dicom-client-python 0.3.1.dev33606
A small dicom client in python
Requires Python: >=3.7

# Dicom Client V1

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### Build Status 
(*Currently Private Build Badges*)

Main: [![Build Status](https://dev.azure.com/CSECodeHub/378940%20-%20PWC%20Health%20OSIC%20Platform%20-%20DICOM/_apis/build/status/dicom-client-python%20release%20pipeline?branchName=main)](https://dev.azure.com/CSECodeHub/378940%20-%20PWC%20Health%20OSIC%20Platform%20-%20DICOM/_build/latest?definitionId=36&branchName=main)

Dev: [![Build Status](https://dev.azure.com/CSECodeHub/378940%20-%20PWC%20Health%20OSIC%20Platform%20-%20DICOM/_apis/build/status/dicom-client%20integration%20and%20dev%20release?branchName=main)](https://dev.azure.com/CSECodeHub/378940%20-%20PWC%20Health%20OSIC%20Platform%20-%20DICOM/_build/latest?definitionId=28&branchName=main)


## API Introduction

There are four core methods that make up DICOM-Client. An interface has been
defined to simplify interaction with DicomClient(). The purpose of these methods
is to upload, download, and delete DCM files from DICOM Server:

```python
class DicomClientInterface(ABC):
    @abstractmethod
    def __init__(self, base_url, token_cache):
        pass
    @abstractmethod
    def upload_dicom_folder(self, folder_name):
        pass
    @abstractmethod
    def upload_dicom_file(self, file_name):
        pass
    @abstractmethod
    def delete_dicom(self, study_id, series_id=None, instance_id=None):
        pass
    @abstractmethod
    def download_dicom(self, output_folder, study_id, series_id=None, instance_id=None):
        pass
    @abstractmethod
    def get_patient_study_ids(self, patient_id):
        pass
```

## To use: 
```
$ pip install dicom_client
$ export AUTH_CONNECTION_INFO="{'authority': 'https://login.microsoftonline.com/72f988bf-86f1-41af-91ab-2d7cd011db47', 'client_id': '9cfb139d-d05d-4f5c-a10c-54e0ec338f53', 'client_secret': 'D.oD1q9SHc77syVRD-8vKi8UhbDXYoi~n~', 'oauth_resource': 'api://9cfb139d-d05d-4f5c-a10c-54e0ec338f53'}"
```

```python
import ast 
import os 
from dicom_client import (
    DicomClient,
    TokenCache,
    make_get_token_func,
)

base_url = "https://tonydicom.azurewebsites.net"

auth = ast.literal_eval(os.environ["AUTH_CONNECTION_INFO"])

token_cache = TokenCache(make_get_token_func(auth))
dicom_client = DicomClient(base_url, token_cache)

dicom_client.upload_dicom_folder("folder_name")
dicom_client.upload_dicom_file("file_name")
dicom_client.delete_dicom("study_id", "series_id", "instance_id")
dicom_client.download_dicom("output_folder", "study_id", "series_id", "instance_id")
dicom_client.get_patient_study_ids("patient_id")
```

This script can be used to validate your DICOM server deployment. 
 
See Microsoft Dicom Server here: https://github.com/microsoft/dicom-server 



# For contributors:

## Pre-reqs
- Provision a dicom server
- Get credentials for dicom server string values
- Export them as environment variables for your debugging environment.

Our .vscode/settings.json point to a .env file:

    "python.envFile": "${workspaceFolder}/.vscode/dev.env",
Our dev.env file needs these values in this format:

```
AUTH_CONNECTION_INFO="{'authority': 'https://login.microsoftonline.com/72f988bf-86f1-41af-91ab-2d7cd011db47', 'client_id': '5bef631a-c4cd-4feb-aaf2-78ff5f7d7347', 'client_secret': 'REPLACE_WITH_YOUR_SECRET_mrpc.lgXK~C0.g146Gu3PcDG.W6Eg0d0I', 'oauth_resource': 'api://REPLACE_WITH_YOUR_RESOURCE_ID5bef631a-c4cd-4feb-aaf2-78ff5f7d7347'}"
```

## Running Tests 

Complete the pre-reqs and set the AUTH_CONNECTION_INFO environment variable, then:  

```
$ git clone our_git_url
$ python3 -m venv .venv
$ pip install -r requirements.txt 
$ pytest tests
```

Make sure you've followed the prerequisites for running the tests locally and validated your dicom server host and exported the correct credentials. See [README.md](README.md) for more details or raise an issue for DICOM server support. 

### Unit tests

To run most of the unit tests (optionally with code coverage reporting), simply run:

```
$ pytest tests/unit [--cov=handler --cov-report=html:htmlcov]
```

Please see `conftest.py` for more information on these test parameters as they can be found with environment variables instead of arguments for development environments.  

### Pylint 

Pylint provides static code analysis for python and uses our `./.pylintrc` file for managing the configuration of the linter. We run pylint in our integration tests to ensure python coding standards. See more info about pylint [here.](https://pypi.org/project/pylint/)

To run pylint locally: 

```
pylint handler --output-format=colorized --rcfile=".pylintrc"
```

### Formatting with Black 

Black is an auto-formatting tool and checker for python that provides further code analysis, it to is run in our integration tests and is helpful to run locally to maintain code clarity and conform to team standards. More info can be found [here.](https://pypi.org/project/black/)

To run black locally: 
```
black --check --line-length 100 .
black --line-length 100 .
```