Hi Josh,
to clarify some of your questions:
I tried to import a folder with 12 images + 12 metadata xmls exported from Zeiss Axiovision.
This is the file list:
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0011.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0011.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0012.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0012.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0002.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0002.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0003.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0003.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0004.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0004.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0013.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0013.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0014.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0014.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0015.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0015.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0005.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0005.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0006.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0006.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0007.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0007.tif_meta.xml
All of them are rather small.
I used this bulk.yml file:
- Code: Select all
---
continue: "true"
transfer: "ln_s"
exclude: "clientpath"
checksum_algorithm: "File-Size-64"
logprefix: "logs/"
output: "yaml"
path: "/OMERO/ManagedRepository/ipimp-11269.tsv"
columns:
- target
- path
and this filelist file:
- Code: Select all
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0011.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0011.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0012.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0012.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0002.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0002.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0003.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0003.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0004.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-2-0004.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0013.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0013.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0014.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0014.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0015.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-0015.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0005.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0005.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0006.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0006.tif_meta.xml
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0007.tif
Dataset:name:von Paddy /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_undiff_D3-2-0007.tif_meta.xml
then I used these two commands entered by hand:
/home/omerouser/OMERO.server/bin/omero --sudo inplace -wpwforinplace -u 'Alex R' login -s 130.83.98.66
/home/omerouser/OMERO.server/bin/omero import --bulk /OMERO/ManagedRepository/bulki-11269.yml
This was independent of my python script, because I wanted to catch the output from the terminal.
I haven't uploaded the script yet, but I upload it, here .py files are not allowed. I am really sorry for the bad code, it is my first python script. If you want to run it you need to change the path in the header to your omero/python/lib and generate a settings file first. Sorry this is still work in progress, I appreciate every input/suggestions.
Best wishes Alex