qpid 0.1.2 → 0.1.3

data/lib/qpid.rb

@@ -6,7 +6,7 @@ require 'cgi'
 require 'happymapper'
 
 class Qpid
-  VERSION = '0.1.2'
+  VERSION = '0.1.3'
   
   class SearchItem
     include HappyMapper
@@ -82,7 +82,7 @@ class Qpid
     case xml = client.get_content(function_uri(:updatestatus, mrn)) 
     when /<message>NO PATIENT<\/message>/
       raise Qpid::NoPatientError.new(mrn)
-    when /<message>NEW<\/message>/
+    when /<message>(?:NEW|UNKNOWN STATUS)<\/message>/
       nil
     when /<lastupdate>(.+)<\/lastupdate>/
       begin
@@ -183,4 +183,4 @@ class Qpid
   def self.ondate(date)
     todate(date) + " AND " + fromdate(date)
   end
-end
+end

data/test/content/3000888_report_pat_4313382_1.xml

@@ -0,0 +1,58 @@
+<table id="report"><tr><td><pre>Accession Number:  BS07W17636                     Report Status:  Final
+Type:  Surgical Pathology
+Specimen Type:  LEFT THIGH MASS
+Procedure Date:
+Ordering Provider:  GAMZE AYATA M.D.
+
+CASE: BS-07-W17636
+PATIENT: PETER RABBITSKI
+
+
+Resident: Peter M Sadow, M.D., Ph.D.
+Pathologist:   Christopher D. M. Fletcher, M.D. FRCPath
+
+PATHOLOGIC DIAGNOSIS:
+
+CONSULT SLIDES FROM UMASS MEMORIAL, WORCESTER, MA
+
+A. LEFT THIGH MASS BIOPSY (S07-16978):
+
+HIGH GRADE SPINDLE CELL SARCOMA, likely myofibroblastic in type.
+
+
+Immunohistochemistry performed at BWH demonstrates the following staining
+profile in tumor cells:
+
+Positive: Desmin, SMA (multifocal)
+Negative: GFAP, S100, CD34, Fast Myosin, Myf4
+
+(See letter)
+
+
+CLINICAL DATA:
+History: 51 year-old male with a large mass in the left thigh.
+
+TISSUE SUBMITTED:
+Consult slides.
+
+GROSS DESCRIPTION:
+Received from UMASS MEMORIAL, THREE BIOTECH, ONE INNOVATION DRIVE, WORCESTER,
+MA, 01655, are four (4) slides and one (1) block.
+
+One (1) block is labeled \"S07-16978\" and sublabeled \"B\" and four (4 HE) stained
+slides are labeled \"S07-16978\" and sublabeled \"FS1\", \"A\", \"B\" and \"D\" which
+correspond to left thigh mass performed on 4/20/2007, according to the
+accompanying pathology report bearing the patient\"s name and a letter from Dr.
+Gamze Ayata.
+
+
+
+By his/her signature below, the senior physician certifies that he/she
+personally conducted a microscopic examination (\"gross only\" exam if so stated)
+of the described specimen(s) and rendered or confirmed the diagnosis(es)
+related thereto.
+
+Final Diagnosis by  Christopher D. M. Fletcher M.D. FRCPath,  Electronically
+signed  on 4/30/2007
+
+</pre></td></tr></table>

