fhirsmith 0.7.5 → 0.7.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +24 -0
- package/README.md +8 -0
- package/library/html.js +4 -0
- package/package.json +1 -1
- package/packages/package-crawler.js +104 -49
- package/packages/packages.js +14 -0
- package/publisher/publisher.js +117 -27
- package/registry/registry.js +97 -89
- package/root-bare-template.html +93 -0
- package/security.md +32 -0
- package/server.js +94 -47
- package/stats.js +6 -4
- package/tx/README.md +6 -6
- package/tx/cs/cs-api.js +3 -0
- package/tx/cs/cs-api.md +285 -0
- package/tx/importers/readme.md +3 -1
- package/tx/library.js +10 -4
- package/tx/provider.js +2 -1
- package/tx/tx-html.js +36 -9
- package/tx/tx.js +34 -11
- package/tx/vs/vs-database.js +42 -5
- package/tx/vs/vs-vsac.js +48 -0
- package/utilities/dashboard.html +274 -0
package/stats.js
CHANGED
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@@ -5,6 +5,7 @@ const escape = require('escape-html');
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class ServerStats {
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started = false;
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requestCount = 0;
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staticRequestCount = 0;
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requestTime = 0;
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// Collect metrics every 10 minutes
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intervalMs = 10 * 60 * 1000;
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@@ -27,7 +28,8 @@ class ServerStats {
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const now = Date.now();
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const currentMem = process.memoryUsage().heapUsed;
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const
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const combinedCount = this.requestCount + this.staticRequestCount;
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const requestsDelta = combinedCount - this.requestCountSnapshot;
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const requestsTat = requestsDelta > 0 ? this.requestTime / requestsDelta : 0;
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const minutesSinceStart = this.history.length > 1
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? this.intervalMs / 60000
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@@ -38,7 +40,7 @@ class ServerStats {
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const idleDelta = currentCpu.idle - this.lastUsage.idle;
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const totalDelta = currentCpu.total - this.lastUsage.total;
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const percent = totalDelta > 0 ? 100 * (1 - idleDelta / totalDelta) : 0;
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const loopDelay = this.eventLoopMonitor.mean / 1e6;
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let cacheCount = 0;
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for (let m of this.cachingModules) {
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@@ -48,11 +50,11 @@ class ServerStats {
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this.history.push({time: now, mem: currentMem - this.startMem, rpm: requestsPerMin, tat: requestsTat, cpu: percent, block: loopDelay, cache : cacheCount});
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this.eventLoopMonitor.reset();
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this.requestCountSnapshot =
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this.requestCountSnapshot = combinedCount;
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this.requestTime = 0;
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this.lastTime = now;
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this.lastUsage = currentCpu;
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// Prune old data (keep 24 hours)
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const cutoff = now - (24 * 60 * 60 * 1000); // 24 hours ago
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this.history = this.history.filter(m => m.time > cutoff);
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package/tx/README.md
CHANGED
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@@ -201,7 +201,7 @@ Loads LOINC from a SQLite database file.
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```
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The filename is downloaded from the base URL if not cached. Database files must be in the server's proprietary format.
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The file is built by importing LOINC (
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The file is built by importing LOINC (see [documentation](importers/readme.md))
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#### `rxnorm` - RxNorm
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@@ -211,7 +211,7 @@ Loads RxNorm drug terminology from a SQLite database file.
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- rxnorm:rxnorm_02032025-a.db
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```
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The file is built by importing RxNorm (
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The file is built by importing RxNorm (see [documentation](importers/readme.md))
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#### `ndc` - NDC (National Drug Code)
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@@ -228,7 +228,7 @@ Loads FDA UNII codes from a SQLite database file.
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```yaml
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- unii:unii_20240622.db
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```
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The file is built by importing UNII (
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The file is built by importing UNII (see [documentation](importers/readme.md))
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#### `snomed` - SNOMED CT
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@@ -254,7 +254,7 @@ Common edition identifiers:
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- `nl` - Netherlands
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- `ips` - IPS (International Patient Summary) Free Set
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The file is built by importing SNOMED CT (
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The file is built by importing SNOMED CT (see [documentation](importers/readme.md))
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#### `cpt` - CPT (Current Procedural Terminology)
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@@ -267,7 +267,7 @@ Loads CPT codes from a SQLite database file.
