Add auto-updating sample database

.gitattributes

@@ -1 +1 @@
-limsdatapull/fakesecrets filter=git-crypt diff=git-crypt
+limsdatapull/updatedata.py filter=git-crypt diff=git-crypt

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

limsdatapull/refresh-lims-data.bat

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+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