psc 0.0.1 → 0.0.2

data/.yardopts

@@ -2,3 +2,4 @@
 --markup markdown
 --hide-void-return
 --files CHANGELOG.md,int-psc/README-int-psc.md
+--readme README.md

data/CHANGELOG.md

@@ -1,3 +1,9 @@
+0.0.2
+=====
+
+- Correct PSC token middleware so it properly continues the
+  faraday "app". (#3)
+
 0.0.1
 =====
 

data/README-ssl.md

@@ -0,0 +1,46 @@
+# @title SSL in psc.rb
+
+SSL in psc.rb
+=============
+
+psc.rb uses Faraday's `net/http` adapter by default. This adapter
+verifies SSL certificates when used with HTTPS-served resources (as it
+should). If the openssl install used by your ruby interpreter doesn't
+have the CA certificate for your PSC instance, you'll get an exception
+like this when you make a request:
+
+`OpenSSL::SSL::SSLError: SSL_connect returned=1 errno=0 state=SSLv3 read server certificate B: certificate verify failed`
+
+There are two ways to resolve this for psc.rb.
+
+Configure OpenSSL with appropriate CA certificates
+--------------------------------------------------
+
+Depending on your OS & distribution, this may be as simple as
+installing another package, or it might be fiendishly
+complex/impossible. References:
+
+* <http://gagravarr.org/writing/openssl-certs/others.shtml>
+* <http://curl.haxx.se/ca/>
+
+Configure PSC::Client or PSC::Connection
+----------------------------------------
+
+You can pass SSL options to the underlying adapter when creating a
+{Psc::Client} or {Psc::Connection} instance:
+
+    psc = Psc::Client.new(
+      'https://demos.nubic.northwestern.edu/psc',
+      :authenticator => { :basic => %w(superuser superuser) },
+      :ssl => { :ca_file => '/etc/ssl/cacert.pem' }
+    )
+
+This example assumes you've put an appropriate CA certificate in
+`/etc/ssl/cacert.pem`. (You can, of course, put it where ever you
+like.) If you need a PEM-formatted version of the common commercial
+certificates, <http://curl.haxx.se/ca/> is a good source.
+
+This option is much easier to get working than the first one. It has
+the downside that it requires that all platforms where you will run
+your code have the CA certs in the same place or that you add a
+another configuration option to your application.

data/README.md

@@ -1,8 +1,3 @@
-(Beware: [Readme-driven development in
-progress](http://tom.preston-werner.com/2010/08/23/readme-driven-development.html). This
-is documentation for expected features, not for the current state of
-the library.)
-
 # psc.rb
 
 `psc.rb` is a ruby client for [Patient Study Calendar][psc]'s RESTful
@@ -31,7 +26,10 @@ site][demo-docs]) before using this library.
 
     pp psc.studies
 
-(This code will run if you have the psc gem installed; try it and see.)
+(This code will run if you have the psc gem installed, so long as your
+ruby's openssl has a reasonable set of commercial CAs configured; try
+it and see. If you get a certificate validation error, check out
+{file:README-ssl.md} for some tips.)
 
 ## Installing
 
@@ -135,7 +133,7 @@ custom classes are in the {Psc::Faraday} module.
 ## Project info
 
 * [Source code][github]
-* [API Documentation][rubydoc]
+* [API documentation][rubydoc]
 * [Bug reports and feature requests][issues]
 * [Continuous integration][ci]
 * Version policy: [semantic versioning][semver]
@@ -143,7 +141,7 @@ custom classes are in the {Psc::Faraday} module.
 [rubydoc]: http://rubydoc.info/gems/psc
 [issues]: https://github.com/NUBIC/psc.rb/issues
 [github]: https://github.com/NUBIC/psc.rb
-[ci]: https://ctms-ci.nubic.northwestern.edu/hudson/jobs/psc.rb
+[ci]: https://public-ci.nubic.northwestern.edu/job/psc.rb
 [semver]: http://semver.org/
 
