src/Services/CodeTypesService.php

   1 <?php
   2
   3 /**
   4  * CodeTypesService.php
   5  *
   6  * @package   openemr
   7  * @link      http://www.open-emr.org
   8  * @author    Stephen Nielson <stephen@nielson.org>
   9  * @copyright Copyright (c) 2021 Stephen Nielson <stephen@nielson.org>
  10  * @license   https://github.com/openemr/openemr/blob/master/LICENSE GNU General Public License 3
  11  */
  12
  13 namespace OpenEMR\Services;
  14
  15 use OpenEMR\Services\FHIR\FhirCodeSystemConstants;
  16
  17 /**
  18  * Service for code type
  19  */
  20 class CodeTypesService
  21 {
  22     /**
  23      * @const string
  24      */
  25     const CODE_TYPE_SNOMED_CT = "SNOMED-CT";
  26     const CODE_TYPE_SNOMED = "SNOMED";
  27     const CODE_TYPE_CPT4 = "CPT4";
  28     const CODE_TYPE_LOINC = "LOINC";
  29     const CODE_TYPE_NUCC = "NUCC";
  30     const CODE_TYPE_RXNORM = "RXNORM";
  31     const CODE_TYPE_RXCUI = "RXCUI";
  32     const CODE_TYPE_ICD10 = 'ICD10';
  33     const CODE_TYPE_ICD10PCS = 'ICD10PCS';
  34     const CODE_TYPE_CPT = 'CPT';
  35     const CODE_TYPE_CVX = 'CVX';
  36     const CODE_TYPE_OID_HEALTHCARE_PROVIDER_TAXONOMY = "2.16.840.1.114222.4.11.1066";
  37     const CODE_TYPE_OID = array(
  38         '2.16.840.1.113883.6.96' => self::CODE_TYPE_SNOMED_CT,
  39         '2.16.840.1.113883.6.12' => self::CODE_TYPE_CPT4,
  40         '2.16.840.1.113883.6.1' => self::CODE_TYPE_LOINC,
  41         '2.16.840.1.113883.6.101' => self::CODE_TYPE_NUCC,
  42         '2.16.840.1.113883.6.88' => self::CODE_TYPE_RXNORM,
  43         '2.16.840.1.113883.6.90' => self::CODE_TYPE_ICD10,
  44         '2.16.840.1.113883.6.103' => 'ICD9-CM',
  45         '2.16.840.1.113883.6.104' => 'ICD9-PCS',
  46         '2.16.840.1.113883.6.4' => 'ICD10-PCS',
  47         '2.16.840.1.113883.6.14' => 'HCP',
  48         '2.16.840.1.113883.6.285' => 'HCPCS',
  49         '2.16.840.1.113883.5.2' => "HL7 Marital Status",
  50         '2.16.840.1.113883.12.292' => 'CVX',
  51         '2.16.840.1.113883.5.83' => 'HITSP C80 Observation Status',
  52         '2.16.840.1.113883.3.26.1.1' => 'NCI Thesaurus',
  53         '2.16.840.1.113883.3.88.12.80.20' => 'FDA',
  54         "2.16.840.1.113883.4.9" => "UNII",
  55         "2.16.840.1.113883.6.69" => "NDC",
  56         '2.16.840.1.113883.5.14' => 'HL7 ActStatus',
  57         '2.16.840.1.113883.6.259' => 'HL7 Healthcare Service Location',
  58         '2.16.840.1.113883.12.112' => 'DischargeDisposition',
  59         '2.16.840.1.113883.5.4' => 'HL7 Act Code',
  60         '2.16.840.1.113883.1.11.18877' => 'HL7 Relationship Code',
  61         '2.16.840.1.113883.6.238' => 'CDC Race',
  62         '2.16.840.1.113883.6.177' => 'NLM MeSH',
  63         '2.16.840.1.113883.5.1076' => "Religious Affiliation",
  64         '2.16.840.1.113883.1.11.19717' => "HL7 ActNoImmunicationReason",
  65         '2.16.840.1.113883.3.88.12.80.33' => "NUBC",
  66         '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
  67         '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
  68         '2.16.840.1.113883.6.13' => 'CDT',
  69         '2.16.840.1.113883.18.2' => 'AdministrativeSex',
  70         '2.16.840.1.113883.5.1' => 'AdministrativeGender',
  71         self::CODE_TYPE_OID_HEALTHCARE_PROVIDER_TAXONOMY => 'HealthCareProviderTaxonomy'
  72     );
  73     /**
  74      * @var array
  75      */
  76     public $installedCodeTypes;
  77     /**
  78      * @var bool
  79      */
  80     private $snomedInstalled;
  81     private $cpt4Installed;
  82     private $rxnormInstalled;
  83
  84     public function __construct()
  85     {
  86         // currently, our installed code types are
  87         global $code_types;
  88         $this->installedCodeTypes = $code_types;
  89
  90         $this->snomedInstalled = isset($code_types[self::CODE_TYPE_SNOMED_CT]);
  91         $this->cpt4Installed = isset($code_types[self::CODE_TYPE_CPT4]);
  92         $this->rxnormInstalled = isset($code_types[self::CODE_TYPE_RXNORM]);
  93     }
  94
  95     /**
  96      * Lookup the description for a series of codes in the database.  Eventually we would want to
  97      * remove the global lookup_code_descriptions and use this so we can mock these codes and improve our unit test speed.
