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fix readme (doc was on the wrong section)
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glyg committed Jan 24, 2024
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27 changes: 7 additions & 20 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -61,15 +61,13 @@ about the files (name, mimetype).

`--metadata` allows you to specify which transfer metadata will be saved in `transfer.xml` as possible MapAnnotation values to the images. Defaults to image ID, timestamp, software version, source hostname, md5, source username, source group.

<<<<<<< HEAD
`--plugin` allows you to export omero data to a desired format by using an external plugin. See for example the [arc plugin](https://github.com/cmohl2013/omero-arc), which exports omero
projects to ARC repositories.
`--server` creates the transfer.xml file but does not copy data
=======
`--metadata_only` creates the transfer.xml file but does not copy data
>>>>>>> ab2fbd3 (changes cli option to avoid collision)
or generate an archive. The last cli argument is the path where the `transfer.xml`
file will be written
`--binaries` allows to specify whether to archive binary data
(e.g images, ROIs, FileAnnotations) or only create the transfer.xml.
Default is `all` and will create the archive. With `none`, only the `transfer.xml`
file is created, in which case the last cli argument is the path where
the `transfer.xml` file will be written.


Examples:
Expand All @@ -78,12 +76,9 @@ omero transfer pack Image:123 transfer_pack.tar
omero transfer pack --zip Image:123 transfer_pack.zip
omero transfer pack Dataset:1111 /home/user/new_folder/new_pack.tar
omero transfer pack 999 tarfile.tar # equivalent to Project:999
<<<<<<< HEAD
omero transfer pack --plugin arc Project:999 path/to/my/arc/repo
omero transfer pack --server Dataset:1111 /home/user/new_folder
=======
omero transfer pack --metadata_only Dataset:1111 /home/user/new_folder
>>>>>>> ab2fbd3 (changes cli option to avoid collision)
omero transfer pack --binaries none Dataset:1111 /home/user/new_folder/
omero transfer pack --binaries all Dataset:1111 /home/user/new_folder/new_pack.tar
```

## `omero transfer unpack`
Expand All @@ -104,19 +99,11 @@ effectively merging the "new" unpacked entities with existing ones.

`--metadata` allows you to specify which transfer metadata will be used from `transfer.xml` as MapAnnotation values to the images. Fields that do not exist on `transfer.xml` will be ignored. Defaults to image ID, timestamp, software version, source hostname, md5, source username, source group.

`--binaries` allows to specify whether to archive binary data
(e.g images, ROIs, FileAnnotations) or only create the transfer.xml.
Default is `all` and will create the archive. With `none`, only the `transfer.xml`
file is created, in which case the last cli argument is the path where
the `transfer.xml` file will be written.

Examples:
```
omero transfer unpack transfer_pack.zip
omero transfer unpack --output /home/user/optional_folder --ln_s
omero transfer unpack --folder /home/user/unpacked_folder/
omero transfer pack --binaries none Dataset:1111 /home/user/new_folder/
omero transfer pack --binaries all Dataset:1111 /home/user/new_folder/new_pack.tar
```

## `omero transfer prepare`
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