fhirsmith 0.18.2 → 1.0.0

package/tx/cs/cs-mimetypes.js

@@ -741,12 +741,16 @@ class MimeTypeServicesFactory extends CodeSystemFactoryProvider {
    * @param {I18nSupport} i18n
    * @param {string} cacheFolder - where the downloaded copy of the IANA registry is kept
    * @param {Logger} log
+   * @param {Object} [options]
+   * @param {boolean} [options.readOnly] - only read the cached copy: never download or write
+   *   it (a tx-worker, cluster.md: the master refreshes it before the workers start)
    */
-  constructor(i18n, cacheFolder = null, log = null) {
+  constructor(i18n, cacheFolder = null, log = null, options = {}) {
     super(i18n);
     this.uses = 0;
     this.cacheFolder = cacheFolder;
     this.log = log;
+    this.readOnly = options.readOnly === true;
     this.registeredTypes = null;
   }
 
@@ -761,7 +765,13 @@ class MimeTypeServicesFactory extends CodeSystemFactoryProvider {
       return; // no cache configured: the registered filter is unavailable
     }
     const target = path.join(this.cacheFolder, IANA_MEDIA_TYPES_FILE);
-    await this.#refresh(target);
+    if (this.readOnly) {
+      if (!fs.existsSync(target)) {
+        this.log?.warn(`Mime types: no cached copy of the IANA registry at ${target} (a tx-worker reads the one the master downloads, and never downloads it)`);
+      }
+    } else {
+      await this.#refresh(target);
+    }
 
     if (fs.existsSync(target)) {
       try {

package/tx/cs/cs-ndc.js

@@ -3,6 +3,7 @@ const assert = require('assert');
 const { CodeSystem } = require('../library/codesystem');
 const { CodeSystemProvider, CodeSystemFactoryProvider} = require('./cs-api');
 const {validateArrayParameter} = require("../../library/utilities");
+const { guarded } = require('../library/sqlite-utilities');
 
 class NdcConcept {
   constructor(code, display, isPackage = false, key = null) {
@@ -31,10 +32,7 @@ class NdcServices extends CodeSystemProvider {
 
   // Clean up database connection when provider is destroyed
   close() {
-    if (this.db) {
-      this.db.close();
-      this.db = null;
-    }
+    this.closeDb();
   }
 
   // Metadata methods
@@ -134,6 +132,14 @@ class NdcServices extends CodeSystemProvider {
     }
   }
 
+  /**
+   * The concept's properties for $expand: built by extendLookup, so that an expansion reports
+   * the same properties $lookup does (see CodeSystemProvider._propertiesFromLookup)
+   */
+  async properties(context, names) {
+    return this._propertiesFromLookup(context, names);
+  }
+
   async extendLookup(ctxt, props, params) {
     validateArrayParameter(props, 'props', String);
     validateArrayParameter(params, 'params', Object);
@@ -248,7 +254,7 @@ class NdcServices extends CodeSystemProvider {
         params = [concept.key];
       }
 
-      this.db.get(sql, params, (err, row) => {
+      this.db.get(sql, params, guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (!row) {
@@ -277,7 +283,7 @@ class NdcServices extends CodeSystemProvider {
 
           resolve(result);
         }
-      });
+      }));
     });
   }
 
@@ -358,7 +364,7 @@ class NdcServices extends CodeSystemProvider {
         LIMIT 1
       `;
 
-      this.db.get(sql, [code, code], (err, row) => {
+      this.db.get(sql, [code, code], guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row) {
@@ -370,7 +376,7 @@ class NdcServices extends CodeSystemProvider {
         } else {
           resolve(null);
         }
-      });
+      }));
     });
   }
 
@@ -383,7 +389,7 @@ class NdcServices extends CodeSystemProvider {
         LIMIT 1
       `;
 
-      this.db.get(sql, [code], (err, row) => {
+      this.db.get(sql, [code], guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row) {
@@ -393,7 +399,7 @@ class NdcServices extends CodeSystemProvider {
         } else {
           resolve(null);
         }
-      });
+      }));
     });
   }
 
@@ -443,10 +449,10 @@ class NdcServices extends CodeSystemProvider {
           return;
       }
 
