From 25625085d30128cdf1182c2d9d8465d3959c5af5 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 26 Mar 2021 14:25:22 -0600
Subject: [PATCH] Add auto-updating sample database

---
 .gitattributes                     |   2 +-
 limsdatapull/fakesecrets           | Bin 84 -> 0 bytes
 limsdatapull/limsdatapull.yaml     |  49 +++++++++++++++++++++++++++++
 limsdatapull/refresh-lims-data.bat |  20 ++++++++++++
 limsdatapull/updatedata.py         | Bin 0 -> 3491 bytes
 5 files changed, 70 insertions(+), 1 deletion(-)
 delete mode 100644 limsdatapull/fakesecrets
 create mode 100755 limsdatapull/limsdatapull.yaml
 create mode 100755 limsdatapull/refresh-lims-data.bat
 create mode 100755 limsdatapull/updatedata.py

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 5c541ba259f3c3dd67b6014fea6296a66c9f4c1a..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 84
zcmV-a0IUB1M@dveQdv+`01l{$p1>09Q!SrU4?0~nu-P;c+w?G!Q}FTh0%fbqG9&5F
q5~{XTGWsR1zm+)AUlT5nIIt;QpbNXj<F52lzO7JEjCrz&)$yVPGbl#@

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 0000000000000000000000000000000000000000..fa5ffa9cbda65c3b45fe9fb931080722b12d6f96
GIT binary patch
literal 3491
zcmV;U4P5d7M@dveQdv+`03Ku;Y*-@4wH{dP6W+$W{4CH=B$F%x0QmS*lBF>;pKkUb
z+9yU;*#?a^8E>o0=Pzal+IDJy7w|9{YLZPe*hv#@3<~khRaT)XLf0Tr5D?qQr3x2;
zQeM9Qz%Cnn9#DBgv1R$RX%nT$eW5AEFVJoG;6jjOoL;S|(?V4JShVwunerEy-X$B@
z#xP#o$YGpL^%e&FMHw3xwS%&|oK9K=9+%X*hvQnJCgc+QFe#qXP$o`0=T{eW+@Rav
z4LRTwQ1>yZiZQQc7?_Uwqa$0FAT7mTSf^Z_(29cT4L#{3D!98fT}*_G@StVyP5v~e
z<{x5M%M_auZz4-<^;z4p+55lu5`v(PO4Pe;?G5<dSrvU14b0%W4?b2ze3V6LSvjql
ztVN^vTV_Qbg`)^w?x*A0R$*20aDw-=0s@lWDuE0ic&3cpW-ZSkZvqLa5P=Aan+E;I
zDWR_hfg8j}?*#mIhR#PaK@FkcZf<|sx9lu2)>83eK9R;-DK4hHQo3aNHT^qoe<?=Z
zG{EA|+Vp^cBO&A?0qt&E9S4v<#$N71GMiC*wfKJkw!2_RPrVC$Y1D>Xw}kPf#^0f1
zN}swl?p}0?1Mp)<1W)V;N*InTxp5vAMZA_hra%k+edN&kcOHuR^rjD40oNNu9he<W
zAUhg?+Q#rAZI>KMfdjJN`ln5Gvpb~5YYuQv@y+|sFTRGQe&E+U`nr&!ZtT_Zv&_c{
