Notebook 1 - The FHIR API.ipynb

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   "cell_type": "markdown",
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   "source": [
    "<img src=\"https://www.hl7.org/fhir/assets/images/fhir-logo-www.png\" style=\"float: left; width: 25%; margin-bottom: 0.5em;\">"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Author: **Lee Surprenant** lmsurpre@us.ibm.com\n",
    "- [Section 1: The FHIR HTTP API](#Section-1.-The-FHIR-REST-API)\n",
    "- [Section 2: FHIR Search](#Section-2:-FHIR-Search)\n",
    "- [Section 3: Search paramater types](#Section-3:-Search-parameter-types)\n",
    "- [Section 4: Chaining and includes](#Section-4:-Chaining-and-includes)\n",
    "- [Section 5: Putting it together](#Section-5:-Putting-it-together)\n",
    "- [Section 6: Bulk export](#Section-6:-Bulk-export)"
   ]
  },
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   "cell_type": "code",
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   "metadata": {},
   "outputs": [],
   "source": [
    "# save the base url of the FHIR server\n",
    "base = 'https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open'\n",
    "\n",
    "# setup imports\n",
    "import os\n",
    "from requests import get\n",
    "from requests import post\n",
    "from requests import put\n",
    "from requests import delete\n",
    "from requests import head\n",
    "from IPython.display import IFrame\n",
    "\n",
    "# a function to print the top x rows and add a newline\n",
    "def peek(string, line_count=25):\n",
    "    print(os.linesep.join(string.split(os.linesep)[:line_count]) + '\\n')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/opt/conda/envs/Python-3.7-main/lib/python3.7/site-packages/secretstorage/dhcrypto.py:16: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead\n",
      "  from cryptography.utils import int_from_bytes\n",
      "/opt/conda/envs/Python-3.7-main/lib/python3.7/site-packages/secretstorage/util.py:25: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead\n",
      "  from cryptography.utils import int_from_bytes\n",
      "Requirement already satisfied: jsonpointer in /opt/conda/envs/Python-3.7-main/lib/python3.7/site-packages (2.1)\n"
     ]
    }
   ],
   "source": [
    "#(Optional)\n",
    "# install jsonpointer\n",
    "!pip install jsonpointer\n",
    "from jsonpointer import resolve_pointer as resolve"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Section 1. The FHIR REST API"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
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      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"1200\"\n",
       "            height=\"330\"\n",
       "            src=\"https://www.hl7.org/fhir/resourcelist.html#tabs\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f323806c050>"
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     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "# HL7 FHIR defines a set of \"resources\" for exchanging information.\n",
    "IFrame('https://www.hl7.org/fhir/resourcelist.html#tabs', width=1200, height=330)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"1200\"\n",
       "            height=\"330\"\n",
       "            src=\"https://www.hl7.org/fhir/http.html#operations\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f323806c790>"
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     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Each resource type supports the same set of interactions, categorized in the spec into \"instance-level\" and \"type-level\" interactions.\n",
    "IFrame('https://www.hl7.org/fhir/http.html#operations', width=1200, height=330)"
   ]
  },
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   "execution_count": 5,
   "metadata": {
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   "outputs": [
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     "name": "stdout",
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     "text": [
      "Response code: 200\n",
      "Server: IBM FHIR Server 4.8.0\n",
      "Security: {'cors': True}\n",
      "Supported types: \n",
      "  Measure: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductIndication: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Organization: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  EvidenceVariable: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Library: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CarePlan: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductAuthorization: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Account: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  OperationOutcome: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MeasureReport: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  PractitionerRole: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Binary: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ImmunizationEvaluation: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicationDispense: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DiagnosticReport: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductUndesirableEffect: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DeviceUseStatement: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  PlanDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Immunization: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  NutritionOrder: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Person: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProduct: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  AdverseEvent: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ClaimResponse: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DeviceDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  GraphDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MolecularSequence: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DeviceMetric: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MessageHeader: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Invoice: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Linkage: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicationKnowledge: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  EventDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ServiceRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ActivityDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SpecimenDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SubstanceReferenceInformation: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ChargeItem: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DetectedIssue: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  EffectEvidenceSynthesis: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  FamilyMemberHistory: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ImplementationGuide: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ClinicalImpression: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CoverageEligibilityRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  EnrollmentRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  OrganizationAffiliation: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  StructureMap: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  EnrollmentResponse: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  List: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SubstanceProtein: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ResearchStudy: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Condition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Practitioner: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  AppointmentResponse: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Task: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Provenance: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Coverage: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  InsurancePlan: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Slot: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Device: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Bundle: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ConceptMap: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  