Uploads images listed in a csv spreadsheet into an xnat server

upload-imagedata.sh

#!/bin/bash

print_usage() {
  echo "
Uploads images listed in a csv spreadsheet into an xnat server
Uses the script create-session.sh

The spreadsheet should contain the following columns, separated by spaces:
<project> <subject-id> <acquisition-date> <session-type (MR or CT)> <session-label> <scan-label> <image-file-path>

The subject ids have to be already present in the database. This can be achieved using the 
'upload spreadsheet' function from the web interface.

Date format: MM\/DD\/YY   (US style, month first!)

Usage:
    ./upload-imagedata.sh (-h|--host) <server URI>  (-u|--user) <username> (-p|--password) <password>
                          (-i|--input) <csv spreadsheet> 
"
  exit 1
}

check_next_arg() {
  if [ $# -lt 2 ]
  then
    echo "Missing argument."
    print_usage
  fi
  next_arg="$2"
  if [ ${#next_arg} -eq 0 ]
  then
    echo "Value is missing for option $1."
    print_usage
  fi
  if [ "${next_arg:0:1}" == "-" ]
  then
    echo "Value is missing for option $1."
    print_usage
  fi
}

while [ $# -gt 0 ]
do
  if [ "$1" == "-h" ] || [ "$1" == "--host" ]
  then
    check_next_arg ${@}
    xnat="$2"
    shift 2
  elif [ "$1" == "-u" ] || [ "$1" == "--user" ]
  then
    check_next_arg ${@}
    user="$2"
    shift 2
  elif [ "$1" == "-p" ] || [ "$1" == "--password" ]
  then
    password="$2"
    shift 2
  elif [ "$1" == "-i" ] || [ "$1" == "--input" ]
  then
    input="$2"
    shift 2
  else
    echo "Unknown argument: $1"
    print_usage
  fi
done

if [ "$user" == "" ] || [ "$xnat" == "" ] || [ "$input" == "" ]
then
  echo "missing one of these required options:"
  echo "xnat, user, input"
  print_usage
fi

if [ "$password" == "" ] 
then 
  read -p "password: " -s password
  echo
fi

if [ $password == "" ]
then
  echo "Invalid password."
  print_usage
fi

# Path to the curl binary
curl_dir=/usr/bin

# Remove the last character of the url if it finishes by "/"
xnat=${xnat%"/"}

echo "input data :"
echo "xnat: $xnat"
echo "user: $user"
echo "password: $password"
echo "input: $input"

# ------------------------------------------------------------------------
#  XNAT
# ------------------------------------------------------------------------

function check_response {
  if [ $1 -ne 0 ]
  then
    echo "Connection to the XNAT server has failed."
    success=0;
  else
    success=1;
  fi

  if grep -q "Login attempt failed" <<< $2
  then
    echo "Login attempt failed."
    echo $2
    success=0;
  else
    success=1;
  fi
}

Curl=$curl_dir/curl

curlArgs="-u $user:$password --insecure --silent"
curlArgsProgress="-u $user:$password --insecure"

while read p; do

  project=`echo $p | awk -F, '{print $1}'`
  subject=`echo $p | awk -F, '{print $2}'`
  date=`echo $p | awk -F, '{print $3}'`
  type=`echo $p | awk -F, '{print $4}' | tr '[A-Z]' '[a-z]'`
  experiment=`echo $p | awk -F, '{print $5}'`
  scan=`echo $p | awk -F, '{print $6}' | awk '{gsub(/[[:punct:]]/,"-")}1'`
  scanType=`echo $p | awk -F, '{print $7}'`
  file=`echo $p | awk -F, '{print $8}'`

  echo "project: $project"
  echo "subject: $subject"
  echo "date: $date"
  echo "type: $type"
  echo "experiment: $experiment"
  echo "scan: $scan"
  echo "scanType: $scanType"
  echo "file: $file"


  # define imageid from the adni xml description (specific ADNI upload)

 # imageid=`echo $file | sed 's/.*_I\(.*\).xml/\1/g'`

  # find the actual image file (specific ADNI upload)

 # imagefile=`ls ../renamed/*_$subject*$imageid*.nii.gz`
  
#  imagefile=`ls $imageid.zip`
  
  # define imageid as the file without extension
  imageid=${file%\.*}
  # find the actual image file full path (more global use)
  imagefile=$(cd $(dirname $file); pwd)/$(basename $file)

  echo "imagefile: $imagefile"

  if [ ! -f "$imagefile" ]; then
    echo "image file not found: $imagefile"
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue
  fi

  if [ "$project" == "" ] || [ "$subject" == "" ] || [ "$experiment" == "" ] ||
      [ "$scan" == "" ] || [ "$date" == "" ] || [ "$type" == "" ] || [ "$scanType" == "" ] || [ "$file" == "" ]
  then
    echo "missing one of these required arguments for upload:"
    echo "project, subject, type, experiment, scan, scanType, date, file"
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue
  fi

  session="${experiment}"
  xnatUri=$xnat/REST
  projectUri=$xnatUri/projects/$project
  subjectUri=$projectUri/subjects/$subject
  experimentUri=$subjectUri/experiments/$session

