fhir | Official source for the HL7 FHIR Specification

I want to do a search in HAPI FHIR server as follows:

• Retrive Observation resources that are referenced in .has-member of other Observation resources that have a specific .device id.

Example:

We use FHIR, but we've had a few customer accidentally create a new Patient instead of finding and adding data to an existing patient creating duplicate entries for the same real-life patient.

I'd like to search for patients with same DOB and similar names and then offer them UI in the app to merge their records.

My questions are:

1. What's the most efficient way to do this search in FHIR without having to retrieve and compare every Patient resource?
2. What's the cleanest way to transfer related patient resources to one of the patients as part of a merge?

Thanks in advance.

I have been working with the FHIR REST API for a while but haven't had any experience with Python. As my first python project I am attempting to create a simple python script that can read and write to an open API. I am able to read but I am stuck on creating a successful POST due to the following: error [TypeError("unhashable type: 'dict'")]. I don't fully understand how the python dictionary works and attempted to use a tuple but get the same error.

I'm trying to build a simple api-gateway using spring-cloud-gateway. So far I understood the basic principle but I'm running in a specific Problem:

The target url which I'm forwarding my request potentially contains zero, one or multiple path segments. Unfortunately, these path segments are ignored.

The short version is this: The /Patient/[ID]/$everything for the example patient shown below has a reference to a procedure that is not also included in the /Patient/$everything resource.

Specifically: This example is from synthea. Synthea is an amazing tool that provides synthetic patients in FHIR format. (https://synthea.mitre.org/)

I have this example patient: https://syntheticmass.mitre.org/v1/fhir/Patient/5acc8bb4-2d14-4461-a560-228d96459cc3

This exists in the $everything resource as part of a claim resource:

One of the brilliant aspects of Firely.Terminal is its ability to interoperate with the local FHIR package cache (~/.fhir) in a way that is fully compatible with HAPI tools using the cache. Sadly, that no longer seems to be the case.

Today I updated Firely.Terminal to version 2.4.2 and it seems that the new version walks all over the FHIR package cache, changing files without having been asked to.

It used to be that the only thing Firely.Terminal changed in existing packages was the generation of a missing .index.json. For newly installed packages, the only difference to a HAPI-installed package was some additional fields in .index.json (presence of some fields containing null which would normally be suppressed, and the addition of a fhirVersion field).

When the new Firely.Terminal is told to add a package to a scope (fhir install) it automatically 'bakes' it, which seems to involve things like snapshotting all StructureDefinition resources and expanding all ValueSet resources. Even resources whose content remains unscathed get their timestamps trashed. The same fate befalls all packages that are listed as dependencies in the manifest of the package being added to the scope.

There is an 'unbake' command (e.g. fhir unbake --package kbv.ita.for@1.0.1) but this does not operate recursively. What's more, when it says 'Bake successfully removed from KBV.ITA.FOR@1.0.1' (note the erroneous capitalisation) then that is an outright lie - the contents of the package directory are completely unchanged, except for the removal of the file .bake.json.

Hence the only way of restoring the package cache to working order is to identify all trashed packages, delete them all, and then reference them with some HAPI tool in order to get them re-cached.

I wouldn't mind so much if Firely.Terminal trashed its own cache. But what it destroys is the global HAPI package cache for the current user, and that is simply not acceptable.

Is there any way of suppressing the destructive behaviour of Firely.Terminal? Ideally globally (with machine-wide effect), but a secret command switch would do in a pinch. If that is not possible: does anyone know which of the older versions is the newest that still works, and where to get it?

Note: if the cached packages are write-protected then Firely.Terminal doesn't take the hint - it tries to clobber the files anyway and spews out oodles of 'access denied' messages. What's more, it doesn't even stop when an error occurs; instead it continues on its merry way and trashes everything that one might have forgotten to write-protect.

Background: one of the properties of the FHIR package cache that is important for our work is that the files in the cache are exactly the same as those in the (normative) published packages. In particular, we need profiles published without snapshots to not contain snapshots, value sets published without expansions to not contain expansions and so on. For one thing, this makes it possible to verify that the cached files are exactly the same as those contained in the published packages (or fixed versions thereof). For another, we need to control the context in which profiles are snapshotted, value sets expanded and so on because it may be necessary to supply dependencies that are different from those declared in the package manifest. The latter is sometimes necessary because the profile/package version management in the context of electronic prescriptions in Germany is a bit, erm, peculiar and can diverge from FHIR standards. For this to work at all the resources must be snapshotted/expanded dynamically (depending on the use context), not statically on disk. Things are moving in a more standards-compliant direction but we are not quite there yet.

I have ndjson file Patients.ndjson

I am trying to build our IG for the first time using the publishler.jar but am getting a NullPointerException. I understand that there is some problem with it not managing to find some code in a CodeSystem but I can't figure it out. One clear problem that you'll see when I paste the output is that, for some reason it is working with r5 but we need r4 (4.0.1) and I have a hunch that this is leading to the problem because in r5 we do seem to have some issue with CodeSystems we still haven't figured out. Maybe someone can figure out what I'm doing wrong.

I actually tried 2 different approaches. the first:

java -jar publisher.jar -ig "c:\FHIR\outburn\fsh-generated\resources\ImplementationGuide-outburn.json" output:

I am new to MongoDB queries and looking for some guidance on how to retrieve documents that fit the search criteria. In particular, I need to find all the id(s) of the documents where the code is JPID i.e, "code": "JPID". We can assume the name of the collection is systems.

Since this is a nested object I thought of using the $unwid - but I am still stuck on how to do it. The example is very trivial. Any help and guidance is appreciated.