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**Note:** CPT is copyrighted by the American Medical Association. Ensure you have appropriate licensing.
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The file is built by importing CPT (
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The file is built by importing CPT (see [documentation](importers/readme.md))
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#### `omop` - OMOP Vocabularies
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@@ -276,7 +276,7 @@ Loads OMOP (Observational Medical Outcomes Partnership) vocabulary mappings from
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```yaml
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- omop:omop_v20250227.db
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```
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The file is built by importing OMOP (
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The file is built by importing OMOP (see [documentation](importers/readme.md))
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#### `npm` - FHIR NPM Packages
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package/tx/cs/cs-api.js
CHANGED
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@@ -9,6 +9,9 @@ const {validateParameter, validateArrayParameter} = require("../../library/utili
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const {I18nSupport} = require("../../library/i18nsupport");
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const {VersionUtilities} = require("../../library/version-utilities");
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/**
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* For documentation, see cs-api.md
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*/
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class FilterExecutionContext {
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filters = [];
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forIterate = false;
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package/tx/cs/cs-api.md
ADDED
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@@ -0,0 +1,285 @@
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# CodeSystem Provider API
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## Introduction
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The CodeSystem Provider API defines the contract between the FHIR terminology server and the
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individual code system implementations that back it. It consists of two abstract base classes:
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- **`CodeSystemProvider`** — represents a live, per-request provider for a specific code system
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(bound to an `OperationContext`). One instance is created per request.
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- **`CodeSystemFactoryProvider`** — a long-lived factory that the server holds in memory and
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uses to construct `CodeSystemProvider` instances on demand.
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Implementors subclass `CodeSystemProvider` and override the methods marked *must override*.
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The remaining methods have sensible defaults that can optionally be overridden to improve
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fidelity or performance.
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### OperationContext
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Every `CodeSystemProvider` is constructed with an `OperationContext` that carries
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per-request state: the requested languages (`opContext.langs`), a usage tracker, and other
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request-scoped information. Providers must store and consult this context when making
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language-sensitive decisions.
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### Supplements
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A provider may be constructed with an array of `CodeSystem` supplement resources. These are
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FHIR CodeSystem resources with `content = supplement`, and they supply additional displays and
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designations for codes that exist in the base code system. The base class provides helper
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methods (`_displayFromSupplements`, `_listSupplementDesignations`, `_hasAnySupplementDisplays`)
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that implementors can call from their `display()` and `designations()` overrides.
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### Codes and Contexts
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Many methods accept either a raw `string` code or a `CodeSystemProviderContext` — an opaque
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handle returned by `locate()` and the iteration/filter machinery. Passing a context instead
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of a string allows implementations to avoid redundant lookups; the pattern is to locate a
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concept once, obtain a context, and then pass that context to subsequent property queries.
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---
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## Metadata
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These methods describe the code system as a whole. All are synchronous.
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### Required overrides
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| Method | Returns | Description |
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|---|---|---|
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| `system()` | `string` | The canonical URI of the code system (e.g. `http://loinc.org`). |
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| `version()` | `string` | The version of the code system. |
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| `description()` | `string` | A human-readable description of the code system. |
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| `totalCount()` | `integer` | The total number of concepts in the code system. |
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### Provided (with defaults)
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| Method | Default | Description |
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|---|---|---|
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| `name()` | `system()` + `\|` + `version()` | The versioned URI for the code system. Returns `system()` alone if there is no version. |
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| `vurl()` | Same as `name()` | Alias for the versioned URI. |
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| `defLang()` | `'en'` | The default language for displays in this code system. |
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| `contentMode()` | `CodeSystemContentMode.Complete` | Whether the code system is complete, a fragment, etc. |
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| `expandLimitation()` | `0` | A cap on expansion size (e.g. for CPT). `0` means no limit. |
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| `sourcePackage()` | `null` | The NPM package that contributed this code system, if known. |
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| `propertyDefinitions()` | `null` | The set of defined properties; override to expose them. |
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| `isNotClosed()` | `false` | Return `true` for grammar-based systems (e.g. UCUM) that cannot be fully enumerated. |
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| `isCaseSensitive()` | `true` | Whether code comparisons are case-sensitive. |
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| `hasParents()` | `false` | Whether the code system has a concept hierarchy. |
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| `specialEnumeration()` | `null` | Override to nominate a substitute enumeration (used by UCUM). |
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| `listFeatures()` | `null` | Return applicable server features. |
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| `status()` | `{}` | Return status metadata: `{ status, standardsStatus, experimental }`. |
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| `versionAlgorithm()` | `null` | The algorithm used for version comparison (e.g. `'semver'`, `'date'`). |
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| `versionNeeded()` | `false` | Whether a version must be specified when using this code system. |
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| `valueSet()` | `null` | The implicit value set URI for this code system, if any. |
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| `versionIsMoreDetailed(check, actual)` | `false` | Return `true` if `actual` is a more specific version than `check` (used by SCT edition handling). |
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| `hasSupplement(url)` | — | Returns `true` if the named supplement is in scope. |
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| `listSupplements()` | — | Returns the versioned URIs of all supplements in scope. |
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| `hasAnyDisplays(languages)` | — | Returns `true` if there are displays available in the requested languages. |
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---
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## Code Properties
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These methods return information about an individual concept. Each accepts either a raw
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`string` code or a `CodeSystemProviderContext` obtained from `locate()`.
