Post Cloning Setup

Setup Relay User

Run relay_setup.sh

clone_setup/relay_setup.sh

Adjust crontab based on prefered schedule.

Copy key to Aspera

run add_relay_user.sh as root on Aspera

Copy key to hcp-ops

run add_relay_user.sh as root on hcp-ops

Configure Logging and Updates

Edit /etc/ozmt/reporting.muttrc

Configure matching shared folder to $HOSTNAME on Owncloud owned by the administrator

Share common folder on Owncloud

Edit /root/relay-data.sh and put proper Owncloud username and password in.

Clean /owncloud and test relay-update.sh

CODE

rm -rf /owncloud/* 
rm -f /owncloud/.csync_journal.db
/opt/relaysync/relay-update.sh

Enable sync via root crontab by un-commenting relay-update.sh line

Replace SSL certificate

In /etc/pki/tls/certs

Setup XNAT relay

Login to https://{IP}

relay / relay123

Set SiteID, site URL and Site Description

click administer -> Site Administration

Create Projects

New -> Project

XNAT User setup

https://wiki.humanconnectome.org/display/CCFPRIV/LifeSpan+Data+Relays

Set password for relay user:

Click relay at top of page

Create site specific system user on relay and Intradb.

Used for Xsync

Create Site Admin user.

grant all privileges

Create additional users for site

Add Users to Project

Administer -> Users

Setup Xsync for each project

Project -> Manage (tab) -> Xsync Configuration -> Begin Configuration

Setup RAW data relay

Configure /raw/scripts/config.yaml

– Can use sample-config.yaml.

CODE

sync:
  logfile: /raw/data/logs/raw-sync.log
  report_name: raw_sync
  host: asp-connect1.wustl.edu
mars:
  ip: 192.168.2.2
  bwlimit: --bwlimit=40000
  cleanup: --remove-source-files
relay:
  ip: 192.168.2.3
  source: /raw/data/staging/
  destination: /data/lifespanRAW
xnat:
  url: https://intradb.humanconnectome.org
  projects:
    - CCF_PHCP_ITK
    - CCF_HCD_ITK
    - CCF_HCA_ITK
web:
  host: hcp-ops.nrg.mir
  log: /var/www/hcp-ops/db/relays

Configure upstream XNAT accounts

Double check username and passwords in /home/${HOSTNAME}_sync/.hcpxnat_intradb.cfg and .hcpxnat_relay.cfg

Testing the Setup

Open port for testing:

iptables -I IN_public_allow -p tcp --dport 8104 -j ACCEPT

Lower DICOM timeout:

Set to 1 min for testing. 5 minutes is default.

DICOM sync:

Open matching session scan (HCAP1017_V1_B scan20) and set headers to match one of the relay's projects (CCF_HCA_ITK, CCF_HCD_ITK, etc.)

Upload to relay using DicomBrowser.

Run Xsync on the relay

Verify session makes it to Intradb in the correct project

RAW sync:

Verify MR_20170130_200809_2cab83d9-62be-4392-94df-8c848751d8be_dMRI_dir98_PA.cplxraw file is in /rawdata on MARS VM

zfs rollback rawdata@before-harvard-test1

Make a snapshot of /rawdata on first run

Run /raw/scripts/mars-to-relay.sh on the relay

Verify data gets pulled into /raw/data/staging/ on relay

Modify access time of file to appease syncing parameters

touch -a -d '1 Jan 2017 12:00' MR_2017*.cplxraw

Run /raw/scripts/relay-to-backup.sh

Verify data made it to asp-connect1.wustl.edu in /data/lifespanRAW/{hostname}

Other:

Run /raw/scripts/find-xnat-raw.py for good measure

Set xnat cleanup interval to 0 and run /raw/scripts/cleanup-local-xnat.py

Change interval back to 30

Remove dsa key fingerprint from ~/.ssh/known_hosts after testing

Delete RelayTest subject from Intradb

Set 5 minute default for dicom receiver

Set Sync Retry interval to 15 minutes, 2 retries

Set Remote Token to 2 days

Remove files from relay staging and asp-connect

Setup LAN

Set SMTP relay IP.

/etc/postfix/main.cf

Set the NTP server in /etc/ntp.conf

Use the console to configure enp0s20f0 for the LAN IP

Set the Identity to "LAN"

Set the IP, Gateway and DNS

Set the timezone

Setup IPMI

Setup Users

Set password for ADMIN

Create hcpadmin

Create Site admin