @option opts [Integer] :result_limit
357
- # @option opts [Integer] :tautomer_limit
358
- # @option opts [String] :extra_query
359
- # @return [Array<StructureSearchHit>]
360
- def v1_indexes_index_search_substructure_get(index, smiles, opts = {})
361
- data, _status_code, _headers = v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts)
362
- data
363
- end
364
-
365
- # Perform substructure search against index
366
- # @param index [String]
367
- # @param smiles [String]
368
- # @param [Hash] opts the optional parameters
369
- # @option opts [Integer] :result_limit
370
- # @option opts [Integer] :tautomer_limit
371
- # @option opts [String] :extra_query
372
- # @return [Array<(Array<StructureSearchHit>, Integer, Hash)>] Array<StructureSearchHit> data, response status code and response headers
373
- def v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts = {})
374
- if @api_client.config.debugging
375
- @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_substructure_get ...'
376
- end
377
- # verify the required parameter 'index' is set
378
- if @api_client.config.client_side_validation && index.nil?
379
- fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_substructure_get"
380
- end
381
- # verify the required parameter 'smiles' is set
382
- if @api_client.config.client_side_validation && smiles.nil?
383
- fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_indexes_index_search_substructure_get"
384
- end
385
- # resource path
386
- local_var_path = '/v1/indexes/{index}/search/substructure'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
387
-
388
- # query parameters
389
- query_params = opts[:query_params] || {}
390
- query_params[:'smiles'] = smiles
391
- query_params[:'result_limit'] = opts[:'result_limit'] if !opts[:'result_limit'].nil?
392
- query_params[:'tautomer_limit'] = opts[:'tautomer_limit'] if !opts[:'tautomer_limit'].nil?
393
- query_params[:'extra_query'] = opts[:'extra_query'] if !opts[:'extra_query'].nil?
394
-
395
- # header parameters
396
- header_params = opts[:header_params] || {}
397
- # HTTP header 'Accept' (if needed)
398
- header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
399
-
400
- # form parameters
401
- form_params = opts[:form_params] || {}
402
-
403
- # http body (model)
404
- post_body = opts[:debug_body]
405
-
406
- # return_type
407
- return_type = opts[:debug_return_type] || 'Array<StructureSearchHit>'
408
-
409
- # auth_names
410
- auth_names = opts[:debug_auth_names] || []
411
-
412
- new_options = opts.merge(
413
- :operation => :"DefaultApi.v1_indexes_index_search_substructure_get",
414
- :header_params => header_params,
415
- :query_params => query_params,
416
- :form_params => form_params,
417
- :body => post_body,
418
- :auth_names => auth_names,
419
- :return_type => return_type
420
- )
421
-
422
- data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
423
- if @api_client.config.debugging
424
- @api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_substructure_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
425
- end
426
- return data, status_code, headers
427
- end
428
-
429
- # List schemas available for creating indexes
430
- # @param [Hash] opts the optional parameters
431
- # @return [Array<Schema>]
432
- def v1_schemas_get(opts = {})
433
- data, _status_code, _headers = v1_schemas_get_with_http_info(opts)
434
- data
435
- end
436
-
437
- # List schemas available for creating indexes
438
- # @param [Hash] opts the optional parameters
439
- # @return [Array<(Array<Schema>, Integer, Hash)>] Array<Schema> data, response status code and response headers
440
- def v1_schemas_get_with_http_info(opts = {})
441
- if @api_client.config.debugging
442
- @api_client.config.logger.debug 'Calling API: DefaultApi.v1_schemas_get ...'
443
- end
444
- # resource path
445
- local_var_path = '/v1/schemas'
446
-
447
- # query parameters
448
- query_params = opts[:query_params] || {}
449
-
450
- # header parameters
451
- header_params = opts[:header_params] || {}
452
- # HTTP header 'Accept' (if needed)
453
- header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
454
-
455
- # form parameters
456
- form_params = opts[:form_params] || {}
457
-
458
- # http body (model)
459
- post_body = opts[:debug_body]
460
-
461
- # return_type
462
- return_type = opts[:debug_return_type] || 'Array<Schema>'
463
-
464
- # auth_names
465
- auth_names = opts[:debug_auth_names] || []
466
-
467
- new_options = opts.merge(
468
- :operation => :"DefaultApi.v1_schemas_get",
469
- :header_params => header_params,
470
- :query_params => query_params,
471
- :form_params => form_params,
472
- :body => post_body,
473
- :auth_names => auth_names,
474
- :return_type => return_type
475
- )
476
-
477
- data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
478
- if @api_client.config.debugging
479
- @api_client.config.logger.debug "API called: DefaultApi#v1_schemas_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
480
- end
481
- return data, status_code, headers
482
- end
483
-
484
- # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
485
- # @param smiles [Array<Smiles>]
486
- # @param [Hash] opts the optional parameters
487
- # @return [Array<StandardizedSmiles>]
488
- def v1_standardize_post(smiles, opts = {})
489
- data, _status_code, _headers = v1_standardize_post_with_http_info(smiles, opts)
490
- data
491
- end
492
-
493
- # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
494
- # @param smiles [Array<Smiles>]
495
- # @param [Hash] opts the optional parameters
496
- # @return [Array<(Array<StandardizedSmiles>, Integer, Hash)>] Array<StandardizedSmiles> data, response status code and response headers
497
- def v1_standardize_post_with_http_info(smiles, opts = {})
498
- if @api_client.config.debugging
499
- @api_client.config.logger.debug 'Calling API: DefaultApi.v1_standardize_post ...'
500
- end
501
- # verify the required parameter 'smiles' is set
502
- if @api_client.config.client_side_validation && smiles.nil?
503
- fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_standardize_post"
37
+ # verify the required parameter 'smile' is set
38
+ if @api_client.config.client_side_validation && smile.nil?
39
+ fail ArgumentError, "Missing the required parameter 'smile' when calling DefaultApi.standardize_post"
504
40
  end
505
41
  # resource path
506
- local_var_path = '/v1/standardize'
42
+ local_var_path = '/standardize'
507
43
 
