first commit for DocumentReference creation

create_mhd.rb

@@ -0,0 +1,104 @@
+# create_mhd.rb
+# This script reads all of the JSON objects contained in the children of the execution directory
+
+require 'bundler'
+require 'yaml'
+require 'logger'
+require 'erb'
+require 'date'
+require 'fileutils'
+
+log = Logger.new(STDOUT)
+
+DEBUG = true
+
+Bundler::require
+
+def generate_id
+	# Generates a 16 digit random number
+	Random.new.random_number(9999999999999999)
+end
+
+if ARGV.length < 1
+	raise "usage:\n\nruby create_mhd.rb path_for_patient\n\nnote: only a single patient is currently supported"
+end
+
+
+# Create directories to hold our objects
+patient_root_directory = File.join(Dir.pwd, ARGV[0])
+
+FileUtils.mkpath (File.join(patient_root_directory, "DocumentReference"))
+FileUtils.mkpath (File.join(patient_root_directory, "DocumentManifest"))
+
+
+# IHE XDS classCode Value Set
+report_class_code = {}
+report_class_code["system"] = "urn:oid:1.3.6.1.4.1.19376.1.2.6.1"
+report_class_code["code"] = "REPORT"
+report_class_code["display"] = "Report"
+
+images_class_code = {}
+images_class_code["system"] = "urn:oid:1.3.6.1.4.1.19376.1.2.6.1"
+images_class_code["code"] = "IMAGES"
+images_class_code["display"] = "Images"
+
+fhir = {}
+
+Dir["#{ARGV[0]}/**/*.json"].each do |data|
+
+	log.info("Processing: #{data}\n")
+    json = JSON.parse(data_string = File.read(data))
+
+    if fhir[json["resourceType"].to_s].nil?
+    	fhir[json["resourceType"].to_s] = []
+    end
+
+    fhir[json["resourceType"].to_s] << json
+
+end
+
+if fhir["Patient"].length > 1
+	raise "Multiple patients not currenlty supported"
+end
+
+
+
+# Will use ERB templates to generate DocumentReference resources
+# ERB template requires the following instance variables:
+# @id - going to be used to uniquely identify this resource
+# @div - human readable (html) rendering of the resource
+# @patient_id - json 
+# @diagnostic_report_code
+
+@patient_id = fhir["Patient"][0]["id"]
+@patient_identifier = fhir["Patient"][0]["identifier"].to_json
+
+fhir["DiagnosticReport"].each do |r|
+
+	@parent_resource_type = r["resourceType"]
+
+	@parent_resource_code = r["code"]["coding"][0].to_json
+
+	@id = generate_id
+
+	@parent_id = r["id"]
+
+	@document_class_code = report_class_code.to_json
+
+	@diagnostic_report_code = r["code"].to_json
+
+	@created = r["issued"]
+
+	b = binding
+	document_reference_template = ERB.new(File.read("document_reference.json.erb"))
+
+	puts document_reference_template.result(b) if DEBUG
+
+	#TODO - Create @div from the object itself
+
+	mhd_hash = JSON.parse(document_reference_template.result(b))
+
+	File.write(File.join(patient_root_directory,  "DocumentReference/document_reference." + @parent_id + ".json"), JSON.pretty_generate(mhd_hash))
+
+end
+

document_reference.json.erb

@@ -0,0 +1,122 @@
+{
+  "resourceType": "DocumentReference",
+  "id": "<%= @id %>",
+  "text": {
+    "status": "generated",
+    "div": "<%= @div %>"
+  },
+  "identifier": [
+    {
+      "system": "https://github.com/ImagingInformatics/hackathon-dataset/",
+      "value": "89573"
+    }
+  ],
+  "subject": {
+    "reference": "Patient/<%= @patient_id %>"
+  },
+  "type": 
+    <%= @diagnostic_report_code %>,
+  "class": {
+    "coding": [
+      <%= @document_class_code %>
+    ]
+  },
+  "author": [
+    {
+      "reference": "Practitioner/siimmd"
+    },
+    {
+      "reference": "#a2"
+    }
+  ],
+  "custodian": {
+    "reference": "Organization/siim"
+  },
+  "authenticator": {
+    "reference": "Practitioner/siimmd"
+  },
+  "created": "<%= @created %>",
+  "indexed": "<%= @created %>",
+  "status": "current",
+  "docStatus": {
+    "coding": [
+      {
+        "system": "http://hl7.org/fhir/composition-status",
+        "code": "final",
+        "display": "Final"
+      }
+    ]
+  },
+  "description": "Physical",
+  "securityLabel": [
+    {
+      "coding": [
+        {
+          "system": "http://hl7.org/fhir/v3/Confidentiality",
+          "code": "V",
+          "display": "very restricted"
+        }
+      ]
+    }
+  ],
+  "content": [
+    {
+      "attachment": {
+        "contentType": "application/json-fhir",
+        "language": "en-US",
+        "url": "<%= @parent_resource_type + "/" + @parent_id %>"
+      },
+      "format": [
+        {
+          "system": "http://hl7.org/fhir/diagnosticreport.html",
+          "display": "FHIR DiagnosticReport Specification"
+        }
+      ]
+    }
+  ],
+  "context": {
+    "encounter": {
+      "reference": "Encounter/xcda"
+    },
+    "event": [
+      {
+        "coding": [
+          <%= @parent_resource_code %>
+        ]
+      }
+    ],
+    "period": {
+      "start": "2004-12-23T08:00:00+11:00",
+      "end": "2004-12-23T08:01:00+11:00"
+    },
+    "facilityType": {
+      "coding": [
+        {
+          "system": "https://loinc.org/document-ontology/",
+          "code": "Outpatient",
+          "display": "Outpatient"
+        }
+      ]
+    },
+    "practiceSetting": {
+      "coding": [
+        {
+          "system": "https://loinc.org/document-ontology/",
+          "code": "Radiology",
+          "display": "Radiology"
+        }
+      ]
+    },
+    "sourcePatientInfo": {
+      "reference": "Patient/<%= @patient_id %>"
+    },
+    "related": [
+      {
+        "identifier": <%= @patient_identifier %>,
+        "ref": {
+          "reference": "Patient/<%= @patient_id %>"
+        }
+      }
+    ]
+  }
+}