Merge FHIR Bug Fixes To Release 6.1.0 (#5160)

* Fixes #5095 Patient,Goals,Immunization (#5097)

Not sure what happened but it looks like provider_uuid got stomped on in
CarePlan and Immunization.  Adding that in to our uuid mappings fixes
the problem with the resources returning 500.

For Patient it looks like the patient/* context was broken in the
Patient resource endpoint when we refactored the parameter name for
documentation purposes.  I've updated the $id parameter in the patient
route to be $uuid.

* Openemr fhir single patient api #5122 (#5129)

* Fix SurgeryService query.

FHIR searchAll was relying on a username column that doesn't exist.  Not
sure if some code got stomped on or how this ever passed our inferno
test suite.

* Fix Provenance queries.

Again not sure if code got stomped on but DiagnosticReports and
DocumentReference and Immunization Provenance were not working with
single patient api.

* FHIR document how medication works inside request

Added comments that explain how medication is embedded via the code
property inside of MedicationRequest.

* Fixes #5125,#5123 FHIR ids,Provenance

Reworked the FHIR ids for Provenance,CarePlan, and Goals.  FHIR R4.0.1
changed the logical id allowed fields (or at least inferno started
validating them) so we had to adjust how we handle these resources.  I
use a different surrogate key string which is valid in 4.0.1.  I also
handle the prior key data so we can still read and return the old format
so people's data doesn't break.

I also fix the issue where clinical notes,procedures and immunization weren't
returning provenance resources

* Fix style issues.

* Fix Care Plan unit tests.

We had too many fixture interdependencies now that the careplan also
joins on the forms table. Since I was testing the
surrogate key logic I stopped the getOne test and just focused on the
surrogateKey.

* Fixes #5137 Vitals save data absent value (#5138)

Make it so we can save a 0 value for columns in vitals to signify the
data is missing.

* Fixes #5127 mapped uuids not saving in registry (#5139)

Made it so the uuids for mapped resources such as vitals are being
populated in the uuid registry.  Users will need to run the
sql_upgrade.php for any existing installation in order for the vitals to
get their registry populated.

_rest_routes.inc.php

@@ -10636,10 +10636,10 @@
     "GET /fhir/Patient/:uuid" => function ($uuid, HttpRestRequest $request) {
         if ($request->isPatientRequest()) {
             // only allow access to data of binded patient
-            if (empty($id) || ($id != $request->getPatientUUIDString())) {
+            if (empty($uuid) || ($uuid != $request->getPatientUUIDString())) {
                 throw new AccessDeniedException("patients", "demo", "patient id invalid");
             }
-            $id = $request->getPatientUUIDString();
+            $uuid = $request->getPatientUUIDString();
         } else {
             RestConfig::authorization_check("patients", "demo");
         }

interface/forms/vitals/templates/vitals/vitals_textbox.tpl

@@ -9,10 +9,10 @@
     <td class='currentvalues p-2'>
         {if isset($vitalsStringFormat) }
         <input type="text" class="form-control" size='5' name='{$input|attr}' id='{$input|attr}_input'
-               value="{if $vitals->$vitalsValue() != 0}{$vitals->$vitalsValue()|string_format:$vitalsStringFormat|attr}{/if}"/>
+               value="{if is_numeric($vitals->$vitalsValue()) }{$vitals->$vitalsValue()|string_format:$vitalsStringFormat|attr}{/if}"/>
         {else}
         <input type="text" class="form-control" size='5' name='{$input|attr}' id='{$input|attr}_input'
-               value="{if $vitals->$vitalsValue() != 0}{$vitals->$vitalsValue()|attr}{/if}"/>
+               value="{if is_numeric($vitals->$vitalsValue())}{$vitals->$vitalsValue()|attr}{/if}"/>
         {/if}
 
