fhir_client 1.0.2 → 1.6.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: c176b2138418157c1fc357c4c1fd18c335625692
+  metadata.gz: d0b559d338d7f9f46f075f1b81519fedaf482ffe
+  data.tar.gz: 5dae2a7c67ee80258a9c56c5c88179dab7dbe44e
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+  data.tar.gz: b70ac6d8e90671845411f85af80db521174b33d5a8f5e8c1989a7d9c1eba50eb56f7849e8d65031b6095b3ef2abbb5623da1a9343c8579e7922726674ba248bd

data/Gemfile.lock

@@ -1,10 +1,10 @@
 PATH
   remote: .
   specs:
-    fhir_client (1.0.2)
+    fhir_client (1.6.0)
       activesupport (>= 3)
       addressable (>= 2.3)
-      fhir_models (>= 0.3.1)
+      fhir_models (>= 1.6.0)
       oauth2 (~> 1.1)
       rest-client (~> 1.8)
       tilt (>= 1.1)
@@ -26,11 +26,11 @@ GEM
     coderay (1.1.1)
     date_time_precision (0.8.1)
     docile (1.1.5)
-    domain_name (0.5.20160310)
+    domain_name (0.5.20160615)
       unf (>= 0.0.5, < 1.0.0)
     faraday (0.9.2)
       multipart-post (>= 1.2, < 3)
-    fhir_models (0.3.1)
+    fhir_models (1.6.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 1.16, < 3)
@@ -40,7 +40,7 @@ GEM
       domain_name (~> 0.5)
     i18n (0.7.0)
     json (1.8.2)
-    jwt (1.5.1)
+    jwt (1.5.4)
     method_source (0.8.2)
     mime-types (2.99.2)
     mini_portile2 (2.1.0)
@@ -52,9 +52,9 @@ GEM
     nokogiri (1.6.8)
       mini_portile2 (~> 2.1.0)
       pkg-config (~> 1.1.7)
-    oauth2 (1.1.0)
+    oauth2 (1.2.0)
       faraday (>= 0.8, < 0.10)
-      jwt (~> 1.0, < 1.5.2)
+      jwt (~> 1.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
@@ -64,7 +64,7 @@ GEM
       method_source (~> 0.8.1)
       slop (~> 3.4)
     rack (1.6.4)
-    rake (11.1.2)
+    rake (11.2.2)
     rest-client (1.8.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 3.0)

data/README.md

@@ -11,35 +11,50 @@ Supports:
 * Operations (e.g. `$everything`, `$validate`)
 * Support for OAuth2
 
-### Getting Started
+## Getting Started
 
     $ bundle install
     $ bundle exec rake fhir:console
 
-### Creating a Client
+## Creating a Client
 ```ruby
 client = FHIR::Client.new(url)
 ```
 
-### Searching
+This client supports two modes of operation: basic and advanced.  The basic mode is useful for simple operations
+because it promotes an ActiveRecord-like style of interaction.  The advanced mode is less developer-friendly, but is currently necessary if you would like to use the entire range of operations exposed by FHIR.
+
+## Basic Usage
+
+Associate the client with the model:
+
 ```ruby
-reply = client.search(FHIR::Patient, search: {parameters: {name: 'P'}})
-bundle = reply.resource
-patient = bundle.entry.first.resource
+FHIR::Model.client = client
 ```
 
-### Fetching a Bundle
+The FHIR models can now be used to directly interact with a FHIR server.
+
 ```ruby
-reply = client.read_feed(FHIR::Patient) # fetch Bundle of Patients
-bundle = reply.resource
-bundle.entry.each do |entry|
-  patient = entry.resource
-  puts patient.name[0].text
-end
-puts reply.code # HTTP 200 (or whatever was returned)
-puts reply.body # Raw XML or JSON
+# read an existing patient with an ID of 'example'
+patient = FHIR::Patient.read('example')
+
+# update a patient
+patient.gender = 'female'
+patient.update # saves the patient 
+
+# create a patient
+patient = FHIR::Patient.create(name: {given: 'John', family: 'Doe'})
+
+# search patients
+results = FHIR::Patient.search(given: 'John', family: 'Doe')
+results.count # results in an enumeration
+
+# delete the recently created patient
+patient.destroy
 ```
 
+## Advanced Usage
+
 ### CRUD Examples
 ```ruby
 # read an existing patient with id "example"
@@ -73,6 +88,25 @@ client.conditional_create(patient, ifNoneExist)
 client.destroy(FHIR::Patient, patient_id)
 ```
 