BodyStructure: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Location: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductContraindication: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  RequestGroup: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  BiologicallyDerivedProduct: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Medication: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  TerminologyCapabilities: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Group: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ValueSet: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductManufactured: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SupplyDelivery: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductInteraction: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CoverageEligibilityResponse: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ChargeItemDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ObservationDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  VerificationResult: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Basic: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CommunicationRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Parameters: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  RelatedPerson: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CompartmentDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  TestScript: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  AllergyIntolerance: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  GuidanceResponse: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MessageDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Substance: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Composition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ImmunizationRecommendation: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SearchParameter: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  AuditEvent: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ImagingStudy: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  NamingSystem: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SubstanceSourceMaterial: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ResearchElementDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  EpisodeOfCare: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Goal: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ResearchDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ExampleScenario: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SubstanceNucleicAcid: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Contract: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  QuestionnaireResponse: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Endpoint: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  StructureDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CodeSystem: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  PaymentReconciliation: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Flag: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  RiskEvidenceSynthesis: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CareTeam: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SubstanceSpecification: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Subscription: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ExplanationOfBenefit: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  VisionPrescription: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DeviceRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  HealthcareService: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Questionnaire: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  OperationDefinition: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Consent: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  RiskAssessment: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SubstancePolymer: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Encounter: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicationRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicationStatement: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CapabilityStatement: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Patient: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Specimen: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductPackaged: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  ResearchSubject: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductIngredient: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Evidence: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  PaymentNotice: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  CatalogEntry: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicinalProductPharmaceutical: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  SupplyRequest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  TestReport: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Appointment: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Communication: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Claim: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DocumentReference: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Observation: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Schedule: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Procedure: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  DocumentManifest: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  Media: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n",
      "  MedicationAdministration: ['create', 'read', 'vread', 'update', 'patch', 'delete', 'history-instance', 'search-type']\n"
     ]
    }
   ],
   "source": [
    "# This notebook focuses on the FHIR Search API, but first we use the \"capabilities\" interaction to learn about our target server.\n",
    "\n",
    "# retrieve the server \"CapabilityStatement\" and print the important bits\n",
    "response = get(base + '/metadata')\n",
    "print('Response code: ' + str(response.status_code))\n",
    "result = response.json()\n",
    "print('Server: ' + result['name'] + ' ' + result['version'])\n",
    "print('Security: ' + str(result['rest'][0]['security']))\n",
    "resources = result['rest'][0]['resource']\n",
    "\n",
    "supported_types = {r['type']: [i['code'] for i in r['interaction']] for r in resources}\n",
    "\n",
    "print('Supported types: ')\n",
    "for k,v in supported_types.items():\n",
    "    print('  ' + k + ': ' + str(v))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Section 2: FHIR Search"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Response code: 200\n",
      "Response body: \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"b6bce8fe-46e4-4618-8f4e-ff3f7323e946\",\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 32655,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&_page=1\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&_page=2\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient/17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Patient\",\n",
      "                \"id\": \"17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "                \"meta\": {\n",
      "                    \"versionId\": \"4\",\n",
      "                    \"lastUpdated\": \"2021-03-12T03:13:48.626Z\",\n",
      "\n",
      "Number of entries: 10\n"
     ]
    }
   ],
   "source": [
    "# Now that we know our server supports the \"search-type\" interaction on all resource types, lets start working with the Patient endpoint.\n",
    "\n",
    "# query for all Patient resources, then print the HTTP status code and the first 25 lines of the response\n",
    "response = get(base + '/Patient')\n",
    "print('Response code: ' + str(response.status_code))\n",
    "peek('Response body: \\n' + response.text)\n",
    "print('Number of entries: ' + str(len(response.json().get('entry'))))\n",
    "\n",
    "# technically you've now performed your first FHIR \"search\" (just with no parameters)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Second page: \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"93e11f34-1abd-4124-bbb1-8cd1edf31dad\",\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 32655,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&_page=2\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&_page=3\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"previous\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&_page=1\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient/17598bf809c-1a099ca4-cdb9-4837-8692-51338082cd97\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Patient\",\n",
