icputrd/platform

ICPUTRD Image Platform

This repository is for the work on the web interface to annotate images.

• It is built on MEANJS stack https://github.com/meanjs/mean

• Example tools that may be relevant:

  1. Annotating image regions: http://annotorious.github.io/demos.html

• Backup database (do that periodically and before any server restarts/docker changes)

  1. connect to a container that is linked to db
  2. DT=$(date +"%Y%m%d")
  3. mkdir -p $DT/mean-dev
  4. mongodump -h db:27017 --db mean-dev --out $DT

• Restore database

  1. connect to a container that is linked to db (/data/DATE/mean-dev is where it was previously dumped)
  2. mongorestore -h db -d mean-dev /data/DATE/mean-dev
  3. if only one collection needs update, drop it and mongoimport -h db -d mean-dev -c tags --type=csv --mode=insert--headerline tags.csv

• Process of porting the database

  1. use a python script named new_tags.py that is located in ~dlee97/ICPUTRD directory on da1 (also here)
  2. connect to a container that is linked to dbNew (where dbNew is a copy of db)
  3. run "python3 new_tags.py" which will update all of the tags the script saves the newly named tags as a new collection named new_tags
     • start the mongo shell in the container using "mongo --host=db"
     • run "db.tags.renameCollection("old_tags")"
     • then "db.new_tags.renameCollection("tags")"

Setup server

• First step is to create a container on the server using the following command. Adjust [user_id], [port] and [container_name].

docker run -d 
     -v /data/icputrd/arf/mean.js/public/2015:/opt/mean.js/public/2015 \ 
     -v /data/icputrd/arf/mean.js/public/2016:/opt/mean.js/public/2016 \
     -v /data/icputrd/arf/mean.js/public/2014:/opt/mean.js/public/2014 \
     -v /data/icputrd/arf/mean.js/public/2013:/opt/mean.js/public/2013 \
     -v /data/icputrd/arf/mean.js/public/2012:/opt/mean.js/public/2012 \
     -v /data/icputrd/arf/mean.js/public/2011:/opt/mean.js/public/2011 \
     -v /data/icputrd/arf/mean.js/public/2017:/opt/mean.js/public/2017 \
     -v /data/icputrd/arf/mean.js/public/sara_img:/opt/mean.js/public/sara_img \
     -v /data/icputrd/arf/mean.js/public/:/opt/mean.js/public/ \
     -v /data/icputrd/arf/mean.js/public/js:/opt/mean.js/public/js \
     -v /data/icputrd/arf/mean.js/public/css:/opt/mean.js/public/css \
     -v /home/[user_id]:/home/[user_id] -p [port]:22 \
     --name [container_name] \
     --link dbNew:dbNew \
     icputrd/platform /bin/startsvc.sh [user_id]    

• Append the user's id_rsa.pub to ~/.ssh/authorized_keys for authorization.

Setup remote connection

• Generating ssh keys
  • For Linux and Mac: ssh-keygen. Once it completes, it should produces the id_rsa.pub and id_rsa files inside your ~/.ssh/ folder.
  • For Windows: Please refer to [***]
    After some experiments, we think the easiest way for Windows users is to use Powershell. You should also get the id_rsa.pub and id_rsa files inside your some_location/.ssh/ folder (Note: some_location should be displayed at the end of the ssh-keygen process)
    (Powershell approach) Create and copy code below to file icputrd.bat; save it on Desktop/ for convenience. (information about batch file in Windows 10)

@echo off
set url="http://localhost:3000"
start chrome %url%
<# You could open with different browsers #>
<# start iexplore.exe %url%
start firefox.exe %url%
start microsoft-edge:%url% #>
<# Powershell.exe ssh da1p #>
Powershell.exe -WindowStyle Minimized ssh da1p
pause

• Copy and paste the public key into https://docs.google.com/forms/d/e/1FAIpQLSe_2zBBTcuKAa1UdAIAZikvkjfXZBrzvvvFU-20A18t-FXcvw/viewform?usp=pp_url.
  Your id_rsa.pub is needed for setting up the connection. To see the public key, simply run cat ~/.ssh/id_rsa.pub.

• Set up your ~/.ssh/config file so that you can login to one of the da servers without having to fully specify the server name each time. Simply copy the content below to ~/.ssh/config.

Host *
  ForwardAgent yes
  
host da1p
    hostname da1.eecs.utk.edu
    identityfile ~/.ssh/id_rsa
    # identityfile C:\Users\Windows_user_name/.ssh/id_rsa // Windows user may have something like this
    user [user_id_on_server]
    Port [port]
    LocalForward 3000 127.0.0.1:3000

• Connect to ICPUTRD and creating an new account
  1. In your Terminal or cmd, type ssh da1p to connect
  2. Go to http://localhost:3000/
  3. Creating an new account