AllergyIntolerance Resource & GET methods FHIR (openemr#3334)

* Implemented Post and Put for FHIR

* Update _rest_routes.inc.php

* Added routes for Patient Put & Post

* Search by address, phone, gender

* Psr2 fixes

* Psr2 fixes

* Psr2 again

* Organization resource with getAll function

* Psr2 fixes

* Updated naming conventions

* Psr2 fixes

* AllergyIntolerance Resource with GET methods

* Small fixes

* small fix

* some fixes

* Few Fixes

* Small fixes

_rest_routes.inc.php

@@ -337,6 +337,7 @@
 
 );
 
+use OpenEMR\RestControllers\FHIR\FhirAllergyIntoleranceRestController;
 use OpenEMR\RestControllers\FHIR\FhirPatientRestController;
 use OpenEMR\RestControllers\FHIR\FhirEncounterRestController;
 use OpenEMR\RestControllers\FHIR\FhirOrganizationRestController;
@@ -384,6 +385,14 @@
  "GET /fhir/Organization/:oid" => function ($oid) {
  return (new FhirOrganizationRestController(null))->getOne($oid);
  },
+ "GET /fhir/AllergyIntolerance" => function () {
+ RestConfig::authorization_check("patients", "med");
+ return (new FhirAllergyIntoleranceRestController(null))->getAll($_GET);
+ },
+ "GET /fhir/AllergyIntolerance/:id" => function ($id) {
+ RestConfig::authorization_check("patients", "med");
+ return (new FhirAllergyIntoleranceRestController(null))->getOne($id);
+ },
  "POST /fhir/QuestionnaireResponse" => function () {
  RestConfig::authorization_check("patients", "demo");
  $data = (array)(json_decode(file_get_contents("php:https://input"), true));

src/RestControllers/FHIR/FhirAllergyIntoleranceRestController.php

@@ -0,0 +1,69 @@
+<?php
+
+namespace OpenEMR\RestControllers\FHIR;
+
+use OpenEMR\Services\FHIR\FhirAllergyIntoleranceService;
+use OpenEMR\Services\FHIR\FhirResourcesService;
+use OpenEMR\RestControllers\RestControllerHelper;
+use OpenEMR\FHIR\R4\FHIRResource\FHIRBundle\FHIRBundleEntry;
+
+class FhirAllergyIntoleranceRestController
+{
+ private $fhirAllergyIntoleranceService;
+ private $fhirService;
+
+ public function __construct($id)
+ {
+ $this->fhirAllergyIntoleranceService = new FhirAllergyIntoleranceService();
+ $this->fhirAllergyIntoleranceService->setId($id);
+ $this->fhirService = new FhirResourcesService();
+ }
+
+ public function getAll($search)
+ {
+ $result = $this->fhirAllergyIntoleranceService->getAll(array('patient' => $search['patient']));
+ if ($result === false) {
+ http_response_code(404);
+ exit;
+ }
+ $entries = array();
+ $resourceURL = \RestConfig::$REST_FULL_URL;
+ foreach ($result as $allergy) {
+ $entryResource = $this->fhirAllergyIntoleranceService->createAllergyIntoleranceResource(
+ $allergy['id'],
+ $allergy,
+ false
+ );
+ $entry = array(
+ 'fullUrl' => $resourceURL . "/" . $allergy['id'],
+ 'resource' => $entryResource
+ );
+ $entries[] = new FHIRBundleEntry($entry);
+ }
+ $result = $this->fhirService->createBundle('AllergyIntolerance', $entries, false);
+ return RestControllerHelper::responseHandler($result, null, 200);
+ }
+
+ public function getOne($id)
+ {
+ $result = $this->fhirAllergyIntoleranceService->getOne($id);
+ if ($result) {
+ $resource = $this->fhirAllergyIntoleranceService->createAllergyIntoleranceResource(
+ $result['id'],
+ $result,
+ false
+ );
+ $statusCode = 200;
+ } else {
+ $statusCode = 404;
+ $resource = $this->fhirValidate->operationOutcomeResourceService(
+ 'error',
+ 'invalid',
+ false,
+ "Resource Id $id does not exist"
+ );
+ }
+
+ return RestControllerHelper::responseHandler($resource, null, $statusCode);
+ }
+}

