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Commit 50a29145 authored by mjbonifa's avatar mjbonifa
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removed conda, notebook and scripts as they are no longer needed

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conda.yaml deleted 100644 → 0
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− 129
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name: acmc
channels:
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- asttokens=3.0.0=pyhd8ed1ab_1
- blosc=1.21.6=he440d0b_1
- brotli-python=1.1.0=py313h46c70d0_2
- bzip2=1.0.8=h4bc722e_7
- c-ares=1.34.4=hb9d3cd8_0
- c-blosc2=2.16.0=h3122c55_0
- ca-certificates=2025.1.31=hbcca054_0
- certifi=2025.1.31=pyhd8ed1ab_0
- cffi=1.17.1=py313hfab6e84_0
- charset-normalizer=3.4.1=pyhd8ed1ab_0
- comm=0.2.2=pyhd8ed1ab_1
- debugpy=1.8.12=py313h46c70d0_0
- decorator=5.1.1=pyhd8ed1ab_1
- exceptiongroup=1.2.2=pyhd8ed1ab_1
- executing=2.1.0=pyhd8ed1ab_1
- h2=4.2.0=pyhd8ed1ab_0
- hdf5=1.14.3=nompi_h2d575fe_109
- hpack=4.1.0=pyhd8ed1ab_0
- hyperframe=6.1.0=pyhd8ed1ab_0
- idna=3.10=pyhd8ed1ab_1
- importlib-metadata=8.6.1=pyha770c72_0
- ipykernel=6.29.5=pyh3099207_0
- ipython=8.32.0=pyh907856f_0
- jedi=0.19.2=pyhd8ed1ab_1
- jupyter_client=8.6.3=pyhd8ed1ab_1
- jupyter_core=5.7.2=pyh31011fe_1
- keyutils=1.6.1=h166bdaf_0
- krb5=1.21.3=h659f571_0
- ld_impl_linux-64=2.43=h712a8e2_2
- libaec=1.1.3=h59595ed_0
- libblas=3.9.0=28_h59b9bed_openblas
- libcblas=3.9.0=28_he106b2a_openblas
- libcurl=8.11.1=h332b0f4_0
- libedit=3.1.20250104=pl5321h7949ede_0
- libev=4.33=hd590300_2
- libexpat=2.6.4=h5888daf_0
- libffi=3.4.6=h2dba641_0
- libgcc=14.2.0=h77fa898_1
- libgcc-ng=14.2.0=h69a702a_1
- libgfortran=14.2.0=h69a702a_1
- libgfortran5=14.2.0=hd5240d6_1
- libgomp=14.2.0=h77fa898_1
- liblapack=3.9.0=28_h7ac8fdf_openblas
- liblzma=5.6.4=hb9d3cd8_0
- libmpdec=4.0.0=h4bc722e_0
- libnghttp2=1.64.0=h161d5f1_0
- libopenblas=0.3.28=pthreads_h94d23a6_1
- libsodium=1.0.20=h4ab18f5_0
- libsqlite=3.48.0=hee588c1_1
- libssh2=1.11.1=hf672d98_0
- libstdcxx=14.2.0=hc0a3c3a_1
- libstdcxx-ng=14.2.0=h4852527_1
- libuuid=2.38.1=h0b41bf4_0
- libzlib=1.3.1=hb9d3cd8_2
- lz4-c=1.10.0=h5888daf_1
- matplotlib-inline=0.1.7=pyhd8ed1ab_1
- ncurses=6.5=h2d0b736_3
- nest-asyncio=1.6.0=pyhd8ed1ab_1
- nomkl=1.0=h5ca1d4c_0
- numexpr=2.10.2=py313h5f97788_100
- numpy=2.2.3=py313h17eae1a_0
- openssl=3.4.1=h7b32b05_0
- packaging=24.2=pyhd8ed1ab_2
- pandas=2.2.3=py313ha87cce1_1
- parso=0.8.4=pyhd8ed1ab_1
- pexpect=4.9.0=pyhd8ed1ab_1
- pickleshare=0.7.5=pyhd8ed1ab_1004
- pip=25.0.1=pyh145f28c_0
- platformdirs=4.3.6=pyhd8ed1ab_1
- prompt-toolkit=3.0.50=pyha770c72_0
- psutil=6.1.1=py313h536fd9c_0
- ptyprocess=0.7.0=pyhd8ed1ab_1
- pure_eval=0.2.3=pyhd8ed1ab_1
- py-cpuinfo=9.0.0=pyhd8ed1ab_1
- pycparser=2.22=pyh29332c3_1
- pygments=2.19.1=pyhd8ed1ab_0
- pysocks=1.7.1=pyha55dd90_7
- pytables=3.10.2=py313hd261420_1
- python=3.13.1=ha99a958_105_cp313
- python-dateutil=2.9.0.post0=pyhff2d567_1
- python-tzdata=2025.1=pyhd8ed1ab_0
- python_abi=3.13=5_cp313
- pytz=2024.1=pyhd8ed1ab_0
- pyzmq=26.2.1=py313h8e95178_0
- readline=8.2=h8228510_1
- requests=2.32.3=pyhd8ed1ab_1
- six=1.17.0=pyhd8ed1ab_0
- snappy=1.2.1=h8bd8927_1
- stack_data=0.6.3=pyhd8ed1ab_1
- tk=8.6.13=noxft_h4845f30_101
- tornado=6.4.2=py313h536fd9c_0
- traitlets=5.14.3=pyhd8ed1ab_1
- typing-extensions=4.12.2=hd8ed1ab_1
