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fhir-kindling-1.0.0a7
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مشاهده بیشترتوضیحات
CRUD Operations against FHIR servers, resource validation and synthetic FHIR resource generation.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | fhir-kindling-1.0.0a7 |
| نام | fhir-kindling |
| نسخه کتابخانه | 1.0.0a7 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Michael Graf |
| ایمیل نویسنده | michael.graf@uni-tuebingen.de |
| آدرس صفحه اصلی | https://github.com/migraf/fhir-kindling |
| آدرس اینترنتی | https://pypi.org/project/fhir-kindling/ |
| مجوز | MIT license |
[](https://github.com/migraf/fhir-kindling/actions/workflows/main_ci.yml)
[](https://codecov.io/gh/migraf/fhir-kindling)
[](https://badge.fury.io/py/fhir-kindling)
# :fire: FHIR Kindling
CRUD library for fhir servers, with resource validation and parsing powered by
the [pydantic](https://github.com/samuelcolvin/pydantic)
models created by [fhir.resources](https://github.com/nazrulworld/fhir.resources). More details in
the [Documentation](https://migraf.github.io/fhir-kindling/).
## Features
- Create, Read, Update, Delete resources using a FHIR server's REST API
- Transfer resources between servers while maintaining referential integrity using server-given IDs
- Bundle creation, validation and data management on a FHIR server via the REST API
- Supports Hapi, Blaze and IBM FHIR servers
- CSV serialization of query results
- Synthetic data generation and
## Installation
Install the package using pip:
```shell
pip install fhir-kindling --user
```
## Usage
### Connecting to a FHIR server
```python
from fhir_kindling import FhirServer
# Connect with basic auth
basic_auth_server = FhirServer("https://fhir.server/fhir", username="admin", password="admin")
# Connect with static token
token_server = FhirServer("https://fhir.server/fhir", token="your_token")
# Connect using oauth2/oidc
oidc_server = FhirServer("https://fhir.server/fhir", client_id="client_id", client_secret="secret",
oidc_provider_url="url")
# Print the server's capability statement
print(basic_auth_server.capabilities)
```
### Query resources from the server
#### Basic resource query
```python
from fhir_kindling import FhirServer
from fhir.resources.patient import Patient
# Connect using oauth2/oidc
oidc_server = FhirServer("https://fhir.server/fhir", client_id="client_id", client_secret="secret",
oidc_provider_url="url")
# query all patients on the server
query = oidc_server.query(Patient, output_format="json").all()
print(query.response)
# Query resources based on name of resource
query = oidc_server.query("Patient", output_format="json").all()
print(query.response)
```
#### Query with filters
Filtering the targeted resource is done using the `where` method on the query object. The filter is created by defining
the target field, the comparison operator and the value to compare.
```python
from fhir_kindling import FhirServer
server = FhirServer(api_address="https://fhir.server/fhir")
query = server.query("Patient").where(field="birthDate", operator="gt", value="1980").all()
```
#### Including related resources in the query
Resources that reference or are referenced by resources targeted by the query can be included in the response using
the `include` method on the query object.
```python
# server initialization omitted
# get the patients along with the queried conditions
query_patient_condition = server.query("Condition").include(resource="Condition", reference_param="subject").all()
# get the conditions for a patient
query_patient_condition = server.query("Patient")
query_patient_condition = query_patient_condition.include(resource="Condition", reference_param="subject", reverse=True)
response = query_patient_condition.all()
```
#### Query resources by reference
If you know the id and resource type of the resource you want to query, you can use the `get` method for a single
reference
for a list of references use `get_many`. The passed references should follow the format of `<resource_type>/<id>`.
```python
# server initialization omitted
patient = server.get("Patient/123")
patients = server.get_many(["Patient/123", "Patient/456"])
```
### Add resources to the server
Resources can be added to the server using the `add` method on the server object. Lists of resources can be added using
'add_all'.
```python
from fhir_kindling import FhirServer
from fhir.resources.patient import Patient
# Connect to the server
server = FhirServer(api_address="https://fhir.server/fhir")
# add a single resource
patient = Patient(name=[{"family": "Smith", "given": ["John"]}])
response = server.add(patient)
# add multiple resources
patients = [Patient(name=[{"family": f"Smith_{i}", "given": ["John"]}]) for i in range(10)]
response = server.add_all(patients)
```
### Deleting/Updating resources
Resources can be deleted from the server using the `delete` method on the server object, it takes as input either
references to the resources or the resources itself.
Similarly the `update` method can be used to update the resources on the server, by passing a list of updated resources.
```python
from fhir_kindling import FhirServer
from fhir.resources.patient import Patient
# Connect to the server
server = FhirServer(api_address="https://fhir.server/fhir")
# add some patients
patients = [Patient(name=[{"family": f"Smith_{i}", "given": ["John"]}]) for i in range(10)]
response = server.add_all(patients)
# change the name of the patients
for patient in response.resources:
patient.name[0].given[0] = "Jane"
# update the patients on the server
updated_patients = server.update(resources=response.resources)
# delete based on reference
server.delete(references=response.references[:5])
# delete based on resources
server.delete(resources=response.resources[5:])
```
### Transfer resources between servers
Transferring resources between servers is done using the `transfer` method on the server object. Using this method
server assigned ids are used for transfer and referential integrity is maintained.
