openbel-api 0.4.0-java

data/app/openbel/api/schemas/evidence_collection.schema.json

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+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "description": "DESCRIBE EVIDENCE COLLECTION",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "evidence_collection",
+    "facets"
+  ],
+  "properties": {
+    "evidence_collection": {
+      "type": "array",
+      "minItems": 0,
+      "title": "",
+      "description": "",
+      "items": {
+        "$ref":"evidence_resource.schema.json"
+      }
+    },
+    "facets": {
+      "type": "array",
+      "minItems": 0,
+      "title": "",
+      "description": "",
+      "items": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": [
+          "category",
+          "name",
+          "value",
+          "filter",
+          "count"
+        ],
+        "properties": {
+          "category": {
+            "type": "string"
+          },
+          "name": {
+            "type": "string"
+          },
+          "value": {
+            "type": "string"
+          },
+          "filter": {
+            "type": "string"
+          },
+          "count": {
+            "type": "integer"
+          }
+        }
+      }
+    },
+    "metadata": {
+      "title": "Metadata",
+      "description": "Data about the evidence collection",
+      "type": "object",
+      "additionalProperties": true,
+      "properties": {
+        "collection_paging": {
+          "type": "object",
+          "properties": {
+            "total": {
+              "title": "Total",
+              "description": "The total number of resources in this collection.",
+              "type": "number",
+              "minimum": 0
+            },
+            "total_filtered": {
+              "title": "Total Filtered",
+              "description": "The total number of resources in the filtered collection.",
+              "type": "number",
+              "minimum": 0
+            },
+            "total_pages": {
+              "title": "Total Pages",
+              "description": "The total number of pages (i.e. sized partitions) in the filtered collection.",
+              "type": "number",
+              "minimum": 0
+            },
+            "current_page": {
+              "title": "Current Page",
+              "description": "The current page of the filtered collection that this resource represents.",
+              "type": "number",
+              "minimum": 0
+            },
+            "current_page_size": {
+              "title": "Current Page Size",
+              "description": "The number of resources in the current page of the filtered collection.",
+              "type": "number",
+              "minimum": 0
+            }
+          }
+        }
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/evidence_resource.schema.json

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+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Evidence Resource",
+  "description": "A single evidence resource.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "evidence"
+  ],
+  "properties": {
+    "allOf": [
+      {
+        "$ref":"evidence.schema.json"
+      },
+      {
+        "type": "object",
+        "additionalProperties": false,
+        "required": [
+          "links"
+        ],
+        "properties": {
+          "links": {
+            "type": "object"
+          }
+        }
+      }
+    ]
+  }
+}

data/app/openbel/api/schemas/namespace_value_collection.schema.json

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+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Namespace Value Collection",
+  "description": "A collection of namespace value resources.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "namespace_value_collection"
+  ],
+  "properties": {
+    "namespace_value_collection": {
+      "type": "array",
+      "minItems": 0,
+      "title": "",
+      "description": "",
+      "items": {
+        "$ref":"http://next.belframework.org/schemas/namespace_value_resource.schema.json"
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/namespace_value_resource.schema.json

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+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Namespace Value Resource",
+  "description": "A single namespace value within a BEL Namespace.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "namespace_value"
+  ],
+  "properties": {
+    "namespace_value": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": [
+        "type",
+        "identifier",
+        "name",
+        "title",
+        "species"
+      ],
+      "properties": {
+        "type": {
+          "type": "string"
+        },
+        "identifier": {
+          "type": "string"
+        },
+        "name": {
+          "type": "string"
+        },
+        "title": {
+          "type": ["null", "string"]
+        },
+        "species": {
+          "type": ["null", "string"]
+        },
+        "match_text": {
+          "type": "string"
+        }
+      }
+    }
+  }
+}

data/app/openbel/api/util.rb

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+require 'pathname'
+
+module OpenBEL
+  module Util
+    def self.path(*args)
+      return nil if args.empty?
+      tokens = args.flatten
+      tokens.reduce(Pathname(tokens.shift)) { |path, t| path += t }
+    end
+  end
+end

