beda-software / fhir-py Goto Github PK

Now, FHIRReference returns None for .id/.resourceType attributes.
But we can extract them from URL: http://another.fhir.server/fhir/Patient/id

Sometimes we need to iterate over thousands of entries and I think it will be very useful if we can have fetch_all() as a generator. Now if we call fetch_all for thousands of entries we firstly wait until all entries are fetched.

Consider implementing lazy fetch for searchset iterating.

Repeat Django's behaviour, just check resource_type and id

It would be great if we could use conditional delete (as described here) to clean up linked resources.

Use Bundle resource from #7

We should transform resource/reference instance in search lookups, for example:

practitioner = clients.resources('Practitioner').first()

# This line should be transformed to
client.resources('Schedule').search(actor=practitioner)

# Something like that
client.resources('Schedule').search(actor=practitioner.reference)

Something like resource.update({'attr': 'new value'}) or client.resources('Patient').update(id=1, {'birthDate': '1905-08-23'})

• Create classes FHIRClient, FHIRResource, FHIRReference, FHIRSearchSet based on classes from base-fhir-py
• Override FHIRReference.id, FHIRReference.resource_type, FHIRReference.reference
• Add validation using FHIRResource.raise_error_if_invalid_keys FHIRReference.raise_error_if_invalid_keys

1. Create alias for execute - fetch()
2. Create fetch_all() which fetches all instances with pagination

client.resources('Patient').limit(10).fetch_all()

Possible implementation:

def fetch_all(self):
    resources = []
    page = 0
    while True:
        new_resources = self.page(page).fetch()
        if not new_resources:
            break
        resources.extend(new_resources)
        page += 1
    
    return new_resources

• Rename FHIRClient -> Client, FHIRResource -> Resource, FHIRBaseResource -> AbstractResource, FHIRReference -> Reference, FHIRSearchSet -> SearchSet
• Make them abstract
• In Client specify searchset_class, resource_class, reference_class and use them in public API (resource, resources, reference)
• Remove load_schema, validation, fhir_version, schema, root_keys make raise_error_if_invalid_keys public and empty by default
• Make Reference.resource_type, Reference.id, Reference.reference abstract
• Make AbstractResource.is_reference non static, abstract and move into Resource
• In SearchSet.clone use self.class to instantiate a copy

It will be very useful to combine complex queries using Q() like it made in Django.

Examples:
OR

client.resources('Slot').search(Q(schedule='id1') | Q(schedule='id2'))

transforms to =>

client.resources('Schedule').search(actor='id1,id2')

and generates =>

?schedule=id1,id2

AND

client.resources('Schedule').search(Q(actor='id1') & Q(actor='id2'))

transforms to =>

client.resources('Schedule').search(actor=['id1', 'id2'])

and generates =>

?actor=id1&actor=id2

Hi
I created a repl.it program using fhirpy. You can test it here
https://repl.it/@fhirinterm/TryFhirPy

It just runs this:

import asyncio
from fhirpy import AsyncFHIRClient

async def main():
# Create an instance
client = AsyncFHIRClient(
'http://test.fhir.org/r4',
fhir_version='4.0.0',
authorization='Bearer TOKEN',
)

# Iterate over search set
org_resources = client.resources('Patient')
async for org_resource in org_resources:
    print(org_resource.serialize())

if name == 'main':
loop = asyncio.get_event_loop()
loop.run_until_complete(main())

I got this error message:

Traceback (most recent call last):
File "main.py", line 22, in
loop.run_until_complete(main())
File "/usr/local/lib/python3.7/asyncio/base_events.py", line 579, in run_until_complete
return future.result()
File "main.py", line 16, in main
async for org_resource in org_resources:
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line496, in aiter
items = await iterable_coroutine
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line522, in fetch
resource = self._perform_resource(data, skip_caching)
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line282, in _perform_resource
resource = self.client.resource(resource_type, **data)
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line90, in resource
return self.resource_class(self, resource_type=resource_type, **kwargs)
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line709, in init
super(BaseResource, self).init(client, **converted_kwargs)
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line597, in init
self._raise_error_if_invalid_keys(kwargs.keys())
File "/home/runner/.local/share/virtualenvs/python3/lib/python3.7/site-packages/fhirpy/base/lib.py", line684, in _raise_error_if_invalid_keys
key, ', '.join(root_attrs)
KeyError: 'Invalid key _birthDate. Possible keys are multipleBirthInteger, text, active, deceasedBoolean, identifier, multipleBirthBoolean, language, extension, contained, address, gender, modifierExtension, id, communication, managingOrganization, resourceType, maritalStatus, photo, telecom, birthDate, name, generalPractitioner, meta, contact, implicitRules, deceasedDateTime, link'

