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Readme update, test infra update (ome#86)
* updated test infra * readme updates
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.omero

README.md

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An OMERO CLI plugin for creating and using transfer packets between OMERO servers.
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Transfer packets contain objects and annotations. This project creates a zip file from an object
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Transfer packets contain objects and annotations. This project creates a single (zip, tar) file from an object
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(Project, Dataset, Image, Screen, Plate) containing all original files necessary to create the images
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in that object, plus an XML file detailing the links between entities, annotations and ROIs thereof.
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`omero-cli-transfer` requires at least Python 3.8. This is due to `ome-types` requiring that as well;
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this package relies heavily on it, and it is not feasible without it.
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Of course, this CAN be an issue, especially given `omero-py` _officially_ only supports Python 3.6. However,
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it is possible to run `omero-py` in Python 3.8 or newer as well. Our recommended way to do so it using `conda`.
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With conda installed, you can do
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```
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conda create -n myenv -c conda-forge python=3.8 zeroc-ice=3.6.5
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conda activate myenv
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pip install omero-cli-transfer
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```
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It is possible to do the same thing without `conda` as long as your python/pip version is at least 3.8,
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but that will require locally building a wheel for `zeroc-ice` (which pip does automatically) - it is a
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but that will require either installing a prebuilt wheel for `zeroc-ice` (Glencoe Software provides them [here](https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases) or locally building a wheel for `zeroc-ice` (which pip does automatically) - the latter is a
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process that can be anything from "completely seamless and without issues" to "I need to install every
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dependency ever imagined". Try at your own risk.
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The syntax for specifying objects is: `<object>:<id>` where `<object>` can be `Image`, `Project`, `Dataset`, `Plate` or `Screen`. `Project` is assumed if `<object>:` 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.
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Currently, only MapAnnotations, Tags, FileAnnotations and CommentAnnotations are packaged into the transfer pack. All kinds of ROI (except Masks) should work.
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If you would like to specify multiple objects, you can use the `<object>:<id1>-<id2>` for packing every object between `id1` and `id2`, or `<object>:<id1>,<id2>,<id3>` to pack only objects with ids `id1`, `id2` and `id3`.
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Note that, if you are packing a `Plate` or `Screen`, default OMERO settings prevent you from downloading Plates and you will generate an empty pack file if you do so. If you want to generate a pack file from these entities, you will need to set `omero.policy.binary_access` appropriately.
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Currently, only MapAnnotations, Tags, FileAnnotations, LongAnnotations (i.e. ratings) and CommentAnnotations are packaged into the transfer pack. All kinds of ROI (except Masks) should work.
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Note that, if you are packing a `Plate` or `Screen`, default OMERO settings prevent you from downloading Plates and you will get errors if you do so. If you want to generate a pack file from these entities, you will need to set `omero.policy.binary_access` appropriately.
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`--zip` packs the object into a compressed zip file rather than a tarball.
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file is created, in which case the last cli argument is the path where
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the `transfer.xml` file will be written.
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`--ignore_errors` gnores any download/export errors during the pack process,
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`--ignore_errors` ignores any download/export errors during the pack process,
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often the result of servers which do not allow Plate downloads (but will
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ignore any non-zero return code from `omero download` or `omero export`).
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Examples:
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```
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omero transfer pack Image:123 transfer_pack.tar
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omero transfer pack --zip Image:123 transfer_pack.zip
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omero transfer pack Dataset:1111 /home/user/new_folder/new_pack.tar
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omero transfer pack --zip Image:123-126 transfer_pack.zip
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omero transfer pack Dataset:1111,1115 /home/user/new_folder/new_pack.tar
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omero transfer pack 999 tarfile.tar # equivalent to Project:999
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omero transfer pack --plugin arc Project:999 path/to/my/arc/repo
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omero transfer pack --binaries none Dataset:1111 /home/user/new_folder/

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