data/bin/openbel-api

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+#!/usr/bin/env jruby
+
+require 'optparse'
+require 'puma/cli'
+
+ORIGINAL_ARGV = ARGV.dup
+OPENBEL_ARGV  = ARGV.slice_before('--').to_a[0]
+PUMA_ARGV     = ARGV.slice_after('--').to_a[1] || []
+
+ROOT          = File.expand_path('..', File.dirname(__FILE__))
+config_file   = ENV['OPENBEL_API_CONFIG_FILE']
+
+exec('puma', '--help') if ['-h', '--help'].any? {|opt| PUMA_ARGV.include?(opt) }
+
+# Parse OpenBEL API arguments.
+options = {}
+parser  = OptionParser.new do |opts|
+	opts.banner = %Q{
+Runs the OpenBEL API application using the Puma HTTP server (Ruby).
+
+Usage:
+
+    openbel-api -f [FILE] -- [Puma options]
+
+Detail:
+
+The command-line is divided into OpenBEL API and Puma options. These options
+are divided using the "--" delimiter.
+
+OpenBEL API
+===========
+
+The first set of options pertain to the OpenBEL API.
+
+A configuration file must be provided for the OpenBEL API application.
+This can be provided by setting the OPENBEL_API_CONFIG_FILE environment
+variable or by passing the "-f" option.
+
+Puma HTTP Server
+================
+
+The second set of options pertain to the Puma HTTP server. This includes
+settings like bind interface, port, PID file, etc. To see all options for
+Puma run:
+
+  openbel-api -- --help
+
+OpenBEL API Options
+===================
+	}
+
+	opts.on('-f', '--file FILE', 'The file where the configuration will be written.') do |file|
+		options[:file] = file
+	end
+end
+
+parser.default_argv = OPENBEL_ARGV
+parser.parse!
+
+if options[:file]
+	config_file = options[:file]
+end
+
+begin
+	File.open(config_file, 'r')
+rescue SystemCallError => err
+	if err.class.name.start_with?('Errno::')
+		$stderr.puts %Q{The configuration file "#{File.expand_path(config_file)}" cannot be read.\nError: #{err.message}}
+		exit 1
+	else
+		raise err
+	end
+end
+
+ENV['OPENBEL_API_CONFIG_FILE'] = config_file
+
+# Run Puma.
+exec('puma', *PUMA_ARGV, "#{File.join(ROOT, 'app', 'openbel', 'api', 'config.ru')}")

data/bin/openbel-config

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+#!/usr/bin/env jruby
+require 'optparse'
+
+# options; any default go here
+options = {}
+
+# parse options from cli
+OptionParser.new do |opts|
+  opts.banner = %Q{
+    Writes an OpenBEL configuration file (YAML format).
+
+    Usage: openbel-config -f [FILE]
+  }.gsub(/^ +/, '')
+
+  opts.on('-f', '--file FILE', 'The file where the configuration will be written.') do |file|
+    options[:file] = file
+  end
+end.parse!
+
+# resolve path for config.yml template
+CONFIG = File.join(File.expand_path('..', File.dirname(__FILE__)), 'config', 'config.yml')
+
+# sanity check
+unless File.readable?(CONFIG)
+  $stderr.puts %Q{The configuration template cannot be read. Path was "#{CONFIG}".}
+  exit 1
+end
+
+# write out the config
+if options[:file]
+  begin
+    File.open(options[:file], 'w') do |f|
+      f.write(File.read(CONFIG))
+    end
+  rescue SystemCallError => err
+    if err.class.name.start_with?('Errno::')
+      $stderr.puts %Q{The file option "#{options[:file]}" cannot be written.\nError: #{err.message}}
+      exit 1
+    else
+      raise err
+    end
+  end
+  $stdout.puts "Wrote configuration template to path #{options[:file]}."
+else
+  $stdout.puts(File.read(CONFIG))
+end

data/config/async_evidence.rb

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+# $LOAD_PATH.unshift File.expand_path('../lib', __FILE__)
+# require 'evidence/mongo'
+# config['evidence'] = OpenBEL::Evidence::Evidence.new(mongo)
+
+# mongo = {
+#   :host     => 'localhost',
+#   :port     => 27017,
+#   :database => 'openbel'
+# }
+
+require 'em-mongo'
+config['evidence_collection'] = EM::Mongo::Connection.new('localhost', 27017).db('openbel').collection('evidence')

data/config/async_jena.rb

@@ -0,0 +1,14 @@
+require 'bel'
+
+# Use Jena RdfRepository plugin from bel.rb.
+config['rdf_repository'] = BEL::RdfRepository.plugins[:jena].create_repository(:tdb_directory => 'data2')
+$stdout.puts "Initialized rdf/jena."
+
+# Include RDF monkeypatch of BEL::Model classes.
+BEL::Translator.plugins[:rdf].create_translator
+$stdout.puts "Loaded monkey patch for BEL RDF methods."
+
+# Bootstrap
+require 'rdf'
+UUID.generate
+$stdout.puts "Bootstrapped RDF (uuid)."

data/config/config.yml

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+# Configuration template for OpenBEL API
+
+# Storage of evidence through the Mongo database.
+evidence_store:
+  mongo:
+    host:     'localhost'
+    port:     27017
+    database: 'openbel'
+
+# RDF dataset for BEL datasets, annotations, and namespaces using Apache Jena.
+resource_rdf:
+  jena:
+    tdb_directory: 'biological-concepts-rdf'
+
+# Full-text search over annotation and namespace values using SQLite.
+resource_search:
+  sqlite:
+    database_file: 'biological-concepts-rdf.db'
+
+# 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'
+

