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diff --git a/python-hcuppy.spec b/python-hcuppy.spec new file mode 100644 index 0000000..80b5edd --- /dev/null +++ b/python-hcuppy.spec @@ -0,0 +1,552 @@ +%global _empty_manifest_terminate_build 0 +Name: python-hcuppy +Version: 0.0.7 +Release: 1 +Summary: hcuppy is a Python implementation of HCUP Tools and Software +License: Apaceh 2.0 +URL: https://github.com/yubin-park/hcuppy +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/ab/ed/760869dfe841b90991d6a463394d02fd8962976e8b2760849348f01e2957/hcuppy-0.0.7.tar.gz +BuildArch: noarch + + +%description +# hcuppy + +A Python package for [H-CUP Tools and Software](https://www.hcup-us.ahrq.gov/tools_software.jsp). +The modules implemented in this package are as follows: +- "[CCS (Clinical Classification Software)](https://www.hcup-us.ahrq.gov/toolssoftware/ccs10/ccs10.jsp)" converts ICD-10 diagnosis and procedure codes to clinically meaningful groups +- "[CCI (Chronic Condition Indicator)](https://www.hcup-us.ahrq.gov/toolssoftware/chronic_icd10/chronic_icd10.jsp)" identifies chronic conditions from ICD-10 diagnosis codes +- "[Elixhauser Comordibity Index](https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp)" calculates both readmission and mortality risks using a set of ICD-10 diagnosis codes +- "[Procedure Classes](https://www.hcup-us.ahrq.gov/toolssoftware/procedureicd10/procedure_icd10.jsp)" identify if a given ICD-10 procedure code is Minor/Major Diagnosis/Therapeutic +- "[Utilization Flags](https://www.hcup-us.ahrq.gov/toolssoftware/utilflagsicd10/utilflag_icd10.jsp)" identify if a combination of UB40 revenue codes and ICD-10 procedure codes indicates (or implies) a certain resource utilization e.g. Intensive Care Unit, Ultrasound, X-Ray, etc. +- "[Surgery Flags](https://www.hcup-us.ahrq.gov/toolssoftware/surgflags/surgeryflags.jsp)" identify if a CPT code is a surgery related or not. *NOTE that, to use this module, users must agree to an additional license agreement with the AMA for using CPT codes [here](https://www.hcup-us.ahrq.gov/toolssoftware/surgflags/surgeryflags_license.jsp)*. + +NOTE that this package does not support for ICD-9. + +## Installing + +Installing from the source: +``` +$ git clone git@github.com:yubin-park/hcuppy.git +$ cd hcuppy +$ python setup.py develop +``` + +Or, simply using `pip`: +``` +$ pip install hcuppy +``` + +## File Structure +- `hcuppy/`: The package source code is located here. + - `data/`: The raw data files downloaded from the H-CUP website. + - `ccs.py`: a module for CCS + - `cci.py`: a module for CCI + - `elixhauser.py`: a module for Elixhauser Comorbidity Index + - `prcls.py`: a module for Procedure Class + - `uflag.py`: a module for Utilization Flags + - `sflag.py`: a module for Surgery Flags + - `utils.py`: utility functions for reading data files. +- `tests/`: test scripts to check the validity of the outputs. +- `LICENSE.txt`: Apache 2.0. +- `README.md`: This README file. +- `setup.py`: a set-up script. + +## Code Examples +`hcuppy` is really simple to use. +Please see some examples below. +NOTE that all functions used below have docstrings. +If you want to see the input parameter specifications, +please type `print(<instance>.<function>.__doc__)`. + +### Using CCS +```python +>>> import json +>>> from hcuppy.ccs import CCSEngine +>>> ce = CCSEngine(mode="dx") +>>> out = ce.get_ccs(["E119", "I10"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "ccs": "49", + "ccs_desc": "Diabetes mellitus without complication", + "ccs_lv1": "3", + "ccs_lv1_desc": "Endocrine; nutritional; and metabolic diseases and immunity disorders", + "ccs_lv2": "3.2", + "ccs_lv2_desc": "Diabetes mellitus without complication [49.]" + }, + { + "ccs": "98", + "ccs_desc": "Essential hypertension", + "ccs_lv1": "7", + "ccs_lv1_desc": "Diseases of the circulatory system", + "ccs_lv2": "7.1", + "ccs_lv2_desc": "Hypertension" + } +] +>>> +``` + +### Using CCI +```python +>>> from hcuppy.cci import CCIEngine +>>> ce = CCIEngine() +>>> out = ce.get_cci(["E119"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "is_chronic": true, + "body_system": "3", + "body_system_desc": "Endocrine, nutritional, and metabolic diseases and immunity disorders" + } +] +``` + +### Using Elixhauser Comorbidity Index +```python +>>> from hcuppy.elixhauser import ElixhauserEngine +>>> ee = ElixhauserEngine() +>>> out = ee.get_elixhauser(["E119", "E108", "I10", "I110", "Z944"]) +>>> print(json.dumps(out, indent=2)) +{ + "cmrbdt_lst": [ + "LIVER", + "DMCX", + "HTNCX", + "CHF" + ], + "rdmsn_scr": 31, + "mrtlt_scr": 9 +} +>>> +``` + +### Using Procedure Class +```python +>>> from hcuppy.prcls import PrClsEngine +>>> pce = PrClsEngine() +>>> out = pce.get_prcls(["B231Y0Z"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "class": "1", + "desc": "Minor Diagnostic" + } +] +>>> +``` + +### Using Utilization Flag +```python +>>> from hcuppy.uflag import UFlagEngine +>>> ufe = UFlagEngine() +>>> out = ufe.get_uflag(rev_lst=["0380"], pr_lst=["BB0DZZZ"]) +>>> print(json.dumps(out, indent=2)) +[ + "Blood", + "Chest X-Ray" +] +>>> +``` + +Please refer to the test scripts under the `tests/` folder if you want to see other example use cases. + +## License +Apache 2.0 + +## Authors +Yubin Park, PhD + +## References +- https://www.hcup-us.ahrq.gov/ +- https://www.hcup-us.ahrq.gov/tools_software.jsp +- https://cran.r-project.org/web/packages/comorbidity/vignettes/comorbidityscores.html +- https://github.com/modusdatascience/ccs + + + + + + + + + + +%package -n python3-hcuppy +Summary: hcuppy is a Python implementation of HCUP Tools and Software +Provides: python-hcuppy +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-hcuppy +# hcuppy + +A Python package for [H-CUP Tools and Software](https://www.hcup-us.ahrq.gov/tools_software.jsp). +The modules implemented in this package are as follows: +- "[CCS (Clinical Classification Software)](https://www.hcup-us.ahrq.gov/toolssoftware/ccs10/ccs10.jsp)" converts ICD-10 diagnosis and procedure codes to clinically meaningful groups +- "[CCI (Chronic Condition Indicator)](https://www.hcup-us.ahrq.gov/toolssoftware/chronic_icd10/chronic_icd10.jsp)" identifies chronic conditions from ICD-10 diagnosis codes +- "[Elixhauser Comordibity Index](https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp)" calculates both readmission and mortality risks using a set of ICD-10 diagnosis codes +- "[Procedure Classes](https://www.hcup-us.ahrq.gov/toolssoftware/procedureicd10/procedure_icd10.jsp)" identify if a given ICD-10 procedure code is Minor/Major Diagnosis/Therapeutic +- "[Utilization Flags](https://www.hcup-us.ahrq.gov/toolssoftware/utilflagsicd10/utilflag_icd10.jsp)" identify if a combination of UB40 revenue codes and ICD-10 procedure codes indicates (or implies) a certain resource utilization e.g. Intensive Care Unit, Ultrasound, X-Ray, etc. +- "[Surgery Flags](https://www.hcup-us.ahrq.gov/toolssoftware/surgflags/surgeryflags.jsp)" identify if a CPT code is a surgery related or not. *NOTE that, to use this module, users must agree to an additional license agreement with the AMA for using CPT codes [here](https://www.hcup-us.ahrq.gov/toolssoftware/surgflags/surgeryflags_license.jsp)*. + +NOTE that this package does not support for ICD-9. + +## Installing + +Installing from the source: +``` +$ git clone git@github.com:yubin-park/hcuppy.git +$ cd hcuppy +$ python setup.py develop +``` + +Or, simply using `pip`: +``` +$ pip install hcuppy +``` + +## File Structure +- `hcuppy/`: The package source code is located here. + - `data/`: The raw data files downloaded from the H-CUP website. + - `ccs.py`: a module for CCS + - `cci.py`: a module for CCI + - `elixhauser.py`: a module for Elixhauser Comorbidity Index + - `prcls.py`: a module for Procedure Class + - `uflag.py`: a module for Utilization Flags + - `sflag.py`: a module for Surgery Flags + - `utils.py`: utility functions for reading data files. +- `tests/`: test scripts to check the validity of the outputs. +- `LICENSE.txt`: Apache 2.0. +- `README.md`: This README file. +- `setup.py`: a set-up script. + +## Code Examples +`hcuppy` is really simple to use. +Please see some examples below. +NOTE that all functions used below have docstrings. +If you want to see the input parameter specifications, +please type `print(<instance>.