fhirsmith 0.14.1 → 0.15.0

package/tx/library.js

@@ -39,6 +39,7 @@ const { OCLValueSetProvider } = require('./ocl/vs-ocl');
 const { OCLConceptMapProvider } = require('./ocl/cm-ocl');
 const {UriServicesFactory} = require("./cs/cs-uri");
 const {debugLog} = require("./operation-context");
+const { checkIdPrefix } = require("./library/resource-ids");
 
 /**
  * This class holds all the loaded content ready for processing
@@ -72,6 +73,17 @@ class Library {
   packageSources = [];
   externalSources = [];
 
+  /**
+   * {Map<Object, string>} the id prefix the library YAML gives for the source a provider was
+   * loaded from (npm:hl7.terminology=tho), by provider
+   */
+  #sourcePrefixes = new Map();
+
+  /**
+   * {Set<string>} every id prefix the library YAML gives - autonumbered prefixes skip them
+   */
+  #givenPrefixes = new Set();
+
   baseUrl = null;
   cacheFolder = null;
   startTime = Date.now();
@@ -171,6 +183,8 @@ class Library {
 
     this.log.info('Fetching Data from '+this.baseUrl);
 
+    this.#checkSourcePrefixes(config.sources);
+
     for (const source of config.sources) {
       try {
         await this.processSource(source, this.packageManager, "fetch");
@@ -223,15 +237,20 @@ class Library {
     this.assignIds();
   }
 
-  async processSource(source, packageManager, mode) {
-    // Parse the source string
+  /**
+   * Parse a source entry from the library YAML: type[!]:details[=prefix]
+   *
+   * @param {string} source
+   * @returns {{type: string, details: string, isDefault: boolean, prefix: string|null}}
+   */
+  #parseSource(source) {
     const colonIndex = source.indexOf(':');
     if (colonIndex === -1) {
       throw new Error(`Invalid source format: ${source}`);
     }
 
     let type = source.substring(0, colonIndex);
-    const details = source.substring(colonIndex + 1);
+    let details = source.substring(colonIndex + 1);
 
     // Handle special markers (like ! for default)
     let isDefault = false;
@@ -240,6 +259,59 @@ class Library {
       isDefault = true;
     }
 
