ASU SHARES CLI

Command-line utilities aimed at supporting FHIR Consent management and CQL (Clinical Quality Language) operations on FHIR servers. Written and maintained in TypeScript using the Commander library.

CLI Usage

asushares --version for CLI utility version information asushares --help for subcommand documentation and examples

Subcommands

1. convert <filePath> [outputPath]

Converts a .cql file to a base64 encoded string.

• Arguments:
  • <filePath>: Path to the .cql file.
  • [outputPath] (optional): Path to save the base64 encoded output.
• Usage:

  ts-node asushares.ts convert myfile.cql output.txt

  • If outputPath is omitted, it outputs the base64 string to the console.

2. create-fhir-bundle <filePath> <outputPath> <description> [ipUrl]

Creates a FHIR bundle from a .cql file and saves it as a JSON file.

• Arguments:
  • <filePath>: Path to the .cql file.
  • <outputPath>: Path to save the generated FHIR bundle JSON file.
  • <description>: Description of the library.
  • [ipUrl] (optional): Base URL for the FHIR Library (default is http://localhost:8080/fhir/Library/).
• Usage:

  ts-node asushares.ts create-fhir-bundle myfile.cql bundle.json "Description of the CQL library"

3. post-fhir <filePath> <url>

Posts a FHIR bundle JSON file to a specified FHIR server.

• Arguments:

  • <filePath>: Path to the JSON file containing the FHIR bundle.
  • <url>: Base URL of the FHIR server.

• Usage:

  ts-node asushares.ts post-fhir bundle.json http://localhost:8080/fhir

4. create-and-post <filePath> <outputPath> <description> <url>

Creates a FHIR bundle from a .cql file, saves it as a JSON file, and posts it to a specified URL.

• Arguments:

  • <filePath>: Path to the .cql file.
  • <outputPath>: Path to save the generated FHIR bundle JSON file.
  • <description>: Description of the library.
  • <url>: URL of the server to post the FHIR bundle.

• Usage:

  ts-node asushares.ts create-and-post myfile.cql bundle.json "Description of the CQL library" http://localhost:8080/fhir

5. synthea-upload <directory> <url> --dry-run -d

Upload a directory of Synthea-generated FHIR resources to a FHIR URL using Synthea file naming conventions and loading order.

• Arguments:

  • <directory>: Directory with Synthea-generate "fhir" resource files.
  • <url>: URL of the FHIR server to upload the resources to.
  • --dry-run -d: Perform a dry run without uploading any resources.

• Usage:

  ts-node asushares.ts synthea-upload /dir/to/synthea-files http://localhost:8080/fhir 

6. verify-codes <fhirPath> <csvFilePath> --delete

Verifies JSON files for relevant codes based on a provided CSV and deletes irrelevant files if the delete flag is set.

• Arguments:

  • <fhirPath>: Path to the directory containing JSON files.
  • <csvFilePath>: Path to the CSV file containing relevant codes. The following columns are expected, with no empty rows - Index,Code_Type,Code,Description,Category. The code maps code types eg. SNOWMED-CT to the required URL in the backend. A sample csv is present in the assets folder for reference purposes.
  • --delete: URL of the server to post the FHIR bundle. Optional.

• Usage:

  ts-node asushares.ts verify-codes /Users/username/Documents/synthea/output/fhir /Users/username/Documents/synthea/Verification_CSV.csv

7. valueset <ids...> [options]

Downloads VSAC ValueSets and optionally uploads them to a HAPI-FHIR server.

• Arguments:

  • <ids...>: VSAC OIDs or canonical URLs to process.

• Options:

  • --mode <m>: Specify the operation mode (definition, expansion, or both). Default: expansion.
  • --version <yyyymmdd>: Specify a specific VSAC ValueSet version.
  • --filter <text>: Apply a server-side filter for $expand (optional).
  • --out <dir>: Output directory for downloaded files. Default: ./valuesets.
  • --post <fhirBaseUrl>: Post the downloaded ValueSets to a FHIR server.
  • --post-mode <m>: Specify the upload mode (definition or expanded). Default: expanded.
  • --bundle: Wrap uploads in a transaction Bundle.
  • --umls-key <key>: UMLS API key (overrides the UMLS_API_KEY environment variable).
  • --count <n>: Expansion page size. Default: 1000.
  • --concurrency <n>: Number of concurrent OIDs to fetch. Default: 4.
  • --retry <n>: Maximum retries for transient errors. Default: 3.
  • --cache <dir>: Cache directory for fetched pages. Default: .vsac_cache.
  • --dry-run: Print actions without making changes. Default: false.

• Usage:

  ts-node asushares.ts valueset 2.16.840.1.113762.1.4.1110.71 2.16.840.1.113883.3.464.1003.106.11.1001 --out ./valuesets

  ts-node asushares.ts valueset 2.16.840.1.113762.1.4.1110.71 --mode both --post http://hapi.fhir.server/baseR4

  ts-node asushares.ts valueset 2.16.840.1.113762.1.4.1110.71 --umls-key your-umls-key --cache ./custom_cache

## Dependencies

 - commander: Command-line argument parsing.
 - fs: File system operations.
 - axios: Making HTTP requests.
 - ts-progress: Simple progress bar.
 - csv-parser: Used for parsing input csvs.

## Attribution

Authors:

- Abhishek Dhadwal
- Preston Lee

Released under the Apache 2.0 license.