palexander

# Thanks to @samsonjs for the cleaned up version:
# https://gist.github.com/samsonjs/4076746

PREFIX=$HOME
VERSION=1.2.3

# Install Protocol Buffers
wget http://protobuf.googlecode.com/files/protobuf-2.4.1.tar.bz2
tar -xf protobuf-2.4.1.tar.bz2 
cd protobuf-2.4.1

palexander

Accessing BioPortal REST API from the browser with JSONP

This is a prototype service. As such, NCBO will not be providing support for its usage.

Signature

• http://bioportal.bioontology.org/ajax/jsonp?path=%2Fontologies&callback=?&apikey=your_api_key&userapikey=user_api_key

Parameters

The endpoint takes a few parameters (* required):

• • path={REST service endpoint path} - this should not include the /bioportal

palexander

module LinkedData
  module Models
    class Review < Goo::Base::Resource
      model :review
      validates :creator, :presence => true, :cardinality => { :maximum => 1 }
      validates :created, :date_time_xsd => true, :presence => true, :cardinality => { :maximum => 1 }
      validates :body, :presence => true, :cardinality => { :maximum => 1 }
      validates :ontologyReviewed, :presence => true, :cardinality => { :maximum => 1 }
      validates :usabilityRating, :cardinality => { :maximum => 1 }
      validates :coverageRating, :cardinality => { :maximum => 1 }

palexander

# Setup for usage in Mac OSX (assuming you are using 4store.app from your /Applications folder)
curl -L https://raw.github.com/gist/4211360/81143f15fd6f9a3defcd38b6c24a922f3fc731ac/gistfile1.sh -o 4s-service
chmod +x 4s-service
mv 4s-service /Applications/4store.app/Contents/MacOS/bin
# Add the following to your (zsh|bash)rc path (this makes it so you don't have to run 4store.app):
# export PATH=/Applications/4store.app/Contents/MacOS/bin:$PATH
# You can also do this for custom installs of 4store, just replace the /Applications path with your own
# THE SCRIPT WILL NOT WORK WITHOUT 4s-backend, 4s-httpd, etc IN YOUR PATH

# Defaults:

palexander

org.ncbo.stanford.service.ontology.AbstractOntologyService ERROR - 2013-02-04 03:51:11,509 - Error in OntologyService:uploadOntologyFile()! - remote file (fileItem) /srv/ncbo/bioportal_resources/uploads/1005/1 (Is a directory)
java.io.FileNotFoundException: /srv/ncbo/bioportal_resources/uploads/1005/1 (Is a directory)
        at java.io.FileOutputStream.open(Native Method)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
        at org.ncbo.stanford.util.CompressionUtils.extractFiles(CompressionUtils.java:126)
        at org.ncbo.stanford.util.CompressionUtils.unzip(CompressionUtils.java:58)
        at org.ncbo.stanford.util.CompressionUtils.uncompress(CompressionUtils.java:41)
        at org.ncbo.stanford.util.ontologyfile.compressedfilehandler.AbstractCompressedFileHandler.handle(AbstractCompressedFileHandler.java:35)
        at org.ncbo.stanford.util.ontologyfile.compressedfilehandler.impl.RRFCompressedFileHandlerImpl

palexander

require 'rack'

class TestPull < LinkedData::TestCase

  def self.before_suite
    # CREATE FILE OBJECT:
    file = File.new("../some/file.owl")
    @@thread = Thread.new do
      Rack::Server.start(
        app: lambda do |e|

palexander

# Base config from Vagrantfile plus additions to support docker
config.vm.provider :virtualbox do |vb|
  config.vm.box = BOX_NAME
  config.vm.box_url = BOX_URI
  vb.customize ["modifyvm", :id, "--natdnshostresolver1", "on"]
  vb.customize ["modifyvm", :id, "--natdnsproxy1", "on"]
  
  # Added for docker
  vb.customize ["modifyvm", :id, "--ioapic", "on"] # needed for multicpu support
  vb.customize ["modifyvm", :id, "--cpus", "4"] # multiple cpus

palexander

namespace :docker do
  desc "Run tasks in parallel using docker"
  task :test do
    forks = 4
    begin
      # Start docker containers (serially, docker seems to have problems with concurrency)
      ports = {}
      forks.times do |i|
        # Start redis and get the mapped port
        `docker run -d -p 6379 -name redis#{i} yourdockeruser/redis`

palexander

namespace :docker do
  desc "Run tests in parallel using docker"
  task :test do
    forks = 4
    begin
      # Start docker containers (serially, docker seems to have problems with concurrency)
      ports = {}
      forks.times do |i|
        # Start redis and get the mapped port
        `docker run -d -p 6379 -name redis#{i} yourdockeruser/redis`

palexander

@@ -41,10 +41,23 @@ namespace :docker do
           # Require the test files for this particular fork
           test_files_sliced[i].each {|f| require_relative f}

+          # redirect stdout
+          require 'stringio'
+          sio = StringIO.new
+          $stdout = sio
+          $stderr = sio
+