openbel-api 0.4.0-java
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- checksums.yaml +7 -0
- data/.gemspec +65 -0
- data/CHANGELOG.md +22 -0
- data/INSTALL.md +19 -0
- data/INSTALL_RUBY.md +107 -0
- data/LICENSE +191 -0
- data/README.md +208 -0
- data/app/openbel/api/app.rb +83 -0
- data/app/openbel/api/config.rb +45 -0
- data/app/openbel/api/config.ru +3 -0
- data/app/openbel/api/helpers/pager.rb +109 -0
- data/app/openbel/api/middleware/auth.rb +112 -0
- data/app/openbel/api/resources/adapters/basic_json.rb +52 -0
- data/app/openbel/api/resources/annotation.rb +141 -0
- data/app/openbel/api/resources/base.rb +16 -0
- data/app/openbel/api/resources/completion.rb +89 -0
- data/app/openbel/api/resources/evidence.rb +115 -0
- data/app/openbel/api/resources/evidence_transform.rb +143 -0
- data/app/openbel/api/resources/function.rb +98 -0
- data/app/openbel/api/resources/match_result.rb +79 -0
- data/app/openbel/api/resources/namespace.rb +174 -0
- data/app/openbel/api/routes/annotations.rb +168 -0
- data/app/openbel/api/routes/authenticate.rb +108 -0
- data/app/openbel/api/routes/base.rb +326 -0
- data/app/openbel/api/routes/datasets.rb +519 -0
- data/app/openbel/api/routes/evidence.rb +330 -0
- data/app/openbel/api/routes/expressions.rb +560 -0
- data/app/openbel/api/routes/functions.rb +41 -0
- data/app/openbel/api/routes/namespaces.rb +382 -0
- data/app/openbel/api/routes/root.rb +39 -0
- data/app/openbel/api/schemas.rb +34 -0
- data/app/openbel/api/schemas/annotation_collection.schema.json +20 -0
- data/app/openbel/api/schemas/annotation_resource.schema.json +36 -0
- data/app/openbel/api/schemas/annotation_value_collection.schema.json +21 -0
- data/app/openbel/api/schemas/annotation_value_resource.schema.json +35 -0
- data/app/openbel/api/schemas/completion_collection.schema.json +21 -0
- data/app/openbel/api/schemas/completion_resource.schema.json +146 -0
- data/app/openbel/api/schemas/evidence.schema.json +198 -0
- data/app/openbel/api/schemas/evidence_collection.schema.json +98 -0
- data/app/openbel/api/schemas/evidence_resource.schema.json +29 -0
- data/app/openbel/api/schemas/namespace_value_collection.schema.json +21 -0
- data/app/openbel/api/schemas/namespace_value_resource.schema.json +43 -0
- data/app/openbel/api/util.rb +11 -0
- data/bin/openbel-api +78 -0
- data/bin/openbel-config +46 -0
- data/config/async_evidence.rb +12 -0
- data/config/async_jena.rb +14 -0
- data/config/config.yml +31 -0
- data/config/server_config.rb +184 -0
- data/lib/openbel/api/cache/cache.rb +30 -0
- data/lib/openbel/api/config/config.rb +33 -0
- data/lib/openbel/api/evidence/api.rb +39 -0
- data/lib/openbel/api/evidence/facet_api.rb +18 -0
- data/lib/openbel/api/evidence/facet_filter.rb +83 -0
- data/lib/openbel/api/evidence/mongo.rb +247 -0
- data/lib/openbel/api/evidence/mongo_facet.rb +105 -0
- data/lib/openbel/api/helpers/dependency_graph.rb +52 -0
- data/lib/openbel/api/model/rdf_resource.rb +74 -0
- data/lib/openbel/api/plugin/cache/kyotocabinet.rb +85 -0
- data/lib/openbel/api/plugin/configure_plugins.rb +97 -0
- data/lib/openbel/api/plugin/evidence/evidence.rb +58 -0
- data/lib/openbel/api/plugin/plugin.rb +99 -0
- data/lib/openbel/api/plugin/plugin_manager.rb +20 -0
- data/lib/openbel/api/plugin/plugin_repository.rb +60 -0
- data/lib/openbel/api/storage/cache_proxy.rb +74 -0
- data/lib/openbel/api/storage/triple_storage.rb +43 -0
- metadata +379 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: 84860112a47f326439806c8f6f81987e31a47121
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data.tar.gz: 55a1281b0db90eae0ba49b6314d3727c29225268
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SHA512:
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metadata.gz: 1a3d631752e68f0be2686c1bf8eb4efa13b19f803fe9dc9a1572a3171f36f881904e5c5279e537587ee9005c49fa12c5ff61cff096ac142f42d870eb5e653562
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data.tar.gz: 094034e7a35004b6e05da1174cad42e1b372a77e526159a939891824e2c20e309a658a15084a001551b9caafd1fc6c68ec6d06cd485dbe0f67c0a1c81762be41
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data/.gemspec
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Gem::Specification.new do |spec|
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spec.name = 'openbel-api'
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spec.version = '0.4.0'
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spec.summary = %q{The OpenBEL API provided over RESTful HTTP endpoints.}
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spec.description = %q{The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.}
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spec.license = 'Apache-2.0'
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spec.authors = [
