alexr wrote:There is the "could not insert: [ome.model.core.OriginalFile]; SQL" error, that I think is the reason I see the datasets generated, but not the actual images.
Seems plausible. Want to upload your server log then?
~Josh
alexr wrote:There is the "could not insert: [ome.model.core.OriginalFile]; SQL" error, that I think is the reason I see the datasets generated, but not the actual images.
I did a complete restart this morning, not only the omero server, but the complete server. Then the locks are gone. When I restart omero and try an other import then I again get only the dataset generated in the server, but no images are added and I end up again with several locks.
I then removed the locks manually and tried the CLI with my above described method using bulk.yml and filelist.tsv. I used the same command that worked yesterday. I get the following output (for one file only):
I uploaded the server logs from /OMERO.server/var/log via the upload interface.
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "originalfile_repo_path_index"
Detail: Key (repo, regexp_split_to_array((('/'::text || path) || name) || '/'::text, '/+'::text))=(842746fd-4734-46bf-b55c-952bcc59e0ec, {"","Alex R_3",2018-06,27,09-58-34.947,250618_J1_undiff_D3-2-0006.tif,""}) already exists.
---
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
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
alexr wrote: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
bin/omero import -f 250618_J1_diff_D3-0010.tif
bin/omero import -f 250618_J1_diff_D3-0010.tif_meta.xml
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.
/home/omerouser/OMERO.server/bin/omero import -f /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA\ replication\ ES\ cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif
#======================================
# Group: /media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif SPW: false Reader: loci.formats.in.ZeissTIFFReader
/media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif
/media/CCHL-User/Patrick/01_PhD/Projects/1_DNA replication ES cells/1_data/Differentiation/250618/Axiovert_overview/250618_J1_diff_D3-0010.tif
/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
I did not get any images imported.
org.openmicroscopy.shoola.env.data.ImportException: File Not Valid
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1077)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:748)
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