src/Services/FHIR/Observation/FhirObservationVitalsService.php

   1 <?php
   2
   3 /**
   4  * FhirObservationVitalsService.php
   5  * @package openemr
   6  * @link      http://www.open-emr.org
   7  * @author    Stephen Nielson <stephen@nielson.org>
   8  * @copyright Copyright (c) 2021 Stephen Nielson <stephen@nielson.org>
   9  * @license   https://github.com/openemr/openemr/blob/master/LICENSE GNU General Public License 3
  10  */
  11
  12 namespace OpenEMR\Services\FHIR\Observation;
  13
  14 use OpenEMR\Common\Logging\SystemLogger;
  15 use OpenEMR\Common\Uuid\UuidMapping;
  16 use OpenEMR\Common\Uuid\UuidRegistry;
  17 use OpenEMR\FHIR\R4\FHIRDomainResource\FHIRObservation;
  18 use OpenEMR\FHIR\R4\FHIRElement\FHIRCodeableConcept;
  19 use OpenEMR\FHIR\R4\FHIRElement\FHIRCoding;
  20 use OpenEMR\FHIR\R4\FHIRElement\FHIRId;
  21 use OpenEMR\FHIR\R4\FHIRElement\FHIRMeta;
  22 use OpenEMR\FHIR\R4\FHIRElement\FHIRQuantity;
  23 use OpenEMR\FHIR\R4\FHIRResource\FHIRObservation\FHIRObservationComponent;
  24 use OpenEMR\Services\FHIR\FhirCodeSystemConstants;
  25 use OpenEMR\Services\FHIR\FhirProvenanceService;
  26 use OpenEMR\Services\FHIR\FhirServiceBase;
  27 use OpenEMR\Services\FHIR\IPatientCompartmentResourceService;
  28 use OpenEMR\Services\FHIR\UtilsService;
  29 use OpenEMR\Services\Search\FhirSearchParameterDefinition;
  30 use OpenEMR\Services\Search\SearchFieldException;
  31 use OpenEMR\Services\Search\SearchFieldType;
  32 use OpenEMR\Services\Search\ServiceField;
  33 use OpenEMR\Services\Search\TokenSearchField;
  34 use OpenEMR\Services\VitalsService;
  35 use OpenEMR\Validators\ProcessingResult;
  36
  37 class FhirObservationVitalsService extends FhirServiceBase implements IPatientCompartmentResourceService
  38 {
  39     // we set this to be 'Final' which has the follow interpretation
  40     // 'The observation is complete and there are no further actions needed.'
  41     // @see http://hl7.org/fhir/R4/valueset-observation-status.html
  42     const VITALS_DEFAULT_OBSERVATION_STATUS = "final";
  43
  44     const VITALS_PANEL_LOINC_CODE = '85353-1';
  45     /**
  46      * @var VitalsService
  47      */
  48     private $service;
  49
  50     const CATEGORY = "vital-signs";
  51
  52     const COLUMN_MAPPINGS = [
  53         // @see http://hl7.org/fhir/R4/observation-vitalsigns.html
  54         self::VITALS_PANEL_LOINC_CODE => [
  55             // this code contains a lot of the other vital sign codes and is treated specially in this service.
