Populate Metadata guide #13
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| **omero-metadata plugin installation** | ||
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| For the best experience, the ``omero-metadata`` plugin should be installed on your OMERO.server. The ``Populate Metadata`` script tries to reuse the code of the ``omero-metadata`` plugin. If the plugin is not found on the server, the ``Populate Metadata`` script falls back on a deprecated code, with limited set of features. The ``omero-metadata`` plugin installation is typically done by the administrator of the OMERO.server. |
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Do you reckon this should be compulsory in the OMERO.server installation instructions?
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fmpov, clear Yes. My main motivation for the Yes is the recent constant stream of external users (on the level of OMERO admins, facility managers etc.) who would like to have the plugin&script as ready as possible for their basic users to handle their metadata.
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The ansible role installs the omero-server python package (not the same as OMERO.server)
https://github.com/ome/ansible-role-omero-server/blob/5bce48f0e238ebd4b37fd1dc1f4483f3fe76acde/defaults/main.yml#L113
which has these compulsory dependencies:
https://github.com/ome/omero-cli-server/blob/e65c0d60a6c6e892fab8533eabb067c770077503/setup.py#L51-L56
You could add open a PR to add it there and see what everyone else thinks?
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@manics Opened ome/omero-cli-server#5
docs/metadata-ui.rst
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| #. Select the Dataset you created and attached to it the CSV. Find the script icon |image6| above the central pane, expand it and find the ``Import scripts`` section. In there, select the ``Populate metadata`` script. |
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Maybe remove "and attached to it the CSV" since that was optional.
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Perhaps make the last sentence longer: "In there, select the Populate metadata script, which will launch the script dialog". Then, when you mention the Browse button in the next sentence, we know where that is.
docs/metadata-ui.rst
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| #. If you did not attach the CSV to the Dataset, you can now click on the ``Browse`` button and select the CSV from your local machine. | ||
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| #. Run the script. |
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"Click OK to run the script, and wait for it to show as complete in the 'Activities' panel". (or something like that)
docs/metadata-ui.rst
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| - Data: example images from | ||
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| - IDR data `idr0021-lawo-pericentriolarmaterial/experimentA <https://idr.openmicroscopy.org/webclient/?show=project-51>`_ |
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Do we really need these images? Any images will do, right? (you ask the user to rename them anyway). If the user thinks they have to download IDR data, this could slow them down or block them.
docs/metadata-ui.rst
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| #. Click on single images inside the Dataset and observe that in the "Tables" harmonica in the right-hand pane there are new values coming originally from your edited CSV. |
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Uppercase "Images" is better. (few other places too).
docs/metadata-ui.rst
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| #. Select the Screen you identified above and (optionally) attached to it the CSV. Find the script icon |image6| above the central pane, expand it and find the ``Import scripts`` section. In there, select the ``Populate metadata`` script. |
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Again, although you have 'optionally' here, you can still simplify by removing "and (optionally) attached to it the CSV". You only have the 1 Screen.
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| **b**: BoolColumn, for true/false | ||
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| **plate, well, image, dataset, roi**: to specify objects |
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specify objects by name? (or is ID used for roi?)
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Ah, I see you specify this is 'Name' below, so can ignore above comment.
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Thanks - all points have been addressed. LGTM for me 👍 |
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Thanks @will-moore . Merging. |
Motivated by the interest in this workflow and #12, this PR is adding a new, completely UI-oriented chapter to the guide, with a separate sub-section specifically on SPW.
To test:
cc @jburel @will-moore @sbesson @manics