cheminee 0.1.5 → 0.1.7

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    cheminee (0.1.5)
+    cheminee (0.1.7)
       typhoeus (~> 1.0, >= 1.0.1)
 
 GEM

data/README.md

@@ -7,7 +7,7 @@ Cheminée: The Chemical Structure Search Engine
 This SDK is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
 - API version: 1.0
-- Package version: 0.1.5
+- Package version: 0.1.7
 - Build package: org.openapitools.codegen.languages.RubyClientCodegen
 For more information, please visit [https://github.com/rdkit-rs/cheminee](https://github.com/rdkit-rs/cheminee)
 
@@ -24,16 +24,16 @@ gem build cheminee.gemspec
 Then either install the gem locally:
 
 ```shell
-gem install ./cheminee-0.1.5.gem
+gem install ./cheminee-0.1.7.gem
 ```
 
-(for development, run `gem install --dev ./cheminee-0.1.5.gem` to install the development dependencies)
+(for development, run `gem install --dev ./cheminee-0.1.7.gem` to install the development dependencies)
 
 or publish the gem to a gem hosting service, e.g. [RubyGems](https://rubygems.org/).
 
 Finally add this to the Gemfile:
 
-    gem 'cheminee', '~> 0.1.5'
+    gem 'cheminee', '~> 0.1.7'
 
 ### Install from Git
 
@@ -60,6 +60,7 @@ require 'cheminee'
 api_instance = Cheminee::DefaultApi.new
 
 begin
+  #List indexes
   result = api_instance.v1_indexes_get
   p result
 rescue Cheminee::ApiError => e
@@ -74,20 +75,26 @@ All URIs are relative to *http://localhost:3000/api*
 
 Class | Method | HTTP request | Description
 ------------ | ------------- | ------------- | -------------
-*Cheminee::DefaultApi* | [**v1_indexes_get**](docs/DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes | 
-*Cheminee::DefaultApi* | [**v1_indexes_index_get**](docs/DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | 
-*Cheminee::DefaultApi* | [**v1_indexes_index_post**](docs/DefaultApi.md#v1_indexes_index_post) | **POST** /v1/indexes/{index} | 
-*Cheminee::DefaultApi* | [**v1_indexes_index_search_substructure_get**](docs/DefaultApi.md#v1_indexes_index_search_substructure_get) | **GET** /v1/indexes/{index}/search/substructure | 
-*Cheminee::DefaultApi* | [**v1_schemas_get**](docs/DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | 
-*Cheminee::DefaultApi* | [**v1_standardize_post**](docs/DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize | 
+*Cheminee::DefaultApi* | [**v1_indexes_get**](docs/DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes | List indexes
+*Cheminee::DefaultApi* | [**v1_indexes_index_bulk_index_post**](docs/DefaultApi.md#v1_indexes_index_bulk_index_post) | **POST** /v1/indexes/{index}/bulk_index | Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
+*Cheminee::DefaultApi* | [**v1_indexes_index_get**](docs/DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | Get extended information about an index
+*Cheminee::DefaultApi* | [**v1_indexes_index_post**](docs/DefaultApi.md#v1_indexes_index_post) | **POST** /v1/indexes/{index} | Create an index
+*Cheminee::DefaultApi* | [**v1_indexes_index_search_substructure_get**](docs/DefaultApi.md#v1_indexes_index_search_substructure_get) | **GET** /v1/indexes/{index}/search/substructure | Perform substructure search against index
+*Cheminee::DefaultApi* | [**v1_schemas_get**](docs/DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | List schemas available for creating indexes
+*Cheminee::DefaultApi* | [**v1_standardize_post**](docs/DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
 
