[ome-users] Multiple groups "in-place import"?
Sebastien Besson (Staff)
s.besson at dundee.ac.uk
Thu Feb 14 13:58:55 GMT 2019
Hi Konrad,
Does the folder /OMERO/in-place-import/SN120-16 exist on the server where you are
running the script and is it accessible to the user who is executing the script?
The initial script is hardcoded to handle the location chosen for holding the primary data of
the OME outreach server. Using this location is definitely not a requirement.
If the data you want to import is stored elsewhere, you probably to update the last argument
of the import line and point at the appropriate location in your use case
Best,
Sebastien
> On 14 Feb 2019, at 12:44, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de> wrote:
>
> Hi Sebastien,
> thanks for getting back; edited as you suggested
>
> $OMEROPATH import -d $DatasetId --transfer=ln_s "/OMERO/in-place-import/$FOLDER"
> right after the command that links the dataset to the project:
> $OMEROPATH obj new ProjectDatasetLink parent=$ProjectId child=$DatasetId
>
> ...
> echo Starting
> SUDOER=${SUDOER:-GrandImporter}
> OMEROPATH=${OMEROPATH:-OMERO.server/bin/omero}
> PASSWORD=${PASSWORD:-ome}
> HOST=${HOST:-omerotest.uk-erlangen.de}
> PROJECT=${PROJECT:-Lightsheet}
> FOLDER=${FOLDER:-SN120-16}
> NUMBER=${NUMBER:-2}
> OMEUSER=${OMEUSER:-trainer}
> DATATYPE=${DATATYPE:-dataset}
> for ((i=1;i<=$NUMBER;i++));
> do $OMEROPATH login --sudo ${SUDOER} -u $OMEUSER-$i -s $HOST -w $PASSWORD
> if [ "$DATATYPE" = "dataset" ]; then
> ProjectId=$($OMEROPATH obj new Project name=$PROJECT)
> DatasetId=$($OMEROPATH obj new Dataset name=$FOLDER)
> $OMEROPATH obj new ProjectDatasetLink parent=$ProjectId child=$DatasetId
> $OMEROPATH import -d $DatasetId --transfer=ln_s "/OMERO/in-place-import/$FOLDER"
>
> elif [ "$DATATYPE" = "plate" ]; then
> $OMEROPATH import --transfer=ln_s "/OMERO/in-place-import/$FOLDER"
>
> fi
> $OMEROPATH logout
> done
> echo Finishing
>
> ran the script & got:
>
> Starting
> Created session f307479d-3ee4-4ce3-adbf-fcc39f022f9f (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session f307479d-3ee4-4ce3-adbf-fcc39f022f9f (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session f307479d-3ee4-4ce3-adbf-fcc39f022f9f (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session f307479d-3ee4-4ce3-adbf-fcc39f022f9f (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> ProjectDatasetLink:1742
> Using session f307479d-3ee4-4ce3-adbf-fcc39f022f9f (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> 2019-02-14 13:32:02,854 180 [ main] INFO ome.formats.importer.ImportConfig - OMERO Version: 5.4.6-ice36-b87
> 2019-02-14 13:32:02,864 190 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 5.8.2 revision: 6bc10be63e934ed12e76c3ffd83ecd2bca6312a1 date: 18 April 2018
> 2019-02-14 13:32:02,894 220 [ main] INFO formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
> 2019-02-14 13:32:02,896 222 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
> 2019-02-14 13:32:03,151 477 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
> 2019-02-14 13:32:03,154 480 [ main] ERROR ome.formats.importer.cli.ErrorHandler - UNREADABLE_FILE: /OMERO/in-place-import/SN120-16
> java.io.FileNotFoundException: /OMERO/in-place-import/SN120-16
> at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:411) [blitz.jar:na]
> at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576) [blitz.jar:na]
> at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384) [blitz.jar:na]
> at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222) [blitz.jar:na]
> at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174) [blitz.jar:na]
> at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:147) [blitz.jar:na]
> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:964) [blitz.jar:na]
> 2019-02-14 13:32:03,155 481 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 0 group(s) with 0 call(s) to setId in 0ms. (4ms total) [0 unknowns]
> 2019-02-14 13:32:13,239 10565 [ main] ERROR ome.system.UpgradeCheck - Error reading from url: http://upgrade.openmicroscopy.org.uk?version=5.4.6-ice36-b87;os.name=Linux;os.arch=amd64;os.version=3.10.0-514.6.1.el7.x86_64;java.runtime.version=1.8.0_121-b13;java.vm.vendor=Oracle+Corporation "connect timed out"
> 2019-02-14 13:32:13,276 10602 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to omerotest.uk-erlangen.de:4064
> 2019-02-14 13:32:13,582 10908 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
> 2019-02-14 13:32:13,753 11079 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.4.6
> 2019-02-14 13:32:13,753 11079 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.4.6-ice36-b87
> 2019-02-14 13:32:13,753 11079 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 1.8.0_121
> 2019-02-14 13:32:13,753 11079 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux
> 2019-02-14 13:32:13,753 11079 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
> 2019-02-14 13:32:13,753 11079 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 3.10.0-514.6.1.el7.x86_64
> No imports found
>
> Usage: importer-cli [OPTION]... [path [path ...]]...
> or: importer-cli [OPTION]... -
>
> Import any number of files into an OMERO instance.
> If "-" is the only path, a list of files or directories
> is read from standard in. Directories will be searched for
> all valid imports.
>
> Session arguments:
> Mandatory arguments for creating a session are 1- either the OMERO server hostname,
> username and password or 2- the OMERO server hostname and a valid session key.
> -s SERVER OMERO server hostname
> -u USER OMERO username
> -w PASSWORD OMERO password
> -k KEY OMERO session key (UUID of an active session)
> -p PORT OMERO server port (default: 4064)
>
> Naming arguments:
> All naming arguments are optional
> -n NAME Image or plate name to use
> -x DESCRIPTION Image or plate description to use
> --name NAME Image or plate name to use
> --description DESCRIPTION Image or plate description to use
>
> Optional arguments:
> -h Display this help and exit
> -f Display the used files and exit
> -c Continue importing after errors
> -l READER_FILE Use the list of readers rather than the default
> -d DATASET_ID OMERO dataset ID to import image into
> -r SCREEN_ID OMERO screen ID to import plate into
> -T TARGET target for imports
> --report Report errors to the OME team
> --upload Upload broken files and log file (if any) with report. Required --report
> --logs Upload log file (if any) with report. Required --report
> --email EMAIL Email for reported errors. Required --report
> --debug LEVEL Turn debug logging on (optional level)
> --annotation-ns ANNOTATION_NS Namespace to use for subsequent annotation
> --annotation-text ANNOTATION_TEXT Content for a text annotation
> --annotation-link ANNOTATION_LINK Comment annotation ID to link all images to
>
> Examples:
>
> $ importer-cli -s localhost -u user -w password -d 50 foo.tiff
> $ importer-cli -s localhost -u user -w password -d Dataset:50 foo.tiff
> $ importer-cli -f foo.tiff
> $ importer-cli -s localhost -u username -w password -d 50 --debug ALL foo.tiff
>
> For additional information, see:
> https://docs.openmicroscopy.org/latest/omero/users/cli/import.html
> Report bugs to <ome-users at lists.openmicroscopy.org.uk>
> ...
> Finishing
>
> Still empty folders!
> What's missing?
>
> Cheers
> Konrad
>
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