automatic import of python-hcuppyopeneuler20.03

3 files changed, 554 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..8d8209c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/hcuppy-0.0.7.tar.gz
diff --git a/python-hcuppy.spec b/python-hcuppy.spec
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+%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
diff --git a/sources b/sources
new file mode 100644
index 0000000..cf251e2
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+1eb2fa0a60dec31a6a6f0aeef7110704  hcuppy-0.0.7.tar.gz