fhir_client 1.6.2 → 1.6.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 489841cb2a8cf3b5f7dcbfc19a49029f0dbaa544
-  data.tar.gz: 7e9587ecdc2fe7748e9a0ed8a3d64fc08762094a
+  metadata.gz: 15449e3ef2e088da8def1b3996ccc17d4a1a333d
+  data.tar.gz: 83cecd3899ccdd1c8672de9fd5d8c283e497e9d6
 SHA512:
-  metadata.gz: 22440c0ab5d28a3df897733a3d1495c49ea6d7356e90f31b38df2b3dc97d769c85ffb39ece753514d689971c99575ca23e1a7a01a435d3fad11a01fa63d1fc52
-  data.tar.gz: 762f8f777505ac955a125060ccd880f796c64216da5b9d4b29bf6d8a7eb9bd7f892968fc20cd47ac4b1209de8fa9acc2d1976ff74f4c57f9a7eadf60155a87f0
+  metadata.gz: f3d906ae7896baee562592e678c1396266ff6cb0d3f9c3d9973ed84e576820e2b998de1eac61e0b8d502a9a5ff7beba04580c2e19d61ed1cd2e1ce4428557c8f
+  data.tar.gz: a0d986ea2a72d00af5c41e22f052863b99e1abc0b2c34d9c07d67f32fbed9091081fae0a925ccb2a78841d026bb42f7710d2af81a11a4b088e5c2b10ee6fd630

data/.gitignore

@@ -26,9 +26,9 @@ build/
 
 # for a library or gem, you might want to ignore these files since the code is
 # intended to run in multiple environments; otherwise, check them in:
-# Gemfile.lock
-# .ruby-version
-# .ruby-gemset
+Gemfile.lock
+.ruby-version
+.ruby-gemset
 
 # unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
 .rvmrc

data/fhir_client.gemspec

@@ -7,7 +7,7 @@ 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 = '1.6.2'
+  s.version = '1.6.3'
 
   s.files = s.files = `git ls-files`.split("\n")
 
@@ -17,8 +17,9 @@ Gem::Specification.new do |s|
   s.add_dependency 'oauth2', '~> 1.1'
   s.add_dependency 'activesupport', '>= 3'
   s.add_dependency 'addressable', '>= 2.3'
-  s.add_dependency 'rack', '~> 1.6'
+  s.add_dependency 'rack', '~> 1.5'
+  s.add_dependency 'nokogiri'
   s.add_development_dependency 'pry'
+  s.add_development_dependency 'minitest'
+  s.add_development_dependency 'test-unit'
 end
-
-

data/lib/client_interface.rb

@@ -19,7 +19,6 @@ module FHIR
     attr_accessor :client
 
     attr_accessor :default_format
-    attr_accessor :default_format_bundle
 
     attr_accessor :cached_conformance
 
@@ -34,10 +33,17 @@ module FHIR
     @baseServiceUrl = baseServiceUrl
     @use_format_param = false
     @default_format = FHIR::Formats::ResourceFormat::RESOURCE_XML
-    @default_format_bundle = FHIR::Formats::FeedFormat::FEED_XML
     set_no_auth
   end
 
+  def default_json
+    @default_format = FHIR::Formats::ResourceFormat::RESOURCE_JSON
+  end
+
+  def default_xml
+    @default_format = FHIR::Formats::ResourceFormat::RESOURCE_XML
+  end
+
   # Set the client to use no authentication mechanisms
   def set_no_auth
     FHIR.logger.info "Configuring the client to use no authentication."
@@ -163,22 +169,22 @@ module FHIR
   end
 
   def try_conformance_formats(default_format)
-    formats = [ FHIR::Formats::ResourceFormat::RESOURCE_XML,
-      FHIR::Formats::ResourceFormat::RESOURCE_JSON,
-      'application/xml',
-      'application/json']
-    formats.insert(0,default_format)
+    formats = [FHIR::Formats::ResourceFormat::RESOURCE_XML,
+               FHIR::Formats::ResourceFormat::RESOURCE_JSON,
+               FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2,
+               FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2,
+               'application/xml',
+               'application/json']
+    formats.insert(0, default_format)
 