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'Anthony Bargnesi',
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'Nick Bargnesi',
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'William Hayes'
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]
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spec.date = %q{2015-12-02}
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spec.email = %q{abargnesi@selventa.com}
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spec.files = [
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Dir.glob('app/**/*.{json,rb,ru}'),
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Dir.glob('config/**/*.{rb,yml}'),
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Dir.glob('lib/**/*.rb'),
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__FILE__,
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'CHANGELOG.md',
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'LICENSE',
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'INSTALL.md',
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'INSTALL_RUBY.md',
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'README.md'
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].flatten!
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spec.executables = Dir.glob('bin/*').map(&File.method(:basename))
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spec.homepage = 'https://github.com/OpenBEL/openbel-server'
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spec.require_paths = ['app', 'lib']
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spec.platform = 'java'
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spec.required_ruby_version = '>= 2.0.0'
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# Dependencies
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## bel.rb
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spec.add_runtime_dependency 'bel', '0.4.0'
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## bel.rb plugin - annotation/namespace search
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spec.add_runtime_dependency 'bel-search-sqlite', '0.4.0'
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## bel.rb plugin - RDF repository using Apache Jena
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spec.add_runtime_dependency 'bel-rdf-jena', '0.4.0'
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## RDF - RDF abstraction
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spec.add_runtime_dependency 'rdf', '1.99.0'
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## Mongo - Faceted search of evidence.
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spec.add_runtime_dependency 'mongo', '1.12.5'
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spec.add_runtime_dependency 'bson', '1.12.5'
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## REST API dependencies
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spec.add_runtime_dependency 'dot_hash', '0.5.9'
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spec.add_runtime_dependency 'jrjackson', '0.3.7'
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spec.add_runtime_dependency 'json_schema', '0.10.0'
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spec.add_runtime_dependency 'multi_json', '1.11.2'
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spec.add_runtime_dependency 'oat', '0.4.6'
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spec.add_runtime_dependency 'puma', '2.15.3'
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spec.add_runtime_dependency 'rack', '1.6.4'
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spec.add_runtime_dependency 'rack-cors', '0.4.0'
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spec.add_runtime_dependency 'rack-handlers', '0.7.0'
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spec.add_runtime_dependency 'sinatra', '1.4.6'
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spec.add_runtime_dependency 'sinatra-contrib', '1.4.6'
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spec.add_runtime_dependency 'jwt', '1.5.2'
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spec.add_runtime_dependency 'rest-client', '1.8.0'
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end
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# vim: ts=2 sw=2:
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# encoding: utf-8
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data/CHANGELOG.md
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# Change Log
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All notable changes to openbel-api will be documented in this file. The curated log begins at changes to version 0.4.0.