      "\n",
      "Number of entries: 10\n"
     ]
    }
   ],
   "source": [
    "# note that results are paged and the \"link\" field in the response Bundle contains links to the previous, current, and next page of results\n",
    "for link in response.json().get('link'):\n",
    "    if link.get('relation') == 'next':\n",
    "        page2 = get(link.get('url'))        \n",
    "peek('Second page: \\n' + page2.text)\n",
    "print('Number of entries: ' + str(len(response.json().get('entry'))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Single resource per page: \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"b0140878-b70b-4130-8a7d-138bca685f6b\",\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 32655,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=1&_page=1\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=1&_page=2\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient/17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Patient\",\n",
      "                \"id\": \"17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "                \"meta\": {\n",
      "                    \"versionId\": \"4\",\n",
      "                    \"lastUpdated\": \"2021-03-12T03:13:48.626Z\",\n",
      "\n",
      "Number of entries: 1\n"
     ]
    }
   ],
   "source": [
    "# we can control the number of resources on each page by passing the _count parameter\n",
    "response = get(base + '/Patient?_count=1')\n",
    "peek('Single resource per page: \\n' + response.text)\n",
    "print('Number of entries: ' + str(len(response.json().get('entry'))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"178e1b23-7962-43c8-87b0-e4863644420b\",\n",
      "    \"meta\": {\n",
      "        \"tag\": [\n",
      "            {\n",
      "                \"system\": \"http://terminology.hl7.org/CodeSystem/v3-ObservationValue\",\n",
      "                \"code\": \"SUBSETTED\",\n",
      "                \"display\": \"subsetted\"\n",
      "            }\n",
      "        ]\n",
      "    },\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 32655,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&_summary=count&_page=1\"\n",
      "        }\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "# if you're only interested in the count, you can specify that via either\n",
    "# A. _count=0 (0 results per page); or\n",
    "# B. _summary=count\n",
    "\n",
    "print(get(base + '/Patient' + '?' + '_summary=count').text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"1200\"\n",
       "            height=\"330\"\n",
       "            src=\"https://hl7.org/fhir/patient.html#resource\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f3238387f10>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# if you want a lot of results per page, you can reduce the amount of data returned via the _summary or _elements parameters\n",
    "\n",
    "# first, lets review the structure of the Patient resource\n",
    "IFrame('https://hl7.org/fhir/patient.html#resource', width=1200, height=330)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Normal: \n",
      "dict_keys(['resourceType', 'id', 'meta', 'text', 'extension', 'identifier', 'name', 'telecom', 'gender', 'birthDate', 'address', 'maritalStatus', 'multipleBirthBoolean', 'communication'])\n",
      "\n",
      "Summary: \n",
      "dict_keys(['resourceType', 'id', 'meta', 'identifier', 'name', 'telecom', 'gender', 'birthDate', 'address'])\n",
      "\n",
      "Elements: \n",
      "dict_keys(['resourceType', 'id', 'meta', 'gender'])\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# print the list of top-level elements in the first Patient resource returned\n",
    "response = get(base + '/Patient')\n",
    "peek('Normal: \\n' + str(response.json().get('entry')[0].get('resource').keys()))\n",
    "\n",
    "# look for the Σ flag in the Resource Content section of the resource page in the specification for what elements are considered \"summary\" elements \n",
    "response = get(base + '/Patient?' + '_summary=true')\n",
    "peek('Summary: \\n' + str(response.json().get('entry')[0].get('resource').keys()))\n",
    "\n",
    "# need more control?\n",
    "# you can use the _elements parameter to ask for specific fields back (although the server should include required fields and modifier fields as well)\n",
    "response = get(base + '/Patient?' + '_elements=id,gender')\n",
    "peek('Elements: \\n' + str(response.json().get('entry')[0].get('resource').keys()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Normal: \t902254 bytes \t(0.327694 s)\n",
      "Summary: \t526541 bytes \t(0.279208 s)\n",
      "Elements: \t114154 bytes \t(0.241758 s)\n"
     ]
    }
   ],
   "source": [
    "# this can add up!\n",
    "\n",
    "response = get(base + '/Patient?_count=100')\n",
    "print('Normal: \\t' + str(len(response.content)) + ' bytes \\t(' + str(response.elapsed.total_seconds()) + ' s)')\n",
    "\n",
    "response = get(base + '/Patient?_count=100&_summary=true')\n",
    "print('Summary: \\t' + str(len(response.content)) + ' bytes \\t(' + str(response.elapsed.total_seconds()) + ' s)')\n",
    "\n",
    "response = get(base + '/Patient?_count=100&_elements=id,gender,birthDate')\n",
    "print('Elements: \\t' + str(len(response.content)) + ' bytes \\t(' + str(response.elapsed.total_seconds()) + ' s)')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"1200\"\n",
       "            height=\"500\"\n",
       "            src=\"https://www.hl7.org/fhir/patient.html#search\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f3238045fd0>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# now add some search parameters\n",
    "\n",
    "# each FHIR resource type has its own set of parameters; find them toward the bottom of the page for that resource type in the specification\n",
    "# for example, for the Patient resource type, see https://www.hl7.org/fhir/patient.html#search\n",
    "IFrame('https://www.hl7.org/fhir/patient.html#search', width=1200, height=500)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Response code: 200\n",
      "Response body: \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"6f3f1954-e5cc-482b-b469-f9c05aa70b3c\",\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 15450,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&gender=male&_page=1\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=10&gender=male&_page=2\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient/17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Patient\",\n",
      "                \"id\": \"17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "                \"meta\": {\n",
      "                    \"versionId\": \"4\",\n",
      "                    \"lastUpdated\": \"2021-03-12T03:13:48.626Z\",\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# for example, lets use the search parameter named \"gender\"\n",
    "response = get(base + '/Patient' + '?' + 'gender=male')\n",
    "print('Response code: ' + str(response.status_code))\n",
    "peek('Response body: \\n' + response.text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "male:   \t15450\n",
      "female: \t17204\n",
      "missing gender: 1\n"
     ]
    }
   ],
   "source": [
    "# pro tip: combine your search query with _summary=count to explore the data\n",
    "print('male:   \\t' + str(get(base + '/Patient' + '?' + 'gender=male' + '&' + '_summary=count').json().get('total')))\n",
    "print('female: \\t' + str(get(base + '/Patient' + '?' + 'gender=female' + '&' + '_summary=count').json().get('total')))\n",
    "\n",
    "# use the \"missing\" modifier to look for resources that do NOT have a value for the target parameter\n",
    "response = get(base + '/Patient' + '?' + 'gender:missing=true' + '&' + '_summary=count')\n",
    "print('missing gender: ' + str(response.json().get('total')))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Section 3: Search parameter types"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "male:\n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"630d24e0-bb85-4aa1-88ad-156e52e8ac8a\",\n",