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All are `async`.
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### Required overrides
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| Method | Returns | Description |
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|---|---|---|
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| `code(code)` | `string` | Returns the canonical form of the code (may normalise case, whitespace, etc.). |
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| `display(code)` | `string` | The best available display for the concept given the languages in `opContext.langs`. Should consult supplements via `_displayFromSupplements()`. |
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| `definition(code)` | `string` | The definition for the concept, or `null`. |
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| `designations(code, displays)` | — | Populates the `ConceptDesignations` object with all available designations across all languages. Should call `_listSupplementDesignations()` to include supplement designations. |
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### Provided (with defaults)
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| Method | Default | Description |
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|---|---|---|
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| `isAbstract(code)` | `false` | Whether the concept is abstract (cannot be used in instances). |
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| `isInactive(code)` | `false` | Whether the concept is inactive. |
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| `isDeprecated(code)` | `false` | Whether the concept is deprecated. |
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| `getStatus(code)` | `null` | The status string for the concept. |
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| `itemWeight(code)` | `null` | The assigned item weight (used in questionnaire scoring). |
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| `parent(code)` | `null` | The parent concept, for hierarchical code systems. |
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| `extensions(code)` | `null` | FHIR extensions on the concept, if any. |
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| `properties(code)` | `[]` | The defined properties for the concept. |
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| `incompleteValidationMessage(code)` | `null` | A message explaining why validation may be incomplete (used by SCT). |
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| `sameConcept(a, b)` | `false` | Returns `true` if `a` and `b` refer to the same concept (e.g. different expression forms). |
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| `isDisplay(designation)` | `false` | Called for designations not already marked with a standard display use code; return `true` to treat the designation as a display. |
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| `subsumesTest(codeA, codeB)` | `'not-subsumed'` | Returns one of `equivalent`, `subsumes`, `subsumed-by`, or `not-subsumed`. |
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| `extendLookup(ctxt, props, params)` | — | Called during `$lookup`; add any additional properties to `params`. |
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---
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## Iteration
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Iteration allows the server to enumerate all concepts in a code system, for use in value set
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expansion. The pattern is:
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```js
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const iter = await provider.iteratorAll();
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let ctxt;
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while ((ctxt = await provider.nextContext(iter)) !== null) {
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const c = await provider.code(ctxt);
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const d = await provider.display(ctxt);
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// ...
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}
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```
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For hierarchical code systems, `iterator(code)` returns an iterator over the *children* of
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the given concept. Pass `null` to iterate the root concepts. `iteratorAll()` iterates
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everything regardless of hierarchy.
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| Method | Returns | Description |
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|---|---|---|
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| `iterator(code)` | `CodeSystemIterator \| null` | Returns an iterator over the children of the given concept, or over the root concepts if `code` is `null`. Return `null` if iteration is not supported. |
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| `iteratorAll()` | `CodeSystemIterator \| null` | Returns an iterator over all concepts. For flat code systems this delegates to `iterator(null)`; for hierarchical systems this must be overridden. |
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| `nextContext(iterator)` | `CodeSystemProviderContext \| null` | Advances the iterator and returns the next concept, or `null` when exhausted. |
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The default `iterator()` returns `null` (iteration not supported). The default `nextContext()`
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returns `null`. Override both to support expansion.
