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Fhirbase

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Build Status

Fhirbase is a command-line utility which enables you to easily import FHIR data into a PostgreSQL database and work with it in a relational way. Also Fhirbase provides set of stored procedures to perform CRUD operations and maintain Resources History.

Status

Sorry guys, this project is frozen untill new hero will support it. Most of ideas from fhirbase is moved and developed in Aidbox FHIR Platform

Getting Started

Please proceed to the Getting Started tutorial for PostgreSQL and Fhirbase installation instructions.

Usage Statistics

Please note that Fhirbase collects anonymous usage statistics. It does not send any FHIR data, only events happened (database initialized, resources imported and error happened). You can check the source code for stats sender yourself.

You can turn off usage statistics sending with --nostats global flag.

Development

To participate in Fhirbase development you'll need to install Golang and Dep package manager.

Fhirbase is Makefile-based project, so building it is as simple as invoking make command.

NB you can put Fhirbase source code outside of GOPATH env variable because Makefile sets GOPATH value to fhirbase-root/.gopath.

To enable hot reload of demo's static assets set DEV env variable like this:

DEV=1 fhirbase web

License

Copyright © 2018 Health Samurai team.

Fhirbase is released under the terms of the MIT License.

fhirbase.net's People

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fhirbase.net's Issues

Polymorphic handling failures

Happy new year :-)

We are using this very helpful utility and have run into issues with polymorphic elements. Please let us know if there is something we are not understanding about how this works or whether this is an issue with the code base.

Regards,
Janet

These examples are for the FHIR v4 MedicationStatement resource, which contains Medication[x] polymorphic element.

The two issues are:

(1) FhirbaseJsonWriter fails to write Medication[x] when it is CodeableConcept.

 The json is:
	{
	  "resourceType": "MedicationStatement",
	  "id": "example005",
	  "status": "entered-in-error",	  
	  "medicationCodeableConcept": {
		"coding": [
		  {
			"system": "http://snomed.info/sct",
			"code": "27658006",
			"display": "Amoxicillin (product)"
		  }
		]
	  },
	  "subject": {
		"reference": "Patient/4d5ed44d-ba1d-41b2-866e-5a9662278ae6",
		"display": "Donald Duck"
	  }
	}
	
   The error is: 
   Newtonsoft.Json.JsonWriterException: Token PropertyName in state Array would result in an invalid JSON object. Path 'medication.codeableconcept.coding'.
       at Newtonsoft.Json.JsonWriter.AutoComplete(JsonToken tokenBeingWritten)

   The failure also occurs just after writing system while the code is attempting to (prematurely)  "WriteEndObject:, but it also occurs without system and display (with just one contained field, the "code"). So there seems to be two issues: (a) the _isPolymorphic is causing the WriteEndObject to fire too soon instead of reading all contained fields, and (b) the WriteEndObject is confused (?) about the value to write for the Array state.

(2) FhirbaseJsonReader fails to read Medication[x] when it is a Resource.

The json is:
	{
	  "resourceType": "MedicationStatement",
	  "id": "example005",
	  "status": "entered-in-error",	  
	  "medicationCodeableConcept": {
		"coding": [
		  {
			"system": "http://snomed.info/sct",
			"code": "27658006",
			"display": "Amoxicillin (product)"
		  }
		]
	  },
	  "subject": {
		"reference": "Patient/4d5ed44d-ba1d-41b2-866e-5a9662278ae6",
		"display": "Donald Duck"
	  }
	}

The error is thrown by: result.Add(_parser.Parse<T>(reader));
The error is: System.ArgumentException: Can not add Newtonsoft.Json.Linq.JValue to Newtonsoft.Json.Linq.JObject.

Lastly, since we cannot read Medication as CodeableConcept we do not know if the Read would fail, but we suspect it would.

add README.md

Just add couple of sentences about what's inside repo and give links to documentation and fhirbase site.

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