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This project adheres to [Semantic Versioning][Semantic Versioning].
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## [0.4.0][0.4.0] - 2015-12-14
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### Added
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- Evidence Store
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- Storage of evidence including creation, retrieval, modification, and deletion actions.
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- Flexible filtering of stored, evidence based on user's custom data requirements.
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- Upload a document (e.g. BEL script, XBEL, or Evidence JSON), to the Evidence Store, as a dataset. These can later be retrieved or deleted from the Evidence Store.
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- Flexible filtering of evidence contained within a dataset.
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- Download a document (e.g. BEL script, XBEL, or Evidence JSON) from a dataset.
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- BEL Expressions
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- Autocomplete a BEL term expression.
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- Retrieve the structural components of a BEL expression.
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- Annotations and Namespaces
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- Retrieve annotation (e.g. Disease Ontology) and namespace (e.g. GO) data.
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- Retrieve equivalent namespace values from the individual.
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- Retrieve orthologous namespace values from the individual.
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[Semantic Versioning]: http://semver.org
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data/INSTALL.md
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Install
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=======
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This library requires [Ruby](https://www.ruby-lang.org) (**>= 2.0.0**). See [how to install ruby](https://github.com/OpenBEL/bel.rb/blob/master/INSTALL_RUBY.md).
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Install from [RubyGems.org](http://rubygems.org/gems/bel)
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```bash
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gem install bel
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```
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Build from master branch
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1. Obtain source for master branch.
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- `git clone git@github.com:OpenBEL/bel.rb.git`
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2. Build
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- `gem build bel.gemspec`
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- `gem install bel-[VERSION].gem`
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data/INSTALL_RUBY.md
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# Install Ruby
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## Install Ruby (Windows)
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1. Download [RubyInstaller](http://rubyinstaller.org/downloads).
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* Versions 2.x.x are supported.
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2. Install RubyInstaller version.
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* Enable the _Add Ruby executables to your PATH_ option presented during installation.
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3. Open a command prompt (Windows Key + R then type `cmd`).
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* Confirm installation by typing `ruby -v`.
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* The output should show the ruby version (e.g. `ruby 2.0.0p451 (2014-02-24) [x64-mingw32]`).
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Continue with <a href="#install_bel_gem">Install the bel gem</a>.
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## Install Ruby (Mac OSX)
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_Option 1: Homebrew_
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1. Install with homebrew by typing `brew install ruby`.
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2. Add ruby commands to your PATH.
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* Add to .bash_profile.
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* `echo 'export PATH="/usr/local/Cellar/ruby/VERSION/bin:$PATH"' >> .bash_profile`
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* Update environment by sourcing .bash_profile.
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* `source ~/.bash_profile`
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3. Confirm installation by typing `ruby -v`.
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_Option 2: rbenv_
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* _Install with homebrew._
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* `brew update`
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* `brew install rbenv ruby-build`
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* More details [here] (https://github.com/sstephenson/rbenv#homebrew-on-mac-os-x).
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* _Install with git._
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* Clone rbenv repository.
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* `git clone https://github.com/sstephenson/rbenv.git ~/.rbenv`
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* Add to .bash_profile.
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* `echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile`
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* Enable shims and autocompletion from the terminal.
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* `echo 'eval "$(rbenv init -)"' >> ~/.bash_profile`
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* Clone ruby-build repository.
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* `git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build`
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* More details [here] (https://github.com/sstephenson/rbenv#installation).
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Continue with <a href="#install_bel_gem">Install the bel gem</a>.
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## Install Ruby (Linux)
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_Option 1: Install via package manager._
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* Example installation with Ubuntu.
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* Type `sudo apt-get install ruby` in the terminal.
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_Option 2: rbenv_
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* _Install with git._
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* Clone rbenv repository.
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* `git clone https://github.com/sstephenson/rbenv.git ~/.rbenv`
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* Add to .bash_profile.
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* `echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile`
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* Enable shims and autocompletion from the terminal.