     @cached_conformance = nil
     @default_format = nil
-    @default_format_bundle = nil
 
     formats.each do |frmt|
       reply = get 'metadata', fhir_headers({format: frmt})
       if reply.code == 200
         @cached_conformance = parse_reply(FHIR::Conformance, frmt, reply)
         @default_format = frmt
-        @default_format_bundle = frmt
         break
       end
     end
@@ -243,10 +249,10 @@ module FHIR
     # Extract the request payload in the specified format, defaults to XML
     def request_payload(resource, headers)
       if headers
-        case headers["format"]
-        when FHIR::Formats::ResourceFormat::RESOURCE_XML
+        format_specified = headers[:format] || headers["format"]
+        if format_specified.downcase.include?('xml')
           resource.to_xml
-        when FHIR::Formats::ResourceFormat::RESOURCE_JSON
+        elsif format_specified.downcase.include?('json')
           resource.to_json
         else
           resource.to_xml
@@ -289,7 +295,7 @@ module FHIR
     end
 
     def get(path, headers)
-      url = URI(build_url(path)).to_s
+      url = URI(URI.escape(build_url(path))).to_s
       FHIR.logger.info "GETTING: #{url}"
       headers = clean_headers(headers)
       if @use_oauth2_auth

data/lib/ext/bundle.rb

@@ -1,6 +1,5 @@
 module FHIR
   class Bundle
-    include Enumerable
 
     def self_link
       link.select {|n| n.relation == 'self'}.first

data/lib/fhir_client.rb

@@ -1,6 +1,5 @@
 # Top level include file that brings in all the necessary code
 require 'bundler/setup'
-require 'rubygems'
 require 'yaml'
 require 'nokogiri'
 require 'fhir_models'
@@ -21,7 +20,6 @@ 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','client_reply.rb')
 require_relative File.join('.','model','tag.rb')

data/lib/model/client_reply.rb

@@ -65,8 +65,17 @@ module FHIR
     end
 
     def version
-      self_link =~ %r{(?<=_history\/)(\w+)}
-      $1
+      version = nil
+      link = self_link
+      if link && link.include?('_history/')
+        begin
+          tokens = link.split('_history/')
+          version = tokens.last.split('/').first
+        rescue Exception => e
+          version = nil
+        end
+      end
+      version
     end
 
     def self_link
@@ -133,7 +142,7 @@ module FHIR
           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)
+#          binding.pry if !(@@header_regexes[header] =~ value)
         elsif !value.nil?
           errors << "#{name}: Should not have header: #{header}"
         end

data/lib/resource_address.rb

@@ -4,7 +4,7 @@ module FHIR
     DEFAULTS = {
       id: nil,
       resource: nil,
-      format: 'application/xml+fhir',
+      format: 'application/fhir+xml'
     }
 
     DEFAULT_CHARSET = 'UTF-8'
@@ -117,11 +117,15 @@ module FHIR
       id = nil
       if !resourceType.nil? && !url.nil?
         token = "#{resourceType}/"
-        start = url.index(token) + token.length
-        t = url[start..-1]
-        stop = (t.index("/") || 0)-1
-        stop = -1 if stop.nil?
-        id = t[0..stop]
+        if url.index(token)
+          start = url.index(token) + token.length
+          t = url[start..-1]
+          stop = (t.index("/") || 0)-1
+          stop = -1 if stop.nil?
+          id = t[0..stop]
+        else
+          id = nil
+        end
       end
       id
     end

data/lib/resource_format.rb

@@ -2,8 +2,11 @@ module FHIR
   module Formats
     class ResourceFormat
 
-      RESOURCE_XML = "application/xml+fhir"
-      RESOURCE_JSON = "application/json+fhir"
+      RESOURCE_XML = "application/fhir+xml"
+      RESOURCE_JSON = "application/fhir+json"
+
+      RESOURCE_XML_DSTU2 = "application/xml+fhir"
+      RESOURCE_JSON_DSTU2 = "application/json+fhir"
 
     end
   end

data/lib/sections/crud.rb

@@ -17,7 +17,7 @@ module FHIR
       #
       # Read a resource bundle (an XML ATOM feed)
       #
-      def read_feed(klass, format=@default_format_bundle)
+      def read_feed(klass, format=@default_format)
         options = { resource: klass, format: format }
         reply = get resource_url(options), fhir_headers(options)
         reply.resource = parse_reply(klass, format, reply)
@@ -89,7 +89,7 @@ module FHIR
       #
       def partial_update(klass, id, patchset, options={}, format=@default_format)
         options = { resource: klass, id: id, format: format }.merge options
-        
+
         if (format == FHIR::Formats::ResourceFormat::RESOURCE_XML)
           options[:format] = FHIR::Formats::PatchFormat::PATCH_XML
           options[:Accept] = format

data/lib/sections/feed.rb

@@ -12,7 +12,7 @@ module FHIR
         link = bundle.method(page).call
         return nil unless link
         reply = get strip_base(link.url), fhir_headers
-        reply.resource = parse_reply(current.resource_class, @default_format_bundle, reply)
+        reply.resource = parse_reply(current.resource_class, @default_format, reply)
         reply.resource_class = current.resource_class
         reply
       end