  98      *
  99      * @param string $codes       - Is of the form "type:code;type:code; etc.".
 100      * @param string $desc_detail - Can choose either the normal description('code_text') or the brief description('code_text_short').
 101      * @return string               - Is of the form "description;description; etc.".
 102      * @see code_types.inc.php
 103      */
 104     public function lookup_code_description($codes, $desc_detail = "code_text"): string
 105     {
 106         if (empty($codes)) {
 107             return "";
 108         }
 109         $code_text = lookup_code_descriptions($codes, $desc_detail);
 110         if (empty($code_text)) {
 111             // let's return a description of code if available.
 112             // sometimes depending on code, long and/or short description may not be available.
 113             $desc_detail = $desc_detail == "code_text" ? "code_text_short" : "code_text";
 114             $code_text = lookup_code_descriptions($codes, $desc_detail);
 115         }
 116         return $code_text;
 117     }
 118
 119     /**
 120      *
 121      * @return bool - Returns true if the snomed-ct codes are installed
 122      */
 123     public function isSnomedCodesInstalled(): bool
 124     {
 125         return $this->snomedInstalled;
 126     }
 127
 128     /**
 129      *
 130      * @return bool - Returns whether the system has the cpt4 codes installed
 131      */
 132     public function isCPT4Installed(): bool
 133     {
 134         return $this->cpt4Installed;
 135     }
 136
 137     /**
 138      *
 139      * @return bool - Returns whether the system has the rxnorm codes installed
 140      */
 141     public function isRXNORMInstalled(): bool
 142     {
 143         return $this->rxnormInstalled;
 144     }
 145
 146     public function isInstalledCodeType($codeType): bool
 147     {
 148         return isset($this->installedCodeTypes[$codeType]);
 149     }
 150
 151     /**
 152      * @param       $code
 153      * @param false $useOid
 154      * @return string|null
 155      */
 156     public function getSystemForCode($code, $useOid = false)
 157     {
 158         $codeType = $this->getCodeTypeForCode($code);
 159         if (!empty($codeType)) {
 160             return $this->getSystemForCodeType($codeType);
 161         }
 162         return null;
 163     }
 164
 165     /**
 166      * @param $code
 167      * @return array
 168      */
 169     public function parseCode($code)
 170     {
 171         $parsedCode = $code;
 172         $parsedType = null;
 173         if (is_string($code) && strpos($code, ":") !== false) {
 174             $parts = explode(":", $code);
 175             $parsedCode = $parts[1];
 176             $parsedType = $parts[0];
 177         }
 178         return ['code' => $parsedCode, 'code_type' => $parsedType];
 179     }
 180
 181     /**
 182      * Returns a code with the code type prefixed
 183      *
 184      * @param $code string The value for the code that exists in the given code_type datadatabse
 185      * @param $type string The code_type that the code belongs to (SNOMED, RXCUI, ICD10, etc).