+    // the id prefix for the resources the source provides: everything after the last '='
+    let prefix = null;
+    const eqIndex = details.lastIndexOf('=');
+    if (eqIndex > -1) {
+      prefix = details.substring(eqIndex + 1);
+      details = details.substring(0, eqIndex);
+      const problem = checkIdPrefix(prefix);
+      if (problem) {
+        throw new Error(`Invalid source '${source}': ${problem}`);
+      }
+    }
+    return { type, details, isDefault, prefix };
+  }
+
+  /**
+   * Check the id prefixes the library YAML gives before anything is loaded - each id space
+   * must belong to one source
+   *
+   * @param {string[]} sources
+   */
+  #checkSourcePrefixes(sources) {
+    const seen = new Map();
+    for (const source of sources) {
+      const { prefix } = this.#parseSource(source);
+      if (prefix) {
+        if (seen.has(prefix)) {
+          throw new Error(`The id prefix '${prefix}' is given for both '${seen.get(prefix)}' and '${source}'`);
+        }
+        seen.set(prefix, source);
+      }
+    }
+  }
+
+  async processSource(source, packageManager, mode) {
+    const { type, details, isDefault, prefix } = this.#parseSource(source);
+
+    // the providers this source adds, so they can be given its id prefix
+    const csCount = this.codeSystemProviders.length;
+    const vsCount = this.valueSetProviders.length;
+    const cmCount = this.conceptMapProviders.length;
+
+    await this.#loadSource(type, details, isDefault, mode, packageManager);
+
+    if (prefix) {
+      this.#givenPrefixes.add(prefix);
+      for (const provider of [...this.codeSystemProviders.slice(csCount),
+        ...this.valueSetProviders.slice(vsCount), ...this.conceptMapProviders.slice(cmCount)]) {
+        this.#sourcePrefixes.set(provider, prefix);
+      }
+    }
+  }
+
+  async #loadSource(type, details, isDefault, mode, packageManager) {
     // Switch statement for different source types
     switch (type) {
       case 'internal':
@@ -664,7 +736,15 @@ class Library {
     const resources = await contentLoader.getResourcesByType("CodeSystem");
     let csc = 0;
     for (const resource of resources) {
-      const cs = new CodeSystem(await contentLoader.loadFile(resource, contentLoader.fhirVersion()));
+      let cs;
+      try {
+        cs = new CodeSystem(await contentLoader.loadFile(resource, contentLoader.fhirVersion()));
+      } catch (e) {
+        // one unacceptable resource (e.g. contained resources the server doesn't support)
+        // must not stop the rest of the package loading
+        this.log.warn(`Package ${contentLoader.pid()}: skipping CodeSystem ${resource.id || resource.filename || ''}: ${e.message}`);
+        continue;
+      }
       if (this.#isIgnored(cs.url, cs.version)) {
         this.log.info(`Ignoring CodeSystem ${cs.url}${cs.version ? '#' + cs.version : ''} (excluded by config)`);
         continue;
@@ -775,7 +855,14 @@ class Library {
     const csEntries = await contentLoader.getResourcesByType("CodeSystem");
     let csc = 0;
     for (const entry of csEntries) {
-      const cs = new CodeSystem(await contentLoader.loadFile(entry, contentLoader.fhirVersion()));
+      let cs;
+      try {
+        cs = new CodeSystem(await contentLoader.loadFile(entry, contentLoader.fhirVersion()));
+      } catch (e) {
+        // one unacceptable resource must not stop the rest of the package loading
+        this.log.warn(`Package ${contentLoader.pid()}: skipping CodeSystem ${entry.id || entry.filename || ''}: ${e.message}`);
+        continue;
+      }
       if (this.#isIgnored(cs.url, cs.version)) {
         this.log.info(`Ignoring CodeSystem ${cs.url}${cs.version ? '#' + cs.version : ''} (excluded by config)`);
         continue;
@@ -985,6 +1072,7 @@ class Library {
     // Now add the existing value set providers after the FHIR core packages
     provider.valueSetProviders.push(...this.valueSetProviders);
     provider.conceptMapProviders.push(...this.conceptMapProviders);
+    provider.applyTHOPrecedence();
 
     // bind UCUM common value set
     let ucum = provider.codeSystemFactories.get("http://unitsofmeasure.org");
@@ -1015,30 +1103,29 @@ class Library {
   }
 
   /**
-   * all the loaded resources must have unique IDs for the get operation
-   * they must be assigned by the library on loading. providers can either assign
-   * ids from the global space at start up, or, if they can provide new resources
-   * later in an ongoing fashion, allocate them in their own space
+   * Every loaded resource is served in the id space of the provider that loaded it: its id is
+   * the provider's spaceId, '-', and the id it had in its source (see
+   * tx/library/resource-ids.js). The spaceId is the prefix the library YAML gives for the
+   * provider's source, or, if it gives none, a number - the next one, counting providers of
+   * the same kind, that the YAML doesn't use as a prefix. Numbers depend on the order of the
+   * sources, so a source whose ids should stay the same when the YAML changes needs a prefix.
+   *
+   * (Code system factories don't have ids - they are not available directly.)
    */
   assignIds() {
-    let ids = new Set();
-    // these don't have ids - not available directly for (const cs of this.codeSystemFactories) { .. }
-    let i = 0;
-    for (const cp of this.codeSystemProviders) {
-      cp.spaceId = String(++i);
-      cp.assignIds(ids);
-    }
-    i = 0;
-    for (const vp of this.valueSetProviders) {
-      vp.spaceId = String(++i);
-      vp.assignIds(ids);
-    }
-    i = 0;
-    for (const cmp of this.conceptMapProviders) {
-      cmp.spaceId = String(++i);
-      cmp.assignIds(ids);
+    for (const providers of [this.codeSystemProviders, this.valueSetProviders, this.conceptMapProviders]) {
+      let n = 0;
+      for (const provider of providers) {
+        let spaceId = this.#sourcePrefixes.get(provider);
+        if (!spaceId) {
+          do {
+            n++;
+          } while (this.#givenPrefixes.has(String(n)));
+          spaceId = String(n);
+        }
+        provider.assignIds(spaceId);
+      }
     }
-
   }
 
