bdunnette

import sys
import os
import json
from csv import DictReader

files_to_parse = sys.argv[1:]
for f in files_to_parse:
    print("Reading cases from %s" % f)
    json_filename = "%s.json" % os.path.splitext(f)[0]
    cases = []

bdunnette

#!/bin/bash

#Read case/slide titles from titles.txt (one case/title per line)
titles=()
while read line
do
  # echo $line
  titles+=("$line")
done < titles.txt
# echo ${titles[@]}

bdunnette

-- Find files from specific data group
SELECT [ImageId],[CompressedFileLocation]
  FROM [Aperio].[dbo].[Image]
  WHERE [DataGroupID]=162
  
-- Update file location of given image
UPDATE [Aperio].[dbo].[Image]
  SET [CompressedFileLocation]='\\gleason\images2\Projects\Giubellino\D17-1452-CompoundSpitzNevus.svs'
  WHERE [ImageId]=76585

bdunnette

for %%f in (*.svs) do (
  echo %%~nf
  vips openslideload --associated thumbnail "%%~nf.svs" "%%~nf.jpg"
  vipsthumbnail -s 256 "%%~nf.jpg"
  del "%%~nf.jpg"
)

bdunnette

#!/bin/bash

# This script requires libvips-tools to be installed

trackingcode="UA-39453866-3"
imagehost="web-basic.oit.umn.edu"

tracking_script="<script>(function(e,t,n,r,i,s,o){e[\"GoogleAnalyticsObject\"]=i;e[i]=e[i]||function(){(e[i].q=e[i].q||[]).push(arguments)},e[i].l=1*new Date;s=t.createElement(n),o=t.getElementsByTagName(n)[0];s.async=1;s.src=r;o.parentNode.insertBefore(s,o)})(window,document,\"script\",\"//www.google-analytics.com/analytics.js\",\"ga\");ga(\"create\",\"$trackingcode\",\"umn.edu\");ga(\"send\",\"pageview\")</script>"

indextitle=${PWD##*/}

bdunnette

SELECT TOP 100 * 
FROM [Aperio].[dbo].[Specimen] Specimen
INNER JOIN [Aperio].[dbo].[Slide] Slide
ON Slide.ParentId=Specimen.Id
INNER JOIN [Aperio].[dbo].[Image] Image
ON Image.ParentId=Slide.Id
WHERE Specimen.ColumnPublishToWeb2 = 'TRUE'

bdunnette

FROM ubuntu:16.04
MAINTAINER Brian Dunnette <[email protected]>

RUN \

  # Install dependencies
  sed "s/archive.ubuntu.com/local-mirror.cs.umn.edu/g; \
    s/security.ubuntu.com/local-mirror.cs.umn.edu/g" \
    -i /etc/apt/sources.list && \
  apt-get update && \

bdunnette

# cd to your Loopback project directory and run:
# curl https://gist.githubusercontent.com/bdunnette/a1854b4f0c5010cb7a539be5f2d63ef8/raw/add-gulp.sh | sh
REPO=https://gist.githubusercontent.com/bdunnette/a1854b4f0c5010cb7a539be5f2d63ef8/raw
echo client/vendor >> .gitignore
mv server/boot/root.js server/boot/root.js.bak
sed 's/\("files\".*\:.*{\)/&\"loopback\#static\"\:\{\"params\"\:\"\$\!\.\.\/client\"\}/' -i server/middleware.json
sed 's/\("compression\".*\:.*{\)/&\"enabled\":false/' -i server/middleware.json
mkdir -p client/js client/css server/fixtures
touch client/css/app.css server/fixtures/.gitkeep
wget -O gulpfile.js $REPO/gulpfile.js

bdunnette

# checkout, compile & install
git clone https://github.com/facebook/watchman.git
cd watchman/
# git checkout v4.7.0
sudo apt install -y autoconf automake build-essential python-dev
./autogen.sh
./configure
make
sudo make install

bdunnette

echo "Using $1 for output..."
for s in *.pdf
do
  i="${s%.*}"
  printf "# $i\n\n" >> $1
  echo $s
  pdftotext $s - >> $1
done