508
44
  # query parameters
509
45
  query_params = opts[:query_params] || {}
@@ -522,16 +58,16 @@ module Cheminee
522
58
  form_params = opts[:form_params] || {}
523
59
 
524
60
  # http body (model)
525
- post_body = opts[:debug_body] || @api_client.object_to_http_body(smiles)
61
+ post_body = opts[:debug_body] || @api_client.object_to_http_body(smile)
526
62
 
527
63
  # return_type
528
- return_type = opts[:debug_return_type] || 'Array<StandardizedSmiles>'
64
+ return_type = opts[:debug_return_type] || 'Array<StandardizedSmile>'
529
65
 
530
66
  # auth_names
531
67
  auth_names = opts[:debug_auth_names] || []
532
68
 
533
69
  new_options = opts.merge(
534
- :operation => :"DefaultApi.v1_standardize_post",
70
+ :operation => :"DefaultApi.standardize_post",
535
71
  :header_params => header_params,
536
72
  :query_params => query_params,
537
73
  :form_params => form_params,
@@ -542,7 +78,7 @@ module Cheminee
542
78
 
543
79
  data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
544
80
  if @api_client.config.debugging
545
- @api_client.config.logger.debug "API called: DefaultApi#v1_standardize_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
81
+ @api_client.config.logger.debug "API called: DefaultApi#standardize_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
546
82
  end
547
83
  return data, status_code, headers
548
84
  end
@@ -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: 7.3.0-SNAPSHOT
9
+ OpenAPI Generator version: 7.0.0-SNAPSHOT
10
10
 
11
11
  =end
12
12
 
@@ -17,7 +17,6 @@ require 'tempfile'
17
17
  require 'time'
18
18
  require 'typhoeus'
19
19
 
