fhirsmith 0.7.6 → 0.8.2

package/tx/cs/cs-rxnorm.js

@@ -331,20 +331,20 @@ class RxNormServices extends CodeSystemProvider {
   async doesFilter(prop, op, value) {
     
 
-    prop = prop.toUpperCase();
+    let propUC = prop.toUpperCase();
 
     // TTY filters
-    if (prop === 'TTY' && ['=', 'in'].includes(op)) {
+    if (propUC === 'TTY' && ['=', 'in'].includes(op)) {
       return true;
     }
 
     // STY filter
-    if (prop === 'STY' && op === '=') {
+    if (propUC === 'STY' && op === '=') {
       return true;
     }
 
     // SAB filter
-    if (prop === 'SAB' && op === '=') {
+    if (propUC === 'SAB' && op === '=') {
       return true;
     }
 
@@ -370,12 +370,12 @@ class RxNormServices extends CodeSystemProvider {
     
 
     const filter = new RxNormFilterHolder();
-    prop = prop.toUpperCase();
+    let propUC = prop.toUpperCase();
 
     let sql = '';
     let params = {};
 
-    if (op === 'in' && prop === 'TTY') {
+    if (op === 'in' && propUC === 'TTY') {
       const values = value.split(',').map(v => v.trim()).filter(v => v);
       const placeholders = values.map((_, i) => `$tty${i}`).join(',');
       sql = `AND TTY IN (${placeholders})`;
@@ -383,36 +383,36 @@ class RxNormServices extends CodeSystemProvider {
         params[`tty${i}`] = this.#sqlWrapString(val);
       });
     } else if (op === '=') {
-      if (prop === 'STY') {
+      if (propUC === 'STY') {
         sql = `AND ${this.getCodeField()} IN (SELECT RXCUI FROM rxnsty WHERE TUI = $sty)`;
         params.sty = this.#sqlWrapString(value);
-      } else if (prop === 'SAB') {
+      } else if (propUC === 'SAB') {
         sql = `AND ${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE SAB = $sab)`;
         params.sab = this.#sqlWrapString(value);
-      } else if (prop === 'TTY') {
+      } else if (propUC === 'TTY') {
         sql = `AND TTY = $tty`;
         params.tty = this.#sqlWrapString(value);
       } else if (this.rels.includes(prop)) {
         if (value.startsWith('CUI:')) {
           const cui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI1 FROM rxnrel WHERE REL = $rel AND RXCUI2 = $cui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI2 FROM rxnrel WHERE REL = $rel AND RXCUI1 = $cui2)))`;
           params.rel = this.#sqlWrapString(prop);
           params.cui2 = this.#sqlWrapString(cui);
         } else if (value.startsWith('AUI:')) {
           const aui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI1 FROM rxnrel WHERE REL = $rel AND RXAUI2 = $aui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI2 FROM rxnrel WHERE REL = $rel AND RXAUI1 = $aui2)))`;
           params.rel = this.#sqlWrapString(prop);
           params.aui2 = this.#sqlWrapString(aui);
         }
       } else if (this.reltypes.includes(prop)) {
         if (value.startsWith('CUI:')) {
           const cui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI1 FROM rxnrel WHERE RELA = $rela AND RXCUI2 = $cui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI2 FROM rxnrel WHERE RELA = $rela AND RXCUI1 = $cui2)))`;
           params.rela = this.#sqlWrapString(prop);
           params.cui2 = this.#sqlWrapString(cui);
         } else if (value.startsWith('AUI:')) {
           const aui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI1 FROM rxnrel WHERE RELA = $rela AND RXAUI2 = $aui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI2 FROM rxnrel WHERE RELA = $rela AND RXAUI1 = $aui2)))`;
           params.rela = this.#sqlWrapString(prop);
           params.aui2 = this.#sqlWrapString(aui);
         }
@@ -429,7 +429,6 @@ class RxNormServices extends CodeSystemProvider {
   }
 
   async searchFilter(filterContext, filter, sort) {
-    
 
     if (!filter || !filter.stems || filter.stems.length === 0) {
       throw new Error('Invalid search filter');
@@ -499,8 +498,6 @@ class RxNormServices extends CodeSystemProvider {
   }
 
   async filterSize(filterContext, set) {
-    
-
     if (!set.executed) {
       await this.#executeFilter(set);
     }
@@ -709,6 +706,11 @@ class RxNormTypeServicesFactory extends CodeSystemFactoryProvider {
     const db = new sqlite3.Database(this.dbPath);
 
     try {
+      await new Promise((resolve, reject) => {
+        db.run(`CREATE INDEX IF NOT EXISTS idx_rxnstems_cui_stem ON RXNSTEMS(CUI, stem)`,
+          err => err ? reject(err) : resolve());
+      });
+
       this._sharedData = {
         version: '',
         rels: [],

package/tx/cs/cs-snomed.js

@@ -12,6 +12,7 @@ const {
 const {DesignationUse} = require("../library/designations");
 const {BaseCSServices} = require("./cs-base");
 const {formatDateMMDDYYYY} = require("../../library/utilities");
+const {ConceptMap} = require("../library/conceptmap");
 
