intervention-engine / fhir

Generic FHIR server implementation in GoLang.

Intervention Engine FHIR Server

NOTE: This project is not under active development. Others have forked and continue work on the code. If you would like your fork added/removed from this list, please file an issue.

Active Forks

• https://github.com/eug48/fhir

This project provides HL7 FHIR DSTU2 models and server components implemented in Go and using MongoDB as storage. Other versions of FHIR are also supported on other branches within this repository:

• stu3_mar2017 - Official FHIR STU3 Release
• stu3_jan2017 - FHIR 1.8 (San Antonio)
• stu3_aug2016 - FHIR 1.6 (Baltimore)
• stu3_mar2016 - FHIR 1.4 (Montreal)

This is a library that can be embedded into other server applications. The library is not a complete implementation of FHIR, as features that are selected are driven by the Intervention Engine, eCQM Engine, Patient Matching Test Harness and Synthetic Mass projects.

Currently, this server library supports:

• JSON representations of all resources
• Create/Read/Update/Delete (CRUD) operations
• Conditional update and delete
• Some but not all search features
  • All defined resource-specific search parameters except composite types and contact (email/phone) searches
  • Chained searches
  • _include and _revinclude searches (without _recurse)
• Batch bundle uploads (POST, PUT, and DELETE entries)

Currently, this server does not support the following major features:

• XML representations of resources
• History (versions, etc.)
• Extension of primitive types and resource sub-components

As mentioned above, this repository contains a library. It does not build into a stand alone application. If you would like to build a server application, please see fhir-server project.

NOTE: Most of the fhir source code is generated by the fhir-golang-generator. In most cases, updates to source code in the fhir repository need to be accompanied by corresponding updates in the fhir-golang-generator.

Development

This project uses Go 1.7 and MongoDB. To test the library, first, install all of the dependencies:

$ go get -t ./...

Once the dependencies are installed, you should make sure that MongoDB is also running. The test suite will create a fhir-test database in a local instance of MongoDB to execute some tests. You can then run the test suite with the following:

$ go test ./...

Usage

Users of this library should work with the FHIRServer struct. Web request handlers in this library are implemented using Gin.

Examples of usage can be found in the server set up of the eCQM Engine or the server set up of Intervention Engine.

License

Copyright 2017 The MITRE Corporation

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

fhir's Issues

"Open Type Elements" have incomplete representation

"Open Type Elements" are those elements whose type is represented as "*" and generally have names like value[x]. Currently, our code has representations for the following types:

• String
• Integer
• DateTime
• Boolean
• CodeableConcept
• Range

According to the spec, however, there are quite a few more types. See 1.19.0.18 Open Type Element for the full list. This affects Parameters, Extension, and ElementDefinition. The generator should be updated to represent the full spectrum of types.

Using PUT to store a Bundle results in an error

An attempt to PUT a Bundle to the endpoint, /Bundle/ with an assigned Id in the uri and in the document results in an error 500.

The console only reports ERROR | echo | Invalid Id

C-CDA

Hi, C-CDA to FHIR and vice versa conversation possible? Any help would be appreciated.

Thanks

Long-Term Organization of This Repo

Now that FHIR 2 has been released, we should consider our long-term organization of this repository. Ideally I'd like to see 4 or 5 tagged releases instead of many branches, one for each of:

• DSTU2
• DSTU3 1.4
• DSTU3 1.6
• DSTU3 1.8
• STU3

Was there a 1.2?

Time for a FHIR STU3 1.8 Release

The latest FHIR candidate is now 1.8, see http://hl7.org/fhir/2017Jan/index.html. Among other things this renames "MedicationOrder" to "MedicationRequest" and changes some attributes of this model. Since Synthea was upgraded to FHIR STU3 1.8 the latest Synthea output is no longer compatible with 1.6.

Bad Entry in the SearchParameterDictionary

ConceptMap.source-uri in the SearchParameterDictionary has no targets. Without any targets this entry cannot be used to perform a search.