     </td>

interface/forms/vitals/templates/vitals/vitals_textbox_conversion.tpl

@@ -24,7 +24,7 @@
         <td class='currentvalues p-2'>
     {/if}
             <input type="text" class="form-control" size='5' name='{$input|attr}' id='{$input|attr}_input'
-                   value="{if $vitals->$vitalsValue() != 0}{$vitals->$vitalsValue()|attr}{/if}"
+                   value="{if is_numeric($vitals->$vitalsValue()) }{$vitals->$vitalsValue()|attr}{/if}"
                    onChange="convUnit('usa', {$unit|attr_js}, '{$input|attr}_input')" title='{$vitalsValueUSAHelpTitle|default:''|xlt}'/>
         </td>
     <td class="editonly">
@@ -61,7 +61,7 @@
     {/if}
             <!-- Note we intentionally use vitalsValue not vitalValuesMetric because of how data is stored internally -->
             <input type="text" class="form-control" size='5' id='{$input|attr}_input_metric'
-                   value="{if $vitals->$vitalsValue() != 0}{$vitals->$vitalsValueMetric()|attr}{/if}"
+                   value="{if is_numeric($vitals->$vitalsValue()) }{$vitals->$vitalsValueMetric()|attr}{/if}"
                    onChange="convUnit('metric', {$unit|attr_js}, '{$input|attr}_input')"/>
         </td>
         <td class="editonly">

src/Common/Forms/FormVitals.php

@@ -226,7 +226,7 @@ public function get_weight_metric()
     }
     public function set_weight($w)
     {
-        if (!empty($w) && is_numeric($w)) {
+        if (is_numeric($w)) {
             $this->weight = $w;
         }
     }
@@ -251,7 +251,7 @@ public function get_height_metric()
     }
     public function set_height($h)
     {
-        if (!empty($h) && is_numeric($h)) {
+        if (is_numeric($h)) {
             $this->height = $h;
         }
     }
@@ -265,7 +265,7 @@ public function get_temperature_metric()
     }
     public function set_temperature($t)
     {
-        if (!empty($t) && is_numeric($t)) {
+        if (is_numeric($t)) {
             $this->temperature = $t;
         }
     }
@@ -286,7 +286,7 @@ public function get_pulse()
     }
     public function set_pulse($p)
     {
-        if (!empty($p) && is_numeric($p)) {
+        if (is_numeric($p)) {
             $this->pulse = $p;
         }
     }
@@ -296,7 +296,7 @@ public function get_respiration()
     }
     public function set_respiration($r)
     {
-        if (!empty($r) && is_numeric($r)) {
+        if (is_numeric($r)) {
             $this->respiration = $r;
         }
     }
@@ -320,7 +320,7 @@ public function get_BMI_short()
     }
     public function set_BMI($bmi)
     {
-        if (!empty($bmi) && is_numeric($bmi)) {
+        if (is_numeric($bmi)) {
             $this->BMI = $bmi;
         }
     }
@@ -342,7 +342,7 @@ public function get_waist_circ_metric()
     }
     public function set_waist_circ($w)
     {
-        if (!empty($w) && is_numeric($w)) {
+        if (is_numeric($w)) {
             $this->waist_circ = $w;
         }
     }
@@ -356,7 +356,7 @@ public function get_head_circ_metric()
     }
     public function set_head_circ($h)
     {
-        if (!empty($h) && is_numeric($h)) {
+        if (is_numeric($h)) {
             $this->head_circ = $h;
         }
     }
@@ -366,7 +366,7 @@ public function get_oxygen_saturation()
     }
     public function set_oxygen_saturation($o)
     {
-        if (!empty($o) && is_numeric($o)) {
+        if (is_numeric($o)) {
             $this->oxygen_saturation = $o;
         }
     }
@@ -377,7 +377,7 @@ public function get_oxygen_flow_rate()
     }
     public function set_oxygen_flow_rate($o)
     {
-        if (!empty($o) && is_numeric($o)) {
+        if (is_numeric($o)) {
             $this->oxygen_flow_rate = $o;
         } else {
             $this->oxygen_flow_rate = 0.00;
@@ -391,7 +391,7 @@ public function get_inhaled_oxygen_concentration()
 