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* `echo 'eval "$(rbenv init -)"' >> ~/.bash_profile`
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* Clone ruby-build repository.
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* `git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build`
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* More details [here] (https://github.com/sstephenson/rbenv#installation).
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Continue with <a href="#install_bel_gem">Install the bel gem</a>.
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<br><br>
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<div id="install_bel_gem"></div>
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## Install the _bel_ gem
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1. Open a terminal or command prompt.
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2. Use the `gem` command to install the `bel` gem.
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* `gem install bel`
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3. You should see the following:
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<pre>
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Fetching: bel-0.2.1.gem (100%)
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Successfully installed bel-0.2.1
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Parsing documentation for bel-0.2.1
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Installing ri documentation for bel-0.2.1
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1 gem installed
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</pre>
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4. Confirm you can access the `bel_upgrade` command.
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5. Continue with <a href="#upgrading_bel">Upgrading BEL</a>.
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<br><br>
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<div id="upgrading_bel"></div>
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## Upgrading BEL
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1. Type `bel_upgrade --help` for option details.
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2. Run command
|
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* Example 1 - convert a BEL file
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* `bel_upgrade --bel small_corpus.bel --changelog "http://resource.belframework.org/belframework/20131211/change_log.json"
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* Example 2 - convert BEL from standard in
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* `curl "http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel" | bel_upgrade --changelog "http://resource.belframework.org/belframework/20131211/change_log.json"`
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* More details [here] (https://github.com/OpenBEL/bel.rb).
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3. The upgraded BEL will be written to standard out. Simply redirect to a file after that.
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* `bel_upgrade ... > upgraded-version.bel`
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<br><br>
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## Issues
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* If you have questions with `bel_upgrade` or the `bel` gem please post to the [openbel-discuss] (https://groups.google.com/forum/#!forum/openbel-discuss) google group.
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* If you encounter errors please post an issue to [github issues] (https://github.com/OpenBEL/bel.rb/issues).
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data/LICENSE
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Apache License
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Version 2.0, January 2004
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http://www.apache.org/licenses/
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TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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1. Definitions.
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"License" shall mean the terms and conditions for use, reproduction, and
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distribution as defined by Sections 1 through 9 of this document.
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"Licensor" shall mean the copyright owner or entity authorized by the copyright
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owner that is granting the License.
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"Legal Entity" shall mean the union of the acting entity and all other entities
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that control, are controlled by, or are under common control with that entity.
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For the purposes of this definition, "control" means (i) the power, direct or
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indirect, to cause the direction or management of such entity, whether by
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contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the
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outstanding shares, or (iii) beneficial ownership of such entity.
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"You" (or "Your") shall mean an individual or Legal Entity exercising
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permissions granted by this License.
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"Source" form shall mean the preferred form for making modifications, including
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but not limited to software source code, documentation source, and configuration
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files.
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"Object" form shall mean any form resulting from mechanical transformation or
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translation of a Source form, including but not limited to compiled object code,
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generated documentation, and conversions to other media types.
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"Work" shall mean the work of authorship, whether in Source or Object form, made
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available under the License, as indicated by a copyright notice that is included
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in or attached to the work (an example is provided in the Appendix below).
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"Derivative Works" shall mean any work, whether in Source or Object form, that
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is based on (or derived from) the Work and for which the editorial revisions,
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annotations, elaborations, or other modifications represent, as a whole, an
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original work of authorship. For the purposes of this License, Derivative Works
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shall not include works that remain separable from, or merely link (or bind by
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name) to the interfaces of, the Work and Derivative Works thereof.
