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|
# ProbeSetData
This is by far the largest table (~100Gb). I need to add disk space to be able to host it on the NVME.
Prototocol from
=> ./move-to-innodb.gmi
Every table update has to follow the template:
### Check recent backups
* [X] ascertain there is a backup
* [ ] copy original files
### Make temporary table
If you have enough space, you can create a copy of the actual table and do the work on that:
```
CREATE TABLE mytest AS SELECT * FROM ProbeSetData;
```
Then you can change the column as desired:
```
ALTER TABLE tbl_name MODIFY COLUMN col_name BIGINT AUTO_INCREMENT;
```
Once the process is done, you can rename the tables:
```
DROP ProbeSetData;
RENAME TABLE tbl_name TO new_tbl_name, tbl_name2 TO ProbeSetData;
```
### Check table structure
```
SHOW CREATE TABLE ProbeSetData;
```
A really simple table
```
| ProbeSetData | CREATE TABLE 'ProbeSetData' (
'Id' int(10) unsigned NOT NULL DEFAULT 0,
'StrainId' int(20) NOT NULL,
'value' float NOT NULL,
UNIQUE KEY 'DataId' ('Id','StrainId'),
KEY 'strainid' ('StrainId')
) ENGINE=MyISAM DEFAULT CHARSET=latin1 |
```
```
MariaDB [db_webqtl]> select * from ProbeSetData limit 2;
+----+----------+-------+
| Id | StrainId | value |
+----+----------+-------+
| 1 | 1 | 5.742 |
| 1 | 2 | 5.006 |
+----+----------+-------+
2 rows in set (0.000 sec)
```
But large
```
MariaDB [db_webqtl]> select count(*) from ProbeSetData;
+------------+
| count(*) |
+------------+
| 5141631478 |
+------------+
1 row in set (0.000 sec)
```
Do this also on Penguin2.
```
| ProbeSetData | CREATE TABLE 'ProbeSetData' (
'Id' int(10) unsigned NOT NULL DEFAULT 0,
'StrainId' smallint(5) unsigned NOT NULL DEFAULT 0,
'value' float NOT NULL,
UNIQUE KEY 'DataId' ('Id','StrainId')
) ENGINE=InnoDB DEFAULT CHARSET=latin1 |
```
The table layout is a bit puzzling.
```
MariaDB [db_webqtl]> select max(StrainId) from ProbeSetData;
+---------------+
| max(StrainId) |
+---------------+
| 65777 |
+---------------+
MariaDB [db_webqtl]> select max(Id) from ProbeSetData;
+----------+
| max(Id) |
+----------+
| 91406791 |
+----------+
```
For StrainID MediumInt is a better fit with unsigned range is 0 to 16777215 and Id should be a INT (instead of BIGINT for the time being). That will make the table+indices smaller and faster.
### Check GN1,2,3 code for use of table
```
rg ProbeSetData --color=always |less -R
rg ProbeSetData --type=py -l|fzf --preview="rg --color=always -A 20 ProbeSetData {}" --preview-window=right:85%:wrap
```
No surprises from the code scan.
### Create test
Some select statement and maybe a page of GN2.
The tests we can share from ProbeSetXRef.
Page of GN2 is the mapping page, e.g.
=> http://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P
### Create primary key
```
ALTER TABLE ProbeSetData
ADD PRIMARY KEY(col1,col2);
```
### Create indices
```
SHOW INDEX FROM ProbeSetData;
DROP INDEX ProbeSetId ON ProbeSetData;
```
### Convert to innodb
```
ALTER TABLE ProbeSetData ENGINE = InnoDB;
```
### Change charset
```
ALTER TABLE ProbeSetSE CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;
```
### Update fulltext
For those cases see bottom of move-to-innodb.gmi.
### Run optimiser
```
OPTIMIZE NO_WRITE_TO_BINLOG TABLE ProbeSetData;
```
After running the optimiser rename the tables
```
RENAME TABLE orig TO orig_old, mytest TO orig;
```
### Check test
|
