Support Stu3ToR4 conversion and update DotLiquid version

CODE_OF_CONDUCT.md

@@ -0,0 +1,9 @@
+# Microsoft Open Source Code of Conduct
+
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+
+Resources:
+
+- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
+- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
+- Contact [[email protected]](mailto:[email protected]) with questions or concerns

GeoPol.xml

@@ -18,7 +18,6 @@
     <!-- Use back slash \ to indicate folder path e.g. src\external\ -->
     <ExcludeFolder>.gitignore</ExcludeFolder>
     <ExcludeFolder>GeoPol.xml</ExcludeFolder>
-    <ExcludeFolder>test</ExcludeFolder>
     <!-- 3rd Party Libraries section below -->
   </Component>
 </GeoPol_Folders>

README.md

@@ -4,45 +4,45 @@ FHIR Converter is an open source project that enables conversion of health data
 
 The first version of the FHIR Converter released to open source on Mar 6th, 2020. It used Handlebars template language and Javascript runtime. A new converter engine was released on Nov 13, 2020 that uses Liquid templating language and .Net runtime.
 
-Currently, Microsoft supports two types of converter engines, Handlebars engine and Liquid engine, along with templates and filters. **We strongly recommend using the Liquid converter** for a better alignment with [Azure Healthcare APIs](https://docs.microsoft.com/azure/healthcare-apis/), [Azure API for FHIR](https://azure.microsoft.com/services/azure-api-for-fhir/), [FHIR Server for Azure](https://github.com/microsoft/fhir-server), and [Microsoft Logic Apps](https://azure.microsoft.com/services/logic-apps/).
+Currently, Microsoft supports two types of converter engines, Handlebars engine and Liquid engine, along with templates and filters. **We strongly recommend using the Liquid converter** for a better alignment with [Azure Healthcare APIs](https://docs.microsoft.com/azure/healthcare-apis/), [Azure Health Data Services](https://azure.microsoft.com/en-us/services/health-data-services/#overview), [FHIR Server for Azure](https://github.com/microsoft/fhir-server), and [Microsoft Logic Apps](https://azure.microsoft.com/services/logic-apps/).
 
 The following table shows the differences between two converter engines:
 
 |  | Handlebars engine | Liquid engine | 
 | ----- | ----- | ----- |
 | **Template language** | [Handlebars](https://handlebarsjs.com/) | [Liquid](https://shopify.github.io/liquid/) |
 | **Template authoring tool** | Self-hosted web-app | [VS Code extension](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-health-fhir-converter)|
-| **Supported conversions** | 1. HL7v2 to FHIR <br> 2. C-CDA to FHIR | 1. HL7v2 to FHIR <br> 2. C-CDA to FHIR <br> 3. JSON to FHIR **(new!)** |
-| **Available as** | 1. Self-deployed web service <br> (on-prem or on Azure)| 1. Command line tool <br> 2. $convert-data operation in  [FHIR Server for Azure (OSS)](https://github.com/microsoft/fhir-server/blob/main/docs/ConvertDataOperation.md) <br> 3. $convert-data operation in both [Azure API for FHIR](https://docs.microsoft.com/azure/healthcare-apis/azure-api-for-fhir/convert-data) and [Azure Healthcare APIs (preview)](https://docs.microsoft.com/azure/healthcare-apis/fhir/convert-data)|
+| **Supported conversions** | 1. HL7v2 to FHIR <br> 2. C-CDA to FHIR | 1. HL7v2 to FHIR <br> 2. C-CDA to FHIR <br> 3. JSON to FHIR <br> 4. FHIR STU3 to FHIR R4 **(new Command Line Tool!)** |
+| **Available as** | 1. Self-deployed web service <br> (on-prem or on Azure)| 1. Command line tool <br> 2. $convert-data operation in  [FHIR Server for Azure (OSS)](https://github.com/microsoft/fhir-server/blob/main/docs/ConvertDataOperation.md) <br> 3. $convert-data operation in both [Azure Health Data Services](https://docs.microsoft.com/en-us/azure/healthcare-apis/fhir/convert-data) and [Azure API for FHIR](https://docs.microsoft.com/azure/healthcare-apis/azure-api-for-fhir/convert-data)|
 
 ⚠ Rest of this document is about the Liquid converter. For the Handlebars converter, please refer to the [Handlebars branch](https://github.com/microsoft/FHIR-Converter/tree/handlebars).
 
-Currently, FHIR Converter supports three types of conversions, **HL7v2 to FHIR**, **C-CDA to FHIR**, and **JSON to FHIR**. The converter uses templates that define mappings between these different data formats. The templates are written in [Liquid](https://shopify.github.io/liquid/) templating language and make use of custom [filters](docs/Filters-and-Tags.md).
+Currently, FHIR Converter supports four types of conversions, **HL7v2 to FHIR**, **C-CDA to FHIR**, **JSON to FHIR** and **FHIR STU3 to FHIR R4**. The converter uses templates that define mappings between these different data formats. The templates are written in [Liquid](https://shopify.github.io/liquid/) templating language and make use of custom [filters](docs/Filters-and-Tags.md).
 