Searching for message:MessageHeader.destination-uri now returns OperationOutcome and no result

Querying FHIR server for /Bundle?message:MessageHeader.destination-uri=urihere is no longer returning search results. Instead, an operation outcome with an error is returned.

Querying for /Bundle?message:MessageHeader works as expected.

A patch file with a suggested unit test is attached.

This uri against the IE FHIR Server embedded with ptmatch returns the json below:
http://localhost:3001/Bundle?message:MessageHeader.destination-uri=http://mitre.org/ptmatchadapter-fril

{
"resourceType": "OperationOutcome",
"issue": [
{
"severity": "error",
"code": "processing",
"details": {
"coding": [
{
"system": "http://hl7.org/fhir/ValueSet/operation-outcome",
"code": "MSG_PARAM_MODIFIER_INVALID",
"display": "Parameter "message" modifier is invalid"
}
],
"text": "Parameter "message" modifier is invalid"
}
}
]

}

Extensions in Contained Resources Not Unmarshaled Correctly

This is a known issue when retrieving resources that inherit from DomainResource and have one or more contained resources. As these resources are unmarshaled from the database the exact type of the contained resources is not known, so they are unmarshaled into the generic interface{} type.

This unmarshaling operation names the fields in this interface{} exactly as they are in the database, meaning the id is actually _id, and the fields used to store the extension (@context, @id, @type) remain that way.

The _id field is corrected to id in the web layer before being returned to a client, but the extensions are not.

Paging Links are Incorrect

The paging links returned by the server are URL escaped. Examples in the FHIR spec show them unescaped. See: http://hl7.org/fhir/2017Jan/http.html#paging

Running IE and FHIR in parrallel

Both of servers, fhit and ie, bind to port 3001. I understand both need to be running but maybe I'm missing something. Is there an up and running guide that outlines setup for all the inter-related components?

XML parsing fails

XML parsing doesn't work at all. The struct tags for XML are all of the form

`xml:"tag"`

but the values are taken from the "value" attribute. The problem is that it is not possible to specify that the value for an element is taken from an attribute of the same element. It is only possible to specify that the value of a field of the element is taken from an attribute. As a result, the struct tags don't correspond to the XML format, and parsing fails. See this Stackoverflow discussion for details.

The solution seems to be to implement a custom unmarshaller/marshaller for XML that is aware of this usage of the "value" attribute.

Content-Type of responses for FHIR Resources should be application/json+fhir

FHIR Spec (DSTU2) Section 2.1.0.6 () states the formal mime type for fhir resources is application/json+fhir.
The formal MIME-type for FHIR resources is application/xml+fhir or application/json+fhir. The correct mime type SHALL be used by clients and servers:
• XML: application/xml+fhir
• JSON: application/json+fhir

The intervention engine FHIR server returns application/json

Bundle composition and message search params do not work

The Bundle composition and message search parameters do not currently work in our server because the paths are defined with indexers (e.g., Bundle.entry.resource(0)). In addition, this is compounded by the issue that we don't support chaining into inlined resources.

Chained search does not work for inlined resources

Some resources contain other resources inlined rather than as references (e.g., bundle.entry.resource). The fhir server does not properly handle chained queries that chain into these inlined resources.

move the fhir model classes to their own project

It's useful for implementors to use the fhir classes without depending on mongodb, have you considered moving those to their own (dependency-less) github project?

Inheritance of Resource, DomainResource, Element and BackboneElement

In the XML Schema Resource, DomainResource, Element and BackboneElement are parent types of most of the data and resource types. In particular, they include fields like Language and Extension. These seem to be absent from the various classes, or am I missing something?

JSON representation of Parameters is missing resourceType property

The Parameters map is missing, "resourceType": "Parameters".

Add a MarshalJSON() method in Parameters.go (I don't know if this would go on ParametersParametersComponent (which is where UnmarshalJSON is located) or directly on Parameters

Requesting the conformace with `Accept: application/fhir+xml` returns a `200` code & JSON response

In testing against the syntheticmass-dev server, I found that requesting /metadata with an Accept header of application/fhir+xml (the new resource format in FHIR 1.6), returns a 200 status code and a JSON response body. It would seem the correct status header in this case should be 406 Not Acceptable.

