Mercurial > repos > lldelisle > max_projections_stack_and_upload_omero
comparison upload_omero.sh @ 0:a02156aa8bda draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero commit 69a86e0a8ef82ce3c2232b99f72717a184f4d4cf
| author | lldelisle |
|---|---|
| date | Thu, 12 Dec 2024 12:42:20 +0000 |
| parents | |
| children | 9be687213bc9 |
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| -1:000000000000 | 0:a02156aa8bda |
|---|---|
| 1 #!/bin/bash | |
| 2 omero_server="$1" | |
| 3 omero_user="$(cat $2 | awk 'NR==2{print $0}')" | |
| 4 omero_password="$(cat $2 | awk 'NR==3{print $0}')" | |
| 5 to_create=$3 | |
| 6 project_name_or_id=$4 | |
| 7 dataset_name_or_id=$5 | |
| 8 | |
| 9 if [ "$to_create" = "both" ]; then | |
| 10 # Create a project: | |
| 11 project_name_or_id=$(${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Project name="${project_name_or_id}" | awk -F ":" 'END{print $NF}') | |
| 12 echo "Just created the new project ${project_name_or_id}" | |
| 13 fi | |
| 14 if [ "$to_create" = "both" ] || [ "$to_create" = "dataset" ]; then | |
| 15 dataset_name_or_id=$(${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Dataset name="${dataset_name_or_id}" | awk -F ":" 'END{print $NF}') | |
| 16 echo "Just created the new dataset ${dataset_name_or_id}" | |
| 17 ${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new ProjectDatasetLink parent=Project:${project_name_or_id} child=Dataset:${dataset_name_or_id} | |
| 18 fi | |
| 19 echo "Start upload" | |
| 20 omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} --depth 1 -T Dataset:id:"${dataset_name_or_id}" output 2>&1 | |
| 21 echo "Upload finished" |