psc 0.0.1

data/int-psc/state/ABC 1200.xml

@@ -0,0 +1,115 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<study xmlns="http://bioinformatics.northwestern.edu/ns/psc" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" assigned-identifier="ABC 1200" last-modified-date="2011-05-12T11:10:29.740Z" xsi:schemaLocation="http://bioinformatics.northwestern.edu/ns/psc http://bioinformatics.northwestern.edu/ns/psc/psc.xsd">
+  <planned-calendar id="9c9c8042-75f1-477a-8855-40e6084f0954"/>
+  <amendment name="[Original]" date="2011-05-12" mandatory="true" released-date="2011-05-12T11:10:29.740Z" updated-date="2011-05-12T10:44:34.568Z">
+    <planned-calendar-delta id="d7adaa30-e2f0-4415-a751-53ccee9433ca" node-id="9c9c8042-75f1-477a-8855-40e6084f0954">
+      <add id="234ae5fa-e712-473d-b395-7e5edf9ef532" index="0">
+        <epoch id="72e7e90a-5f09-49b7-9dc4-785d56cf4414" name="Treatment">
+          <study-segment id="f174f7c2-ceed-4c6c-8392-1688f34b7905" name="A">
+            <period id="e74bbe38-46ad-410c-acd8-fb70f9527c0b" name="Surgery" repetitions="1" start-day="1" duration-quantity="1" duration-unit="day">
+              <planned-activity id="db2ffa63-8c28-43cd-94c4-e8f6801ce42b" day="1">
+                <activity-reference code="1041" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+            <period id="1d8227b3-8f40-424c-a238-bffcda982014" name="Frequent monitoring" repetitions="24" start-day="1" duration-quantity="1" duration-unit="week">
+              <planned-activity id="2da856a4-3d40-4d04-8804-c9ee2b9f90b3" day="1">
+                <activity-reference code="360" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="09791bfb-eaf6-418a-8516-fae296df23f0" day="1">
+                <activity-reference code="253" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+            <period id="e93b9f37-43de-4873-a776-1e7fcefbec59" name="Infrequent monitoring" repetitions="6" start-day="1" duration-quantity="1" duration-unit="month">
+              <planned-activity id="3ad03935-5bdf-448e-88ee-ee656d12afe3" day="1">
+                <activity-reference code="701" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="6fdbfd73-6cc3-41a6-a388-b19cf2bf7b25" day="1">
+                <activity-reference code="451" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+            <period id="0c7852e2-eca1-4b57-9e7a-2d222abf43ea" name="Intervention" repetitions="8" start-day="8" duration-quantity="3" duration-unit="week">
+              <planned-activity id="845b63f0-389d-4b7c-b9df-986b7dd3e4ad" day="1">
+                <activity-reference code="211" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="0be23936-1621-49b3-862e-90eee0b03bf4" day="15">
+                <activity-reference code="211" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="7f599ee3-f45f-4af1-bcfd-3d377b3bbc4a" day="8">
+                <activity-reference code="43" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+          </study-segment>
+          <study-segment id="fe329f59-1253-405a-9933-ea2d70bdf0dc" name="B">
+            <period id="538baa4e-6e4f-4e67-a112-b5a5d1200ba9" name="Frequent monitoring" repetitions="24" start-day="1" duration-quantity="1" duration-unit="week">
+              <planned-activity id="e742696d-c066-4e59-9bd2-f064a468ca87" day="1">
+                <activity-reference code="360" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="d882f175-13ae-4c16-9aa2-38f27c2ea2a6" day="1">
+                <activity-reference code="253" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+            <period id="d54584c4-acc5-4de9-8323-ed36cbced4bc" name="Infrequent monitoring" repetitions="6" start-day="1" duration-quantity="1" duration-unit="month">
+              <planned-activity id="b23569f5-1268-4264-8c4d-bae166616d16" day="1">
+                <activity-reference code="701" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="3c54d7b4-f2ec-4b9e-9fe4-b6d13b92aeba" day="1">
+                <activity-reference code="451" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+            <period id="b85661ef-ff19-462f-83a4-3e53ed69cd84" name="Intervention" repetitions="8" start-day="8" duration-quantity="3" duration-unit="week">
+              <planned-activity id="23a0aac4-87f6-4cd3-8df1-71bee82505ae" day="1">
+                <activity-reference code="211" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="24deeecc-cba8-4d8c-bc55-35048970bb8e" day="15">
+                <activity-reference code="211" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="40cce9be-3a32-4477-9c8d-79104b8625f0" day="8">
+                <activity-reference code="43" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+          </study-segment>
+        </epoch>
+      </add>
+      <add id="1b02eb68-d1c8-4d11-88f2-4785ff91f0bb" index="1">
+        <epoch id="1d0d08cc-ed40-4ebb-923f-ebe0c29e814d" name="Follow up">
+          <study-segment id="4c01e031-1fe9-41ad-970c-368cb57c0c8e" name="Follow up">
+            <period id="3b8bff21-4d30-475f-a9b7-a39afed63b94" name="QoL" repetitions="18" start-day="1" duration-quantity="1" duration-unit="quarter">
+              <planned-activity id="a33a6a83-2b27-4678-a395-4025b399882b" details="Administer by phone" day="1">
+                <activity-reference code="941" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+          </study-segment>
+        </epoch>
+      </add>
+      <add id="aefbcdc5-ac5b-4c0d-b092-b6e9e337969e" index="2">
+        <epoch id="9d7bf8eb-6413-4286-97c0-f44f489883e6" name="Run-in">
+          <study-segment id="14969b7b-e49e-48e0-b081-ba94d9448479" name="Run-in">
+            <period id="3970c8a8-89e3-4d7e-98ac-4f27232cc624" repetitions="3" start-day="1" duration-quantity="7" duration-unit="day">
+              <planned-activity id="cdd73e03-1410-4ae6-9d86-4a8929cd1678" day="1">
+                <activity-reference code="360" source="Northwestern University"/>
+              </planned-activity>
+              <planned-activity id="0df8ccf3-2067-47c6-bbf3-dfbf8512968e" day="7">
+                <activity-reference code="593" source="Northwestern University"/>
+              </planned-activity>
+            </period>
+          </study-segment>
+        </epoch>
+      </add>
+      <reorder id="a455e585-1bee-4770-b191-63fb8ec70066" child-id="9d7bf8eb-6413-4286-97c0-f44f489883e6" old-index="2" new-index="0"/>
+    </planned-calendar-delta>
+  </amendment>
+  <sources>
+    <source name="Northwestern University">
+      <activity name="Ketones (Acetone)" code="593" type="Lab Test"/>
+      <activity name="Taxol" code="211" type="Intervention"/>
+      <activity name="Dialysis Chemistry Panel" code="451" type="Lab Test"/>
+      <activity name="24 hr urine, protein electrophoresis" code="253" type="Lab Test"/>
+      <activity name="Carboplatin" code="43" type="Intervention"/>
+      <activity name="Pregnancy Test" code="701" type="Lab Test"/>
+      <activity name="CBC" code="360" type="Lab Test"/>
+      <activity name="QOL Survey" code="941" type="Other"/>
+      <activity name="Surgery" code="1041" type="Procedure"/>
+    </source>
+  </sources>
+</study>

