Add metadata import section

[pwalczysko]

Adding metadata import section.

Possibly the order could be reversed, and possibly a new section showing how to create a quick and easy, simple bulkmap config could come in.

cc @francesw @manics @jburel

[manics]

It's not clear to me who this guide is targetted at:

• People using the outreach server during a workshop given by us?
• People using their own OMERO server?

[pwalczysko]

@manics

It's not clear to me who this guide is targetted at:

People using the outreach server during a workshop given by us?
People using their own OMERO server?

Both. We need simply both. And we do not have the margin to produce two parallel lines.
If you could specify the main unclear points (for potential users who are not within our workshop) ?

[manics]

I think you need to tell people how to obtain and import idr0021, otherwise they can't follow the guide on their own server. Alternatively you could write your own bulkmap-config.yml for a smaller dataset?

For example, https://omero-guides.readthedocs.io/en/latest/introduction/docs/annotate.html says

The data used are from the siRNAi-HeLa folder available at https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/

Perhaps you could annotate those images instead?

[manics]

pwalczysko#1 adds a simple-annotation-bulkmap-config.yml file corresponding to simple-annotation.csv

[pwalczysko]

@manics thank you for the simple-bulkmap-config.yml

After reading the description in the commit and the comments in the file itself, I have two questions.

Can we have the KVPs listed under the "Default namespace" organized in the "Others" header in the webclient ? What governs this ? @francesw was meaning that this might be the indentations of the blocks such as d9acb71#diff-e2d81d8cdbf9ac42c679d54ca6b0af06R51 (in her example these blocks had indentations, in yours d9acb71#diff-e2d81d8cdbf9ac42c679d54ca6b0af06R51 they are unindented. Is that the crucial point which decides about the "Others" header in webclient later ?

We do not have all the mapr categories defined in the outreach servers, and, somehow, the mapr on these servers does not seem to work for these newly added KVPs using the simple... csv and bulkmap files. Only the "old" annotated idr0021 seem to be handled correctly by mapr on outreach.

This (and also the fact that mapr is complex, needs an extra install, we do not have a walkthrough for it, etc.) leads me to another question:

Can I have a nice header like Phenotypes for my KVP group, but not have a mapr category defined ? (as you see, I would like to offer a step 1. no-mapr-yet and step 2. mapr-if-you-want approach).

[pwalczysko]

@manics Is this jinja magic d9acb71#diff-e2d81d8cdbf9ac42c679d54ca6b0af06R107 logic encoded in the omero metadata plugin ? This is a nice feature.

[pwalczysko]

Addressed the comments. Now we have two options, one using the IDR data, one using the siRNAi-HeLa data, which are easier to get.

[jburel]

maybe create a folder with the csv, yml files and not mix them with the .rst doc file

[manics]

Looks fine to me