      "    \"meta\": {\n",
      "        \"tag\": [\n",
      "            {\n",
      "                \"system\": \"http://terminology.hl7.org/CodeSystem/v3-ObservationValue\",\n",
      "                \"code\": \"SUBSETTED\",\n",
      "                \"display\": \"subsetted\"\n",
      "            }\n",
      "        ]\n",
      "    },\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 15450,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=1&gender=http://hl7.org/fhir/administrative-gender%7Cmale&_elements=gender&_page=1\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=1&gender=http://hl7.org/fhir/administrative-gender%7Cmale&_elements=gender&_page=2\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient/17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Patient\",\n",
      "                \"id\": \"17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c\",\n",
      "                \"meta\": {\n",
      "                    \"versionId\": \"4\",\n",
      "                    \"lastUpdated\": \"2021-03-12T03:13:48.626Z\",\n",
      "                    \"profile\": [\n",
      "                        \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient\"\n",
      "                    ],\n",
      "                    \"tag\": [\n",
      "                        {\n",
      "                            \"system\": \"http://terminology.hl7.org/CodeSystem/v3-ObservationValue\",\n",
      "                            \"code\": \"SUBSETTED\",\n",
      "                            \"display\": \"subsetted\"\n",
      "                        }\n",
      "                    ]\n",
      "                },\n",
      "                \"gender\": \"male\"\n",
      "            },\n",
      "            \"search\": {\n",
      "                \"mode\": \"match\",\n",
      "                \"score\": 1\n",
      "            }\n",
      "        }\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "# search parameters have types\n",
    "\n",
    "# gender is considered a \"token\" search parameter\n",
    "\n",
    "# Token search\n",
    "# this parameter type is common for 'coded' values (Code, Coding, and CodeableConcept) and identifiers\n",
    "# token values consist of a system and a code, although sometimes the system is implicit (like in the case of gender)\n",
    "# users can search on the system and code (system|code), the code alone (code), system-less codes (|code), or even the system alone (system|)\n",
    "response = get(base + '/Patient' + '?' + 'gender=http://hl7.org/fhir/administrative-gender|male' + '&_count=1&_elements=gender')\n",
    "print('male:\\n' + response.text)\n",
    "\n",
    "\n",
    "# there are also Number, Date/DateTime, String, Reference, Quantity, URI, and Composite parameter types"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Smiths:\n",
      "17598d8e9df-706d630f-784d-473d-a0d2-37af26e3c36e: Smitham\n",
      "17598dc69c4-fe632367-ce4f-413b-9639-5f409631fdbd: Smith\n",
      "17598e7faf2-37231ae2-90fa-4668-90cc-9d413e44ff73: Smitham\n",
      "17598fe2d81-8588df6c-a4e5-486f-8de7-f2a457e1ecbb: Smitham\n",
      "175991c2ff1-8b5aef81-6ed2-4173-8ee0-3a38612ece43: Smitham\n",
      "175991de90e-b9364b28-a200-4d19-9bba-1cd4d5d9f037: Heller, Smith\n",
      "175992f962b-159acf20-e5d5-4370-bf38-8e02eef6d761: Smith\n",
      "17599326aa9-40e01d7e-1d5b-4f1b-9bed-9c0a0b031df1: Smith\n",
      "175993420d0-eb6a0968-589a-4a71-a010-19e84056c44e: Smitham\n",
      "17599375dc6-21078467-b048-499a-b8c4-9f5ddfc6ffd3: Haley, Smitham\n"
     ]
    }
   ],
   "source": [
    "# String search\n",
    "response = get(base + '/Patient' + '?' + 'family=Smith' + '&_elements=name')\n",
    "print('Smiths:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(', '.join(map(lambda n: n.get('family'), resource.get('name'))))\n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Smiths:\n",
      "17598dc69c4-fe632367-ce4f-413b-9639-5f409631fdbd: Smith\n",
      "175991de90e-b9364b28-a200-4d19-9bba-1cd4d5d9f037: Heller, Smith\n",
      "175992f962b-159acf20-e5d5-4370-bf38-8e02eef6d761: Smith\n",
      "17599326aa9-40e01d7e-1d5b-4f1b-9bed-9c0a0b031df1: Smith\n",
      "175993c2874-5f898109-a18d-4d6e-8cfb-ecd69eb37862: Smith\n",
      "17599522520-bdb4311f-3765-45f2-bd5d-1f1aca14a931: Smith\n",
      "17599539a99-bccf02f3-57ef-4399-a4c6-0296aa8356c1: Purdy, Smith\n",
      "1759954cc00-9def2bdc-a444-4e84-bf77-a0e79e449d19: Rosenbaum, Smith\n",
      "175995a5564-869be93e-c7c2-4cab-9951-d15063f39975: Wintheiser, Smith\n",
      "175995ad366-3722d3d9-c56e-4d06-ba32-1b662e18bfbe: Wehner, Smith\n",
      "\n",
      "Skis:\n",
      "17598bf6496-92b7682f-d882-4b3c-8e37-178b11cde674: Gusikowski, West\n",
      "17598c069d0-3b1b68c5-13e0-4c46-b929-1fea6d13454f: Osinski\n",
      "17598c0689e-e60c055e-c166-406d-a9b0-f6d113292dcc: Gutkowski\n",
      "17598c10cbc-642eb489-8d83-4220-8591-a31adc7a9189: Gusikowski\n",
      "17598c3ebc7-63c73ac0-7cc7-492f-b1f5-661c9da0b95e: Gulgowski\n",
      "17598c45f73-e1ac3687-ae53-4591-b9f7-65deb78c8a1b: Jaskolski\n",
      "17598c61295-bf40a9c1-ebc2-46cb-b4e5-c1ea732c0960: Gusikowski\n",
      "17598c88bd6-e98052ab-8f37-46c5-ade7-c3b441573a90: Swaniawski\n",
      "17598cbac2b-5b5193d4-9b35-48a9-88b1-b2912fd0c896: Jaskolski, Erdman\n",
      "17598ccda87-246aadea-59a6-4287-a472-7a9117e89059: Powlowski\n"
     ]
    }
   ],
   "source": [
    "# wait, \"Smitham\" !?\n",
    "\n",
    "# string search performs a case-insensitive \"begins-with\" search by default!\n",
    "# use the modifier \":exact\" if you want exact matches (and improved performance)\n",
    "response = get(base + '/Patient' + '?' + 'family:exact=Smith' + '&_elements=name')\n",
    "print('Smiths:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(', '.join(map(lambda n: n.get('family'), resource.get('name'))))\n",
    "print()\n",
    "\n",
    "# string search also has a \":contains\" modifier\n",
    "response = get(base + '/Patient' + '?' + 'family:contains=ski' + '&_elements=name')\n",
    "print('Skis:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(', '.join(map(lambda n: n.get('family'), resource.get('name'))))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Born in 1984:\n",
      "17598c01014-694ba51f-a02d-4686-b956-7d6eb9d7e5fa: 1984-12-05\n",
      "17598c330b0-817d8bac-b275-449d-8163-0ae095d6a7d5: 1984-03-23\n",
      "17598d78d31-639632e7-4f79-4b1a-81e8-f462de2c5912: 1984-09-18\n",
      "17598dc812f-37fd8fe9-e900-4f11-b166-5515fd7b4125: 1984-12-26\n",
      "17598dda658-9243965e-f6e2-4909-b2f6-89dcd7dcf799: 1984-05-04\n",
      "17598de13a7-c2c48b25-a1cc-498a-9b98-08629619ae15: 1984-03-04\n",
      "17598e32314-d67c7847-5ca3-4b0c-86df-195e40626a65: 1984-10-05\n",
      "17598e54dfe-683137bf-6a96-4b94-9218-7be5ff4ee2fb: 1984-04-21\n",
      "17598eed38d-eb24c019-4ab9-4f14-9c66-db95a1ed22dc: 1984-10-23\n",
      "17598f52f36-17f4bfd8-c305-468f-9c38-792a461e28a3: 1984-04-26\n"
     ]
    }
   ],
   "source": [
    "# Date search\n",
    "response = get(base + '/Patient' + '?' + 'birthdate=1984' + '&_elements=birthDate')\n",
    "print('Born in 1984:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(resource.get('birthDate'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Born before 1984:\n",
      "17598bf0165-6eda45e2-f9c1-4c4c-9ef2-1776cfbb0a7d: 1976-10-11\n",
      "17598bf1688-037fcb72-18af-40ce-a96b-c393a595dd49: 1975-07-10\n",
      "17598bf28f3-257b9fe9-9084-41d6-bb0f-43b4729a7f0d: 1982-01-13\n",
      "17598bf36c7-fedcedc3-b78c-4688-82ef-622e0cc71b22: 1973-03-03\n",
      "17598bf6cd6-d8388338-897d-48a0-b334-a877459941b2: 1979-03-01\n",
      "17598bf3d06-15fa6deb-59ad-4bd2-b8a1-8a2fa606d084: 1924-10-07\n",
      "17598bf6496-92b7682f-d882-4b3c-8e37-178b11cde674: 1948-12-25\n",
      "17598bf98b2-789821a7-b30c-48d4-b388-5343a933d8ad: 1972-06-15\n",
      "17598bfb281-9ca10cb0-6ba0-4691-85f4-424423b1869d: 1970-12-02\n",
      "17598bfa2da-9c19d3ed-5bef-49ab-b6b0-1d731446ddf6: 1960-11-21\n",
      "\n",
      "Born after 1984:\n",
      "17598bed122-d90e0186-8458-4482-a580-5b18b554ed3c: 1990-02-05\n",
      "17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f: 1986-07-15\n",
      "17598bf4a5d-185e291b-d0e3-42d3-9b70-eeae60debeec: 2005-11-09\n",
