fhir_client 1.0.1

data/lib/feed_format.rb

@@ -0,0 +1,10 @@
+module FHIR
+  module Formats
+    class FeedFormat
+
+      FEED_XML = "application/xml+fhir"
+      FEED_JSON = "application/json+fhir"
+
+    end
+  end
+end

data/lib/fhir_api_validation.json

@@ -0,0 +1,360 @@
+[
+  {
+    "interaction": "read",
+    "path": ["/[type]/[id]"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false,
+        "ETag": "optional",
+        "If-Modified-Since": "optional",
+        "If-None-Match": "optional"
+      },
+      "body": false
+    },
+    "response": {
+      "status": [200,404,410],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": true,
+        "Last-Modified": true
+      },
+      "body": { "types": ["Resource"] }
+    }
+  },{
+    "interaction": "vread",
+    "path": ["/[type]/[id]/_history/[vid]"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false 
+    },
+    "response": {
+      "status": [200,404],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": true,
+        "Last-Modified": true
+      },
+      "body": { "types": ["Resource"] }
+    }
+  },{
+    "interaction": "update",
+    "path": ["/[type]/[id]"],
+    "verb": "PUT",
+    "request": {
+      "headers": {
+        "Content-Type": true,
+        "Accept": "optional",
+        "Prefer": "optional",
+        "If-Match": "optional"
+      },
+      "body": { "types": ["Resource"] }
+    },
+    "response": {
+      "status": [200,201,400,404,405,409,412,422],
+      "headers": {
+        "Content-Type": "optional",
+        "Location": "optional",
+        "ETag": true,
+        "Last-Modified": true
+      },
+      "body": { "types": ["Resource"] }
+    }
+  },{
+    "interaction": "delete",
+    "path": ["/[type]/[id]"],
+    "verb": "DELETE",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200,204,404,405,409,412],
+      "headers": {
+        "Content-Type": "optional",
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["OperationOutcome"] }
+    }
+  },{
+    "interaction": "create",
+    "path": ["/[type]"],
+    "verb": "POST",
+    "request": {
+      "headers": {
+        "Content-Type": true,
+        "Accept": "optional",
+        "Prefer": "optional",
+        "If-None-Exist": "optional"
+      },
+      "body": { "types": ["Resource"] }
+    },
+    "response": {
+      "status": [201,400,404,405,422],
+      "headers": {
+        "Content-Type": true,
+        "Location": true,
+        "ETag": true,
+        "Last-Modified": true
+      },
+      "body": { "types": ["Resource"] }
+    }
+  },{
+    "interaction": "search",
+    "path": ["/[type]?"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200,403],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{
+    "interaction": "search",
+    "path": ["/[type]/_search?"],
+    "verb": "POST",
+    "request": {
+      "headers": {
+        "Content-Type": "application/x-www-form-urlencoded",
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": "form data"      
+    },
+    "response": {
+      "status": [200,403],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{
+    "interaction": "search-all",
+    "path": ["/_search?"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200,403],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{
+    "interaction": "conformance",
+    "path": ["/","/metadata"],
+    "verb": ["GET","OPTIONS"],
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200,404],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Conformance"] }
+    }
+  },{      
+    "interaction": "transaction",
+    "path": ["/"],
+    "verb": "POST",
+    "request": {
+      "headers": {
+        "Content-Type": true,
+        "Accept": "optional",
+        "Prefer": "optional"
+      },
+      "body": { "types": ["Bundle"] }      
+    },
+    "response": {
+      "status": [200,400,404,405,409,412,422],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{      
+    "interaction": "history",
+    "path": ["/[type]/[id]/_history"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{      
+    "interaction": "history-type",
+    "path": ["/[type]/_history"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{      
+    "interaction": "history-all",
+    "path": ["/_history"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false      
+    },
+    "response": {
+      "status": [200],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Bundle"] }
+    }
+  },{      
+    "interaction": "operation",
+    "path": ["/$[name]","/[type]/$[name]","/[type]/[id]/$[name]"],
+    "verb": "POST",
+    "request": {
+      "headers": {
+        "Content-Type": true,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": { "types": ["Parameters"] }
+    },
+    "response": {
+      "status": [200],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Parameters","Resource"] }
+    }
+  },{      
+    "interaction": "operation",
+    "path": ["/$[name]","/[type]/$[name]","/[type]/[id]/$[name]"],
+    "verb": "GET",
+    "request": {
+      "headers": {
+        "Content-Type": false,
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": false
+    },
+    "response": {
+      "status": [200],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Parameters","Resource"] }
+    }
+  },{      
+    "interaction": "operation",
+    "path": ["/$[name]","/[type]/$[name]","/[type]/[id]/$[name]"],
+    "verb": "POST",
+    "request": {
+      "headers": {
+        "Content-Type": "application/x-www-form-urlencoded",
+        "Accept": "optional",
+        "Prefer": false
+      },
+      "body": { "regex": "([\w\-]+(=[\w\-.:\/\|]*)?(&[\w\-]+(=[\w\-.:\/\|]*)?)*)?" }
+    },
+    "response": {
+      "status": [200],
+      "headers": {
+        "Content-Type": true,
+        "Location": false,
+        "ETag": false,
+        "Last-Modified": false
+      },
+      "body": { "types": ["Parameters","Resource"] }
+    }
+  }
+]

