fhir-pyrate 0.2.0b9__tar.gz → 0.2.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- fhir_pyrate-0.2.0b9/README.md → fhir_pyrate-0.2.2/PKG-INFO +106 -17
- fhir_pyrate-0.2.0b9/PKG-INFO → fhir_pyrate-0.2.2/README.md +72 -51
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/ahoy.py +14 -7
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/dicom_downloader.py +140 -68
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/miner.py +17 -18
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/pirate.py +106 -80
- fhir_pyrate-0.2.2/fhir_pyrate/util/__init__.py +4 -0
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/util/bundle_processing_templates.py +7 -4
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/util/fhirobj.py +2 -2
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/util/imports.py +3 -3
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/util/token_auth.py +27 -23
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/util/util.py +9 -5
- fhir_pyrate-0.2.2/pyproject.toml +101 -0
- fhir_pyrate-0.2.0b9/fhir_pyrate/util/__init__.py +0 -8
- fhir_pyrate-0.2.0b9/pyproject.toml +0 -56
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/LICENSE +0 -0
- {fhir_pyrate-0.2.0b9 → fhir_pyrate-0.2.2}/fhir_pyrate/__init__.py +1 -1
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Metadata-Version: 2.1
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Name: fhir-pyrate
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Version: 0.2.2
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Summary: FHIR-PYrate is a package that provides a high-level API to query FHIR Servers for bundles of resources and return the structured information as pandas DataFrames. It can also be used to filter resources using RegEx and SpaCy and download DICOM studies and series.
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Home-page: https://github.com/UMEssen/FHIR-PYrate
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License: MIT
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Keywords: python,fhir,data-science,fhirpath,healthcare
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Author: Rene Hosch
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Author-email: rene.hosch@uk-essen.de
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Requires-Python: >=3.10,<4.0
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Provides-Extra: all
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Provides-Extra: downloader
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Requires-Dist: dicomweb-client (>=0.52.0,<0.53.0) ; extra == "downloader" or extra == "all"
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Requires-Dist: fhirpathpy (>=0.2.2,<0.3.0)
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Requires-Dist: numpy (>=2.0.0,<3.0.0)
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Requires-Dist: pandas (>=2.0.0,<3.0.0)
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Requires-Dist: pydicom (>=2.1.2,<3.0.0) ; extra == "downloader" or extra == "all"
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Requires-Dist: requests (>=2.28.0,<3.0.0)
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Requires-Dist: tqdm (>=4.56.0,<5.0.0)
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Project-URL: Repository, https://github.com/UMEssen/FHIR-PYrate
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Description-Content-Type: text/markdown
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[](https://opensource.org/licenses/MIT)
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[](https://www.python.org/downloads/release/python-31011/)
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[](https://pypi.org/project/fhir-pyrate/)
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[](https://pypi.org/project/fhir-pyrate/#history)
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[](https://zenodo.org/badge/latestdoi/456893108)
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[](https://wispermed.org/)
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<!-- PROJECT LOGO -->
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<div align="center">
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<a href="https://github.com/UMEssen/FHIR-PYrate">
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<img src="https://raw.githubusercontent.com/UMEssen/FHIR-PYrate/main/images/logo.svg" alt="Logo" width="440" height="338">
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</div>
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This package is meant to provide a simple abstraction to query and structure FHIR resources as
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pandas DataFrames. Want to use R instead? Try out [fhircrackr](https://github.com/POLAR-fhiR/fhircrackr)!
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**If you use this package, please cite:**
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Hosch, R., Baldini, G., Parmar, V. et al. FHIR-PYrate: a data science friendly Python package to query FHIR servers. BMC Health Serv Res 23, 734 (2023). https://doi.org/10.1186/s12913-023-09498-1
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There are four main classes:
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* [Ahoy](https://github.com/UMEssen/FHIR-PYrate/blob/main/fhir_pyrate/ahoy.py): Authenticate on the FHIR API
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([Example 1](https://github.com/UMEssen/FHIR-PYrate/blob/main/examples/1-simple-json-to-df.ipynb),
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problems with the authentication (or anything else really), please just create an issue or
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<div align="center">
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<img src="https://raw.githubusercontent.com/UMEssen/FHIR-PYrate/main/images/resources.svg" alt="Resources" width="630" height="385">
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</div>
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<!-- TABLE OF CONTENTS -->
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Table of Contents:
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| trade_rows_for_dataframe | 3 | Yes | Yes | DataFrame |
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**CACHING**: It is also possible to cache the bundles using the `cache_folder` parameter.
