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awatson1978 / procure-wip

App for patients to retrieve and share their raw clinical data using SMART-on-FHIR

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Procure

Procure is early stage software and should not be deployed for broad production use at this time. Health records or information accessed using the software may not reflect a complete or accurate medical history and should not be used as a substitute for seeking official health records or professional medical judgment. The software may contain viruses, worms, spyware or other malware or defects that may alter health information or cause it to be inaccurate or incomplete. Individuals accessing their health records should consult with their health care provider prior to making any decisions related to their health.

Overview

Procure is an open source, web based application that that enables users to retrieve their clinical data from their healthcare providers, browse the data, download it as structured files in JSON FHIR format, download a subset of the data in Excel or CSV format, and send it with third parties. Patients can use the app to review their medical records for accuracy, perform analysis to obtain insights, or share their information with a research project. Unlike many apps that retrieve medical data, such as Apple Health, Procure does not store or interpret the data, instead acting as a conduit to empower patients with direct access to their raw data.

The app can connect to any healthcare provider that has an electronic health record system supporting the SMART-on-FHIR specification which currently includes most sites in the United States that use the Epic EHR. Many providers that use other EHR vendors are expected to deploy this connectivity later this year.

Developers can also use the app to test SMART on FHIR servers, or demonstrate the capabilities of these servers.

You can follow the instructions below to run a local copy of the app on your machine and retrieve data from test sandboxes. However, to access real medical data (even your own), you'll need to use a publicly hosted copy of the app, or host the app yourself at a public web URL that supports "HTTPS". If you host the app yourself, you'll also need to register the URL where it's posted with the systems you intend to connect to (see the Registering Procure section below for guidance).

Procure is compatible with the latest versions of Google Chrome, IE Edge, Safari and Firefox.

As early stage software, Procure has bugs. If you run into an issue, please review the "issues" tab on Github and, if the problem isn't listed, open a new issue ticket to let us know! Also, if you're a software developer and are able to fix the code, git pull requests are very welcome, but please get in touch before coding large changes.

Demo

Wizard UI - sample integration with historical data collection for a study

Patient UI - interface for patients interested in obtaining their own raw healthcare data or developers testing a FHIR server

Installing and Running Procure

Procure runs entirely as a web page in the user's browser and can be hosted from any web server that can serve static html, CSS, and javascript files (such as Amazon S3, Heroku, or even Github pages). Once the code is more stable, we may provide pre-complied releases, however, currently you can download and build the app using the following steps.

  1. Install prerequisites

  2. Clone this repository and install dependencies

    git clone [github path]/procure
cd procure
curl https://open.epic.com/MyApps/EndpointsJson -o ./public/config/epic_endpoints.json
npm i

  3. Start the Procure development server

    npm run start

Building and Deploying Procure

Before deploying Procure, you'll probably want to register your deployment URL with EHR vendors and update the Procure configuration. See the relevant sections below.

To build a production version of Procure, run the following command from the Procure directory npm run build. This will create (or update) a build sub-directory containing files that you can copy to your web server.

Registering Procure with EHR Vendors

Epic

Visit https://fhir.epic.com and navigate to the Build Apps item in the top menu bar (you'll need to register and verify your identity). Complete the create app form, making sure that the Redirect Url field is set to the URL where you'll be hosting Procure followed by /callback.html (eg. https://example.com/callback.html). Epic will generate a client id value for your instance of the app (note that it can take up to 24 hours for this value to propagate to EHRs and be ready for use). You'll want to add this value to the public/config/config-override.json file in Procure, so it looks something like this:

{
	"credentials": {
		"epic": {"clientId": "YOUR CLIENT ID HERE"}
	}
}

Configuring Procure

Much of Procure's functionality can be customized by changing or overriding values in its configuration file. These parameters are described in the sections below and there are examples of the parameters in the app's default configuration file.

Overriding Configuration Properties

You can modify Procure's settings by altering values in the public/config/config.json file. However, this file may be updated in new releases of Procure, requiring you to re-apply your changes. A better approach is to override specific configuration properties by adding them to the public/config/config-override.json file, which is unique to your Procure deployment. When Procure is run in development mode, the path to a config override file can be specified in the config querystring parameter. If this parameter isn't populated, the file public/config/config-override-dev.json will be loaded instead.

The root structure in the config-override.json or config-override-dev.json file must be a JSON object. At runtime, the properties of this object are merged with those in the config.json file. Additional properties will be added, and altered values will be replaced. For example, to change the title of the Argonaut (Epic) query profile, you would create the following object in your override file that mirrors the structure of the config file, setting a new title property. None of the other properties in the object hierarchy will be altered.