 The converter comes with a few ready-to-use templates. If needed, you can create a new template, or modify existing templates to meet your specific conversion requirements.
 
-FHIR Converter with DotLiquid engine transforms the input data into FHIR bundles that are persisted to a FHIR server. The converter is integrated into both [Azure API for FHIR](https://docs.microsoft.com/azure/healthcare-apis/azure-api-for-fhir/) and [Azure Healthcare APIs (preview)](https://docs.microsoft.com/azure/healthcare-apis/), as well as in the open-source [FHIR Server](https://github.com/microsoft/fhir-server) as a [`$convert-data` operation](#using-convert-data-in-fhir-server). It is also available as a [command line tool](#using-command-line-tool).
+FHIR Converter with DotLiquid engine transforms the input data into FHIR bundles that are persisted to a FHIR server. The converter is integrated into both [Azure Health Data Services](https://azure.microsoft.com/en-us/services/health-data-services/#overview) and [Azure API for FHIR](https://docs.microsoft.com/azure/healthcare-apis/azure-api-for-fhir/), as well as in the open-source [FHIR Server](https://github.com/microsoft/fhir-server) as a [`$convert-data` operation](#using-convert-data-in-fhir-server). It is also available as a [command line tool](#using-command-line-tool).
 
 ## Using $convert-data in FHIR server
 
-The `$convert-data` operation is integrated into both Azure API for FHIR and FHIR server to run as part of the service. After enabling `$convert-data` in your server, you can make API calls in the form of ```<<your FHIR server URL>>/$convert-data``` to the server to convert your data into FHIR. In the API call request body, you would include parameters such as `inputData`, `inputDataType`, `templateCollectionReference`, and `rootTemplate`, to specify the message and the type of message you are converting. 
+The `$convert-data` operation is integrated into Azure Health Data Services, Azure API for FHIR and FHIR server to run as part of the service. After enabling `$convert-data` in your server, you can make API calls in the form of ```<<your FHIR server URL>>/$convert-data``` to the server to convert your data into FHIR. In the API call request body, you would include parameters such as `inputData`, `inputDataType`, `templateCollectionReference`, and `rootTemplate`, to specify the message and the type of message you are converting. 
 
 For more information on configuring and using `$convert-data` operation on your server, please refer to these documentation:
 
+- [$convert-data for Azure Health Data Services](https://docs.microsoft.com/en-us/azure/healthcare-apis/fhir/convert-data)
 - [$convert-data for Azure API for FHIR](https://docs.microsoft.com/azure/healthcare-apis/azure-api-for-fhir/convert-data)
-- [$convert-data for Azure Healthcare APIs](https://docs.microsoft.com/azure/healthcare-apis/fhir/convert-data)
 - [$convert-data for FHIR Server](https://github.com/microsoft/fhir-server/blob/main/docs/ConvertDataOperation.md)
 
 ## Using Command line tool
 
 ### Supported parameters
 
-The command line tool is another way of converting data, as well as managing templates. The tool converts a folder containing input messages (HL7v2, C-CDA, or JSON) into FHIR resources. It accepts the following parameters in the command line:
+The command line tool is another way of converting data, as well as managing templates. The tool converts a folder containing input messages (HL7v2, C-CDA, JSON or FHIR STU3) into FHIR R4 resources. It accepts the following parameters in the command line:
 