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This unfortunately does not currently work with multiprocessing, but saves a lot of time if you
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need to download a lot of data and you are always doing the same requests.
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parameter. There is an example of this in the docstrings of the Pirate class.
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A toy request for ImagingStudy:
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You can find an example in [Example 3](https://github.com/UMEssen/FHIR-PYrate/blob/main/examples/3-patients-for-condition.ipynb).
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Additionally, you can specify the `with_columns` parameter, which can add any columns from the original
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DataFrame. The columns can be either specified as a list of columns `[col1, col2, ...]` or as a
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list of tuples `[(new_name_for_col1, col1), (new_name_for_col2, col2), ...]
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list of tuples `[(new_name_for_col1, col1), (new_name_for_col2, col2), ...]`.
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Currently, whenever a column is completely empty (i.e., no resources
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have a corresponding value for that column), it is just removed from the DataFrame.
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This is to ensure that we output clean DataFrames when we are handling multiple resources.
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More on that in the following section.
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#### Note on Querying Multiple Resources
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Not all FHIR servers allow this (at least not the public ones that we have tried),
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but it is also possible to obtain multiple resources with just one query:
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```python
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search = ...
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result_dfs = search.steal_bundles_to_dataframe(
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resource_type="ImagingStudy",
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request_params={
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"_lastUpdated": "ge2022-12",
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"_count": "3",
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"_include": "ImagingStudy:subject",
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},
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fhir_paths=[
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"id",
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"started",
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("modality", "modality.code"),
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("procedureCode", "procedureCode.coding.code"),
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(
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"study_instance_uid",
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"identifier.where(system = 'urn:dicom:uid').value.replace('urn:oid:', '')",
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),
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("series_instance_uid", "series.uid"),
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("series_code", "series.modality.code"),
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("numberOfInstances", "series.numberOfInstances"),
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("family_first", "name[0].family"),
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("given_first", "name[0].given"),
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)
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```
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In this case, a dictionary of DataFrames is returned, where the keys are the resource types.
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or `result_dfs["Patient"]`.
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You can find an example of this in [Example 2](https://github.com/UMEssen/FHIR-PYrate/blob/main/examples/2-condition-to-imaging-study.ipynb)
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where the `ImagingStudy` resource is queried.
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e.g. `ImagingStudy.series.uid` instead of `series.uid`, and for each DataFrame only return the
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corresponding attributes.
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However, we do not want to force the user to always specify the resource type, and in the current
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version the DataFrames
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coming from multiple resources have the same columns, because
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we cannot filter which resource was actually intended.
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Which means however, that if you are actually requesting an attribute for a specific resource and it
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is not found, that that column will not appear.
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In the future, [we plan to do a smarter filtering of the FHIRPaths](https://github.com/UMEssen/FHIR-PYrate/issues/120),
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such that only the ones containing
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the actual resource name are kept if the resource name is specified in the path,
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and that a column full of `None`s is obtained in case no resource type is specified.
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### [Miner](https://github.com/UMEssen/FHIR-PYrate/blob/main/fhir_pyrate/miner.py)
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## Project status
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The project is in active development.
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Metadata-Version: 2.1
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Name: fhir-pyrate
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Version: 0.2.0b9
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Summary: FHIR-PYrate is a package that provides a high-level API to query FHIR Servers for bundles of resources and return the structured information as pandas DataFrames. It can also be used to filter resources using RegEx and SpaCy and download DICOM studies and series.
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Home-page: https://github.com/UMEssen/FHIR-PYrate
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License: MIT
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Keywords: python,fhir,data-science,fhirpath,healthcare
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Author: Rene Hosch
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Author-email: rene.hosch@uk-essen.de
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.8
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Project-URL: Repository, https://github.com/UMEssen/FHIR-PYrate
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Description-Content-Type: text/markdown
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<!-- PROJECT LOGO -->
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This package is meant to provide a simple abstraction to query and structure FHIR resources as
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pandas DataFrames. Want to use R instead? Try out [fhircrackr](https://github.com/POLAR-fhiR/fhircrackr)!