 ### Running the tests

data/Rakefile

@@ -65,5 +65,5 @@ namespace :ci do
   end
 
   # currently bypassing ci_reporter due to https://github.com/nicksieger/ci_reporter/issues/5
-  task :build => %w(int-psc:war int-psc:clean_logs rake:spec cucumber)
+  task :build => %w(int-psc:unlock_database int-psc:war int-psc:clean_logs rake:spec cucumber)
 end

data/ci-exec.sh

@@ -0,0 +1,44 @@
+#!/bin/bash -xe
+
+BUNDLER_VERSION=1.1.rc
+GEMSET=psc-rb
+
+if [ -z $CI_RUBY ]; then
+    echo "CI_RUBY must be set"
+    exit 1
+fi
+
+set +xe
+echo "Initializing RVM"
+source ~/.rvm/scripts/rvm
+set -xe
+
+# On the overnight build, reinstall all gems
+if [ `date +%H` -lt 5 ]; then
+    set +xe
+    echo "Purging gemset to verify that all deps can still be installed"
+    rvm --force $CI_RUBY gemset delete $GEMSET
+    set -xe
+fi
+
+RVM_CONFIG="${CI_RUBY}@${GEMSET}"
+set +xe
+echo "Switching to ${RVM_CONFIG}"
+rvm use $RVM_CONFIG
+set -xe
+
+which ruby
+ruby -v
+
+set +e
+gem list -i bundler -v $BUNDLER_VERSION
+if [ $? -ne 0 ]; then
+  set -e
+  gem install bundler -v $BUNDLER_VERSION
+fi
+set -e
+
+bundle update
+
+# Temporarily skipping integrated tests due to issue #2.
+bundle exec rake ci:spec --trace

data/features/studies.feature

@@ -11,8 +11,8 @@ Scenario: List studies
    When I evaluate the following code:
     """
     s = client.studies
-    puts "Study count: #{s.size}"
-    puts "First study: #{s.first['assigned_identifier']}"
+    $stdout.puts "Study count: #{s.size}"
+    $stdout.puts "First study: #{s.first['assigned_identifier']}"
     """
    Then I should see this output:
     """

data/features/support/int_psc.rb

@@ -94,7 +94,7 @@ class IntPsc
     Timeout.timeout(90) do
       while true
         begin
-          open(File.join(self.url, '/api/v1/docs')) { |f| f.read }
+          open(File.join(self.url, '/api/v1/docs/psc.xsd')) { |f| f.read }
           break
         rescue RuntimeError
           sleep(1)
@@ -103,12 +103,25 @@ class IntPsc
         end
       end
     end
+  rescue Timeout::Error => e
+    $stderr.puts "PSC's API did not become available within 90s."
+    if ENV['CI_RUBY']
+      $stderr.puts "Output from the runner may help figure out the problem:"
+      $stderr.puts File.read(path('deploy-base', 'logs', 'jetty.out'))
+    else
+      $stderr.puts "Take a look at the logs in #{path('deploy-base', 'logs')} for hints."
+    end
+    raise e
+  end
+
+  def jdbc_url
+    "jdbc:hsqldb:file:#{path('hsqldb', configuration_name)};shutdown=true"
   end
 
   def create_hsql_psc_configuration
     File.open(path("#{configuration_name}.properties"), 'w') do |f|
       f.puts [
-        "datasource.url=jdbc:hsqldb:file:#{path('hsqldb', configuration_name)};shutdown=true",
+        "datasource.url=#{jdbc_url}",
         'datasource.username=sa',
         'datasource.password=',
         'datasource.driver=org.hsqldb.jdbcDriver'
@@ -128,8 +141,24 @@ class IntPsc
     end
   end
 
+  def hsqldb_shutdown_compact
+    sqltool 'SHUTDOWN COMPACT;'
+  end
+
   private
 
+  def sqltool(commands)
+    cmd =
+      "java -jar #{hsqldb_jar} --inlineRc 'URL=#{jdbc_url}',USER=sa,PASSWORD= --sql '#{commands}'"
+    $stderr.puts cmd
+    system(cmd)
+  end
+
+  def hsqldb_jar
+    @hsqldb_jar ||=
+      Dir[File.join(expanded_war_directory, 'WEB-INF/lib/*.jar')].detect { |p| p =~ /hsqldb/ }
+  end
+
   def expand_if_necessary
     dirtime = File.directory?(expanded_war_directory) ?
       File.mtime(expanded_war_directory) :

data/int-psc/README-int-psc.md

@@ -1,3 +1,5 @@
+# @title Integration Test PSC README
+
 # Integration test PSC
 
 This directory contains artifacts related to the PSC instance that

data/lib/psc/faraday/psc_token.rb

@@ -29,7 +29,7 @@ module Psc
       def call(env)
         env[:request_headers]['Authorization'] = "psc_token #{token}"
 