zbB(3ftSWq$YLs)Jx^qP^)?IxkUf==b+_j|R7=HLiDB_FqqkP9+v_xJIP-c0-YyhO3
z#?XgBr*bP$#1ySxUy8PpN@v$vS0g+1>Ib&no*J8zM@4{^rsB~1RX*3(Y-%@l1|hXE
zNW;(~`@}a#G(B4WuJQLszk{zkWKft`P4Tzqqt$e1^2+yL1a|p+W+%>f^}}-w@4K&_
zg`V^i*m)FkZo~jMUX&~C9b@%zJU!eoHhhTw!|EWdkJU{tiS38z_Wt$&ztq<N-#*26
zjcOwT`s}gN^~1RKn6+D!7R^@x&dsqR->^JjFOtN|B3o&vM6~5BcWfdq7U?_qJE7t&
zQ6qEOn3kriAZgLOtqVsD55C;e@oAm4P0Y-SMi9et!Jaj)V}3)rL;KD?W65S@c7yf>
zNS<DW9Y4(bA=gK@VX2?}It?v4e;*&~%CpR5&_=cu=rJY=%jFJjUeCDx2+Aa!m76L1
zucz?EfSh(EB~eEZ^p*Kqf=OSR*i~T~x24<&3%Js@=;<Ye);zREqc?`p#xUVPoiO*N
z659grYP3P>*0;6d=M5IbCi_f8)c-ZdI)Fm4&--7{<-H9cO}nuA-sRopohP{~S3Sfc
zs`Tx%)cm5B3X`1>E6O;J4c?NOv^&b2l7_P#bW9dBxxQ?z{W<tOcl{Z+fAR(oc!1BC
zXZ%9$p#+ffATrPC>a_Uu{X4|y%CU#u33=tK<XDS22{i;V@y(qjOFE7bdM3WsMBZlZ
z(6^$2d;Fi<Q7`TUBEvST$C*^TOFY~^@~@rgEyvv~m0c3x)3ubKQ`W{6qZWm6EonB2
ze~$6ch#+Qg(-&gvb1^vvkP+M^vlz%KUPf#-b5R?bD|V>_fvzR<!!ERHz(F2dp?&Ma
zIc+-&XkK?F6(S6q9ey@%02vdH+P9y!8f0B_e<8{Vc6~-XfLj9Mpf@5xHE%=8`kfuD
z&qFkH-Xz(c2%=tnDA?Yk1{!D8s)F<^Mt{3rYB4U5G}@=@^g_^BCNAZ1hjt(M=r-r<
zSZ1r*w<#ypt&SVcsb(&wt=Iuvxo+ngR>J(3I%w>nHp#%RjjDlWiiF3F&_W9NM4+7K
z!8VX-C;=d#A~k3$49*p(M%FnSqjr$b7PsWKIZcR3GAGl3+0+)F#Lx}B*o_TFN}S{c
zu0Kg@;pls%93959>~aJF*`llJ|9NakgS@S#)&LS`yScAf@6OUH@j$1=#CScIerN5g
zndQgg&<!pXtN6bL0;+1`fgyFPcdt_|E2HRpeK~%xxbL_5^(+SrMP^h5ti`tB9I%O1
zC@@$mH^I^cEk~G_&m4Y>WUIN}g@x%d$=TOK5Er|XR!iwS?oel{=}CpUxVh2P`rtsG
zvt)nQ1{|zQJDrN4z*xz4|C91?ri2!heiInY;_7M)cdFCqg-{)nD(}*47vQn`2C{)q
zabc)icVQ_(<VQ#iQiGA``HQU|$4A7+0R0PcZ?wii>QDSyus2$C;W&M|xpIUES~6NM
zPuB9-LAc-G;E(x$)!Vdexo~z7K=R;u5#V@WM2LIhxpy;|=5Dva`9SUN=c~H$c!wp~
zb~bywmNM0&UVS#?#5TdqX9U|&YWJ?t59azC8VEbZ8FDs%qym2)b>@_x81c7mO1Rf^
zZ~Emw()&RgH<?nAo&c$(DYN==mu5OWMc96~qr{M$6>L$ZrNI+Tv?w_4l#85t`Hi9F
zU(8g<jv-3DRXI-|42#~b2?W%iCbRK{d=o)u0j%TtiB&(jfn^CXOJA6mEyY18^p4c^
zaWTEo!oYKhKlOq}6DPLGZgX;ea2XyLaq6JbSe}*tb*&OyTk<{H6PQunxMp&2{QhbJ
zN<}GJj7~*;6u||?1ryb85-J!c?81eJOf@!2d2F{Jw>Ay9Yj&+4l!tu+Rtd5htGw7L
