src/Services/ClinicalNotesService.php

   1 <?php
   2
   3 /**
   4  * ClinicalNotesService.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;
  13
  14 use OpenEMR\Common\Database\QueryUtils;
  15 use OpenEMR\Common\Uuid\UuidRegistry;
  16 use OpenEMR\Services\Search\FhirSearchWhereClauseBuilder;
  17 use OpenEMR\Services\Search\ISearchField;
  18 use OpenEMR\Services\Search\SearchFieldException;
  19 use OpenEMR\Services\Search\TokenSearchField;
  20 use OpenEMR\Services\Search\TokenSearchValue;
  21 use OpenEMR\Validators\ProcessingResult;
  22
  23 class ClinicalNotesService extends BaseService
  24 {
  25     const TABLE_NAME = "form_clinical_notes";
  26
  27     const ACTIVITY_ACTIVE = 1;
  28     const ACTIVITY_INACTIVE = 0;
  29
  30     public function __construct()
  31     {
  32         parent::__construct(self::TABLE_NAME);
  33         UuidRegistry::createMissingUuidsForTables(['form_clinical_notes']);
  34     }
  35
  36     /**
  37      * Returns a list of records matching the search criteria.
  38      * Search criteria is conveyed by array where key = field/column name, value is an ISearchField
  39      * If an empty array of search criteria is provided, all records are returned.
  40      *
  41      * The search will grab the intersection of all possible values if $isAndCondition is true, otherwise it returns
  42      * the union (logical OR) of the search.
  43      *
  44      * More complicated searches with various sub unions / intersections can be accomplished through a CompositeSearchField
  45      * that allows you to combine multiple search clauses on a single search field.
  46      *
  47      * @param ISearchField[] $search Hashmap of string => ISearchField where the key is the field name of the search field
  48      * @param bool $isAndCondition Whether to join each search field with a logical OR or a logical AND.
  49      * @return ProcessingResult The results of the search.
  50      */
  51     public function search($search, $isAndCondition = true)
  52     {
  53         // because we can have two clinical note table options (one from contrib etc), we will return an empty search
  54         // result for now if the table does not conform to our CORE clinical_notes
  55         $fields = $this->getFields();
  56         $processingResult = new ProcessingResult();
  57         if (array_search('code', $fields) === false) {
  58             // there is no data right now for the other form so we leave it be.
  59             return $processingResult;
  60         }
  61
  62         // we leave status to be current, if we ever support entered-in-error, or superseded we can do that here.
  63         try {
  64             $sql = "
  65             SELECT
  66                 notes.id
  67                 ,notes.uuid AS uuid
  68                 ,notes.activity
  69                 ,notes.date
  70                 ,notes.code
  71                 ,notes.codetext
  72                 ,notes.description
  73                 ,notes.external_id
  74                 ,notes.clinical_notes_type
  75                 ,notes.note_related_to
  76                 ,notes.clinical_notes_category
  77                 ,lo_category.category_code
  78                 ,lo_category.category_title
  79                 ,patients.pid
  80                 ,patients.puuid
  81                 ,encounters.eid
  82                 ,encounters.euuid
  83                 ,encounters.encounter_date
  84                 ,users.username
  85                 ,users.user_uuid
  86                 ,users.npi
  87                 ,users.physician_type
  88             FROM
  89                 (
  90                     select
  91                         id
  92                         ,uuid
  93                         ,activity
  94                         ,`date`
  95                         ,`code`
  96                         ,codetext
  97                         ,`description`
  98                         ,external_id
  99                         ,clinical_notes_type
 100                         ,note_related_to
 101                         ,clinical_notes_category
 102                         ,form_id
 103                         ,user
 104                  FROM
 105                     form_clinical_notes
 106              ) notes
 107             JOIN (
 108                 SELECT
 109                     id AS form_id,
 110                     encounter
 111                     ,pid AS form_pid
 112                 FROM
 113                     forms
 114             ) forms ON forms.form_id = notes.form_id
 115             LEFT JOIN (
 116                 select
 117                     encounter AS eid
 118                     ,uuid AS euuid
 119                     ,`date` AS encounter_date
 120                 FROM
 121                     form_encounter
 122             ) encounters ON encounters.eid = forms.encounter
 123             LEFT JOIN
 124             (
 125                 SELECT
 126                     uuid AS puuid
 127                     ,pid
 128                     FROM patient_data
 129             ) patients ON forms.form_pid = patients.pid
 130             LEFT JOIN
 131             (
 132                 SELECT
 133                     uuid AS user_uuid
 134                     ,username
