.. _cli_omero_fs: 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 :omerocmd:`fs` command. See :: $ bin/omero fs -h Listing repositories ^^^^^^^^^^^^^^^^^^^^ The :omerocmd:`fs repos` subcommand lists the repositories used by OMERO. For example :: bin/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: .. program:: omero fs repos .. option:: -h, --help Display the help for this subcommand. .. option:: --style <{plain,csv,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. .. option:: --managed This option lists only Managed repositories. For example :: bin/omero fs repos --managed --style=csv #,Id,UUID,Type,Path 0,1,83bf5c68-8236-47ff-ae3e-728674eb0103,Managed,/OMERO/ManagedRepository Listing filesets ^^^^^^^^^^^^^^^^ The :omerocmd:`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 :: bin/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: .. program:: omero fs sets .. option:: -h, --help Display the help for this subcommand. .. option:: --style <{plain,csv,sql}> See :option:`omero fs repos --style`. .. option:: --limit This option specifies the maximum number of return values, the default is 25. .. option:: --offset This option specifies the number of entries to skip before starting the listing, the default, 0, is to skip no entries. .. option:: --order <{newest,oldest,prefix}> This option determines the order of the rows returned, `newest` is the default. .. option:: --without-images This option lists only those filesets without images, these may be corrupt filesets. .. option:: --with-transfer This option lists only those filesets imported using the given in-place import methods. .. option:: --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.** .. option:: --extended With this option more details are provided for each returned value. This may be slow. For example :: bin/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 :omerocmd:`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 :: bin/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: .. program:: omero fs images .. option:: -h, --help Display the help for this subcommand. .. option:: --style {plain,csv,sql} See :option:`omero fs repos --style`. .. option:: --limit See :option:`omero fs sets --limit`. .. option:: --offset See :option:`omero fs sets --offset` .. option:: --order <{newest,oldest,prefix}> See :option:`omero fs sets --order`. .. option:: --archived With this option the subcommand lists only images with archived data. .. option:: --extended With this option more details are provided for each returned value. This may be slow. For example :: bin/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 :omerocmd:`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 (:property:`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 chnaging the date format :: $ bin/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: .. program:: omero fs rename .. option:: -h, --help Display the help for this subcommand. .. option:: --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 :: $ bin/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 Detailing disk usage ^^^^^^^^^^^^^^^^^^^^ The :omerocmd:`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 :: bin/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 :: bin/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: .. program:: omero fs usage .. option:: -h, --help Display the help for this subcommand. .. option:: --style {plain,csv,sql} See :option:`omero fs repos --style`. .. option:: --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. .. option:: --size_only Print total bytes used, in bytes, with no extra text, this is useful for automated scripting. .. option:: --report Print detailed breakdown of disk usage by types of files. This option is ignored if `--size_only` is used. .. option:: --units {K,M,G,T,P} Units to use for disk usage for the total size using base-2. The default is bytes. .. option:: --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 :: bin/omero fs usage --groups --size_only -C -u user-1 4576108188820 bin/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)