Plugin to create PDF at the end of a run for Ion Torrent

launch.sh

#!/bin/bash

VERSION="0.1"

#Set the URL for the API requests
plugin_url=http://127.0.0.1/rundb/api/v1/results/${RUNINFO__PK}/plugin/
page_url=http://127.0.0.1/${RUNINFO__URL_ROOT}/

#Set the HTTP Headers
api_header="Content-Type: application/json;Accept: application/json"

#Count the number of plugins with status of "Started" 
running=`curl --silent \
 --header ${api_header} \
 --location ${plugin_url} |
jsonpipe |
grep pluginState/ |
grep -v ${RUNINFO__PLUGIN_NAME} |
awk '{print $2}'|
grep "Started" |
wc -l`

#write out the json to rerun the plugin
echo {\"plugin\":[\"${RUNINFO__PLUGIN_NAME}\"]} > post.json

if [ "$running" -ne "0" ]
then
  #if there are plugins still "started" then call this plugin again
  echo "There are still plugins running, calling this plugin again."
  #wait a few seconds first
  sleep 10 
  curl --silent --header ${api_header} \
   --location ${plugin_url} \
   --request POST \
   --data "@post.json"
else   
  #All of the other plugins have finished -- do your final step here
  /opt/ion/iondb/bin/wkhtmltopdf-amd64 -q --javascript-delay 1000 --margin-top 15 --header-spacing 5 --header-right "Page [page] of [toPage]" --header-font-size 9 --disable-internal-links --disable-external-links  ${page_url}?no_header=True report.pdf
  #now you have to do something with report.pdf, maybe scp it? Maybe email? 
  echo "Done!"
fi