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---
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## Filters
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Filters are used when expanding value sets that use `include.filter` clauses. The filter
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workflow has two phases:
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**Phase 1 — preparation.** The server calls `getPrepContext(iterate)` to obtain a
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`FilterExecutionContext`, then calls `filter()` once for each filter clause in the include.
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After all filters have been registered, `executeFilters()` is called to obtain one or more
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`FilterConceptSet` objects.
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**Phase 2 — evaluation.** The server either iterates the result set
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(`filterMore` / `filterConcept`) or checks membership (`filterLocate` / `filterCheck`).
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```js
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const ctx = await provider.getPrepContext(true);
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await provider.filter(ctx, 'concept', 'is-a', 'some-code');
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const sets = await provider.executeFilters(ctx);
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const set = sets[0];
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while (await provider.filterMore(ctx, set)) {
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const concept = await provider.filterConcept(ctx, set);
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// ...
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}
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await provider.filterFinish(ctx);
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```
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+
| Method | Default | Description |
|
|
172
|
+
|---|---|---|
|
|
173
|
+
| `doesFilter(prop, op, value)` | `false` | Return `true` if the given filter property/operator/value combination is supported. |
|
|
174
|
+
| `getPrepContext(iterate)` | Returns a `FilterExecutionContext` | Returns the shared context object that will be passed to all subsequent filter calls. |
|
|
175
|
+
| `filter(ctx, prop, op, value)` | *must override if filters supported* | Registers a single filter clause. |
|
|
176
|
+
| `searchFilter(ctx, text, sort)` | throws | Registers a free-text search filter. |
|
|
177
|
+
| `specialFilter(ctx, sort)` | throws if `specialEnumeration()` set | Registers a special enumeration filter (UCUM). |
|
|
178
|
+
| `executeFilters(ctx)` | *must override if filters supported* | Finalises filter setup and returns `FilterConceptSet[]` for iteration or membership testing. |
|
|
179
|
+
| `filterSize(ctx, set)` | *must override* | Returns the number of concepts in the filter set. |
|
|
180
|
+
| `filtersNotClosed(ctx)` | `false` | Return `true` if the filter set is open-ended (grammar-based system). |
|
|
181
|
+
| `filterMore(ctx, set)` | *must override* | Advances the iterator; returns `true` if there is a current concept. |
|
|
182
|
+
| `filterConcept(ctx, set)` | *must override* | Returns the current concept as a `CodeSystemProviderContext`. |
|
|
183
|
+
| `filterLocate(ctx, set, code)` | *must override* | Finds a specific code in the filter set. Returns a `CodeSystemProviderContext` if found, or an error string if not. |
|
|
184
|
+
| `filterCheck(ctx, set, concept)` | *must override* | Returns `true` if the concept is in the filter set, or an error string if not. |
|
|
185
|
+
| `filterFinish(ctx)` | no-op | Called when the filter session is complete; release any resources held. |
|
|
186
|
+
|
|
187
|
+
### Alternative: `handlesSelecting` / `processSelection`
|
|
188
|
+
|
|
189
|
+
For large code systems where a value set selects codes from only that system, the server can
|
|
190
|
+
hand the entire include/exclude list to the provider in one call rather than using the filter
|
|
191
|
+
workflow above.
|
|
192
|
+
|
|
193
|
+
Override `handlesSelecting()` to return `true` and then implement `processSelection()`.
|
|
194
|
+
The method receives the full lists of includes and excludes, along with pagination parameters
|
|
195
|
+
if applicable, and returns `FilterConceptSet[]`.
|
|
196
|
+
|
|
197
|
+
---
|
|
198
|
+
|
|
199
|
+
## Lookup
|
|
200
|
+
|
|
201
|
+
Lookup supports the `$lookup` and `$validate-code` operations.
|
|
202
|
+
|
|
203
|
+
| Method | Description |
|
|
204
|
+
|---|---|
|
|
205
|
+
| `locate(code)` | Look up a code by string. Returns `{ context, message }`. If found, `context` is a `CodeSystemProviderContext` and `message` is `null`. If not found, `context` is `null` and `message` explains why. **Must override.** |
|
|
206
|
+
| `locateIsA(code)` | Look up a code within the scope of a parent concept. Required only if `hasParents()` returns `true`. |
|
|
207
|
+
| `extendLookup(ctxt, props, params)` | Called during `$lookup` to allow the provider to add extra properties to the response `Parameters`. The `props` array lists the property names requested by the client. |
|
|
208
|
+
|
|
209
|
+
The server calls `locate()` first to confirm the code exists, then uses the returned context
|
|
210
|
+
to call `display()`, `definition()`, `designations()`, `properties()`, `extensions()`, and
|
|
211
|
+
`extendLookup()` as needed to build the lookup response.