   async close() {

package/tx/ocl/cm-ocl.cjs

@@ -3,6 +3,7 @@ const { ConceptMap } = require('../library/conceptmap');
 const { PAGE_SIZE } = require('./shared/constants');
 const { createOclHttpClient } = require('./http/client');
 const { fetchAllPages, extractItemsAndNext } = require('./http/pagination');
+const { stripIdPrefix } = require('../library/resource-ids');
 
 const DEFAULT_MAX_SEARCH_PAGES = 10;
 
@@ -24,7 +25,7 @@ class OCLConceptMapProvider extends AbstractConceptMapProvider {
     this._canonicalBySourceUrl = new Map();
   }
 
-  assignIds(ids) {
+  prefixIds() {
     if (!this.spaceId) {
       return;
     }
@@ -33,13 +34,18 @@ class OCLConceptMapProvider extends AbstractConceptMapProvider {
     this._idMap.clear();
 
     for (const cm of unique) {
-      if (!cm.id.startsWith(`${this.spaceId}-`)) {
-        const nextId = `${this.spaceId}-${cm.id}`;
-        cm.id = nextId;
-        cm.jsonObj.id = nextId;
-      }
+      this.#prefixId(cm);
       this._idMap.set(cm.id, cm);
-      ids.add(`ConceptMap/${cm.id}`);
+    }
+  }
+
+  // concept maps are served in this provider's id space - including the ones that arrive
+  // after the spaceId is assigned
+  #prefixId(cm) {
+    if (this.spaceId && cm.id && !cm.id.startsWith(`${this.spaceId}-`)) {
+      const nextId = `${this.spaceId}-${cm.id}`;
+      cm.id = nextId;
+      cm.jsonObj.id = nextId;
     }
   }
 
@@ -56,7 +62,7 @@ class OCLConceptMapProvider extends AbstractConceptMapProvider {
 
     const mappingId = this.#extractMappingId(url);
     if (mappingId) {
-      return await this.fetchConceptMapById(mappingId);
+      return await this.#fetchMappingById(mappingId);
     }
 
     try {
@@ -81,14 +87,15 @@ class OCLConceptMapProvider extends AbstractConceptMapProvider {
     if (this._idMap.has(id)) {
       return this._idMap.get(id);
     }
+    // only ids in this provider's space - the rest is the OCL mapping id
+    const rawId = stripIdPrefix(id, this.spaceId);
+    return rawId ? await this.#fetchMappingById(rawId) : null;
+  }
 
-    let rawId = id;
-    if (this.spaceId && id.startsWith(`${this.spaceId}-`)) {
-      rawId = id.substring(this.spaceId.length + 1);
-    }
-
-    if (this._idMap.has(rawId)) {
-      return this._idMap.get(rawId);
+  async #fetchMappingById(rawId) {
+    const id = this.spaceId ? `${this.spaceId}-${rawId}` : rawId;
+    if (this._idMap.has(id)) {
+      return this._idMap.get(id);
     }
 
     try {
@@ -378,6 +385,7 @@ class OCLConceptMapProvider extends AbstractConceptMapProvider {
   }
 
   #indexConceptMap(cm) {
+    this.#prefixId(cm);
     this.conceptMapMap.set(cm.url, cm);
     if (cm.version) {
       this.conceptMapMap.set(`${cm.url}|${cm.version}`, cm);

package/tx/ocl/cs-ocl.cjs

@@ -92,15 +92,12 @@ class OCLCodeSystemProvider extends AbstractCodeSystemProvider {
     }
   }
 