      "17598bf2ea9-7238cb29-0108-47a7-bf50-c94c6468ad2b: 2020-01-19\n",
      "17598bf555d-8e5857a0-4da9-4e6c-b9be-8624f80cf080: 1990-01-07\n",
      "17598bf809c-1a099ca4-cdb9-4837-8692-51338082cd97: 2019-09-05\n",
      "17598bf8b6a-ef83ac85-d722-406a-893a-7b016f060867: 1994-08-22\n",
      "17598bf9bf3-72e9d777-a355-4e7c-9b61-6a7dd30a61f4: 1999-10-06\n",
      "17598bfb106-0f9d95e0-84de-4b28-b8ad-d6a0f4caa980: 1993-01-07\n",
      "17598bfd0cf-22472597-7a8f-47b4-abb9-b36ab298ee12: 2007-08-05\n",
      "\n",
      "Born \"around\" 1984:\n",
      "17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f: 1986-07-15\n",
      "17598bf28f3-257b9fe9-9084-41d6-bb0f-43b4729a7f0d: 1982-01-13\n",
      "17598c01014-694ba51f-a02d-4686-b956-7d6eb9d7e5fa: 1984-12-05\n",
      "17598c05638-14568b50-6d51-4ab4-a94c-096c49ac8a4e: 1982-04-20\n",
      "17598c0a7ca-46d519f3-9866-427f-91b3-75f834a5eb72: 1983-10-29\n",
      "17598c1650a-20726259-3909-46b4-8d70-effe09390d7c: 1982-09-15\n",
      "17598c31418-c137d962-05b5-4f50-aec7-70033c0de3c1: 1983-05-29\n",
      "17598c330b0-817d8bac-b275-449d-8163-0ae095d6a7d5: 1984-03-23\n",
      "17598c38744-b7e7533a-5d2d-40bd-8f34-ab16eedd8062: 1988-06-29\n",
      "17598c41945-9802183c-797e-48ef-8f92-da84f0c00aa1: 1980-04-24\n"
     ]
    }
   ],
   "source": [
    "# date searches support lt(<), le(<=), gt(>), ge(>=), sa(starts after), and eb(ends before) \"prefixes\"\n",
    "response = get(base + '/Patient' + '?' + 'birthdate=eb1984' + '&_elements=birthDate')\n",
    "print('Born before 1984:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(resource.get('birthDate'))\n",
    "\n",
    "response = get(base + '/Patient' + '?' + 'birthdate=sa1984' + '&_elements=birthDate')\n",
    "print('\\n' + 'Born after 1984:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(resource.get('birthDate'))\n",
    "\n",
    "# some servers support ap(approximately equal) as well, although the spec lets the server decide exactly what that means...\n",
    "response = get(base + '/Patient' + '?' + 'birthdate=ap1984' + '&_elements=birthDate')\n",
    "print('\\n' + 'Born \"around\" 1984:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('id'), end=': ')\n",
    "    print(resource.get('birthDate'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Patients with a general-practitioner:   \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"0b24f3ee-94b9-4bde-8dd1-5a5479c3c53f\",\n",
      "    \"meta\": {\n",
      "        \"tag\": [\n",
      "            {\n",
      "                \"system\": \"http://terminology.hl7.org/CodeSystem/v3-ObservationValue\",\n",
      "                \"code\": \"SUBSETTED\",\n",
      "                \"display\": \"subsetted\"\n",
      "            }\n",
      "        ]\n",
      "    },\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 0,\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Reference search\n",
    "response = get(base + '/Patient?general-practitioner:missing=false&_elements=generalPractitioner,link,managingOrganization&_count=1')\n",
    "peek('Patients with a general-practitioner:   \\n' + response.text, 15)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"1200\"\n",
       "            height=\"480\"\n",
       "            src=\"https://hl7.org/fhir/condition.html#resource\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f3230ea73d0>"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# since our model doesn't have any reference fields on the Patient resources, lets look at Conditions instead\n",
    "IFrame('https://hl7.org/fhir/condition.html#resource', width=1200, height=480)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Conditions for patient 17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f:\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '10509002', 'display': 'Acute bronchitis (disorder)'}], 'text': 'Acute bronchitis (disorder)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '195662009', 'display': 'Acute viral pharyngitis (disorder)'}], 'text': 'Acute viral pharyngitis (disorder)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '68235000', 'display': 'Nasal congestion (finding)'}], 'text': 'Nasal congestion (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '267102003', 'display': 'Sore throat symptom (finding)'}], 'text': 'Sore throat symptom (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '248595008', 'display': 'Sputum finding (finding)'}], 'text': 'Sputum finding (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '84229001', 'display': 'Fatigue (finding)'}], 'text': 'Fatigue (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '267036007', 'display': 'Dyspnea (finding)'}], 'text': 'Dyspnea (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '56018004', 'display': 'Wheezing (finding)'}], 'text': 'Wheezing (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '43724002', 'display': 'Chill (finding)'}], 'text': 'Chill (finding)'}\n",
      "{'coding': [{'system': 'http://snomed.info/sct', 'code': '386661006', 'display': 'Fever (finding)'}], 'text': 'Fever (finding)'}\n",
      "\n",
      "Result entries match? True\n",
      "\n",
      "Result entries match? True\n"
     ]
    }
   ],
   "source": [
    "# get all conditions that reference a specific patient\n",
    "response = get(base + '/Condition' + '?' + 'subject=Patient/17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f' + '&_elements=code')\n",
    "print('Conditions for patient 17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f:')\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('code'))\n",
    "\n",
    "# when the type of the reference is fixed to a single value, it can be omitted (Patient/x -> x)\n",
    "response2 = get(base + '/Condition' + '?' + 'patient=17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f' + '&_elements=code')\n",
    "print('\\n' + 'Result entries match? ' + str(response.json().get('entry') == response2.json().get('entry')))\n",
    "\n",
    "# a reference to a resource's full url on the server should be equivalent to the relative reference format mentioned above\n",
    "response3 = get(base + '/Condition' + '?' + 'patient=' + base + '/Patient/17598beef3c-73a65dab-c8e5-4756-a60a-69bbc48cef4f' + '&_elements=code')\n",
    "print('\\n' + 'Result entries match? ' + str(response.json().get('entry') == response3.json().get('entry')))\n",
    "\n",
    "# references can also reference resources on other servers"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Section 4: Chaining and includes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Type II Diabetes in female patients:   \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"6824f74d-3375-489d-8204-e11448d6d959\",\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 600,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Condition?_count=1&code=http://snomed.info/sct%7C44054006&patient:Patient.gender=female&_page=1\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Condition?_count=1&code=http://snomed.info/sct%7C44054006&patient:Patient.gender=female&_page=2\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Condition/17598ca24de-8a64595d-1f7f-4a9d-af9b-9623bbd3db6d\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Condition\",\n",
      "                \"id\": \"17598ca24de-8a64595d-1f7f-4a9d-af9b-9623bbd3db6d\",\n",
      "                \"meta\": {\n",
      "                    \"versionId\": \"2\",\n",
      "                    \"lastUpdated\": \"2021-03-12T03:09:00.332Z\",\n",
      "                    \"profile\": [\n",
      "                        \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"\n",
      "                    ]\n",
      "                },\n",
      "                \"clinicalStatus\": {\n",
      "                    \"coding\": [\n",
      "                        {\n",
      "                            \"system\": \"http://terminology.hl7.org/CodeSystem/condition-clinical\",\n",
      "                            \"code\": \"active\"\n",
      "                        }\n",
      "                    ]\n",
      "                },\n",
      "                \"verificationStatus\": {\n",
      "                    \"coding\": [\n",
      "                        {\n",
      "                            \"system\": \"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\n",