 
 ## Documentation for Models
 
+ - [Cheminee::BulkRequest](docs/BulkRequest.md)
+ - [Cheminee::BulkRequestDoc](docs/BulkRequestDoc.md)
  - [Cheminee::CreateIndexError](docs/CreateIndexError.md)
  - [Cheminee::GetIndexesResponseError](docs/GetIndexesResponseError.md)
  - [Cheminee::IndexMeta](docs/IndexMeta.md)
  - [Cheminee::ListIndexResponseErr](docs/ListIndexResponseErr.md)
+ - [Cheminee::PostIndexBulkResponseError](docs/PostIndexBulkResponseError.md)
+ - [Cheminee::PostIndexBulkResponseOk](docs/PostIndexBulkResponseOk.md)
+ - [Cheminee::PostIndexBulkResponseOkStatus](docs/PostIndexBulkResponseOkStatus.md)
  - [Cheminee::Schema](docs/Schema.md)
  - [Cheminee::Smile](docs/Smile.md)
  - [Cheminee::StandardizedSmile](docs/StandardizedSmile.md)

data/docs/BulkRequest.md

@@ -0,0 +1,18 @@
+# Cheminee::BulkRequest
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **docs** | [**Array<BulkRequestDoc>**](BulkRequestDoc.md) |  |  |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::BulkRequest.new(
+  docs: null
+)
+```
+

data/docs/BulkRequestDoc.md

@@ -0,0 +1,20 @@
+# Cheminee::BulkRequestDoc
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **smile** | **String** |  |  |
+| **extra_data** | **Object** | This value can store an arbitrary JSON object like '{}' | [optional] |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::BulkRequestDoc.new(
+  smile: null,
+  extra_data: null
+)
+```
+

data/docs/DefaultApi.md

@@ -4,19 +4,20 @@ All URIs are relative to *http://localhost:3000/api*
 
 | Method | HTTP request | Description |
 | ------ | ------------ | ----------- |
-| [**v1_indexes_get**](DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes |  |
-| [**v1_indexes_index_get**](DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} |  |
-| [**v1_indexes_index_post**](DefaultApi.md#v1_indexes_index_post) | **POST** /v1/indexes/{index} |  |
-| [**v1_indexes_index_search_substructure_get**](DefaultApi.md#v1_indexes_index_search_substructure_get) | **GET** /v1/indexes/{index}/search/substructure |  |
-| [**v1_schemas_get**](DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas |  |
-| [**v1_standardize_post**](DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize |  |
+| [**v1_indexes_get**](DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes | List indexes |
+| [**v1_indexes_index_bulk_index_post**](DefaultApi.md#v1_indexes_index_bulk_index_post) | **POST** /v1/indexes/{index}/bulk_index | Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable |
+| [**v1_indexes_index_get**](DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | Get extended information about an index |
+| [**v1_indexes_index_post**](DefaultApi.md#v1_indexes_index_post) | **POST** /v1/indexes/{index} | Create an index |
+| [**v1_indexes_index_search_substructure_get**](DefaultApi.md#v1_indexes_index_search_substructure_get) | **GET** /v1/indexes/{index}/search/substructure | Perform substructure search against index |
+| [**v1_schemas_get**](DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | List schemas available for creating indexes |
+| [**v1_standardize_post**](DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines |
 