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**If you use this package, please cite:**
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Hosch, R., Baldini, G., Parmar, V. et al. FHIR-PYrate: a data science friendly Python package to query FHIR servers. BMC Health Serv Res 23, 734 (2023). https://doi.org/10.1186/s12913-023-09498-1
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There are four main classes:
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* [Ahoy](https://github.com/UMEssen/FHIR-PYrate/blob/main/fhir_pyrate/ahoy.py): Authenticate on the FHIR API
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([Example 1](https://github.com/UMEssen/FHIR-PYrate/blob/main/examples/1-simple-json-to-df.ipynb),
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problems with the authentication (or anything else really), please just create an issue or
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<!-- TABLE OF CONTENTS -->
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**CACHING**: It is also possible to cache the bundles using the `cache_folder` parameter.
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This unfortunately does not currently work with multiprocessing, but saves a lot of time if you
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need to download a lot of data and you are always doing the same requests.
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You can also specify how long the cache should be valid with the `cache_expiry_time` parameter.
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Additionally, you can also specify whether the requests should be retried using the `retry_requests`
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parameter. There is an example of this in the docstrings of the Pirate class.
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A toy request for ImagingStudy:
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@@ -429,7 +393,65 @@ parameters specified in `df_constraints` as columns of the final DataFrame.
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You can find an example in [Example 3](https://github.com/UMEssen/FHIR-PYrate/blob/main/examples/3-patients-for-condition.ipynb).
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Additionally, you can specify the `with_columns` parameter, which can add any columns from the original
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DataFrame. The columns can be either specified as a list of columns `[col1, col2, ...]` or as a
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-
list of tuples `[(new_name_for_col1, col1), (new_name_for_col2, col2), ...]
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list of tuples `[(new_name_for_col1, col1), (new_name_for_col2, col2), ...]`.
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+
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Currently, whenever a column is completely empty (i.e., no resources
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have a corresponding value for that column), it is just removed from the DataFrame.
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This is to ensure that we output clean DataFrames when we are handling multiple resources.
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More on that in the following section.
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+
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+
#### Note on Querying Multiple Resources
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+
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Not all FHIR servers allow this (at least not the public ones that we have tried),
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but it is also possible to obtain multiple resources with just one query:
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+
```python
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+
search = ...
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+
result_dfs = search.steal_bundles_to_dataframe(
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+
resource_type="ImagingStudy",
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+
request_params={
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+
"_lastUpdated": "ge2022-12",
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|
+
"_count": "3",
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|
+
"_include": "ImagingStudy:subject",
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+
},
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|
+
fhir_paths=[
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|
+
"id",
|
|
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|
+
"started",
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|
+
("modality", "modality.code"),
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|
+
("procedureCode", "procedureCode.coding.code"),
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|
+
(
|
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|
+
"study_instance_uid",
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|
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|
+
"identifier.where(system = 'urn:dicom:uid').value.replace('urn:oid:', '')",
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|
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|
+
),
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|
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|
+
("series_instance_uid", "series.uid"),
|
|
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|
+
("series_code", "series.modality.code"),
|
|
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|
+
("numberOfInstances", "series.numberOfInstances"),
|
|
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|
+
("family_first", "name[0].family"),
|
|
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|
+
("given_first", "name[0].given"),
|
|
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|
+
],
|
|
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|
+
num_pages=1,
|
|
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|
+
)
|
|
433
|
+
```
|
|
434
|
+
In this case, a dictionary of DataFrames is returned, where the keys are the resource types.
|
|
435
|
+
You can then select the single dictionary by doing `result_dfs["ImagingStudy"]`
|
|
436
|
+
or `result_dfs["Patient"]`.
|
|
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|
+
You can find an example of this in [Example 2](https://github.com/UMEssen/FHIR-PYrate/blob/main/examples/2-condition-to-imaging-study.ipynb)
|
|
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|
+
where the `ImagingStudy` resource is queried.
|
|
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|
+
|
|
440
|
+
In theory, it would be smarter to specify the resource name in front of the FHIRPaths,
|
|
441
|
+
e.g. `ImagingStudy.series.uid` instead of `series.uid`, and for each DataFrame only return the
|
|
442
|
+
corresponding attributes.
