alohaUploadAndTagOutputs

#!/bin/bash

#
# Probably want the SubjectJsonFile path
#

CmdName=$(basename "$0")
Syntax="${CmdName} {-B BaselineDate} {-F FollowupDate} {-f FwFilePathJsonFile} {-i FollowupIndex} {-d FollowupDir}[-n][-v] SubjectAlohaJsonFile"

function sys {
	[ -n "${opt_n}${opt_v}" ] && echo "$@" 1>&2
	[ -n "$opt_n" ] || "$@"
}

while getopts B:d:F:f:i:nv arg
do
	case "$arg" in
	     B|d|F|f|i|n|v)
		eval "opt_${arg}='${OPTARG:=1}'"
		;;
	esac
done

shift $(("$OPTIND" - 1))

if [ -z "$opt_d" ]
then
	echo "${CmdName} : missing -d FollowupDir" 1>&2
	echo "$Syntax" 1>&2
	exit 1
fi

FollowupDir="$opt_d"
FollowupUploadDir="${FollowupDir}/Uploads"

if [ -z "$opt_i" ]
then
	echo "${CmdName} : missing -i FollowupIndex" 1>&2
	echo "$Syntax" 1>&2
	exit 2
fi

FollowupIndex="$opt_i"

if [ -z "$opt_B " ]
then
	echo "${CmdName} : missing -B BaselineDate" 1>&2
	echo "$Syntax" 1>&2
	exit 2
fi
BaselineDate=$(date -d "$opt_B" '+%Y-%m-%d')

if [ -z "$opt_F " ]
then
	echo "${CmdName} : missing -F FollowupDate" 1>&2
	echo "$Syntax" 1>&2
	exit 2
fi
FollowupDate=$(date -d "$opt_F" '+%Y-%m-%d')
SubjectAlohaJsonFile="$1"

SubjectId=$(jq -r '.SubjectId' "$SubjectAlohaJsonFile")
SubjectLabel=$(jq -r '.SubjectLabel' "$SubjectAlohaJsonFile")

FollowupJson=$(jq ".Followup[$FollowupIndex].FollowupT2" "$SubjectAlohaJsonFile")
FollowupSessionId=$(jq -r -n --argjson FollowupJson "$FollowupJson" "($FollowupJson).SessionId")

AlohaOutputJson='{
  "FileNameTemplate": "aloha-%s-%s_%s-%s",
  "FilenameSources": [ ".SubjectLabel", ".FromDate", ".ToDate", ".FileName" ],
  "Metadata": "???",
  "FollowupOutputFiles": [
         {
	      "AlohaFileName": "deformable/bltrim_left_to_hw.nii.gz"
	    , "FwFileName": "BaselineT2LeftTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Left"]
         }
       , {
	      "AlohaFileName": "deformable/bltrim_right_to_hw.nii.gz"
	    , "FwFileName": "BaselineT2RightTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
       , {
	      "AlohaFileName": "deformable/futrim_om_left_to_hw.nii.gz"
	    , "FwFileName": "FollowupT2LeftTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Left" ]
         }
       , {
	      "AlohaFileName": "deformable/futrim_om_right_to_hw.nii.gz"
	    , "FwFileName": "FollowupT2RightTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
       , {
	      "AlohaFileName": "deformable/blmptrim_left_to_hw.nii.gz"
	    , "FwFileName": "BaselineT1LeftTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Left" ]
         }
       , {
	      "AlohaFileName": "deformable/blmptrim_right_to_hw.nii.gz"
	    , "FwFileName": "BaselineT1RightTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
       , {
	      "AlohaFileName": "deformable/fumptrim_om_left_to_hw.nii.gz"
	    , "FwFileName": "FollowupT1LeftTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Left" ]
         }
       , {
	      "AlohaFileName": "deformable/fumptrim_om_right_to_hw.nii.gz"
	    , "FwFileName": "FollowupT1RightTrimmedHalfwaySpace"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
       , {
	      "AlohaFileName": "deformable/mp_antsreg3d_left1Warp.nii.gz"
	    , "FwFileName": "T1LeftWarpField"
	    , "Tags": [ "Aloha", "Output", "Left" ]
         }
       , {
	      "AlohaFileName": "deformable/mp_antsreg3d_right1Warp.nii.gz"
	    , "FwFileName": "T1RightWarpField"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
       , {
	      "AlohaFileName": "deformable/tse_antsreg3d_left1Warp.nii.gz"
	    , "FwFileName": "T2LeftWarpField"
	    , "Tags": [ "Aloha", "Output", "Left" ]
         }
       , {
	      "AlohaFileName": "deformable/tse_antsreg3d_right1Warp.nii.gz"
	    , "FwFileName": "T2RightWarpField"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
       , {
	      "AlohaFileName": "results/volumes_left.txt"
	    , "FwFileName": "LeftVolumes"
	    , "Tags": [ "Aloha", "Output", "Left" ]
         }
       , {
	      "AlohaFileName": "results/volumes_right.txt"
	    , "FwFileName": "RightVolumes"
	    , "Tags": [ "Aloha", "Output", "Right" ]
         }
  ]
}'

FollowupUploadFilesRegEx=$(echo $(echo "$AlohaOutputJson" | jq -r '.FollowupOutputFiles[].AlohaFileName') | sed 's/ /)|(/g; s/^.*$/(&)/' )

echo "$AlohaOutputJson" > /tmp/json

[ -e "$FollowupUploadDir" ] || mkdir "$FollowupUploadDir"

FileNameTemplate=$(echo "$AlohaOutputJson" | jq -r '.FileNameTemplate')
FilenameSources=$(echo "$AlohaOutputJson" | jq -r '.FilenameSources[]')

while read f
do
	Basename=$(basename "$f")

	FwFileJson=$(echo "$AlohaOutputJson" | jq -r --argjson AlohaFileName "\"$Basename\"" '.. | select(.AlohaFileName | test($AlohaFileName)) ?')
	FwFileName=$(echo "$FwFileJson" | jq -r '.FwFileName')
	Tags=$(echo "$FwFileJson" | jq -r '.Tags|@csv' | sed 's/"//g')
	FwTemplatedFileName=$(printf "$FileNameTemplate" "$SubjectLabel" "$BaselineDate" "$FollowupDate" "$FwFileName")
	FwUploadFilename="${FollowupUploadDir}/${FwTemplatedFileName}"
	sys cp "$f" "$FwUploadFilename"
	sys fwuploadfile -t "$Tags" -p "$FollowupSessionId" "$FwUploadFilename" 
	
done < <(find "$FollowupDir" -type f | grep -E "${FollowupUploadFilesRegEx}$" )


# naming: Want a name template: "
# and sources [ .followup.timestamp, .baseline.timestamp, subject, session, filename ]
#
# Copy file to new name
# upload renamed file to FollowupT2 and tag it
# 

exit 0