|
|
212
|
+
|
|
213
|
+
---
|
|
214
|
+
|
|
215
|
+
## Translations
|
|
216
|
+
|
|
217
|
+
Code systems that define implicit concept maps (for example, cross-version extension mappings)
|
|
218
|
+
can surface translations via the `$translate` operation.
|
|
219
|
+
|
|
220
|
+
These methods are on **`CodeSystemProvider`**:
|
|
221
|
+
|
|
222
|
+
| Method | Default | Description |
|
|
223
|
+
|---|---|---|
|
|
224
|
+
| `registerConceptMaps(list)` | no-op | Called at startup; the provider should add any implicit `ConceptMap` resources it owns to `list`. |
|
|
225
|
+
| `getTranslations(coding, target)` | `null` | Returns `CodeTranslation[]` mapping the given `coding` to the `target` system, or `null` if no translation is available. |
|
|
226
|
+
|
|
227
|
+
These methods are on **`CodeSystemFactoryProvider`**:
|
|
228
|
+
|
|
229
|
+
| Method | Default | Description |
|
|
230
|
+
|---|---|---|
|
|
231
|
+
| `findImplicitConceptMaps(conceptMaps, source, dest)` | `null` | Returns concept maps between `source` and `dest` that are implicitly defined by this code system. |
|
|
232
|
+
| `findImplicitConceptMap(url, version)` | `null` | Returns a single implicit concept map by URL and version. |
|
|
233
|
+
|
|
234
|
+
---
|
|
235
|
+
|
|
236
|
+
## Known Value Sets and Concept Maps
|
|
237
|
+
|
|
238
|
+
Code system providers may have built-in knowledge of value sets and concept maps that are
|
|
239
|
+
defined as part of the code system's specification (for example, the FHIR core code systems
|
|
240
|
+
ship with a number of defined value sets).
|
|
241
|
+
|
|
242
|
+
These methods are on **`CodeSystemFactoryProvider`**:
|
|
243
|
+
|
|
244
|
+
| Method | Default | Description |
|
|
245
|
+
|---|---|---|
|
|
246
|
+
| `buildKnownValueSet(url, version)` | `null` | If the factory knows of a value set at `url` (optionally at `version`), build and return it as a `ValueSet` resource. Return `null` if not known. |
|
|
247
|
+
| `registerSupplements()` | `[]` | Returns a list of `CodeSystem` supplement resources whose metadata is known to the factory. Content may be omitted; the server will call `fillOutSupplement()` if it needs the full content. |
|
|
248
|
+
| `fillOutSupplement(supplement)` | no-op | Called by the server when it needs the full content of a supplement that was registered with partial content. The factory should populate `supplement` in-place. |
|
|
249
|
+
|
|
250
|
+
---
|
|
251
|
+
|
|
252
|
+
## CodeSystemFactoryProvider
|
|
253
|
+
|
|
254
|
+
The factory is a long-lived singleton that the server registers at startup and holds in
|
|
255
|
+
memory for the lifetime of the server process. Its responsibilities are:
|
|
256
|
+
|
|
257
|
+
- Holding data loaded from disk or a database (call `load()` at startup).
|
|
258
|
+
- Creating per-request `CodeSystemProvider` instances via `build()`.
|
|
259
|
+
- Declaring implicit value sets, concept maps, and supplements.
