Note
This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.
The CLI import options -d or -r can be used to specify, respectively, the import target Dataset or Screen by ID. The option -T, --target adds more ways of specifying the import target.
The general form of the target argument is:
<action or Class>[:<discriminator>]:<pattern>
where the discriminator is optional. Thus a target must contain one or two colons. Any further colons will be read as part of the pattern. If the discriminator is omitted a default will be used depending on the action or Class. Currently the following actions and classes are supported: Dataset, Screen and regex.
For Dataset and Screen the currently supported discriminators are name and id. If the discriminator is omitted the default used is id. So:
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:id:2
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:2
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -d 2
will all have the same effect of importing the image to the Dataset with ID 2.
The name discriminator can be used to select the target by name, and so:
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:name:Sample01
will import the image to the Dataset with name Sample01. If more than one Dataset exists with the specified name the most recently created will be used. If no Dataset exists with the specified name a new Dataset will be created for the import.
The choice of Dataset can be specified by adding a qualifying character to the discriminator: + to use the most recent, - to use the oldest, % to only import if there is a unique target or @ to create a new container even if one with the correct name already exists.
For example:
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:+name:Samples
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:-name:Samples
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:%name:Samples
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:@name:Samples
The first case is equivalent to the previous example, the most recent Dataset will be used. In the second case the oldest Dataset will be used. In the third case the import should fail if multiple datasets with that name exist. In the first three cases a new Dataset will be created if none exists. In the last case a new Dataset should be created even if one or more already exist.
If the name contains spaces or other characters that cannot be used on the command line the pattern should be enclosed in quotes:
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:name:"New Dataset"
To import a plate to a Screen target the same syntax can be used as in all the examples above, for example:
$ bin/omero import ~/images/bd-pathway/2015-12-01_000/ -T Screen:+name:Pathway
The local path of the file to be imported can be used to specify the target Dataset or Screen using a regular expression using the action regex. For this action the only discriminator is name and if the discriminator is omitted the qualified form of this +name will be used. The sequence (?<Container1>.*?) is a named-capturing group used to specify the Dataset or Screen name in the regular expression, the specific name Container1 must be used here. For example:
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T "regex:^.*images/(?<Container1>.*?)"
would use a Dataset with name being the path following images/, in this case dv.
The name discriminator can be explicitly used and, as in the previous section, also qualified:
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T "regex:+name:^.*images/(?<Container1>.*?)"
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T "regex:-name:^.*images/(?<Container1>.*?)"
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T "regex:%name:^.*images/(?<Container1>.*?)"
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T "regex:@name:^.*images/(?<Container1>.*?)"
These each work in the same way as the previous Dataset examples.
In some cases the importable files may be in nested directories, this is often the case with plates and some multi-image formats. A regular expression can be used to pick a higher level directory as the Screen or Dataset name. For example, if several BD Pathway HCS files are under the following paths:
~/images/bd-pathway/week-1/2015-12-01_000/
~/images/bd-pathway/week-2/2015-12-09_000/
~/images/bd-pathway/week-2/2015-12-11_000/
and the intended Screens for the import are week-1 and week-2 then the following could be used:
$ bin/omero import ~/images/bd-pathway/ -T "regex:+name:^.*bd-pathway/(?<Container1>[^/]*)/.*"
which would import one Plate into the Screen week-1 and two Plates into the Screen week-2, creating those Screens if necessary.
A useful way of determining the nested structure to help in constructing regular expressions is the option -f which displays the used files but does not import them:
$ bin/omero import -f ~/images/bd-pathway/week-1
...
2016-03-30 15:58:56,574 701 [ main] INFO ome.formats.importer.ImportCandidates - 59 file(s) parsed into 1 group(s) with 1 call(s) to setId in 92ms. (99ms total) [0 unknowns]
#======================================
# Group: /Users/colin/images/bd-pathway/week-1/2009-05-01_000/Experiment.exp SPW: true Reader: loci.formats.in.BDReader
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/Experiment.exp
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/20X NA 075 Olympus Confocal.geo
...
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/Well D11/DsRed - Confocal - n000000.tif
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/Well D11/DsRed - Confocal - n000001.tif
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/Well D11/DsRed - Confocal - n000002.tif
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/Well D11/Transmitted Light - n000000.tif
which shows that all the files for one particular Plate from the example above are under:
/Users/colin/images/bd-pathway/week-1/2009-05-01_000/
For more information on the regular expression syntax that can be used in templates see: java.util.regex.Pattern documentation.
Currently, in all the above cases the import target must be in the user’s current group for the import to succeed. It is hoped that this limitation can be removed in a later version of OMERO. This is also pertinent if the target is likely to be created as it will be created in the current group, which may not be the group intended.
If no group is specified by using the -g login option as part of the import, the current group will be dependent on the user’s login status:
If the user knows which group the import target is in, or needs to be created in, then one of the following methods can be used to ensure the target group is the current group for the import:
Explicitly log in using the -g login option before running the import command:
$ bin/omero login -g group_name
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:2
Provide the -g login option as part of the import command:
$ bin/omero import -g group_name ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:2
Use omero sessions group to switch group before running the import command:
$ bin/omero sessions group 51
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:2
Use the -k login option to reconnect to an active session for the target group:
$ bin/omero login -k c41a6f78-ba6e-4caf-aba3-a94378d5484c
$ bin/omero import ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:2
# or alternatively
$ bin/omero import -k c41a6f78-ba6e-4caf-aba3-a94378d5484c ~/images/dv/SMN10ul03_R3D_D3D.dv -T Dataset:2
The session ID can be found using the omero sessions list command.
For further information on the commands omero login and omero sessions see Manage sessions.
Note
The -g login option requires the group name as its argument, while the omero sessions group subcommand uses either the group ID or the group name.