|
|
443
|
+
However, we do not want to force the user to always specify the resource type, and in the current
|
|
444
|
+
version the DataFrames
|
|
445
|
+
coming from multiple resources have the same columns, because
|
|
446
|
+
we cannot filter which resource was actually intended.
|
|
447
|
+
Currently, we solved this by just removing all columns that do not have any results.
|
|
448
|
+
Which means however, that if you are actually requesting an attribute for a specific resource and it
|
|
449
|
+
is not found, that that column will not appear.
|
|
450
|
+
In the future, [we plan to do a smarter filtering of the FHIRPaths](https://github.com/UMEssen/FHIR-PYrate/issues/120),
|
|
451
|
+
such that only the ones containing
|
|
452
|
+
the actual resource name are kept if the resource name is specified in the path,
|
|
453
|
+
and that a column full of `None`s is obtained in case no resource type is specified.
|
|
454
|
+
|
|
433
455
|
|
|
434
456
|
### [Miner](https://github.com/UMEssen/FHIR-PYrate/blob/main/fhir_pyrate/miner.py)
|
|
435
457
|
|
|
@@ -559,4 +581,3 @@ This project is licenced under the [MIT Licence](LICENSE).
|
|
|
559
581
|
|
|
560
582
|
## Project status
|
|
561
583
|
The project is in active development.
|
|
562
|
-
|
|
@@ -33,18 +33,22 @@ class Ahoy:
|
|
|
33
33
|
:param token_refresh_delta: Either a timedelta object that tells us how often the token
|
|
34
34
|
should be refreshed, or a number of minutes; this does not need to be specified for JWT tokens
|
|
35
35
|
that contain the expiry date
|
|
36
|
+
:param session: The session that can be used for the authentication. This is particularly
|
|
37
|
+
useful if you have some particular requirements for your authentication (e.g. you need to
|
|
38
|
+
support for cusum self-signed certificates).
|
|
36
39
|
"""
|
|
37
40
|
|
|
38
41
|
def __init__(
|
|
39
42
|
self,
|
|
40
|
-
auth_url: str = None,
|
|
43
|
+
auth_url: Optional[str] = None,
|
|
41
44
|
auth_type: Optional[str] = "token",
|
|
42
|
-
refresh_url: str = None,
|
|
43
|
-
username: str = None,
|
|
45
|
+
refresh_url: Optional[str] = None,
|
|
46
|
+
username: Optional[str] = None,
|
|
44
47
|
auth_method: Optional[str] = "password",
|
|
45
|
-
token: str = None,
|
|
48
|
+
token: Optional[str] = None,
|
|
46
49
|
max_login_attempts: int = 5,
|
|
47
|
-
token_refresh_delta: Union[int, timedelta] = None,
|
|
50
|
+
token_refresh_delta: Optional[Union[int, timedelta]] = None,
|
|
51
|
+
session: Optional[requests.Session] = None,
|
|
48
52
|
) -> None:
|
|
49
53
|
self.auth_type = auth_type
|
|
50
54
|
self.auth_method = auth_method
|
|
@@ -54,7 +58,10 @@ class Ahoy:
|
|
|
54
58
|
self._user_env_name = "FHIR_USER"
|
|
55
59
|
self._pass_env_name = "FHIR_PASSWORD"
|
|
56
60
|
self.token = token
|
|
57
|
-
|
|
61
|
+
if session is None:
|
|
62
|
+
self.session = requests.Session()
|
|
63
|
+
else:
|
|
64
|
+
self.session = session
|
|
58
65
|
self.max_login_attempts = max_login_attempts
|
|
59
66
|
self.token_refresh_delta = token_refresh_delta
|
|
60
67
|
if self.auth_type is not None and self.auth_method is not None:
|
|
@@ -75,7 +82,7 @@ class Ahoy:
|
|
|
75
82
|
self.close()
|
|
76
83
|
|
|
77
84
|
def change_environment_variable_name(
|
|
78
|
-
self, user_env: str = None, pass_env: str = None
|
|
85
|
+
self, user_env: Optional[str] = None, pass_env: Optional[str] = None
|
|
79
86
|
) -> None:
|
|
80
87
|
"""
|
|
81
88
|
Change the name of the variables used to retrieve username and password.
|