Interestingly, if you replace 'Patient' with 'Organization'
It works perfectly
KInd regards
DK

When making a get call on multiple end points, both open (http://hapi.fhir.org/baseDstu3) and EMR Vendor based (Epic 2018, Epic August 2018) receive error

the JSON object must be str, not 'bytes'

This is caused by a missing .decode() call on r.content, here's the broken piece of code. Notice the 200 call is the only one without a .decode()

        if 200 <= r.status_code < 300:
            return json.loads(r.content) if r.content else None

        if r.status_code == 404:
            raise FHIRResourceNotFound(r.content.decode())

        raise FHIROperationOutcome(r.content.decode())

This simple example shows the issue

from fhirpy import FHIRClient

client = FHIRClient(url='http://hapi.fhir.org/baseDstu3')
resources = client.resources('Practitioner').get(id=1700173)

I have a fix in place I'm using currently and will submit a pull request.

For example, if I have a list of Patient Id's I want to look up, how can I iterate the list and make an asynchronous request for each one? Here is what I tried so far:

import asyncio
from fhirpy import AsyncFHIRClient

async def main():
    # Create an instance
    client = AsyncFHIRClient(
        'https://myfhirendpoint.com',
        fhir_version='4.0.0',
    )
    client.schema = None

    pat_ids = [
        "patient1",
        "patient2",
        "patient3",
        "patient4",
        "patient5",
    ]

    resources = client.resources('Patient')
    tasks = [
        resources.search(_id=pat_id).limit(10)
        for pat_id in pat_ids
    ]

    patients = [await task.fetch() for task in tasks]
    return patients

if __name__ == '__main__':
    loop = asyncio.get_event_loop()
    loop.run_until_complete(main())

The above works, but I don't think it is executing asynchronously. What is the proper way to do this using fhirpy?

I've started adding issues and pull requests, though the project's license file is empty. While the beda software site speaks to a commitment to open source, it would make folks, including myself, more comfortable contributing if the licensing was clearly stated in the repo.

https://choosealicense.com/no-permission/

When we use revinclude or include we have a bundle with multiple types of resources, but fetch/fetch_all returns only main resource.

We can add fetch_raw/fetch_all_raw that should always return a dict with fetched resources.

Example:

client.resources('Schedule').revinclude('Slot', 'schedule').fetch_all_raw()

returns

{'Slot': [SlotResource, SlotResource, ...],
'Schedule': [ScheduleResource, ScheduleResource, ...],}

And

client.resources('Schedule').fetch_all_raw()

returns

{'Schedule': [ScheduleResource, ScheduleResource, ...],}

TBD

Not sure if this problem is specific to the FHIR Server I am pulling from, but supplying a page number will always return a bundle with resources. The current fetch_all() code uses this:

while True:
    new_resources = await self.page(page).fetch()
        if not new_resources:
            break

Since my server always returns something regardless of the page number, it gets stuck in the loop above. The way I've gotten around this in the past is to refer to the next link in the Bundle .

I suppose a quick and dirty solution would be something like the following:

async def fetch(self):
    bundle_data = await self.client._fetch_resource(
        self.resource_type, self.params
    )
    bundle_resource_type = bundle_data.get('resourceType', None)

    ...
    
    next_link = None
    for link in bundle_data.get('link', []):
        if link['relation'] == 'next':
            next_link = link['url']
    
    return resources, next_link

async def fetch_all(self):
    page = 1
    resources = []

    while True:
        new_resources, next_link = await self.page(page).fetch()
        resources.extend(new_resources)
        
        if not next_link:
            break
            
        page += 1

    return resources

The documentation mentions you can use Raw Parameters using the following:

from fhirpy.base.searchset import Raw

patients = client.resources('Patient')
patients.search(Raw('general-practitioner.name=Hospital'))
# /Patient?general-practitioner.name=Hospital

However, after downloading the source code for 1.0.0 it appears that searchset.py was not included in the release. Is this a mistake?

/Questionnaire/<id>/$populate

/Valuest/<id>/$expand

/Valuest/$expand

$ operation should be a string parameter and accept any string. It should work on both levels.

When using a bearer token, is there a way to refresh it when it expires?
Or will I have to create a new client instance each time?