src/Services/FHIR/FhirAllergyIntoleranceService.php

@@ -0,0 +1,223 @@
+<?php
+
+namespace OpenEMR\Services\FHIR;
+
+use OpenEMR\FHIR\R4\FHIRDomainResource\FHIRAllergyIntolerance;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRAllergyIntoleranceCategory;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRAllergyIntoleranceCriticality;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRAllergyIntoleranceType;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRAnnotation;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRCodeableConcept;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRCoding;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRDateTime;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRId;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRMeta;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRReference;
+use OpenEMR\FHIR\R4\FHIRElement\FHIRUrl;
+use OpenEMR\FHIR\R4\FHIRResource\FHIRAllergyIntolerance\FHIRAllergyIntoleranceReaction;
+use OpenEMR\FHIR\R4\FHIRResource\FHIRBundle;
+use OpenEMR\FHIR\R4\FHIRResource\FHIRBundle\FHIRBundleLink;
+use OpenEMR\FHIR\R4\PHPFHIRResponseParser;
+use OpenEMR\Services\ListService;
+
+class FhirAllergyIntoleranceService
+{
+
+ private $id;
+
+ public function __construct()
+ {
+ }
+
+ public function setId($id)
+ {
+ $this->id = $id;
+ }
+
+ public function getAll($search)
+ { 
+ $SQL = "SELECT id,
+ date as recorded_date,
+ type,
+ subtype,
+ title,
+ begdate,
+ enddate,
+ returndate,
+ referredby,
+ extrainfo,
+ diagnosis,
+ pid,
+ outcome,
+ reaction,
+ severity_al
+ FROM lists
+ WHERE type = 'allergy'";
+
+ if (isset($search['patient']))
+ $SQL .= " AND pid = ?;";
+
+ $allergyIntolerenceresults = sqlStatement($SQL, $search['patient']);
+ $results = array();
+ while ($row = sqlFetchArray($allergyIntolerenceresults)) {
+ $codeSQL = "SELECT dx_code 
+ FROM icd10_dx_order_code
+ WHERE short_desc = ?;";
+ $code = sqlQuery($codeSQL, array($row['reaction']));
+ $row['code'] = $code['dx_code'];
+ array_push($results, $row);
+ }
+ return $results;
+ }
+
+ public function getOne($id)
+ {
+ $SQL = "SELECT id,
+ date as recorded_date,
+ type,
+ subtype,
+ title,
+ begdate,
+ enddate,
+ returndate,
+ referredby,
+ extrainfo,
+ diagnosis,
+ pid,
+ outcome,
+ reaction,
+ severity_al
+ FROM lists
+ WHERE type = 'allergy'
+ AND id = ?;";
+
+ $sqlResult = sqlStatement($SQL, $id);
+ $result = sqlFetchArray($sqlResult);
+ $codeSQL = "SELECT dx_code
+ FROM icd10_dx_order_code
+ WHERE short_desc = ?;";
+
+ $code = sqlQuery($codeSQL, array($result['reaction']));
+ $result['code'] = $code['dx_code'];
+ return $result; 
+ }
+
+ public function createAllergyIntoleranceResource($id = '', $data = '', $encode = true)
+ { 
+ $typeCoding = new FHIRCoding();
+ $typeCoding->setSystem("http:https://terminology.hl7.org/CodeSystem/allergyintolerance-clinical");
+ $typeCoding->setCode($data['type']);
+ $typeCoding->setDisplay(ucwords($data['type']));
+ $type = new FHIRAllergyIntoleranceType();
+ $type->setValue($typeCoding);
+
+ $onSetDateTime = new FHIRDateTime();
+ $onSetDateTime->setValue($data['begdate']);
+
+ $recordedDate = new FHIRDateTime();
+ $recordedDate->setValue($data['recorded_date']);
+
+ $clinicalStatus = '';
+ if ($data['outcome'] == '1' && isset($data['enddate']))
+ $clinicalStatus = "resolved";
+ else if (!isset($data['enddate'])) 
+ $clinicalStatus = "active";
+ else
+ $clinicalStatus = "inactive";
+ $clinicalStatusCoding = new FHIRCoding();