zUZ>#t61XCX?u8pG^<BN*4$@Ar96(tHxX^Lsj@@U8YrIn-B6kwjO88cOz+BCf)%T~&
z>)8oD<*tB7<iy}Qm0Tm4;7ZRGo*Y4&hd6lOp{24KDyqHDl%bkWHEK3yz~1`F!#@D@
z1D@w)3~hOs>JZ(jEMhamN{_#$CKoWgKO~*a+4W2)9Eyz2==RQ%81`jdIk`|swlha9
zDo5+Qt;{U!{j7d~WPi2bVx%yJZ`c0mz*qOH`wuw_EId-8s2KgLF^MAn^5*2NP%~y9
zX5!VWNY3HtFJ<JxokV(qIIn%JkK-CM`(dW6A8#azA08$Zp;nVkXT&<I%)VY=Y6T>n
z)VttHA9gPU53r%>0bth4&%mZE(a;4ZJ6Zd$pWE=VDy>WXlcw``FXj72i$@Vwhrv2I
zURI1cRynU<3O=dXAkV!9!?u1ft=lRc-FL8tAS?Cu*C##0)x61(ZmH+KUiDMj;m{=D
zWWf0`Mpd(W^BVd5Wlf&xMaWZ$B3d0kxj7Z5|3g>UVucGIA^!0@)4AmbZ$xzqDSC*M
zB$UI33%(Tn{MWfu&ii~2uf3vCNf=<bHT*^aH${ZQ(NyqEGUVL0A$m|^@1eIA_b&Q}
zF2tmY@6jvjV4@!w>>cw{rBH|AWi2RM)}qT;|F5|Oi7m{RWSf!fNYalv#nCXUXDx17
z+D8P?jGAa*x;|#FaeAS25tk839SI<v?19lAStc?lqa^#u?XcM3r`fhd<;MMmF=EqA
z^^GbEOZD7ZVGxUUM->DZUWZEcl%~Tq3b;#%Gyv<m!zpYjuCo}LezN<CG=jO6{xQ_i
zpoz_G8y5CvmuYeCw0^eMXl`&9;TXR64i9V4%%O3}u$-T4c$oVu0<3QrG(rbw_R$MQ
zmBhR^^s7~0KQ=SWMi0l97+*v_<p7hR9jtOL=qYK0!P3mSxAm#_cncZ>tSTeD=0*Ks
z;S+AY(x71X&~}#9S<}XZByidija8)-z@WERX}8_HOr_Z2=_0KKpW7U1Ve|l9Mq)7u
zJK+I&>s4`_8aqh=W@6jR*u9aMHmYCEVjOd&sofRa?LvEGtj3YT<-pX|DHYi^9LE{-
zf-!47Cz%AW^k<y2Dq_XuF;y)b_p5l(7&_gVRUma)3dw<(^)~jZ8AAC0saK0VjcL0_
z@48macuhK+x%=)4fR8^Dq(Il`mC6QtvM_t3j4X8$G$JnRnwTj<i6t0WqiTeV&+<Cw
zQe<MHtfBLC{eCak`+H&^3}1|7)SCi63Y)VgFEwg-c@0>`2$Z%1z5J+-X}n}_W`$me
zl5--^59Qeq>h^VsjWn6)YOfRb^5kk0X>fb7@!?(~m&ATM*^qpYELo-Zyg1%^?Wh)M
z8dK6C%hz9CdIo{)fH!lofCo0)#Hd-(C+>oZi=}EX*CcVkGj;L?V7^?`bP0B>Lis40
ztfJ~EmKL)Gk+k}efvp75P{e%j1ze?WF}x*bV%TJ}>0%KhWvK^>fex!QnzpbP-^C|h
z<+w*?R-q7g<Y_GIInveuhqd5gc&sI$(|p(jd--L<fHv!wo5W2jp!mUoQ3qmS@NKZ&
z>8werXUBZG8bW784+eacp~sgg-^I;Vx|zh+F()7qKli}`ZHh?vw7>Yn<DLcWNU))w
z8G9!Y;~wv7PTP;;p=SvJ7P|au>HW+%UGO%R*XiTcd}OkzVV|<%=A~rRqI)tuv~v;R
zgeVz&XP3jT(*x*YoXC9@rfF}<r2#}n(qNI3=<IeVM~k`815)i!y3L7ew5y*WQG@zD
z*rM$b`K<sVD$6YHS<zJf6V_71DT!KV`3R31ZDax?W$@&fu(dCS+`7>JpCXj67Hc@q
z1#HVDg?-T<_ez1P$GKHG0^0&~hx|0vWG~l*5vvnICthYQ@a_BtA8MvP{&jzWRin6I
RIO{OqbB`VowJL3F`ebi@<>LSV

literal 0
HcmV?d00001