 // Context kinds matching Pascal enum
 const SnomedProviderContextKind = {
@@ -371,6 +372,29 @@ class SnomedServices {
     return result;
   }
 
+  filterInactive(state) {
+    const result = new SnomedFilterContext();
+    result.inactive = state;
+    return result;
+  }
+
+  filterModuleId(id) {
+    const result = new SnomedFilterContext();
+    let concept = this.concepts.findConcept(id);
+    result.moduleId = concept.index;
+    return result;
+  }
+
+  filterByProperty(prop, value) {
+    const result = new SnomedFilterContext();
+    let p = this.concepts.findConcept(prop);
+    let v = this.concepts.findConcept(value);
+    result.propProp = p.index;
+    result.propValue = v.index;
+    return result;
+
+  }
+
   searchFilter(searchText, includeInactive = false, exactMatch = false) {
     const result = new SnomedFilterContext();
 
@@ -765,6 +789,12 @@ class SnomedProvider extends BaseCSServices {
           this._addCodeProperty(params, 'property', 'child', code, null, description);
         }
 
+        const moduleId = this.sct.concepts.getModuleId(ctxt.getReference());
+        if (moduleId) {
+          const code = this.sct.getConceptId(moduleId);
+          this._addCodeProperty(params, 'property', 'module', code, null, null);
+        }
+
         const relationships = this.sct.getConceptRelationships(ctxt.getReference());
         let set = new Set();
         for (let relationshipRef of relationships) {
@@ -812,10 +842,25 @@ class SnomedProvider extends BaseCSServices {
         return this.sct.conceptExists(value);
       }
     }
+    if (prop === 'inactive') {
+      return op === '=' && ['true', 'false'].includes(value);
+    }
+
+    if (prop === 'moduleId') {
+      const id = this.sct.stringToIdOrZero(value);
+      return id !== 0n && op === '=';
+    }
+
     if (prop == 'expressions' && op == '=' && ['true', 'false'].includes(value)) {
       return true;
     }
 
+    const cid = this.sct.stringToIdOrZero(prop);
+    if (cid != 0) {
+      const id = this.sct.stringToIdOrZero(value);
+      return id !== 0n && op === '=';
+    }
+
     return false;
   }
 
@@ -851,7 +896,38 @@ class SnomedProvider extends BaseCSServices {
           return null;
         }
         default:
-          throw new Error(`Unsupported filter operation: ${op}`);
+          throw new Error(`Unsupported filter operation: concept ${op} ${value}`);
+      }
+    }
+
+    if (prop === 'inactive') {
+      if (value !== 'true' && value !== 'false') {
+        throw new Error(`Invalid filter value: ${value}`);
+      }
+
+      switch (op) {
+        case '=': {
+          filterContext.filters.push(this.sct.filterInactive(value === 'true'));
+          return null;
+        }
+        default:
+          throw new Error(`Unsupported filter operation: inactive ${op} ${value}`);
+      }
+    }
+
+    if (prop === 'moduleId') {
+      const id = this.sct.stringToIdOrZero(value);
+      if (id === 0n) {
+        throw new Error(`Invalid concept ID: ${value}`);
+      }
+
+      switch (op) {
+        case '=': {
+          filterContext.filters.push(this.sct.filterModuleId(id));
+          return null;
+        }
+        default:
+          throw new Error(`Unsupported filter operation: moduleId ${op} ${value}`);
       }
     }
 
@@ -862,6 +938,24 @@ class SnomedProvider extends BaseCSServices {
       return null;
     }
 
+    const cid = this.sct.stringToIdOrZero(prop);
+    if (cid != 0) {
+
+      const id = this.sct.stringToIdOrZero(value);
+      if (id === 0n) {
+        throw new Error(`Invalid concept ID: ${value}`);
+      }
+
+      switch (op) {
+        case '=': {
+          filterContext.filters.push(this.sct.filterByProperty(cid, id));
+          return null;
+        }
+        default:
+          throw new Error(`Unsupported filter operation: ${prop} ${op} ${value}`);
+      }
+    }
+
     throw new Error(`Unsupported filter property: ${prop}`);
   }
 