  56             'fullcode' => 'LOINC:' . self::VITALS_PANEL_LOINC_CODE
  57             ,'code' => self::VITALS_PANEL_LOINC_CODE
  58             ,'description' => 'Vital signs, weight, height, head circumference, oxygen saturation and BMI panel'
  59             ,'column' => ''
  60             ,'in_vitals_panel' => false
  61         ],
  62         '9279-1' => [
  63             'fullcode' => 'LOINC:9279-1'
  64             ,'code' => '9279-1'
  65             ,'description' => 'Respiratory Rate'
  66             ,'column' => ['respiration', 'respiration_unit', 'respiration_interpretation_code', 'respiration_interpretation_title']
  67             ,'in_vitals_panel' => true
  68         ]
  69         ,'8867-4' => [
  70             'fullcode' => 'LOINC:8867-4'
  71             ,'code' => '8867-4'
  72             ,'description' => 'Heart rate'
  73             ,'column' => ['pulse', 'pulse_unit', 'pulse_interpretation_code', 'pulse_interpretation_title']
  74             ,'in_vitals_panel' => true
  75         ]
  76         ,'2708-6' => [
  77             'fullcode' => 'LOINC:2708-6'
  78             ,'code' => '2708-6'
  79             ,'description' => 'Oxygen saturation in Arterial blood'
  80             ,'column' => ['oxygen_saturation', 'oxygen_saturation_unit', 'oxygen_saturation_interpretation_code', 'oxygen_saturation_interpretation_title']
  81             ,'in_vitals_panel' => true
  82         ]
  83         ,'59408-5' => [
  84             'fullcode' => 'LOINC:59408-5',
  85             'code' => '59408-5',
  86             'description' => 'Oxygen saturation in Arterial blood by Pulse oximetry',
  87             'column' => ['oxygen_saturation', 'oxygen_saturation_unit', 'oxygen_flow_rate', 'oxygen_flow_rate_unit', '_interpretation_code', '_interpretation_title'],
  88             'in_vitals_panel' => true
  89         ]
  90         ,'3151-8' => [
  91             'fullcode' => 'LOINC:3151-8'
  92             ,'code' => '3151-8',
  93             'description' => 'Inhaled oxygen flow rate',
  94             'column' => ['oxygen_flow_rate', 'oxygen_flow_rate_unit', 'oxygen_flow_rate_interpretation_code', 'oxygen_flow_rate_interpretation_title'],
  95             'in_vitals_panel' => true
  96         ]
  97         ,'8310-5' => [
  98             'fullcode' => 'LOINC:8310-5',
  99             'code' => '8310-5',
 100             'description' => 'Body Temperature',
 101             'column' => ['temperature', 'temperature_unit', 'temperature_interpretation_code', 'temperature_interpretation_title'],
 102             'in_vitals_panel' => true
 103         ]
 104         ,'8327-9' => [
 105             'fullcode' => 'LOINC:8327-9',
 106             'code' => '8327-9',
 107             'description' => 'Temperature Location',
 108             'column' => 'temp_method',
 109             'in_vitals_panel' => true
 110         ]
 111         ,'8302-2' => [
 112             'fullcode' => 'LOINC:8302-2',
 113             'code' => '8302-2',
 114             'description' => 'Body height',
 115             'column' => ['height', 'height_unit', 'height_interpretation_code', 'height_interpretation_title'],
 116             'in_vitals_panel' => true
 117         ]
 118         ,'9843-4' => [
 119             'fullcode' => 'LOINC:9843-4'
 120             ,'code' => '9843-4'
 121             ,'description' => 'Head Occipital-frontal circumference'
 122             ,'column' => ['head_circ', 'head_circ_unit', 'head_circ_interpretation_code', 'head_circ_interpretation_title']
 123             ,'in_vitals_panel' => true
 124         ]
 125         ,'29463-7' => [
 126             'fullcode' => 'LOINC:29463-7'
 127             ,'code' => '29463-7'
 128             ,'description' => 'Body weight'
 129             ,'column' => ['weight', 'weight_unit', 'weight_interpretation_code', 'weight_interpretation_title']
 130             ,'in_vitals_panel' => true
 131         ]
 132         ,'39156-5' => [
 133             'fullcode' => 'LOINC:39156-5'
 134             ,'code' => '39156-5'
 135             ,'description' => 'Body mass index (BMI) [Ratio]'
 136             ,'column' =>  ['BMI', 'BMI_status', 'BMI_unit', 'BMI_interpretation_code', 'BMI_interpretation_title']
 137             ,'in_vitals_panel' => true
 138         ]
 139         ,'85354-9' => [
 140             'fullcode' => 'LOINC:85354-9'
 141             ,'code' => '85354-9'
 142             ,'description' => 'Blood pressure systolic and diastolic'
 143             // we hack this a bit to make it work by having our systolic and diastolic together
 144             ,'column' => ['bps', 'bps_unit', 'bpd', 'bpd_unit', 'bps_interpretation_code'
 145                 , 'bps_interpretation_title', 'bpd_interpretation_code', 'bpd_interpretation_title']
 146             ,'in_vitals_panel' => true
 147         ]
 148         ,'8480-6' => [
 149             'fullcode' => 'LOINC:8480-6'
 150             ,'code' => '8480-6'
 151             ,'description' => 'Systolic blood pressure'
 152             // we hack this a bit to make it work by having our systolic and diastolic together
 153             ,'column' => ['bps', 'bps_unit', 'bps_interpretation_code', 'bps_interpretation_title']
 154             ,'in_vitals_panel' => true
 155         ]
 156         ,'8462-4' => [
 157             'fullcode' => 'LOINC:8462-4'
 158             ,'code' => '8462-4'
 159             ,'description' => 'Diastolic blood pressure'
 160             // we hack this a bit to make it work by having our systolic and diastolic together
 161             ,'column' => ['bpd', 'bpd_unit', 'bpd_interpretation_code', 'bpd_interpretation_title']
 162             ,'in_vitals_panel' => true
 163         ]
 164
 165
 166
 167         // pediatric profiles are different...
