Repository management

Since 5.0.3 it is possible to list images, filesets and the repositories that contain them. At an administrator-only level it is also possible to move filesets. This functionality is provided by the omero fs command. See

$ omero fs -h

Listing repositories

The omero fs repos subcommand lists the repositories used by OMERO. For example

omero fs repos

 # | Id | UUID                                 | Type    | Path
---+----+--------------------------------------+---------+--------------------------
 0 | 1  | 83bf5c68-8236-47ff-ae3e-728674eb0103 | Managed | /OMERO/ManagedRepository
 1 | 2  | ad899754-bff0-4605-a234-acd4da178f3b | Public  | /OMERO
 2 | 3  | ScriptRepo                           | Script  | /dist/lib/scripts

The options available to this subcommand are:

-h, --help

Display the help for this subcommand.

--style {plain,csv,json,sql}

This option determines the output style, tabular sql being the default as in the previous example. The csv style is comma-separated values with an initial header row, plain is the same as csv but without the header row. json returns an array of JSON objects that can be piped to other tools.

--managed

This option lists only Managed repositories.

For example

omero fs repos --managed --style=csv

#,Id,UUID,Type,Path
0,1,83bf5c68-8236-47ff-ae3e-728674eb0103,Managed,/OMERO/ManagedRepository

Listing filesets

The omero fs sets subcommand lists filesets by various criteria. Filesets are bundles of original data imported into OMERO 5 and above, which represent one or more images. For example

omero fs sets

 #  | Id    | Prefix                            | Images | Files | Transfer
----+-------+-----------------------------------+--------+-------+----------
 0  | 79853 | user-3_9/2014-07/22/16-41-04.244/ | 1      | 1     |
 1  | 79852 | user-3_9/2014-07/22/10-44-11.235/ | 1      | 1     |
 2  | 79851 | user-3_9/2014-07/22/10-44-07.300/ | 1      | 1     |
 3  | 79813 | user-3_9/2014-07/21/14-13-02.353/ | 1      | 1     |
 4  | 79812 | user-3_9/2014-07/21/14-13-00.182/ | 1      | 1     |
 5  | 79811 | user-3_9/2014-07/21/14-12-59.212/ | 1      | 1     |
 6  | 79810 | user-3_9/2014-07/21/14-12-57.896/ | 1      | 1     |
 7  | 79809 | user-3_9/2014-07/21/14-10-22.436/ | 3      | 600   |
 ...
 24 | 79772 | user-4_5/2014-07/18/17-14-43.631/ | 1      | 1     |
(25 rows, starting at 0 of approx. 50173)

The options available to this subcommand are:

-h, --help

Display the help for this subcommand.

--style {plain,csv,json,sql}

See omero fs repos --style.

--limit LIMIT

This option specifies the maximum number of return values, the default is 25.

--offset OFFSET

This option specifies the number of entries to skip before starting the listing, the default, 0, is to skip no entries.

--order {newest,oldest,prefix}

This option determines the order of the rows returned, newest is the default.

--without-images

This option lists only those filesets without images, these may be corrupted filesets.

--with-transfer WITH_TRANSFER [WITH_TRANSFER ...]

This option lists only those filesets imported using the given in-place import methods.

--check

This option checks each fileset for validity by recalculating each file’s checksum and comparing it with the checksum recorded upon import. This may be slow. This option is available to administrators only.

--extended

With this option more details are provided for each returned value. This may be slow.

For example

omero fs sets --order oldest --limit 3 --offset 5 --check

 # | Id | Prefix                            | Images | Files | Transfer | Check
---+----+-----------------------------------+--------+-------+----------+-------
 0 | 54 | user-3_9/2014-06/09/09-24-28.037/ | 1      | 1     |          | OK
 1 | 55 | user-3_9/2014-06/09/09-24-31.354/ | 1      | 1     |          | OK
 2 | 57 | user-5_4/2014-06/09/11-01-00.557/ | 1      | 1     |          | OK
(3 rows, starting at 5 of approx. 78415)

Listing images

The omero fs images subcommand lists imported images by various criteria. This subcommand is useful for showing pre-FS (i.e. OMERO 4.4 and before) images which have their original data archived with them. For example

omero fs images

 #  | Image  | Name                              | FS    | # Files | Size
----+--------+-----------------------------------+-------+---------+----------
 0  | 102803 | kidney_TFl_1.bmp.ome.tiff         | 79853 | 1       | 435.1 KB
 1  | 102802 | 4kx4k.jpg                         | 79852 | 1       | 1.7 MB
 2  | 102801 | 2kx2k.jpg                         | 79851 | 1       | 486.3 KB
 3  | 102773 | multi-channel.ome.tif             | 79813 | 1       | 220.3 KB
 4  | 102772 | multi-channel-z-series.ome.tif    | 79812 | 1       | 1.1 MB
 5  | 102771 | multi-channel-time-series.ome.tif | 79811 | 1       | 1.5 MB
 6  | 102770 | multi-channel-4D-series.ome.tif   | 79810 | 1       | 7.4 MB
 7  | 102769 | 001_001_000_000.tif [Well B6]     | 79809 | 600     | 1.1 GB
...
 24 | 102732 | 00027841.png                      | 79774 | 1       | 235 B
(25 rows, starting at 0 of approx. 117393)

The options available to this subcommand are:

-h, --help

Display the help for this subcommand.

--style {plain,csv,json,sql}

See omero fs repos --style.

