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| Run the Java-based command-line importer | ||
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| This is a Python wrapper around the Java importer. Login is handled by Python | ||
| OMERO.cli. To see more options, use "--javahelp". | ||
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| Options marked with "**" are passed strictly to Java. If they interfere with | ||
| any of the Python arguments, you may need to end precede your arguments with a | ||
| "--". | ||
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| Bulk imports: | ||
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| Rather than passing one or more files to the import command, a single | ||
| dictionary-like file (e.g. yml or json) can be passed to the `--bulk` | ||
| argument. Most keys in the bulk file will be treated like additional | ||
| command-line arguments. Special keys include: | ||
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| * columns A list of columns for parsing the value of path | ||
| * continue Like the "-c" changes error handling | ||
| * dry_run If true, print out additional arguments rather than run them. | ||
| If another string other than false, use as a template for | ||
| storing the import commands. (e.g. /tmp/%s.sh) | ||
| * include Relative path (from the bulk file) of a parent bulk file | ||
| * path A file which will be parsed line by line based on its file | ||
| ending. Lines containing zero or more keys along with a | ||
| single file to be imported. Options for formats include: | ||
| - .tsv and .csv files will be parsed by the existing library | ||
| - other files will be parsed with shlex | ||
| - unless no columns are specified, in which case each line | ||
| is treated as a file | ||
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| Optional Arguments: | ||
| In addition to any higher level options | ||
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| -h, --help show this help message and exit | ||
| --javahelp, --java-help Show the Java help text | ||
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| Login arguments: | ||
| Environment variables: | ||
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| OMERO_USERDIR Set the base directory containing the user's files. | ||
| Default: $HOME/omero | ||
| OMERO_SESSIONDIR Set the base directory containing local sessions. | ||
| Default: $OMERO_USERDIR/sessions | ||
| OMERO_TMPDIR Set the base directory containing temporary files. | ||
| Default: $OMERO_USERDIR/tmp | ||
| OMERO_PASSWORD Set the user's password for creating new sessions. | ||
| Ignored if -w or --password is used. | ||
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| Optional session arguments: | ||
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| -C, --create Create a new session regardless of existing ones | ||
| -s SERVER, --server SERVER OMERO server hostname | ||
| -p PORT, --port PORT OMERO server port | ||
| -g GROUP, --group GROUP OMERO server default group | ||
| -u USER, --user USER OMERO username | ||
| -w PASSWORD, --password PASSWORD OMERO password | ||
| -k KEY, --key KEY OMERO session key (UUID of an active session) | ||
| --sudo ADMINUSER Create session as this admin. Changes meaning of password! | ||
| -q, --quiet Quiet mode. Causes most warning and diagnostic messages to be suppressed. | ||
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| Python arguments: | ||
| Optional arguments which are used to configure import. | ||
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| --bulk [BULK] Bulk YAML file for driving multiple imports | ||
| --logprefix [LOGPREFIX] Directory or file prefix for --file and --errs | ||
| --file [FILE] File for storing the standard output from the Java process | ||
| --errs [ERRS] File for storing the standard error from the Java process | ||
| --clientdir CLIENTDIR Path to the directory containing the client JARs. Default: lib/client | ||
| --logback LOGBACK Path to a logback xml file. Default: etc/logback-cli.xml | ||
| --fetch-jars FETCH_JARS Download this version of OMERO.java jars and exit | ||
| --depth DEPTH Number of directories to scan down for files | ||
| --skip {all,checksum,minmax,thumbnails,upgrade} | ||
| Optional step to skip during import | ||
| path Path to be passed to the Java process | ||
| 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. | ||
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| 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) | ||
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| Naming arguments: | ||
| Optional arguments passed strictly to Java. | ||
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| -n NAME, --name NAME Image or plate name to use (**) | ||
| -x DESCRIPTION, --description DESCRIPTION | ||
| Image or plate description to use (**) | ||
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| Feedback arguments: | ||
| Optional arguments passed strictly to Java allowing to report errors to the OME team. | ||
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| --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 (**) | ||
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| Annotation arguments: | ||
| Optional arguments passed strictly to Java allowing to annotate imports. | ||
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| --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 (**) | ||
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| Java arguments: | ||
| Optional arguments passed strictly to Java. | ||
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| -f Display the used files and exit (**) | ||
| -c Continue importing after errors (**) | ||
| -l READER_FILE, --readers 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 TARGET OMERO target specification (**) | ||
| --debug LEVEL Turn debug logging on (**) | ||
| --output TYPE Set an alternative output style | ||
| --encrypted TYPE Whether the import should use SSL or not | ||
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| Advanced Java arguments: | ||
| Optional arguments passed strictly to Java. For more information, see --advanced-help. | ||
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| --advanced-help Show the advanced help text | ||
| --transfer [TYPE] Transfer methods like in-place import | ||
| --exclude [TYPE] Exclusion filters for preventing re-import | ||
| --checksum-algorithm [TYPE] Alternative hashing mechanisms balancing speed & accuracy | ||
| --parallel-upload COUNT Number of file upload threads to run at the same time | ||
| --parallel-fileset COUNT Number of fileset candidates to import at the same time | ||
| 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 | ||
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| 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 | ||
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| Examples: | ||
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| # Display help | ||
| $ omero import -h | ||
| # Import foo.tiff using current login | ||
| $ omero import ~/Data/my_file.dv | ||
| # Import foo.tiff using input credentials | ||
| $ omero import -s localhost -u user -w password foo.tiff | ||
| # Set Java debugging level to ALL | ||
| $ omero import foo.tiff -- --debug=ALL | ||
| # Display used files for importing foo.tiff | ||
| $ omero import foo.tiff -f | ||
| # Limit debugging output | ||
| $ omero import -- --debug=ERROR foo.tiff | ||
| $ 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 | ||
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| For additional information, see: | ||
| https://docs.openmicroscopy.org/latest/omero/users/cli/import.html | ||
| Report bugs at https://forum.image.sc/ | ||
| Report bugs at https://www.openmicroscopy.org/forums |
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