 168         // need pediatric BMI
 169         // need pediatric head-occipetal
 170         // TODO: @adunsulag figure out where these values come from...
 171
 172         // Birth - 36 months @see https://www.cdc.gov/growthcharts/html_charts/hcageinf.htm
 173         // @see
 174         ,'8289-1' => [
 175             'fullcode' => 'LOINC:8289-1'
 176             ,'code' => '8289-1'
 177             ,'description' => 'Head Occipital-frontal circumference Percentile'
 178             ,'column' => ['ped_head_circ', 'ped_head_circ_unit', 'ped_head_circ_interpretation_code', 'ped_head_circ_interpretation_title']
 179             ,'in_vitals_panel' => false
 180         ]
 181         // 2-20yr @see https://www.cdc.gov/growthcharts/html_charts/bmiagerev.htm
 182         ,'59576-9' => [
 183             'fullcode' => 'LOINC:59576-9'
 184             ,'code' => '59576-9'
 185             ,'description' => 'Body mass index (BMI) [Percentile] Per age and sex'
 186             ,'column' => ['ped_bmi', 'ped_bmi_unit', 'ped_bmi_interpretation_code', 'ped_bmi_interpretation_title']
 187             ,'in_vitals_panel' => false
 188         ]
 189         // @see https://www.cdc.gov/growthcharts/html_charts/wtstat.htm
 190         // grab min(height) and find where weight <= 50
 191         // could do this with 3 columns representing height, weight & %
 192         // height, weight, %
 193         // select % WHERE height <= usrheight & weight <= usrweight ORDER BY height DESC, weight DESC LIMIT 1
 194         ,'77606-2' => [
 195             'fullcode' => 'LOINC:77606-2'
 196             ,'code' => '77606-2'
 197             ,'description' => 'Weight-for-length Per age and sex'
 198             ,'column' => ['ped_weight_height', 'ped_weight_height_unit', 'ped_weight_height_interpretation_code', 'ped_weight_height_interpretation_title']
 199             ,'in_vitals_panel' => false
 200         ]
 201         // need pediatric weight for height observations...