data/lib/sections/history.rb

@@ -4,17 +4,17 @@ module FHIR
       #
       # Create a new resource with a server assigned id. Return the newly created
       # resource with the id the server assigned. Associates tags with newly created resource.
-      # 
+      #
       # @param resourceClass
       # @param resource
       # @return
       #
       # public <T extends Resource> AtomEntry<OperationOutcome> create(Class<T> resourceClass, T resource, List<AtomCategory> tags);
-      
+
       #
-      # Retrieve the update history for a resource with given id since last update time. 
+      # Retrieve the update history for a resource with given id since last update time.
       # Last update may be null TODO - ensure this is the case.
-      # 
+      #
       # @param lastUpdate
       # @param resourceClass
       # @param id
@@ -22,10 +22,10 @@ module FHIR
       #
       # public <T extends Resource> AtomFeed history(Calendar lastUpdate, Class<T> resourceClass, String id);
       # public <T extends Resource> AtomFeed history(DateAndTime lastUpdate, Class<T> resourceClass, String id);
-      
+
       def history(options)
         reply = get resource_url(options), fhir_headers(options).except(:history)
-        reply.resource = parse_reply(options[:resource], @default_format_bundle, reply)
+        reply.resource = parse_reply(options[:resource], @default_format, reply)
         reply.resource_class = options[:resource]
         reply
       end
@@ -33,7 +33,7 @@ module FHIR
       #
       # Retrieve the entire update history for a resource with the given id.
       # Last update may be null TODO - ensure this is the case.
-      # 
+      #
       # @param resourceClass
       # @param id
       # @param lastUpdate
@@ -54,18 +54,18 @@ module FHIR
       def resource_history_as_of(klass, lastUpdate)
         history(resource: klass, history:{since: lastUpdate})
       end
-      
+
       #
       # Retrieve the update history for all resource types since the start of server records.
-      # 
+      #
       def all_history
         history(history:{})
       end
 
       #
       # Retrieve the update history for all resource types since a specific last update date/time.
-      # 
-      # Note: 
+      #
+      # Note:
       # @param lastUpdate
       # @return
       #

data/lib/sections/search.rb

@@ -1,15 +1,15 @@
 module FHIR
   module Sections
     module Search
-      
+
       #
       # Search a set of resources of a given type.
-      # 
+      #
       # @param klass The type of resource to be searched.
       # @param options A hash of options used to construct the search query.
       # @return FHIR::ClientReply
       #
-      def search(klass, options={}, format=@default_format_bundle)
+      def search(klass, options={}, format=@default_format)
         options.merge!({ resource: klass, format: format })
 
         if options[:search] && options[:search][:flag]
@@ -23,7 +23,7 @@ module FHIR
         reply
       end
 
-      def search_existing(klass, id, options={}, format=@default_format_bundle)
+      def search_existing(klass, id, options={}, format=@default_format)
         options.merge!({ resource: klass, id: id, format: format })
         #if options[:search][:flag]
         if options[:search] && options[:search][:flag]
@@ -36,7 +36,7 @@ module FHIR
         reply
       end
 
-      def search_all(options={}, format=@default_format_bundle)
+      def search_all(options={}, format=@default_format)
         options.merge!({ format: format })
         if options[:search] && options[:search][:flag]
           reply = post resource_url(options), nil, fhir_headers(options)

data/lib/tasks/tasks.rake

@@ -58,14 +58,26 @@ namespace :fhir do
   task :clean, [:url] do |t, args|
     client = FHIR::Client.new(args.url)
     fhir_resources.each do | klass |
+      puts "Reading #{klass.name.demodulize}..."
+      skipped = []
       reply = client.read_feed(klass)
       while !reply.nil? && !reply.resource.nil? && reply.resource.total > 0
+        puts "  Cleaning #{reply.resource.entry.length} #{klass.name.demodulize} resources..."
         reply.resource.entry.each do |entry|
-          client.destroy(klass,entry.resource.id) unless entry.resource.nil?
+          unless entry.resource.nil?
+            del_reply = client.destroy(klass,entry.resource.id) 
+            skipped << "#{klass.name.demodulize}/#{entry.resource.id}" if [405,409].include?(del_reply.code)
+          end
+        end
+        if skipped.empty?
+          reply = client.read_feed(klass) 
+        else
+          puts "  *** Unable to delete some #{klass.name.demodulize}s ***"
+          reply = nil
         end
-        reply = client.read_feed(klass)
       end
     end
+    puts "Done cleaning."
     Rake::Task['fhir:count'].invoke(args.url)
   end
 

data/test/unit/bundle_test.rb

@@ -13,7 +13,7 @@ class BundleTest < Test::Unit::TestCase
     }
     clientReply = FHIR::ClientReply.new('feed-test', response)
 
