diff options
Diffstat (limited to 'topics/systems')
| -rw-r--r-- | topics/systems/mariadb/ProbeSetData.gmi | 43 |
1 files changed, 40 insertions, 3 deletions
diff --git a/topics/systems/mariadb/ProbeSetData.gmi b/topics/systems/mariadb/ProbeSetData.gmi index 5feb384..047cc3b 100644 --- a/topics/systems/mariadb/ProbeSetData.gmi +++ b/topics/systems/mariadb/ProbeSetData.gmi @@ -6,6 +6,31 @@ I disabled these and they need to be restored: * [ ] binary log * [ ] backup script +* [ ] flush db +* [ ] cron system-check +* [ ] systemd MYSQLD_OPTS setting + +The following fetches the data to be used for mapping: + +SELECT + Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2 + FROM + (ProbeSetData, ProbeSetFreeze, + Strain, ProbeSet, ProbeSetXRef) + left join ProbeSetSE on + (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) + left join NStrain on + (NStrain.DataId = ProbeSetData.Id AND + NStrain.StrainId = ProbeSetData.StrainId) + WHERE + ProbeSet.Name = '4336695' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA' AND + ProbeSetXRef.DataId = ProbeSetData.Id AND + ProbeSetData.StrainId = Strain.Id + Order BY + Strain.Name; + Prototocol from @@ -27,6 +52,14 @@ Every table update has to follow the template: ### Make temporary table +``` +mysql 1.5K Jun 27 2021 ProbeSetData.frm +mysql 63G Dec 4 22:15 ProbeSetData.MYD +mysql 118G Dec 28 08:52 ProbeSetData.MYI +mysql 1.5K Jan 1 20:45 mytest.frm +mysql 20G Jan 1 21:34 mytest.ibd +``` + If you have enough space, you can create a copy of the actual table and do the work on that: Original: @@ -47,7 +80,7 @@ New: DROP table mytest; CREATE table mytest( Id INT unsigned NOT NULL DEFAULT 0, - StrainId MediumINT unsigned NOT NULL, + StrainId MediumINT unsigned NOT NULL DEFAULT 0, value float NOT NULL, primary key(Id,StrainId), key (StrainId)) CHARACTER SET utf8mb4; @@ -56,10 +89,10 @@ CREATE table mytest( And fill it killing quite a few birds with one stone :). You may want to disable the binary logger before running: ``` -INSERT INTO mytest (Id,StrainId,value) SELECT Id,StrainId,value FROM ProbeSetData; +INSERT INTO mytest1 (Id,StrainId,value) SELECT Id,StrainId,value FROM ProbeSetData LIMIT 51631478; ``` -(it may be faster to use mysqldump for this!). +Makes a table at 1% of size - a table of 2.3GB. I wonder why the full thing took up 330Gb before we ran out of disk space. Once the process is done, you can rename the tables: @@ -218,3 +251,7 @@ RENAME TABLE orig TO orig_old, mytest TO orig; ``` ### Check test + +## Notes + +I found it is a bad idea to remove large .ibd files by hand because mariadb wants to recreate them to play the transaction log. |