Fixes openemr#7002 FHIR api warnings missing keys (openemr#7005)

Allergy intollerance was failing when the unassigned reaction was given
since there are no codes and that threw a warning.

social history was relying on columns that didn't exist that also threw
warnings.

Vitals services temp_method was not being set properly and threw a
warning.

Procedure service had a number of columns it attempted to populate but
the actual data values did not match with the array keys.

src/Services/FHIR/FhirAllergyIntoleranceService.php

@@ -171,7 +171,8 @@ public function parseOpenEMRRecord($dataRecord = array(), $encode = false)
 
  // cardinality is 0..*
  // however in OpenEMR we currently only track a single reaction, we will populate it if we have it.
- if (!empty($dataRecord['reaction'])) {
+ // if a reaction is unassigned, it has no codes and so we will skip over this as it has no meaning in FHIR.
+ if (!empty($dataRecord['reaction']) && $dataRecord['reaction'] !== 'unassigned') {
  $reaction = new FHIRAllergyIntoleranceReaction();
  $reactionConcept = new FHIRCodeableConcept();
  $conceptText = $dataRecord['reaction_title'] ?? "";

src/Services/FHIR/Observation/FhirObservationSocialHistoryService.php

@@ -212,8 +212,6 @@ private function parseSocialHistoryIntoObservationRecords(ProcessingResult $proc
  ,"description" => $this->getDescriptionForCode($code)
  ,"category" => "social-history"
  , "puuid" => $record['puuid']
- , "euuid" => $record['euuid']
- , "user_uuid" => $record['user_uuid']
  ,"uuid" => UuidRegistry::uuidToString($uuidMappings[$code])
  ,"date" => $record['date']
  ];

src/Services/FHIR/Observation/FhirObservationVitalsService.php

@@ -105,7 +105,7 @@ class FhirObservationVitalsService extends FhirServiceBase implements IPatientCo
  'fullcode' => 'LOINC:8327-9',
  'code' => '8327-9',
  'description' => 'Temperature Location',
- 'column' => 'temp_method',
+ 'column' => ['temp_method'],
  'in_vitals_panel' => true
  ]
  ,'8302-2' => [
@@ -696,8 +696,12 @@ private function populateComponentColumn(FHIRObservation $observation, $dataReco
 
  private function populateBodyTemperatureLocation(FHIRObservation $observation, $record)
  {
- // no guidance on how to pass this on, so we are using the value string to pass this on.
- $observation->setValueString($record['temp_method']);
+ if (empty($record['temp_method'])) {
+ $observation->setDataAbsentReason(UtilsService::createDataAbsentUnknownCodeableConcept());
+ } else {
+ // no guidance on how to pass this on, so we are using the value string to pass this on.
+ $observation->setValueString($record['temp_method']);
+ }
  }
 
  /**

src/Services/ProcedureService.php

@@ -62,14 +62,14 @@ public function search($search, $isAndCondition = true)
  ,porder.order_diagnosis
  ,porder.order_encounter_id
  ,porder.order_lab_id
- 
+
  ,preport.report_date
  ,preport.procedure_report_id
  ,preport.report_uuid
  ,preport.report_notes
- 
+
  ,presult.procedure_result_id
- ,presult.result_uuid 
+ ,presult.result_uuid
  ,presult.result_code
  ,presult.result_text
  ,presult.result_units
@@ -78,18 +78,18 @@ public function search($search, $isAndCondition = true)
  ,presult.result_abnormal
  ,presult.result_comments
  ,presult.result_status
- 
+
  ,order_codes.procedure_name
  ,order_codes.procedure_code
  ,order_codes.procedure_type
- 
+
  ,pcode_types.standard_code
 
  ,labs.lab_id
  ,labs.lab_uuid
  ,labs.lab_npi
  ,labs.lab_name
- 
+
  ,patients.puuid
  ,patients.pid
 
@@ -99,7 +99,7 @@ public function search($search, $isAndCondition = true)
 
  ,docs.doc_id
  ,docs.doc_uuid
- 
+
  ,provider.provider_uuid
  ,provider.provider_id
  ,provider.provider_fname
@@ -118,7 +118,7 @@ public function search($search, $isAndCondition = true)
  procedure_report
  ) preport
  LEFT JOIN (
- SELECT 
+ SELECT
  procedure_result_id
  ,procedure_report_id
  ,uuid AS result_uuid
@@ -137,10 +137,10 @@ public function search($search, $isAndCondition = true)
  FROM
  `procedure_result`
  ) presult
- ON 
+ ON
  preport.procedure_report_id = presult.procedure_report_id
  LEFT JOIN (
- SELECT 
+ SELECT
  procedure_order_id
  ,uuid AS order_uuid
  ,provider_id AS order_provider_id
@@ -154,7 +154,7 @@ public function search($search, $isAndCondition = true)
  FROM
  procedure_order
  ) porder
- ON 
+ ON
  porder.procedure_order_id = preport.procedure_order_id
  LEFT JOIN
  (
@@ -173,12 +173,12 @@ public function search($search, $isAndCondition = true)
  ,npi AS lab_npi
  ,`name` AS lab_name
  ,`active` AS lab_active
- FROM 
+ FROM
  procedure_providers
  ) labs
- ON 
+ ON
  labs.lab_id = porder.order_lab_id
- LEFT JOIN 
+ LEFT JOIN
  (
  select
  procedure_order_id
@@ -190,7 +190,7 @@ public function search($search, $isAndCondition = true)
  FROM procedure_order_code
  )
  order_codes
- ON 
+ ON
  order_codes.procedure_order_id = porder.procedure_order_id AND order_codes.procedure_order_seq = preport.procedure_order_seq
  LEFT JOIN (
  select
@@ -199,17 +199,17 @@ public function search($search, $isAndCondition = true)
  FROM procedure_type
  ) pcode_types ON order_codes.procedure_code = pcode_types.proc_code
  LEFT JOIN (
- select 
+ select
  pid
  ,uuid AS puuid
  FROM
  patient_data
  ) patients
- ON 
- patients.pid = porder.order_patient_id 
- 
+ ON
+ patients.pid = porder.order_patient_id
+
  LEFT JOIN (
- select 
+ select
  id AS doc_id
  ,uuid AS doc_uuid
  FROM
@@ -298,10 +298,10 @@ private function hydrateSearchResultsFromQueryResource($queryResource)
  $procedure['provider'] = [
  'id' => $record['provider_id']
  ,'uuid' => $record['provider_uuid']
- ,'fname' => $record['fname']
- ,'mname' => $record['mname']
- ,'lname' => $record['lname']
- ,'npi' => $record['npi']
+ ,'fname' => $record['provider_fname']
+ ,'mname' => $record['provider_mname']
+ ,'lname' => $record['provider_lname']
+ ,'npi' => $record['provider_npi']
  ];
  }
  if (!empty($record['lab_id'])) {
@@ -366,7 +366,7 @@ private function hydrateSearchResultsFromQueryResource($queryResource)
  , 'range' => $record['result_range']
  , 'abnormal' => $record['result_abnormal']
  , 'comments' => $record['result_comments']
- , 'document_id' => $record['result_document_id']
+ , 'document_id' => $record['doc_id']
  , 'status' => $record['result_status']
  ];
  $report['results'][] = $result;

src/Services/SocialHistoryService.php

@@ -188,7 +188,7 @@ function getUuidFields(): array
  {
  // note the uuid here is the uuid_mapping table's uuid since each column in the table has its own distinct uuid
  // in the system.
- return ['puuid', 'euuid', 'uuid', 'user_uuid'];
+ return ['puuid', 'uuid'];
  }