20
-
21
20
  module Cheminee
22
21
  class ApiClient
23
22
  # The Configuration object holding settings to be used in the API client.
@@ -46,10 +45,9 @@ module Cheminee
46
45
  # Call an API with given options.
47
46
  #
48
47
  # @return [Array<(Object, Integer, Hash)>] an array of 3 elements:
49
- # the data deserialized from response body (may be a Tempfile or nil), response status code and response headers.
48
+ # the data deserialized from response body (could be nil), response status code and response headers.
50
49
  def call_api(http_method, path, opts = {})
51
50
  request = build_request(http_method, path, opts)
52
- tempfile = download_file(request) if opts[:return_type] == 'File'
53
51
  response = request.run
54
52
 
55
53
  if @config.debugging
@@ -71,9 +69,7 @@ module Cheminee
71
69
  end
72
70
  end
73
71
 
74
- if opts[:return_type] == 'File'
75
- data = tempfile
76
- elsif opts[:return_type]
72
+ if opts[:return_type]
77
73
  data = deserialize(response, opts[:return_type])
78
74
  else
79
75
  data = nil
@@ -128,7 +124,9 @@ module Cheminee
128
124
  end
129
125
  end
130
126
 
131
- Typhoeus::Request.new(url, req_opts)
127
+ request = Typhoeus::Request.new(url, req_opts)
128
+ download_file(request) if opts[:return_type] == 'File'
129
+ request
132
130
  end
133
131
 
134
132
  # Builds the HTTP request body
@@ -166,8 +164,6 @@ module Cheminee
166
164
  # process can use.
167
165
  #
168
166
  # @see Configuration#temp_folder_path
169
- #
170
- # @return [Tempfile] the tempfile generated
171
167
  def download_file(request)
172
168
  tempfile = nil
173
169
  encoding = nil
@@ -182,24 +178,21 @@ module Cheminee
182
178
  prefix = prefix + '-' unless prefix.end_with?('-')
183
179
  encoding = response.body.encoding
184
180
  tempfile = Tempfile.open(prefix, @config.temp_folder_path, encoding: encoding)
181
+ @tempfile = tempfile
185
182
  end
186
183
  request.on_body do |chunk|
187
184
  chunk.force_encoding(encoding)
188
185
  tempfile.write(chunk)
189
186
  end
190
- # run the request to ensure the tempfile is created successfully before returning it
191
- request.run
192
- if tempfile
193
- tempfile.close
194
- @config.logger.info "Temp file written to #{tempfile.path}, please copy the file to a proper folder "\
195
- "with e.g. `FileUtils.cp(tempfile.path, '/new/file/path')` otherwise the temp file "\
196
- "will be deleted automatically with GC. It's also recommended to delete the temp file "\
197
- "explicitly with `tempfile.delete`"
198
- else
199
- fail ApiError.new("Failed to create the tempfile based on the HTTP response from the server: #{request.inspect}")
187
+ request.on_complete do |response|
188
+ if tempfile
189
+ tempfile.close
190
+ @config.logger.info "Temp file written to #{tempfile.path}, please copy the file to a proper folder "\
191
+ "with e.g. `FileUtils.cp(tempfile.path, '/new/file/path')` otherwise the temp file "\
192
+ "will be deleted automatically with GC. It's also recommended to delete the temp file "\
193
+ "explicitly with `tempfile.delete`"
194
+ end
200
195
  end
201
-
202
- tempfile
203
196
  end
204
197
 
205
198
  # Check if the given MIME is a JSON MIME.
@@ -220,10 +213,15 @@ module Cheminee
220
213
  # @param [String] return_type some examples: "User", "Array<User>", "Hash<String, Integer>"
221
214
  def deserialize(response, return_type)
222
215
  body = response.body
216
+
217
+ # handle file downloading - return the File instance processed in request callbacks
218
+ # note that response body is empty when the file is written in chunks in request on_body callback
219
+ return @tempfile if return_type == 'File'
220
+
223
221
  return nil if body.nil? || body.empty?
224
222
 
225
223
  # return response body directly for String return type
226
- return body.to_s if return_type == 'String'
224
+ return body if return_type == 'String'
227
225
 
228
226
  # ensuring a default content type
229
227
  content_type = response.headers['Content-Type'] || 'application/json'
@@ -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: 7.3.0-SNAPSHOT
9
+ OpenAPI Generator version: 7.0.0-SNAPSHOT
10
10
 
11
11
  =end
12
12