CV title

[floradanna]

Describe the bug When creating a new sample_controlled_vocabs (in both Template and Sample Type), if I give an existing CV title SEEK gives warning error, since CV titles must be unique and no duplicates are allowed. However, if I look at the list of existing CV titles I see many duplicates (e.g., library source is listed 4 times at least).

To Reproduce See screenshot below and then:

1. Go to Create --> Template or Sample type
2. Click on Attribute Type --> Controlled Vocabulary or Ontology --> use dropdown to see the existing ones
3. Scroll down and see titles such as "library source" listed multiple times.

This is in contrast with the following error:

Expected behavior Consistent behaviour, although I don't know yet what that would be. To be discussed.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]

Additional context In DataHub, the same attribute (like, library source) with the same CV list (titled library source as well) will be "used" many many times by derived templates (via Create Template based on existing templates) and derived sample types (via applying the same template to many studies or assays). So, I think this is what it is causing having repeated CV list titles in the dropdown menu. However, this is in contrast with default SEEK rule that prohibits having repetition of the same title in CV list.

Questions:

• does SEEK only check if the CV title exist, independently of the listed terms being identical or different? probably, yes.
• should the content of the list be checked?
• is this a big limit for users since all CV lists are listed together, meaning CV lists created by anyone in any project at any point in time in a given SEEK instance?
• should lists be also restricted somehow (by project, by template...)?
• should lists make use of unique identifiers (seek ID) to check unicity?
• how does DataHub differentiate between Ontology and CV? Currently, the GUI to create an Ontology list is identical to the one for creating a CV list.
• It might be necessary now to define what's an Ontology list vs a CV list
  • Ontology list:
    • only one root ontology term and all children are fetched
    • no editing allow (no deletion, no addition of free terms)
    • Ontology list take the name of the root term as title
  • CV list:
    • no direct fetching of ontology terms from OLS (but still possible to paste URL to a ontology term)
    • possibility to add, delete, edit terms
    • free text for CV list title

[floradanna]

@rabuono something to figure out

[floradanna]

• [ ] Add sharing permission to CV list: by default the same as the Sample type that uses it (sharing permission for Sample type are still to be implemented).

• [ ] Keep possibility

  • to add terms to the CV list via Edit ISA study and Edit ISA Assay (even if samples exist)
  • to delete terms from the CV list if the terms are not already used

• [ ] hide dropdown for CV

[kdp-cloud]

Requirements: https://docs.google.com/document/d/1h_LEL8keDyKrnUJRVyuZUjE-xSRap1_yf9xDTkrJKGc/edit