+### Searching
+```ruby
+reply = client.search(FHIR::Patient, search: {parameters: {name: 'P'}})
+bundle = reply.resource
+patient = bundle.entry.first.resource
+```
+
+### Fetching a Bundle
+```ruby
+reply = client.read_feed(FHIR::Patient) # fetch Bundle of Patients
+bundle = reply.resource
+bundle.entry.each do |entry|
+  patient = entry.resource
+  puts patient.name[0].text
+end
+puts reply.code # HTTP 200 (or whatever was returned)
+puts reply.body # Raw XML or JSON
+```
+
 ### Transactions
 ```ruby
 # Create a patient

data/fhir_client.gemspec

@@ -7,11 +7,11 @@ Gem::Specification.new do |s|
   s.email = "aquina@mitre.org"
   s.homepage = "https://github.com/hl7-fhir/fhir-svn"
   s.authors = ["Andre Quina", "Jason Walonoski", "Janoo Fernandes"]
-  s.version = '1.0.2'
+  s.version = '1.6.0'
 
   s.files = s.files = `git ls-files`.split("\n")
 
-  s.add_dependency 'fhir_models', '>= 0.3.1'
+  s.add_dependency 'fhir_models', '>= 1.6.0'
   s.add_dependency 'tilt', '>= 1.1'
   s.add_dependency 'rest-client', '~> 1.8'
   s.add_dependency 'oauth2', '~> 1.1'

data/lib/client_exception.rb

@@ -0,0 +1,10 @@
+class ClientException < Exception
+
+  attr_accessor :reply
+
+  def initialize(message, reply = nil)
+    super(message)
+    @reply = reply
+  end
+
+end

data/lib/client_interface.rb

@@ -196,25 +196,20 @@ module FHIR
 
   def fhir_headers(options={})
     FHIR::ResourceAddress.new.fhir_headers(options, @use_format_param)
-  end  
+  end
 
   def parse_reply(klass, format, response)
     $LOG.info "Parsing response with {klass: #{klass}, format: #{format}, code: #{response.code}}."
     return nil if ![200,201].include? response.code
     res = nil
     begin
-      res = nil
-      if(format.downcase.include?('xml'))
-        res = FHIR::Xml.from_xml(response.body)
-      else
-        res = FHIR::Json.from_json(response.body)
-      end
+      res = FHIR.from_contents(response.body)
+      res.client = self if !res.nil?
       $LOG.warn "Expected #{klass} but got #{res.class}" if res.class!=klass
     rescue Exception => e
       $LOG.error "Failed to parse #{format} as resource #{klass}: #{e.message} %n #{e.backtrace.join("\n")} #{response}"
       nil
     end
-    res.client = self
     res
   end
 
@@ -226,7 +221,7 @@ module FHIR
     if [:get, :delete, :head].include?(request['method'])
       method(request['method']).call(request['url'], request['headers'])
     elsif [:post, :put].include?(request['method'])
-      resource = request['headers']['resource'].constantize.from_xml(request['payload'])
+      resource = FHIR.from_contents(request['payload']) unless request['payload'].nil?
       method(request['method']).call(request['url'], resource, request['headers'])
     end
   end
@@ -295,7 +290,7 @@ module FHIR
 
     def get(path, headers)
       url = URI(build_url(path)).to_s
-      puts "GETTING: #{url}"
+      $LOG.info "GETTING: #{url}"
       headers = clean_headers(headers)
       if @use_oauth2_auth
         # @client.refresh!
@@ -320,22 +315,28 @@ module FHIR
         @reply = FHIR::ClientReply.new(req, res)
       else
         headers.merge!(@security_headers) if @use_basic_auth
-        @client.get(url, headers){ |response, request, result|
-          $LOG.info "GET - Request: #{request.to_json}, Response: #{response.force_encoding("UTF-8")}"
-          request.args[:path] = url.gsub(@baseServiceUrl,'')
-          res = {
-            :code => result.code,
-            :headers => scrubbed_response_headers(result.each_key{}),
-            :body => response
-          }
-          @reply = FHIR::ClientReply.new(request.args, res)
+        begin
+          response = @client.get(url, headers)
+        rescue Exception => e
+          response = e.response if e.response
+        end
+
+        $LOG.info "GET - Request: #{response.request.to_json}, Response: #{response.body.force_encoding("UTF-8")}"
+        response.request.args[:path] = response.request.args[:url].gsub(@baseServiceUrl,'')
+        headers = response.headers.inject({}){ |h,(k,v)| h[k.to_s.gsub('_','-')] = v.to_s; h}
+        res = {
+          :code => response.code,
+          :headers => scrubbed_response_headers(headers),
+          :body => response.body
         }
+
+        @reply = FHIR::ClientReply.new(response.request.args, res)
       end
     end
 
     def post(path, resource, headers)
       url = URI(build_url(path)).to_s
