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New Tools: OMERO get and OMERO filter using ezomero #61

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merged 33 commits into from
Oct 22, 2024

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rmassei
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@rmassei rmassei commented Oct 11, 2024

New tools

  • OMERO get - Tool to fetch project, dataset, images and ROIs IDs from a user defined OMERO.server. Additionally, this tool fetch attachments and tables linked to an Image
  • OMERO filter - Tool to filter images IDs by filename, Key-Value Pairs and Tag value. IDs are a list of image IDs which can be fetched using the omero_get tool.
    Both output are .tsv file with the get/filtered IDs.

Additionally, the cr/ci pipeline was updated to enrich the OMERO dummy set. A tag value is added to an image to test the OMERO filter tool.

UPDATE - omero.get was splitted in 2 tools (rmassei#3):
omero_get_id -> fetch project, dataset, images, annotations, tags, table and ROIs IDs
omero_get_value -> Tool to fetch Annotation, Tag and Tables from IDs.

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rmassei commented Oct 11, 2024

@lldelisle what do you think about it?

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@bernt-matthias bernt-matthias left a comment

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Great additions. Added some suggestions.

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This is great, here are more comments. And I will try the get with my instance because I am not sure I understand what it does.

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I am working on a PR to your branch for omero_get

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Please check rmassei#3

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rmassei commented Oct 16, 2024

@bernt-matthias we just need to create the macro for username and password and then we should be trought :)

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Good to go @rmassei and @lldelisle ?

@bernt-matthias bernt-matthias merged commit 19d84fd into Helmholtz-UFZ:main Oct 22, 2024
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3 participants