 
 ## v1_indexes_get
 
 > <Array<IndexMeta>> v1_indexes_get
 
-
+List indexes
 
 ### Examples
 
@@ -27,7 +28,7 @@ require 'cheminee'
 api_instance = Cheminee::DefaultApi.new
 
 begin
-  
+  # List indexes
   result = api_instance.v1_indexes_get
   p result
 rescue Cheminee::ApiError => e
@@ -43,7 +44,7 @@ This returns an Array which contains the response data, status code and headers.
 
 ```ruby
 begin
-  
+  # List indexes
   data, status_code, headers = api_instance.v1_indexes_get_with_http_info
   p status_code # => 2xx
   p headers # => { ... }
@@ -71,11 +72,75 @@ No authorization required
 - **Accept**: application/json; charset=utf-8
 
 
+## v1_indexes_index_bulk_index_post
+
+> <PostIndexBulkResponseOk> v1_indexes_index_bulk_index_post(index, bulk_request)
+
+Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
+
+### Examples
+
+```ruby
+require 'time'
+require 'cheminee'
+
+api_instance = Cheminee::DefaultApi.new
+index = 'index_example' # String | 
+bulk_request = Cheminee::BulkRequest.new({docs: [Cheminee::BulkRequestDoc.new({smile: 'smile_example'})]}) # BulkRequest | 
+
+begin
+  # Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
+  result = api_instance.v1_indexes_index_bulk_index_post(index, bulk_request)
+  p result
+rescue Cheminee::ApiError => e
+  puts "Error when calling DefaultApi->v1_indexes_index_bulk_index_post: #{e}"
+end
+```
+
+#### Using the v1_indexes_index_bulk_index_post_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<PostIndexBulkResponseOk>, Integer, Hash)> v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request)
+
+```ruby
+begin
+  # Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
+  data, status_code, headers = api_instance.v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <PostIndexBulkResponseOk>
+rescue Cheminee::ApiError => e
+  puts "Error when calling DefaultApi->v1_indexes_index_bulk_index_post_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **index** | **String** |  |  |
+| **bulk_request** | [**BulkRequest**](BulkRequest.md) |  |  |
+
+### Return type
+
+[**PostIndexBulkResponseOk**](PostIndexBulkResponseOk.md)
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+- **Content-Type**: application/json; charset=utf-8
+- **Accept**: application/json; charset=utf-8
+
+
 ## v1_indexes_index_get
 
 > <Array<IndexMeta>> v1_indexes_index_get(index)
 
-
+Get extended information about an index
 
 ### Examples
 
@@ -87,7 +152,7 @@ api_instance = Cheminee::DefaultApi.new
 index = 'index_example' # String | 
 
 begin
-  
+  # Get extended information about an index
   result = api_instance.v1_indexes_index_get(index)
   p result
 rescue Cheminee::ApiError => e
@@ -103,7 +168,7 @@ This returns an Array which contains the response data, status code and headers.
 
 ```ruby
 begin
-  
+  # Get extended information about an index
   data, status_code, headers = api_instance.v1_indexes_index_get_with_http_info(index)
   p status_code # => 2xx
   p headers # => { ... }
@@ -137,7 +202,7 @@ No authorization required
 
 > <IndexMeta> v1_indexes_index_post(index, schema, opts)
 
-
+Create an index
 
 ### Examples
 
@@ -153,7 +218,7 @@ opts = {
 }
 
 begin
-  
+  # Create an index
   result = api_instance.v1_indexes_index_post(index, schema, opts)
   p result
 rescue Cheminee::ApiError => e
@@ -169,7 +234,7 @@ This returns an Array which contains the response data, status code and headers.
 
 ```ruby
 begin
-  
+  # Create an index
   data, status_code, headers = api_instance.v1_indexes_index_post_with_http_info(index, schema, opts)
   p status_code # => 2xx
   p headers # => { ... }
@@ -205,7 +270,7 @@ No authorization required
 
 > <Array<SubstructureSearchHit>> v1_indexes_index_search_substructure_get(index, q)
 
-
+Perform substructure search against index
 
 ### Examples
 
@@ -218,7 +283,7 @@ index = 'index_example' # String |
 q = 'q_example' # String | 
 
 begin
-  
+  # Perform substructure search against index
   result = api_instance.v1_indexes_index_search_substructure_get(index, q)
   p result
 rescue Cheminee::ApiError => e
@@ -234,7 +299,7 @@ This returns an Array which contains the response data, status code and headers.
 