data/int-psc/state/int-psc-state.xml

@@ -0,0 +1,64 @@
+<!-- To rebuild the integration test PSC when you change this data, run `rake int-psc:rebuild` -->
+
+<psc-state>
+  <!--
+      General note: Anywhere a date is specified, the value may either
+      be a date string in the form yyyy-mm-dd or an integer. An
+      integer indicates a date relative to today (negative, before
+      today; positive, after today).
+  -->
+
+  <site name="Northwestern University" assigned-identifier="IL036"/>
+  <site name="Mayo Clinic Rochester" assigned-identifier="MN026"/>
+  <site name="Thomas Jefferson University" assigned-identifier="PA121"/>
+
+  <!--
+      The assigned-identifier attribute for template is mandatory;
+      file is optional. If the file is omitted, it is assumed to be a
+      file named [assigned-identifier].xml in the same directory as
+      this state XML file.
+  -->
+  <template assigned-identifier="ABC 1200">
+    <!--
+        approval indicates whether the template should be marked as
+        approved for use by the site. It can be either a date or
+        false; the default is 0 (i.e., today). All released amendments
+        will have the same approval status.
+    -->
+    <participating-site assigned-identifier="IL036" approval="2008-01-07"/>
+    <participating-site assigned-identifier="PA121" approval="2010-01-02"/>
+  </template>
+
+
+  <registration>
+    <subject
+        first-name="Jo"
+        last-name="Fredricksson"
+        gender="Female"
+        birth-date="1950-06-01"
+        person-id="XC56700077"
+        >
+      <subject-property name="Hat size" value="7"/>
+    </subject>
+    <!-- template-identifier and site-identifier are mandatory attributes -->
+    <study-site
+        template="ABC 1200"
+        site="IL036"
+        study-subject-identifier="A0001"
+        desired-assignment-identifier="POP-2702">
+      <!--
+          * segment is either the ID for the segment or its "epoch: segment" name (mandatory).
+          * start is the start date for the segment (default: 0 for the first segment;
+            the end of the previous for subsequent). [TODO: the second part isn't implemented yet]
+          * mode is the transition mode for the segment (default: per-protocol).
+      -->
+      <scheduled-segment segment="Run-in" start="2010-01-01"/>
+      <scheduled-segment segment="Treatment: A" start="2010-02-01" mode="per-protocol"/>
+      <scheduled-segment segment="Follow up" start="2010-03-15" mode="immediate"/>
+    </study-site>
+
+    <!-- multiple study-sites allowed per registration to reuse the same subject -->
+  </registration>
+
+  <!-- multiple registrations allowed -->
+</psc-state>