 202     ];
 203
 204     public function __construct($fhirApiURL = null)
 205     {
 206         parent::__construct($fhirApiURL);
 207         $this->service = new VitalsService();
 208         $this->populateResourceMappingUuidsForAllVitals();
 209     }
 210
 211     public function getResourcePathForCode($code)
 212     {
 213         return "category=" . self::CATEGORY . "&code=" . $code;
 214     }
 215     public function getCodeFromResourcePath($resourcePath)
 216     {
 217         $query_vars = [];
 218         parse_str($resourcePath, $query_vars);
 219         return $query_vars['code'] ?? null;
 220     }
 221
 222     public function populateResourceMappingUuidsForAllVitals()
 223     {
 224         $resourcePathList = [];
 225         foreach (self::COLUMN_MAPPINGS as $column => $mapping) {
 226             // TODO: @adunsulag make this a single function call so we can be more effecient
 227 //            $resourcePathList[] = "category=vital-signs&code=" . $mapping['code'];
 228             $resourcePath = $this->getResourcePathForCode($mapping['code']);
 229             UuidMapping::createMissingResourceUuids('Observation', 'form_vitals', $resourcePath);
 230         }
 231     }
 232
 233     public function supportsCategory($category)
 234     {
 235         return ($category === self::CATEGORY);
 236     }
 237
 238     public function supportsCode($code)
 239     {
 240         return array_search($code, array_keys(self::COLUMN_MAPPINGS)) !== false;
 241     }
 242
 243
 244     /**
 245      * Returns an array mapping FHIR Resource search parameters to OpenEMR search parameters
 246      */
 247     protected function loadSearchParameters()
 248     {
 249         return [
 250             'patient' => $this->getPatientContextSearchField(),
 251             'code' => new FhirSearchParameterDefinition('code', SearchFieldType::TOKEN, ['code']),
 252             'category' => new FhirSearchParameterDefinition('category', SearchFieldType::TOKEN, ['category']),
 253             'date' => new FhirSearchParameterDefinition('date', SearchFieldType::DATETIME, ['date']),
 254             '_id' => new FhirSearchParameterDefinition('_id', SearchFieldType::TOKEN, [new ServiceField('uuid', ServiceField::TYPE_UUID)]),
 255         ];
 256     }
 257
 258
 259     /**
 260      * Inserts an OpenEMR record into the sytem.
 261      * @return The OpenEMR processing result.
 262      */
 263     protected function insertOpenEMRRecord($openEmrRecord)
 264     {
 265         // TODO: Implement insertOpenEMRRecord() method.
 266     }
 267
 268     /**
 269      * Updates an existing OpenEMR record.
 270      * @param $fhirResourceId The OpenEMR record's FHIR Resource ID.
 271      * @param $updatedOpenEMRRecord The "updated" OpenEMR record.
 272      * @return The OpenEMR Service Result
 273      */
 274     protected function updateOpenEMRRecord($fhirResourceId, $updatedOpenEMRRecord)
 275     {
 276         // TODO: Implement updateOpenEMRRecord() method.
 277     }
 278
 279     /**
 280      * Searches for OpenEMR records using OpenEMR search parameters
 281      * @param openEMRSearchParameters OpenEMR search fields
 282      * @param $puuidBind - Optional variable to only allow visibility of the patient with this puuid.
 283      * @return OpenEMR records
 284      */
 285     protected function searchForOpenEMRRecords($openEMRSearchParameters): ProcessingResult
 286     {
 287         $processingResult = new ProcessingResult();
 288
 289         try {
 290             $observationCodesToReturn = [];
 291
 292             if (isset($openEMRSearchParameters['category']) && $openEMRSearchParameters['category'] instanceof TokenSearchField) {
 293                 if (!$openEMRSearchParameters['category']->hasCodeValue(self::CATEGORY)) {
 294                     throw new SearchFieldException("category", "invalid value");
 295                 }
 296                 // we only support one category and then we remove it.
 297                 unset($openEMRSearchParameters['category']);
 298             }
 299
 300             if (isset($openEMRSearchParameters['code'])) {
 301                 /**
 302                  * @var TokenSearchField
 303                  */
 304                 $code = $openEMRSearchParameters['code'];
 305                 if (!($code instanceof TokenSearchField)) {
 306                     throw new SearchFieldException('code', "Invalid code");
 307                 }
 308                 foreach ($code->getValues() as $value) {
 309                     $code = $value->getCode();
 310                     $observationCodesToReturn[$code] = $code;
 311                 }
 312                 unset($openEMRSearchParameters['code']);
 313             }
 314
 315
 316             if (empty($observationCodesToReturn)) {
 317                 // grab everything
 318                 $observationCodesToReturn = array_keys(self::COLUMN_MAPPINGS);
 319                 $observationCodesToReturn = array_combine($observationCodesToReturn, $observationCodesToReturn);
 320             }
 321
 322             // convert vital sign records from 1:many
 323
