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Open-source FHIR Server to support patient- and clinician-facing apps

Home Page: http://smartplatforms.org

License: Other

Groovy 84.93% CSS 10.55% JavaScript 0.13% Batchfile 4.39%

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POST example

Josh,
I got the server running. However, when I try to POST Patient-example.xml with command:

curl 'h0/DiagnosticOrder/example' -X PUT -H 'Authorization: Basic Y2xpZW50OnNlY3JldA=='-H 'Content-Type: text/xml' --data @grails-app/conf/examples/Patient-example.xml

I get this message:
Warning: Couldn't read data from file
Warning: "grails-app/conf/examples/Patient-example.xml", this makes an empty
Warning: POST.

curl: (6) Couldn't resolve host 'Content-Type: text'

On the server side, I see this:
Evaluating request org.apache.catalina.core.ApplicationHttpRequest@f62d719 with null
Formats: xml + xml
errors.GrailsExceptionResolver IOException occurred when processing request: [PUT] /DiagnosticOrder/example
Stream closed. Stacktrace follows:
java.io.IOException: Stream closed
at fhir.ApiController.parseResourceFromRequest(ApiController.groovy:131)
at fhir.ApiController.update(ApiController.groovy:149)
at com.brandseye.cors.CorsFilter.doFilter(CorsFilter.java:82)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
fhir.ErrorController Rendering a 500 error
fhir.ResponseFilters rendered after: 14

Any pointers? Thank you for the help!

Latest implementation of FHIR removes xpath from the Conformance resource

At present, smart-on-fhir uses the XPath found in the Conformance resource to build search indexes to enable searching the documents it stores. Unfortunately, the latest version of FHIR (me.fhir:fhir-0.12:0.2) removes this XPath, meaning that grails-app/conf/profile.xml can't be parsed when using the latest version of FHIR. As the information stored in that resource is used by the SearchIndexService to determine how to provide search information, this effectively breaks smart-on-fhir.

I'm not entirely clear on whether this information is entirely removed from the FHIR spec or just moved to a different location, but it does present an issue moving forward.

Abstract "token" into an authorization object

Should merge authorization data from the auth server's token introspection endpoint with (nominal) data about users and their actual permissions. This would encapsulate:

allowed compartments
user details
authorization scopes

xpath performance

Parse a resource once outside of searchParamHandlers, rather than inside deach
http://stackoverflow.com/questions/6471861/faster-api-than-javax-xml-xpath-to-parse-the-xml-for-a-value

smart-on-fhir/api-server: URL "Sample Patients:" points to old sample data project

https://github.com/smart-on-fhir/api-server

URL "Sample Patients:" point to https://github.com/chb/smart_sample_patients/tree/fhir

should be https://github.com/smart-on-fhir/sample-patients

Getting more sample data

You can load sample data from SMART's Sample Patients:

$ sudo apt-get install python-jinja2
$ git clone --recursive https://github.com/smart-on-fhir/sample-patients
$ cd sample-patients/bin
$ git checkout fhir
$ python generate.py --write-fhir ../generated-data
$ ls ../generated-data # a bunch of XML files

FHIR `read` on non-existing resource returns 404 with HTML

I'm getting the following response with this call (but would expect an OperationOutcome in JSON):

curl -H "Accept: application/json+fhir" https://fhir-open-api-dstu2.smarthealthit.org/Patient/xxx

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Error 404 Not Found</title>
</head>
<body><h2>HTTP ERROR 404</h2>
<p>Problem accessing /WEB-INF/grails-app/views/api/read.jsp. Reason:
<pre>    Not Found</pre></p><hr><i><small>Powered by Jetty://</small></i><hr/>

</body>
</html>

URL value mismatch in the fhir response bundle

The "url" value in the fhir response bundle inside the attribute "link" refers to a different port(9080), however the grails-app is running on port 8080(default) inside tomcat using the gradle wrapper...

Host a live copy + document links in README

Unable to update the records on your server

I am trying to update the record in the FHIR server it is throwing me following exception with 500 status. I am not sure some this is missing.
Below is the Exception I am getting

" Exception in thread "main" java.io.IOException: Server returned HTTP response code: 500 for URL: http://fhir.dev.aimsplatform.com/Patient/1272431_format=xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at com.test.HttpURLConnectionExample.updatePatientRecord(HttpURLConnectionExample.java:157)
at com.test.HttpURLConnectionExample.main(HttpURLConnectionExample.java:30)"

Following is the code snippet I am using. Please help me on this

//update particular patient record
private void updatePatientRecord(int PatientID) throws Exception {

        String url = "http://fhir.dev.aimsplatform.com/Patient/" + PatientID +"_format=xml";            
        //PUT https://example.com/path/{resourceType}/{id}

        URL obj = new URL(url);
        HttpURLConnection con = (HttpURLConnection) obj.openConnection();

         String authStr = "client"+":"+"secret";
            System.out.println("Original String is " + authStr);

        // encode data on your side using BASE64
            byte[] bytesEncoded = Base64.getEncoder().encode(authStr .getBytes());
            String authEncoded = new String(bytesEncoded);
            con.setRequestProperty("Authorization", "Basic "+authEncoded);  
        // optional default is PUT
        con.setRequestMethod("PUT");  


        con.setDoOutput(true);
        con.setDoInput(true);
        con.setRequestProperty("Content-Type", "application/json");
        con.setRequestProperty("Accept", "application/json");             