|
|
260
|
+
|
|
261
|
+
### Required overrides
|
|
262
|
+
|
|
263
|
+
| Method | Description |
|
|
264
|
+
|---|---|
|
|
265
|
+
| `system()` | The canonical URI of the code system. |
|
|
266
|
+
| `name()` | A human-readable name including version information. |
|
|
267
|
+
| `version()` | The version of the code system data held by this factory. |
|
|
268
|
+
| `defaultVersion()` | The latest known version, used when no version is requested. |
|
|
269
|
+
| `id()` | A short identifier for this provider (used in logging and diagnostics). |
|
|
270
|
+
| `build(opContext, supplements)` | Construct and return a `CodeSystemProvider` bound to the given `OperationContext` and supplements. |
|
|
271
|
+
|
|
272
|
+
### Provided (with defaults)
|
|
273
|
+
|
|
274
|
+
| Method | Default | Description |
|
|
275
|
+
|---|---|---|
|
|
276
|
+
| `load()` | no-op | Called once at startup; load data from disk, database, or network here. |
|
|
277
|
+
| `nameBase()` | Delegates to `name()` | The name without version information. |
|
|
278
|
+
| `content()` | `'complete'` | The content mode of the code system (`complete`, `fragment`, etc.). |
|
|
279
|
+
| `getPartialVersion()` | Major.minor of `version()` if semver | A partial version string for flexible version matching. |
|
|
280
|
+
| `describeVersion(version)` | `'v' + version` | A display string for a version. |
|
|
281
|
+
| `useCount()` | — | The number of times `build()` has been called. |
|
|
282
|
+
| `recordUse()` | — | Increments the use count. |
|
|
283
|
+
| `iteratable()` | `false` | Return `true` if the code system supports iteration. |
|
|
284
|
+
| `codeLink(code)` | `undefined` | Return a URL linking to documentation for the given code, if available. |
|
|
285
|
+
| `close()` | no-op | Called at server shutdown; release database connections and other resources here. |
|
package/tx/importers/readme.md
CHANGED
|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
# TX-Import: Medical Terminology Import Tool
|
|
2
2
|
|
|
3
|
-
A comprehensive CLI tool for importing various medical terminology standards into SQLite databases and other formats
|
|
3
|
+
A comprehensive CLI tool for importing various medical terminology standards into SQLite databases and other formats
|
|
4
|
+
for use by FHIRsmith. The tool supports LOINC, SNOMED CT, UNII, NDC, and provides extensible architecture for
|
|
5
|
+
additional terminologies.
|
|
4
6
|
|
|
5
7
|
## Table of Contents
|
|
6
8
|
|
package/tx/library.js
CHANGED
|
@@ -65,7 +65,8 @@ class Library {
|
|
|
65
65
|
*/
|
|
66
66
|
conceptMapProviders;
|
|
67
67
|
|
|
68
|
-
|
|
68
|
+
packageSources = [];
|
|
69
|
+
externalSources = [];
|
|
69
70
|
|
|
70
71
|
baseUrl = null;
|
|
71
72
|
cacheFolder = null;
|
|
@@ -360,6 +361,9 @@ class Library {
|
|
|
360
361
|
const codeSystemProvider = new OCLCodeSystemProvider(config);
|
|
361
362
|
const valueSetProvider = new OCLValueSetProvider(config);
|
|
362
363
|
const conceptMapProvider = new OCLConceptMapProvider(config);
|
|
364
|
+
this.externalSources.push(codeSystemProvider);
|
|
365
|
+
this.externalSources.push(valueSetProvider);
|
|
366
|
+
this.externalSources.push(conceptMapProvider);
|
|
363
367
|
providerSet = {
|
|
364
368
|
config,
|
|
365
369
|
codeSystemProvider,
|
|
@@ -470,6 +474,7 @@ class Library {
|
|
|
470
474
|
let vsac = new VSACValueSetProvider(this.vsacCfg, this.stats);
|
|
471
475
|
vsac.initialize();
|
|
472
476
|
this.valueSetProviders.push(vsac);
|
|
477
|
+
this.externalSources.push(vsac);
|
|
473
478
|
//const mem = process.memoryUsage();
|
|
474
479
|
let time = Math.floor(Date.now() - this.lastTime).toString().padStart(5)+" ";
|
|
475
480
|
let system = "vsac".padEnd(50);
|
|
@@ -597,7 +602,7 @@ class Library {
|
|
|
597
602
|
const contentLoader = new PackageContentLoader(fullPackagePath);
|
|
598
603
|
await contentLoader.initialize();
|
|
599
604
|
|
|
600
|
-
this.
|
|
605
|
+
this.packageSources.push(contentLoader.id()+"#"+contentLoader.version());
|
|
601
606
|
|
|
602
607
|
let cp = new ListCodeSystemProvider();
|
|
603
608
|
const resources = await contentLoader.getResourcesByType("CodeSystem");
|
|
@@ -635,7 +640,7 @@ class Library {
|
|
|
635
640
|
const contentLoader = new PackageContentLoader(fullPackagePath);
|
|
636
641
|
await contentLoader.initialize();
|
|
637
642
|
|
|
638
|
-
this.
