Opened 14 years ago
Closed 14 years ago
#1232 closed enhancement (worksforme)
Long running getAllInheritedAnnotations query
| Reported by: | base | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | BASE 2.11 |
| Component: | core | Version: | |
| Keywords: | experiment overview inherited annotations query | Cc: |
Description
The query that retrieves all inherited (directly and indirectly) annotations for an annotation set is not efficient. It results in long waiting time for experiment overview and experiment re-validation. The issue and a simple fix is described in more detail here http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01650.html
Change History (7)
comment:1 Changed 14 years ago by
| Milestone: | → BASE 2.11 |
|---|
comment:2 Changed 14 years ago by
| Type: | defect → enhancement |
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comment:3 Changed 14 years ago by
| Owner: | changed from everyone to Martin Svensson |
|---|---|
| Status: | new → assigned |
comment:4 Changed 14 years ago by
| Owner: | changed from Martin Svensson to Nicklas Nordborg |
|---|---|
| Status: | assigned → new |
comment:5 Changed 14 years ago by
| Status: | new → assigned |
|---|
comment:6 Changed 14 years ago by
comment:7 Changed 14 years ago by
| Resolution: | → worksforme |
|---|---|
| Status: | assigned → closed |
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I am not able to reproduce this on either PostgreSQL 8.3.6 or MySQL 5.0.67. I have tested with an experiment that has 128 annotated raw bioassays on both databases. In both cases the getAllInheritedAnnotations() query takes about 5-10 milliseconds to execute. There is an additional 5-10 milliseconds to return the resulting Annotation objects and then about 10-20 milliseconds to load/validate the actual annotation values. On averge each node requires about 30 milliseconds to fully load.