openbel-api 0.4.0-java

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data/.gemspec

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+Gem::Specification.new do |spec|
+  spec.name                  = 'openbel-api'
+  spec.version               = '0.4.0'
+  spec.summary               = %q{The OpenBEL API provided over RESTful HTTP endpoints.}
+  spec.description           = %q{The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.}
+  spec.license               = 'Apache-2.0'
+  spec.authors               = [
+                                 'Anthony Bargnesi',
+                                 'Nick Bargnesi',
+                                 'William Hayes'
+                               ]
+  spec.date                  = %q{2015-12-02}
+  spec.email                 = %q{abargnesi@selventa.com}
+  spec.files                 = [
+                                 Dir.glob('app/**/*.{json,rb,ru}'),
+                                 Dir.glob('config/**/*.{rb,yml}'),
+                                 Dir.glob('lib/**/*.rb'),
+                                 __FILE__,
+                                 'CHANGELOG.md',
+                                 'LICENSE',
+                                 'INSTALL.md',
+                                 'INSTALL_RUBY.md',
+                                 'README.md'
+                               ].flatten!
+  spec.executables           = Dir.glob('bin/*').map(&File.method(:basename))
+  spec.homepage              = 'https://github.com/OpenBEL/openbel-server'
+  spec.require_paths         = ['app', 'lib']
+  spec.platform              = 'java'
+  spec.required_ruby_version = '>= 2.0.0'
+
+  # Dependencies
+
+  ## bel.rb
+  spec.add_runtime_dependency 'bel',               '0.4.0'
+
+  ## bel.rb plugin - annotation/namespace search
+  spec.add_runtime_dependency 'bel-search-sqlite', '0.4.0'
+
+  ## bel.rb plugin - RDF repository using Apache Jena
+  spec.add_runtime_dependency 'bel-rdf-jena',      '0.4.0'
+
+  ## RDF - RDF abstraction
+  spec.add_runtime_dependency 'rdf',               '1.99.0'
+
+  ## Mongo - Faceted search of evidence.
+  spec.add_runtime_dependency 'mongo',             '1.12.5'
+  spec.add_runtime_dependency 'bson',              '1.12.5'
+
+  ## REST API dependencies
+  spec.add_runtime_dependency 'dot_hash',          '0.5.9'
+  spec.add_runtime_dependency 'jrjackson',         '0.3.7'
+  spec.add_runtime_dependency 'json_schema',       '0.10.0'
+  spec.add_runtime_dependency 'multi_json',        '1.11.2'
+  spec.add_runtime_dependency 'oat',               '0.4.6'
+  spec.add_runtime_dependency 'puma',              '2.15.3'
+  spec.add_runtime_dependency 'rack',              '1.6.4'
+  spec.add_runtime_dependency 'rack-cors',         '0.4.0'
+  spec.add_runtime_dependency 'rack-handlers',     '0.7.0'
+  spec.add_runtime_dependency 'sinatra',           '1.4.6'
+  spec.add_runtime_dependency 'sinatra-contrib',   '1.4.6'
+  spec.add_runtime_dependency 'jwt',               '1.5.2'
+  spec.add_runtime_dependency 'rest-client',       '1.8.0'
+end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/CHANGELOG.md

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+# Change Log
+All notable changes to openbel-api will be documented in this file. The curated log begins at changes to version 0.4.0.
+
+This project adheres to [Semantic Versioning][Semantic Versioning].
+
+## [0.4.0][0.4.0] - 2015-12-14
+### Added
+- Evidence Store
+  - Storage of evidence including creation, retrieval, modification, and deletion actions.
+  - Flexible filtering of stored, evidence based on user's custom data requirements.
+  - 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.
+  - Flexible filtering of evidence contained within a dataset.
+  - Download a document (e.g. BEL script, XBEL, or Evidence JSON) from a dataset.
+- BEL Expressions
+  - Autocomplete a BEL term expression.
+  - Retrieve the structural components of a BEL expression.
+- Annotations and Namespaces
+  - Retrieve annotation (e.g. Disease Ontology) and namespace (e.g. GO) data.
+  - Retrieve equivalent namespace values from the individual.
+  - Retrieve orthologous namespace values from the individual.
+
+[Semantic Versioning]: http://semver.org