- typing_extensions=4.12.2=pyha770c72_1
- tzdata=2025a=h78e105d_0
- urllib3=2.3.0=pyhd8ed1ab_0
- wcwidth=0.2.13=pyhd8ed1ab_1
- zeromq=4.3.5=h3b0a872_7
- zipp=3.21.0=pyhd8ed1ab_1
- zlib-ng=2.2.4=h7955e40_0
- zstandard=0.23.0=py313h80202fe_1
- zstd=1.5.6=ha6fb4c9_0
- pip:
- aiosqlite==0.21.0
- click==8.1.8
- cramjam==2.9.1
- et-xmlfile==2.0.0
- fastparquet==2024.11.0
- fsspec==2025.2.0
- gitdb==4.0.12
- gitpython==3.1.44
- greenlet==3.1.1
- iniconfig==2.0.0
- lxml==5.3.1
- openpyxl==3.1.5
- pluggy==1.5.0
- pyarrow==19.0.0
- pyomop==4.3.0
- pytest==8.3.4
- simpledbf==0.2.6
- smmap==5.0.2
- sqlalchemy==2.0.38
prefix: /opt/conda/envs/acmc
notebook/process_codes_WP.ipynb deleted 100644 → 0
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script/import.sh deleted 100644 → 0
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#! /usr/bin/bash
echo "Removing Corrupted Files from Ho"
rm codes/GitHub_TG_repository/lymphoma_prevalence_birm_cam/lymphoma_prevalence_birm_cam_ICD10.csv
rm codes/GitHub_TG_repository/Menieresdisease_birm_cam/Menieresdisease_birm_cam_ICD10.csv
rm codes/GitHub_TG_repository/peripheral_neuropathy_birm_cam/peripheral_neuropathy_birm_cam_ICD10.csv
rm codes/GitHub_TG_repository/Sjogrenssyndrome_Bham_CAM/Sjogrenssyndrome_Bham_CAM_ICD10.csv
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script/run.sh deleted 100644 → 0
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#! /usr/bin/bash
version="V3_2_10"
previous="V3_2_9"
python main.py -r2 PHEN_assign_v3.json CONC_summary_working.xlsx
mv output/MELD_concepts_read.csv output/${version}_MELD_concepts_readv2.csv
python main.py -i PHEN_assign_v3.json CONC_summary_working.xlsx --no-translate
mv output/MELD_concepts_read.csv output/${version}_MELD_icd10_no_translate.csv
python main.py -s PHEN_assign_v3.json CONC_summary_working.xlsx --no-translate
mv output/MELD_concepts_read.csv output/${version}_MELD_snomed_no_translate.csv
# python main.py -o PHEN_assign_v3.json CONC_summary_working.xlsx --no-translate
# mv output/MELD_concepts_read.csv output/${version}_MELD_opcs4_no_translate.csv
python main.py -a PHEN_assign_v3.json CONC_summary_working.xlsx --no-translate
mv output/MELD_concepts_read.csv output/${version}_MELD_atc_no_translate.csv
# python main.py -m PHEN_assign_v3.json CONC_summary_working.xlsx --no-translate
# mv output/MELD_concepts_read.csv output/${version}_MELD_med_no_translate.csv
mv output/MELD_errors.csv output/${version}_MELD_errors.csv
#Generate Report
rm concepts-output/MELD-report.md
python report.py PHEN_assign_v3.json CONC_summary_working.xlsx codes/ concepts-output/MELD-report.md ${version} ${previous}
#Divide Concepts to Output Repo
rm -rf concepts-output/readv2/*
rm -rf concepts-output/icd10/*
rm -rf concepts-output/snomed/*
rm -rf concepts-output/atc/*
python publish.py output/${version}_MELD_concepts_readv2.csv concepts-output/readv2/
python publish.py output/${version}_MELD_icd10_no_translate.csv concepts-output/icd10/
python publish.py output/${version}_MELD_snomed_no_translate.csv concepts-output/snomed/
python publish.py output/${version}_MELD_atc_no_translate.csv concepts-output/atc/
cp output/${version}_MELD_errors.csv concepts-output/${version}_MELD_errors.csv
# Show Changes in Output repo (should be same as report)
cd concepts-output
git diff --stat
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