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data/README.md
ADDED
@@ -0,0 +1,208 @@
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+
# openbel-api
|
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+
|
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+
The OpenBEL API provides RESTful API access to your BEL content. It is part of [OpenBEL Platform][OpenBEL Platform].
|
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|
+
|
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## Features
|
6
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+
|
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+
- Evidence Store
|
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- Storage of evidence including creation, retrieval, modification, and deletion actions.
|
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|
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- Flexible filtering of stored, evidence based on user's custom data requirements.
|
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|
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- Upload a document (e.g. BEL script, XBEL, or Evidence JSON), to the Evidence Store, as a dataset. These can later be retrieved or deleted from the Evidence Store.
|
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- Flexible filtering of evidence contained within a dataset.
|
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|
+
- Download a document (e.g. BEL script, XBEL, or Evidence JSON) from a dataset.
|
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|
+
- BEL Expressions
|
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|
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- Autocomplete a BEL term expression.
|
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|
+
- Retrieve the structural components of a BEL expression.
|
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|
+
- Annotations and Namespaces
|
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|
+
- Retrieve annotation (e.g. Disease Ontology) and namespace (e.g. GO) data.
|
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|
+
- Retrieve equivalent namespace values from the individual.
|
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|
+
- Retrieve orthologous namespace values from the individual.
|
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|
+
|
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|
+
## Vocabulary
|
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|
+
|
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|
+
*Annotation*
|
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A name/value property that describes an aspect of an *Evidence*. For example *Ncbi Taxonomy*:*Homo sapiens* is an annotation for the Human species.
|
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|
+
|
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|
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*Namespace*
|
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A biological identifier that is curated and maintained by an organization. For example the *Gene Ontology* (i.e. *GO*) or *HGNC* (i.e. *HUGO Gene Nomenclature Committee*) database.
|
28
|
+
|
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|
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*Evidence*
|
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|
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A biological interaction curated from scientific literature. It is comprised of five parts.
|
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|
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|
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|
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- *Citation*: The identification for the scientific literature where the interaction was stated.
|
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|
+
- *BEL Statement*: The biological interaction curated from the *Citation*.
|
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|
+
- *Summary text*: The text (i.e. *quotation*) within the *Citation* that supports the *BEL Statement*.
|
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|
+
- *Experiment Context*: The biological context within the experiment where the *BEL Statement* was observed. For example if the experiment sample was a biopsy on Human, Lung tissue then you might provide *Ncbi Taxonomy*: *Homo sapiens* and *Uberon*: *lung epithelium*.
|
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|
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- *Metadata*: Additional data about this *Evidence* that is not part of the experiment (i.e. in *Experiment Context*). For example the evidence's *Reviewer*, *Create Date*, or *Reviewed Date* would be considered metadata.
|
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|
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- *References*: The annotation and namespace sources used in the *BEL Statement*, *Experiment Context*, and *Metadata*. For example *Ncbi Taxonomy* may refer to an annotation identified by the URI http://www.openbel.org/bel/namespace/ncbi-taxonomy.
|
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|
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|
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*Document*: A file containing a collection of *Evidence* with document metadata like *Name*, *Description*, and *Version*. The supported document formats are BEL script, XBEL, and JSON Evidence.
|
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|
+
|
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|
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*Dataset*: The representation of a *BEL Document* within the OpenBEL API. This provides access to document metadata as well as the collection of *Evidence* stored in the OpenBEL API that originate from the *BEL Document*.
|
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|
+
|
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|
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*Expression*: A string encoded in BEL that may represent a parameter (e.g. *AKT1*, *GO:"apoptotic process"*), term (e.g. *bp(GO:"apoptotic process")*), or statement (e.g. *p(HGNC:AKT1) increases bp(GO:"apoptotic process")*).
|
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+
|
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|
+
*Evidence Store*: A database used for *Evidence*. It facilitates storage, filtering, and transformation of *Evidence*.
|
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|
+
|
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|
+
## Technical requirements
|
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|
+
|
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|
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The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
|
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|
+
|
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|
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*System Requirements*
|
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|
+
|
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|
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- [Java 8][Java 8]
|
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|
+
- [JRuby][JRuby], 1.7.x or 9.x series (9.0.x.0 is recommended)
|
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|
+
- Follow [JRuby Getting Started][JRuby Getting Started] for installation instructions.
|
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|
+
- [MongoDB][MongoDB], version 3.0 or greater
|
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|
+
- Follow [MongoDB download][MongoDB download] page for download and installation instructions.