data/lib/psc.rb

@@ -0,0 +1,47 @@
+require 'builder'
+
+##
+# The namespace for `psc.rb`.
+module Psc
+  autoload :Faraday,    'psc/faraday'
+  autoload :Client,     'psc/client'
+  autoload :Connection, 'psc/connection'
+
+  ##
+  # Wraps `Builder::XmlMarkup` to ease the construction of PSC XML
+  # entities. For example:
+  #
+  #     Psc.xml('study-snapshot', :assigned_identifier => 'YUV 1234') do |snap|
+  #       snap.tag!('long-title', 'Why you validly counting?')
+  #       snap.tag!('planned-calendar') { |pc|
+  #         pc.epoch(:name => 'Run-in') { |e|
+  #           # and so on
+  #         }
+  #       }
+  #       snap.sources { |sources|
+  #         sources.source { |src|
+  #           # and so on
+  #         }
+  #       }
+  #     }
+  #
+  # @see http://builder.rubyforge.org/classes/Builder/XmlMarkup.html
+  # @return [String] the constructed XML
+  def self.xml(root_name, root_attributes={}, &block)
+    root_attributes['xmlns'] = xml_namespace['psc']
+    Builder::XmlMarkup.new(:indent => 2).tag!(root_name, root_attributes, &block)
+  end
+
+  ##
+  # @private
+  XML_NAMESPACE = { 'psc' => 'http://bioinformatics.northwestern.edu/ns/psc' }.freeze
+
+  ##
+  # Provides an XML namespace mapping suitable for use with
+  # Nokogiri. The prefix `psc` is mapped to PSC's namespace.
+  #
+  # @return [Hash<String, String>] the mapping
+  def self.xml_namespace
+    XML_NAMESPACE
+  end
+end

data/lib/psc/client.rb

@@ -0,0 +1,35 @@
+require 'psc'
+
+module Psc
+  ##
+  # A high-level interface to a PSC instance's API. This class does
+  # not expose everything you can do with the API — only a few
+  # of the more common elements. Refer to the API documentation and
+  # use {Psc::Connection} for complete access.
+  class Client
+    ##
+    # The connection that the client is using to access PSC. Use it to
+    # make requests that the high-level interface doesn't support.
+    #
+    # @return [Psc::Connection]
+    attr_reader :connection
+
+    ##
+    # Create a new client instance. The given url and options will be
+    # used to create a {Psc::Connection} for the client to use; see
+    # that class for more details about what is permitted
+    def initialize(url, options, &block)
+      @connection = Psc::Connection.new(url, options, &block)
+    end
+
+    ##
+    # Returns an array of hashes describing the studies in the system.
+    # The contents are from the JSON representation of the `/studies`
+    # resource.
+    #
+    # @return [Array<Hash>]
+    def studies
+      connection.get('studies.json').body['studies']
+    end
+  end
+end