-      this.db.get(sql, (err, row) => {
+      this.db.get(sql, guarded(reject, (err, row) => {
         if (err) reject(err);
         else resolve(row.count);
-      });
+      }));
     });
   }
 
@@ -495,7 +501,7 @@ class NdcServices extends CodeSystemProvider {
           return;
       }
 
-      this.db.get(sql, [set._iterator.offset], (err, row) => {
+      this.db.get(sql, [set._iterator.offset], guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row) {
@@ -514,7 +520,7 @@ class NdcServices extends CodeSystemProvider {
           set._iterator.hasMore = false;
           resolve(null);
         }
-      });
+      }));
     });
   }
 
@@ -571,9 +577,14 @@ class NdcServices extends CodeSystemProvider {
 }
 
 class NdcServicesFactory extends CodeSystemFactoryProvider {
-  constructor(i18n, dbPath) {
+  /**
+   * @param {Object} [options] - {readOnly: true} in a tx-worker (cluster.md): the file is
+   *   the master's; this process opens it read-only
+   */
+  constructor(i18n, dbPath, options = {}) {
     super(i18n);
     this.dbPath = dbPath;
+    this.readOnly = !!options.readOnly;
     this.uses = 0;
     this._loaded = false;
     this._lookupTables = null;
@@ -601,17 +612,21 @@ class NdcServicesFactory extends CodeSystemFactoryProvider {
     }
   }
 
+  #open() {
+    return this.readOnly ? new sqlite3.Database(this.dbPath, sqlite3.OPEN_READONLY) : new sqlite3.Database(this.dbPath);
+  }
+
   async load() {
     // Use temporary database connection for loading
-    const tempDb = new sqlite3.Database(this.dbPath);
+    const tempDb = this.#open();
 
     try {
       // Load version
       this._version = await new Promise((resolve, reject) => {
-        tempDb.get('SELECT Version FROM NDCVersion ORDER BY Version DESC LIMIT 1', (err, row) => {
+        tempDb.get('SELECT Version FROM NDCVersion ORDER BY Version DESC LIMIT 1', guarded(reject, (err, row) => {
           if (err) reject(err);
           else resolve(row ? row.Version : 'unknown');
-        });
+        }));
       });
 
       // Initialize lookup tables
@@ -632,30 +647,30 @@ class NdcServicesFactory extends CodeSystemFactoryProvider {
 
       for (const table of tables) {
         await new Promise((resolve, reject) => {
-          tempDb.all(table.sql, (err, rows) => {
+          tempDb.all(table.sql, guarded(reject, (err, rows) => {
             if (err) reject(err);
             else {
               const map = this._lookupTables[table.name];
               rows.forEach(row => map.set(row.NDCKey, row.Name));
               resolve();
             }
-          });
+          }));
         });
       }
 
       // Load counts
       this._packageCount = await new Promise((resolve, reject) => {
-        tempDb.get('SELECT COUNT(NDCKey) as count FROM NDCPackages', (err, row) => {
+        tempDb.get('SELECT COUNT(NDCKey) as count FROM NDCPackages', guarded(reject, (err, row) => {
           if (err) reject(err);
           else resolve(row.count);
-        });
+        }));
       });
 
       this._productCount = await new Promise((resolve, reject) => {
-        tempDb.get('SELECT COUNT(NDCKey) as count FROM NDCProducts', (err, row) => {
+        tempDb.get('SELECT COUNT(NDCKey) as count FROM NDCProducts', guarded(reject, (err, row) => {
           if (err) reject(err);
           else resolve(row.count);
-        });
+        }));
       });
 
     } finally {
@@ -673,7 +688,7 @@ class NdcServicesFactory extends CodeSystemFactoryProvider {
     this.recordUse();
 
     // Create fresh database connection for this provider instance
-    const db = new sqlite3.Database(this.dbPath);
+    const db = this.#open();
 
     return new NdcServices(
       opContext, supplements,

package/tx/cs/cs-omop.js

@@ -5,6 +5,7 @@ const { FilterExecutionContext, CodeSystemFactoryProvider } = require('./cs-api'
 const {validateOptionalParameter, validateArrayParameter} = require("../../library/utilities");
 const {ConceptMap} = require("../library/conceptmap");
 const {BaseCSServices} = require("./cs-base");
+const { guarded } = require('../library/sqlite-utilities');
 
 class OMOPConcept {
   constructor(code, display, domain, conceptClass, standard, vocabulary) {
@@ -135,10 +136,7 @@ class OMOPServices extends BaseCSServices {
   }
 
   close() {
-    if (this.db) {
-      this.db.close();
-      this.db = null;
-    }
+    this.closeDb();
   }
 