data/INSTALL.md

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+Install
+=======
+
+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).
+
+Install from [RubyGems.org](http://rubygems.org/gems/bel)
+
+```bash
+    gem install bel
+```
+
+Build from master branch
+
+1. Obtain source for master branch.
+  - `git clone git@github.com:OpenBEL/bel.rb.git`
+
+2. Build
+  - `gem build bel.gemspec`
+  - `gem install bel-[VERSION].gem`

data/INSTALL_RUBY.md

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+# Install Ruby
+
+
+## Install Ruby (Windows)
+
+1. Download [RubyInstaller](http://rubyinstaller.org/downloads).
+   * Versions 2.x.x are supported.
+2. Install RubyInstaller version.
+   * Enable the _Add Ruby executables to your PATH_ option presented during installation.
+3. Open a command prompt (Windows Key + R then type `cmd`).
+   * Confirm installation by typing `ruby -v`.
+   * The output should show the ruby version (e.g. `ruby 2.0.0p451 (2014-02-24) [x64-mingw32]`).
+
+Continue with <a href="#install_bel_gem">Install the bel gem</a>.
+
+## Install Ruby (Mac OSX)
+
+_Option 1: Homebrew_
+
+1. Install with homebrew by typing `brew install ruby`.
+2. Add ruby commands to your PATH.
+   * Add to .bash_profile.
+     * `echo 'export PATH="/usr/local/Cellar/ruby/VERSION/bin:$PATH"' >> .bash_profile`
+   * Update environment by sourcing .bash_profile.
+     * `source ~/.bash_profile`
+3. Confirm installation by typing `ruby -v`.
+
+_Option 2: rbenv_
+
+* _Install with homebrew._
+   * `brew update`
+   * `brew install rbenv ruby-build`
+   * More details [here] (https://github.com/sstephenson/rbenv#homebrew-on-mac-os-x).
+
+* _Install with git._
+   * Clone rbenv repository.
+     * `git clone https://github.com/sstephenson/rbenv.git ~/.rbenv`
+   * Add to .bash_profile.
+     * `echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile`
+   * Enable shims and autocompletion from the terminal.
+     * `echo 'eval "$(rbenv init -)"' >> ~/.bash_profile`
+   * Clone ruby-build repository.
+     * `git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build`
+   * More details [here] (https://github.com/sstephenson/rbenv#installation).
+
+Continue with <a href="#install_bel_gem">Install the bel gem</a>.
+
+## Install Ruby (Linux)
+
+_Option 1: Install via package manager._
+
+* Example installation with Ubuntu.
+   * Type `sudo apt-get install ruby` in the terminal.
+
+_Option 2: rbenv_
+
+* _Install with git._
+   * Clone rbenv repository.
+     * `git clone https://github.com/sstephenson/rbenv.git ~/.rbenv`
+   * Add to .bash_profile.
+     * `echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile`
+   * Enable shims and autocompletion from the terminal.
+     * `echo 'eval "$(rbenv init -)"' >> ~/.bash_profile`
+   * Clone ruby-build repository.
+     * `git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build`
+   * More details [here] (https://github.com/sstephenson/rbenv#installation).
+
+Continue with <a href="#install_bel_gem">Install the bel gem</a>.
+
+<br><br>
+<div id="install_bel_gem"></div>
+## Install the _bel_ gem
+
+1. Open a terminal or command prompt.
+2. Use the `gem` command to install the `bel` gem.
+   * `gem install bel`
+3. You should see the following:
+
+<pre>
+    Fetching: bel-0.2.1.gem (100%)
+    Successfully installed bel-0.2.1
+    Parsing documentation for bel-0.2.1
+    Installing ri documentation for bel-0.2.1
+    1 gem installed
+</pre>
+4. Confirm you can access the `bel_upgrade` command.
+5. Continue with <a href="#upgrading_bel">Upgrading BEL</a>.
+
+<br><br>
+<div id="upgrading_bel"></div>
+## Upgrading BEL
+
+1. Type `bel_upgrade --help` for option details.
+2. Run command
+   * Example 1 - convert a BEL file
+     * `bel_upgrade --bel small_corpus.bel --changelog "http://resource.belframework.org/belframework/20131211/change_log.json"
+   * Example 2 - convert BEL from standard in
+     * `curl "http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel" | bel_upgrade --changelog "http://resource.belframework.org/belframework/20131211/change_log.json"`
+   * More details [here] (https://github.com/OpenBEL/bel.rb).
+3. The upgraded BEL will be written to standard out.  Simply redirect to a file after that.
+   * `bel_upgrade ... > upgraded-version.bel`
+
+<br><br>
+## Issues
+
+* 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.
+* If you encounter errors please post an issue to [github issues] (https://github.com/OpenBEL/bel.rb/issues).