 | Option | Name | Optionality | Default | Description |
 | ----- | ----- | ----- |----- |----- |
 | -d | TemplateDirectory | Required | | Root directory of templates. |
-| -r | RootTemplate | Required | | Name of root template.<br><br> **HL7v2 to FHIR**: "ADT_A01", "ADT_A02", "ADT_A03", "ADT_A04", "ADT_A05", "ADT_A08", "ADT_A11",  "ADT_A13", "ADT_A14", "ADT_A15", "ADT_A16", "ADT_A25", "ADT_A26", "ADT_A27", "ADT_A28", "ADT_A29", "ADT_A31", "ADT_A47", "ADT_A60", "OML_O21", "ORU_R01", "ORM_O01", "VXU_V04", "SIU_S12", "SIU_S13", "SIU_S14", "SIU_S15", "SIU_S16", "SIU_S17", "SIU_S26", "MDM_T01", "MDM_T02" <br><br> **C-CDA to FHIR**: "CCD", "ConsultationNote", "DischargeSummary", "HistoryandPhysical", "OperativeNote", "ProcedureNote", "ProgressNote", "ReferralNote", "TransferSummary" <br><br> **JSON to FHIR**: "Stu3ChargeItem", "ExamplePatient" <br> (*These JSON templates are sample templates for use, not default templates that adhere to any pre-defined JSON message types. JSON does not have any standardized message types, unlike HL7v2 messages or C-CDA documents. Therefore, instead of "default" templates we provide you with some sample templates that you can use as a starting guide for you to modify and customize.*)  |
+| -r | RootTemplate | Required | | Name of root template.<br><br> **HL7v2 to FHIR**: "ADT_A01", "ADT_A02", "ADT_A03", "ADT_A04", "ADT_A05", "ADT_A08", "ADT_A11",  "ADT_A13", "ADT_A14", "ADT_A15", "ADT_A16", "ADT_A25", "ADT_A26", "ADT_A27", "ADT_A28", "ADT_A29", "ADT_A31", "ADT_A47", "ADT_A60", "OML_O21", "ORU_R01", "ORM_O01", "VXU_V04", "SIU_S12", "SIU_S13", "SIU_S14", "SIU_S15", "SIU_S16", "SIU_S17", "SIU_S26", "MDM_T01", "MDM_T02" <br><br> **C-CDA to FHIR**: "CCD", "ConsultationNote", "DischargeSummary", "HistoryandPhysical", "OperativeNote", "ProcedureNote", "ProgressNote", "ReferralNote", "TransferSummary" <br><br> **JSON to FHIR**: "Stu3ChargeItem", "ExamplePatient" <br> (*These JSON templates are sample templates for use, not default templates that adhere to any pre-defined JSON message types. JSON does not have any standardized message types, unlike HL7v2 messages or C-CDA documents. Therefore, instead of "default" templates we provide you with some sample templates that you can use as a starting guide for you to modify and customize.*) <br><br> **FHIR STU3 to R4**: Name of the root template that is the same as the STU3 resource name e.g., "Patient", "Observation", "Organization". Some of the STU3 resources are renamed or removed from R4. Please refer to [Resource differences and constraints for STU3 to R4](docs/Stu3R4-resources-differences.md). |
 | -c | InputDataContent | Optional| | Input data content. Specify OutputDataFile to get the results. |
 | -n | InputDataFile | Optional| | Input data file. Specify OutputDataFile to get the results. |
 | -f | OutputDataFile | Optional | | Output data file. |

SECURITY.md

@@ -0,0 +1,41 @@
+<!-- BEGIN MICROSOFT SECURITY.MD V0.0.3 BLOCK -->
+
+## Security
+
+Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/Microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet), [Xamarin](https://github.com/xamarin), and [our GitHub organizations](https://opensource.microsoft.com/).
+
+If you believe you have found a security vulnerability in any Microsoft-owned repository that meets Microsoft's [Microsoft's definition of a security vulnerability](https://docs.microsoft.com/en-us/previous-versions/tn-archive/cc751383(v=technet.10)) of a security vulnerability, please report it to us as described below.
+
+## Reporting Security Issues
+
+**Please do not report security vulnerabilities through public GitHub issues.**
+
+Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://msrc.microsoft.com/create-report).
+
+If you prefer to submit without logging in, send email to [[email protected]](mailto:[email protected]).  If possible, encrypt your message with our PGP key; please download it from the the [Microsoft Security Response Center PGP Key page](https://www.microsoft.com/en-us/msrc/pgp-key-msrc).
+
+You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://www.microsoft.com/msrc).
+
+Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
+
+  * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
+  * Full paths of source file(s) related to the manifestation of the issue
+  * The location of the affected source code (tag/branch/commit or direct URL)
+  * Any special configuration required to reproduce the issue
+  * Step-by-step instructions to reproduce the issue
+  * Proof-of-concept or exploit code (if possible)
+  * Impact of the issue, including how an attacker might exploit the issue
+
+This information will help us triage your report more quickly.
+
+If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://microsoft.com/msrc/bounty) page for more details about our active programs.
+
+## Preferred Languages
+
+We prefer all communications to be in English.
+
+## Policy
+
+Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://www.microsoft.com/en-us/msrc/cvd).
+
+<!-- END MICROSOFT SECURITY.MD BLOCK -->

data/SampleData/Stu3/Account.json

@@ -0,0 +1,56 @@
+{
+  "resourceType": "Account",
+  "id": "example",
+  "text": {
+    "status": "generated",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">HACC Funded Billing for Peter James Chalmers</div>"
+  },
+  "identifier": [
+    {
+      "system": "urn:oid:0.1.2.3.4.5.6.7",
+      "value": "654321"
+    }
+  ],
+  "status": "active",
+  "type": {
+    "coding": [
+      {
+        "system": "http://hl7.org/fhir/v3/ActCode",
+        "code": "PBILLACCT",
+        "display": "patient billing account"
+      }
+    ],
+    "text": "patient"
+  },
+  "name": "HACC Funded Billing for Peter James Chalmers",
+  "subject": {
+    "reference": "Patient/example",
+    "display": "Peter James Chalmers"
+  },
+  "period": {
+    "start": "2016-01-01",
+    "end": "2016-06-30"
+  },
+  "active": {
+    "start": "2016-01-01",
+    "end": "2016-06-30"
+  },
+  "balance": {
+    "value": -1200,
+    "unit": "USD",
+    "system": "urn:iso:std:iso:4217",
+    "code": "USD"
+  },
+  "coverage": [
+    {
+      "coverage": {
+        "reference": "Coverage/7546D"
+      },
+      "priority": 1
+    }
+  ],
+  "owner": {
+    "reference": "Organization/hl7"
+  },
+  "description": "Hospital charges"
+}