        JSONObject details = new JSONObject();      

        details.put("city","california");
        details.put("country","usa");

        OutputStreamWriter wr= new OutputStreamWriter(con.getOutputStream());
        wr.write(details.toString());;
        wr.flush(); 


         InputStream ins = con.getInputStream();
         InputStreamReader isr = new InputStreamReader(ins);
         BufferedReader in = new BufferedReader(isr);

         //output the information        

         String inputLine;
         while ((inputLine = in.readLine()) != null)
         {
             System.out.println(inputLine);
         }
         in.close();
    }

ᐧ

Cut "/fhir" from UrlMappings

Allow the server to determine URL via context. This allows "clean" API service urls like https://api.fhir.me

UI "Loading" logic on server switch

Avoid removing/adding table on update. Just hide/cover to prevent up/downs in small viewports.

Demos's link is broken

oauth

•Turn authentication or off with fhir.oauth.enabled : true | false

Where do we pass this flag or add this flag? I tried to pass it on the command line as:

./grailsw run-app --fhir-oauth.enabled:false

That did not work and got an error about oauth not being setup.

Thanks!

Implement Atom feed (+JSON) for `search` results

Allow clients to leave off `:ResourceType` modifiers from searches when unambiguous

For instance allow:
GET /MedicationPrescription?patient.name=john
instead of insisting on
GET /MedicationPrescription?patient:Patient.name=john

But continue to insist on disambiguation when there's >1 possible type, as in:
GET /Observation?subject.name=john
(In this case, provide a friendly error message.)

_sort order in queries

Consider support for ordered results. May need to derive the order client-side, or split resourceIndex into resource-specific collections (because MongoDB has a limit of 64 indexes per collection, and while k:v works for search queries via $elemMatch, it doesn't work for sort.)

Search params are double XML encoded in Atom `feed.id`

Implement resource-wise and server-wide history API

... and when done, update conformance profile to indicate support.

Load SMART sample data

Add a set of SMART export scripts for FHIR... at least for

Meds
Problems
Labs
Vitals
Demographics

Port the static CCDA Receiver UI and apps

Rewrite the main UI to launch with administration level privileges and support listing patients, arching, launching an app on a record...

Port growth chart, Cardiac Risk, BP Centiles, and time permitting, med rec depending on how lists can be handled.

FHIR DSTU3 issue

Hello,

Our organization just went from DSTU2 to DSTU3. In the DSTU2 version the encounter object has a method "class_" that accepts an enumeration of consisting of states of the patient such as "Inpatient", "Outpatient","Ambulatory", etc... The DSTU3 version has modified the class_ method to take a Coding object that consists of a CodeID(string) and DisplayText (string). So the question is, with the enumeration gone, how are the states to be persisted in this Coding object? We certainly cannot rely on a string for determining state as there may be a plethora of fat fingered patient states hydrating the object.

Total result count in JSON feed results

Currently the property is omitted

Pick and code for a FHIR Connectathon 4 Track

http://wiki.hl7.org/index.php?title=FHIR_Connectathon_4

Host an up-to-date conformance (profile.xml) resource

Implement support for patient-level comparments

will need a clear way to determine which resources belong in a given compartment! Maybe something simple like "Everything that links to a patient"?

Add new data to the server via HTTP PUT

when I follow the instructions and successfully run the project.and I can access http://localhost:8080/
but when i try the following code,I get a error 10061 access denied
curl 'http://localhost:8080/DiagnosticOrder/example'
-X PUT
-H 'Content-Type: text/xml'
--data @grails-app/conf/examples/diagnosticorder.xml

Expose SMART sample meds and fulfillments

Build an app that acts as a FHIR client

rather than hard-coding the UI into the server. Ideally this would handle

consuming a conformance profile or defaulting to a full feature set
list available resources + calls
support auto-population of search params
errors
content-types

Should be totally client-side using CORS requests -- but should also have a built-in server side pure proxy to support interaction with non-CORS FHIR servers.

Integrate OAuth2 (proxy to MITREid Connect)

Rely on an external OAuth2 authorization server to issue tokens, and check with that server (via introspection endpoints) when protected resource requests arrive.

Documentasample patient generation and loading

Get the rdflib versions right or eliminate dependency

OperationOutcome does not honor Accept header

I noticed our API server doesn't honor Accept: application/json+fhir and just returns an XML formatted OperationOutcome.

To replicate using HTTPie:

http https://fhir-api-dstu2.smarthealthit.org/Patient family==Argonaut given==Jason Authorization:"Bearer xOoZyp" Accept:application/json+fhir

smart-on-fhir/api-server ./grailsw run-script scripts/LoadCCDA.groovy run-script: command not found

Storing Documents + DocumentReferences

BASE_URL="http://localhost:8080"
CLIENT_ID=client
CLIENT_SECRET=secret
PATIENT_ID="1234"
CCDA="grails-app/conf/examples/ccda.xml"
./grailsw run-script scripts/LoadCCDA.groovy
ERROR: -bash: run-script: command not found

ERROR: file does not exist grails-app/conf/examples/ccda.xml

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should be https://github.com/smart-on-fhir/sample-patients

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