pylantir 0.1.3__py3-none-any.whl → 0.2.1__py3-none-any.whl

pylantir-0.1.3.dist-info/METADATA

@@ -1,193 +0,0 @@
-Metadata-Version: 2.4
-Name: pylantir
-Version: 0.1.3
-Summary: Python - DICOM Modality WorkList
-Author-email: Milton Camacho <miltoncamachoicc@gmail.com>
-Requires-Python: >=3.11.1
-Description-Content-Type: text/markdown
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-License-File: LICENSE
-Requires-Dist: pynetdicom
-Requires-Dist: sqlalchemy
-Requires-Dist: PyCap
-Requires-Dist: uuid
-Requires-Dist: coloredlogs
-Requires-Dist: python-dotenv
-Requires-Dist: pandas
-Requires-Dist: pyspark>=3.0.0 ; extra == "spark"
-Requires-Dist: bandit[toml]==1.7.5 ; extra == "test"
-Requires-Dist: black==23.3.0 ; extra == "test"
-Requires-Dist: check-manifest==0.49 ; extra == "test"
-Requires-Dist: flake8-bugbear==23.5.9 ; extra == "test"
-Requires-Dist: flake8-docstrings ; extra == "test"
-Requires-Dist: flake8-formatter_junit_xml ; extra == "test"
-Requires-Dist: flake8 ; extra == "test"
-Requires-Dist: flake8-pyproject ; extra == "test"
-Requires-Dist: pre-commit==3.3.1 ; extra == "test"
-Requires-Dist: pylint==3.3.6 ; extra == "test"
-Requires-Dist: pylint_junit ; extra == "test"
-Requires-Dist: pytest-cov==4.0.0 ; extra == "test"
-Requires-Dist: pytest-mock<3.10.1 ; extra == "test"
-Requires-Dist: pytest-runner ; extra == "test"
-Requires-Dist: pytest==7.3.1 ; extra == "test"
-Requires-Dist: pytest-github-actions-annotate-failures ; extra == "test"
-Requires-Dist: shellcheck-py==0.9.0.2 ; extra == "test"
-Project-URL: Documentation, https://github.com/miltoncamacho/pylantir/tree/main#readme
-Project-URL: Source, https://github.com/miltoncamacho/pylantir
-Project-URL: Tracker, https://github.com/miltoncamacho/pylantir/issues
-Provides-Extra: spark
-Provides-Extra: test
-
-<div style="text-align: center;">
-    <h1>Pylantir</h1>
-</div>
-<div style="text-align: center;">
-    <img src="pylantir.png" alt="Pylantir" width="50%">
-</div>
-
-This project's goal is to significantly reduce the number of human-related errors when manualy registering participants for medical imaging procedures.
-
-It effectively provides a python based DICOM Modality Worklist Server (SCP) and Modality Performed Procedure Step (SCP) able to receive requests from medical imaging equipemnt based on DICOM network comunication (e.g., a C-FIND, N-CREATE, N-SET requests).
-
-It will build/update a database based on the information entered in the study-related REDCap database using a REDCap API (You will require to have API access to the study).
-
-## Getting Started
-
-To get started simply install using:
-
-```bash
-pip install pylantir
-```
-
-You need to provide your REDCap API URL and API token before starting the server.
-Set up environmental variables before starting the server:
-
-```bash
-export REDCAP_API_URL=<your API url>
-export REDCAP_API_TOKEN=<your API token>
-```
-
-Start a server called with AEtitle MWL_SERVER.
-
-```bash
-pylantir start --ip 127.0.0.1 --port 4242 --AEtitle MWL_SERVER --pylantir_config Path/to/your/config.json
-```
-
-## Tests
-
-If you want to run the tests make sure to clone the repository and run them from there.
-
-Git clone the repository:
-
-```bash
-git clone https://github.com/miltoncamacho/pylantir
-cd pylantir/tests
-```
-
-Query the worklist database to check that you have some entries using:
-
-```bash
-python query-db.py
-```
-
-Then, you can get a StudyUID from one of the entries to test the MPPS workflow. For example: 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
-
-Take this and run a create action to mark the worklist Procedure Step Status as IN_PROGRESS
-
-```bash
-python test-mpps.py --AEtitle MWL_SERVER --mpps_action create --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632