      "                            \"code\": \"confirmed\"\n",
      "                        }\n",
      "                    ]\n",
      "                },\n",
      "                \"category\": [\n",
      "                    {\n",
      "                        \"coding\": [\n",
      "                            {\n",
      "                                \"system\": \"http://terminology.hl7.org/CodeSystem/condition-category\",\n",
      "                                \"code\": \"encounter-diagnosis\",\n",
      "                                \"display\": \"Encounter Diagnosis\"\n",
      "                            }\n",
      "                        ]\n",
      "                    }\n",
      "                ],\n",
      "                \"code\": {\n",
      "                    \"coding\": [\n",
      "                        {\n",
      "                            \"system\": \"http://snomed.info/sct\",\n",
      "                            \"code\": \"44054006\",\n",
      "                            \"display\": \"Diabetes\"\n",
      "                        }\n",
      "                    ],\n",
      "                    \"text\": \"Diabetes\"\n",
      "                },\n",
      "                \"subject\": {\n",
      "                    \"reference\": \"Patient/17598ca24dd-04a58485-e8ac-4b6d-b85f-de4f55bf0787\"\n",
      "                },\n",
      "                \"encounter\": {\n",
      "                    \"reference\": \"Encounter/17598ca24de-40d4ed3a-1b8a-4551-a89a-eca22e717f48\"\n",
      "                },\n",
      "                \"onsetDateTime\": \"2017-12-18T16:16:32-05:00\",\n",
      "                \"recordedDate\": \"2017-12-18T16:16:32-05:00\"\n",
      "            },\n",
      "            \"search\": {\n",
      "                \"mode\": \"match\",\n",
      "                \"score\": 1\n",
      "            }\n",
      "        }\n",
      "    ]\n",
      "}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Chaining\n",
    "\n",
    "# where reference parameters get really interesting is when you want to query one resource type based on a property of another resource to which its linked\n",
    "# for example, here is a search for Type II Diabetes in female patients\n",
    "response = get(base + '/Condition' + '?' + 'code=http://snomed.info/sct|44054006' + '&' + 'patient:Patient.gender=female' + '&_count=1')\n",
    "peek('Type II Diabetes in female patients:   \\n' + str(response.text), 100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Patients with Type II Diabetes:   \n",
      "{\n",
      "    \"resourceType\": \"Bundle\",\n",
      "    \"id\": \"b984c979-395c-455e-bc74-bda8718a87d1\",\n",
      "    \"type\": \"searchset\",\n",
      "    \"total\": 1063,\n",
      "    \"link\": [\n",
      "        {\n",
      "            \"relation\": \"self\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=1&_has:Condition:patient:code=http://snomed.info/sct%7C44054006&_page=1\"\n",
      "        },\n",
      "        {\n",
      "            \"relation\": \"next\",\n",
      "            \"url\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient?_count=1&_has:Condition:patient:code=http://snomed.info/sct%7C44054006&_page=2\"\n",
      "        }\n",
      "    ],\n",
      "    \"entry\": [\n",
      "        {\n",
      "            \"fullUrl\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/Patient/17598c0ea1f-f838725e-91e0-4a98-9eb6-f3e7323e9dfa\",\n",
      "            \"resource\": {\n",
      "                \"resourceType\": \"Patient\",\n",
      "                \"id\": \"17598c0ea1f-f838725e-91e0-4a98-9eb6-f3e7323e9dfa\",\n",
      "                \"meta\": {\n",
      "                    \"versionId\": \"4\",\n",
      "                    \"lastUpdated\": \"2021-03-12T03:09:46.128Z\",\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Reverse chaining\n",
    "\n",
    "# references can be searched the other way around via the \"_has\" parameter\n",
    "response = get(base + '/Patient' + '?' + '_has:Condition:patient:code=http://snomed.info/sct|44054006' + '&_count=1')\n",
    "peek('Patients with Type II Diabetes:   \\n' + response.text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Response contains both Conditions and Patients, but only the Conditions are counted in the page size and total:\n",
      "\n",
      "Total: 1063\n",
      "Condition: 17598c0ea20-7b251c64-b10a-4942-b72b-3014af79875f\n",
      "Condition: 17598c6d269-b8bd24cc-0280-48f8-a835-db262812387e\n",
      "Patient: 17598c0ea1f-f838725e-91e0-4a98-9eb6-f3e7323e9dfa\n",
      "Patient: 17598c6d269-6c393947-fbeb-44b7-9ec7-fbaede13bc8a\n"
     ]
    }
   ],
   "source": [
    "# Includes\n",
    "\n",
    "# its also possible to get a resource and its related resources back in a single query\n",
    "response = get(base + '/Condition?code=http://snomed.info/sct|44054006' + '&' + '_include=Condition:patient' + '&_count=2')\n",
    "peek('Response contains both Conditions and Patients, but only the Conditions are counted in the page size and total:')\n",
    "print('Total: ' + str(response.json().get('total')))\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('resourceType'), end=': ')\n",
    "    print(resource.get('id'))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Response contains both Patients and Conditions, but only the Patients are counted in the page size and total:\n",
      "\n",
      "Total: 17204\n",
      "Patient: 17598bf36c7-fedcedc3-b78c-4688-82ef-622e0cc71b22\n",
      "Patient: 17598bf4a5d-185e291b-d0e3-42d3-9b70-eeae60debeec\n",
      "Condition: 17598bf36c8-5800bd67-4c08-4a68-8968-054c670ef2a6\n",
      "Condition: 17598bf36c8-7d2861ad-e607-4122-90b3-74265240aaca\n",
      "Condition: 17598bf36c9-d53628c0-8fc4-4570-bb9a-25af21328712\n",
      "Condition: 17598bf36c9-9dec87f6-1a92-4b8a-b02a-ad1ab3dabd30\n",
      "Condition: 17598bf36c9-5c6f054a-eb02-4eac-ae3e-f02d3472b15c\n",
      "Condition: 17598bf36c9-4fb95111-885e-421f-8a5b-a9942a759020\n",
      "Condition: 17598bf36c9-a8f8bb3d-c403-4fb9-8f18-5a8c0cbe2b78\n",
      "Condition: 17598bf36c9-b1f1fc40-ef31-49b5-8579-4a45cca657b2\n",
      "Condition: 17598bf4a5e-b9e99052-25a6-4400-a8b8-da48b8cbb22d\n",
      "Condition: 17598bf4a65-ee99ca87-65c3-4a14-900f-02e90ec4db4a\n",
      "Condition: 17598bf4a66-49d7afde-a7f1-42e4-858d-990f49a2f1ca\n",
      "Condition: 17598bf4a66-39d8080e-27ee-488d-9e35-59275a486457\n",
      "Condition: 17598bf4a6f-b87ac7b6-6faf-49b5-95fd-3eddf4f7494c\n",
      "Condition: 17598bf4a6f-ec9abd6f-ee59-4f71-8fa5-c737ac1be63b\n",
      "Condition: 17598bf4a70-b98f87d7-d469-4b3d-987e-02b78336b82e\n",
      "Condition: 17598bf4a70-6e7537b4-1a90-4a3c-842c-6c5c1db45ad3\n",
      "Condition: 17598bf4a70-ca048f40-02a3-4c24-a1b6-f53ffb3c1667\n"
     ]
    }
   ],
   "source": [
    "# Reverse Includes\n",
    "\n",
    "response = get(base + '/Patient?gender=female' + '&' + '_revinclude=Condition:patient' + '&_count=2')\n",
    "peek('Response contains both Patients and Conditions, but only the Patients are counted in the page size and total:')\n",
    "print('Total: ' + str(response.json().get('total')))\n",
    "for entry in response.json().get('entry'):\n",
    "    resource = entry.get('resource')\n",
    "    print(resource.get('resourceType'), end=': ')\n",
    "    print(resource.get('id'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Section 5: Putting it together"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Patients with Type II Diabetes:  1063\n"
     ]
    }
   ],
   "source": [
    "response = get(base + '/Condition' + '?' + 'code=http://snomed.info/sct|44054006' + '&_count=1')\n",
    "print('Patients with Type II Diabetes:  ' + str(response.json().get('total')))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CHD: \t\t\t1059\n",
      "CKD: \t\t\t0\n",
      "AFib: \t\t\t359\n",
      "stroke: \t\t1008\n",
      "hypertension: \t\t0\n",
      "heart failure: \t\t84\n",
      "PVD: \t\t\t0\n",
      "arthritis: \t\t48\n",
      "cancer: \t\t0\n",
      "osteoporosis: \t\t762\n",
      "depression: \t\t0\n",
      "asthma: \t\t24\n",
      "COPD: \t\t\t0\n",
      "dementia: \t\t0\n",
      "SMI: \t\t\t0\n",
      "epilepsy: \t\t546\n",
      "hypothyroidism: \t0\n",
      "learning disability: \t0\n"
