[ome-users] Multiple groups "in-place import"?
Kölble, Konrad
Konrad.Koelble at uk-erlangen.de
Thu Feb 14 12:44:48 GMT 2019
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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