-        @app.call
+        @app.call(env)
       end
 
       private

data/lib/psc/version.rb

@@ -1,3 +1,3 @@
 module Psc
-  VERSION = '0.0.1'
+  VERSION = '0.0.2'
 end

data/psc.gemspec

@@ -23,11 +23,12 @@ Gem::Specification.new do |s|
   s.add_dependency 'nokogiri', '~> 1.4'
   s.add_dependency 'activesupport', '>= 2.3' # for the JSON adapter
 
+  s.add_development_dependency 'rake', '~> 0.9.2'
   s.add_development_dependency 'rspec', '~> 2.6'
   s.add_development_dependency 'ci_reporter', '~> 1.6'
-  s.add_development_dependency 'cucumber', '~> 0.10.2'
+  s.add_development_dependency 'cucumber', '0.10.7'
   s.add_development_dependency 'childprocess', '~> 0.1'
   s.add_development_dependency 'highline'
   s.add_development_dependency 'webmock', '~> 1.6'
-  s.add_development_dependency 'yard', '~> 0.6.8'
+  s.add_development_dependency 'yard', '~> 0.7.1'
 end

data/spec/middleware_helper.rb

@@ -12,7 +12,7 @@ end
 
 shared_examples 'unconditional middleware' do
   it 'continues the chain' do
-    app.should_receive(:call)
+    app.should_receive(:call).with(env)
     subject.call(env)
   end
 end

data/tasks/int-psc.rake

@@ -14,7 +14,7 @@ namespace 'int-psc' do
       sh [
         'curl',
         '-o', task.name,
-        "'https://ctms-ci.nubic.northwestern.edu/hudson/job/PSC%20nightly%20distribution/lastSuccessfulBuild/artifact/*zip*/archive.zip'"
+        "'https://public-ci.nubic.northwestern.edu/job/PSC%20nightly%20distribution/lastSuccessfulBuild/artifact/*zip*/archive.zip'"
       ].join(' ')
     end
 
@@ -65,8 +65,11 @@ namespace 'int-psc' do
     IntPsc.run do |int_psc|
       int_psc.apply_state_and_mark_readonly
     end
+
+    IntPsc.new.hsqldb_shutdown_compact
+
     # the copied log file is not needed in the locked database
-    rm path('hsqldb', 'datasource.log')
+    rm_rf IntPsc.path('hsqldb', 'datasource.log')
   end
 
   desc 'Start up the integrated test PSC instance to poke around'
@@ -81,4 +84,9 @@ namespace 'int-psc' do
   task :clean_logs do
     rm_rf IntPsc.path('deploy-base', 'logs')
   end
+
+  desc 'Remove the database lock if it was left over by a previous run'
+  task :unlock_database do
+    rm_rf IntPsc.path('hsqldb', 'datasource.lck')
+  end
 end