     ]
    }
   ],
   "source": [
    "# SNOMED concepts for comorbidities of Type II Diabetes\n",
    "#coronary heart disease (CHD), 53741008\n",
    "#chronic kidney disease (CKD), 709044004\n",
    "#atrial fibrillation, 49436004\n",
    "#stroke, 230690007\n",
    "#hypertension, 38341003\n",
    "#heart failure, 84114007\n",
    "#peripheral vascular disease (PVD), 400047006\n",
    "#rheumatoid arthritis, 69896004\n",
    "#Malignant neoplasm, primary (morphologic abnormality), 86049000\n",
    "#Malignant neoplastic disease (disorder), 363346000\n",
    "#osteoporosis, 64859006\n",
    "#depression, 35489007\n",
    "#asthma, 195967001\n",
    "#chronic obstructive pulmonary disease (COPD), 13645005\n",
    "#dementia, 52448006\n",
    "#severe mental illness (SMI), 391193001\n",
    "#epilepsy, 84757009\n",
    "#hypothyroidism, 40930008\n",
    "#learning disability, 1855002\n",
    "\n",
    "print('CHD: \\t\\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '53741008').json().get('total')))\n",
    "print('CKD: \\t\\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '709044004').json().get('total')))\n",
    "print('AFib: \\t\\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '49436004').json().get('total')))\n",
    "print('stroke: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '230690007').json().get('total')))\n",
    "print('hypertension: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '38341003').json().get('total')))\n",
    "print('heart failure: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '84114007').json().get('total')))\n",
    "print('PVD: \\t\\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '400047006').json().get('total')))\n",
    "print('arthritis: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '69896004').json().get('total')))\n",
    "print('cancer: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '86049000').json().get('total') + get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '363346000').json().get('total')))\n",
    "print('osteoporosis: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '64859006').json().get('total')))\n",
    "print('depression: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '35489007').json().get('total')))\n",
    "print('asthma: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '195967001').json().get('total')))\n",
    "print('COPD: \\t\\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '13645005').json().get('total')))\n",
    "print('dementia: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '52448006').json().get('total')))\n",
    "print('SMI: \\t\\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '391193001').json().get('total')))\n",
    "print('epilepsy: \\t\\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '84757009').json().get('total')))\n",
    "print('hypothyroidism: \\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '40930008').json().get('total')))\n",
    "print('learning disability: \\t' + str(get(base + '/Condition?_summary=count&code=http://snomed.info/sct|' + '1855002').json().get('total')))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CHD:\n",
      "Total: 30\n",
      "1759a06f11a-77b7ee76-ae8d-47a8-9a8e-17e7278e4137, 1759bccd5dc-a4192660-b224-4d88-acf6-bfb538fc0052, 1759c042626-da786c63-fcd4-4a86-aaec-54ec28458861, 1759c7179ab-cdc927fb-ec72-4c10-961e-a424bb8241f3, 1759c906bce-6fcc151d-240e-441f-aa3f-3a8123222d0c, 1759c9d0e32-10946dda-2ac9-4f8e-a6ba-eade9aba6ac8, 175b90993dc-7568b0d3-91ce-4862-be00-7cb99389f323, 175ba73ffc5-86182577-c52f-4c24-b09c-acfdc0043b8c, 175babfca99-31bcaafc-876a-453a-905c-b0482607b2c5, 175bb745e4f-1f3f83a8-6f6c-43da-adf1-fdc5440d88b5, \n",
      "\n",
      "AFib:\n",
      "Total: 23\n",
      "1759b62a9bc-650fc722-8bb1-4a81-827c-95b73a83d7b4, 1759be696c1-fd6cfa13-8e69-454f-ad73-d3b27a051f6f, 1759c1d61ec-500b2890-fcc9-428c-86c2-bcb15a5cbaa5, 1759c4dfa60-d50fbfcb-dda0-4669-82c8-42e73c5bb239, 1759c76bdcd-dfc226a9-37b6-4a72-b303-1613ed7ec838, 175b9f4c2a0-e971ee19-f55e-4319-85bd-57737b23ba26, 175ba948672-bc9ba458-81df-4def-8064-da02406e9f62, 175ba9518ee-29c6291a-ae29-4c62-8283-6c5a1264c404, 175ba9ca813-0a7f0565-f701-4c66-9d11-7b2754dddf6d, 175baa492a2-c7306451-8ede-4d55-9a21-2da3932f036c, \n",
      "\n",
      "stroke:\n",
      "Total: 36\n",
      "175998f05f8-29eebaa9-2179-4d7b-9603-ca9c7cf25e23, 1759b62a9bc-650fc722-8bb1-4a81-827c-95b73a83d7b4, 1759b7179b6-d3d28532-15b8-41db-8781-fbde5c781fab, 1759b91f0bf-5a8bf1c3-7aa4-4d8b-a4d3-83d5097f18c4, 1759bcaf1a7-188d7217-1e1d-4664-bc7a-e07bc658539d, 1759c048c78-1e94db2f-f936-4a12-b427-a89667db2ee8, 1759c363589-398bc35f-8c6c-41f7-8840-572e653a30e5, 1759c3a8255-0131fdfe-0db6-47e3-9cb9-d770efee0012, 1759c4dfa60-d50fbfcb-dda0-4669-82c8-42e73c5bb239, 1759c51e871-214856d2-a5be-47ca-99a7-e9b43b21dc26, \n",
      "\n",
      "heart failure:\n",
      "Total: 5\n",
      "1759b62a9bc-650fc722-8bb1-4a81-827c-95b73a83d7b4, 175b9f4c2a0-e971ee19-f55e-4319-85bd-57737b23ba26, 175c0fd9b65-022a8b08-76b1-481e-bef9-82866c621bd9, 175c1151cca-345c1f27-af3e-403f-8aad-42be1a128b73, 175c2e6aa49-7a8d5bae-e376-41fc-8d51-659148290cbe, \n",
      "\n",
      "arthritis:\n",
      "Total: 0\n",
      "\n",
      "\n",
      "osteoporosis:\n",
      "Total: 25\n",
      "175998be983-6278fae0-a059-467f-8637-3cbff69d9b4e, 1759b7afa3c-e89ecf98-c0b2-4e69-866b-ef6e89f6fba0, 1759bfa2d15-72ddae5b-292a-40f5-8558-8c062211dd42, 1759c0c9587-ab5bdbf5-56e3-4328-b347-089d17ea59b8, 1759c14d16a-fa7ed5df-d034-4b8c-bc74-296cc4b32c31, 1759c51e871-214856d2-a5be-47ca-99a7-e9b43b21dc26, 1759c64e1fd-de32b308-29ab-4a04-8850-564e574b20fd, 1759c685bbc-bff3331b-d71e-4987-8246-657b653a77c2, 175b98dc155-70c909ff-7125-414d-beff-ff17bd202c40, 175ba10c839-3767563a-d7f3-4dbd-88a4-cf54a587d310, \n",
      "\n",
      "asthma:\n",
      "Total: 1\n",
      "175c2b7c38a-61ab893b-7b40-45ae-9955-6f26107de9cc, \n",
      "\n",
      "epilepsy:\n",
      "Total: 8\n",
      "1759ba18cd9-617df281-8a07-4a25-919d-d320d53f4da2, 1759c181967-bd8686d0-bcf5-475c-932d-e41f1f3769bc, 175ba3d7afe-c2a50287-ebb2-48b0-90f8-3654e28244c1, 175bae212ec-e15e067c-7a7a-4d60-9635-213cdfcae928, 175bae68708-0423d3ed-55d0-4f64-ac98-717649009b04, 175c0c66c0a-f500462c-e568-47ac-ad35-045a11eb8b8f, 175c15e0a00-c2dcdc18-a2f6-4cd1-b9f4-e78a940e8064, 175c2ac659d-cc743967-f254-43bb-b345-17a5282088fe, \n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Patients with Type II Diabetes *and* comorbidities\n",
    "hasDiabetes = base + '/Patient?_elements=id&_has:Condition:patient:code=http://snomed.info/sct|44054006'\n",
    "\n",
    "def printPatientsWithComorbidity(conceptId):\n",
    "    responseJSON = get(hasDiabetes + '&_has:Condition:patient:code=http://snomed.info/sct|' + conceptId).json()\n",
    "    print('Total: ' + str(responseJSON.get('total')))\n",
    "    if 'entry' in responseJSON:\n",
    "        for entry in responseJSON.get('entry'):\n",
    "            print(entry.get('resource').get('id'), end=\", \")\n",
    "    print('\\n')\n",
    "\n",
    "print('CHD:')\n",
    "printPatientsWithComorbidity('53741008')\n",
    "\n",
    "print('AFib:')\n",
    "printPatientsWithComorbidity('49436004')\n",
    "\n",
    "print('stroke:')\n",
    "printPatientsWithComorbidity('230690007')\n",
    "\n",
    "print('heart failure:')\n",
    "printPatientsWithComorbidity('84114007')\n",
    "\n",
    "print('arthritis:')\n",
    "printPatientsWithComorbidity('69896004')\n",
    "\n",
    "print('osteoporosis:')\n",
    "printPatientsWithComorbidity('64859006')\n",
    "\n",
    "print('asthma:')\n",
    "printPatientsWithComorbidity('195967001')\n",
    "\n",
    "print('epilepsy:')\n",
    "printPatientsWithComorbidity('84757009')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Section 6: Bulk export"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Response code: 202\n",
      "{'Date': 'Wed, 05 May 2021 18:12:57 GMT', 'Content-Length': '0', 'Connection': 'keep-alive', 'Content-Location': 'https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/$bulkdata-status?job=060hzfxJyNUqyFck7t7tpg', 'Content-Language': 'en-US', 'Strict-Transport-Security': 'max-age=86400; includeSubDomains'}\n"
     ]
    }
   ],
   "source": [
    "# To perform deeper analysis of the data, it can be useful to export some or all of the data into \"bulk fhir\" format\n",