-  assignIds(ids) {
+  prefixIds() {
+    const codeSystems = [...new Set(this._idToCodeSystem.values())];
     this._usedIds.clear();
-    for (const cs of this._idToCodeSystem.values()) {
-      if (!cs.id || ids.has(`CodeSystem/${cs.id}`)) {
-        cs.id = String(ids.size);
-        cs.jsonObj.id = cs.id;
-      }
-      ids.add(`CodeSystem/${cs.id}`);
-      this._usedIds.add(cs.id);
+    this._idToCodeSystem.clear();
+    for (const cs of codeSystems) {
+      this.#trackCodeSystemId(cs);
       this._idToCodeSystem.set(cs.id, cs);
     }
   }
@@ -358,9 +355,11 @@ class OCLCodeSystemProvider extends AbstractCodeSystemProvider {
       return;
     }
 
-    if (!cs.id || this._usedIds.has(cs.id)) {
+    // code systems are served in this provider's id space
+    const prefix = this.spaceId ? `${this.spaceId}-` : '';
+    if (!cs.id || !cs.id.startsWith(prefix) || this._usedIds.has(cs.id)) {
       const raw = cs.id || cs.name || cs.url || 'ocl-cs';
-      const base = this.spaceId ? `${this.spaceId}-${raw}` : String(raw);
+      const base = raw.startsWith(prefix) ? String(raw) : `${prefix}${raw}`;
       let candidate = base;
       let index = 1;
       while (this._usedIds.has(candidate)) {

package/tx/ocl/vs-ocl.cjs

@@ -114,6 +114,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
             id: cached.canonicalUrl
           }, 'R5');
           this.#applyCachedCompose(valueSetObj, paramsKey);
+          this.#prefixId(valueSetObj);
           // Indexa o ValueSet restaurado para torná-lo disponível via fetchValueSet
           this.valueSetMap.set(valueSetObj.url, valueSetObj);
           if (valueSetObj.version) {
@@ -224,7 +225,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     }
   }
 
-  assignIds(ids) {
+  prefixIds() {
     if (!this.spaceId) {
       return;
     }
@@ -233,13 +234,18 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     this._idMap.clear();
 
     for (const vs of unique) {
-      if (!vs.id.startsWith(`${this.spaceId}-`)) {
-        const nextId = `${this.spaceId}-${vs.id}`;
-        vs.id = nextId;
-        vs.jsonObj.id = nextId;
-      }
+      this.#prefixId(vs);
       this._idMap.set(vs.id, vs);
-      ids.add(`ValueSet/${vs.id}`);
+    }
+  }
+
+  // value sets are served in this provider's id space - including the ones that arrive
+  // after the spaceId is assigned
+  #prefixId(vs) {
+    if (this.spaceId && vs.id && !vs.id.startsWith(`${this.spaceId}-`)) {
+      const nextId = `${this.spaceId}-${vs.id}`;
+      vs.id = nextId;
+      vs.jsonObj.id = nextId;
     }
   }
 
@@ -345,16 +351,9 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
   }
 
   #getLocalValueSetById(id) {
-    if (this._idMap.has(id)) {
-      return this._idMap.get(id);
-    }
-
-    if (this.spaceId && id.startsWith(`${this.spaceId}-`)) {
-      const unprefixed = id.substring(this.spaceId.length + 1);
-      return this._idMap.get(id) || this._idMap.get(unprefixed) || this.valueSetMap.get(unprefixed) || null;
-    }
-
-    return this._idMap.get(id) || this.valueSetMap.get(id) || null;
+    // _idMap is keyed by the ids the value sets are served with - prefixed, once the
+    // spaceId is assigned
+    return this._idMap.get(id) || null;
   }
 
   // eslint-disable-next-line no-unused-vars
@@ -391,6 +390,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
   }
 
   #indexValueSet(vs) {
+    this.#prefixId(vs);
     const existing = this.valueSetMap.get(vs.url) || null;
 
     // When fresh discovery metadata replaces a cold-cached entry, carry over