 324             $result = $this->service->search($openEMRSearchParameters, true);
 325             $data = $result->getData() ?? [];
 326
 327             // need to transform these into something we can consume
 328             foreach ($data as $record) {
 329                 // each vital record becomes a 1 -> many record for our observations
 330                 $this->parseVitalsIntoObservationRecords($processingResult, $record, $observationCodesToReturn);
 331             }
 332         } catch (SearchFieldException $exception) {
 333             $processingResult->setValidationMessages([$exception->getField() => $exception->getMessage()]);
 334         }
 335
 336         return $processingResult;
 337     }
 338
 339     private function parseVitalsIntoObservationRecords(ProcessingResult $processingResult, $record, $observationCodesToReturn)
 340     {
 341         $uuidMappings = $this->getVitalSignsUuidMappings(UuidRegistry::uuidToBytes($record['uuid']));
 342         // convert each record into it's own openEMR record array
 343
 344         if (!empty($observationCodesToReturn[self::VITALS_PANEL_LOINC_CODE])) {
 345             if (!empty($uuidMappings[self::VITALS_PANEL_LOINC_CODE])) {
 346                 $vitalsRecord = [
 347                     "code" => self::VITALS_PANEL_LOINC_CODE
 348                     , "description" => $this->getDescriptionForCode(self::VITALS_PANEL_LOINC_CODE)
 349                     , "category" => self::CATEGORY
 350                     , "puuid" => $record['puuid']
 351                     , "euuid" => $record['euuid']
 352                     , "members" => []
 353                     , "uuid" => UuidRegistry::uuidToString($uuidMappings[self::VITALS_PANEL_LOINC_CODE])
 354                     , "user_uuid" => $record['user_uuid']
 355                     , "date" => $record['date']
 356                 ];
 357                 foreach ($uuidMappings as $code => $uuid) {
 358                     if (!$this->isVitalSignPanelCodes($code)) {  // we will skip over our vital signs code, and any pediatric stuff
 359                         continue;
 360                     }
 361                     $vitalsRecord["members"][$code] = UuidRegistry::uuidToString($uuid);
 362                 }
 363                 $processingResult->addData($vitalsRecord);
 364                 unset($observationCodesToReturn[self::VITALS_PANEL_LOINC_CODE]);
 365             } else {
 366                 (new SystemLogger())->error("FhirVitalsService->parseVitalsIntoObservationRecords() Cannot return vitals panel as mapping uuid is missing for code " . self::VITALS_PANEL_LOINC_CODE);
 367             }
 368         }
 369         foreach ($observationCodesToReturn as $code) {
 370             $vitalsRecord = [
 371                 "code" => $code
 372                 ,"description" => $this->getDescriptionForCode($code)
 373                 ,"category" => self::CATEGORY
 374                 , "puuid" => $record['puuid']
 375                 , "euuid" => $record['euuid']
 376                 , "user_uuid" => $record['user_uuid']
 377                 ,"uuid" => UuidRegistry::uuidToString($uuidMappings[$code])
 378                 ,"date" => $record['date']
 379             ];
 380
 381             $columns = $this->getColumnsForCode($code);
 382             $columns[] = 'details'; // make sure to grab our detail columns
 383             // if any value of the column is populated we will return that the record has a value.
 384             foreach ($columns as $column) {
 385                 if (isset($record[$column]) && $record[$column] != "") {
 386                     $vitalsRecord[$column] = $record[$column];
 387                 }
 388             }
 389             $processingResult->addData($vitalsRecord);
 390         }
 391     }
 392
 393     private function getVitalSignsUuidMappings($uuid)
 394     {
 395         $mappedRecords = UuidMapping::getMappedRecordsForTableUUID($uuid);
 396         $codeMappings = [];
 397         if (!empty($mappedRecords)) {
 398             foreach ($mappedRecords as $record) {
 399                 $resourcePath = $record['resource_path'] ?? '';
 400                 $code = $this->getCodeFromResourcePath($resourcePath);
 401                 if (empty($code)) {
 402                     // TODO: @adunsulag handle this exception
 403                     continue;
 404                 }
 405                 $codeMappings[$code] = $record['uuid'];
 406             }
 407         }
 408         return $codeMappings;
 409     }
 410
 411
 412     /**
 413      * Parses a FHIR Resource, returning the equivalent OpenEMR record.
 414      *
 415      * @param $fhirResource The source FHIR resource
 416      * @return a mapped OpenEMR data record (array)
 417      */
 418     public function parseFhirResource($fhirResource = array())
 419     {
 420     }
 421
 422
 423     /**
 424      * Parses an OpenEMR data record, returning the equivalent FHIR Resource
 425      *
 426      * @param $dataRecord The source OpenEMR data record
 427      * @param $encode Indicates if the returned resource is encoded into a string. Defaults to True.