data/lib/fhir_client.rb

@@ -0,0 +1,41 @@
+# Top level include file that brings in all the necessary code
+require 'bundler/setup'
+require 'rubygems'
+require 'yaml'
+require 'nokogiri'
+require 'fhir_models'
+require 'rest_client'
+require 'addressable/uri'
+require 'oauth2'
+require 'active_support/core_ext'
+
+begin
+	generator = FHIR::Boot::Generator.new
+	# 1. generate the lists of primitive data types, complex types, and resources
+	generator.generate_metadata
+	# 2. generate the complex data types
+	generator.generate_types
+	# 3. generate the base Resources
+	generator.generate_resources
+rescue Exception => e 
+	$LOG.error("Could not re-generate fhir models... this can happen in production, but the code does not need to be re-generated")
+end
+
+# Simple and verbose loggers
+RestClient.log = Logger.new("fhir_client.log", 10, 1024000)
+$LOG = Logger.new("fhir_client_verbose.log", 10, 1024000)
+
+root = File.expand_path '..', File.dirname(File.absolute_path(__FILE__))
+Dir.glob(File.join(root, 'lib','sections','**','*.rb')).each do |file|
+  require file
+end
+
+require_relative File.join('.','client_interface.rb')
+require_relative File.join('.','resource_address.rb')
+require_relative File.join('.','resource_format.rb')
+require_relative File.join('.','feed_format.rb')
+require_relative File.join('.','patch_format.rb')
+require_relative File.join('.','model','bundle.rb')
+require_relative File.join('.','model','client_reply.rb')
+require_relative File.join('.','model','tag.rb')
+

data/lib/model/bundle.rb

@@ -0,0 +1,32 @@
+module FHIR
+  class Bundle
+
+    def self_link
+      link.select {|n| n.relation == 'self'}.first
+    end
+
+    def first_link
+      link.select {|n| n.relation == 'first'}.first
+    end
+
+    def last_link
+      link.select {|n| n.relation == 'last'}.first
+    end
+
+    def next_link
+      link.select {|n| n.relation == 'next'}.first
+    end
+
+    def previous_link
+      link.select {|n| n.relation == 'previous' || n.relation == 'prev'}.first
+    end
+
+    def get_by_id(id)
+      entry.each do |item|
+        return item.resource if item.id == id || item.resource.id == id
+      end
+      nil
+    end
+
+  end
+end