|
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|
+
- [SQLite][SQLite], version 3.8.0 or greater
|
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|
+
- Follow [SQLite download][SQLite download] page for download and installation instructions.
|
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|
+
|
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|
+
## Getting up and Running
|
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|
+
|
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|
+
### Installation
|
64
|
+
|
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|
+
The OpenBEL API is packaged and installed as a Ruby gem. A Ruby gem is packed library or application that runs on the Ruby virtual machine. In this case OpenBEL API runs only on [JRuby][JRuby].
|
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|
+
|
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|
+
Installation uses the [RubyGems][RubyGems] site to download and install the gem from. To install the OpenBEL API gem run the `gem install` command available within your [JRuby][JRuby] installation.
|
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|
+
|
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|
+
```bash
|
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|
+
gem install openbel-api
|
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|
+
```
|
72
|
+
|
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|
+
All of the application dependencies needed by `openbel-api` will be installed during this process.
|
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|
+
|
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|
+
### Configuration
|
76
|
+
|
77
|
+
The OpenBEL API requires a configuration file to set up a few things. You can create an initial configuration file using the `openbel-config` command.
|
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|
+
|
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|
+
```bash
|
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|
+
openbel-config --file openbel-api-config.yml
|
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|
+
```
|
82
|
+
|
83
|
+
*Configure the Evidence Store*
|
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|
+
The Evidence Store is backed by a [MongoDB][MongoDB] database. You will need to provide the *host*, *port*, and *database* option.
|
85
|
+
|
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|
+
The default configuration is:
|
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|
+
|
88
|
+
```yaml
|
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|
+
evidence_store:
|
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|
+
mongo:
|
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|
+
host: 'localhost'
|
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|
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port: 27017
|
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|
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database: 'openbel'
|
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|
+
```
|
95
|
+
|
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|
+
*Resource RDF data*
|
97
|
+
Annotations, namespaces, and dataset storage are represented as [RDF][RDF] data. The data is stored in an on-disk database using Apache Jena (Java library included with `openbel-api`).
|
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|
+
|
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|
+
You will need to configure the location of the Apache Jena TDB database that holds this data.
|
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|
+
|
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|
+
The default configuration is:
|
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|
+
|
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|
+
```yaml
|
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|
+
resource_rdf:
|
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|
+
jena:
|
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|
+
tdb_directory: 'biological-concepts-rdf'
|
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|
+
```
|
108
|
+
|
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|
+
**Tip**
|
110
|
+
You can obtain the latest Resource RDF database (20150611) from the [OpenBEL build server][Resource RDF 20150611].
|
111
|
+
|
112
|
+
*Resource search*
|
113
|
+
Annotations and namespaces can be full-text searched using a [SQLite][SQLite] database. The data is stored in an on-disk file.
|
114
|
+
|
115
|
+
The default configuration is:
|
116
|
+
|
117
|
+
```yaml
|
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|
+
resource_search:
|
119
|
+
sqlite:
|
120
|
+
database_file: 'biological-concepts-rdf.db'
|
121
|
+
```
|
122
|
+
|
123
|
+
|
124
|
+
**Tip**
|
125
|
+
You can obtain the latest Resource Search database (20150611) from the [OpenBEL build server][Resource Search 20150611].
|
126
|
+
|
127
|
+
*Token-based authentication*
|
128
|
+
The OpenBEL API is equipped to require authentication for specific API paths (e.g. Evidence, Datasets). The implementation uses [Auth0][Auth0] as a single sign-on service.
|
129
|
+
|
130
|
+
By default authentication is disabled.