data/test/content/3000888_report_rad_63580395.xml

@@ -0,0 +1,86 @@
+<table id="report"><tr><th class="report_header">CDR Lab: RAD - CTBxRetper 07/01/2010</th></tr><tr><th>Site: MGH Acc: 301654345 Status: Final</th></tr><a href= "http://radamicas1.mgh.harvard.edu/servlet/com.amicas.servlet.integration.EmbeddedGateway?AN=301654345"> Image </a><tr><td><pre>Exam Number:  301654345                        Report Status:  Final
+Type:  CTBxRetper
+Date/Time:  07/01/2010 10:41
+Exam Code:  CTBXRE
+Ordering Provider:  Temel, Jennifer S MD
+
+HISTORY:  
+     SEE HX - LUNG CA WITH NEW RP SOFT TISSUE
+     
+
+REPORT     PROCEDURE: 
+     CT-Guided Retroperitoneal Soft Tissue Biopsy
+      
+     INDICATION:  T2N1M0 stage IIB NSCLC s/p RM and RL bilobectomy, s/p 4 
+     cycles of adjuvant chemotherapy. Follow-up PET/CT dated 6/16/10 
+     revealed a PET positive retroperitoneal soft tissue new from CT of 
+     2009.
+     Allergies: Penicillin 
+     Patient held 81 mg Aspirin approximately 10 days before the procedure.
+      
+     OPERATORS:
+     FELLOW:  Dr. Nisha Sainani
+     ATTENDING:  Dr. Ronald Arellano was present for the entire procedure
+      
+     CONSENT:
+     The patient was informed of the nature of the proposed procedure.  
+     The purposes, alternatives, risks, and benefits were explained and 
+     discussed.  All questions were answered and written consent was 
+     obtained.
+      
+     ANESTHESIA: Intravenous conscious sedation was administered by 
+     radiology nursing. Continuous hemodynamic and respiratory monitoring 
+     was performed, including the use of pulse oximetry.
+      
+     START TIME:   9:25 am
+     STOP TIME:     10:45 am  
+      
+     MEDICATIONS:
+     Fentanyl (mcg) IV  200 mcg
+     Versed (mg) IV  4 mg
+     1% Local Lidocaine
+      
+     SUPPLIES:
+     22 G x 20 cm Chiba needle (Cook)
+     18 G x 20 cm Temno (CardinalHealth) co-axial biopsy needle set
+      
+     INFECTION CONTROL: All elements of maximal sterile barrier technique 
+     followed including: cap, mask, sterile gown, sterile gloves, a large 
+     sterile sheet, hand hygiene, 2% chlorhexidine for cutaneous 
+     antisepsis (or acceptable alternative antiseptics, per current 
+     guideline).  
+      
+     PROCEDURE:  
+     The patient was placed in right lateral decubitus position on the CT 
+     table.  A &quot;timeout&quot; was performed before the start of the procedure 
+     with the patient on the table to verify the correct patient, 
+     procedure and position. Preliminary axial CT images were obtained 
+     with radioopaque cutaneous grid.  The retroperitoneal peri-aortic 
+     soft tissue was localized.  After assessing the most direct access to 
+     the lesion from the left side, the patient's skin was prepped and 
+     draped in the usual sterile fashion.  1% Lidocaine local anesthetic 
+     was infiltrated in the skin and subcutaneous tissues.  Subsequently, 
+     a 17 gauge introducer needle was advanced through left 
+     retroperitoneum into the lesion.  Fine needle aspirations (22 gauge) 
+     and and 18 gauge core biopsy samples (three) of the mass obtained and 
+     were sent for cytology and surgical pathology analysis.  
+      
+     Postbiopsy images demonstrated no hemorrhage and few pockets of air 
+     in the retroperitoneum.
+      
+     The patient tolerated the procedure well and was transported to the 
+     recovery area in stable condition. 
+      
+     
+     IMPRESSION:
+     CT GUIDED BIOPSY OF RETROPERITONEAL SOFT TISSUE.
+      
+     PLAN:
+     Follow up on biopsy results.
+     
+       
+RADIOLOGISTS:                           SIGNATURES:
+     Sainani, Nisha I MBBS                   
+     Arellano, Ronald S Attending            Arellano, Ronald S Attending
+
+</pre></td></tr></table>

data/test/content/3000888_search_type.xml

@@ -0,0 +1 @@
+<?xml version='1.0'?><searchlist><mrn>3000888</mrn><request>type:PAT</request><query><search>{type:PAT}</search><searchitem><type>PAT</type><MID>4417067</MID><Scheduledate>2007-07-17</Scheduledate><site></site><status></status><desc><![CDATA[Surgical Pathology]]></desc><context><![CDATA[]]></context></searchitem><searchitem><type>PAT</type><MID>4318532</MID><Scheduledate>2007-04-26</Scheduledate><site></site><status></status><desc><![CDATA[Surgical Pathology]]></desc><context><![CDATA[]]></context></searchitem><searchitem><type>PAT</type><MID>4313382</MID><Scheduledate>2007-04-23</Scheduledate><site></site><status></status><desc><![CDATA[Surgical Pathology]]></desc><context><![CDATA[]]></context></searchitem></query></searchlist>

data/test/content/3000888_search_type_fromdate.xml

@@ -0,0 +1 @@
+<?xml version='1.0'?><searchlist><request>type:PAT and fromdate:\"07/01/2007\"</request><query><search>({type:PAT} AND {fromdate:07/01/2007})</search><searchitem><type>PAT</type><MRN>3000888</MRN><MID>4417067</MID><Scheduledate>2007-07-17</Scheduledate><site></site><status></status><desc><![CDATA[Surgical Pathology]]></desc><context><![CDATA[]]></context></searchitem></query></searchlist>

data/test/content/3000888_search_type_rad.xml

@@ -0,0 +1,17 @@
+<?xml version='1.0'?>
+<searchlist>
+  <mrn>3000888</mrn>
+  <request>type:RAD</request>
+  <query>
+    <search>{type:RAD}</search>
+    <searchitem>
+      <type>RAD</type>
+      <MID>63580395</MID>
+      <Scheduledate>2010-07-01</Scheduledate>
+      <site></site>
+      <status></status>
+      <desc><![CDATA[CTBxRetper]]></desc>
+      <context><![CDATA[]]></context>
+    </searchitem>
+  </query>
+</searchlist>

