cheminee 0.0.15
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- checksums.yaml +7 -0
- data/Gemfile +9 -0
- data/Gemfile.lock +72 -0
- data/README.md +90 -0
- data/Rakefile +10 -0
- data/cheminee.gemspec +38 -0
- data/docs/DefaultApi.md +70 -0
- data/docs/Smile.md +18 -0
- data/docs/StandardizedSmile.md +20 -0
- data/git_push.sh +57 -0
- data/lib/cheminee/api/default_api.rb +86 -0
- data/lib/cheminee/api_client.rb +391 -0
- data/lib/cheminee/api_error.rb +58 -0
- data/lib/cheminee/configuration.rb +290 -0
- data/lib/cheminee/models/smile.rb +221 -0
- data/lib/cheminee/models/standardized_smile.rb +223 -0
- data/lib/cheminee/version.rb +15 -0
- data/lib/cheminee.rb +42 -0
- data/openapi-generator-config.json +7 -0
- data/openapi.json +77 -0
- data/pkg/cheminee-0.0.15.gem +0 -0
- data/spec/api/default_api_spec.rb +45 -0
- data/spec/api_client_spec.rb +228 -0
- data/spec/configuration_spec.rb +42 -0
- data/spec/models/smile_spec.rb +34 -0
- data/spec/models/standardized_smile_spec.rb +40 -0
- data/spec/spec_helper.rb +111 -0
- metadata +115 -0
checksums.yaml
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---
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SHA256:
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SHA512:
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metadata.gz: bc6a0005d9bc67f6a9a8224e1a293e615fada51873b3a3d2ca06bfabe906538051e0d3c09530dcb0727cdad7cf27bdd25655ebe6e3791ab64c89c5171bcc34f4
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data/Gemfile
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data/Gemfile.lock
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PATH
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remote: .
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specs:
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cheminee (0.0.15)
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typhoeus (~> 1.0, >= 1.0.1)
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GEM
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remote: https://rubygems.org/
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specs:
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ast (2.4.2)
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byebug (11.1.3)
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coderay (1.1.3)
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diff-lcs (1.5.0)
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ethon (0.16.0)
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ffi (>= 1.15.0)
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ffi (1.15.5)
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jaro_winkler (1.5.6)
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method_source (1.0.0)
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parallel (1.23.0)
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parser (3.2.2.3)
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ast (~> 2.4.1)
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racc
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pry (0.14.2)
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coderay (~> 1.1)
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method_source (~> 1.0)
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pry-byebug (3.10.1)
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byebug (~> 11.0)
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pry (>= 0.13, < 0.15)
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psych (5.1.0)
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stringio
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racc (1.7.1)
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rainbow (3.1.1)
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rake (13.0.6)
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rspec (3.12.0)
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rspec-core (~> 3.12.0)
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rspec-expectations (~> 3.12.0)
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rspec-mocks (~> 3.12.0)
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rspec-core (3.12.2)
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rspec-support (~> 3.12.0)
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rspec-expectations (3.12.3)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.12.0)
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rspec-mocks (3.12.6)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.12.0)
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rspec-support (3.12.1)
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rubocop (0.66.0)
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jaro_winkler (~> 1.5.1)
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parallel (~> 1.10)
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parser (>= 2.5, != 2.5.1.1)
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psych (>= 3.1.0)
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rainbow (>= 2.2.2, < 4.0)
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ruby-progressbar (~> 1.7)
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unicode-display_width (>= 1.4.0, < 1.6)
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ruby-progressbar (1.13.0)
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stringio (3.0.8)
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typhoeus (1.4.0)
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ethon (>= 0.9.0)
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unicode-display_width (1.5.0)
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PLATFORMS
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x86_64-linux
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DEPENDENCIES
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cheminee!
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pry-byebug
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rake (~> 13.0.1)
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rspec (~> 3.6, >= 3.6.0)
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rubocop (~> 0.66.0)
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BUNDLED WITH
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2.4.10
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data/README.md
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# cheminee
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Cheminee - the Ruby gem for the Cheminée
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Cheminée: The Chemical Structure Search Engine
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This SDK is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
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- API version: 1.0
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- Package version: 0.0.15
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- Build package: org.openapitools.codegen.languages.RubyClientCodegen
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For more information, please visit [https://github.com/rdkit-rs/cheminee](https://github.com/rdkit-rs/cheminee)
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## Installation
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### Build a gem
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To build the Ruby code into a gem:
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```shell
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gem build cheminee.gemspec
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```
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Then either install the gem locally:
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```shell
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gem install ./cheminee-0.0.15.gem
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```
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(for development, run `gem install --dev ./cheminee-0.0.15.gem` to install the development dependencies)
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or publish the gem to a gem hosting service, e.g. [RubyGems](https://rubygems.org/).
