Add Sample IDs to the dynamic table and exported table

[rabuono]

• [ ] Add output/current Assay/child Sample ID to the dynamic table
• [x] Add Input Sample ID to the dynamic table
• [x] Add Input Sample ID as a new column in the exported table

[rabuono]

This will help with a few scenarios, including the following:

• In DataHub, Assay A with two samples named S1 and S1 (same name, different samples)
• In DataHub, Assay B
  • Input “S1” --> Output “S1a”
• User download Assay B table to fill in the table with a new sample

Table: Assay B table contains

• Output ID = ID_S1a123 (the user has never seen this before)
• Input ID = ID_S123 (the user has never seen this before)
• Input name = S1
• [N attributes describing S1a] = xxx
• Output name = S1a

User:

• wonders what Output ID = ID_S1a123 is and ignores it
• wonders what Input ID = ID_S123 is and ignores it
• Under Input name, the user adds “S1”
• Fills in N attributes describing the new sample
• Under Output name, the user add “S1b”
• Copy-paste the new row of the table into DataHub dynamic table

DataHub

• Checks the value for Output ID = EMPTY —> create new sample
  • assign Output ID = XX when user hits SAVE
  • assign Output name = S1b when user hits SAVE
• Checks the value for Input name = S1, search for input sample name = S1 and finds 2 samples with the same name
  • —> ERROR. Asks the user to choose between “S1 with ID_S123” and “S1 with ID_S145” as input
• User checks the downloaded table and choose “S1 with ID_S123”

[floradanna]

Before any development can be done, there is some GUI to be defined.

1) in the dynamic table, multiple inputs get all listed in the same column as coma separated values. How do we envision the visualisation of ID for these inputs?

Having the IDs all listed as coma separated values in a separated column might not improve clarity for the users.

[floradanna]

Features of the exported/imported excel sheet:

• Headers contain controlled vocabulary (as dropdown); users can only choose from the listed terms.
• ID column is locked and cannot be edited by users (it can begin copied though)
• All samples in the sample type will be exported (for now). See issue #1422 for improved feature.
• Export/Import for editing and creating samples is only allowed for each single sample type, not for the overview table

[rabuono]

Short update on the testing:

• [x] Currently, the downloaded spreadsheet has many blank values in the dropdown for ontology. GIF below

• [x] The Sources Table (and likely Samples table and Assay tables) display FAIRDOM-SEEK id and uuid of Samples that the User should not have access to.
• [x] The downloaded spreadsheet contains Samples that the User downloading it shouldn't have access to. Alice is added to the Project and makes Sample 5 (yellow). Alice changed the Sample sharing permissions so that it is only visible to Project members. Rafael is not part of the Project, but has access to Samples 1 through 4 (but not 5). Sources Table has expected behavior below for values about Sample 5, but should not be displaying FAIRDOM-SEEK id nor uuid for Sample 5 (as Rafael does not have access to it). The downloaded spreadsheet contains information on Sample 5, but should contain no mention to Sample 5 at all, as Rafael has no access to Sample 5.

[rabuono]

Best might be to substitute MANDATORY with REQUIRED to keep consistency with vocabulary used in FAIRDOM-SEEK

[floradanna]

Visualisation:

• In excel, list of inputs is visualised as [{"id"=>24, "title"=>"Sample 1"}, {"id"=>25, "title"=>"Sample 2"}]. Users must follow this syntax to update/make samples link via excel.
• In dynamic table, in "Input" attribute, the sample name is shown (sample ID could be shown when hovering over it and in dropdown list)
• when uploading the excel to the assay
  • SEEK check user's sample permissions --> list samples that cannot be edited by the user because the user has no managing permission on those samples
  • provide overview of the changes that the user is about to make and provide option for deleting each sample in case user doesn't want to continue with those changes
  • for newly created samples, the user is then redirect to batch sharing permission page to apply sharing permission to the new samples