diff --git a/.gitattributes b/.gitattributes index 6ae3868..14641d9 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -limsdatapull/fakesecrets filter=git-crypt diff=git-crypt +limsdatapull/updatedata.py filter=git-crypt diff=git-crypt diff --git a/limsdatapull/fakesecrets b/limsdatapull/fakesecrets deleted file mode 100644 index 5c541ba..0000000 Binary files a/limsdatapull/fakesecrets and /dev/null differ diff --git a/limsdatapull/limsdatapull.yaml b/limsdatapull/limsdatapull.yaml new file mode 100755 index 0000000..56c58a3 --- /dev/null +++ b/limsdatapull/limsdatapull.yaml @@ -0,0 +1,49 @@ +name: limsdatapull +channels: + - conda-forge + - defaults +dependencies: + - blas=1.0=mkl + - brotlipy=0.7.0=py39hb82d6ee_1001 + - ca-certificates=2021.1.19=haa95532_0 + - certifi=2020.12.5=py39haa95532_0 + - cffi=1.14.5=py39h0878f49_0 + - chardet=4.0.0=py39hcbf5309_1 + - cryptography=3.4.4=py39h7bc7c5c_0 + - et_xmlfile=1.0.1=py_1001 + - filelock=3.0.12=pyh9f0ad1d_0 + - gdown=3.12.2=pyh9f0ad1d_0 + - idna=2.10=pyh9f0ad1d_0 + - intel-openmp=2020.2=254 + - jdcal=1.4.1=py_0 + - mkl=2020.2=256 + - mkl-service=2.3.0=py39h196d8e1_0 + - mkl_fft=1.3.0=py39h46781fe_0 + - mkl_random=1.0.2=py39h848d8c7_0 + - numpy=1.19.2=py39h729668d_0 + - numpy-base=1.19.2=py39hbd0edd7_0 + - openpyxl=3.0.6=pyhd3eb1b0_0 + - openssl=1.1.1j=h2bbff1b_0 + - pandas=1.2.3=py39hf11a4ad_0 + - pip=21.0.1=pyhd8ed1ab_0 + - pycparser=2.20=pyh9f0ad1d_2 + - pyopenssl=20.0.1=pyhd8ed1ab_0 + - pysocks=1.7.1=py39hcbf5309_3 + - python=3.9.2=h7840368_0_cpython + - python-dateutil=2.8.1=pyhd3eb1b0_0 + - python_abi=3.9=1_cp39 + - pytz=2021.1=pyhd3eb1b0_0 + - requests=2.25.1=pyhd3deb0d_0 + - setuptools=49.6.0=py39hcbf5309_3 + - six=1.15.0=pyh9f0ad1d_0 + - sqlite=3.34.0=h8ffe710_0 + - tqdm=4.58.0=pyhd8ed1ab_0 + - tzdata=2021a=he74cb21_0 + - urllib3=1.26.3=pyhd8ed1ab_0 + - vc=14.2=hb210afc_4 + - vs2015_runtime=14.28.29325=h5e1d092_4 + - wheel=0.36.2=pyhd3deb0d_0 + - win_inet_pton=1.1.0=py39hcbf5309_2 + - wincertstore=0.2=py39hcbf5309_1006 + - xlrd=2.0.1=pyhd3eb1b0_0 +prefix: C:\Users\jim.mildenberger\Miniconda3\envs\limsdatapull diff --git a/limsdatapull/refresh-lims-data.bat b/limsdatapull/refresh-lims-data.bat new file mode 100755 index 0000000..1480011 --- /dev/null +++ b/limsdatapull/refresh-lims-data.bat @@ -0,0 +1,20 @@ +rem Set Conda environment stuff up +set CONDAPATH=%USERPROFILE%\miniconda3 +set ENVNAME=limsdatapull +set ENVPATH=%CONDAPATH%\envs\%ENVNAME% +set DATAPATH=%USERPROFILE%\limsdatapull + +rem Activate the Conda environment +call %CONDAPATH%\Scripts\activate.bat %ENVPATH% + +rem Go to the remote drive +cd /D %DATAPATH% + +rem Perform the data pull using Python +python updatedata.py + +rem Deactivate Conda just in case +call conda deactivate + +rem Cleanup all of the temp files +del "Aliquoted Samples.xlsx" "Already Shipped Samples for Sequencing.xlsx" coverage.xlsx df_full.pkl Discarded.xlsx merge.xlsx diff --git a/limsdatapull/updatedata.py b/limsdatapull/updatedata.py new file mode 100755 index 0000000..fa5ffa9 Binary files /dev/null and b/limsdatapull/updatedata.py differ