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| author | Munyoki Kilyungi | 2023-12-14 01:33:41 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2023-12-14 01:33:41 +0300 |
| commit | 3d6fec1bc267cfa0a64dfc57318372ee6133f034 (patch) | |
| tree | a05a00159c377c7298c23f73ee44bfac2b439000 /issues/handling-resource-links-in-probeset-page.gmi | |
| parent | 503e78e497e56b320b2bdc07f84b5c74bf2cf368 (diff) | |
| download | gn-gemtext-3d6fec1bc267cfa0a64dfc57318372ee6133f034.tar.gz | |
Add basic performance analysis for ProbeSet RDF dump.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'issues/handling-resource-links-in-probeset-page.gmi')
| -rw-r--r-- | issues/handling-resource-links-in-probeset-page.gmi | 15 |
1 files changed, 15 insertions, 0 deletions
diff --git a/issues/handling-resource-links-in-probeset-page.gmi b/issues/handling-resource-links-in-probeset-page.gmi index bcd50ed..2f18c19 100644 --- a/issues/handling-resource-links-in-probeset-page.gmi +++ b/issues/handling-resource-links-in-probeset-page.gmi @@ -55,3 +55,18 @@ Identifying duplicates: ``` SELECT GeneSymbol, GeneId, SpeciesId, COUNT(CONCAT(GeneSymbol, "_", GeneId, "_", SpeciesId)) AS `count` FROM GeneList GROUP BY BINARY GeneSymbol, GeneId, chromosome, txStart, txEnd HAVING COUNT(CONCAT(GeneSymbol, "_", GeneId, "_", SpeciesId)) > 1; ``` + +Transforming ProbeSet metadata takes long. The exact command: + +```shell +time guix shell guile-dbi \ +guile-hashing -m manifest.scm -- ./pre-inst-env ./examples/probeset.scm --settings conn.scm --output /export/data/genenetwork-virtuoso/probeset-metadata.ttl --documentation ./docs/probeset-metadata.md +``` + +The aforementioned command takes: + +* real: 89m1.715s +* user: 175m47.684s +* sys: 6m15.076s + +Optimisations---perhaps using guile-fibers---can be considered later. |