Conformance Statement?

Any thoughts on how to include/generate a conformance statement for this server? (from implementer's check list)

Ideas could be - create a conformance model (Resource) and manually populate it, or find a way to introspect the go code to determine which models and parameters are implemented and then generate the conformance model?

Tests fail on git clone (mongo_indexes_test.go)

Perhaps I am doing it wrong, but I am getting a fail in the mongo index test. I have mongo installed and running, missing another prereq?

ok fhir/auth 0.024s
ok fhir/models 0.025s
ok fhir/search 1.904s
--- FAIL: TestMongoIndexes (0.00s)
panic: mkdir ./testdb: file exists [recovered]
panic: mkdir ./testdb: file exists

goroutine 6 [running]:
testing.tRunner.func1(0xc4202120f0)
/usr/local/go/src/testing/testing.go:711 +0x2d2
panic(0xf049e0, 0xc4201df080)
/usr/local/go/src/runtime/panic.go:491 +0x283
fhir/server.(*MongoIndexesTestSuite).SetupSuite(0xc42016ab40)
/home/plamar/go/src/fhir/server/mongo_indexes_test.go:54 +0x84f
github.com/stretchr/testify/suite.Run(0xc4202120f0, 0x178c4a0, 0xc42016ab40)
/home/plamar/go/src/github.com/stretchr/testify/suite/suite.go:64 +0x63b
fhir/server.TestMongoIndexes(0xc4202120f0)
/home/plamar/go/src/fhir/server/mongo_indexes_test.go:96 +0x51
testing.tRunner(0xc4202120f0, 0x10b3a88)
/usr/local/go/src/testing/testing.go:746 +0xd0
created by testing.(*T).Run
/usr/local/go/src/testing/testing.go:789 +0x2de
FAIL fhir/server 0.035s
ok fhir/upload 0.025s

Fix for search parameters missing from STU3 branch

It looks like this commit, which is present on master, hasn't made it to STU3: 3f6fef6

When GETting a Bundle, the embedded resources don't appear to get unmarshalled as desired

POST a Bundle to the FHIR Server. Note the new Bundle identifier. Open a new browser window and request the bundle from the FHIR server.

The resource identifier for embedded resources will be _id.
Also, it appears the timestamp is cominb back in the BSON format rather than then FHIR format.

    "timestamp": {
      "precision": "timestamp",
      "time": "2016-09-07T12:14:51-04:00"
    }

RequestMessageReturnedFromFhirServer.txt
RequestMessageBeforePostingToServer.txt

Reverse Chained Searches Return no Results

Reverse chained searches that return no results return a 500 error instead of a 200 status and an empty FHIR bundle.

Incorrect type

Seems like inside HumanName type field Family should be string instead of []string:

https://www.hl7.org/fhir/datatypes.html#humanname

A POSTed Bundle containing an Id is processed without error

The FHIR server accepts a Bundle containing an Id, changes the value of the Id, and returns success.

FHIR Spec Section 2.1.0.13 states: “If the client wishes to have control over the id of a newly submitted resource, it should use the update interaction instead.” In fact, if we’re accepting the post and re-assigning the ID, we’re in violation of the spec ourselves, as it further states: “If an ID element is provided, the server SHALL respond with a HTTP 400 error code, and SHOULD provide an operation outcome identifying the issue.” .

date comparison operator for _lastUpdated is not supported in search query

Invoking something like the following results in a Operation Outcome with Error 500

http://localhost:8881/Bundle?_lastUpdated=%3E%3D2016-02-09T13%3A57%3A01.686-05%3A00

The above is seeking resources that have been updated since a specified time. The need is to allow message recipients to query for "new" messages addressed to them.

_include and _revinclude not working when included param references array

If the included param references a field that is an array, then the included results are not returned (for example, _include=Observation:performer). This is because MongoDB's left-join (a.k.a. $lookup) doesn't work with array fields. You need to unwind the arrays and then group them back together again.