data/config/server_config.rb

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+#!/usr/bin/env puma
+
+tag 'OBP - API'
+
+pidfile 'openbel-api.pid'
+
+# if ENV['SERVER_AS_DAEMON'].to_i == 1
+#   daemonize true
+#
+#   require 'fileutils'
+#   stdout_file = ENV['OUT_SERVER_STDOUT']
+#   FileUtils.mkdir_p File.dirname(stdout_file)
+#   stderr_file = ENV['OUT_SERVER_STDERR']
+#   FileUtils.mkdir_p File.dirname(stderr_file)
+#   stdout_redirect stdout_file, stderr_file
+# end
+
+bind 'tcp://0.0.0.0:9000'
+
+threads 1, 8
+
+# The directory to operate out of.
+#
+# The default is the current directory.
+#
+# directory '/u/apps/lolcat'
+
+# Use an object or block as the rack application. This allows the
+# config file to be the application itself.
+#
+# app do |env|
+#   puts env
+#
+#   body = 'Hello, World!'
+#
+#   [200, { 'Content-Type' => 'text/plain', 'Content-Length' => body.length.to_s }, [body]]
+# end
+
+# Load “path” as a rackup file.
+#
+# The default is “config.ru”.
+#
+# rackup '/u/apps/lolcat/config.ru'
+
+# Set the environment in which the rack's app will run. The value must be a string.
+#
+# The default is “development”.
+#
+# environment 'production'
+
+# Daemonize the server into the background. Highly suggest that
+# this be combined with “pidfile” and “stdout_redirect”.
+#
+# The default is “false”.
+#
+# daemonize
+# daemonize false
+
+# Store the pid of the server in the file at “path”.
+#
+# pidfile '/u/apps/lolcat/tmp/pids/puma.pid'
+
+# Use “path” as the file to store the server info state. This is
+# used by “pumactl” to query and control the server.
+#
+# state_path '/u/apps/lolcat/tmp/pids/puma.state'
+
+# Redirect STDOUT and STDERR to files specified. The 3rd parameter
+# (“append”) specifies whether the output is appended, the default is
+# “false”.
+#
+# stdout_redirect '/u/apps/lolcat/log/stdout', '/u/apps/lolcat/log/stderr'
+# stdout_redirect '/u/apps/lolcat/log/stdout', '/u/apps/lolcat/log/stderr', true
+
+# Disable request logging.
+#
+# The default is “false”.
+#
+# quiet
+
+# Configure “min” to be the minimum number of threads to use to answer
+# requests and “max” the maximum.
+#
+# The default is “0, 16”.
+#
+# threads 0, 16
+
+# Bind the server to “url”. “tcp://”, “unix://” and “ssl://” are the only
+# accepted protocols.
+#
+# The default is “tcp://0.0.0.0:9292”.
+#
+# bind 'tcp://0.0.0.0:9292'
+# bind 'unix:///var/run/puma.sock'
+# bind 'unix:///var/run/puma.sock?umask=0111'
+# bind 'ssl://127.0.0.1:9292?key=path_to_key&cert=path_to_cert'
+
+# Instead of “bind 'ssl://127.0.0.1:9292?key=path_to_key&cert=path_to_cert'” you
+# can also use the “ssl_bind” option.
+#
+# ssl_bind '127.0.0.1', '9292', { key: path_to_key, cert: path_to_cert }
+
+# Code to run before doing a restart. This code should
+# close log files, database connections, etc.
+#
+# This can be called multiple times to add code each time.
+#
+# on_restart do
+#   puts 'On restart...'
+# end
+
+# Command to use to restart puma. This should be just how to
+# load puma itself (ie. 'ruby -Ilib bin/puma'), not the arguments
+# to puma, as those are the same as the original process.
+#
+# restart_command '/u/app/lolcat/bin/restart_puma'
+
+# === Cluster mode ===
+
+# How many worker processes to run.
+#
+# The default is “0”.
+#
+# workers 2
+
+# Code to run when a worker boots to setup the process before booting
+# the app.
+#
+# This can be called multiple times to add hooks.
+#
+# on_worker_boot do
+#   puts 'On worker boot...'
+# end
+
+# Code to run when a worker boots to setup the process after booting
+# the app.
+#
+# This can be called multiple times to add hooks.
+#
+# after_worker_boot do
+#   puts 'On worker boot...'
+# end
+
+# Code to run when a worker shutdown.
+#
+#
+# on_worker_shutdown do
+#   puts 'On worker boot...'
+# end
+
+# Allow workers to reload bundler context when master process is issued
+# a USR1 signal. This allows proper reloading of gems while the master
+# is preserved across a phased-restart. (incompatible with preload_app)
+# (off by default)
+
+# prune_bundler
+
+# Preload the application before starting the workers; this conflicts with
+# phased restart feature. (off by default)
+
+# preload_app!
+
+# Additional text to display in process listing
+#
+# tag 'app name'
+
+# Change the default timeout of workers
+#
+# worker_timeout 60
+
+# === Puma control rack application ===
+
+# Start the puma control rack application on “url”. This application can
+# be communicated with to control the main server. Additionally, you can
+# provide an authentication token, so all requests to the control server
+# will need to include that token as a query parameter. This allows for
+# simple authentication.
+#
+# Check out https://github.com/puma/puma/blob/master/lib/puma/app/status.rb
+# to see what the app has available.
+#
+# activate_control_app 'unix:///var/run/pumactl.sock'
+# activate_control_app 'unix:///var/run/pumactl.sock', { auth_token: '12345' }
+# activate_control_app 'unix:///var/run/pumactl.sock', { no_token: true }