 428      * @return the FHIR Resource. Returned format is defined using $encode parameter.
 429      */
 430     public function parseOpenEMRRecord($dataRecord = array(), $encode = false)
 431     {
 432         $observation = new FHIRObservation();
 433         $meta = new FHIRMeta();
 434         $meta->setVersionId('1');
 435         $meta->setLastUpdated(gmdate('c'));
 436         $observation->setMeta($meta);
 437
 438         $id = new FHIRId();
 439         $id->setValue($dataRecord['uuid']);
 440         $observation->setId($id);
 441
 442         if (!empty($dataRecord['date'])) {
 443             $observation->setEffectiveDateTime(gmdate('c', strtotime($dataRecord['date'])));
 444         } else {
 445             $observation->setEffectiveDateTime(UtilsService::createDataMissingExtension());
 446         }
 447
 448         $code = $dataRecord['code'];
 449         $description = $this->getDescriptionForCode($code);
 450
 451         $categoryCoding = new FHIRCoding();
 452         $categoryCode = new FHIRCodeableConcept();
 453         if (!empty($dataRecord['code'])) {
 454             $categoryCoding->setCode($dataRecord['code']);
 455             $categoryCoding->setDisplay($description);
 456             $categoryCoding->setSystem(FhirCodeSystemConstants::LOINC);
 457             $categoryCode->addCoding($categoryCoding);
 458             $observation->setCode($categoryCode);
 459         }
 460
 461
 462         $observation->setStatus(self::VITALS_DEFAULT_OBSERVATION_STATUS);
 463
 464         // TODO: @adunsulag if our provenance needs to be more detailed we can use performer to set the user
 465
 466         $obsConcept = new FHIRCodeableConcept();
 467         $obsCategoryCoding = new FhirCoding();
 468         $obsCategoryCoding->setSystem(FhirCodeSystemConstants::HL7_OBSERVATION_CATEGORY);
 469         $obsCategoryCoding->setCode($dataRecord['category']);
 470         $obsConcept->addCoding($obsCategoryCoding);
 471         $observation->addCategory($obsConcept);
 472
 473         $observation->setSubject(UtilsService::createRelativeReference("Patient", $dataRecord['puuid']));
 474
 475         if (!empty($dataRecord['notes'])) {
 476             $observation->addNote(['text' => $dataRecord['notes']]);
 477         }
 478
 479         $basic_codes = [
 480             "9279-1" => 'respiration', "8867-4" => 'pulse', '2708-6' => 'oxygen_saturation', '8310-5' => 'temperature'
 481             ,'8302-2' => 'height', '9843-4' => 'head_circ', '29463-7' => 'weight', '39156-5' => 'BMI'
 482             ,'59576-9' => 'ped_bmi', '8289-1' => 'ped_head_circ', '77606-2' => 'ped_weight_height'
 483         ];
 484
 485         if (isset($basic_codes[$code])) {
 486             $this->populateBasicQuantityObservation($basic_codes[$code], $observation, $dataRecord);
 487         }
 488         // more complicated codes
 489         switch ($code) {
 490             case self::VITALS_PANEL_LOINC_CODE: // vital-signs panel
 491                 $this->populateVitalSignsPanelObservation($observation, $dataRecord);
 492                 break;
 493             case '8327-9':
 494                 $this->populateBodyTemperatureLocation($observation, $dataRecord);
 495                 break;
 496             case '85354-9': // blood pressure panel that includes systolic & diastolic pressure
 497                 $this->populateBloodPressurePanel($observation, $dataRecord);
 498                 break;
 499             case '8480-6':
 500                 $this->populateComponentColumn(
 501                     $observation,
 502                     $dataRecord,
 503                     'bps',
 504                     '8480-6',
 505                     $this->getDescriptionForCode('8480-6')
 506                 );
 507                 break;
 508             case '8462-4':
 509                 $this->populateComponentColumn(
 510                     $observation,
 511                     $dataRecord,
 512                     'bpd',
 513                     '8462-4',
 514                     $this->getDescriptionForCode('8462-4')
 515                 );
 516                 break;
 517             case '2708-6':
 518                 $this->populateCoding($observation, '59408-5');
 519                 break;
 520             case '59408-5':