<function>.__doc__)`. + +### Using CCS +```python +>>> import json +>>> from hcuppy.ccs import CCSEngine +>>> ce = CCSEngine(mode="dx") +>>> out = ce.get_ccs(["E119", "I10"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "ccs": "49", + "ccs_desc": "Diabetes mellitus without complication", + "ccs_lv1": "3", + "ccs_lv1_desc": "Endocrine; nutritional; and metabolic diseases and immunity disorders", + "ccs_lv2": "3.2", + "ccs_lv2_desc": "Diabetes mellitus without complication [49.]" + }, + { + "ccs": "98", + "ccs_desc": "Essential hypertension", + "ccs_lv1": "7", + "ccs_lv1_desc": "Diseases of the circulatory system", + "ccs_lv2": "7.1", + "ccs_lv2_desc": "Hypertension" + } +] +>>> +``` + +### Using CCI +```python +>>> from hcuppy.cci import CCIEngine +>>> ce = CCIEngine() +>>> out = ce.get_cci(["E119"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "is_chronic": true, + "body_system": "3", + "body_system_desc": "Endocrine, nutritional, and metabolic diseases and immunity disorders" + } +] +``` + +### Using Elixhauser Comorbidity Index +```python +>>> from hcuppy.elixhauser import ElixhauserEngine +>>> ee = ElixhauserEngine() +>>> out = ee.get_elixhauser(["E119", "E108", "I10", "I110", "Z944"]) +>>> print(json.dumps(out, indent=2)) +{ + "cmrbdt_lst": [ + "LIVER", + "DMCX", + "HTNCX", + "CHF" + ], + "rdmsn_scr": 31, + "mrtlt_scr": 9 +} +>>> +``` + +### Using Procedure Class +```python +>>> from hcuppy.prcls import PrClsEngine +>>> pce = PrClsEngine() +>>> out = pce.get_prcls(["B231Y0Z"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "class": "1", + "desc": "Minor Diagnostic" + } +] +>>> +``` + +### Using Utilization Flag +```python +>>> from hcuppy.uflag import UFlagEngine +>>> ufe = UFlagEngine() +>>> out = ufe.get_uflag(rev_lst=["0380"], pr_lst=["BB0DZZZ"]) +>>> print(json.dumps(out, indent=2)) +[ + "Blood", + "Chest X-Ray" +] +>>> +``` + +Please refer to the test scripts under the `tests/` folder if you want to see other example use cases. + +## License +Apache 2.0 + +## Authors +Yubin Park, PhD + +## References +- https://www.hcup-us.ahrq.gov/ +- https://www.hcup-us.ahrq.gov/tools_software.jsp +- https://cran.r-project.org/web/packages/comorbidity/vignettes/comorbidityscores.html +- https://github.com/modusdatascience/ccs + + + + + + + + + + +%package help +Summary: Development documents and examples for hcuppy +Provides: python3-hcuppy-doc +%description help +# hcuppy + +A Python package for [H-CUP Tools and Software](https://www.hcup-us.ahrq.gov/tools_software.jsp). +The modules implemented in this package are as follows: +- "[CCS (Clinical Classification Software)](https://www.hcup-us.ahrq.gov/toolssoftware/ccs10/ccs10.jsp)" converts ICD-10 diagnosis and procedure codes to clinically meaningful groups +- "[CCI (Chronic Condition Indicator)](https://www.hcup-us.ahrq.gov/toolssoftware/chronic_icd10/chronic_icd10.jsp)" identifies chronic conditions from ICD-10 diagnosis codes +- "[Elixhauser Comordibity Index](https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp)" calculates both readmission and mortality risks using a set of ICD-10 diagnosis codes +- "[Procedure Classes](https://www.hcup-us.ahrq.gov/toolssoftware/procedureicd10/procedure_icd10.jsp)" identify if a given ICD-10 procedure code is Minor/Major Diagnosis/Therapeutic +- "[Utilization Flags](https://www.hcup-us.ahrq.gov/toolssoftware/utilflagsicd10/utilflag_icd10.jsp)" identify if a combination of UB40 revenue codes and ICD-10 procedure codes indicates (or implies) a certain resource utilization e.g. Intensive