Implemented python ids7client

ids7client/python/.bandit.yml

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+skips:
+  - B311
+  - B113

ids7client/python/.gitignore

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+# These are some examples of commonly ignored file patterns.
+# You should customize this list as applicable to your project.
+# Learn more about .gitignore:
+#     https://www.atlassian.com/git/tutorials/saving-changes/gitignore
+
+# Node artifact files
+node_modules/
+dist/
+
+# Compiled Java class files
+*.class
+
+# Compiled Python bytecode
+*.py[cod]
+
+# Log files
+*.log
+
+# Package files
+*.jar
+
+# Maven
+target/
+dist/
+
+# JetBrains IDE
+.idea/
+
+# Unit test reports
+TEST*.xml
+
+# Generated by MacOS
+.DS_Store
+
+# Generated by Windows
+Thumbs.db
+
+# Applications
+*.app
+*.exe
+*.war
+
+# Large media files
+*.mp4
+*.tiff
+*.avi
+*.flv
+*.mov
+*.wmv
+
+**/*.egg-info
+**/*build

ids7client/python/Makefile

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+SHELL=bash
+
+.PHONY: format
+format:
+	isort .;
+	black .
+
+.PHONY: lint
+lint:
+	flake8 ids7client/
+	bandit -c .bandit.yml -r ids7client/
+	isort --check ids7client/
+	black ids7client/ --check --diff
+	mypy ids7client/

ids7client/python/README.md

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+# Python Client for Sectra IDS7 PACS
+
+## Introduction
+
+This python package aims to facilite the development of AI applications integrated in Sectra IDS7 PACS.
+
+Please note that for now, not every feature is implemented but the package can easily be enriched:
+
+* some endpoints are missing (e.g., slide downloading)
+* QIDO client is pretty basic
+
+### What it implements
+
+* A client for the IDS7 AI API (`IDS7AIClient`)
+* A client for the IDS7 QIDO API (`IDS7QidoClient`)
+* A set of pydantic models to encapsulate and validate data sent and received from IDS7
+
+
+### What it does not implement, but might, at some point
+
+* A server to receive analysis requests from IDS7
+
+## Installation
+
+To install ids7client (until it is published in pypi):
+
+```pip install .```
+
+To install ids7client with development dependencies (linting and formating, see below):
+
+```pip install ./[dev]```
+
+## Usage
+
+Before using the client, make sure you have access to a valid authentication token, sent in the analysis requests.
+
+### Example 1: Retrieve image information
+
+```python
+from ids7client.ai import IDS7AIClient
+
+# Callback info, sent by IDS7 in the request
+callback_url = "https://sectrapacs.com"
+callback_token = "abc"
+
+# Slide id, sent by IDS7 in the request
+slide_id = "blabla"
+
+client = IDS7AIClient(
+    url=callback_url,
+    token=callback_token
+)
+
+# Returns the image info with extended and personal health information data
+image_info = client.get_image_info(slide_id, extended=True, phi=True)
+```
+
+### Example 2: Returning basic results
+
+The following code creates a result payload that can be sent as response to display a frame on the whole slide and a label telling the user that the analysis is pending.
+
+```python
+from ids7client.ai import (
+    ResultContent,
+    ResultType,
+    PrimitiveItem,
+    Style,
+    Polygon,
+    Point,
+    Label,
+    Result
+)
+
+# Slide id, sent by IDS7 in the request
+slide_id = "blabla"
+
+data = ResultContent(
+    type=ResultType.PRIMITIVES,
+    content=[
+        PrimitiveItem(
+            style=Style(
+                strokeStyle="#000000",
+            ),
+            polygons=[
+                Polygon(
+                    points=[
+                        Point(x=0.0, y=0.0),
+                        Point(x=1.0, y=0.0),
+                        Point(x=1.0, y=1.0),
+                        Point(x=0.0, y=1.0),
+                    ]
+                )
+            ],
+            labels=[
+                Label(
+                    location=Point(x=0.00, y=0.0),
+                    label="Analysis running",
+                )
+            ],
+        )
+    ],
+)
+
+result = Result(
+    slideId=slide_id,
+    displayResult="Analysis running",
+    applicationVersion="1.0.0",
+    data=data
+)
+```
+
+### Example 3: Retrieving patient, request and exam id
+
+```python
+from IDS7Client.ai import IDS7AIClient
+from IDS7Client.qido import IDS7QidoClient, DicomCodes
+
+# Callback info, sent by IDS7 in the request
+callback_url = "https://sectrapacs.com"
+callback_token = "abc"
+
+# Slide id, sent by IDS7 in the request
+slide_id = "blabla"
+
+ai_client = IDS7AIClient(
+    url=callback_url,
+    token=callback_token
+)
+
+# Returns the image info with extended and personal health information data
+image_info = client.get_image_info(slide_id, extended=True, phi=True)
+
+# Instanciates QIDO client with provided url, username and password
+qido_client = IDS7QidoClient(qido_url, qido_username, qido_password)
+
+# Retrieve study from QIDO API
+study = qido_client.find_one_study(studyInstanceUid=data.study_id)
+
+# Retrieve patient, request and exam id from the response
+patient_id = study.get_value_as_string(DicomCodes.PATIENT_ID)
+request_id = study.get_value_as_string(DicomCodes.REQUEST_ID)
+exam_id = study.get_value_as_string(DicomCodes.EXAM_ID)
+```
+
+### Error handling and retries
+
+Any request to the IDS7 server is retried 5 times with exponential delays if there is a connection error. Any other error is not handled by the clients.
+
+Clients raise `IDS7RequestError` if the IDS7 server returns an error status code (e.g., 400, 404, 500, etc.). The error includes the returned status code, text and the requested path.
+
+## Code quality
+
+Code quality is ensured with the following tools:
+
+* flake8 for formating
+* mypy for static typing analysis
+* bandit for security
+* black for formating
+* isort for imports order
+
+One can format the code using the following command:
+
+```make format```
+
+One can lint the code using the following command:
+
+```make lint```
+
+
+## What's next?
+
+* HL7 API client
+* More detailed data validation (e.g., min and max lengths of arrays)
+* Missing IDS7 endpoints

ids7client/python/extra_requirements.txt

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+bandit
+black
+flake8
+isort
+mypy
+types-requests
+types-setuptools

ids7client/python/ids7client/__init__.py

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+from .errors import IDS7RequestError

ids7client/python/ids7client/ai/__init__.py

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+from .client import IDS7AIClient
+from .schemas import (
+    Action,
+    ApplicationInfo,
+    Attachment,
+    AttachmentState,
+    CallbackInfo,
+    Context,
+    CreateInput,
+    DisplayedName,
+    DisplayProperties,
+    FocalPlane,
+    ImageInfo,
+    ImageNotification,
+    InputTemplate,
+    InputType,
+    Invocation,
+    Label,
+    MultiAreaContent,
+    OpticalPath,
+    Patch,
+    PatchContent,
+    Point,
+    Polygon,
+    Polyline,
+    PrimitiveItem,
+    Registration,
+    Result,
+    ResultContent,
+    ResultData,
+    ResultResponse,
+    ResultType,
+    Size,
+    SlideFormat,
+    Specimen,
+    Status,
+    Style,
+    TaggedPolygonContent,
+    TaggedPolygonInputContent,
+    TileFormat,
+)