 186      * @return string  The fully typed code (TYPE:CODE)
 187      */
 188     public function getCodeWithType($code, $type, $oe_format = false)
 189     {
 190         if (empty($type) || empty($code)) {
 191             return "";
 192         }
 193         $tmp = explode(':', $code);
 194         if (is_array($tmp) && count($tmp ?? []) === 2) {
 195             if (!$oe_format) {
 196                 return $code;
 197             }
 198             // rebuild when code type format flag is set
 199             $type = $tmp[0];
 200             $code = $tmp[1];
 201         }
 202         if ($oe_format) {
 203             $type = $this->formatCodeType($type ?? "");
 204         }
 205         return ($type ?? "") . ":" . ($code ?? "");
 206     }
 207
 208     /**
 209      * @param $code
 210      * @return mixed
 211      */
 212     public function getCodeTypeForCode($code)
 213     {
 214         $parsedCode = $this->parseCode($code);
 215         return $parsedCode['code_type'];
 216     }
 217
 218     /**
 219      * @param string $codeType
 220      * @param false  $useOid
 221      * @return string|null
 222      */
 223     public function getSystemForCodeType($codeType, $useOid = false)
 224     {
 225         $system = null;
 226
 227         if ($useOid) {
 228             if (self::CODE_TYPE_SNOMED_CT == $codeType) {
 229                 $system = '2.16.840.1.113883.6.96';
 230             } elseif (self::CODE_TYPE_SNOMED == $codeType) {
 231                 $system = '2.16.840.1.113883.6.96';
 232             } elseif (self::CODE_TYPE_CPT4 == $codeType) {
 233                 $system = '2.16.840.1.113883.6.12';
 234             } elseif (self::CODE_TYPE_LOINC == $codeType) {
 235                 $system = '2.16.840.1.113883.6.1';
 236             } elseif (self::CODE_TYPE_ICD10 == $codeType) {
 237                 $system = '2.16.840.1.113883.6.90';
 238             } elseif (self::CODE_TYPE_RXCUI == $codeType || self::CODE_TYPE_RXNORM == $codeType) {
 239                 $system = '2.16.840.1.113883.6.88';
 240             } elseif (self::CODE_TYPE_CPT == $codeType) {
 241                 $system = '2.16.840.1.113883.6.12';
 242             } elseif (self::CODE_TYPE_CVX == $codeType) {
 243                 $system = '2.16.840.1.113883.12.292';
 244             } elseif (self::CODE_TYPE_ICD10PCS == $codeType) {
 245                 $system = '2.16.840.1.113883.6.4';
 246             }
 247         } else {
 248             if (self::CODE_TYPE_SNOMED_CT == $codeType) {
 249                 $system = FhirCodeSystemConstants::SNOMED_CT;
 250             } elseif (self::CODE_TYPE_SNOMED == $codeType) {
 251                 $system = FhirCodeSystemConstants::SNOMED_CT;
 252             } elseif (self::CODE_TYPE_NUCC == $codeType) {
 253                 $system = FhirCodeSystemConstants::NUCC_PROVIDER;
 254             } elseif (self::CODE_TYPE_LOINC == $codeType) {
 255                 $system = FhirCodeSystemConstants::LOINC;
 256             } elseif (self::CODE_TYPE_RXNORM == $codeType || self::CODE_TYPE_RXCUI == $codeType) {
 257                 $system = FhirCodeSystemConstants::RXNORM;
 258             }
 259         }
 260         if (empty($system)) {
 261             foreach (self::CODE_TYPE_OID as $oid => $system_code) {
 262                 if ($system_code == $codeType) {
 263                     return $oid;
 264                 }
 265             }
 266         }
 267         return $system;
 268     }
 269
 270     /**
 271      * @param string $type
 272      * @return string
 273      */
 274     public function formatCodeType($type)
 275     {
 276         switch (strtoupper(trim($type))) {
 277             case 'ICD10':
 278             case 'ICD10-CM':
 279             case 'ICD-10-CM':
 280             case 'ICD10CM':
 281                 $type = 'ICD10';
 282                 break;
 283             case 'SNOMED CT':
 284             case 'SNOMED-CT':
 285             case 'SNOMEDCT':
 286                 $type = 'SNOMED-CT';
 287                 if (!$this->isSnomedCodesInstalled()) {
 288                     $type = 'SNOMED CT'; // for valueset table lookups
 289                     break;
 290                 }
 291                 break;
 292             case 'RXCUI':
 293             case 'RXNORM':
 294                 if (!$this->isRXNORMInstalled() && $this->isInstalledCodeType('RXCUI')) {
 295                     $type = 'RXCUI'; // then let's use RxCUI for lookups
 296                 } else {
 297                     $type = 'RXNORM';
 298                 }
 299                 break;
 300             case 'CPT':
 301             case 'CPT4':
 302                 $type = 'CPT4';
 303                 break;
 304             default:
 305                 if (strpos($type, '2.16.840.1.113883.') !== false) {
 306                     $type = $this->getCodeSystemNameFromSystem($type);
 307                 }
 308         }
 309         return $type ?? "";
 310     }
 311
 312     public function getCodeSystemNameFromSystem($oid): string
 313     {
 314         return self::CODE_TYPE_OID[$oid] ?? '';
 315     }
 316
 317     /**
 318      * Returns a resolved code set including using valueset table to try and get a code set.