--limit LIMIT

See omero fs sets --limit.

--offset OFFSET

See omero fs sets --offset.

--order {newest,oldest,prefix}

See omero fs sets --order.

--archived

With this option the subcommand lists only images with archived data.

--extended

With this option more details are provided for each returned value. This may be slow.

For example

omero fs images --archived --offset 16 --limit 3

 # | Image | Name                      | FS | # Files | Size
---+-------+---------------------------+----+---------+---------
 0 | 15481 | UMD001_ORO.svs [Series 1] |    | 1       | 12.7 MB
 1 | 15478 | biosamplefullframetif.tif |    | 1       | 32.0 MB
 2 | 10018 | 050118.lei [07-13-a]      |    | 4       | 4.8 MB
(3 rows, starting at 16 of approx. 833)

Renaming filesets

The omero fs rename subcommand moves an existing fileset, specified by its ID, to a new location. This subcommand is available to administrators only.

It may be useful to rename an existing fileset after the import template (omero.fs.repo.path) has been changed to match the new template. By default the files in the fileset and the accompanying import log are moved. For example, after adding the group name and group ID to template and changing the date format

$ omero fs rename 9

Renaming Fileset:9 to pg-0_3/user-0_2/2014-07-23/16-48-20.786/
Moving user-0_2/2014-07/23/16-31-51.070/ to pg-0_3/user-0_2/2014-07-23/16-48-20.786/
Moving user-0_2/2014-07/23/16-31-51.070.log to pg-0_3/user-0_2/2014-07-23/16-48-20.786.log

The ID can be given as a number or in the form Fileset:ID.

The options available to this subcommand are:

-h, --help

Display the help for this subcommand.

--no-move

With this option the files will be left in place to be moved later. Advice will be given as to which files need to be moved to complete the renaming process. Note that if the files are not moved then the renamed filesets will not be accessible until the files have been moved into the new positions.

For example

$ omero fs rename Fileset:8 --no-move

Renaming Fileset:8 to pg-0_3/user-0_2/2014-07-23/16-49-23.543/
Done. You will now need to move these files manually:
-----------------------------------------------------
mv /OMERO/ManagedRepository/user-0_2/2014-07/23/16-29-14.809/ /OMERO/ManagedRepository/pg-0_3/user-0_2/2014-07-23/16-49-23.543/
mv /OMERO/ManagedRepository/user-0_2/2014-07/23/16-29-14.809.log /OMERO/ManagedRepository/pg-0_3/user-0_2/2014-07-23/16-49-23.543.log

Note

The omero fs rename subcommand is currently disabled pending a bug-fix.

Detailing disk usage

The omero fs usage subcommand provides details of the underlying disk usage for various types of objects. This subcommand takes optional positional arguments of object types with ids and returns the total disk usage of the specified objects.

For example

omero fs usage Image:30001,30051 Plate:1051 --report

Total disk usage: 1064320138 bytes in 436 files
 component    | size (bytes) | files
--------------+--------------+-------
 Thumbnail    | 582030       | 256
 Job          | 1772525      | 2
 Pixels       | 49545216     | 12
 FilesetEntry | 1011947729   | 124
 Annotation   | 472638       | 42
(5 rows)

If no positional argument is given then the total usage for the current user across all of that user’s groups is returned.

For example

omero fs usage --report

Total disk usage: 4526436430274 bytes in 26078 files
 component    | size (bytes)  | files
--------------+---------------+-------
 Pixels       | 14654902013   | 2961
 FilesetEntry | 4510839804505 | 8820
 Thumbnail    | 17337131      | 8110
 Job          | 265665153     | 2792
 OriginalFile | 1757277       | 109
 Annotation   | 13167582976   | 3910
(6 rows)

If multiple objects are given and those objects contain common data then that usage will not be counted twice. For example, if two datasets contain the same image then the fileset for that image will not be double-counted in the total disk usage.

The options available to this subcommand are:

-h, --help

Display the help for this subcommand.

--style {plain,csv,json,sql}

See omero fs repos --style.

--wait WAIT

Number of seconds to wait for the processing to complete. To wait indefinitely use < 0, for no wait use 0. The default is to wait indefinitely.

--size_only

Print total bytes used, in bytes, with no extra text, this is useful for automated scripting.

--report

Print detailed breakdown of disk usage by types of files. This option is ignored if –size_only is used.

--units {K,M,G,T,P}

Units to use for disk usage for the total size using base-2. The default is bytes.

--groups

Print size for all of the current user’s groups, this includes the user’s own data and the data of other group members visible to the user. This option only applies if no positional arguments are given.

For example

omero fs usage --groups --size_only -C -u user-1

4576108188820


omero fs usage Project:1,2 Dataset:5 --units M --report

Total disk usage: 1432 MiB in 121 files
 component  | size (bytes) | files
------------+--------------+-------
 Thumbnail  | 73710        | 34
 Pixels     | 1499341282   | 34
 Annotation | 3000028      | 53
(3 rows)

Creating directories

For directory creation in a Managed repository use omero fs mkdir: this creates both the directory on the underlying filesystem and the corresponding entry in the OMERO server’s database. The new directory will be owned by the root user and in the user group. The options available to this subcommand are:

-h, --help

Display the help for this subcommand.

--parents

Ensure that the whole given path exists in the Managed repository. Analogous to the common mkdir’s --parents option, originally simply -p in IEEE Std 1003.1-2008.