metadata

@@ -1,225 +1,176 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: psc
-version: !ruby/object:Gem::Version 
-  hash: 29
+version: !ruby/object:Gem::Version
+  version: 0.0.2
   prerelease: 
-  segments: 
-  - 0
-  - 0
-  - 1
-  version: 0.0.1
 platform: ruby
-authors: 
+authors:
 - Rhett Sutphin
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-05-17 00:00:00 -05:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2011-10-11 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: faraday
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &2156680720 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        - 7
-        - 0
+      - !ruby/object:Gem::Version
         version: 0.7.0
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: builder
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *2156680720
+- !ruby/object:Gem::Dependency
+  name: builder
+  requirement: &2156680200 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 2
-        - 1
-        - 2
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 2.1.2
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: faraday-stack
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *2156680200
+- !ruby/object:Gem::Dependency
+  name: faraday-stack
+  requirement: &2156679660 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 25
-        segments: 
-        - 0
-        - 1
-        - 1
+      - !ruby/object:Gem::Version
         version: 0.1.1
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: nokogiri
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: *2156679660
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: &2156679180 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 1
-        - 4
-        version: "1.4"
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: activesupport
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: *2156679180
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: &2156678720 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 2
-        - 3
-        version: "2.3"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '2.3'
   type: :runtime
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: rspec
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: *2156678720
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &2156678260 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 2
-        - 6
-        version: "2.6"
+      - !ruby/object:Gem::Version
+        version: 0.9.2
   type: :development
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: ci_reporter
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  version_requirements: *2156678260
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &2156677800 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 1
-        - 6
-        version: "1.6"
+      - !ruby/object:Gem::Version
+        version: '2.6'
   type: :development
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  name: cucumber
   prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  version_requirements: *2156677800
+- !ruby/object:Gem::Dependency
+  name: ci_reporter
+  requirement: &2156677280 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 51
-        segments: 
-        - 0
-        - 10
-        - 2
-        version: 0.10.2
+      - !ruby/object:Gem::Version
+        version: '1.6'
   type: :development
-  version_requirements: *id008
-- !ruby/object:Gem::Dependency 
-  name: childprocess
   prerelease: false
-  requirement: &id009 !ruby/object:Gem::Requirement 
+  version_requirements: *2156677280
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: &2156676820 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
+    - - =
+      - !ruby/object:Gem::Version
+        version: 0.10.7
+  type: :development
+  prerelease: false
+  version_requirements: *2156676820
+- !ruby/object:Gem::Dependency
+  name: childprocess
+  requirement: &2156676360 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 9
-        segments: 
-        - 0
-        - 1
-        version: "0.1"
+      - !ruby/object:Gem::Version
+        version: '0.1'
   type: :development
-  version_requirements: *id009
-- !ruby/object:Gem::Dependency 
-  name: highline
   prerelease: false
-  requirement: &id010 !ruby/object:Gem::Requirement 
+  version_requirements: *2156676360
+- !ruby/object:Gem::Dependency
+  name: highline
+  requirement: &2156675980 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id010
-- !ruby/object:Gem::Dependency 
-  name: webmock
   prerelease: false
-  requirement: &id011 !ruby/object:Gem::Requirement 
+  version_requirements: *2156675980
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: &2156620280 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 1
-        - 6
-        version: "1.6"
+      - !ruby/object:Gem::Version
+        version: '1.6'
   type: :development
-  version_requirements: *id011
-- !ruby/object:Gem::Dependency 
-  name: yard
   prerelease: false
-  requirement: &id012 !ruby/object:Gem::Requirement 
+  version_requirements: *2156620280
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: &2156619460 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 0
-        - 6
-        - 8
-        version: 0.6.8
+      - !ruby/object:Gem::Version
+        version: 0.7.1
   type: :development
-  version_requirements: *id012
+  prerelease: false
+  version_requirements: *2156619460
 description: A lightweight ruby client for Patient Study Calendar's RESTful HTTP API
-email: 
+email:
 - r-sutphin@northwestern.edu
 executables: []
-
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - .gitignore
 - .rvmrc
 - .yardopts
 - CHANGELOG.md
 - Gemfile
 - LICENSE
+- README-ssl.md
 - README.md
 - Rakefile
+- ci-exec.sh
 - cucumber.yml
 - features/step_definitions/eval_steps.rb
 - features/step_definitions/setup_steps.rb
@@ -244,7 +195,6 @@ files:
 - lib/psc/faraday/psc_token.rb
 - lib/psc/faraday/string_is_xml.rb
 - lib/psc/version.rb
-- meta.rakefile
 - psc.gemspec
 - spec/fixtures/studies-json.http
 - spec/middleware_helper.rb
@@ -259,41 +209,31 @@ files:
 - tasks/int-psc.rake
 - tasks/psc/TODO
 - tasks/psc/state.rb
-has_rdoc: true
 homepage: https://github.com/NUBIC/psc.rb
 licenses: []
-
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.5.2
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: A lightweight ruby client for Patient Study Calendar's RESTful HTTP API
-test_files: 
+test_files:
 - features/step_definitions/eval_steps.rb
 - features/step_definitions/setup_steps.rb
 - features/studies.feature

data/meta.rakefile

@@ -1,30 +0,0 @@
-PLATFORMS = {
-  :ruby18 => 'ruby-1.8.7-p334',
-  :jruby  => 'jruby-1.6.1',
-  :ruby19 => 'ruby-1.9.2-p180'
-}
-
-BUNDLER_VERSION = '1.0.13'
-
-def ci_env
-  (ENV["PSC_RB_ENV"] || :ruby18).to_sym
-end
-
-namespace :ci do
-  task :rvmrc do
-    puts "#{PLATFORMS[ci_env]}@psc-rb"
-  end
-
-  task :ensure_bundler_available do
-    unless Gem.available?('bundler', BUNDLER_VERSION)
-      puts "Installing bundler"
-      sh "gem install bundler -v '#{BUNDLER_VERSION}'"
-    end
-  end
-
-  task :setup => [:ensure_bundler_available] do
-    sh "bundle _#{BUNDLER_VERSION}_ update"
-  end
-end
-
-task :default => 'ci:setup'