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Bulk Match Client: A CLI Application

The Bulk Match Client is an open-source command-line interface for matching FHIR Patient resources on a FHIR server based on a set of patient demographic information.

Installation

To install and use the Bulk Match Client CLI, you need to have Node.js installed on your system. This project requires Node v21 or above. We recommend using NVM to switch between different node versions.

# Use this if you have NVM; otherwise, use node >= v21
nvm use

# Then, install the relevant dependencies to run the CLI
npm install

Usage

After cloning and installing the project onto your machine, you can run the CLI using node .:

# Generic formula for running the CLI
node . [options]

# To see all available CLI options
node . --help

# An example of running the CLI with a custom config, and a CLI-specified FHIR URL and pointer to a patients.ndjson file
node . --config config/my-config.json -f https://bulk-match.smarthealthit.org/fhir/ --resource data/patients-to-match.ndjson

Options

There are many options for configuring the bulk-match-client. Default values are set by the client for many of them, but there are two ways of specifying custom options to suit your use case: Config Files and CLI arguments:

  1. First, you can create a new configuration files by duplicating our default config in config/template-config.js and specifying your options there. These will override the default values used by the client.
  2. Additionally, you can provide some options as CLI arguments, which will override the client's default values as well as those specified in custom config-files.

Below we break down which options are available to using these methods.

Config File Options

The Bulk Match Client uses js configuration files, but you can think of them as JSON configuration objects. The only reason to use JS is to allow for comments and type suggestions. Below are all the options that can be set in a configuration file.

Auth and FHIR Server Options:

  • string fhirUrl - FHIR server base URL. Can be overridden by the -f or --fhir-url CLI parameter.
  • string tokenUrl - The Bulk Data server token URL (use "none" or "" for open servers and "auto" to try to auto-detect it)
  • object privateKey - The private key (as JWK) used to sign authentication tokens. This is not needed for open servers
  • string clientId - This is not needed for open servers, but identifies the client when making requests. Important for connecting to protected servers
  • number accessTokenLifetime - The access token lifetime in seconds. Note that the authentication server may ignore or restrict this to its own boundaries

Bulk Match Parameter Options:

  • string resource - The patients to match; can be inline FHIR resources, a path to a FHIR JSON, a path to an NDJSON file, or a path to a directory containing FHIR JSON. Can be overridden using CLI parameter -r or --resource.
  • boolean onlySingleMatch - If there are multiple potential matches, the server should only return the single most appropriate match; defaults to false. Can be overridden using CLI flag -s or --onlySingleMatch
  • boolean onlyCertainMatches - If there are multiple potential matches, the server should be certain that each of the records are for the same patient. defaults to false. Can be overridden using CLI flag -C or --onlyCertainMatches
  • number count - Specifies the maximum number of records to return per resource. If no value is provided, the server may decide how many matches to return. Can be overridden using CLI parameter -c or --count
  • string _outputFormat - The value of the _outputFormat parameter for Bulk Data kick-off requests. Will be ignored if empty or falsy. Can be overridden from terminal parameter -F or --_outputFormat

Download related options:

  • string destination: Where to save the patient matches. Can be overridden from terminal parameter -d or --destination. Examples:
    • ./downloads - Save to local folder (relative to the config file)
    • downloads - Save to local folder (relative to the config file)
    • /path/to/downloads - Save to local folder (absolute path)
    • file:///path/to/downloads - Save to local folder (file url)
    • "" - do nothing
    • "none" - do nothing
    • "/dev/null" - do nothing
  • boolean saveManifest - In some cases it might be useful to also save the match manifest file along with the downloaded NDJSON files.
  • boolean addDestinationToManifest - The original match manifest will have an url property for each file, containing the source location. It his is set to true, add a destination property to each file containing the path (relative to the manifest file) to the saved file. This is ONLY used if saveManifest is set to true.

Logging related options:

  • string reporter - The default reporter is "cli". However, this format can look bloated when your STDOUT ends up in log files. For example, if you are using this tool as part of some kind of pipeline and want to maintain clean logs, then consider changing this to "text". Can be overridden from terminal parameter --reporter.
  • object log - Optional logging options (see below):
    • boolean log.enabled - Set this to false to disable logging. Optional (defaults to true).
    • string log.file - Path to the log file. Absolute, or relative to process CWD. If not provided, the file will be called log.ndjson and will be stored in the downloads folder.
    • object log.metadata - Key/value pairs to be added to every log entry. Can be used to add useful information (for example which site imported this data).
  • complex logResponseHeaders - ResponseHeaders to include in error logs for debugging purposes.
    • As for the complex type, valid values are "all" | "none" | string | RegExp | (string | RegExp)[]
    • When "all" is specified, all responseHeaders are returned. When "none" is specified, no responseHeaders are returned. Otherwise, log any responseHeaders matches against 1...* strings/regexp

Options relating to HTTP requests:

  • number retryAfterMSec - If the server does not provide Retry-after header use this number of milliseconds before checking the status again.
  • object requests - Custom options for every request. Many options are available so be careful what you specify here! See https://developer.mozilla.org/en-US/docs/Web/API/Fetch#options. Example: 
    requests: {
    headers: {
        "x-client-id": "whatever" // pass custom headers
    }
}
  • boolean autoRetryOnTransientError - Should requests be automatically retried when server's respond with Transient errors. Defaults to false, in which case users will be prompted before retrying.

CLI Parameters

Note that you can pass a --help parameter with the CLI to see this listed in your terminal.

short long description
--config [config] Relative path to config file. These options are merged with those defined in config/default.js
-f --fhir-url [url] FHIR server base URL. Must be set either as parameter or in the configuration file
-r --resource [resource/filepath] The patients to match; can be inline FHIR resources, a path to a FHIR JSON, a path to an NDJSON file, or a path to a directory containing FHIR JSON
-s --onlySingleMatch If there are multiple potential matches, the server should only return the single most appropriate match; defaults to false
-C --onlyCertainMatches If there are multiple potential matches, the server should be certain that each of the records are for the same patient. defaults to false
-c --count [number] Specifies the maximum number of records to return per resource. If no value is provided, the server may decide how many matches to return
-F --_outputFormat [file-format] The output format you expect back from the server
-d --destination [destination] Specifies the download destination. See config/template-config.js for examples
--reporter [reporterType] Reporter to use to render the output. cli renders fancy progress bars and tables. text is better for log files. Defaults to cli
--status [url] If a status request fails for some reason the client will exit. However, if the status endpoint is printed in the output, you can retry by passing it as --status option here

Environment Variables

There are two environment that can be passed to the client to modify it's logging behavior:

  • NODE_DEBUG - By setting this to "bulk-*", you will see all verbose debug-friendly logging that's be written across the app. This is (unsurprisingly) helpful when debugging. Additionally, you can increase the specificity of the ENV variable here to drill in on logs for a specific part of the app. To see what kinds of options are available, run a global find across the project searching for debuglog("bulk-.
  • ALL_TEST_OUTPUT - When running tests, some tests are performed by spawning a child process and running the client through that process (the helper responsible for this is the invoke method). Because this is a spawn-process, by default the output of that process is piped elsewhere. To align the child-process' output with the main-process' output pipes, set this variable to true or any other value.

License

This project is licensed under the Apache 2.0 License - see the LICENSE file for details.

Support

If you encounter any issues or have questions, please open an issue on GitHub.