     public function set_inhaled_oxygen_concentration($value)
     {
-        if (!empty($value) && is_numeric($value)) {
+        if (is_numeric($value)) {
             $this->inhaled_oxygen_concentration = $value;
         } else {
             $this->inhaled_oxygen_concentration = 0.00;
@@ -404,7 +404,7 @@ public function get_ped_weight_height()
     }
     public function set_ped_weight_height($o)
     {
-        if (!empty($o) && is_numeric($o)) {
+        if (is_numeric($o)) {
             $this->ped_weight_height = $o;
         } else {
             $this->ped_weight_height = 0.00;
@@ -417,7 +417,7 @@ public function get_ped_bmi()
     }
     public function set_ped_bmi($o)
     {
-        if (!empty($o) && is_numeric($o)) {
+        if (is_numeric($o)) {
             $this->ped_bmi = $o;
         } else {
             $this->ped_bmi = 0.00;
@@ -430,7 +430,7 @@ public function get_ped_head_circ()
     }
     public function set_ped_head_circ($o)
     {
-        if (!empty($o) && is_numeric($o)) {
+        if (is_numeric($o)) {
             $this->ped_head_circ = $o;
         } else {
             $this->ped_head_circ = 0.00;

src/Common/Uuid/UuidMapping.php

@@ -91,6 +91,8 @@ public static function createMappingRecordForResourcePaths($targetUuid, $resourc
                 sqlStatementNoLog($insertStatement, $bindValues, true);
                 $index++;
             }
+            // now insert the mapped uuids into the registry
+            $uuidRegistry->insertUuidsIntoRegistry($uuids);
         }
         return $uuids;
     }

src/Common/Uuid/UuidRegistry.php

@@ -134,6 +134,11 @@ public static function populateAllMissingUuids($log = true)
             self::appendPopulateLog('uuid_mapping', $mappedCounter, $logEntryComment);
         }
 
+        // To rectify a bug where mapped uuids were created but nothing in the UUID register for vital observations we
+        // will populate the UUIDRegistry
+        $mappedRegistryUuidCounter = self::createMissingMappedUuids();
+        self::appendPopulateLog('uuid_registry', $mappedRegistryUuidCounter, $logEntryComment);
+
         if (!empty($logEntryComment)) {
             $logEntryComment = rtrim($logEntryComment, ', ');
         }
@@ -151,6 +156,23 @@ public static function populateAllMissingUuids($log = true)
         }
     }
 
+    /**
+     * Creates registry entries for missing uuids in uuid_mapping that are not in uuid_registry.  Returns the count of
+     * the records that were created.
+     * @return int
+     */
+    private static function createMissingMappedUuids()
+    {
+        $createdRows = 0;
+        $sql = "INSERT INTO `uuid_registry`(`uuid`,`table_name`,`table_id`,`mapped`) "
+            . " SELECT `uuid_mapping`.`uuid`,'uuid_mapping','id',1 FROM `uuid_mapping` LEFT JOIN `uuid_registry` registry2 ON `uuid_mapping`.`uuid` = registry2.uuid WHERE registry2.uuid IS NULL";
+        $result = sqlStatementNoLog($sql, []);
+        if ($result !== false) {
+            $createdRows = generic_sql_affected_rows();
+        }
+        return $createdRows;
+    }
+
     /**
      * Returns the uuid registry record for a given uuid.
      * @param string|binary $uuid The uuid to search

src/Services/CarePlanService.php

@@ -30,7 +30,17 @@
 
 class CarePlanService extends BaseService
 {
-    const SURROGATE_KEY_SEPARATOR = "_";
+    // Note: FHIR 4.0.1 id columns put a constraint on ids such that:
+    // Ids can be up to 64 characters long, and contain any combination of upper and lowercase ASCII letters,
+    // numerals, "-" and ".".  Logical ids are opaque to the resource server and should NOT be changed once they've
+    // been issued by the resource server
+    // Up to OpenEMR 6.1.0 patch 0 we used underscores as our separator
+    const SURROGATE_KEY_SEPARATOR_V1 = "_";
+    // use the abbreviation SK for Surrogate key and hyphens.  Since Logical ids are opaque we can do this as long as
+    // our UUID NEVER generates a two digit hyphenated id which none of the standards currently do.
+    // the best approach would be to completely overhaul Careplan but for historical reasons we aren't doing that right now.
+    const SURROGATE_KEY_SEPARATOR_V2 = "-SK-";
+    const V2_TIMESTAMP = 1649476800; // strtotime("2022-04-09");
     private const PATIENT_TABLE = "patient_data";
     private const ENCOUNTER_TABLE = "form_encounter";
     private const CARE_PLAN_TABLE = "form_care_plan";
@@ -52,7 +62,7 @@ class CarePlanService extends BaseService
 