   // Metadata methods
@@ -166,10 +164,10 @@ class OMOPServices extends BaseCSServices {
 
   async totalCount() {
     return new Promise((resolve, reject) => {
-      this.db.get('SELECT COUNT(*) as count FROM Concepts', (err, row) => {
+      this.db.get('SELECT COUNT(*) as count FROM Concepts', guarded(reject, (err, row) => {
         if (err) reject(err);
         else resolve(row.count);
-      });
+      }));
     });
   }
 
@@ -245,7 +243,7 @@ class OMOPServices extends BaseCSServices {
             AND ConceptSynonyms.concept_id = ?
       `;
 
-      this.db.all(sql, [code], (err, rows) => {
+      this.db.all(sql, [code], guarded(reject, (err, rows) => {
         if (err) {
           reject(err);
         } else {
@@ -255,10 +253,26 @@ class OMOPServices extends BaseCSServices {
           }));
           resolve(synonyms);
         }
-      });
+      }));
     });
   }
 
+  /**
+   * The concept's properties for $expand: built by extendLookup, so that an expansion reports
+   * the same properties $lookup does (see CodeSystemProvider._propertiesFromLookup)
+   */
+  async properties(context, names) {
+    // a concept from a filter is partial (domain_id is the domain's concept id, no concept class
+    // or vocabulary): the properties are those of the concept itself
+    if (names && names.length > 0 && context instanceof OMOPConcept && context.conceptClass === '') {
+      const located = await this.locate(String(context.code));
+      if (located.context) {
+        context = located.context;
+      }
+    }
+    return this._propertiesFromLookup(context, names);
+  }
+
   async extendLookup(ctxt, props, params) {
     validateArrayParameter(props, 'props', String);
     validateArrayParameter(params, 'params', Object);
@@ -307,7 +321,7 @@ class OMOPServices extends BaseCSServices {
     return new Promise((resolve, reject) => {
       const sql = 'SELECT * FROM Concepts WHERE concept_id = ?';
 
-      this.db.get(sql, [ctxt.code], (err, row) => {
+      this.db.get(sql, [ctxt.code], guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row) {
@@ -337,7 +351,7 @@ class OMOPServices extends BaseCSServices {
         } else {
           resolve();
         }
-      });
+      }));
     });
   }
 
@@ -354,7 +368,7 @@ class OMOPServices extends BaseCSServices {
             AND ConceptRelationships.concept_id_1 = ?
       `;
 
-      this.db.all(sql, [ctxt.code], (err, rows) => {
+      this.db.all(sql, [ctxt.code], guarded(reject, (err, rows) => {
         if (err) {
           reject(err);
         } else {
@@ -367,7 +381,7 @@ class OMOPServices extends BaseCSServices {
           }
           resolve();
         }
-      });
+      }));
     });
 
     // Reverse relationships
@@ -380,7 +394,7 @@ class OMOPServices extends BaseCSServices {
             AND ConceptRelationships.concept_id_2 = ?
       `;
 
-      this.db.all(sql, [ctxt.code], (err, rows) => {
+      this.db.all(sql, [ctxt.code], guarded(reject, (err, rows) => {
         if (err) {
           reject(err);
         } else {
@@ -394,7 +408,7 @@ class OMOPServices extends BaseCSServices {
           }
           resolve();
         }
-      });
+      }));
     });
   }
 
@@ -512,7 +526,7 @@ class OMOPServices extends BaseCSServices {
             AND concept_id = ?
       `;
 
-      this.db.get(sql, [code], (err, row) => {
+      this.db.get(sql, [code], guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row && row.concept_id.toString() === code) {
@@ -528,7 +542,7 @@ class OMOPServices extends BaseCSServices {
         } else {
           resolve({ context: null, message: undefined });
         }
-      });
+      }));
     });
   }
 