|
|
643
|
+
this.packageSources.push(contentLoader.id()+"#"+contentLoader.version());
|
|
639
644
|
|
|
640
645
|
let cp = new ListCodeSystemProvider();
|
|
641
646
|
const resources = await contentLoader.getResourcesByType("CodeSystem");
|
|
@@ -847,7 +852,8 @@ class Library {
|
|
|
847
852
|
provider.lastTime = this.lastTime;
|
|
848
853
|
provider.lastMemory = this.lastMemory;
|
|
849
854
|
provider.totalDownloaded = this.totalDownloaded;
|
|
850
|
-
provider.
|
|
855
|
+
provider.packageSources = this.packageSources;
|
|
856
|
+
provider.externalSources = this.externalSources;
|
|
851
857
|
|
|
852
858
|
|
|
853
859
|
// Now add the existing value set providers after the FHIR core packages
|
package/tx/provider.js
CHANGED
package/tx/tx-html.js
CHANGED
|
@@ -234,24 +234,44 @@ class TxHtmlRenderer {
|
|
|
234
234
|
html += await this.buildSearchForm(req);
|
|
235
235
|
|
|
236
236
|
// ===== Packages and Factories Section =====
|
|
237
|
-
html += '<hr/><h3>Content
|
|
237
|
+
html += '<hr/><h3>Source Content</h3>';
|
|
238
238
|
|
|
239
|
-
// List
|
|
240
|
-
html += '<h6>
|
|
241
|
-
if (provider.
|
|
242
|
-
const sorted = [...provider.
|
|
239
|
+
// List Packages
|
|
240
|
+
html += '<h6>FHIR Packages</h6>';
|
|
241
|
+
if (provider.packageSources && provider.packageSources.length > 0) {
|
|
242
|
+
const sorted = [...provider.packageSources].sort();
|
|
243
243
|
html += '<ul>';
|
|
244
244
|
for (const source of sorted) {
|
|
245
245
|
html += `<li>${escape(source)}</li>`;
|
|
246
246
|
}
|
|
247
247
|
html += '</ul>';
|
|
248
248
|
} else {
|
|
249
|
-
html += '<p><em>No
|
|
249
|
+
html += '<p><em>No FHIR Packages Loaded</em></p>';
|
|
250
250
|
}
|
|
251
251
|
|
|
252
|
-
//
|
|
253
|
-
|
|
254
|
-
|
|
252
|
+
// List Packages
|
|
253
|
+
html += '<h6>External Sources</h6>';
|
|
254
|
+
if (provider.externalSources && provider.externalSources.length > 0) {
|
|
255
|
+
const sorted = [...provider.externalSources].sort();
|
|
256
|
+
html += '<ul>';
|
|
257
|
+
for (const source of sorted) {
|
|
258
|
+
let n = source.name();
|
|
259
|
+
if (!n) {
|
|
260
|
+
n = source.sourcePackage();
|
|
261
|
+
}
|
|
262
|
+
let ii = source.infoName();
|
|
263
|
+
if (ii) {
|
|
264
|
+
html += `<li>${escape(n)} (<a href="info/${source.id()}">${ii}</a>)</li>`;
|
|
265
|
+
} else {
|
|
266
|
+
html += `<li>${escape(n)}</li>`;
|
|
267
|
+
}
|
|
268
|
+
}
|
|
269
|
+
html += '</ul>';
|
|
270
|
+
} else {
|
|
271
|
+
html += '<p><em>No External Sources Configured</em></p>';
|
|
272
|
+
}
|
|
273
|
+
|
|
274
|
+
html += '<h6 class="mt-4">Special CodeSystems</h6>';
|
|
255
275
|
html += '<table class="grid">';
|
|
256
276
|
html += '<thead><tr><th>Name</th><th>URI</th><th>Version</th><th>Use Count</th></tr></thead>';
|
|
257
277
|
html += '<tbody>';
|
|
@@ -1290,6 +1310,13 @@ class TxHtmlRenderer {
|
|
|
1290
1310
|
});
|
|
1291
1311
|
}
|
|
1292
1312
|
|
|
1313
|
+
async buildInfoPage(source, req) {
|
|
1314
|
+
let html = '';
|
|
1315
|
+
const infoContent = await source.info(req);
|
|
1316
|
+
html += infoContent;