    "export_response = get(base + '/$export' + '?' + '_type=Patient,Condition')\n",
    "print('Response code: ' + str(export_response.status_code))\n",
    "print(export_response.headers)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Response code: 202\n",
      "Response code: 200\n",
      "Response body: \n",
      "{\n",
      "    \"transactionTime\": \"2021-05-05T18:13:26.251Z\",\n",
      "    \"request\": \"https://cluster1-573846-250babbbe4c3000e15508cd07c1d282b-0000.us-east.containers.appdomain.cloud/open/$export?_type=Patient,Condition\",\n",
      "    \"requiresAccessToken\": false,\n",
      "    \"output\": [\n",
      "        {\n",
      "            \"type\": \"Patient\",\n",
      "            \"url\": \"https://s3.us-east.cloud-object-storage.appdomain.cloud/fhir-export-2fbaaea5-68b5-4775-8a40-c1eb3c4f12d5/rjEjBkGMmlfuzFJjtMOk6Z2eF-GMLPaFXll9lxVLaPE/Patient_1.ndjson?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=972a2cff12b94328b3f020c1a8e14e9b%2F20210505%2Fus-east%2Fs3%2Faws4_request&X-Amz-Date=20210505T181328Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=a2528b4d1647ce8bfa1369a9843983f423962368487f2eb1e35d2497a16b8571\",\n",
      "            \"count\": 32655\n",
      "        },\n",
      "        {\n",
      "            \"type\": \"Condition\",\n",
      "            \"url\": \"https://s3.us-east.cloud-object-storage.appdomain.cloud/fhir-export-2fbaaea5-68b5-4775-8a40-c1eb3c4f12d5/rjEjBkGMmlfuzFJjtMOk6Z2eF-GMLPaFXll9lxVLaPE/Condition_1.ndjson?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=972a2cff12b94328b3f020c1a8e14e9b%2F20210505%2Fus-east%2Fs3%2Faws4_request&X-Amz-Date=20210505T181328Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=3d56444e07212c39008fbe8399d26abeeb839176d3a7208b57314b1f3d55e7a8\",\n",
      "            \"count\": 197224\n",
      "        },\n",
      "        {\n",
      "            \"type\": \"Condition\",\n",
      "            \"url\": \"https://s3.us-east.cloud-object-storage.appdomain.cloud/fhir-export-2fbaaea5-68b5-4775-8a40-c1eb3c4f12d5/rjEjBkGMmlfuzFJjtMOk6Z2eF-GMLPaFXll9lxVLaPE/Condition_2.ndjson?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=972a2cff12b94328b3f020c1a8e14e9b%2F20210505%2Fus-east%2Fs3%2Faws4_request&X-Amz-Date=20210505T181328Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=2bef855c1ace93d533f694df588bb45a5b66531ee225502cb1acc90a55712283\",\n",
      "            \"count\": 163153\n",
      "        }\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "import time\n",
    "\n",
    "# poll the status endpoint (returned in the Content-Location header of the $export response)\n",
    "status_response = get(export_response.headers['Content-Location'])\n",
    "print('Response code: ' + str(status_response.status_code))\n",
    "\n",
    "while(status_response.status_code != 200):\n",
    "    time.sleep(20)\n",
    "    status_response = get(export_response.headers['Content-Location'])\n",
    "    print('Response code: ' + str(status_response.status_code))\n",
    "    \n",
    "print('Response body: ' + str(status_response.text))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "{\"resourceType\":\"Condition\",\"id\":\"1759925ccc0-9c57a4a7-afeb-4921-aa48-004861296c0f\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:03:20.869Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"resolved\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"444814009\",\"display\":\"Viral sinusitis (disorder)\"}],\"text\":\"Viral sinusitis (disorder)\"},\"subject\":{\"reference\":\"Patient/1759925ccbf-6adbc8f2-0ee8-4bd3-b57a-9bc4dcf55ee8\"},\"encounter\":{\"reference\":\"Encounter/1759925ccc0-02d7382f-c6d3-4e21-8dfe-7c6627b0b3a6\"},\"onsetDateTime\":\"2017-12-09T23:35:59-05:00\",\"abatementDateTime\":\"2017-12-23T23:35:59-05:00\",\"recordedDate\":\"2017-12-09T23:35:59-05:00\"}\n",
      "{\"resourceType\":\"Condition\",\"id\":\"175992c73bf-ee56bd69-92a1-4490-91f0-e3d8fcc07cd9\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:10:33.461Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"resolved\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"386661006\",\"display\":\"Fever (finding)\"}],\"text\":\"Fever (finding)\"},\"subject\":{\"reference\":\"Patient/175992c73be-5fb46052-093a-44d1-ad04-55f0488d4390\"},\"encounter\":{\"reference\":\"Encounter/175992c73bf-ffd404eb-197d-4791-bb85-e90ae6be0e64\"},\"onsetDateTime\":\"2020-03-06T06:55:23-05:00\",\"abatementDateTime\":\"2020-03-28T09:12:23-04:00\",\"recordedDate\":\"2020-03-06T06:55:23-05:00\"}\n",
      "{\"resourceType\":\"Condition\",\"id\":\"17599325f8f-ecb82619-ba37-420d-b5ce-257dbce2177d\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:16:59.868Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"resolved\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"36955009\",\"display\":\"Loss of taste (finding)\"}],\"text\":\"Loss of taste (finding)\"},\"subject\":{\"reference\":\"Patient/17599325f8f-2eb4384f-bbb4-4f88-80fa-e478d2d4b116\"},\"encounter\":{\"reference\":\"Encounter/17599325f8f-cd773def-fb3e-4460-835f-e63d528d7327\"},\"onsetDateTime\":\"2020-03-09T00:41:00-04:00\",\"abatementDateTime\":\"2020-04-14T02:06:00-04:00\",\"recordedDate\":\"2020-03-09T00:41:00-04:00\"}\n",
      "{\"resourceType\":\"Condition\",\"id\":\"175993848db-f26f11f8-855f-4c23-941c-23eef2f3e6cf\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:23:35.161Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"active\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"36955009\",\"display\":\"Loss of taste (finding)\"}],\"text\":\"Loss of taste (finding)\"},\"subject\":{\"reference\":\"Patient/175993848d9-90779ddf-a0c4-4052-8051-1c7bc1581add\"},\"encounter\":{\"reference\":\"Encounter/175993848db-a5362f40-ee21-41f6-8413-0c7d58875cf8\"},\"onsetDateTime\":\"2020-03-06T14:40:01-05:00\",\"recordedDate\":\"2020-03-06T14:40:01-05:00\"}\n",
      "{\"resourceType\":\"Condition\",\"id\":\"175993e337e-9c6dcc25-7f46-4b9b-9739-9630d8a5a265\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:29:53.501Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"resolved\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"16114001\",\"display\":\"Fracture of ankle\"}],\"text\":\"Fracture of ankle\"},\"subject\":{\"reference\":\"Patient/175993e337e-57854f5d-6b14-46ba-b6fa-2a2cd7e1fa23\"},\"encounter\":{\"reference\":\"Encounter/175993e337e-bd75e82c-ce79-4a93-9ef2-69c7ac952985\"},\"onsetDateTime\":\"2013-03-30T21:49:05-04:00\",\"abatementDateTime\":\"2013-05-29T22:27:05-04:00\",\"recordedDate\":\"2013-03-30T21:49:05-04:00\"}\n",
      "{\"resourceType\":\"Condition\",\"id\":\"1759944ebac-b92fdc8d-0849-48ff-93b9-7010774fe889\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:37:20.091Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"active\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"40055000\",\"display\":\"Chronic sinusitis (disorder)\"}],\"text\":\"Chronic sinusitis (disorder)\"},\"subject\":{\"reference\":\"Patient/1759944ebab-22fa6c7e-dc9f-49ec-897f-c8300a988d57\"},\"encounter\":{\"reference\":\"Encounter/1759944ebac-58caa8bb-1c81-4e4f-80e6-05ffb30ea358\"},\"onsetDateTime\":\"2017-08-15T08:41:05-04:00\",\"recordedDate\":\"2017-08-15T08:41:05-04:00\"}\n",
      "{\"resourceType\":\"Condition\",\"id\":\"175994b17ae-a55091ab-ec13-44f4-b129-7a9e8784f2f8\",\"meta\":{\"versionId\":\"1\",\"lastUpdated\":\"2020-11-05T16:43:56.779Z\",\"profile\":[\"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"active\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\"}]},\"category\":[{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-category\",\"code\":\"encounter-diagnosis\",\"display\":\"Encounter Diagnosis\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"19169002\",\"display\":\"Miscarriage in first trimester\"}],\"text\":\"Miscarriage in first trimester\"},\"subject\":{\"reference\":\"Patient/175994b17ae-428989d4-e791-4525-b95b-b39a058b0ecc\"},\"encounter\":{\"reference\":\"Encounter/175994b17ae-5a8f7850-e8c5-4820-b67c-cda707544e4c\"},\"onsetDateTime\":\"1992-06-07T15:12:53-04:00\",\"recordedDate\":\"1992-06-07T15:12:53-04:00\"}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# retrieve one of the NDJSON files and view the first 25 rows\n",
    "ndjson = get(status_response.json().get('output')[1].get('url'))\n",
    "peek(ndjson.text)"
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