@@ -605,7 +619,7 @@ class OMOPServices extends BaseCSServices {
     set.cursor++;
 
     return new OMOPConcept(
-      row.concept_id,
+      String(row.concept_id), // a code is a string (the expansion's code was a JSON number)
       row.concept_name,
       row.domain_id,
       '', // concept_class not in basic filter query
@@ -657,7 +671,9 @@ class OMOPServices extends BaseCSServices {
   }
 
 
-  // Subsumption testing - not implemented
+  // Subsumption: this provider has no hierarchy (the OMOP concept_ancestor table isn't
+  // imported), so two concepts that both exist are not-subsumed (the caller deals with equal
+  // codes: equivalent)
   async subsumesTest(codeA, codeB) {
     await this.#ensureContext(codeA);
     await this.#ensureContext(codeB);
@@ -683,7 +699,7 @@ class OMOPServices extends BaseCSServices {
           WHERE concept_id = ? AND vocabulary_id = ?
       `;
 
-      this.db.all(sql, [coding.code, vocabId], (err, rows) => {
+      this.db.all(sql, [coding.code, vocabId], guarded(reject, (err, rows) => {
         if (err) {
           reject(err);
         } else {
@@ -696,7 +712,7 @@ class OMOPServices extends BaseCSServices {
           }));
           resolve(translations);
         }
-      });
+      }));
     });
   }
 
@@ -712,7 +728,7 @@ class OMOPServices extends BaseCSServices {
             AND Domains.domain_concept_id = Concepts.concept_id
       `;
 
-      this.db.get(sql, [domain], (err, row) => {
+      this.db.get(sql, [domain], guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row && row.domain_id === domain) {
@@ -740,7 +756,7 @@ class OMOPServices extends BaseCSServices {
         } else {
           reject(new Error(`Unknown Value Domain ${id}`));
         }
-      });
+      }));
     });
   }
 
@@ -749,7 +765,7 @@ class OMOPServices extends BaseCSServices {
     return new Promise((resolve, reject) => {
       const sql = 'SELECT DISTINCT vocabulary_id FROM Concepts';
 
-      this.db.all(sql, (err, rows) => {
+      this.db.all(sql, guarded(reject, (err, rows) => {
         if (err) {
           reject(err);
         } else {
@@ -774,7 +790,7 @@ class OMOPServices extends BaseCSServices {
           }
           resolve();
         }
-      });
+      }));
     });
   }
 
@@ -784,9 +800,14 @@ class OMOPServices extends BaseCSServices {
 }
 
 class OMOPServicesFactory extends CodeSystemFactoryProvider {
-  constructor(i18n, dbPath) {
+  /**
+   * @param {Object} [options] - {readOnly: true} in a tx-worker (cluster.md): the file is
+   *   the master's; this process opens it read-only
+   */
+  constructor(i18n, dbPath, options = {}) {
     super(i18n);
     this.dbPath = dbPath;
+    this.readOnly = !!options.readOnly;
     this.uses = 0;
     this._loaded = false;
     this._sharedData = null;
@@ -855,8 +876,12 @@ class OMOPServicesFactory extends CodeSystemFactoryProvider {
     }
   }
 
+  #open() {
+    return this.readOnly ? new sqlite3.Database(this.dbPath, sqlite3.OPEN_READONLY) : new sqlite3.Database(this.dbPath);
+  }
+
   async load() {
-    const db = new sqlite3.Database(this.dbPath);
+    const db = this.#open();
 
     try {
       this._sharedData = {
@@ -880,7 +905,7 @@ class OMOPServicesFactory extends CodeSystemFactoryProvider {
           WHERE vocabulary_id = 'OMOP Extension'
       `;
 
-      db.get(sql, (err, row) => {
+      db.get(sql, guarded(reject, (err, row) => {
         if (err) {
           reject(err);
         } else if (row) {
@@ -894,7 +919,7 @@ class OMOPServicesFactory extends CodeSystemFactoryProvider {
           this._sharedData._version = 'unknown';
           resolve();
         }
-      });
+      }));
     });
   }
 
@@ -907,7 +932,7 @@ class OMOPServicesFactory extends CodeSystemFactoryProvider {
     this.recordUse();
 
     // Create fresh database connection for this provider instance
-    const db = new sqlite3.Database(this.dbPath);
+    const db = this.#open();
 
     return new OMOPServices(opContext, supplements, db, this._sharedData);
   }