|
|
1317
|
+
return html;
|
|
1318
|
+
}
|
|
1319
|
+
|
|
1293
1320
|
buildSourceOptions(provider) {
|
|
1294
1321
|
let result = '<option value=""></option>';
|
|
1295
1322
|
result += `<option value="internal">internal</option>`;
|
package/tx/tx.js
CHANGED
|
@@ -9,7 +9,7 @@ const express = require('express');
|
|
|
9
9
|
const path = require('path');
|
|
10
10
|
const Logger = require('../library/logger');
|
|
11
11
|
const { Library } = require('./library');
|
|
12
|
-
const { OperationContext, ResourceCache, ExpansionCache } = require('./operation-context');
|
|
12
|
+
const { OperationContext, ResourceCache, ExpansionCache, debugLog} = require('./operation-context');
|
|
13
13
|
const { LanguageDefinitions } = require('../library/languages');
|
|
14
14
|
const { I18nSupport } = require('../library/i18nsupport');
|
|
15
15
|
const { CodeSystemXML } = require('./xml/codesystem-xml');
|
|
@@ -965,6 +965,29 @@ class TXModule {
|
|
|
965
965
|
this.countRequest('home', Date.now() - start);
|
|
966
966
|
}
|
|
967
967
|
});
|
|
968
|
+
|
|
969
|
+
// External source info pages
|
|
970
|
+
router.get('/info/:id', async (req, res) => {
|
|
971
|
+
const start = Date.now();
|
|
972
|
+
try {
|
|
973
|
+
const source = req.txEndpoint.provider.externalSources.find(s => s.id() === req.params.id);
|
|
974
|
+
if (!source) {
|
|
975
|
+
res.status(404).send('Not found');
|
|
976
|
+
return;
|
|
977
|
+
}
|
|
978
|
+
let txhtml = new TxHtmlRenderer(new Renderer(req.txOpContext, req.txEndpoint.provider), this.liquid, this.languages, this.i18n, req.txEndpoint.path);
|
|
979
|
+
const content = await txhtml.buildInfoPage(source, req);
|
|
980
|
+
const html = await txhtml.renderPage(source.name(), content, req.txEndpoint, start);
|
|
981
|
+
res.setHeader('Content-Type', 'text/html');
|
|
982
|
+
res.send(html);
|
|
983
|
+
} catch (error) {
|
|
984
|
+
debugLog(error);
|
|
985
|
+
this.log.error(`Error rendering info page for ${req.params.id}: ${error.message}`);
|
|
986
|
+
res.status(500).send('Internal server error');
|
|
987
|
+
} finally {
|
|
988
|
+
this.countRequest('info', Date.now() - start);
|
|
989
|
+
}
|
|
990
|
+
});
|
|
968
991
|
}
|
|
969
992
|
|
|
970
993
|
/**
|
|
@@ -1153,16 +1176,16 @@ class TXModule {
|
|
|
1153
1176
|
ec = 0;
|
|
1154
1177
|
|
|
1155
1178
|
checkProperJson() { // jsonStr) {
|
|
1156
|
-
|
|
1157
|
-
|
|
1158
|
-
|
|
1159
|
-
|
|
1160
|
-
|
|
1161
|
-
|
|
1162
|
-
|
|
1163
|
-
|
|
1164
|
-
|
|
1165
|
-
|
|
1179
|
+
// const errors = [];
|
|
1180
|
+
// if (jsonStr.includes("[]")) errors.push("Found [] in json");
|
|
1181
|
+
// if (jsonStr.includes('""')) errors.push('Found "" in json');
|
|
1182
|
+
//
|
|
1183
|
+
// if (errors.length > 0) {
|
|
1184
|
+
// this.ec++;
|
|
1185
|
+
// const filename = `/Users/grahamegrieve/temp/tx-err-log/err${this.ec}.json`;
|
|
1186
|
+
// writeFileSync(filename, jsonStr);
|
|
1187
|
+
// throw new Error(errors.join('; '));
|
|
1188
|
+
// }
|
|
1166
1189
|
}
|
|
1167
1190
|
|
|
1168
1191
|
transformResourceForVersion(data, fhirVersion) {
|