@@ -893,7 +987,7 @@ class SnomedProvider extends BaseCSServices {
 
   async filterMore(filterContext, set) {
     set.cursor = set.cursor || 0;
-
+    this.#ensurePopulated(set);
     const size = await this.filterSize(filterContext, set);
     return set.cursor < size;
   }
@@ -927,12 +1021,27 @@ class SnomedProvider extends BaseCSServices {
     }
 
     const ctxt = conceptResult.context;
-
-
     const reference = ctxt.getReference();
     let found = false;
 
-    if (set.matches && set.matches.length > 0) {
+    if (set.inactive !== undefined) {
+      let concept = this.sct.concepts.getConcept(reference);
+      let active = (concept.flags & 0x0F) === 0;
+      found = active !== set.inactive
+    } else if (set.moduleId) {
+      let concept = this.sct.concepts.getConcept(reference);
+      let moduleId = this.sct.concepts.getModuleId(concept.index);
+      found = moduleId === set.moduleId;
+    } else if (set.propProp || set.propValue) {
+      found = false;
+      const relationships = this.sct.getConceptRelationships(reference);
+      for (let relationshipRef of relationships) {
+        const relationship = this.sct.relationships.getRelationship(relationshipRef);
+        if (set.propProp === relationship.relType && set.propValue === relationship.target) {
+          found = true;
+        }
+      }
+    } else if (set.matches && set.matches.length > 0) {
       found = set.matches.some(m => m.index === reference);
     } else if (set.members && set.members.length > 0) {
       found = set.members.some(m => m.ref === reference);
@@ -958,6 +1067,23 @@ class SnomedProvider extends BaseCSServices {
     }
 
     const reference = concept.getReference();
+    if (set.inactive !== undefined) {
+      return this.sct.isActive(reference) !== set.inactive;
+    }
+
+    if (set.moduleId) {
+      return this.sct.concepts.getModuleId(reference) === set.moduleId;
+    }
+
+    if (set.propProp || set.propValue) {
+      const relationships = this.sct.getConceptRelationships(reference);
+      for (let relationshipRef of relationships) {
+        const relationship = this.sct.relationships.getRelationship(relationshipRef);
+        if (set.propProp === relationship.relType && set.propValue === relationship.target) {
+          return true;
+        }
+      }
+    }
 
     if (set.matches && set.matches.length > 0) {
       return set.matches.some(m => m.index === reference);
@@ -970,6 +1096,42 @@ class SnomedProvider extends BaseCSServices {
     return false;
   }
 
+  #ensurePopulated(set) {
+    if (set.populationDone) {
+      return;
+    }
+    if (set.inactive !== undefined && set.descendants.length === 0) {
+      for (let i = 0; i < this.sct.concepts.count(); i++) {
+        let concept = this.sct.concepts.getConceptByCount(i);
+        let active = (concept.flags & 0x0F) === 0;
+        if (active !== set.inactive) {
+          set.descendants.push(concept.index);
+        }
+      }
+    }
+    if (set.moduleId) {
+      for (let i = 0; i < this.sct.concepts.count(); i++) {
+        let concept = this.sct.concepts.getConceptByCount(i);
+        let moduleId = this.sct.concepts.getModuleId(concept.index);
+        if (moduleId === set.moduleId) {
+          set.descendants.push(concept.index);
+        }
+      }
+    }
+    if (set.propProp || set.propValue) {
+      for (let i = 0; i < this.sct.concepts.count(); i++) {
+        let concept = this.sct.concepts.getConceptByCount(i);
+        const relationships = this.sct.getConceptRelationships(concept.getReference());
+        for (let relationshipRef of relationships) {
+          const relationship = this.sct.relationships.getRelationship(relationshipRef);
+          if (set.propProp === relationship.relType && set.propValue === relationship.target) {
+            set.descendants.push(concept.index);
+          }
+        }
+      }
+    }
+    set.populationDone = true;
+  }
 
   // Search filter
   async searchFilter(filterContext, filter, sort) {
@@ -1052,6 +1214,64 @@ class SnomedProvider extends BaseCSServices {
            (cd.use.code === '900000000000013009' || cd.use.code === '900000000000003001');
   }
 