-```
-
-You can verify that this in fact modified your database re-running:
-
-```bash
-python query-db.py
-```
-
-Finally, you can also simulate the pocedure completion efectively updating the Procedure Step Status to COMPLETED or DISCONTINUED:
-
-```bash
-python test-mpps.py --AEtitle MWL_SERVER --mpps_action set --mpps_status COMPLETED --callingAEtitle MWL_TESTER --ip 127.0.0.1 --port 4242 --study_uid 1.2.840.10008.3.1.2.3.4.55635351412689303463019139483773956632 --sop_uid 1.2.840.10008.3.1.2.3.4.187176383255263644225774937658729238426
-```
-
-## Usage
-
-```bash
-usage: pylantir [-h] [--AEtitle AETITLE] [--ip IP] [--port PORT] [--pylantir_config PYLANTIR_CONFIG] [--mpps_action {create,set}] [--mpps_status {COMPLETED,DISCONTINUED}] [--callingAEtitle CALLINGAETITLE] [--study_uid STUDY_UID] [--sop_uid SOP_UID] {start,query-db,test-client,test-mpps}
-```
-
-**pylantir** - Python DICOM Modality WorkList and Modality Performed Procedure Step compliance
-
-### Positional Arguments:
-
-- **{start,query-db,test-client,test-mpps}**: Command to run:
-  - **start**: Start the MWL server
-  - **query-db**: Query the MWL database
-  - **test-client**: Run tests for MWL
-  - **test-mpps**: Run tests for MPPS
-
-### Options:
-
-- **-h, --help**: Show this help message and exit
-- **--AEtitle AETITLE**: AE Title for the server
-- **--ip IP**: IP/host address for the server
-- **--port PORT**: Port for the server
-- **--pylantir_config PYLANTIR_CONFIG**: Path to the configuration JSON file containing pylantir configs:
-  - **allowed_aet**: List of allowed AE titles e.g. `["MRI_SCANNER", "MRI_SCANNER_2"]`
-  - **site**: Site ID:string
-  - **protocol**: `{"site": "protocol_name", "mapping": "HIS/RIS mapping"}`
-  - **redcap2wl**: Dictionary of REDCap fields to worklist fields mapping e.g., `{"redcap_field": "worklist_field"}`
-  - **db_update_interval**: How often to reload the database e
-  - **operation_interval**: What is the time range in a day in which the database will be updated e.g., `{"start_time":[hours,minutes],"end_time":[hours,minutes]}`
-- **--mpps_action {create,set}**: Action to perform for MPPS either create or set
-- **--mpps_status {COMPLETED,DISCONTINUED}**: Status to set for MPPS either COMPLETED or DISCONTINUED
-- **--callingAEtitle CALLINGAETITLE**: Calling AE Title for MPPS, it helps when the MWL is limited to only accept certain AE titles
-- **--study_uid STUDY_UID**: StudyInstanceUID to test MPPS
-- **--sop_uid SOP_UID**: SOPInstanceUID to test MPPS
-
-## Configuration JSON file
-
-As a default pylantir will try to read a JSON structured file with the following structure:
-
-```json
-{
-  "db_path": "/path/to/worklist.db",
-  "db_echo": "False",
-  "db_update_interval": 60,
-  "operation_interval": {"start_time": [0,0],"end_time": [23,59]},
-  "allowed_aet": [],
-  "site": "792",
-  "redcap2wl": {
-    "study_id": "study_id",
-    "instrument": "redcap_repeat_instrument",
-    "session_id" : "mri_instance",
-    "family_id": "family_id",
-    "youth_dob_y": "youth_dob_y",
-    "t1_date": "t1_date",
-    "demo_sex": "demo_sex",
-    "scheduled_date": "mri_date",
-    "scheduled_time": "mri_time",
-    "mri_wt_lbs": "patient_weight_lb",
-    "referring_physician": "referring_physician_name",
-    "performing_physician": "performing_physician",
-    "station_name": "station_name",
-    "status": "performed_procedure_step_status"
-  },
-  "protocol": {
-    "792": "BRAIN_MRI_3T",
-    "mapping": "GEHC"
-  }
-}
-```
-
-## Clean Stop of the MWL and Database Sync
-
-To cleanly stop the MWL server and ensure the database syncronization properly, press `Ctrl + C` (you might need to press it twice).
-

pylantir-0.1.3.dist-info/RECORD

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