 521                 $this->populatePulseOximetryObservation($observation, $dataRecord);
 522                 break;
 523         }
 524         return $observation;
 525     }
 526
 527     private function getColumnsForCode($code)
 528     {
 529         $codeMapping = self::COLUMN_MAPPINGS[$code] ?? null;
 530         if (isset($codeMapping)) {
 531             return is_array($codeMapping['column']) ? $codeMapping['column'] : [$codeMapping['column']];
 532         }
 533         return [];
 534     }
 535
 536     private function getDescriptionForCode($code)
 537     {
 538         $codeMapping = self::COLUMN_MAPPINGS[$code] ?? null;
 539         if (isset($codeMapping)) {
 540             return $codeMapping['description'];
 541         }
 542         return "";
 543     }
 544
 545     private function populateCoding(FHIRObservation $observation, $code)
 546     {
 547         // add additional oxygen-saturation coding
 548         $oxSaturation = new FHIRCoding();
 549         $oxSaturation->setCode($code);
 550         $oxSaturation->setDisplay($this->getDescriptionForCode($code));
 551         $oxSaturation->setSystem(FhirCodeSystemConstants::LOINC);
 552
 553         $observation->getCode()->addCoding($oxSaturation);
 554     }
 555
 556     private function populatePulseOximetryObservation(FHIRObservation $observation, $dataRecord)
 557     {
 558         $this->populateCoding($observation, '2708-6');
 559         if (
 560             $this->columnHasPositiveFloatValue('oxygen_flow_rate', $dataRecord)
 561             || $this->columnHasPositiveFloatValue('oxygen_saturation', $dataRecord)
 562         ) {
 563             $this->populateComponentColumn(
 564                 $observation,
 565                 $dataRecord,
 566                 'oxygen_flow_rate',
 567                 '3151-8',
 568                 $this->getDescriptionForCode('3151-8')
 569             );
 570             $this->populateComponentColumn(
 571                 $observation,
 572                 $dataRecord,
 573                 'oxygen_saturation',
 574                 '3150-0',
 575                 // only place this is used.
 576                 'Oxygen saturation in Arterial blood'
 577             );
 578         } else {
 579             $observation->setDataAbsentReason(UtilsService::createDataAbsentUnknownCodeableConcept());
 580         }
 581     }
 582
 583     private function populateVitalSignsPanelObservation(FHIRObservation $observation, $record)
 584     {
 585         if (!empty($record['members'])) {
 586             foreach ($record['members'] as $code => $uuid) {
 587                 $reference = UtilsService::createRelativeReference("Observation", $uuid);
 588                 $reference->setDisplay($this->getDescriptionForCode($code));
 589                 $observation->addHasMember($reference);
 590             }
 591         }
 592     }
 593
 594     private function isVitalSignPanelCodes($code)
 595     {
 596         $codeMapping = self::COLUMN_MAPPINGS[$code] ?? null;
 597         if (isset($codeMapping)) {
 598             return $codeMapping['in_vitals_panel'];
 599         }
 600         return false;
 601     }
 602
 603     private function populateBasicQuantityObservation($column, FHIRObservation $observation, $record)
 604     {
 605         $quantity = $this->getFHIRQuantityForColumn($column, $record);
 606         if ($quantity != null) {
 607             $observation->setValueQuantity($quantity);
 608         } else {
 609             $observation->setDataAbsentReason(UtilsService::createDataAbsentUnknownCodeableConcept());
 610         }
 611
 612         if (isset($record['details'][$column])) {
 613             $observation->addInterpretation($this->getInterpretationForColumn($record, $column));
 614         }
 615     }
 616
 617     private function getInterpretationForColumn($record, $column): ?FHIRCodeableConcept
 618     {
 619         if (isset($record['details'][$column])) {
 620             $code = $record['details'][$column]['interpretation_codes'];
 621             $text = $record['details'][$column]['interpretation_title'];
 622             return UtilsService::createCodeableConcept([$code => $text], FhirCodeSystemConstants::HL7_V3_OBSERVATION_INTERPRETATION);
 623         }
 624         return null;
 625     }
 626
