omero-cli-transfer

An OMERO CLI plugin for creating and using transfer packets between OMERO servers.

Transfer packets contain objects and annotations. This project creates a zip file from an object (Project, Dataset, Image, Screen, Plate) containing all original files necessary to create the images in that object, plus an XML file detailing the links between entities, annotations and ROIs thereof.

The CLI plugin add the subcommand transfer, which in its turn has two further subcommands omero transfer pack and omero transfer unpack. Both subcommands (pack and unpack) will use an existing OMERO session created via CLI or prompt the user for parameters to create one.

Installation

tl;dr: if you have python>=3.7, a simple pip install omero-cli-transfer might do. We recommend conda, though.

omero-cli-transfer requires at least Python 3.7. This is due to ome-types requiring that as well; this package relies heavily on it, and it is not feasible without it.

Of course, this CAN be an issue, especially given omero-py officially only supports Python 3.6. However, it is possible to run omero-py in Python 3.7 or newer as well. Our recommended way to do so it using conda. With conda installed, you can do

conda create -n myenv -c ome python=3.7 zeroc-ice36-python
conda activate myenv
pip install omero-cli-transfer

It is possible to do the same thing without conda as long as your python/pip version is at least 3.7, but that will require locally building a wheel for zeroc-ice (which pip does automatically) - it is a process that can be anything from "completely seamless and without issues" to "I need to install every dependency ever imagined". Try at your own risk.

Usage

omero transfer pack

Creates a transfer packet for moving objects between OMERO server instances.

The syntax for specifying objects is: : where can be Image, Project or Dataset. Project is assumed if : is omitted. A file path needs to be provided; a tar file with the contents of the packet will be created at the specified path.

Currently, only MapAnnotations, Tags, FileAnnotations and CommentAnnotations are packaged into the transfer pack, and only Point, Line, Ellipse, Rectangle and Polygon-type ROIs are packaged.

--zip packs the object into a compressed zip file rather than a tarball.

--barchive creates a package compliant with Bioimage Archive submission standards - see below for more detail.

Examples:

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

omero transfer unpack

Unpacks an existing transfer packet, imports images as orphans and uses the XML contained in the transfer packet to re-create links, annotations and ROIs.

--ln_s forces imports to use the transfer=ln_s option, in-place importing files. Same restrictions of regular in-place imports apply.

--output allows for specifying an optional output folder where the packet will be unzipped.

--folder allows the user to point to a previously-unpacked folder rather than a single file.

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/

Bioimage Archive submission contents

• Folder structure in the generated zip/tar follows project/dataset structure rather than original ManagedRepository folder structure, and instead of a transfer.xml file, a submission.tsv file is generated.

• submission.tsv file has:

  • one line per file being submitted, between Image files and FileAnnotation files;
  • a column indicating whether that file was originally an Image or FileAnnotation;
  • a "comment" column if any Image has a CommentAnnotation;
  • a column per key in a MapAnnotation inside the pack, with an empty value for all images but the ones with a MapAnnotation with that key; for those images, it has the value for that annotation;
  • a final original_omero_ids column listing all OMERO IDs associated to that file in the origin server: for images, that is all Image IDs that use that file, and for file annotations that is all Image IDs that had that FileAnnotation attached to them.