diff upload_omero.sh @ 0:e1cba36becb2 draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/upload_omero.sh	Tue Dec 19 15:02:41 2023 +0000
@@ -0,0 +1,17 @@
+#!/bin/bash
+omero_server="$1"
+omero_user="$(cat $2 | awk 'NR==2{print $0}')"
+omero_password="$(cat $2 | awk 'NR==3{print $0}')"
+to_create=$3
+screen_name_or_id=$4
+
+if [ "$to_create" = "create" ]; then
+    # Create a screen:
+    screen_name_or_id=$(omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Screen name="${screen_name_or_id}" | awk -F ":" 'END{print $NF}')
+    echo "Just created the new screen ${screen_name_or_id}"
+fi
+
+echo "Start upload"
+companion_file=$(ls output/*.companion.ome)
+omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} -T Screen:id:"${screen_name_or_id}" "${companion_file}" 2>&1
+echo "Upload finished"