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qbicsoftware / data-manager-app

A web-based life science omics and imaging data management solution
https://qbicsoftware.github.io/research-data-management
MIT License
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Link between Sample and Measurement metadata #788

Open oquendoM opened 1 month ago

oquendoM commented 1 month ago

What are you missing?

Link between the sample metadata and measurement metadata.

Why do you need a solution?

The user may want to get the measurement ID only for a subset of samples. If the filtering is depending on a biological parameter (analyte, treatment...) it is not possible. It is also difficult to visualize in the sample tab which samples already have data.

Ideas

I would go 2 ways:

  1. Add column "raw data available: yes/no" in the sample metadata
  2. Add the sample information in the measurement downloaded metadata after the measurement part. ngs_measurements_example.xlsx

Code of Conduct

sven1103 commented 4 weeks ago

Hi @oquendoM ,

thank you for your feedback!

I am unsure, what the user's goal is here. Can you elaborate? Why is only a subset of the measurement IDs relevant, based on what information?

Thanks, Sven

oquendoM commented 4 weeks ago

Hi,

Let's say a user submit RNA and DNA samples but only want to download the RNA samples. Or they have 4 conditions, but only want to download from 3 conditions. The reason to do that will vary from user to user. If I try to get the URL list, I cannot filter for any sample characteristic.

Best, Morgana

sven1103 commented 4 weeks ago

Hi @oquendoM ,

If I try to get the URL list, I cannot filter for any sample characteristic.

I think that coins it, right? Enable users to filter measurements based on sample properties?

sven1103 commented 4 weeks ago

Last question (hopefully :D):

Is it only relevant for the download of data, or to have an overview in general? I am trying to understand, for what reason(s) the measurement ID is of interest.

oquendoM commented 4 weeks ago

The measurement ID is indeed only interesting to the download portion in my opinion.

sven1103 commented 4 weeks ago

ok, and for the raw data availability, i would like to create an own issue, since it is independent from the download selection

sven1103 commented 3 weeks ago

So talking to @oquendoM, we confirmed that it is about an quick overview AND selection of datasets of interest based on their a) availability, b) sequencing run (future feature) and some c) sample properties.

@Steffengreiner or @Shraddha0903, we need to look into feasibility of this request and what the Vaadin framework is providing us.

@oquendoM also underlined, that the current Grid support for multi-select of items in a Grid is not very user-friendly. Based on a filtered request, can we have an easy select all, that applies to the filtered items?