cheminee 0.0.14 → 0.0.15

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
@@ -1,221 +0,0 @@
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- =begin
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- #Cheminée
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-
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- #Cheminée: The Chemical Structure Search Engine
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-
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- The version of the OpenAPI document: 1.0
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-
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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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-
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- =end
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-
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- require 'date'
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- require 'time'
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-
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- module Cheminee
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- class StructureResponseError
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- attr_accessor :error
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-
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- # Attribute mapping from ruby-style variable name to JSON key.
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- def self.attribute_map
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- {
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- :'error' => :'error'
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- }
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- end
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-
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- # Returns all the JSON keys this model knows about
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- def self.acceptable_attributes
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- attribute_map.values
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- end
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-
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- # Attribute type mapping.
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- def self.openapi_types
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- {
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- :'error' => :'String'
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- }
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- end
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-
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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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- ])
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- end
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-
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- # Initializes the object
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- # @param [Hash] attributes Model attributes in the form of hash
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- def initialize(attributes = {})
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- if (!attributes.is_a?(Hash))
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- fail ArgumentError, "The input argument (attributes) must be a hash in `Cheminee::StructureResponseError` initialize method"
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- end
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-
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- # check to see if the attribute exists and convert string to symbol for hash key
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- attributes = attributes.each_with_object({}) { |(k, v), h|
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- if (!self.class.attribute_map.key?(k.to_sym))
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- fail ArgumentError, "`#{k}` is not a valid attribute in `Cheminee::StructureResponseError`. Please check the name to make sure it's valid. List of attributes: " + self.class.attribute_map.keys.inspect
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- end
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- h[k.to_sym] = v
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- }
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-
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- if attributes.key?(:'error')
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- self.error = attributes[:'error']
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- else
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- self.error = nil
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- end
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- end
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-
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- # Show invalid properties with the reasons. Usually used together with valid?
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- # @return Array for valid properties with the reasons
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- def list_invalid_properties
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- warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
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- invalid_properties = Array.new
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- if @error.nil?
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- invalid_properties.push('invalid value for "error", error cannot be nil.')
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- end
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-
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- invalid_properties
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- end
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-
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- # Check to see if the all the properties in the model are valid
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- # @return true if the model is valid
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- def valid?
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- warn '[DEPRECATED] the `valid?` method is obsolete'
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- return false if @error.nil?
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- true
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- end
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-
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- # Checks equality by comparing each attribute.
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- # @param [Object] Object to be compared
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- def ==(o)
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- return true if self.equal?(o)
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- self.class == o.class &&
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- error == o.error
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- end
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-
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- # @see the `==` method
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- # @param [Object] Object to be compared
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- def eql?(o)
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- self == o
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- end
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-
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- # Calculates hash code according to all attributes.
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- # @return [Integer] Hash code
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- def hash
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- [error].hash
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- end
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-
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- # Builds the object from hash
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- # @param [Hash] attributes Model attributes in the form of hash
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- # @return [Object] Returns the model itself
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- def self.build_from_hash(attributes)
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- return nil unless attributes.is_a?(Hash)
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- attributes = attributes.transform_keys(&:to_sym)
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- transformed_hash = {}
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- openapi_types.each_pair do |key, type|
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- if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
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- transformed_hash["#{key}"] = nil
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- elsif type =~ /\AArray<(.*)>/i
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- # check to ensure the input is an array given that the attribute
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- # is documented as an array but the input is not
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- if attributes[attribute_map[key]].is_a?(Array)
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- transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
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- end
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- elsif !attributes[attribute_map[key]].nil?
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- transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
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- end
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- end
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- new(transformed_hash)
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- end
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-
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- # Deserializes the data based on type
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- # @param string type Data type
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- # @param string value Value to be deserialized
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- # @return [Object] Deserialized data
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- def self._deserialize(type, value)
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- case type.to_sym
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- when :Time
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- Time.parse(value)
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- when :Date
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- Date.parse(value)
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- when :String
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- value.to_s
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- when :Integer
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- value.to_i
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- when :Float
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- value.to_f
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- when :Boolean
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- if value.to_s =~ /\A(true|t|yes|y|1)\z/i
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- true
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- else
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- false
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- end
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- when :Object
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- # generic object (usually a Hash), return directly
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- value
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- when /\AArray<(?<inner_type>.+)>\z/
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- inner_type = Regexp.last_match[:inner_type]
157
- value.map { |v| _deserialize(inner_type, v) }
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- when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
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- k_type = Regexp.last_match[:k_type]
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- v_type = Regexp.last_match[:v_type]
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- {}.tap do |hash|
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- value.each do |k, v|
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- hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
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- end
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- end
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- else # model
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- # models (e.g. Pet) or oneOf
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- klass = Cheminee.const_get(type)
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- klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
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- end
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- end
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-
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- # Returns the string representation of the object
174
- # @return [String] String presentation of the object
175
- def to_s
176
- to_hash.to_s
177
- end
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-
179
- # to_body is an alias to to_hash (backward compatibility)
180
- # @return [Hash] Returns the object in the form of hash
181
- def to_body
182
- to_hash
183
- end
184
-
185
- # Returns the object in the form of hash
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- # @return [Hash] Returns the object in the form of hash
187
- def to_hash
188
- hash = {}
189
- self.class.attribute_map.each_pair do |attr, param|
190
- value = self.send(attr)
191
- if value.nil?