 ```ruby
 begin
-  
+  # Perform substructure search against index
   data, status_code, headers = api_instance.v1_indexes_index_search_substructure_get_with_http_info(index, q)
   p status_code # => 2xx
   p headers # => { ... }
@@ -269,7 +334,7 @@ No authorization required
 
 > <Array<Schema>> v1_schemas_get
 
-
+List schemas available for creating indexes
 
 ### Examples
 
@@ -280,7 +345,7 @@ require 'cheminee'
 api_instance = Cheminee::DefaultApi.new
 
 begin
-  
+  # List schemas available for creating indexes
   result = api_instance.v1_schemas_get
   p result
 rescue Cheminee::ApiError => e
@@ -296,7 +361,7 @@ This returns an Array which contains the response data, status code and headers.
 
 ```ruby
 begin
-  
+  # List schemas available for creating indexes
   data, status_code, headers = api_instance.v1_schemas_get_with_http_info
   p status_code # => 2xx
   p headers # => { ... }
@@ -328,7 +393,7 @@ No authorization required
 
 > <Array<StandardizedSmile>> v1_standardize_post(smile)
 
-
+Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
 
 ### Examples
 
@@ -340,7 +405,7 @@ api_instance = Cheminee::DefaultApi.new
 smile = [Cheminee::Smile.new({smile: 'smile_example'})] # Array<Smile> | 
 
 begin
-  
+  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
   result = api_instance.v1_standardize_post(smile)
   p result
 rescue Cheminee::ApiError => e
@@ -356,7 +421,7 @@ This returns an Array which contains the response data, status code and headers.
 
 ```ruby
 begin
-  
+  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
   data, status_code, headers = api_instance.v1_standardize_post_with_http_info(smile)
   p status_code # => 2xx
   p headers # => { ... }

data/docs/PostIndexBulkResponseError.md

@@ -0,0 +1,18 @@
+# Cheminee::PostIndexBulkResponseError
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **error** | **String** |  |  |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::PostIndexBulkResponseError.new(
+  error: null
+)
+```
+

data/docs/PostIndexBulkResponseOk.md

@@ -0,0 +1,18 @@
+# Cheminee::PostIndexBulkResponseOk
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **statuses** | [**Array<PostIndexBulkResponseOkStatus>**](PostIndexBulkResponseOkStatus.md) |  |  |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::PostIndexBulkResponseOk.new(
+  statuses: null
+)
+```
+

data/docs/PostIndexBulkResponseOkStatus.md

@@ -0,0 +1,20 @@
+# Cheminee::PostIndexBulkResponseOkStatus
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **opcode** | **Integer** |  | [optional] |
+| **error** | **String** |  | [optional] |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::PostIndexBulkResponseOkStatus.new(
+  opcode: null,
+  error: null
+)
+```
+

data/lib/cheminee/api/default_api.rb

@@ -19,6 +19,7 @@ module Cheminee
     def initialize(api_client = ApiClient.default)
       @api_client = api_client
     end
+    # List indexes
     # @param [Hash] opts the optional parameters
     # @return [Array<IndexMeta>]
     def v1_indexes_get(opts = {})
@@ -26,6 +27,7 @@ module Cheminee
       data
     end
 
+    # List indexes
     # @param [Hash] opts the optional parameters
     # @return [Array<(Array<IndexMeta>, Integer, Hash)>] Array<IndexMeta> data, response status code and response headers
     def v1_indexes_get_with_http_info(opts = {})
@@ -72,6 +74,79 @@ module Cheminee
       return data, status_code, headers
     end
 