 135                     ,id AS uid
 136                     ,npi
 137                     ,physician_type
 138                     FROM
 139                         users
 140             ) users ON notes.`user` = users.username
 141             LEFT JOIN
 142             (
 143                 SELECT
 144                     notes AS category_code
 145                     ,title AS category_title
 146                     ,option_id
 147                 FROM
 148                     list_options
 149                 WHERE
 150                     list_id = 'Clinical_Note_Category'
 151             ) lo_category ON notes.clinical_notes_category = lo_category.option_id
 152         ";
 153             $whereClause = FhirSearchWhereClauseBuilder::build($search, $isAndCondition);
 154
 155             $sql .= $whereClause->getFragment();
 156             $sqlBindArray = $whereClause->getBoundValues();
 157
 158             $statementResults =  QueryUtils::sqlStatementThrowException($sql, $sqlBindArray);
 159             while ($row = sqlFetchArray($statementResults)) {
 160                 $resultRecord = $this->createResultRecordFromDatabaseResult($row);
 161                 $processingResult->addData($resultRecord);
 162             }
 163         } catch (SearchFieldException $exception) {
 164             $processingResult->setValidationMessages([$exception->getField() => $exception->getMessage()]);
 165         }
 166         return $processingResult;
 167     }
 168
 169     protected function createResultRecordFromDatabaseResult($row)
 170     {
 171         // TODO: @adunsulag this is just for testing until we can figure out the right uuid schematic
 172         if (!empty($row['code'])) {
 173             $row['code'] = $this->addCoding($row['code']);
 174         }
 175         return parent::createResultRecordFromDatabaseResult($row);
 176     }
 177
 178     public function getUuidFields(): array
 179     {
 180         return ['uuid', 'puuid', 'euuid', 'user_uuid'];
 181     }
 182
 183     /**
 184      * Sets the activity status flag for the given form_clinical_notes record to either be active(1) or inactive(0).
 185      * @param $clinicalNoteId The unique record id for the form_clinical_notes table
 186      * @param $pid The unique patient pid from the patient_data table
 187      * @param $encounter The unique encounter id from the form_encounters table
 188      * @param $activity The activity status: active(1) or inactive(0).
 189      */
 190     public function setActivityForClinicalRecord($clinicalNoteId, $pid, $encounter, $activity)
 191     {
 192         $sql = "UPDATE `form_clinical_notes` SET activity = ? WHERE id=? AND pid = ? AND encounter = ?";
 193         $bindings = array($activity, $clinicalNoteId, $pid, $encounter);
 194         QueryUtils::sqlStatementThrowException($sql, $bindings);
 195     }
 196
 197     /**
 198      * Given a form id remove all of the clinical note records connected to that form.
 199      * @param $formId The unique id from the forms table
 200      * @param $pid The unique patient pid from the patient_data table
 201      * @param $encounter The unique encounter id from the form_encounters table
 202      */
 203     public function clearClinicalRecordsForForm($formId, $pid, $encounter)
 204     {
 205         QueryUtils::sqlStatementThrowException(
 206             "DELETE FROM `form_clinical_notes` WHERE form_id=? AND pid = ? AND encounter = ?",
 207             array($formId, $pid, $encounter)
 208         );
 209     }
 210
 211     public function getClinicalRecordNoteById($id)
 212     {
 213         $sql = "select * from `form_clinical_notes` WHERE id = ? ";
 214         $records = QueryUtils::fetchRecords($sql, [$id]);
 215         if (!empty($records)) {
 216             return $records[0];
 217         }
 218         return null;
 219     }
 220
 221     public function createClinicalNotesParentForm($pid, $encounter, $userauthorized)
 222     {
 223         $largestId = QueryUtils::fetchSingleValue("SELECT COALESCE(MAX(form_id), 0) as largestId FROM `form_clinical_notes`", 'largestId');
 224
 225         if ($largestId > 0) {
 226             $form_id = $largestId + 1;
 227         } else {
 228             $form_id = 1;
 229         }
 230
 231         addForm($encounter, "Clinical Notes Form", $form_id, "clinical_notes", $pid, $userauthorized);
 232         return $form_id;
 233     }
 234
 235     public function saveArray(array $record)
 236     {
 237         $form_id = $record['form_id'] ?? null;
 238         $id = $record['id'] ?? null;
 239         $pid = $record['pid'] ?? null;
 240         $encounter = $record['encounter'] ?? null;
 241         $userauthorized = $record['authorized'] ?? null;
 242         $existingRecord = [];
 243
 244
 245         if (empty($form_id) || empty($pid) || empty($encounter) || empty($record) || $userauthorized === null) {
 246             throw new \InvalidArgumentException("Record, form_id, pid, authorized and encounter must be populated");
 247         }
 248
 249         unset($record['id']);
 250         // we grab the existing record so we can populate the uuid if necessary
 251         if (isset($id)) {
 252             $existingRecord = $this->getClinicalRecordNoteById($id);
 253         }
 254
 255         if (empty($form_id)) {