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- is_nullable = self.class.openapi_nullable.include?(attr)
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- next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
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- end
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-
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- hash[param] = _to_hash(value)
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- end
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- hash
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- end
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-
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- # Outputs non-array value in the form of hash
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- # For object, use to_hash. Otherwise, just return the value
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- # @param [Object] value Any valid value
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- # @return [Hash] Returns the value in the form of hash
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- def _to_hash(value)
206
- if value.is_a?(Array)
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- value.compact.map { |v| _to_hash(v) }
208
- elsif value.is_a?(Hash)
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- {}.tap do |hash|
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- value.each { |k, v| hash[k] = _to_hash(v) }
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- end
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- elsif value.respond_to? :to_hash
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- value.to_hash
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- else
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- value
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- end
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- end
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-
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- end
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-
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- end
@@ -1,281 +0,0 @@
1
- =begin
2
- #Cheminée
3
-
4
- #Cheminée: The Chemical Structure Search Engine
5
-
6
- The version of the OpenAPI document: 1.0
7
-
8
- Generated by: https://openapi-generator.tech
9
- OpenAPI Generator version: 7.3.0-SNAPSHOT
10
-
11
- =end
12
-
13
- require 'date'
14
- require 'time'
15
-
16
- module Cheminee
17
- class StructureSearchHit
18
- attr_accessor :extra_data
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-
20
- attr_accessor :smiles
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-
22
- attr_accessor :score
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-
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- attr_accessor :query
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-
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- attr_accessor :used_tautomers
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-
28
- # Attribute mapping from ruby-style variable name to JSON key.
29
- def self.attribute_map
30
- {
31
- :'extra_data' => :'extra_data',
32
- :'smiles' => :'smiles',
33
- :'score' => :'score',
34
- :'query' => :'query',
35
- :'used_tautomers' => :'used_tautomers'
36
- }
37
- end
38
-
39
- # Returns all the JSON keys this model knows about
40
- def self.acceptable_attributes
41
- attribute_map.values
42
- end
43
-
44
- # Attribute type mapping.
45
- def self.openapi_types
46
- {
47
- :'extra_data' => :'Object',
48
- :'smiles' => :'String',
49
- :'score' => :'Float',
50
- :'query' => :'String',
51
- :'used_tautomers' => :'Boolean'
52
- }
53
- end
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-
55
- # List of attributes with nullable: true
56
- def self.openapi_nullable
57
- Set.new([
58
- :'extra_data',
59
- ])
60
- end
61
-
62
- # Initializes the object
63
- # @param [Hash] attributes Model attributes in the form of hash
64
- def initialize(attributes = {})
65
- if (!attributes.is_a?(Hash))
66
- fail ArgumentError, "The input argument (attributes) must be a hash in `Cheminee::StructureSearchHit` initialize method"
67
- end
68
-
69
- # check to see if the attribute exists and convert string to symbol for hash key
70
- attributes = attributes.each_with_object({}) { |(k, v), h|
71
- if (!self.class.attribute_map.key?(k.to_sym))
72
- fail ArgumentError, "`#{k}` is not a valid attribute in `Cheminee::StructureSearchHit`. Please check the name to make sure it's valid. List of attributes: " + self.class.attribute_map.keys.inspect
73
- end
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- h[k.to_sym] = v
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- }
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-
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- if attributes.key?(:'extra_data')
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- self.extra_data = attributes[:'extra_data']
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- else
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- self.extra_data = nil
81
- end
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-
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- if attributes.key?(:'smiles')
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- self.smiles = attributes[:'smiles']
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- else
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- self.smiles = nil
87
- end
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-
89
- if attributes.key?(:'score')
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- self.score = attributes[:'score']
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- else
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- self.score = nil
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- end
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-
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- if attributes.key?(:'query')
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- self.query = attributes[:'query']
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- else
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- self.query = nil
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- end
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-
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- if attributes.key?(:'used_tautomers')
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- self.used_tautomers = attributes[:'used_tautomers']
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- else
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- self.used_tautomers = nil
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- end
106
- end
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-
108
- # Show invalid properties with the reasons. Usually used together with valid?
109
- # @return Array for valid properties with the reasons
110
- def list_invalid_properties
111
- warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
112
- invalid_properties = Array.new
113
- if @smiles.nil?
114
- invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
115
- end
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-
117
- if @score.nil?
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- invalid_properties.push('invalid value for "score", score cannot be nil.')
119
- end
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-
121
- if @query.nil?