data/LICENSE

@@ -0,0 +1,191 @@
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+9. Accepting Warranty or Additional Liability.
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+
+APPENDIX: How to apply the Apache License to your work
+
+To apply the Apache License to your work, attach the following boilerplate
+notice, with the fields enclosed by brackets "[]" replaced with your own
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+   Copyright 2013 OpenBEL Consortium
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data/README.md

@@ -0,0 +1,208 @@
+# openbel-api
+
+The OpenBEL API provides RESTful API access to your BEL content. It is part of [OpenBEL Platform][OpenBEL Platform].
+
+## Features
+
+- Evidence Store
+  - Storage of evidence including creation, retrieval, modification, and deletion actions.
+  - Flexible filtering of stored, evidence based on user's custom data requirements.
+  - 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.
+  - Flexible filtering of evidence contained within a dataset.
+  - Download a document (e.g. BEL script, XBEL, or Evidence JSON) from a dataset.
+- BEL Expressions
+   - Autocomplete a BEL term expression.
+   - Retrieve the structural components of a BEL expression.
+- Annotations and Namespaces
+   - Retrieve annotation (e.g. Disease Ontology) and namespace (e.g. GO) data.
+   - Retrieve equivalent namespace values from the individual.
+   - Retrieve orthologous namespace values from the individual.
+
+## Vocabulary
+
+*Annotation*
+A name/value property that describes an aspect of an *Evidence*. For example *Ncbi Taxonomy*:*Homo sapiens* is an annotation for the Human species.
+
+*Namespace*
+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.
+
+*Evidence*
+A biological interaction curated from scientific literature. It is comprised of five parts.
+
+- *Citation*: The identification for the scientific literature where the interaction was stated.
+- *BEL Statement*: The biological interaction curated from the *Citation*.
+- *Summary text*: The text (i.e. *quotation*) within the *Citation* that supports the *BEL Statement*.
+- *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*.
+- *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.
+- *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.
+
+*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.
+
+*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*.
+
+*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")*).
+
+*Evidence Store*: A database used for *Evidence*. It facilitates storage, filtering, and transformation of *Evidence*.
+
+## Technical requirements
+
+The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
+
+*System Requirements*
+
+- [Java 8][Java 8]
+- [JRuby][JRuby], 1.7.x or 9.x series (9.0.x.0 is recommended)
+  - Follow [JRuby Getting Started][JRuby Getting Started] for installation instructions.
+- [MongoDB][MongoDB], version 3.0 or greater
+  - Follow [MongoDB download][MongoDB download] page for download and installation instructions.
+- [SQLite][SQLite], version 3.8.0 or greater
+  - Follow [SQLite download][SQLite download] page for download and installation instructions. 
+
+## Getting up and Running
+
+### Installation
+
+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].
+
+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.
+
+```bash
+gem install openbel-api
+```
+
+All of the application dependencies needed by `openbel-api` will be installed during this process.
+
+### Configuration
+
+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.
+
+```bash
+openbel-config --file openbel-api-config.yml
+```
+
+*Configure the Evidence Store*
+The Evidence Store is backed by a [MongoDB][MongoDB] database. You will need to provide the *host*, *port*, and *database* option.
