Design Canfield Total Body Photography Upload Solution

[RyanPSullivan7]

Create configuration script for the Canfield TB-Photography instrument. This has a dependency on on the vendor.

[anzhao]

**Use the following shell script to upload the ACEMID data to XNAT: the command to run is: ./acemid_upload.sh subjectID/sessionID/your_zip_file.zip. For instance: if you have the follwing folder structure: acemid_123/acemid_session_123/hospital_123.zip, you can run it as ./acemid_upload.sh acemid_123/acemid_session_123/hospital_123.zip **

#!/bin/bash

# XNAT server URL
XNAT_URL="your_xnat_url"

# XNAT credentials
USERNAME="your_username"
PASSWORD="your_password"

# ACEMID Project ID
PROJECT_ID="ACEMID_NSW_HospitalOne"

# verify the full path
FILENAME=$1
echo "Filename: $FILENAME"

# Extract SUBJECT_ID and SESSION_ID from the filename
SUBJECT_ID=$(echo $FILENAME | cut -d'/' -f1)
SESSION_ID=$(echo $FILENAME | cut -d'/' -f2)

# Subject label and session label can be the same as their IDs 
SUBJECT_LABEL=$SUBJECT_ID
SESSION_LABEL=$SESSION_ID
echo "Subject ID: $SUBJECT_ID"
echo "Session ID: $SESSION_ID"

# Create a subject
curl -u $USERNAME:$PASSWORD -X PUT "$XNAT_URL/data/archive/projects/$PROJECT_ID/subjects/$SUBJECT_ID?label=$SUBJECT_LABEL" -H "Content-Type: application/json" -H "Content-Length: 0"

# Create a session (experiment) with session type
SESSION_TYPE="ais:xcpSessionData"  # Replace with the session type you want
RESPONSE=$(curl -u $USERNAME:$PASSWORD -X PUT "$XNAT_URL/data/archive/projects/$PROJECT_ID/subjects/$SUBJECT_ID/experiments/$SESSION_ID?xsiType=$SESSION_TYPE&label=$SESSION_LABEL" -H "Content-Type: application/json" -H "Content-Length: 0" -w "%{http_code}" -o /dev/null)

# Check if the session creation was successful
if [ "$RESPONSE" -eq 200 ] || [ "$RESPONSE" -eq 201 ]; then
  echo "XCPSession created successfully."
else
  echo "Failed to create XCPSession. HTTP response code: $RESPONSE"
  exit 1
fi

# Create a scan
SCAN_ID="1"  # Replace with the scan ID you want
SCAN_TYPE="ais:xcpScanData"  # Replace with the correct scan type you want
RESPONSE=$(curl -u $USERNAME:$PASSWORD -X PUT "$XNAT_URL/data/archive/projects/$PROJECT_ID/subjects/$SUBJECT_ID/experiments/$SESSION_ID/scans/$SCAN_ID?xsiType=$SCAN_TYPE" -H "Content-Type: application/json" -H "Content-Length: 0" -w "%{http_code}" -o /dev/null)

# Check if the scan creation was successful
if [ "$RESPONSE" -eq 200 ] || [ "$RESPONSE" -eq 201 ]; then
  echo "XCPScan created successfully."
else
  echo "Failed to create XCPScan. HTTP response code: $RESPONSE"
  exit 1
fi

# Upload the file
curl -u $USERNAME:$PASSWORD -X PUT "$XNAT_URL/data/projects/$PROJECT_ID/subjects/$SUBJECT_ID/experiments/$SESSION_ID/scans/$SCAN_ID/resources/TEST/files?extract=true" -F "file=@$FILENAME"