Care Unit, Ultrasound, X-Ray, etc. +- "[Surgery Flags](https://www.hcup-us.ahrq.gov/toolssoftware/surgflags/surgeryflags.jsp)" identify if a CPT code is a surgery related or not. *NOTE that, to use this module, users must agree to an additional license agreement with the AMA for using CPT codes [here](https://www.hcup-us.ahrq.gov/toolssoftware/surgflags/surgeryflags_license.jsp)*. + +NOTE that this package does not support for ICD-9. + +## Installing + +Installing from the source: +``` +$ git clone git@github.com:yubin-park/hcuppy.git +$ cd hcuppy +$ python setup.py develop +``` + +Or, simply using `pip`: +``` +$ pip install hcuppy +``` + +## File Structure +- `hcuppy/`: The package source code is located here. + - `data/`: The raw data files downloaded from the H-CUP website. + - `ccs.py`: a module for CCS + - `cci.py`: a module for CCI + - `elixhauser.py`: a module for Elixhauser Comorbidity Index + - `prcls.py`: a module for Procedure Class + - `uflag.py`: a module for Utilization Flags + - `sflag.py`: a module for Surgery Flags + - `utils.py`: utility functions for reading data files. +- `tests/`: test scripts to check the validity of the outputs. +- `LICENSE.txt`: Apache 2.0. +- `README.md`: This README file. +- `setup.py`: a set-up script. + +## Code Examples +`hcuppy` is really simple to use. +Please see some examples below. +NOTE that all functions used below have docstrings. +If you want to see the input parameter specifications, +please type `print(<instance>.<function>.__doc__)`. + +### Using CCS +```python +>>> import json +>>> from hcuppy.ccs import CCSEngine +>>> ce = CCSEngine(mode="dx") +>>> out = ce.get_ccs(["E119", "I10"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "ccs": "49", + "ccs_desc": "Diabetes mellitus without complication", + "ccs_lv1": "3", + "ccs_lv1_desc": "Endocrine; nutritional; and metabolic diseases and immunity disorders", + "ccs_lv2": "3.2", + "ccs_lv2_desc": "Diabetes mellitus without complication [49.]" + }, + { + "ccs": "98", + "ccs_desc": "Essential hypertension", + "ccs_lv1": "7", + "ccs_lv1_desc": "Diseases of the circulatory system", + "ccs_lv2": "7.1", + "ccs_lv2_desc": "Hypertension" + } +] +>>> +``` + +### Using CCI +```python +>>> from hcuppy.cci import CCIEngine +>>> ce = CCIEngine() +>>> out = ce.get_cci(["E119"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "is_chronic": true, + "body_system": "3", + "body_system_desc": "Endocrine, nutritional, and metabolic diseases and immunity disorders" + } +] +``` + +### Using Elixhauser Comorbidity Index +```python +>>> from hcuppy.elixhauser import ElixhauserEngine +>>> ee = ElixhauserEngine() +>>> out = ee.get_elixhauser(["E119", "E108", "I10", "I110", "Z944"]) +>>> print(json.dumps(out, indent=2)) +{ + "cmrbdt_lst": [ + "LIVER", + "DMCX", + "HTNCX", + "CHF" + ], + "rdmsn_scr": 31, + "mrtlt_scr": 9 +} +>>> +``` + +### Using Procedure Class +```python +>>> from hcuppy.prcls import PrClsEngine +>>> pce = PrClsEngine() +>>> out = pce.get_prcls(["B231Y0Z"]) +>>> print(json.dumps(out, indent=2)) +[ + { + "class": "1", + "desc": "Minor Diagnostic" + } +] +>>> +``` + +### Using Utilization Flag +```python +>>> from hcuppy.uflag import UFlagEngine +>>> ufe = UFlagEngine() +>>> out = ufe.get_uflag(rev_lst=["0380"], pr_lst=["BB0DZZZ"]) +>>> print(json.dumps(out, indent=2)) +[ + "Blood", + "Chest X-Ray" +] +>>> +``` + +Please refer to the test scripts under the `tests/` folder if you want to see other example use cases. + +## License +Apache 2.0 + +## Authors +Yubin Park, PhD + +## References +- https://www.hcup-us.ahrq.gov/ +- https://www.hcup-us.ahrq.gov/tools_software.jsp +- https://cran.r-project.org/web/packages/comorbidity/vignettes/comorbidityscores.html +- https://github.com/modusdatascience/ccs + + + + + + + + + + +%prep +%autosetup -n hcuppy-0.0.7 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-hcuppy -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 0.0.7-1 +- Package Spec generated |