+    # Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
+    # @param index [String] 
+    # @param bulk_request [BulkRequest] 
+    # @param [Hash] opts the optional parameters
+    # @return [PostIndexBulkResponseOk]
+    def v1_indexes_index_bulk_index_post(index, bulk_request, opts = {})
+      data, _status_code, _headers = v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request, opts)
+      data
+    end
+
+    # Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
+    # @param index [String] 
+    # @param bulk_request [BulkRequest] 
+    # @param [Hash] opts the optional parameters
+    # @return [Array<(PostIndexBulkResponseOk, Integer, Hash)>] PostIndexBulkResponseOk data, response status code and response headers
+    def v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request, opts = {})
+      if @api_client.config.debugging
+        @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_bulk_index_post ...'
+      end
+      # verify the required parameter 'index' is set
+      if @api_client.config.client_side_validation && index.nil?
+        fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_bulk_index_post"
+      end
+      # verify the required parameter 'bulk_request' is set
+      if @api_client.config.client_side_validation && bulk_request.nil?
+        fail ArgumentError, "Missing the required parameter 'bulk_request' when calling DefaultApi.v1_indexes_index_bulk_index_post"
+      end
+      # resource path
+      local_var_path = '/v1/indexes/{index}/bulk_index'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
+
+      # query parameters
+      query_params = opts[:query_params] || {}
+
+      # header parameters
+      header_params = opts[:header_params] || {}
+      # HTTP header 'Accept' (if needed)
+      header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
+      # HTTP header 'Content-Type'
+      content_type = @api_client.select_header_content_type(['application/json; charset=utf-8'])
+      if !content_type.nil?
+          header_params['Content-Type'] = content_type
+      end
+
+      # form parameters
+      form_params = opts[:form_params] || {}
+
+      # http body (model)
+      post_body = opts[:debug_body] || @api_client.object_to_http_body(bulk_request)
+
+      # return_type
+      return_type = opts[:debug_return_type] || 'PostIndexBulkResponseOk'
+
+      # auth_names
+      auth_names = opts[:debug_auth_names] || []
+
+      new_options = opts.merge(
+        :operation => :"DefaultApi.v1_indexes_index_bulk_index_post",
+        :header_params => header_params,
+        :query_params => query_params,
+        :form_params => form_params,
+        :body => post_body,
+        :auth_names => auth_names,
+        :return_type => return_type
+      )
+
+      data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
+      if @api_client.config.debugging
+        @api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_bulk_index_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
+      end
+      return data, status_code, headers
+    end
+
+    # Get extended information about an index
     # @param index [String] 
     # @param [Hash] opts the optional parameters
     # @return [Array<IndexMeta>]
@@ -80,6 +155,7 @@ module Cheminee
       data
     end
 
+    # Get extended information about an index
     # @param index [String] 
     # @param [Hash] opts the optional parameters
     # @return [Array<(Array<IndexMeta>, Integer, Hash)>] Array<IndexMeta> data, response status code and response headers
@@ -131,6 +207,7 @@ module Cheminee
       return data, status_code, headers
     end
 
+    # Create an index
     # @param index [String] 
     # @param schema [String] 
     # @param [Hash] opts the optional parameters
@@ -141,6 +218,7 @@ module Cheminee
       data
     end
 
+    # Create an index
     # @param index [String] 
     # @param schema [String] 
     # @param [Hash] opts the optional parameters
@@ -200,6 +278,7 @@ module Cheminee
       return data, status_code, headers
     end
 
+    # Perform substructure search against index
     # @param index [String] 
     # @param q [String] 
     # @param [Hash] opts the optional parameters
@@ -209,6 +288,7 @@ module Cheminee
       data
     end
 
+    # Perform substructure search against index
     # @param index [String] 
     # @param q [String] 
     # @param [Hash] opts the optional parameters
@@ -266,6 +346,7 @@ module Cheminee
       return data, status_code, headers
     end
 
+    # List schemas available for creating indexes
     # @param [Hash] opts the optional parameters
     # @return [Array<Schema>]
     def v1_schemas_get(opts = {})
@@ -273,6 +354,7 @@ module Cheminee
       data
     end
 
+    # List schemas available for creating indexes
     # @param [Hash] opts the optional parameters
     # @return [Array<(Array<Schema>, Integer, Hash)>] Array<Schema> data, response status code and response headers
     def v1_schemas_get_with_http_info(opts = {})
@@ -319,6 +401,7 @@ module Cheminee
       return data, status_code, headers
     end
 
+    # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
     # @param smile [Array<Smile>] 
     # @param [Hash] opts the optional parameters
     # @return [Array<StandardizedSmile>]
@@ -327,6 +410,7 @@ module Cheminee
       data
     end
 
+    # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
     # @param smile [Array<Smile>] 
     # @param [Hash] opts the optional parameters
     # @return [Array<(Array<StandardizedSmile>, Integer, Hash)>] Array<StandardizedSmile> data, response status code and response headers