-    bundle = client.parse_reply(FHIR::Bundle, FHIR::Formats::FeedFormat::FEED_XML, clientReply)
+    bundle = client.parse_reply(FHIR::Bundle, FHIR::Formats::ResourceFormat::RESOURCE_XML, clientReply)
 
     assert !bundle.nil?, "Failed to parse example Bundle."
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_client
 version: !ruby/object:Gem::Version
-  version: 1.6.2
+  version: 1.6.3
 platform: ruby
 authors:
 - Andre Quina
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-24 00:00:00.000000000 Z
+date: 2016-09-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: fhir_models
@@ -102,14 +102,28 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.5'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -124,6 +138,34 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: A Gem for handling FHIR client requests in ruby
 email: aquina@mitre.org
 executables: []
@@ -134,7 +176,6 @@ files:
 - .simplecov
 - .travis.yml
 - Gemfile
-- Gemfile.lock
 - LICENSE
 - README.md
 - Rakefile
@@ -144,7 +185,6 @@ files:
 - lib/ext/bundle.rb
 - lib/ext/model.rb
 - lib/ext/reference.rb
-- lib/feed_format.rb
 - lib/fhir_api_validation.json
 - lib/fhir_client.rb
 - lib/model/client_reply.rb

data/Gemfile.lock

@@ -1,101 +0,0 @@
-PATH
-  remote: .
-  specs:
-    fhir_client (1.6.1)
-      activesupport (>= 3)
-      addressable (>= 2.3)
-      fhir_models (>= 1.6.1)
-      oauth2 (~> 1.1)
-      rack (~> 1.6)
-      rest-client (~> 1.8)
-      tilt (>= 1.1)
-
-GEM
-  remote: http://rubygems.org/
-  specs:
-    activesupport (4.0.13)
-      i18n (~> 0.6, >= 0.6.9)
-      minitest (~> 4.2)
-      multi_json (~> 1.3)
-      thread_safe (~> 0.1)
-      tzinfo (~> 0.3.37)
-    addressable (2.4.0)
-    ansi (1.5.0)
-    awesome_print (1.6.1)
-    bcp47 (0.3.3)
-      i18n
-    coderay (1.1.1)
-    date_time_precision (0.8.1)
-    docile (1.1.5)
-    domain_name (0.5.20160615)
-      unf (>= 0.0.5, < 1.0.0)
-    faraday (0.9.2)
-      multipart-post (>= 1.2, < 3)
-    fhir_models (1.6.2)
-      bcp47 (>= 0.3)
-      date_time_precision (>= 0.8)
-      mime-types (>= 1.16, < 3)
-      nokogiri (>= 1.6)
-      rake (>= 0.8.7)
-    http-cookie (1.0.2)
-      domain_name (~> 0.5)
-    i18n (0.7.0)
-    json (2.0.2)
-    jwt (1.5.4)
-    method_source (0.8.2)
-    mime-types (2.99.2)
-    mini_portile2 (2.1.0)
-    minitest (4.7.5)
-    multi_json (1.12.1)
-    multi_xml (0.5.5)
-    multipart-post (2.0.0)
-    netrc (0.11.0)
-    nokogiri (1.6.8)
-      mini_portile2 (~> 2.1.0)
-      pkg-config (~> 1.1.7)
-    oauth2 (1.2.0)
-      faraday (>= 0.8, < 0.10)
-      jwt (~> 1.0)
-      multi_json (~> 1.3)
-      multi_xml (~> 0.5)
-      rack (>= 1.2, < 3)
-    pkg-config (1.1.7)
-    pry (0.10.3)
-      coderay (~> 1.1.0)
-      method_source (~> 0.8.1)
-      slop (~> 3.4)
-    rack (1.6.4)
-    rake (11.2.2)
-    rest-client (1.8.0)
-      http-cookie (>= 1.0.2, < 2.0)
-      mime-types (>= 1.16, < 3.0)
-      netrc (~> 0.7)
-    simplecov (0.12.0)
-      docile (~> 1.1.0)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.0)
-    slop (3.6.0)
-    thread_safe (0.3.5)
-    tilt (2.0.5)
-    turn (0.9.7)
-      ansi
-      minitest (~> 4)
-    tzinfo (0.3.51)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.7.2)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  awesome_print
-  fhir_client!
-  minitest (~> 4.0)
-  pry
-  simplecov
-  turn
-
-BUNDLED WITH
-   1.12.5

data/lib/feed_format.rb

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