data/lib/psc/connection.rb

@@ -0,0 +1,96 @@
+require 'psc'
+require 'faraday'
+require 'faraday_stack'
+
+module Psc
+  ##
+  # A `Faraday::Connection` set up for use with Patient Study
+  # Calendar. See the {file:README.md} for a couple of examples.
+  #
+  # @see https://github.com/technoweenie/faraday
+  # @see https://github.com/mislav/faraday-stack
+  class Connection < ::Faraday::Connection
+    ##
+    # Create a new PSC connection. This is a `Faraday::Connection`
+    # with the following middleware:
+    #
+    #  * Either {Psc::Faraday::HttpBasic} or {Psc::Faraday::PscToken}
+    #    depending on the contents of the `:authenticator` option
+    #  * {Psc::Faraday::StringIsXml}
+    #  * `::Faraday::Request::JSON`
+    #  * `::Faraday::Request::UrlEncoded`
+    #  * `::FaradayStack::ResponseXML` for content-type text/xml
+    #  * `::FaradayStack::ResponseJSON` for content-type application/json
+    #  * `::Faraday::Adapter::NetHttp`
+    #
+    # If a block is provided, it will receive the Faraday builder so
+    # that you can append more middleware. If you provide your own
+    # adapter, the `net/http` adapter will not be appended.
+    #
+    # @param [String] url the base URL for your PSC instance
+    # @param [Hash] options the options for the connection. These are
+    #   same as accepted by `Faraday::Connection`, plus:
+    # @option options [Hash] :authenticator parameters for the
+    #   authentication middleware. These are detailed in the {file:README.md}.
+    # @yield [builder] (optional)
+    def initialize(url, options)
+      super do |builder|
+        builder.use *authentication_middleware(options[:authenticator])
+        builder.use Psc::Faraday::StringIsXml
+        builder.request :json
+        builder.request :url_encoded
+        builder.use FaradayStack::ResponseXML, :content_type => 'text/xml'
+        builder.use FaradayStack::ResponseJSON, :content_type => 'application/json'
+
+        if block_given?
+          yield builder
+        end
+
+        builder.adapter :net_http unless has_adapter?(builder)
+      end
+
+      unless self.path_prefix =~ %r{/api/v1$}
+        self.path_prefix = if self.path_prefix == '/'
+                             '/api/v1'
+                           else
+                             self.path_prefix + '/api/v1'
+                           end
+      end
+    end
+
+    private
+
+    def authentication_middleware(authenticator)
+      unless authenticator
+        raise 'No authentication method specified. Please include the :authenticator option.'
+      end
+
+      kind = authenticator.keys.first
+
+      case kind
+      when :basic
+        [Psc::Faraday::HttpBasic, *authenticator[kind]]
+      when :token
+        [Psc::Faraday::PscToken, authenticator[kind]]
+      else
+        raise "Unsupported authentication method #{kind.inspect}."
+      end
+    end
+
+    def has_adapter?(builder)
+      builder.handlers.detect { |h| has_superclass?(h.klass, ::Faraday::Adapter) }
+    end
+
+    # It seems like there must be a builtin for this, but I'm not
+    # finding it.
+    def has_superclass?(child, ancestor)
+      if child.superclass == ancestor
+        true
+      elsif child.superclass.nil?
+        false
+      else
+        has_superclass?(child.superclass, ancestor)
+      end
+    end
+  end
+end

data/lib/psc/faraday.rb

@@ -0,0 +1,11 @@
+require 'psc'
+
+require 'faraday'
+
+##
+# The custom Faraday middleware used in `psc.rb`.
+module Psc::Faraday
+  autoload :HttpBasic,   'psc/faraday/http_basic'
+  autoload :PscToken,    'psc/faraday/psc_token'
+  autoload :StringIsXml, 'psc/faraday/string_is_xml'
+end

data/lib/psc/faraday/http_basic.rb

@@ -0,0 +1,35 @@
+require 'psc/faraday'
+
+require 'base64'
+
+module Psc::Faraday
+  ##
+  # Faraday middleware that implements [HTTP Basic][]. This is not
+  # PSC-specific, and Faraday even includes HTTP Basic support, but
+  # Faraday's support is not implemented as middleware. Using
+  # middleware makes setting up a connection based on the
+  # `:authenticator` option cleaner.
+  #
+  # [HTTP Basic]: http://www.ietf.org/rfc/rfc2617.txt
+  class HttpBasic
+    ##
+    # Create an instance of the middleware.
+    #
+    # @param [#call] app
+    # @param [String] username
+    # @param [String] password
+    def initialize(app, username, password)
+      @app = app
+      @header_value = "Basic #{Base64.encode64([username, password].join(':')).strip}"
+    end
+
+    ##
+    # Sets the `Authorization` request header using the HTTP Basic
+    # scheme.
+    def call(env)
+      env[:request_headers]['Authorization'] = @header_value
+
+      @app.call(env)
+    end
+  end
+end

data/lib/psc/faraday/psc_token.rb

@@ -0,0 +1,42 @@
+require 'psc/faraday'
+
+module Psc
+  module Faraday
+    ##
+    # Faraday middleware that implements the `psc_token`
+    # authentication type. Tokens may either be static or computed
+    # per request.
+    class PscToken
+      ##
+      # Create a new instance of the middleware.
+      #
+      # @param [#call] app
+      # @param [#call,String] token_or_creator if the value for this
+      #   parameter responds to `call`, it will be called to create a
+      #   token on each request. Otherwise it will be used as a static
+      #   token value.
+      def initialize(app, token_or_creator)
+        @app = app
+        if token_or_creator.respond_to?(:call)
+          @token_creator = token_or_creator
+        else
+          @token_creator = lambda { token_or_creator }
+        end
+      end
+
+      ##
+      # Adds the `Authorization` header using the configured token creator.
+      def call(env)
+        env[:request_headers]['Authorization'] = "psc_token #{token}"
+
+        @app.call
+      end
+
+      private
+
+      def token
+        @token_creator.call
+      end
+    end
+  end
+end