|
131
|
+
|
132
|
+
The default configuration is:
|
133
|
+
|
134
|
+
```yaml
|
135
|
+
# Set a secret used during session creation....
|
136
|
+
session_secret: 'changeme'
|
137
|
+
|
138
|
+
# User authentication using Auth0.
|
139
|
+
auth:
|
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|
+
enabled: false
|
141
|
+
redirect: 'https://openbel.auth0.com/authorize?response_type=code&scope=openid%20profile&client_id=K4oAPUaROjbWWTCoAhf0nKYfTGsZWbHE'
|
142
|
+
default_connection: 'linkedin'
|
143
|
+
domain: 'openbel.auth0.com'
|
144
|
+
id: 'K4oAPUaROjbWWTCoAhf0nKYfTGsZWbHE'
|
145
|
+
# secret: 'auth0 client secret here'
|
146
|
+
```
|
147
|
+
|
148
|
+
### Running the OpenBEL API
|
149
|
+
|
150
|
+
The OpenBEL API can be run using the `openbel-api` command and passing a configuration file.
|
151
|
+
|
152
|
+
The configuration file can be provided in two ways:
|
153
|
+
- Command option (`--file`)
|
154
|
+
- Environment variable named `OPENBEL_API_CONFIG_FILE`
|
155
|
+
|
156
|
+
*Command option*
|
157
|
+
```
|
158
|
+
openbel-api --file "/path/to/openbel-api-config.yml"
|
159
|
+
```
|
160
|
+
|
161
|
+
*Environment variable*
|
162
|
+
```
|
163
|
+
export OPENBEL_API_CONFIG_FILE="/path/to/openbel-api-config.yml"
|
164
|
+
|
165
|
+
openbel-api
|
166
|
+
```
|
167
|
+
|
168
|
+
To configure server options such as port, background execution, or number of threads you will need to provide an extra set of arguments to the `openbel-api` command. These options help configure the [Puma HTTP server][Puma HTTP server] that is included with OpenBEL API.
|
169
|
+
|
170
|
+
*Example running on port 9000 with up to 16 threads.*
|
171
|
+
|
172
|
+
```bash
|
173
|
+
openbel-api --file openbel-api-config.yml -- --port 9000 --threads 1:16
|
174
|
+
```
|
175
|
+
|
176
|
+
**Note**
|
177
|
+
Run `openbel-api --help` for more information and options.
|
178
|
+
|
179
|
+
## API Documentation
|
180
|
+
|
181
|
+
The REST API is defined by a [RAML][RAML] specification. The specification is published [here][OpenBEL API RAML specification].
|
182
|
+
|
183
|
+
API documentation with *Try it* functionality is available [here][OpenBEL API documentation].
|
184
|
+
|
185
|
+
-----
|
186
|
+
|
187
|
+
Built with collaboration and :heart: by the [OpenBEL][OpenBEL] community.
|
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|
+
|
189
|
+
[OpenBEL]: http://www.openbel.org
|
190
|
+
[OpenBEL Platform]: https://github.com/OpenBEL/openbel-platform
|
191
|
+
[RAML]: http://raml.org/
|
192
|
+
[OpenBEL API RAML specification]: http://next.belframework.org/openbel-api.raml
|
193
|
+
[OpenBEL API documentation]: http://next.belframework.org/
|
194
|
+
[Evidence API documentation]: http://next.belframework.org/#evidence
|
195
|
+
[JRuby]: http://jruby.org
|
196
|
+
[JRuby Getting Started]: http://jruby.org/getting-started
|
197
|
+
[Java 8]: http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html
|
198
|
+
[MongoDB]: https://www.mongodb.org/
|
199
|
+
[MongoDB download]: https://www.mongodb.org/downloads#production
|
200
|
+
[SQLite]: https://www.sqlite.org
|
201
|
+
[SQLite download]: https://www.sqlite.org/download.html
|
202
|
+
[RubyGems]: https://rubygems.org
|
203
|
+
[RDF]: http://www.w3.org/RDF/
|
204
|
+
[Auth0]: https://auth0.com/
|
205
|
+
[Puma HTTP server]: http://puma.io/
|
206
|
+
[Resource RDF 20150611]: http://build.openbel.org/browse/OR-RRD2/latestSuccessful/artifact
|
207
|
+
[Resource Search 20150611]: http://build.openbel.org/browse/OR-RSD2/latestSuccessful/artifact
|
208
|
+
|