+
+The default configuration is:
+
+```yaml
+evidence_store:
+  mongo:
+    host:     'localhost'
+    port:     27017
+    database: 'openbel'
+```
+
+*Resource RDF data*
+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`).
+
+You will need to configure the location of the Apache Jena TDB database that holds this data.
+
+The default configuration is:
+
+```yaml
+resource_rdf:
+  jena:
+    tdb_directory: 'biological-concepts-rdf'
+```
+
+**Tip**
+You can obtain the latest Resource RDF database (20150611) from the [OpenBEL build server][Resource RDF 20150611].
+
+*Resource search*
+Annotations and namespaces can be full-text searched using a [SQLite][SQLite] database. The data is stored in an on-disk file.
+
+The default configuration is:
+
+```yaml
+resource_search:
+  sqlite:
+    database_file: 'biological-concepts-rdf.db'
+```
+
+
+**Tip**
+You can obtain the latest Resource Search database (20150611) from the [OpenBEL build server][Resource Search 20150611].
+
+*Token-based authentication*
+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.
+
+By default authentication is disabled.
+
+The default configuration is:
+
+```yaml
+# Set a secret used during session creation....
+session_secret: 'changeme'
+
+# User authentication using Auth0.
+auth:
+  enabled: false
+  redirect: 'https://openbel.auth0.com/authorize?response_type=code&scope=openid%20profile&client_id=K4oAPUaROjbWWTCoAhf0nKYfTGsZWbHE'
+  default_connection: 'linkedin'
+  domain:   'openbel.auth0.com'
+  id:       'K4oAPUaROjbWWTCoAhf0nKYfTGsZWbHE'
+  # secret:   'auth0 client secret here'
+```
+
+### Running the OpenBEL API
+
+The OpenBEL API can be run using the `openbel-api` command and passing a configuration file.
+
+The configuration file can be provided in two ways:
+- Command option (`--file`)
+- Environment variable named `OPENBEL_API_CONFIG_FILE`
+
+*Command option*
+```
+openbel-api --file "/path/to/openbel-api-config.yml"
+```
+
+*Environment variable*
+```
+export OPENBEL_API_CONFIG_FILE="/path/to/openbel-api-config.yml"
+
+openbel-api
+```
+
+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.
+
+*Example running on port 9000 with up to 16 threads.*
+
+```bash
+openbel-api --file openbel-api-config.yml -- --port 9000 --threads 1:16
+```
+
+**Note**
+Run `openbel-api --help` for more information and options.
+
+## API Documentation
+
+The REST API is defined by a [RAML][RAML] specification. The specification is published [here][OpenBEL API RAML specification].
+
+API documentation with *Try it* functionality is available [here][OpenBEL API documentation].
+
+-----
+
+Built with collaboration and :heart: by the [OpenBEL][OpenBEL] community.
+
+[OpenBEL]: http://www.openbel.org
+[OpenBEL Platform]: https://github.com/OpenBEL/openbel-platform
+[RAML]: http://raml.org/
+[OpenBEL API RAML specification]: http://next.belframework.org/openbel-api.raml
+[OpenBEL API documentation]: http://next.belframework.org/
+[Evidence API documentation]: http://next.belframework.org/#evidence
+[JRuby]: http://jruby.org
+[JRuby Getting Started]: http://jruby.org/getting-started
+[Java 8]: http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html
+[MongoDB]: https://www.mongodb.org/
+[MongoDB download]: https://www.mongodb.org/downloads#production
+[SQLite]: https://www.sqlite.org
+[SQLite download]: https://www.sqlite.org/download.html
+[RubyGems]: https://rubygems.org
+[RDF]: http://www.w3.org/RDF/
+[Auth0]: https://auth0.com/
+[Puma HTTP server]: http://puma.io/
+[Resource RDF 20150611]: http://build.openbel.org/browse/OR-RRD2/latestSuccessful/artifact
+[Resource Search 20150611]: http://build.openbel.org/browse/OR-RSD2/latestSuccessful/artifact
+