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Finally add this to the Gemfile:
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gem 'cheminee', '~> 0.0.15'
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### Install from Git
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If the Ruby gem is hosted at a git repository: https://github.com/GIT_USER_ID/GIT_REPO_ID, then add the following in the Gemfile:
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gem 'cheminee', :git => 'https://github.com/GIT_USER_ID/GIT_REPO_ID.git'
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### Include the Ruby code directly
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Include the Ruby code directly using `-I` as follows:
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```shell
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ruby -Ilib script.rb
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```
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## Getting Started
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Please follow the [installation](#installation) procedure and then run the following code:
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```ruby
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# Load the gem
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require 'cheminee'
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api_instance = Cheminee::DefaultApi.new
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smile = [Cheminee::Smile.new({smile: 'smile_example'})] # Array<Smile> |
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begin
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result = api_instance.standardize_post(smile)
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p result
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rescue Cheminee::ApiError => e
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puts "Exception when calling DefaultApi->standardize_post: #{e}"
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end
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```
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## Documentation for API Endpoints
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All URIs are relative to *http://localhost:3000/api/v1*
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Class | Method | HTTP request | Description
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------------ | ------------- | ------------- | -------------
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*Cheminee::DefaultApi* | [**standardize_post**](docs/DefaultApi.md#standardize_post) | **POST** /standardize |
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## Documentation for Models
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- [Cheminee::Smile](docs/Smile.md)
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- [Cheminee::StandardizedSmile](docs/StandardizedSmile.md)
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## Documentation for Authorization
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Endpoints do not require authorization.
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data/Rakefile
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data/cheminee.gemspec
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# -*- encoding: utf-8 -*-
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=begin
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#Cheminée
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#Cheminée: The Chemical Structure Search Engine
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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: 7.0.0-SNAPSHOT
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=end
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$:.push File.expand_path("../lib", __FILE__)
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require "cheminee/version"
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Gem::Specification.new do |s|
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s.name = "cheminee"
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s.version = Cheminee::VERSION
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s.platform = Gem::Platform::RUBY
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s.authors = ["Xavier Lange"]
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s.email = ["xrlange@gmail.com"]
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s.homepage = "https://github.com/rdkit-rs/cheminee-ruby"
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s.summary = "Cheminée Ruby Gem"
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s.description = "Cheminée: The Chemical Structure Search Engine"
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s.license = "Unlicense"
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s.required_ruby_version = ">= 3.0"
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s.add_runtime_dependency 'typhoeus', '~> 1.0', '>= 1.0.1'
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s.add_development_dependency 'rspec', '~> 3.6', '>= 3.6.0'
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s.files = `find *`.split("\n").uniq.sort.select { |f| !f.empty? }
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s.test_files = `find spec/*`.split("\n")
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s.executables = []
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s.require_paths = ["lib"]
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end
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data/docs/DefaultApi.md
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# Cheminee::DefaultApi
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All URIs are relative to *http://localhost:3000/api/v1*
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| Method | HTTP request | Description |
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| ------ | ------------ | ----------- |
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| [**standardize_post**](DefaultApi.md#standardize_post) | **POST** /standardize | |
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## standardize_post
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> <Array<StandardizedSmile>> standardize_post(smile)
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### Examples
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```ruby
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require 'time'
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require 'cheminee'
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api_instance = Cheminee::DefaultApi.new
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smile = [Cheminee::Smile.new({smile: 'smile_example'})] # Array<Smile> |
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begin
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result = api_instance.standardize_post(smile)
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p result
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rescue Cheminee::ApiError => e
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puts "Error when calling DefaultApi->standardize_post: #{e}"
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end
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```
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#### Using the standardize_post_with_http_info variant
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This returns an Array which contains the response data, status code and headers.
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> <Array(<Array<StandardizedSmile>>, Integer, Hash)> standardize_post_with_http_info(smile)
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```ruby
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begin
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data, status_code, headers = api_instance.standardize_post_with_http_info(smile)
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p status_code # => 2xx
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p headers # => { ... }
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p data # => <Array<StandardizedSmile>>
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rescue Cheminee::ApiError => e
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puts "Error when calling DefaultApi->standardize_post_with_http_info: #{e}"
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end
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```
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### Parameters
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **smile** | [**Array<Smile>**](Smile.md) | | |
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### Return type
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[**Array<StandardizedSmile>**](StandardizedSmile.md)
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### Authorization
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No authorization required
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### HTTP request headers
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- **Content-Type**: application/json; charset=utf-8
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- **Accept**: application/json; charset=utf-8
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data/docs/Smile.md
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# Cheminee::Smile
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## Properties
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
|
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| **smile** | **String** | | |
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## Example
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10
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```ruby
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require 'cheminee'
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instance = Cheminee::Smile.new(
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smile: null
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)
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```
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|
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# Cheminee::StandardizedSmile
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## Properties
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **smile** | **String** | | [optional] |
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| **error** | **String** | | [optional] |
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## Example
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11
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|
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```ruby
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require 'cheminee'
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|
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instance = Cheminee::StandardizedSmile.new(
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smile: null,
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error: null
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)
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```
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|
data/git_push.sh
ADDED
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#!/bin/sh
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# ref: https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/
|
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#
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# Usage example: /bin/sh ./git_push.sh wing328 openapi-petstore-perl "minor update" "gitlab.com"
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git_user_id=$1
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git_repo_id=$2
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release_note=$3
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git_host=$4
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if [ "$git_host" = "" ]; then
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git_host="github.com"
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echo "[INFO] No command line input provided. Set \$git_host to $git_host"
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fi
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+
|
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if [ "$git_user_id" = "" ]; then
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git_user_id="GIT_USER_ID"
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echo "[INFO] No command line input provided. Set \$git_user_id to $git_user_id"
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fi
|
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+
|
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if [ "$git_repo_id" = "" ]; then
|
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git_repo_id="GIT_REPO_ID"
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echo "[INFO] No command line input provided. Set \$git_repo_id to $git_repo_id"
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fi
|
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+
|
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if [ "$release_note" = "" ]; then
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release_note="Minor update"
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echo "[INFO] No command line input provided. Set \$release_note to $release_note"
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fi
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|
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# Initialize the local directory as a Git repository
|
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git init
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|
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# Adds the files in the local repository and stages them for commit.