+ $clinicalStatusCoding->setSystem("http:https://terminology.hl7.org/CodeSystem/allergyintolerance-clinical");
+ $clinicalStatusCoding->setCode($clinicalStatus);
+ $clinicalStatusCoding->setDisplay($clinicalStatus);
+
+ $categoryCoding = new FHIRCoding();
+ $categoryCoding->setSystem("http:https://hl7.org/fhir/allergy-intolerance-category");
+ $categoryCoding->setCode("medication");
+ $categoryCoding->setDisplay("Medication");
+ $category = new FHIRAllergyIntoleranceCategory();
+ $category->setValue($categoryCoding);
+
+ $criticalityCoding = new FHIRCoding();
+ $criticality = new FHIRAllergyIntoleranceCriticality();
+ if (isset($data['severity_al'])) {
+ $severityToCriticalityCode = array(
+ "mild" => "low",
+ "moderate" => "high",
+ "severe" => "unable-to-assess"
+ );
+ $severityToCriticalityDisplay = array(
+ "mild" => "Low Risk",
+ "moderate" => "High Risk",
+ "severe" => "Unable to Assess Risk"
+ );
+ $criticalityCoding->setSystem("http:https://hl7.org/fhir/allergy-intolerance-criticality");
+ $criticalityCoding->setCode($severityToCriticalityCode[strtolower($data['severity_al'])]);
+ $criticalityCoding->setDisplay($severityToCriticalityDisplay[strtolower($data['severity_al'])]); 
+ $criticality->setValue($criticalityCoding);
+ }
+ else {
+ $criticalityCoding->setSystem("http:https://terminology.hl7.org/CodeSystem/data-absent-reason");
+ $criticalityCoding->setCode("unknown");
+ $criticalityCoding->setDisplay("Unknown"); 
+ $criticality->setValue($criticalityCoding);
+ }
+
+ $patient = new FHIRReference();
+ $patient->setReference('Patient/'.$data['pid']);
+
+ $recorder = new FHIRReference();
+ $recorder->setReference('Practitioner/'.$data['referredby']);
+
+ $asserter = new FHIRReference();
+ $asserter->setReference('Patient/'.$data['pid']);
+
+ $note = new FHIRAnnotation();
+ $note->setText($data['extrainfo']);
+
+ $lastOccurrence = new FHIRDateTime();
+ $lastOccurrence->setValue($data['returndate']);
+
+ $manifestation = new FHIRCoding();
+ $manifestation->setSystem("http:https://hl7.org/fhir/sid/icd-10-cm");
+ $manifestation->setCode($data['code']);
+ $manifestation->setDisplay($data['reaction']);
+
+ $description = $data['comments'];
+
+ $reaction = new FHIRAllergyIntoleranceReaction();
+ $reaction->addManifestation($manifestation->jsonSerialize());
+ $reaction->setDescription($description);
+ $reaction->setOnset($data['begdate']);
+ $severityCoding = new FHIRCoding();
+ if (isset($data['severity_al'])) {
+ $severityCoding->setSystem("http:https://hl7.org/fhir/reaction-event-severity");
+ $severityCoding->setCode($data['severity_al']);
+ $severityCoding->setDisplay(ucwords($data['severity_al'])); 
+ $reaction->setSeverity($severityCoding);
+ }
+ else {
+ $severityCoding->setSystem("http:https://terminology.hl7.org/CodeSystem/data-absent-reason");
+ $severityCoding->setCode("unknown");
+ $severityCoding->setDisplay("Unknown"); 
+ $reaction->setSeverity($severityCoding);
+ }
+
+ $resource = new FHIRAllergyIntolerance();
+ $resource->setClinicalStatus($clinicalStatusCoding);
+ $resource->setType($type);
+ $resource->addCategory($category);
+ $resource->setOnsetDateTime($onSetDateTime);
+ $resource->setRecordedDate($recordedDate);
+ $resource->setCriticality($criticality);
+ $resource->setPatient($patient);
+ $resource->setRecorder($recorder);
+ $resource->setAsserter($asserter);
+ $resource->setLastOccurrence($lastOccurrence);
+ $resource->addNote($note);
+ $resource->addReaction($reaction);
+ if ($encode) {
+ return json_encode($resource);
+ } else {
+ return $resource;
+ }
+ }
+}