This method will also attempt to get all the resources that are referenced by the resources being transferred from the
origin
server and transfer them to the destination server as well.
```python
from fhir_kindling import FhirServer
# initialize the two servers
server_1 = FhirServer(api_address="https://fhir.server/fhir")
server_2 = FhirServer(api_address="https://fhir.server/fhir")
# query some resources from server 1
conditions = server_1.query("Condition").limit(10)
# transfer the resources to server 2
response = server_1.transfer(server_2, conditions)
```
## Performance
This library performs request at least 1.5 times faster than other popular fhir libraries.
See [Benchmarks](benchmarks/README.md) for a more detailed description of the benchmarks.
## Credits
This package was created with Cookiecutter and
the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter) project template.
# Change Log
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/)
and this project adheres to [Semantic Versioning](http://semver.org/).
## [0.9.0] - 2022-07-21
Asynchronous API for CRUD operations against fhir servers.
### Changed
- Switched http client library from requests [httpx](https://www.python-httpx.org/)
- removed requests-oauthlib in favor of authlib for oauth2 authentication flow
- `FHIRQuery` class renamed to `FHIRQuerySync` to allow for sync and async version
- moved resolving response pagination from `QueryReponse` to the sync and async query classes
- getting multiple resources via `server.get_many()` now uses proper batch requests
### Added
- `FHIRQueryAsync` class for async queries against a server
- asynchronous counterparts for CRUD operations in the `FHIRServer` class using the same API:
- `query_async()`
- `raw_query_async()`
- `get_async()`
- `get_many_async()`
- `add_async()`
- `add_all_async()`
- `add_bundle_async()`
- `update_async()`
- `delete_async()`
## [0.8.0] - 2022-03-18
Resource transfer between servers and querying resources by reference.
`get`, `get_many` for querying resource by reference
`server.transfer(other_server, query_result)` for transferring resources
### Changed
- `FhirServer` constructor now accepts two additional optional parameters, `auth` and `headers` that will be used for the
instance's `requests` session.
### Added
- [x] `server.get(reference)` get a single resource from the server, based on relative path/reference.
- [x] `server.get_many(references)` get multiple resources from the server, based on relative path/reference.
- [x] `server.transfer(other_server, query)` transfer resources matching the query from one server to another. Also requests
resources referenced by the resources matching to maintain referential integrity on the new server.
- [x] `query.all(page_callback=callback, count=50)` callback functions and count for pagination resolving in query responses.
## [0.7.0] - 2022-01-31
Update a list of resources on the server. CSV/Pandas serialization of resources and query responses.
### Added
- [x] `server.update(resources)` which updates a list of resources stored on the server
- [x] Recursive resource flattening for csv/tabular serialization
- [x] `query_response.save(path, format="csv)` to save the results of a query to csv
### Changed
- `server.query(params)` the query method now directly accepts query parameters
## [0.6.0] - 2022-01-19
Query Response with included resources. Reworked Generators
### Added
- [x] Query response now stores and parses included resources
- [x] Generator parameters for Resources and Fields
- [x] Field generators for generating resource fields based on probabilistic choices or a generator function
- [x] Resource generator field values based on static value or list
- [x] Patient based data set generator
### Changed
- Query interface `where, include, has` now can add query parameters based on method arguments or parameter objects.
## [0.5.0] - 2021-11-12
Query Parameters, include/revinclude, reverse chaining.
### Added
- [x] Query Parameters classes, for regular queries, including resources and reverse chaining
- [x] Support for `_include` and `_revinclude` via `query.include()`
- [x] Reverse chaining support via `query.has()`
- [x] Parsing parameters from given URL/ coverting parameters to query url
### Changed
- Query interface `where, include, has` now can add query parameters based on method arguments or parameter objects.
## [0.4.0] - 2021-11-12
Server summary, deleting resources, removed initial CLI.
### Added
- [x] Getting a list of all resources on the server based on capabilities
- [x] Plots for server and resource summary
- [x] `server.delete()` method to delete resources based on ids
## [0.3.0] - 2021-10-30
Response classes, reference parsing and basic xml support
### Added
XML output format and resolving xml pagination. Response objects containig resources and references
### Changed
Outsourced resolving of response pagination into response classes
### Fixed
## [0.2.0] - 2021-09-18
FHIR server and query API
### Added
Classes for fhir servers and queries. Oauth2/OIDC support.
### Changed
Moved location of cli
### Fixed
## [0.1.0] - 2021-08-24
Initial cli
### Added
### Changed
### Fixed
Hashing order guarantees the right index of the query.json file in the hash
نیازمندی
| مقدار | نام |
|---|---|
| - | python-dotenv |
| - | fhir.resources |
| - | httpx |
| - | pandas |
| - | authlib |
| - | pendulum |
| - | orjson |
| - | xmltodict |
| - | pydantic |
| - | networkx |
| - | pandas |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl fhir-kindling-1.0.0a7:
pip install fhir-kindling-1.0.0a7.whl
نصب پکیج tar.gz fhir-kindling-1.0.0a7:
pip install fhir-kindling-1.0.0a7.tar.gz