data/test/mock_http_client.rb

@@ -0,0 +1,113 @@
+require 'cgi'
+require 'yaml'
+require 'logger'
+require 'date'
+require 'active_support'
+require 'fake_web'
+
+class MockHttpClient
+  attr_accessor :data, :logger, :username, :password, :next_response_nil
+  attr_reader :updatetimes, :delays, :reload_times
+
+  FakeWeb.allow_net_connect = false
+
+  def initialize(yaml_file, logger = nil)
+    self.logger = logger || Logger.new(STDERR)
+    config = YAML.load_file(yaml_file)
+    config[:content].each do |item|
+      content = File.open(File.join(File.dirname(__FILE__), "content", item[:content])) do |f|
+        f.read
+      end
+      self.logger.info("Setting up test URI #{item[:url]}")
+      FakeWeb.register_uri(:get, item[:url], :body => content)
+    end
+    @updatetimes = {}
+    @reload_times = {}
+    @delays = {}
+    config[:patients].each_pair do |mrn, times|
+      @updatetimes[mrn] = DateTime.parse(times[:updatetime])
+      @delays[mrn] = times[:delay]
+    end
+    yield self if block_given?
+    self
+  end
+  
+  def set_auth(foo, username, password)
+    logger.info("Setting username and password, username is \"#{username}\"")
+    self.username = username
+    self.password = password
+    self
+  end
+  
+  def self.parse_uri(uri)
+    uri = uri.respond_to?(:query) ? uri : URI::parse(uri)
+    terms = Hash.new(nil)
+    uri.query.split('&').each do |el|
+      el =~ /^(.+)=(.+)$/
+      terms[$1] = CGI.unescape($2)
+    end
+    terms
+  end
+
+  def get_content(uri)
+    uri = uri.respond_to?(:host) ? uri : URI::parse(uri)
+    logger.info("Getting content for URI [#{uri.to_s}]")
+    req = MockHttpClient.parse_uri(uri)
+    raise "Must specify a USER in a QPID URI (got [#{uri.to_s}])" unless req["USER"]
+    raise "Must specify a MRN in a QPID URI (got [#{uri.to_s}])" unless req["MRN"]
+
+    # Check if we're giving junk next
+    if next_response_nil && next_response_nil > 0
+      logger.warn "Giving null response (#{next_response_nil - 1} left)"
+      self.next_response_nil = next_response_nil - 1
+      return nil
+    end
+    
+    # Check to see if we know about this patient
+    unless updatetimes[req["MRN"]]
+      return no_patient_response
+    end
+    
+    # Otherwise, figure out what we're doing
+    case req["function"]
+    when "updatestatus"
+      updatestatus_response(req["MRN"])
+    when "reload"
+      status = "UPDATING"
+      delay = delays[req["MRN"]] || 5
+      if reload_times[req["MRN"]]
+        if DateTime.now > reload_times[req["MRN"]].since(delay)
+          updatetimes[req["MRN"]] = reload_times[req["MRN"]].since(delay)
+          reload_times.delete(req["MRN"])
+          status = "OK"
+        end
+      else
+        reload_times[req["MRN"]] = DateTime.now
+      end
+      updatestatus_response(req["MRN"], status)
+    when "search"
+      raise "Tried to use the search function without a search parameter [#{uri.to_s}]" unless req["search"]
+      Net::HTTP.get(uri)
+    when "report"
+      raise "Tried to use the report function without a type parameter" unless req["type"]
+      raise "Tried to use the report function without a MID parameter" unless req["MID"]
+      Net::HTTP.get(uri)
+    else
+      raise "Got an apparently invalid QPID function \"#{req.function}\" [#{uri.to_s}]"
+    end
+  end
+  
+  def updatestatus_response(mrn, status = nil)
+    if updatetime = updatetimes[mrn]
+      hours_ago = (DateTime.now - updatetime).to_f * 24.0
+      status ||= (hours_ago < 1) ? "OK" : "STALE"
+      "<updatestatus><lastupdate>#{updatetime.strftime("%Y-%m-%dT%H:%M:%S")}</lastupdate><message>#{status}</message></updatestatus>"
+    else
+      no_patient_response
+    end
+  end
+  
+  def no_patient_response
+    "<updatestatus><message>NO PATIENT</message></updatestatus>"    
+  end
+end

data/test/qpid.yml

@@ -0,0 +1,6 @@
+host: qpid.example.org
+path: /path/to/servlet
+user: realuser
+http_user: servicename
+http_password: servicepw
+query_interval: 1.0