{
	"queryProfiles": {
		"argonaut_epic": {
			"title": "Epic EHR"
		}
	}
}

Sometimes you may wish to replace the object associated with a property entirely instead of merging properties. To do this, prefix the property name with an underscore in the override object. The following example replaces all of the queries in the argonaut_epic query profile with the single query from the override file.

{
	"queryProfiles": {
		"argonaut_epic": {
			"_queries": [{
				"resourcePath": "Patient/{{patientId}}",
				"retrieveReferences": "careProvider"
			}]
		}
	}
}

Root Configuration Parameters

Property Type Description
appName string Text to show in title bar and header.
credentials object SMART on FHIR OAuth credentials that can be referenced by id from one or more endpoints defined in the endpointList configuration item. The property names of the object are credential ids and the values are objects with a clientId and, optionally, a clientSecret property.
mimeTypeMappings object Specifies how to convert the mime types of downloaded attachments into file names. The property names of the object are mime type strings, and the values are file extension strings.
dateSortElements object Defines which fields in each FHIR ResourceType are used when ordering the resources for a user to browse in Procure's UI. Each property name is a FHIR ResourceType, with a value that's an array of FHIR elements. These are evaluated in order, and the first element name that exists is used as the sort date for a resource. All resources fall back to their FHIR lastUpdated date if no clinically relevant date is found.
endpointLists object Populates the list of organizations a user can select from in Procure. The property names of the object are endpoint list ids and the values are endpoint list item objects. See details below.
showWizard boolean When set to true, Procure will open in a simplified wizard workflow that streamlines the process for users to collect and share data with an upload enndpoint such as a research study. This property can also set to true by including a wizard querystring parameter in the url. Note that when showWizard is set to true, the upload enndpoint configuration parameters must also be specified.
warnOnPageNavigate boolean If set to true, a dialog box will be shown when a user tries to navigate away from the Procure webpage without first exporting modified settings.
redirectUri string Advanced - overrides the redirectUri Procure builds based on the page URL. You probably don't need to change this.
queryProfiles object Defines the set of queries Procure runs against a FHIR server to download FHIR resources. The supported FHIR resources and search parameters vary by vendor and creating tailored query profiles for different endpoints accommodates this. The property names of the object are query profile ids and the values are query profile objects. See details below.
ignoreState boolean Advanced - if set to true, will prevent the validation of the state parameter as part of the OAuth flow. Should never be set to true in production deployments.
spreadsheetTemplates object Defines transforms to "flatten" FHIR Resources and represent them as spreadsheets. Drives the items that appear in the "Export as Spreadsheet" menu in Procure. The property names of the object are spreadsheet template ids and the values are template objects . See details below.
upload object Identifies a web based endpoint and related information to enable users to upload their data, for example, to share it with a research study. See details below.
noCustomEndpoints boolean Prevents users from specifying an endpoint that is not in a pre-defined endpoint list, editing a pre-defined endpoint, or importing saved settings with an endpoint.

Endpoint Lists

Endpoint list files populate the entries in Procure's organizations list that shows when a user adds a provider in the app. At runtime, users can also add a custom organization that is not included in a directory file, or override the default properties of any of these endpoints.

Epic makes directory files available for FHIR DSTU2 and FHIR R4 that are included in Procure's public directory as epic_endpoints_r2.json and epic_endpoints_r4.json. You can update these files at any time by running scripts/update_epic_endpoints.sh from the command line. Procure also includes a directory of test sandboxes in a file named sandbox_endpoints.json.

Each of these endpoint list files are referenced from the endpointLists > [id] > path property of config.json, and you can remove these endpoint lists or add others by altering the config-override.json file as described above. Endpoint lists are loaded in alphabetical order by their key.

An endpoint list may be represented as a bundle of FHIR Endpoint resources that each populate the name, status and address elements. Alternatively, an endpoint list may be structured as a custom JSON object with a single Entry (or entry) property that is an array of objects containing the fields listed below. Entries in a non-bundle list may have an id or orgId field that will be used to de-duplicate endpoints within and between lists, retaining the last endpoint loaded with that identifier. If neither of these fields are populated, or if the endpoint list is a bundle of FHIR Endpoint resources, the endpoint will be assigned an identifier at load time based on its name.

Property Type Description
name (or OrganizationName) string, required Displayed in the Procure UI to identify the healthcare organization.
fhirEndpoint (or FHIRPatientFacingURI) string, required URL of the provider's FHIR endpoint
queryProfile string, optional Reference to the id of the set of FHIR queries to retrieve data from this provider that are defined in the queryProfile configuration item.
isOpen boolean, optional Whether the endpoint requires authentication for access. Will be true for all production endpoints, may be false for sandbox environments.
credentialId string Reference to the id of an object that's defined in the credentials configuration item, containing the client id (and optionally client secret) for this provider.
scope array of strings The SMART-on-FHIR scopes for this endpoint. Ignored for open endpoints.
patient string FHIR id of patient to retrieve. Ignored for secure endpoints.
clientId string OAuth client_id for the endpoint. Ignored for open endpoints. Will override a clientId referenced through the credentialId property.
clientSecret string OAuth client_secret for the endpoint. Ignored for open endpoints and not applicable to many secure endpoints. Will override a clientId referenced through the credentialId property.

