Release 2024.2.1

[ashsny]

I think the only problem here is that the backend portion hasn’t gone to staging yet because no one has approved the PR :)

On Sun, Jun 30, 2024 at 5:55 PM EstelleDa @.***> wrote:

@.**** commented on this pull request.

In src/mavedb/routers/experiments.py https://github.com/VariantEffect/mavedb-api/pull/234#discussion_r1660348563 :

@@ -125,7 +125,7 @@ def get_experiment_score_sets( #

TODO(#182): A side effect of this implementation is that only the user who has created the experiment may view all the Score sets

associated with a given experiment. This could be solved with user impersonation for certain user roles.

• score_sets = db.query(ScoreSet).filter(ScoreSet.experiment_id == experiment.id)
• score_sets = db.query(ScoreSet).filter(ScoreSet.experiment_id == experiment.id).filter(~ScoreSet.superseding_score_set.has())

@afrubin https://github.com/afrubin The problem is both urn:mavedb:00000674-a-3 and urn:mavedb:00000674-a-4 replace urn:mavedb:00000674-a-1. It leads to the codes being confused. It should be only one superseded score set or do we allow multiple score sets replacing the same score set? I think we need to modify the data in database.

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[EstelleDa]

I think the only problem here is that the backend portion hasn’t gone to staging yet because no one has approved the PR :) … On Sun, Jun 30, 2024 at 5:55 PM EstelleDa @.> wrote: @*.*** commented on this pull request. ------------------------------ In src/mavedb/routers/experiments.py <#234 (comment)> : > @@ -125,7 +125,7 @@ def get_experiment_score_sets( # # TODO(#182): A side effect of this implementation is that only the user who has created the experiment may view all the Score sets # associated with a given experiment. This could be solved with user impersonation for certain user roles. - score_sets = db.query(ScoreSet).filter(ScoreSet.experiment_id == experiment.id) + score_sets = db.query(ScoreSet).filter(ScoreSet.experiment_id == experiment.id).filter(~ScoreSet.superseding_score_set.has()) @afrubin https://github.com/afrubin The problem is both urn:mavedb:00000674-a-3 and urn:mavedb:00000674-a-4 replace urn:mavedb:00000674-a-1. It leads to the codes being confused. It should be only one superseded score set or do we allow multiple score sets replacing the same score set? I think we need to modify the data in database. — Reply to this email directly, view it on GitHub <#234 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKTI3W4R7LGJPLA5ZCKU43ZKCSITAVCNFSM6AAAAABKCX6KQ6VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDCNJQGI2DGMRWHE . You are receiving this because you authored the thread.Message ID: @.>

lol~ Thanks Ashley. It makes sense for other score sets. I'll review it soon.

[EstelleDa]

I get error in /api/v1/publication-identifiers/search/{db_name}/{identifier} Testing identifier is 23376099 and db_name is PubMed. I think it links to search_publications_by_identifier_and_db, not the fetch_publication_by_dbname_and_identifier.

[EstelleDa]

@ashsny I created a pull request to solve the above problem and added you as the reviewer. Feel free to change the merged branch or do anything to it. It's based on release-2024.2.1. https://github.com/VariantEffect/mavedb-api/pull/236