-      puts "POSTING: #{url}"
+      $LOG.info "POSTING: #{url}"
       headers = clean_headers(headers)
       payload = request_payload(resource, headers) if resource
       if @use_oauth2_auth
@@ -376,7 +377,7 @@ module FHIR
 
     def put(path, resource, headers)
       url = URI(build_url(path)).to_s
-      puts "PUTTING: #{url}"
+      $LOG.info "PUTTING: #{url}"
       headers = clean_headers(headers)
       payload = request_payload(resource, headers) if resource
       if @use_oauth2_auth
@@ -417,7 +418,7 @@ module FHIR
 
     def patch(path, patchset, headers)
       url = URI(build_url(path)).to_s
-      puts "PATCHING: #{url}"
+      $LOG.info "PATCHING: #{url}"
       headers = clean_headers(headers)
       payload = request_patch_payload(patchset, headers['format'])
       if @use_oauth2_auth
@@ -459,7 +460,7 @@ module FHIR
 
     def delete(path, headers)
       url = URI(build_url(path)).to_s
-      puts "DELETING: #{url}"
+      $LOG.info "DELETING: #{url}"
       headers = clean_headers(headers)
       if @use_oauth2_auth
         # @client.refresh!
@@ -500,7 +501,7 @@ module FHIR
     def head(path, headers)
       headers.merge!(@security_headers) unless @security_headers.blank?
       url = URI(build_url(path)).to_s
-      puts "HEADING: #{url}"
+      $LOG.info "HEADING: #{url}"
       RestClient.head(url, headers){ |response, request, result|
         $LOG.info "HEAD - Request: #{request.to_json}, Response: #{response.force_encoding("UTF-8")}"
         request.args[:path] = url.gsub(@baseServiceUrl,'')

data/lib/ext/model.rb

@@ -22,46 +22,85 @@ module FHIR
     end
 
     def self.read(id, client = self.client)
-      client.read(self, id).resource
+      handle_response client.read(self, id)
     end
 
     def self.read_with_summary(id, summary, client = self.client)
-      client.read(self, id, client.default_format, summary).resource
+      handle_response client.read(self, id, client.default_format, summary)
+    end
+
+    def self.vread(id, version_id, client = self.client)
+      handle_response client.vread(self, id, version_id)
+    end
+
+    def self.resource_history(client = self.client)
+      handle_response client.resource_history(self)
+    end
+
+    def self.resource_history_as_of(last_update)
+      handle_response client.resource_history_as_of(self, last_update)
+    end
+
+    def self.resource_instance_history(id, client = self.client)
+      handle_response client.resource_instance_history(self, id)
+    end
+
+    def self.resource_instance_history_as_of(id, last_update, client = self.client)
+      handle_response client.resource_instance_history_as_of(self, id, last_update)
     end
 
     def self.search(params = {}, client = self.client)
-      client.search(self, search: { parameters: params }).resource
+      handle_response client.search(self, search: { parameters: params })
     end
 
     def self.create(model, client = self.client)
       model = new(model) unless model.is_a?(self)
-      client.create(model).resource
+      handle_response client.create(model)
     end
 
     def self.conditional_create(model, params, client = self.client)
       model = new(model) unless model.is_a?(self)
-      client.conditional_create(model, params)
+      handle_response client.conditional_create(model, params)
+    end
+
+    def self.all
+      handle_response client.read_feed(self)
+    end
+
+    def vread(version_id)
+      self.class.vread(id, version_id, client)
     end
 
     def create
-      client.create(self).resource
+      handle_response client.create(self)
     end
 
     def conditional_create(params)
-      client.conditional_create(self, params)
+      handle_response client.conditional_create(self, params)
     end
 
     def update
-      client.update(self, id).resource
+      handle_response client.update(self, id)
     end
 
     def conditional_update(params)
-      client.conditional_update(self, self.id, params).resource
+      handle_response client.conditional_update(self, self.id, params)
     end
 
     def destroy
-      client.destroy(self.class, id) unless id.nil?
+      handle_response client.destroy(self.class, id) unless id.nil?
       nil
     end
+
+    private
+
+    def self.handle_response(response)
+      raise ClientException.new "Server returned #{response.code}.", response if response.code.between?(400,599)
+      response.resource
+    end
+