+  async getTranslations(map, coding, target, reverse) {
+    if (!map || (target && target !== this.system()) || reverse) {
+      return [];
+    }
+    let ref = this.sct.concepts.findConcept(map.id);
+    if (!ref.found) {
+      return [];
+    }
+    let rref = this.sct.refSetIndex.getRefSetByConcept(ref.index);
+    if (rref == -1) {
+      return [];
+    }
+    let refSetRecord = this.sct.refSetIndex.getReferenceSet(rref);
+    let members = this.sct.refSetMembers.getMembers(refSetRecord.membersByRef);
+    let srcConcept = this.sct.concepts.findConcept(coding.code);
+    if (!srcConcept.found) {
+      return [];
+    }
+
+    let result = [];
+    let L = 0;
+    let H = members.length - 1;
+    while (L <= H) {
+      const I = Math.floor((L + H) / 2);
+      const ref = members[I].ref;
+      if (ref < srcConcept.index) {
+        L = I + 1;
+      } else if (ref > srcConcept.index) {
+        H = I - 1;
+      } else {
+        // Found — but scan left for first match in case of duplicates
+        let first = I;
+        while (first > 0 && members[first - 1].ref === srcConcept.index) {
+          first--;
+        }
+        // Process all matching members
+        for (let i = first; i < members.length && members[i].ref === srcConcept.index; i++) {
+          let values = this.sct.refs.getReferences(members[i].values);
+          if (values && values.length >= 1) {
+            let tgtId = String(this.sct.concepts.getConceptId(values[0]));
+            let ct = {
+              map: map.vurl,
+              code: tgtId,
+              system: this.system(),
+              version : this.version(),
+              display: await this.display(tgtId),
+              relationship: map.jsonObj.relationship
+            }
+            result.push(ct);
+          }
+        }
+        break;
+      }
+    }
+
+    return result;
+  }
+
 }
 
 /**
@@ -1178,7 +1398,7 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
         return null;
       }
       let rref = this.snomedServices.refSetIndex.getRefSetByConcept(ref.index);
-      if (rref == 0) {
+      if (rref == -1) {
         return null;
       }
       return {
@@ -1287,6 +1507,59 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
 
     return edition + ' ' + formatDateMMDDYYYY(match[2].substring(4, 6) + match[2].substring(6, 8) + match[2].substring(0, 4));
   }
+
+  async findImplicitConceptMap(url, version) {
+    if (version && (version !== this.version())) {
+      return null;
+    }
+    if (!url || !url.startsWith(this.system()+"?fhir_cm=")) {
+      return null;
+    }
+    let id = url.substring(url.indexOf("=")+1);
+    if (['900000000000523009', '900000000000526001', '900000000000527005', '900000000000530003'].includes(id)) {
+      let name = '';
+      let relationship = '';
+      switch (id) {
+        case '900000000000523009':
+          name = 'POSSIBLY EQUIVALENT TO';
+          relationship = 'inexact';
+          break;
+        case '900000000000526001':
+          name = 'REPLACED BY';
+          relationship = 'equivalent';
+          break;
+        case '900000000000527005':
+          name = 'SAME AS';
+          relationship = 'equal';
+          break;
+        case '900000000000530003':
+          name = 'ALTERNATIVE';
+          relationship = 'inexact';
+          break;
+      }
+      let cm = {
+        resourceType: 'ConceptMap',
+        internalSource : this,
+        relationship: relationship,
+        id : id,
+        url: `${this.system}?fhir_cm=${id}`,
+        version: this.version(),
+        name: `SNOMED CT ${name} Concept Map`,
+        description: `The concept map implicitly defined by the ${name} Association Reference Set`,
+        copyright: 'This value set includes content from SNOMED CT, which is copyright © 2002+ International Health Terminology Standards Development Organisation (SNOMED International), and distributed by agreement between SNOMED International and HL7',
+        status: 'active',
+        sourceUri: `${this.system}?fhir_vs`,
+        targetUri: `${this.system}?fhir_vs`,
+        group: [{
+          source: 'http://snomed.info/sct',
+          target: 'http://snomed.info/sct'
+        }]
+      }
+      return new ConceptMap(cm);
+    } else {
+      return null;
+    }
+  }
 }
 