data/lib/model/client_reply.rb

@@ -0,0 +1,172 @@
+module FHIR
+  class ClientReply
+
+    @@validation_rules = JSON.parse( File.open(File.join(File.expand_path('..',File.dirname(File.absolute_path(__FILE__))),'fhir_api_validation.json'),'r:UTF-8',&:read) )
+    @@path_regexes = {
+      '[type]' => "(#{FHIR::RESOURCES.join('|')})",
+      '[id]' => FHIR::PRIMITIVES['id']['regex'],
+      '[vid]' => FHIR::PRIMITIVES['id']['regex'],
+      '[name]' => "([A-Za-z\-]+)"
+    }
+    @@rfs1123 = /\A\s*
+      (?:(?:Mon|Tue|Wed|Thu|Fri|Sat|Sun)\s*,\s*)?
+      (\d{1,2})\s+
+      (Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)\s+
+      (\d{2,})\s+
+      (\d{2})\s*
+      :\s*(\d{2})\s*
+      (?::\s*(\d{2}))?\s+
+      ([+-]\d{4}|
+       UT|GMT|EST|EDT|CST|CDT|MST|MDT|PST|PDT|[A-IK-Z])/ix
+
+    @@header_regexes = {
+      'Content-Type' => Regexp.new("(#{FHIR::Formats::ResourceFormat::RESOURCE_XML.gsub('+','\\\+')}|#{FHIR::Formats::ResourceFormat::RESOURCE_JSON.gsub('+','\\\+')})(([ ;]+)(charset)([ =]+)(UTF-8|utf-8))?"),
+      'Accept' => Regexp.new("(#{FHIR::Formats::ResourceFormat::RESOURCE_XML.gsub('+','\\\+')}|#{FHIR::Formats::ResourceFormat::RESOURCE_JSON.gsub('+','\\\+')})"),
+      'Prefer' => Regexp.new("(return=minimal|return=representation)"),
+      'ETag' => Regexp.new('(W\/)?"[\dA-Za-z]+"'),
+      'If-Modified-Since' => @@rfs1123,
+      'If-Match' => Regexp.new('(W\/)?"[\dA-Za-z]+"'),
+      'If-None-Match' => Regexp.new('(W\/)?"[\dA-Za-z]+"'),
+      'If-None-Exist' => Regexp.new('([\w\-]+(=[\w\-.:\/\|]*)?(&[\w\-]+(=[\w\-.:\/\|]*)?)*)?'),
+      'Location' => Regexp.new("http(s)?:\/\/[A-Za-z0-9\/\\-\\.]+\/#{@@path_regexes['[type]']}\/#{@@path_regexes['[id]']}\/_history\/#{@@path_regexes['[vid]']}"),
+      'Last-Modified' => @@rfs1123
+    }
+
+    # {
+    #   :method => :get,
+    #   :url => 'http://bonfire.mitre.org/fhir/Patient/123/$everything',
+    #   :path => 'Patient/123/$everything'
+    #   :headers => {},
+    #   :payload => nil # body of request goes here in POST
+    # }
+    attr_accessor :request  
+    # {
+    #   :code => '200',
+    #   :headers => {},
+    #   :body => '{xml or json here}'
+    # }
+    attr_accessor :response 
+    attr_accessor :resource # a FHIR resource
+    attr_accessor :resource_class # class of the :resource
+
+    def initialize(request, response)
+      @request = request
+      @response = response
+    end
+
+    def code
+      @response[:code].to_i unless @response.nil?
+    end
+
+    def id
+      return nil if @resource_class.nil?
+      (self_link || @request[:url]) =~ %r{(?<=#{@resource_class.name.demodulize}\/)([^\/]+)}
+      $1
+    end
+
+    def version
+      self_link =~ %r{(?<=_history\/)(\w+)}
+      $1
+    end
+
+    def self_link
+      (@response[:headers]['content-location'] || @response[:headers]['location']) unless @response.nil? || @response[:headers].nil?
+    end
+
+    def body
+      @response[:body] unless @response.nil?
+    end
+
+    def to_hash
+      hash = {}
+      hash['request'] = @request
+      hash['response'] = @response
+      hash
+    end
+
+    def is_valid?
+      validate.empty?
+    end
+
+    def validate
+      errors = []
+      @@validation_rules.each do |rule|
+        if rule['verb']==@request[:method].to_s.upcase
+          rule_match = false
+          rule['path'].each do |path|
+            rule_regex = path.gsub('/','(\/)').gsub('?','\?')
+            @@path_regexes.each do |token,regex|
+              rule_regex.gsub!(token,regex)
+            end
+            rule_match = true if(Regexp.new(rule_regex) =~ @request[:path])
+          end
+          if rule_match
+            # check the request headers
+            errors << validate_headers("#{rule['interaction'].upcase} REQUEST",@request[:headers],rule['request']['headers'])
+            # check the request body
+            errors << validate_body("#{rule['interaction'].upcase} REQUEST",@request[:payload],rule['request']['body'])
+            # check the response codes
+            if !rule['response']['status'].include?(@response[:code].to_i)
+              errors << "#{rule['interaction'].upcase} RESPONSE: Invalid response code: #{@response[:code]}" 
+            end
+            if @response[:code].to_i < 400
+              # check the response headers
+              errors << validate_headers("#{rule['interaction'].upcase} RESPONSE",@response[:headers],rule['response']['headers'])
+              # check the response body
+              errors << validate_body("#{rule['interaction'].upcase} RESPONSE",@response[:body],rule['response']['body'])
+            end
+          end
+        end
+      end
+      errors.flatten
+    end
+
+    def validate_headers(name,headers,header_rules)
+      errors = []
+      header_rules.each do |header,present|
+        value = headers[header]
+        if present==true
+          if value
+            errors << "#{name}: Malformed value for header #{header}: #{value}" if !(@@header_regexes[header] =~ value)
+          else
+            errors << "#{name}: Missing header: #{header}"
+          end
+        elsif (present=='optional' && value)
+          errors << "#{name}: Malformed value for optional header #{header}: #{value}" if !(@@header_regexes[header] =~ value)
+          binding.pry if !(@@header_regexes[header] =~ value)
+        elsif !value.nil?
+          errors << "#{name}: Should not have header: #{header}"
+        end
+      end
+      errors
+    end
+
+    def validate_body(name,body,body_rules)
+      errors = []
+      if body && body_rules
+        if body_rules['types']
+          body_type_match = false
+          body_rules['types'].each do |type|
+            begin
+              content = FHIR.from_contents(body)
+              body_type_match = true if content.resourceType==type
+              body_type_match = true if type=='Resource' && FHIR::RESOURCES.include?(content.resourceType)
+            rescue
+            end
+          end
+          errors << "#{name}: Body does not match allowed types: #{body_rules['types'].join(', ')}" if !body_type_match              
+        end
+        if body_rules['regex']
+          regex = Regexp.new(body_rules['regex'])
+          errors << "#{name}: Body does not match regular expression: #{body_rules['regex']}" if !(regex =~ body)
+        end
+      elsif body && !body_rules
+        errors "#{name}: Body not allowed"
+      end
+      errors
+    end
+
+    private :validate_headers, :validate_body
+
+  end
+end