 627     private function getFHIRQuantityForColumn($column, $record)
 628     {
 629         if ($this->columnHasPositiveFloatValue($column, $record)) {
 630             $quantity = new FHIRQuantity();
 631             $quantity->setValue(floatval($record[$column]));
 632             $quantity->setSystem(FhirCodeSystemConstants::UNITS_OF_MEASURE);
 633             $unit = $record[$column . '_unit'] ?? null;
 634             $code = $unit;
 635             // @see http://hl7.org/fhir/R4/observation-vitalsigns.html for the codes on this
 636             if ($unit === 'in') {
 637                 $unit = 'in_i';
 638                 $code = "[" . $unit . "]";
 639             } else if ($unit === 'lb') {
 640                 $unit = 'lb_av';
 641                 $code = "[" . $unit . "]";
 642             } else if ($unit === 'degF') {
 643                 $code = "[" . $unit . "]";
 644             }
 645             $quantity->setCode($code);
 646             $quantity->setUnit($unit);
 647             return $quantity;
 648         }
 649         return null;
 650     }
 651
 652     private function columnHasPositiveFloatValue($column, $record)
 653     {
 654         return (isset($record[$column]) && floatval($record[$column]) > 0.00);
 655     }
 656
 657     private function populateBloodPressurePanel(FHIRObservation $observation, $dataRecord)
 658     {
 659             $this->populateComponentColumn(
 660                 $observation,
 661                 $dataRecord,
 662                 'bps',
 663                 '8480-6',
 664                 $this->getDescriptionForCode('8480-6')
 665             );
 666             $this->populateComponentColumn(
 667                 $observation,
 668                 $dataRecord,
 669                 'bpd',
 670                 '8462-4',
 671                 $this->getDescriptionForCode('8462-4')
 672             );
 673     }
 674
 675     private function populateComponentColumn(FHIRObservation $observation, $dataRecord, $column, $code, $description)
 676     {
 677         $component = new FHIRObservationComponent();
 678         $coding = UtilsService::createCodeableConcept([$code => xlt($description)], FhirCodeSystemConstants::LOINC);
 679         $component->setCode($coding);
 680         $quantity = $this->getFHIRQuantityForColumn($column, $dataRecord);
 681         if ($quantity != null) {
 682             $component->setValueQuantity($quantity);
 683         } else {
 684             $component->setDataAbsentReason(UtilsService::createDataAbsentUnknownCodeableConcept());
 685         }
 686         if (isset($dataRecord['details'][$column])) {
 687             $component->addInterpretation($this->getInterpretationForColumn($dataRecord, $column));
 688         }
 689         $observation->addComponent($component);
 690     }
 691
 692     private function populateBodyTemperatureLocation(FHIRObservation $observation, $record)
 693     {
 694         // no guidance on how to pass this on, so we are using the value string to pass this on.
 695         $observation->setValueString($record['temp_method']);
 696     }
 697
 698     /**
 699      * Creates the Provenance resource  for the equivalent FHIR Resource
 700      *
 701      * @param $dataRecord The source OpenEMR data record
 702      * @param $encode Indicates if the returned resource is encoded into a string. Defaults to True.
 703      * @return the FHIR Resource. Returned format is defined using $encode parameter.
 704      */
 705     public function createProvenanceResource($dataRecord, $encode = false)
 706     {
 707         if (!($dataRecord instanceof FHIRObservation)) {
 708             throw new \BadMethodCallException("Data record should be correct instance class");
 709         }
 710         $fhirProvenanceService = new FhirProvenanceService();
 711         $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord);
 712         if ($encode) {
 713             return json_encode($fhirProvenance);
 714         } else {
 715             return $fhirProvenance;
 716         }
 717     }
 718
 719     public function getPatientContextSearchField(): FhirSearchParameterDefinition
 720     {
 721         return new FhirSearchParameterDefinition('patient', SearchFieldType::REFERENCE, [new ServiceField('puuid', ServiceField::TYPE_UUID)]);
 722     }
 723 }