Conversation
Contributor
Author
|
@chris-s-friedman Can you test this reimplemented delete function to see if it runs better? |
chris-s-friedman
left a comment
Contributor
There was a problem hiding this comment.
i had an issue where it stopped deleting things after 248 sequencing experiments got deleted
| delete_kfids(host, STUDIES, [study_id], safety_check=safety_check) | ||
| ) | ||
| kfids = yield_kfids(host, endpoint, {"study_id": study_id}) | ||
| delete_kfids(host, kfids, safety_check=safety_check) |
Contributor
There was a problem hiding this comment.
delete_kfids prints how many things are being deleted at the current endpoint. there should be a statement before deleting printing what endpoint is currently being deleted e.g:
Suggested change
| delete_kfids(host, kfids, safety_check=safety_check) | |
| print(f"Deleting kfids from {endpoint}.") | |
| delete_kfids(host, kfids, safety_check=safety_check) |
Otherwise it's not clear where in the process of deleting the script is.
7c15130 to
f030fa6
Compare
chris-s-friedman
left a comment
Contributor
There was a problem hiding this comment.
I'm still getting an issue where delete_kfids gets to the 248th item and then stops.
Comment on lines
+107
to
+110
| print(f"Finding all {endpoint}.") | ||
| kfids = yield_kfids(host, endpoint, {}, show_progress=True) | ||
| print(f"Deleting all {endpoint}.") | ||
| delete_kfids(host, kfids, safety_check=safety_check) |
Contributor
There was a problem hiding this comment.
I'm now getting
Deleting all studies from http://localhost:5000
Finding all read-groups.
Deleting all read-groups.
oFinding all read-group-genomic-files.
Deleting all read-group-genomic-files.
oFinding all sequencing-experiments.
Deleting all sequencing-experiments.
oFinding all sequencing-experiment-genomic-files.
Deleting all sequencing-experiment-genomic-files.
oFinding all genomic-files.
Deleting all genomic-files.
i'm thinking that leading o is printed from delete_kfids?
maybe something like below so that we don't try to delete nothing?
Suggested change
| print(f"Finding all {endpoint}.") | |
| kfids = yield_kfids(host, endpoint, {}, show_progress=True) | |
| print(f"Deleting all {endpoint}.") | |
| delete_kfids(host, kfids, safety_check=safety_check) | |
| print(f"Finding all {endpoint}.") | |
| kfids = yield_kfids(host, endpoint, {}, show_progress=True) | |
| if len(kfids) > 0: | |
| print(f"Deleting all {endpoint}.") | |
| delete_kfids(host, kfids, safety_check=safety_check) | |
| else: | |
| print(f"Nothing found at {endpoint}.") |
Contributor
Author
There was a problem hiding this comment.
ok try again. you'll have to install dependencies again because I added a new one for cleaner scraping progress display
0d8a35b to
07f25e0
Compare
fiendish
added a commit
that referenced
this pull request
Jun 18, 2021
## Release 0.4.0 ### Summary - Emojis: ♻️ x1, ⚡ x2, ✅ x1, 🧐 x1, ✨ x2 - Categories: Additions x2, Other Changes x5 ### New features and changes - [#36](#36) - ⚡♻️ Consolidate and speed up delete method - [089b62f](089b62f) by [fiendish](https://github.com/fiendish) - [#35](#35) - ✅ Reduce size of some tests - [b143fd9](b143fd9) by [fiendish](https://github.com/fiendish) - [#34](#34) - ⚡ Only patch descendant visibility if needed (also adds dry_run) - [196ee2b](196ee2b) by [fiendish](https://github.com/fiendish) - [#33](#33) - 🧐 Populate starting entities in descendant tree - [a696fc5](a696fc5) by [fiendish](https://github.com/fiendish) - [#32](#32) - ✨ Add whole entity hiding function to only hide visible entities - [77bc428](77bc428) by [fiendish](https://github.com/fiendish) - [#31](#31) - ✨ Add yielding entity contents from kfids - [7420fa6](7420fa6) by [fiendish](https://github.com/fiendish)
Merged
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.