Default values for these properties may be included in the config or config-override files in the endpointLists > [id] > defaults object, however, properties in the endpoint list files will take precedence.

Upload Endpoint

Optionally, Procure can be configured to enable users to share their data by uploading a zip archive file containing the FHIR resources (JSON FHIR bundles by resource type) and related attachments (XML, PDF and other file types) to a web server, (for example, to share their data with a research study they're participating in). The upload endpoint and related information can be specified directly in Procure's configuration file through the upload key. Alternatively, the upload key can be used to provide a URL that points to a manifest file that contains this information (for example, if the upload location URL needs to be generated dynamically, as is the case for a signed AWS S3 endpoint). Lastly, the upload key can be used provide a whitelist of valid manifest URL patterns and the actual manifest location can be passed to the app as a querystring url parameter.

Example backend servers that can generate manifests and receive uploads are in the upload-backends folder.

Pre-Configured Upload Settings

The upload property object has the following properties:

Property Type Description
uploadUrl string, required HTTP URL or HTTPS URL supporting CORS and PUT operation.
name string, required Name for the project accepting the upload. Displayed in the upload dialog box before the user initiates the transfer.
infoUrl string, required URL to web page describing the project accepting the upload. This page should incorporate or link to the project's privacy policy and terms of use. Displayed in the upload dialog box before the user initiates the transfer.
successMessage string, optional Text displayed to the user after an upload successfully completes.
continueUrl string, optional URL that will be opened in a new window following a successful transfer. May be used to support having the user log in and link the uploaded data to an existing account, review the uploaded data for accuracy, configure granular access permissions, etc.
continueLabel string, optional Label for the button that triggers launch of the continue URL following a successful upload.
label string, optional Label for upload button in UI. Defaults to "Share Data".
simulate boolean When set to true, the upload will appear to take place, but no file will be PUT to the upload server. Useful for demos.

Pre-Configured Manifest Location

The upload property object has the following properties:

Property Type Description
manifestUrl string, required HTTP URL or HTTPS URL supporting CORS that returns a JSON manifest object containing the uploadUrl, name and infoUrl properties described above. The manifest may also contain the optional successMessage, continueUrl and continueLabel properties described above.
label string, optional Label for upload button in UI. Defaults to "Share Data".

Dynamic Manifest Location

The upload property object has the following properties:

Property Type Description
whitelist array, required Array of URL patterns (indicate wildcard segments with an *) . Used to evaluate the manifestUrl being passed in to Procure as a querystring parameter.
label string, optional Label for upload button in UI. Defaults to "Share Data".

URL querystring parameters:

Parameter Type Description
upload_manifest_url string, required HTTP URL or HTTPS URL supporting CORS that returns a JSON manifest object containing the uploadUrl, name and infoUrl properties described above. The manifest may also contain the optional successMessage, continueUrl and continueLabel properties described above.
upload_label string, optional Label for upload button in UI. Defaults to "Share Data".

Query Profiles

Query Profiles defines the set of FHIR endpoints and parameters that Procure uses to retrieve an entire patient record. The FHIR capabilities exposed by each vendor vary, so in general, each vendor will need a custom query profile. Additionally, query profiles can be used to restrict the data retrieved to a subset of a patient's record (for example, by only querying Observations with a category of "vital-sign" if other data aren't needed).

Property Type Description
title string, optional Informational - useful for administrators reviewing configurations and used in error messages.
fhirVersion string, optional Defaults to R2, but values of R3 and R4 are also valid.
retryLimit integer, optional Sets how many times Procure retries a single query before failing and reporting an error. Defaults to 0.
queries array of query objects See details below