     function getUuidFields(): array
     {
-        return ['puuid', 'euuid'];
+        return ['puuid', 'euuid', 'provider_uuid'];
     }
 
     public function __construct($carePlanType = self::TYPE_PLAN_OF_CARE)
@@ -134,7 +144,9 @@ public function search($search, $isAndCondition = true)
                 ,patients.pid
                 ,encounters.euuid
                 ,encounters.eid
-                ,fcp.form_id
+                ,fcp_forms.form_id
+                ,fcp_forms.creation_date
+                ,UNIX_TIMESTAMP(fcp_forms.creation_date) AS 'creation_timestamp'
                 ,fcp.code
                 ,fcp.codetext
                 ,fcp.description
@@ -147,7 +159,7 @@ public function search($search, $isAndCondition = true)
                  FROM
                  (
                     select
-                        id AS form_id
+                        id
                         ,code
                         ,codetext
                         ,description
@@ -171,6 +183,16 @@ public function search($search, $isAndCondition = true)
                     FROM
                         form_encounter
                  ) encounters ON fcp.encounter = encounters.eid
+                -- we need the form date information
+                 JOIN (
+                      SELECT
+                      id
+                      ,form_id
+                      ,encounter AS form_encounter
+                      ,date AS creation_date
+                      FROM forms
+                      WHERE form_name = 'Care Plan Form'
+                 ) fcp_forms ON fcp.id = fcp_forms.form_id AND encounters.eid = fcp_forms.form_encounter
                  LEFT JOIN (
                     select
                         pid
@@ -270,9 +292,15 @@ private function populateSurrogateSearchFieldsForUUID(TokenSearchField $fieldUUI
      */
     public function getSurrogateKeyForRecord(array $record)
     {
+        // note that logical ids are allowed to be 64 characters.  Our UUID is 32 characters so as long as
+        // the form_id + separator never exceeds 64 characters we are good here.
         $form_id = $record['form_id'] ?? '';
         $encounter = $record['euuid'] ?? '';
-        return $encounter . self::SURROGATE_KEY_SEPARATOR . $form_id;
+        $separator = self::SURROGATE_KEY_SEPARATOR_V2;
+        if (intval($record['creation_timestamp'] ?? 0) <= self::V2_TIMESTAMP) {
+            $separator = self::SURROGATE_KEY_SEPARATOR_V1;
+        }
+        return $encounter . $separator . $form_id;
     }
 
     /**
@@ -282,7 +310,11 @@ public function getSurrogateKeyForRecord(array $record)
      */
     public function splitSurrogateKeyIntoParts($key)
     {
-        $parts = explode(self::SURROGATE_KEY_SEPARATOR, $key);
+        $delimiter = self::SURROGATE_KEY_SEPARATOR_V2;
+        if (strpos($key, self::SURROGATE_KEY_SEPARATOR_V1) !== false) {
+            $delimiter = self::SURROGATE_KEY_SEPARATOR_V1;
+        }
+        $parts = explode($delimiter, $key);
         $key = [
             "euuid" => $parts[0] ?? ""
             ,"form_id" => $parts[1] ?? ""

src/Services/FHIR/DocumentReference/FhirClinicalNotesService.php

@@ -230,7 +230,12 @@ public function createProvenanceResource($dataRecord, $encode = false)
             throw new \BadMethodCallException("Data record should be correct instance class");
         }
         $fhirProvenanceService = new FhirProvenanceService();
-        $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord, $dataRecord->getAuthor());
+        $authors = $dataRecord->getAuthor();
+        $author = null;
+        if (!empty($authors)) {
+            $author = reset($authors); // grab the first one, as we only populate one anyways.
+        }
+        $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord, $author);
         if ($encode) {
             return json_encode($fhirProvenance);
         } else {

src/Services/FHIR/DocumentReference/FhirPatientDocumentReferenceService.php

@@ -212,7 +212,12 @@ public function createProvenanceResource($dataRecord, $encode = false)
         }
 