+    def handle_response(response)
+      self.class.handle_response(response)
+    end
   end
 end

data/lib/ext/reference.rb

@@ -5,7 +5,7 @@ module FHIR
       type, id = reference.to_s.split("/")
       return unless [type, id].all?(&:present?)
       klass = "FHIR::#{type}".constantize
-      klass.read(client, id)
+      klass.read(id, client)
     end
   end
 end

data/lib/fhir_client.rb

@@ -28,4 +28,4 @@ require_relative File.join('.','feed_format.rb')
 require_relative File.join('.','patch_format.rb')
 require_relative File.join('.','model','client_reply.rb')
 require_relative File.join('.','model','tag.rb')
-
+require_relative File.join('.','client_exception.rb')

data/lib/resource_address.rb

@@ -70,6 +70,8 @@ module FHIR
           url += "/$lookup"
         elsif (opr  && opr[:name]== :concept_map_translate)
           url += "/$translate"
+        elsif (opr  && opr[:name]== :closure_table_maintenance)
+          url += "/$closure"
         end
       end
 

data/lib/sections/operations.rb

@@ -77,13 +77,20 @@ module FHIR
         terminology_operation(options, format)
       end
 
-      #
+      # ConceptMap Translation
       def concept_map_translate(params={}, format=@default_format)
         options = { resource: FHIR::ConceptMap, operation: { name: :concept_map_translate } }
         options.deep_merge!(params)
         terminology_operation(options, format)
       end
 
+      # ConceptMap Closure Table Maintenance
+      def closure_table_maintenance(params={}, format=@default_format)
+        options = { operation: { name: :closure_table_maintenance } }
+        options.deep_merge!(params)
+        terminology_operation(options, format)        
+      end
+
       def terminology_operation(params={}, format=@default_format)
         options = { format: format }
         # params = [id, code, system, version, display, coding, codeableConcept, date, abstract]

data/lib/tasks/tasks.rake

@@ -36,12 +36,15 @@ namespace :fhir do
   end
 
   desc 'count all resources for a given server'
-  task :count, [:url] do |t, args|
+  task :count, [:url,:display_zero] do |t, args|
     client = FHIR::Client.new(args.url)
+    display_zero = (args.display_zero == 'true')
     counts = {}
-    fhir_resources.map do | klass |
+    fhir_resources.each do | klass |
       reply = client.read_feed(klass)
-      counts["#{klass.name.demodulize}"] = reply.resource.total unless reply.resource.nil?
+      if !reply.resource.nil? && (reply.resource.total > 0 || display_zero)
+        counts["#{klass.name.demodulize}"] = reply.resource.total
+      end
     end
     printf "  %-30s %5s\n", 'Resource', 'Count'
     printf "  %-30s %5s\n", '--------', '-----'
@@ -54,7 +57,7 @@ namespace :fhir do
   desc 'delete all resources for a given server'
   task :clean, [:url] do |t, args|
     client = FHIR::Client.new(args.url)
-    fhir_resources.map do | klass |
+    fhir_resources.each do | klass |
       reply = client.read_feed(klass)
       while !reply.nil? && !reply.resource.nil? && reply.resource.total > 0
         reply.resource.entry.each do |entry|
@@ -67,7 +70,7 @@ namespace :fhir do
   end
 
   def fhir_resources
-    Mongoid.models.select {|c| c.name.include?('FHIR') && !c.included_modules.find_index(FHIR::Resource).nil?}
+    FHIR::RESOURCES.map {|r| Object::const_get("FHIR::#{r}")}
   end
 
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_client
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.6.0
 platform: ruby
 authors:
 - Andre Quina
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-10 00:00:00.000000000 Z
+date: 2016-08-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: fhir_models
@@ -18,14 +18,14 @@ dependencies:
     requirements:
     - - '>='
       - !ruby/object:Gem::Version
-        version: 0.3.1
+        version: 1.6.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '>='
       - !ruby/object:Gem::Version
-        version: 0.3.1
+        version: 1.6.0
 - !ruby/object:Gem::Dependency
   name: tilt
   requirement: !ruby/object:Gem::Requirement
@@ -124,6 +124,7 @@ files:
 - README.md
 - Rakefile
 - fhir_client.gemspec
+- lib/client_exception.rb
 - lib/client_interface.rb
 - lib/ext/bundle.rb
 - lib/ext/model.rb
@@ -172,7 +173,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.6
+rubygems_version: 2.0.14.1
 signing_key: 
 specification_version: 4
 summary: A Gem for handling FHIR client requests in ruby