 function getEditionName(edition) {

package/tx/data/cs-de.json

@@ -0,0 +1,186 @@
+{
+  "resourceType" : "CodeSystem",
+  "language" : "de",
+  "id" : "de-multi",
+  "url" : "http://hl7.org/fhir/test/CodeSystem/de-multi",
+  "name" : "TestCodeSystemMultiLangDE",
+  "title" : "Testcodesystem mit mehreren Sprachen",
+  "title:en" : "Test Code System with Multiple Languages",
+  "_title" : {
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+      "extension" : [{
+        "url" : "lang",
+        "valueCode" : "en"
+      },{
+        "url" : "content",
+        "valueString" : "Test Code System with Multiple Languages"
+      }]
+    }]
+  },
+  "status" : "active",
+  "experimental" : false,
+  "date" : "2023-04-01",
+  "publisher" : "FHIR Project",
+  "caseSensitive" : true,
+  "content" : "complete",
+  "concept" : [{
+    "code" : "code1",
+    "display" : "Anzeige 1",
+    "definition" : "Mein erster Code",
+    "definition:en" : "My first code",
+    "_definition" : {
+      "extension" : [{
+        "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+        "extension" : [{
+          "url" : "lang",
+          "valueCode" : "en"
+        },{
+          "url" : "content",
+          "valueString" : "My first code"
+        }]
+      }]
+    },
+    "designation" : [{
+      "language" : "en",
+      "value" : "Display 1"
+    }]
+  },
+  {
+    "code" : "code2",
+    "display" : "Anzeige 2",
+    "definition" : "Mein zweiter Code, mit Kindern",
+    "definition:en" : "My second code, with children",
+    "_definition" : {
+      "extension" : [{
+        "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+        "extension" : [{
+          "url" : "lang",
+          "valueCode" : "en"
+        },{
+          "url" : "content",
+          "valueString" : "My second code, with children"
+        }]
+      }]
+    },
+    "designation" : [{
+      "language" : "de-CH",
+      "value" : "Anzeige 2"
+    },{
+      "language" : "es",
+      "value" : "Mostrar 2"
+    },{
+      "language" : "en",
+      "value" : "Display 2"
+    }],
+    "concept" : [{
+      "code" : "code2a",
+      "display" : "Anzeige 2a",
+      "definition" : "Mein erster Second-Level-Code",
+      "definition:en" : "My first second level code",
+      "_definition" : {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+          "extension" : [{
+            "url" : "lang",
+            "valueCode" : "en"
+          },{
+            "url" : "content",
+            "valueString" : "My first second level code"
+          }]
+        }]
+      },
+      "designation" : [{
+        "language" : "en",
+        "value" : "Display 2a"
+      },{
+        "language" : "es",
+        "value" : "Mostrar 2a"
+      }],
+      "concept" : [{
+        "code" : "code2aI",
+        "display" : "Anzeige 2aI",
+        "definition" : "Mein erster Third-Level-Code",
+        "definition:en" : "My first third level code",
+        "_definition" : {
+          "extension" : [{
+            "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+            "extension" : [{
+              "url" : "lang",
+              "valueCode" : "en"
+            },{
+              "url" : "content",
+              "valueString" : "My first third level code"
+            }]
+          }]
+        },
+        "designation" : [{
+          "language" : "es",
+          "value" : "Mostrar 2aI"
+        }]
+      },
+      {
+        "code" : "code2aII",
+        "display" : "Anzeige 2aII",
+        "definition" : "Mein zweiter Third-Level-Code",
+        "definition:en" : "My second third level code",
+        "_definition" : {
+          "extension" : [{
+            "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+            "extension" : [{
+              "url" : "lang",
+              "valueCode" : "en"
+            },{
+              "url" : "content",
+              "valueString" : "My second third level code"
+            }]
+          }]
+        }
+      }]
+    },
+    {
+      "code" : "code2b",
+      "display" : "Anzeige 2b",
+      "definition" : "Mein zweiter Second-Level-Code",
+      "definition:en" : "My second second level code",
+      "_definition" : {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+          "extension" : [{
+            "url" : "lang",
+            "valueCode" : "en"
+          },{
+            "url" : "content",
+            "valueString" : "My second second level code"
+          }]
+        }]
+      },
+      "designation" : [{
+        "language" : "en",
+        "value" : "Display 2b"
+      }]
+    }]
+  },
+  {
+    "code" : "code3",
+    "display" : "Anzeige 3",
+    "definition" : "Mein Third-Level-Code",
+    "definition:en" : "My Third Level Code",
+    "_definition" : {
+      "extension" : [{
+        "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+        "extension" : [{
+          "url" : "lang",
+          "valueCode" : "en"
+        },{
+          "url" : "content",
+          "valueString" : "My Third Level Code"
+        }]
+      }]
+    },
+    "designation" : [{
+      "language" : "en",
+      "value" : "Display 3"
+    }]
+  }]
+}