data/test/qpid_test_data.yml

@@ -0,0 +1,21 @@
+---
+:patients:
+  "3000888": 
+    :updatetime: 2010-06-12 12:15:23 0
+    :delay: 3
+  "1358881":
+    :updatetime: 2010-07-15 13:15:55 0
+    :delay: 2
+:content:
+  - :url: http://qpid.example.org/path/to/servlet?xml=1&search=type%3APAT&function=search&MRN=3000888&USER=realuser
+    :content: 3000888_search_type.xml
+  - :url: http://qpid.example.org/path/to/servlet?xml=1&search=type%3ARAD&function=search&MRN=3000888&USER=realuser
+    :content: 3000888_search_type_rad.xml
+  - :url: http://qpid.example.org/path/to/servlet?xml=1&search=type%3APAT+and+fromdate%3A%2207%2F01%2F2007%22&function=search&MRN=3000888&USER=realuser
+    :content: 3000888_search_type_fromdate.xml
+  - :url: http://qpid.example.org/path/to/servlet?type=PAT&xml=1&function=report&MID=4417067&MRN=3000888&USER=realuser
+    :content: 3000888_report_pat_4313382_1.xml
+  - :url: http://qpid.example.org/path/to/servlet?type=PAT&xml=1&function=report&MID=4313382&MRN=3000888&USER=realuser
+    :content: 3000888_report_pat_4313382_1.xml
+  - :url: http://qpid.example.org/path/to/servlet?type=RAD&xml=1&function=report&MID=63580395&MRN=3000888&USER=realuser
+    :content: 3000888_report_rad_63580395.xml

metadata

@@ -1,128 +1,149 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: qpid
-version: !ruby/object:Gem::Version 
-  hash: 31
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 2
-  version: 0.1.2
+version: !ruby/object:Gem::Version
+  version: 0.1.3
+  prerelease: 
 platform: ruby
-authors: 
-- Tarik K. Alkasab
+authors:
+- Tarik K. Alkasab, MD, PhD
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2009-10-21 00:00:00 -04:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-10-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: happymapper
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 19
-        segments: 
-        - 0
-        - 3
-        - 0
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.3.0
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: httpclient
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+- !ruby/object:Gem::Dependency
+  name: httpclient
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 119
-        segments: 
-        - 2
-        - 1
-        - 5
-        - 2
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 2.1.5.2
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: hoe
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.1.5.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 2
-        - 3
-        - 3
-        version: 2.3.3
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.10'
   type: :development
-  version_requirements: *id003
-description: The QPID (Queriable Patient Inference Dossier, developed at Massachusetts General Hospital) aggregates and permits semantic searching of electronic medical record systems. The Qpid gem provides a ruby interface to the web service which QPID-based systems offer for searching and accessing medical record information.
-email: 
-- tarik.alkasab@gmail.com
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.10'
+- !ruby/object:Gem::Dependency
+  name: newgem
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+- !ruby/object:Gem::Dependency
+  name: hoe
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
+description: Interface to QPID, the Queriable Patient Inference Dossier system.
+email:
+- talkasab@partners.org
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - History.txt
 - Manifest.txt
-files: 
+- README.rdoc
+files:
 - History.txt
 - Manifest.txt
 - README.rdoc
 - Rakefile
 - lib/qpid.rb
 - script/console
-- script/destroy
-- script/generate
 - test/test_helper.rb
 - test/test_qpid.rb
-has_rdoc: true
+- test/content/3000888_report_pat_4313382_1.xml
+- test/content/3000888_report_rad_63580395.xml
+- test/content/3000888_search_type.xml
+- test/content/3000888_search_type_fromdate.xml
+- test/content/3000888_search_type_rad.xml
+- test/mock_http_client.rb
+- test/qpid.yml
+- test/qpid_test_data.yml
+- .gemtest
 homepage: http://github.com/talkasab/qpid
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --main
 - README.rdoc
-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: qpid
-rubygems_version: 1.3.7
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
-summary: Interface to medical record search systems based on the QPID (Queriable Patient Inference Dossier) system.
-test_files: 
+summary: Interface to QPID, the Queriable Patient Inference Dossier system.
+test_files:
 - test/test_helper.rb
 - test/test_qpid.rb

data/script/destroy

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
-
-begin
-  require 'rubigen'
-rescue LoadError
-  require 'rubygems'
-  require 'rubigen'
-end
-require 'rubigen/scripts/destroy'
-
-ARGV.shift if ['--help', '-h'].include?(ARGV[0])
-RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
-RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
-
-begin
-  require 'rubigen'
-rescue LoadError
-  require 'rubygems'
-  require 'rubigen'
-end
-require 'rubigen/scripts/generate'
-
-ARGV.shift if ['--help', '-h'].include?(ARGV[0])
-RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
-RubiGen::Scripts::Generate.new.run(ARGV)