 319      *
 320      * @param        $code
 321      * @param        $codeType
 322      * @param string $currentCodeText
 323      * @param string $codeDescriptionType
 324      * @return array
 325      */
 326     public function resolveCode($code, $codeType, $currentCodeText = '', $codeDescriptionType = 'code_text')
 327     {
 328         $valueset = '';
 329         $valueset_name = '';
 330         $default = array(
 331             'code' => $code ?? '',
 332             'formatted_code' => $code . ':' . $codeType,
 333             'formatted_code_type' => $codeType ?? '',
 334             'code_text' => $currentCodeText,
 335             'system_oid' => '',
 336             'valueset' => '',
 337             'valueset_name' => ''
 338         );
 339         if (empty($code)) {
 340             $default['formatted_code'] = '';
 341             return $default;
 342         }
 343
 344         $formatted_type = $this->formatCodeType($codeType ?: '');
 345         $oid = $this->getSystemForCodeType($formatted_type, true);
 346         $formatted_code = $this->getCodeWithType($code ?? '', $formatted_type);
 347         if (empty($currentCodeText) && $this->isInstalledCodeType($formatted_type)) {
 348             $currentCodeText = $this->lookup_code_description($formatted_code, $codeDescriptionType);
 349         }
 350
 351         // use valueset table if code description not found.
 352         if (empty($currentCodeText)) {
 353             if (strpos($codeType, '2.16.840.1.113883.') !== false) {
 354                 $oid = trim($codeType);
 355                 $codeType = "";
 356             }
 357             $value = $this->lookupFromValueset($code, $formatted_type, $oid);
 358             $formatted_type = ($value['code_type'] ?? null) ?: $formatted_type;
 359             if (!empty($code) && !empty($formatted_type)) {
 360                 $formatted_code = $formatted_type . ':' . $code;
 361             }
 362             $oid = $value['code_system'] ?? '';
 363             $currentCodeText = $value['description'] ?? '';
 364             $valueset_name = $value['valueset_name'] ?? '';
 365             $valueset = $value['valueset'] ?? '';
 366         }
 367
 368         return array(
 369             'code' => $code ?? "",
 370             'formatted_code' => $formatted_code ?: $code,
 371             'formatted_code_type' => $formatted_type ?: $codeType,
 372             'code_text' => trim($currentCodeText),
 373             'system_oid' => $oid ?? "",
 374             'valueset' => $valueset ?? "",
 375             'valueset_name' => $valueset_name ?? ""
 376         );
 377     }
 378
 379     public function getInstalledCodeTypes()
 380     {
 381         return $this->installedCodeTypes ?? null;
 382     }
 383
 384     public function lookupFromValueset($code, $codeType, $codeSystem)
 385     {
 386         if (empty($codeSystem) && empty($codeType)) {
 387             $value = sqlQuery(
 388                 "Select * From valueset Where code = ? LIMIT 1",
 389                 array($code)
 390             );
 391         } else {
 392             $value = sqlQuery(
 393                 "Select * From valueset Where code = ? And (code_type = ? Or code_type LIKE ? Or code_system = ?)",
 394                 array($code, $codeType, "$codeType%", $codeSystem)
 395             );
 396         }
 397         return $value;
 398     }
 399
 400     public function dischargeOptionIdFromCode($formatted_code)
 401     {
 402         $listService = new ListService();
 403         $ret = $listService->getOptionsByListName('discharge-disposition', ['codes' => $formatted_code]) ?? '';
 404         return $ret[0]['option_id'] ?? '';
 405     }
 406
 407     public function dischargeCodeFromOptionId($option_id)
 408     {
 409         $listService = new ListService();
 410         return $listService->getListOption('discharge-disposition', $option_id)['codes'] ?? '';
 411     }
 412
 413     public function parseCodesIntoCodeableConcepts($codes)
 414     {
 415         $codes = explode(";", $codes);
 416         $codeableConcepts = array();
 417         foreach ($codes as $codeItem) {
 418             $parsedCode = $this->parseCode($codeItem);
 419             $codeType = $parsedCode['code_type'];
 420             $code = $parsedCode['code'];
 421             $system = $this->getSystemForCodeType($codeType);
 422             $codedesc = $this->lookup_code_description($codeItem);
 423             $codeableConcepts[$code] = [
 424                 'code' => $code
 425                 , 'description' => $codedesc
 426                 , 'code_type' => $codeType
 427                 , 'system' => $system
 428             ];
 429         }
 430         return $codeableConcepts;
 431     }
 432 }