Adding first data manipulation files and automatic uploads to orthanc

scripts/countUnzipped.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+if [ $# -lt 1 ] ; then
+	echo Usage $0 DIR;
+	exit 0;
+fi;
+
+aDirs=($(echo $1/*/)); 
+aZips=($(echo $1/*.zip));
+
+nDir=${#aDirs[@]}
+
+echo $nDir/${#aZips[@]};
+
+for ((i=0;i<nDir;i++)) ; do
+	echo ${aDirs[$i]};
+done;
+
+
+

scripts/doZip.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+N=1;
+echo Narg $#;
+if [ $# -gt 0 ] ; 
+then
+	N=$1;
+	echo Setting N to $N;
+fi;
+
+arr=($(echo */)); 
+echo Processing $N/${#arr[@]};
+for ((i=0;i<$N;i++)) ; do 
+	q=$(echo ${arr[i]} |sed 's/\///'); 
+	zip -r $q.zip $q/*; 
+	rm -rf $q/*; 
+	rmdir $q; 
+	chown tomcat8:tomcat8 $q.zip; 
+done;
+
+

scripts/uploadFiles.sh

@@ -0,0 +1,49 @@
+#copy content of directory to orthanc
+
+if [ $# -lt 1 ] ; then
+	echo $#;
+	echo Usage $0 DIR;
+	exit 0;
+fi;
+
+CFG=$2;
+USER=$(jq -r ".orthanc.user" $CFG);
+PASSWORD=$(jq -r ".orthanc.password" $CFG);
+SERVER=$(jq -r ".orthanc.server" $CFG);
+
+CURL="curl -u $USER:$PASSWORD"
+
+arr=($(echo $1/*.zip));
+
+Nall=${#arr[@]};
+N=$Nall
+
+echo Loading $N/$Nall;
+i=0
+for ((j=0;j<Nall;j++)) ; do
+	#ls ${arr[j]};
+	R=$($CURL -X POST $SERVER/instances --data-binary "@${arr[j]}" |jq -r ".[] | .Status");
+
+		
+	for x in $R ; do
+		#echo $x;
+		if [ $x == "AlreadyStored" ] ; then
+			#echo Done
+			break;
+		else
+			#echo New
+			i=$((i+1));
+			break;
+		fi;
+	done;
+
+	if [ $i -eq $N ] ; then
+		#echo "[$i/$N] Done"
+		break;
+	else
+		#echo "[$i/$N] Not done"
+		:
+	fi;
+	echo "Done [$j/$Nall, new $i]"
+
+done;