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Create example phenotypic inputs for no-session-layer BIDS case #100

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alyssadai opened this issue Mar 15, 2023 · 4 comments
Open
2 tasks

Create example phenotypic inputs for no-session-layer BIDS case #100

alyssadai opened this issue Mar 15, 2023 · 4 comments
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good first issue Good issue for a new contributor. maint:coverage Test coverage improvements that were not included in feature prioritization type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs

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@alyssadai
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alyssadai commented Mar 15, 2023

At the moment, we have tests which check that:

  • A custom PhenotypicSession called ses-unnamed is created by the bagel pheno command when it receives a phenotypic TSV with missing session column values
  • A custom ImagingSession called ses-unnamed (that has pipeline metadata) is created by the bagel derivatives command when it receives a proc status TSV w/ missing session column values
  • The session file path stored by bagel bids for a BIDS subject missing a session layer points to the BIDS subject directory (i.e., instead of inserting a fake session directory layer)

What we don't have:

  • A test of the bagel bids command that checks that when a BIDS directory with no session layer is provided, the output JSONLD file contains at least one ImagingSession called ses-unnamed, where the file path for the session still points to the subject directory

This would test, explicitly, that ses-unnamed ImagingSessions are correctly created from BIDS datasets without sessions, and that the same sessions still have accurate paths to the data. At the moment, the combination of existing tests can be argued to test this implicitly.

To be able to create the above test, we would need:

  1. A BIDS dataset with no session layer (e.g., ds001 or eeg_ds000117 from `bids-examples)
  2. A custom phenotypic JSONLD to provide as input to bagel bids, that includes all subjects in the BIDS dataset above
  3. In order to generate 2., we would need to create:
    a. a new valid phenotypic TSV with all subjects in the missing-session-layer BIDS dataset
    b. a corresponding valid Neurobagel data dictionary JSON

Add to tests/data:

  • example_no_session.tsv
  • example_no_session.json
@alyssadai alyssadai added type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs maint:coverage Test coverage improvements that were not included in feature prioritization labels Mar 15, 2023
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@github-actions github-actions bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Apr 15, 2023
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@surchs surchs added good first issue Good issue for a new contributor. and removed _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again labels Dec 5, 2023
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days.
We have applied the _flag:stale label to indicate that this issue should be reviewed again.
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@github-actions github-actions bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Feb 19, 2024
@alyssadai
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@surchs I'm rereading this issue I created (quite a while ago) and would like a second opinion on whether this is still worth addressing.

What gives me pause is the potential overhead related to adding these new examples: we will either need a test that runs both the bagel pheno and bagel bids commands, which seems kind of complex, or a new example JSONLD corresponding to another bids-examples dataset (one missing sessions) that we will have to maintain.

Wdyt? Do you think the intended handling of missing sessions in BIDS data is sufficiently covered by existing tests?

@github-actions github-actions bot removed the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Oct 9, 2024
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Labels
good first issue Good issue for a new contributor. maint:coverage Test coverage improvements that were not included in feature prioritization type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs
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