  # ------------------------------------------------------------------------
  #  Checking project
  # ------------------------------------------------------------------------

  echo -n "Checking project...          "
  response=$($Curl $curlArgs -X GET "$projectUri?format=xml")
  exitVal=$?

  check_response $exitVal $response
  if [ $success -eq 0 ]
  then
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue
  fi

  if grep -q "Unable to find the specified subjectThe server has not found anything matching the request URI" <<< $response
  then
    echo "Project does not exist"
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  else
      echo "OK"
  fi

  # ------------------------------------------------------------------------
  #  Checking subject
  # ------------------------------------------------------------------------

  echo -n "Checking subject...          "
  response=$($Curl $curlArgs -X GET "$subjectUri?format=xml")
  exitVal=$?

  check_response $exitVal $response
  if [ $success -eq 0 ]
  then
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  fi

  if grep -q "Unable to find the specified subject" <<< $response
  then
    echo "Subject does not exist: $subject"
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  else
      echo "OK"
  fi

  # ------------------------------------------------------------------------
  #  Checking experiment
  # ------------------------------------------------------------------------

  echo -n "Checking experiment...       "
  response=$($Curl $curlArgs -X GET "$experimentUri?format=xml")
  exitVal=$?

  check_response $exitVal $response
  if [ $success -eq 0 ]
  then
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  fi

  grep -q "Unable to find the specified experiment." <<< $response
  sessionDoesNotExist=$?

  if [ $sessionDoesNotExist -eq 0 ]
  then
      # ------------------------------------------------------------------------
      #  Creating session
      # ------------------------------------------------------------------------
      echo
      echo "Session does not exist."
      echo -n "Creating session...          "

      experimentArgs="?xsi:type=xnat:"$type"SessionData"
      experimentArgs+="&xnat:"$type"SessionData/date=$date"
      experimentArgs+="&xnat:"$type"SessionData/label=$session"

      command="$Curl $curlArgs -X PUT \"$experimentUri$experimentArgs\""
      echo "command: $command"
      response=$($Curl $curlArgs -X PUT "$experimentUri$experimentArgs")
      exitVal=$?

      check_response $exitVal $response
      if [ $success -eq 0 ]
      then
	echo "skipping imageid $imageid"
	skippedids=$skippedids$imageid"\n"; 
	continue;
      fi

      grep -q "The server encountered an unexpected condition which prevented it from fulfilling the request" <<< $response
      creatingSessionFailed=$?
      
      if [ $creatingSessionFailed -eq 0 ]
      then
	echo
	echo "Cannot create the session."
	echo "Exit code: $exitVal"
	echo "Response from server: $response"
	echo "skipping imageid $imageid"
	skippedids=$skippedids$imageid"\n"; 
	continue;
      else
	echo "OK"
      fi
      
      experimentId=$response
      echo "New experiment created: $experimentId"
  else
      echo "OK"
  fi

  # ------------------------------------------------------------------------
  #  Creating scan
  # ------------------------------------------------------------------------

  #scan="1"

  if [ "$experimentId" != "" ]
  then
      experimentUri="$subjectUri/experiments/$experimentId"
  fi

  scanUri=$experimentUri/scans/$scan

  echo -n "Creating scan...          "

  scanArgs="?xsi:type=xnat:"$type"ScanData"
  scanArgs+="&xnat:"$type"ScanData/type=$scanType"
  scanArgs+="&xnat:"$type"ScanData/quality=usable"
  
  
  command="$Curl $curlArgs -X PUT \"$scanUri$scanArgs\""
  echo "command: $command"
  response=$($Curl $curlArgs -X PUT "$scanUri$scanArgs")
  exitVal=$?

  check_response $exitVal $response
  if [ $success -eq 0 ]
  then
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  fi
  grep -q "The server encountered an unexpected condition which prevented it from fulfilling the request" <<< $response
  creatingScanFailed=$?

  if [ $creatingScanFailed -eq 0 ]
  then
      echo
      echo "Cannot create the scan."
      echo "Exit code: $exitVal"
      echo "Response from server: $response"
      echo "skipping imageid $imageid"
      skippedids=$skippedids$imageid"\n"; 
      continue;
  else
      echo "OK"
  fi

  # ------------------------------------------------------------------------
  #  Uploading file (specific for DICOM file upload)
  # ------------------------------------------------------------------------

  echo -n "Uploading file...          "

  fileName=${imagefile##*/}
  fileUri="$scanUri/resources/DICOM/files/$fileName"

  fileArgs="?format=DICOM"
  fileArgs+="&content=RAW"
  fileArgs+="&overwrite=true"
  fileArgs+="&inbody=true"

  response=$($Curl $curlArgsProgress -X PUT --data-binary @$imagefile "$fileUri$fileArgs" )
  exitVal=$?

  check_response $exitVal $response
  if [ $success -eq 0 ]
  then
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  fi
  grep -q "Status page" <<< $response
  commandFailed=$?

  if [ $commandFailed -eq 0 ]
  then
    echo
    echo "Cannot upload the file."
    echo "Exit code: $exitVal"
    echo "Response from server: $response"
    echo "skipping imageid $imageid"
    skippedids=$skippedids$imageid"\n"; 
    continue;
  else
    echo "OK"
  fi

done < "$input"

echo -e $skippedids > skippedids.log