         $fhirProvenanceService = new FhirProvenanceService();
-        $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord, $dataRecord->getAuthor());
+        $authors = $dataRecord->getAuthor();
+        $author = null;
+        if (!empty($authors)) {
+            $author = reset($authors); // grab the first one, as we only populate one anyways.
+        }
+        $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord, $author);
         if ($encode) {
             return json_encode($fhirProvenance);
         } else {

src/Services/FHIR/FhirCarePlanService.php

@@ -113,7 +113,7 @@ public function parseOpenEMRRecord($dataRecord = array(), $encode = false)
         }
 
         if (!empty($dataRecord['provider_uuid']) && !empty($dataRecord['provider_npi'])) {
-            $carePlanResource->getAuthor(UtilsService::createRelativeReference("Practitioner", $dataRecord['provider_uuid']));
+            $carePlanResource->setAuthor(UtilsService::createRelativeReference("Practitioner", $dataRecord['provider_uuid']));
         }
 
         if ($encode) {

src/Services/FHIR/FhirImmunizationService.php

@@ -3,6 +3,7 @@
 namespace OpenEMR\Services\FHIR;
 
 use OpenEMR\FHIR\R4\FHIRElement\FHIRMeta;
+use OpenEMR\FHIR\R4\FHIRResource\FHIRImmunization\FHIRImmunizationPerformer;
 use OpenEMR\Services\FHIR\FhirServiceBase;
 use OpenEMR\Services\FHIR\Traits\BulkExportSupportAllOperationsTrait;
 use OpenEMR\Services\FHIR\Traits\FhirBulkExportDomainResourceTrait;
@@ -165,7 +166,9 @@ public function parseOpenEMRRecord($dataRecord = array(), $encode = false)
         }
 
         if (!empty($dataRecord['provider_uuid']) && !empty($dataRecord['provider_npi'])) {
-            $immunizationResource->addPerformer(UtilsService::createRelativeReference("Practitioner", $dataRecord['provider_uuid']));
+            $performer = new FHIRImmunizationPerformer();
+            $performer->setActor(UtilsService::createRelativeReference("Practitioner", $dataRecord['provider_uuid']));
+            $immunizationResource->addPerformer($performer);
         }
 
         // education is failing ONC validation, since we don't need it for ONC we are going to leave it off for now.
@@ -201,11 +204,12 @@ public function createProvenanceResource($dataRecord = array(), $encode = false)
             throw new \BadMethodCallException("Data record should be correct instance class");
         }
         $fhirProvenanceService = new FhirProvenanceService();
-        $performer = null;
+        $author = null;
         if (!empty($dataRecord->getPerformer())) {
             $performer = current($dataRecord->getPerformer());
+            $author = $performer->getActor();
         }
-        $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord, $performer);
+        $fhirProvenance = $fhirProvenanceService->createProvenanceForDomainResource($dataRecord, $author);
         if ($encode) {
             return json_encode($fhirProvenance);
         } else {

src/Services/FHIR/FhirMedicationRequestService.php

@@ -180,6 +180,17 @@ public function parseOpenEMRRecord($dataRecord = array(), $encode = false)
         $medRequestResource->setReportedBoolean(self::MEDICATION_REQUEST_REPORTED_PRIMARY_SOURCE);
 
         // medication[x] required
+        /**
+         * US Core Requirements
+         * The MedicationRequest resources can represent a medication using either a code, or reference a Medication resource.
+         * When referencing a Medication resource, the resource may be contained or an external resource.
+         * The server systems are not required to support both a code and a reference, but SHALL support at least one of these methods.
+         * If an external reference to Medication is used, the server SHALL support the _include parameter for searching this element.
+         * The client application SHALL support all methods.
+         *
+         * NOTE: for our requirements we support ONLY the medicationCodeableConcept requirement ie code option and NOT the
+         * embedded medication.
+         */
         if (!empty($dataRecord['drugcode'])) {
 //            $rxnormCoding = new FHIRCoding();
             $rxnormCode = UtilsService::createCodeableConcept($dataRecord['drugcode'], FhirCodeSystemConstants::RXNORM);