 256             $largestId = QueryUtils::fetchSingleValue("SELECT COALESCE(MAX(form_id), 0) as largestId FROM `form_clinical_notes`", 'largestId');
 257
 258             if ($largestId > 0) {
 259                 $record['form_id'] = $largestId + 1;
 260             } else {
 261                 $record['form_id'] = 1;
 262             }
 263
 264             addForm($encounter, "Clinical Notes Form", $record['form_id'], "clinical_notes", $pid, $userauthorized);
 265         }
 266         if (empty($existingRecord['uuid'])) {
 267             $record['uuid'] = (new UuidRegistry(['table_name' => 'form_clinical_notes']))->createUuid();
 268         }
 269
 270         $keys = array_keys($record);
 271         $setValues = array_map(function ($val) {
 272             return $val . " = ? ";
 273         }, $keys);
 274         if (!empty($id)) {
 275             $sql = "UPDATE " . self::TABLE_NAME . " SET " . implode(", ", $setValues) . " WHERE id = ? ";
 276             $bindValues = array_values($record);
 277             $bindValues[] = $id;
 278             QueryUtils::sqlStatementThrowException($sql, $bindValues);
 279         } else {
 280             $sql = "INSERT INTO " . self::TABLE_NAME . " SET " . implode(", ", $setValues);
 281             $bindValues = array_values($record);
 282             $recordId = QueryUtils::sqlInsert($sql, $bindValues);
 283             $record['id'] = $recordId;
 284         }
 285         // if we want the id&uuid back we need to return the record here
 286         return $record;
 287     }
 288
 289     public function getClinicalNoteIdsForPatientForm(int $formid, $pid, $encounter)
 290     {
 291         if (empty($formid) || empty($pid) || empty($encounter)) {
 292             throw new \InvalidArgumentException("formid, pid, and encounter must all be populated");
 293         }
 294
 295         $sql = "SELECT id FROM `form_clinical_notes` WHERE `form_id`=? AND `pid` = ? AND `encounter` = ?";
 296         return QueryUtils::fetchTableColumn($sql, 'id', array($formid, $pid, $encounter));
 297     }
 298
 299     /**
 300      * Retrieve all of the clinical notes for a given patient
 301      * @param $pid
 302      * @return ProcessingResult
 303      */
 304     public function getClinicalNotesForPatient($pid): ProcessingResult
 305     {
 306         $search['pid'] = new TokenSearchField('pid', new TokenSearchValue($pid));
 307         return $this->search($search);
 308     }
 309
 310     public function getClinicalNotesForPatientForm(int $formid, $pid, $encounter)
 311     {
 312         if (empty($formid) || empty($pid)) {
 313             throw new \InvalidArgumentException("formid, and pid must all be populated");
 314         }
 315
 316         $sql = "SELECT fcn.*, lo_category.title AS category_title, lo_category.notes AS category_code
 317                 FROM `form_clinical_notes` fcn
 318                 LEFT JOIN list_options lo_category ON lo_category.list_id = `Clinical_Notes_Category` AND lo_category.option_id = fcn.clinical_notes_category
 319                 LEFT JOIN list_options lo_type ON lo_type.list_id = `Clinical_Notes_Type` AND lo_type.option_id = fcn.clinical_notes_type
 320                 WHERE fcn.`form_id`=? AND fcn.`pid` = ? AND fcn.`encounter` = ?";
 321         return QueryUtils::fetchRecords($sql, array($formid, $pid, $encounter));
 322     }
 323
 324     public function deleteClinicalNoteRecordForPatient($recordId, $pid, $encounter)
 325     {
 326         $sql = "DELETE FROM `form_clinical_notes` WHERE id = ? AND pid= ? AND encounter = ?";
 327         QueryUtils::sqlStatementThrowException($sql, [$recordId, $pid, $encounter]);
 328     }
 329
 330     /**
 331      * Given a code (with or without LOINC prefix) determine if its a valid clinical note code that this service can
 332      * respond to.
 333      * @param $code string
 334      * @return bool true if the code is valid, false otherwise
 335      */
 336     public function isValidClinicalNoteCode($code)
 337     {
 338         // make it a LOINC code
 339         if (strpos($code, ":") === false) {
 340             $code = "LOINC:" . $code;
 341         }
 342         $listService = new ListService();
 343         $options = $listService->getOptionsByListName('Clinical_Note_Type', ['notes' => $code]);
 344         return !empty($options);
 345     }
 346
 347     public function getClinicalNoteTypes()
 348     {
 349         $listService = new ListService();
 350         $options = $listService->getOptionsByListName('Clinical_Note_Type');
 351         return $this->getListAsSelectList($options);
 352     }
 353
 354     public function getClinicalNoteCategories()
 355     {
 356         $listService = new ListService();
 357         $options = $listService->getOptionsByListName('Clinical_Note_Category');
 358         return $this->getListAsSelectList($options);
 359     }
 360
 361     private function getListAsSelectList($optionsList)
 362     {
 363         if (empty($optionsList)) {
 364             return [];
 365         }
 366
 367         $selectList = [];
 368         foreach ($optionsList as $option) {
 369             $selectList[] = ['value' => $option['option_id'], 'code' => $option['notes'], 'title' => $option['title']];
 370         }
 371         return $selectList;
 372     }
 373 }