Query Object

Property Type Description
resourcePath string, required Segment appended to the server's FHIR Base URL to create the query URL. Should not have a leading slash. May be a simple resource name or a more complex path that can include a patientId template parameter that will be replaced at runtime (eg. Patient/{{patientId}}).
params object, optional Object with properties that are FHIR search parameters. The value for a parameter can be a string or an array of strings. Arrays are converted into a comma delimited string in the FHIR query, representing an "or" structure where there server will respond with matches for any of the values. Parameter values can also incorporate a patientId template parameter. For example, a patient search parameter would be represented as the follow property in the params object: "patient": "{{patientId}}").
retrieveReferences string or array of strings, optional One or more limited FHIR path expressions (only dot delimited segments are supported). If populated, Procure will walk the resources returned by this query, and retrieve any resources referenced at the paths in this parameter, including them in the result set.
containReferences string or array of strings, optional Follows the same logic as retrieveReferences, however retrieved resources are embedded as contained resources in the resources that reference them and the reference elements themselves are converted to relative references. Contained references will only be retrieved once, but will be embedded in each resource that references them.
downloadAttachments string or array of strings, optional One or more limited FHIR path expressions (only dot delimited segments are supported). If populated, Procure will walk the resources returned by this query, and retrieve any attachments referenced at the paths in this parameter. Attachments will be named as sequential integers, saved as files, and included in the result set. The file extension appended to each attachment is dictated by the mimeTypeMappings configuration item described above.
pageLimit integer, optional Used for testing - do not set in production. If the FHIR response is paginated so that bundles only contain a portion of the result set, this parameter will set the maximum number of subsequent requests to retrieve additional resources in the result set.

Spreadsheet Templates

Each property in the spreadsheetTemplates configuration object represents a transformation template that will show up in the app's "Export as Spreadsheet" menu. The property name represents an identifier for the template that can be used when referencing it from other templates. The value is an object with the following properties:

Property Type Description
name string, required Displayed in the Procure UI to identify the template.
sortBy array of objects, required Specifies the sort order for rows in the export. Each object has a name property that corresponds to a field name in the template and a dir property that can be asc for an ascending sort order or desc for a descending sort order. Sort objects in the array are applied to the template output in the order they are listed.
extends string, optional Ids (property names) of templates that will be merged with this template (see the Template Inheritance section below)
template array of template item objects Mappings from hierarchical FHIR elements to flat spreadsheet rows. See Spreadsheet Template Item section below.

Spreadsheet Template Item

Property Type Description
path string or array of strings, required Limited FHIR path expression (only dot delimited values are supported), or array of such expressions, that identifies the element that will be mapped to a spreadsheet field. Paths that result in an array of values will be spread across multiple rows in the output spreadsheet, with other fields being repeated on each row. If multiple paths are listed, they will be tested in sequence and the first path that results in a value will be used. A path value of "*" indicates that the item should match the root of the resource when no other path matches.
name string, optional Column heading for this field. If omitted, field will not be included in output spreadsheet, but can still be used to filter rows.
test string, optional Name of built-in function that is used to evaluate if this row should be included in the output spreadsheet, filtering the row if the test function does not return true. See Test Functions section below for available options.
id string, optional Identifier for this field, used for template inheritance. See Template Inheritance below.
transform string, optional Name of built-in function that is used to convert the result of this template item's path expression into the data included in the spreadsheet field. If omitted, field will be populated with the unmodified item. Note that Test Functions are applied to the untransformed values. See Transform Functions below for available options.
children array of template item objects Paths for these child template items will be evaluated relative to this template item's path.

Template Inheritance

If a template has one or more template id values in its extends property (described above), the values in the template will be merged onto the values of the referenced templates using the following logic. Items without an id property or with an id property that doesn't match one of an item in one of the template being extended will be appended to the template. Items that do match an id property of another template item will have their properties merged, with properties from the extended template being replaced in the case of two properties with the same name. Template items that include underscore property (eg.{"_": true}) will entirely replace any template item with the same id, instead of merging properties.

Transform functions

  • stringifyCodings - merges codings from a CodeableConcept into a space delimited list of system|code values.
  • parseDateForExcel - converts date values into Excel dates rather than leaving them as strings. Dates aren't converted when spreadsheet is downloaded as a CSV.
  • getHelperData - incorporate metadata values into export populating this field with the data type specified in the helperDataField property. Currently supports source (the provider name that the data is coming from) and format (xlsx or csv export).

Test functions

  • validateCode - ensures a code value specified in the template item's target property is present in the matched coding (or array of codings).
  • validateValue - ensures the matched value equals the value specified in the template item's target property.
  • validateExists - ensures the path is populated in the FHIR Resource being evaluated.

Contributing

As early stage software, Procure has bugs. If you run into an issue, please review the "issues" tab on Github and, if the problem isn't listed, open a new issue ticket to let us know! Also, if you're a software developer and are able to fix the code, git pull requests are very welcome, but please get in touch before coding large changes.

Developers submitting code should install Git Secrets and configure it as a pre-commit hook on their local Github repository to prevent inadvertent disclosure of confidential information. Pull requests will be screened using this tool prior to being merged.

Third Party Libraries Used

Core

Export

UI

Misc

About

App for patients to retrieve and share their raw clinical data using SMART-on-FHIR

License:MIT License

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