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git add .
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+
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# Commits the tracked changes and prepares them to be pushed to a remote repository.
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+
git commit -m "$release_note"
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39
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+
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40
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+
# Sets the new remote
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+
git_remote=$(git remote)
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+
if [ "$git_remote" = "" ]; then # git remote not defined
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43
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+
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+
if [ "$GIT_TOKEN" = "" ]; then
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+
echo "[INFO] \$GIT_TOKEN (environment variable) is not set. Using the git credential in your environment."
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+
git remote add origin https://${git_host}/${git_user_id}/${git_repo_id}.git
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+
else
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48
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+
git remote add origin https://${git_user_id}:"${GIT_TOKEN}"@${git_host}/${git_user_id}/${git_repo_id}.git
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+
fi
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50
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+
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+
fi
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52
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+
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git pull origin master
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54
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+
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55
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+
# Pushes (Forces) the changes in the local repository up to the remote repository
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+
echo "Git pushing to https://${git_host}/${git_user_id}/${git_repo_id}.git"
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57
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+
git push origin master 2>&1 | grep -v 'To https'
|
@@ -0,0 +1,86 @@
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1
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+
=begin
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2
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+
#Cheminée
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3
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+
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4
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+
#Cheminée: The Chemical Structure Search Engine
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5
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+
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6
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+
The version of the OpenAPI document: 1.0
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7
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+
|
8
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+
Generated by: https://openapi-generator.tech
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9
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+
OpenAPI Generator version: 7.0.0-SNAPSHOT
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+
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+
=end
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+
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+
require 'cgi'
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+
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+
module Cheminee
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+
class DefaultApi
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+
attr_accessor :api_client
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+
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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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+
# @param smile [Array<Smile>]
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+
# @param [Hash] opts the optional parameters
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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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29
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+
|
30
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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<StandardizedSmile>, Integer, Hash)>] Array<StandardizedSmile> data, response status code and response headers
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33
|
+
def standardize_post_with_http_info(smile, opts = {})
|
34
|
+
if @api_client.config.debugging
|
35
|
+
@api_client.config.logger.debug 'Calling API: DefaultApi.standardize_post ...'
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36
|
+
end
|
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"
|
40
|
+
end
|
41
|
+
# resource path
|
42
|
+
local_var_path = '/standardize'
|
43
|
+
|
44
|
+
# query parameters
|
45
|
+
query_params = opts[:query_params] || {}
|
46
|
+
|
47
|
+
# header parameters
|
48
|
+
header_params = opts[:header_params] || {}
|
49
|
+
# HTTP header 'Accept' (if needed)
|
50
|
+
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
51
|
+
# HTTP header 'Content-Type'
|
52
|
+
content_type = @api_client.select_header_content_type(['application/json; charset=utf-8'])
|
53
|
+
if !content_type.nil?
|
54
|
+
header_params['Content-Type'] = content_type
|
55
|
+
end
|
56
|
+
|
57
|
+
# form parameters
|
58
|
+
form_params = opts[:form_params] || {}
|
59
|
+
|
60
|
+
# http body (model)
|
61
|
+
post_body = opts[:debug_body] || @api_client.object_to_http_body(smile)
|
62
|
+
|
63
|
+
# return_type
|
64
|
+
return_type = opts[:debug_return_type] || 'Array<StandardizedSmile>'
|
65
|
+
|
66
|
+
# auth_names
|
67
|
+
auth_names = opts[:debug_auth_names] || []
|
68
|
+
|
69
|
+
new_options = opts.merge(
|
70
|
+
:operation => :"DefaultApi.standardize_post",
|
71
|
+
:header_params => header_params,
|
72
|
+
:query_params => query_params,
|
73
|
+
:form_params => form_params,
|
74
|
+
:body => post_body,
|
75
|
+
:auth_names => auth_names,
|
76
|
+
:return_type => return_type
|
77
|
+
)
|
78
|
+
|
79
|
+
data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
|
80
|
+
if @api_client.config.debugging
|
81
|
+
@api_client.config.logger.debug "API called: DefaultApi#standardize_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
82
|
+
end
|
83
|
+
return data, status_code, headers
|
84
|
+
end
|
85
|
+
end
|
86
|
+
end
|