See:

• https://jira.mongodb.org/browse/SERVER-21469
• http://stackoverflow.com/questions/34967482/lookup-on-objectids-in-an-array

Invalid Observation search parameter returning results

The following query does not cause an error, and returns a set of 100 random Observation results:
https://syntheticmass.mitre.org/fhir/Observation?code:50050

This should cause an error, no?

FHIR commercial server

Do you know any FHIR commercial server available with exposed apis? On prem/cloud?

Installation Issues on Mac OS X

First I clone to github.com/intervention-engine\fhir. MongoDB 3+ is already running. The tests fail and the server startup fails although it does appear to connect to MongoDB.

Here is the test output:

$ go test ./...
# github.com/intervention-engine/fhir/models
models/bundle_test.go:8:2: cannot find package "github.com/bitly/go-simplejson" in any of:
/usr/local/go/src/github.com/bitly/go-simplejson (from $GOROOT)
/Users/alan/Documents/work/src/github.com/bitly/go-simplejson (from $GOPATH)
FAIL    github.com/intervention-engine/fhir/models [setup failed]
# github.com/intervention-engine/fhir/search
search/mongo_search_test.go:15:2: cannot find package "github.com/pebbe/util" in any of:
/usr/local/go/src/github.com/pebbe/util (from $GOROOT)
/Users/alan/Documents/work/src/github.com/pebbe/util (from $GOPATH)
FAIL    github.com/intervention-engine/fhir/search [setup failed]
# github.com/intervention-engine/fhir/server
search/mongo_search_test.go:15:2: cannot find package "github.com/pebbe/util" in any of:
/usr/local/go/src/github.com/pebbe/util (from $GOROOT)
/Users/alan/Documents/work/src/github.com/pebbe/util (from $GOPATH)
FAIL    github.com/intervention-engine/fhir/server [setup failed]
# github.com/intervention-engine/fhir/upload
search/mongo_search_test.go:15:2: cannot find package "github.com/pebbe/util" in any of:
/usr/local/go/src/github.com/pebbe/util (from $GOROOT)
/Users/alan/Documents/work/src/github.com/pebbe/util (from $GOPATH)
FAIL    github.com/intervention-engine/fhir/upload [setup failed]
?       github.com/intervention-engine/fhir [no test files]

Here is the output from the server start attempt:

$go run server.go
panic: no reachable servers

goroutine 1 [running]:
github.com/intervention-engine/fhir/server.(*FHIRServer).Run(0xc820101ee8)
/Users/alan/Documents/work/src/github.com/intervention-engine/fhir/server/server_setup.go:34 +0xa8
main.main()
/Users/alan/Documents/work/src/github.com/intervention-engine/fhir/server.go:13 +0x15f

goroutine 17 [syscall, locked to thread]:
runtime.goexit()
/usr/local/go/src/runtime/asm_amd64.s:1721 +0x1

goroutine 20 [sleep]:
time.Sleep(0x1dcd6500)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoCluster).syncServersLoop(0xc8200bc200)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/cluster.go:386 +0x484
created by gopkg.in/mgo%2ev2.newCluster
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/cluster.go:78 +0x1d0

goroutine 55 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc82019e540, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 26 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc8201480e0, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 31 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc8201481c0, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 32 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc8201482a0, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 45 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc82015ac40, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 80 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc820148a80, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 61 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc82019eb60, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 70 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc820148700, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 75 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc8201488c0, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 82 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc82015ad20, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160

goroutine 102 [sleep]:
time.Sleep(0x37e11d600)
/usr/local/go/src/runtime/time.go:59 +0xf9
gopkg.in/mgo%2ev2.(*mongoServer).pinger(0xc82020a1c0, 0x1)
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:296 +0x1b0
created by gopkg.in/mgo%2ev2.newServer
/Users/alan/Documents/work/src/gopkg.in/mgo.v2/server.go:89 +0x160
exit status 2