Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

See if we can speed things up with ancpBIDS #8

Closed
3 tasks
surchs opened this issue Sep 6, 2022 · 8 comments
Closed
3 tasks

See if we can speed things up with ancpBIDS #8

surchs opened this issue Sep 6, 2022 · 8 comments
Labels
flag:discuss Flag issue that needs to be discussed before it can be implemented. _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again

Comments

@surchs
Copy link
Contributor

surchs commented Sep 6, 2022

Right now, parsing a large dataset takes an annoyingly long time. ancpBIDS is known to be faster. It should also support the core queries that we are interested in. So maybe we can remove the pyBIDS dependency, use ancpBIDS instead, and speed things up

  • take a look to see if we could use ancpBIDS instead of pyBIDS
  • migrate to ancpBIDS
  • make a speed comparison for a large dataset and then decide what to keep
@surchs surchs added this to Neurobagel Sep 6, 2022
@surchs surchs moved this to Inbox in Neurobagel Sep 6, 2022
@surchs surchs moved this from Inbox to Backlog in Neurobagel Sep 6, 2022
@stale
Copy link

stale bot commented Nov 29, 2022

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Nov 29, 2022
@stale stale bot closed this as completed Dec 6, 2022
Repository owner moved this from Backlog to Done in Neurobagel Dec 6, 2022
@surchs surchs reopened this Dec 6, 2022
Repository owner moved this from Done to Inbox in Neurobagel Dec 6, 2022
@stale stale bot removed the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Dec 6, 2022
@surchs surchs added feature:enhancement flag:discuss Flag issue that needs to be discussed before it can be implemented. and removed feature:enhancement labels Jan 3, 2023
@github-actions
Copy link

github-actions bot commented Feb 3, 2023

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 Feb 3, 2023
@surchs surchs moved this from Inbox to Backlog in Neurobagel Feb 3, 2023
@surchs
Copy link
Contributor Author

surchs commented Mar 21, 2023

I would close this issue. It makes sense, but I don't think we'll get to it anytime soon. What do you think @alyssadai? If you agree, feel free to just close

@surchs surchs removed the status in Neurobagel Mar 21, 2023
@alyssadai
Copy link
Contributor

@surchs I'm not super familiar with ancpBIDS, but I wonder if it'd be worth leaving this issue open at least until we've attempted to run the CLI on the PPMI and QPN datasets (which I think are a couple hundred subjects each)? I just did a quick search of "ancpBIDS" in the PyBIDS issues and based on this post/comment I suspect the long runtime might become an issue sooner than we think - it looks like it can take almost 6 min to validate a dataset of ~500 subjects. We can always just wait it out if that's the case, but I think at that point this issue might be worth revisiting, if only to figure out a game plan for the migration. Thoughts?

@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 Mar 22, 2023
@surchs
Copy link
Contributor Author

surchs commented Mar 22, 2023

I put it on the roadmap for "Next", we can move it up if it becomes a more pressing problem

@github-actions
Copy link

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 22, 2023
@surchs
Copy link
Contributor Author

surchs commented Jun 6, 2023

I'm closing this. It's stale, we may eventually do it, but right now it does not seem to be the priority.

@surchs surchs closed this as completed Jun 6, 2023
@github-project-automation github-project-automation bot moved this to Review - Done in Neurobagel Jun 6, 2023
@alyssadai
Copy link
Contributor

@surchs minor - but should we close as "not planned" instead?

@alyssadai alyssadai mentioned this issue Mar 18, 2024
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
flag:discuss Flag issue that needs to be discussed before it can be implemented. _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again
Projects
Neurobagel
Archived in project
Milestone
No milestone
Development

No branches or pull requests
2 participants
@surchs @alyssadai