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- invalid_properties.push('invalid value for "query", query cannot be nil.')
123
- end
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-
125
- if @used_tautomers.nil?
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- invalid_properties.push('invalid value for "used_tautomers", used_tautomers cannot be nil.')
127
- end
128
-
129
- invalid_properties
130
- end
131
-
132
- # Check to see if the all the properties in the model are valid
133
- # @return true if the model is valid
134
- def valid?
135
- warn '[DEPRECATED] the `valid?` method is obsolete'
136
- return false if @smiles.nil?
137
- return false if @score.nil?
138
- return false if @query.nil?
139
- return false if @used_tautomers.nil?
140
- true
141
- end
142
-
143
- # Checks equality by comparing each attribute.
144
- # @param [Object] Object to be compared
145
- def ==(o)
146
- return true if self.equal?(o)
147
- self.class == o.class &&
148
- extra_data == o.extra_data &&
149
- smiles == o.smiles &&
150
- score == o.score &&
151
- query == o.query &&
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- used_tautomers == o.used_tautomers
153
- end
154
-
155
- # @see the `==` method
156
- # @param [Object] Object to be compared
157
- def eql?(o)
158
- self == o
159
- end
160
-
161
- # Calculates hash code according to all attributes.
162
- # @return [Integer] Hash code
163
- def hash
164
- [extra_data, smiles, score, query, used_tautomers].hash
165
- end
166
-
167
- # Builds the object from hash
168
- # @param [Hash] attributes Model attributes in the form of hash
169
- # @return [Object] Returns the model itself
170
- def self.build_from_hash(attributes)
171
- return nil unless attributes.is_a?(Hash)
172
- attributes = attributes.transform_keys(&:to_sym)
173
- transformed_hash = {}
174
- openapi_types.each_pair do |key, type|
175
- if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
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- transformed_hash["#{key}"] = nil
177
- elsif type =~ /\AArray<(.*)>/i
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- # check to ensure the input is an array given that the attribute
179
- # is documented as an array but the input is not
180
- if attributes[attribute_map[key]].is_a?(Array)
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- transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
182
- end
183
- elsif !attributes[attribute_map[key]].nil?
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- transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
185
- end
186
- end
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- new(transformed_hash)
188
- end
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-
190
- # Deserializes the data based on type
191
- # @param string type Data type
192
- # @param string value Value to be deserialized
193
- # @return [Object] Deserialized data
194
- def self._deserialize(type, value)
195
- case type.to_sym
196
- when :Time
197
- Time.parse(value)
198
- when :Date
199
- Date.parse(value)
200
- when :String
201
- value.to_s
202
- when :Integer
203
- value.to_i
204
- when :Float
205
- value.to_f
206
- when :Boolean
207
- if value.to_s =~ /\A(true|t|yes|y|1)\z/i
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- true
209
- else
210
- false
211
- end
212
- when :Object
213
- # generic object (usually a Hash), return directly
214
- value
215
- when /\AArray<(?<inner_type>.+)>\z/
216
- inner_type = Regexp.last_match[:inner_type]
217
- value.map { |v| _deserialize(inner_type, v) }
218
- when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
219
- k_type = Regexp.last_match[:k_type]
220
- v_type = Regexp.last_match[:v_type]
221
- {}.tap do |hash|
222
- value.each do |k, v|
223
- hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
224
- end
225
- end
226
- else # model
227
- # models (e.g. Pet) or oneOf
228
- klass = Cheminee.const_get(type)
229
- klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
230
- end
231
- end
232
-
233
- # Returns the string representation of the object
234
- # @return [String] String presentation of the object
235
- def to_s
236
- to_hash.to_s
237
- end
238
-
239
- # to_body is an alias to to_hash (backward compatibility)
240
- # @return [Hash] Returns the object in the form of hash
241
- def to_body
242
- to_hash
243
- end
244
-
245
- # Returns the object in the form of hash
246
- # @return [Hash] Returns the object in the form of hash
247
- def to_hash
248
- hash = {}
249
- self.class.attribute_map.each_pair do |attr, param|
250
- value = self.send(attr)
251
- if value.nil?
252
- is_nullable = self.class.openapi_nullable.include?(attr)
253
- next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
254
- end
255
-
256
- hash[param] = _to_hash(value)
257
- end
258
- hash
259
- end
260
-
261
- # Outputs non-array value in the form of hash
262
- # For object, use to_hash. Otherwise, just return the value
263
- # @param [Object] value Any valid value
264
- # @return [Hash] Returns the value in the form of hash
265
- def _to_hash(value)
266
- if value.is_a?(Array)
267
- value.compact.map { |v| _to_hash(v) }
268
- elsif value.is_a?(Hash)
269
- {}.tap do |hash|
270
- value.each { |k, v| hash[k] = _to_hash(v) }
271
- end
272
- elsif value.respond_to? :to_hash
273
- value.to_hash
274
- else
275
- value
276
- end
277
- end
278
-
279
- end
280
-
281
- end