The following examples should work:

client.resources('Patient').search(general_practitioner__name='test')

client.resources('Patient').search(general_practitioner__Practitioner__name='test')

In #35 we've done lazy fetching using __iter__/__aiter__. I think In 2.0.0 we can remove fetch/fetch_all/fetch_raw due to __iter__/__aiter__ (always returns all results) and some methods such as to_list() and to_bundle()

Several EHR vendors, including Epic, require headers that cannot be passed in, or make no sense to be passed in, with the current state of the object constructor. These are typically used for things like client IDs and additional authorization for access.

I have a solution currently implemented and being used with a large EHR installation. I add an extra_headers attribute to the object, defaulted to None. When not None, the extra_headers attribute is unpacked into the headers variable.

If you can please assign this bug to me, I will submit a pull request for the solution within the next few days.

datetime.date should be transformed into %Y-%m-%d, and datetime.datetime into %Y-%m-%dT%H:%M:%S

Now we have a bug when using client.resources('...').search(active=True)
It creates a query ?active=True, but it should be ?active=true

TBD

Example:

p = client.resource('Patient', managingOrganization=[...])

p['managingOrganization'] = None
p.save()

should remove managingOrganization key for POST/PUT query.
For PATCH - TBD, but it hasn't implemented yet

Just re-write FHIRResource._get_path

It will be useful if we can provide this API for search() with prefixies and modifiers.
See:

• https://www.hl7.org/fhir/search.html#prefix
• https://www.hl7.org/fhir/search.html#string
• https://www.hl7.org/fhir/search.html#token

Examples:

client.resources('Schedule').search(date__eq='2000-01-01')

transforms to =>

client.resources('Schedule').search(date='eq2000-01-01')

generates =>

?date=eq2000-01-01

Let's remove self.client to self._client

I am trying to resolve references from a resource, with AsyncReference.to_resource()
This seems to fail.

example

import asyncio
from fhirpy import AsyncFHIRClient
from py2neo import Graph, Node, Relationship


async def main():
    # Create an instance
    client = AsyncFHIRClient(
        "http://hapi.fhir.org/baseR4",
        # "http://localhost:8080/fhir",
        authorization="Bearer TOKEN",
    )

    obser_client = client.resources("Observation")  # Return lazy search set
    obser_query = obser_client.search().limit(5)
    observations = await obser_query.fetch()
    for obser in observations:
        if "subject" in obser:
            # This will fail
            patient = await obser.subject.to_resource()


if __name__ == "__main__":
    loop = asyncio.get_event_loop()
    loop.run_until_complete(main())

It looks like a typo on line

because when changing the line

self.resource_type).search(id=self.id).get()

to

self.resource_type).search(_id=self.id).get()

it seems to work.
Im just starting to work with fhir, and do not have a good overview of the subject matter.
Do I use the function in a wrong way?
Is the fhir test server data corrupt?
If i found a bug, i can provide a merge request.

Now it is hard to extract details

p = client.resource('Observation', code={'coding': [{'code': '123'}]})

p['code'] should return wrapped dict and provide get_by_path method

Now it accepts only id. get should accept any search parameters and assert that exactly one result was returned. Otherwise, an exception should be fired.

Now we update only id and meta. But sometimes the resource can be mutated

Critical fix for get_by_path beda-software/base-fhir-py@cf02ff9

It should make a POST request to the /resourceType/$validate and return OperationOutcome if raise_exception arg passed or just True/False.
TBD

GET /EpisodeOfCare?patient:Patient.name=Ivan

We need to support both sync and async interfaces

We should add a new SearchSet (e.g. HistorySearchSet) and provide methods .history() for Resource/Reference, SearchSet and Client.

It should be something like that:

client.history('User') - returns HistorySearchSet for /User/_history/
client.history('User', 'id') - returns HistorySearchSet for /User/id/_history/

clients.resources('User').history() - returns HistorySearchSet for /User/_history/
clients.resources('User').history('id') - returns HistorySearchSet for /User/id/_history/

And resource/reference methods:

resource = client.resource('User').get('id')
resource.history() - returns HistorySearchSet for /User/id/_history/

And HistorySearchSet should provide:

history = client.history('User', 'id')

history.fetch()/history.fetch_all() - executes and returns list of resources
history.count() - executes and returns history count
history.limit()/history.page() - the same as in the SearchSet
history.at('date')/history.since('date') - returns new HistorySearchSet
history.get('vid') - executes and returns /User/id/_history/vid

And also we can support some useful helpers:

resource.history().get_previous() - returns the previous version of the resource if possible or None