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Allow use of prepared SQL statements in {{#get_db_data:}}
Allow use of prepared SQL statements in {{#get_db_data:}}
for ODBC connections and mySQL.
Define prepared SQL statements in LocalSettings.php per database
connection.
Examples:
One statement per connection:
In LocalSettings.php:
$edgDBServer ['rfam'] = 'mysql-rfam-public.ebi.ac.uk:4497';
$edgDBServerType['rfam'] = 'mysql';
$edgDBName ['rfam'] = 'Rfam';
$edgDBUser ['rfam'] = 'rfamro';
$edgDBPass ['rfam'] = '';
$edgDBPrepared ['rfam'] = <<<'SQL'
SELECT fr.rfam_acc, fr.rfamseq_acc, fr.seq_start, fr.seq_end
FROM full_region fr, rfamseq rf, taxonomy tx
WHERE rf.ncbi_id = tx.ncbi_id
AND fr.rfamseq_acc = rf.rfamseq_acc
AND tx.ncbi_id = ?
AND is_significant = 1 -- exclude low-scoring matches from the same clan
SQL;
$edgDBTypes ['rfam'] = 's'; // optional.
In wikitext:
{{#get_db_data:
db = rfam
| parameters=10116 <!-- substitutes ?'s in prepared statement -->
| data=account=rfam_acc,sec=rfamseq_acc,start=seq_start,end=seq_end
}}
Several statements per connection:
In LocalSettings.php:
$edgDBServer ['rfam'] = 'mysql-rfam-public.ebi.ac.uk:4497';
$edgDBServerType['rfam'] = 'mysql';
$edgDBName ['rfam'] = 'Rfam';
$edgDBUser ['rfam'] = 'rfamro';
$edgDBPass ['rfam'] = '';
$edgDBPrepared ['rfam'] = [
'sequences' => <<<'SEQ'
SELECT fr.rfam_acc, fr.rfamseq_acc, fr.seq_start, fr.seq_end
FROM full_region fr, rfamseq rf, taxonomy tx
WHERE rf.ncbi_id = tx.ncbi_id
AND fr.rfamseq_acc = rf.rfamseq_acc
AND tx.ncbi_id = ?
AND is_significant = 1 -- exclude low-scoring matches from the same clan
SEQ,
'sno' => <<<'SNO'
SELECT fr.rfam_acc, fr.rfamseq_acc, fr.seq_start, fr.seq_end, f.type
FROM full_region fr, rfamseq rf, taxonomy tx, family f
WHERE
rf.ncbi_id = tx.ncbi_id
AND f.rfam_acc = fr.rfam_acc
AND fr.rfamseq_acc = rf.rfamseq_acc
AND tx.tax_string LIKE ?
AND f.type LIKE '%snoRNA%'
AND is_significant = 1 -- exclude low-scoring matches from the same clan
SNO];
In wikitext:
{{#get_db_data:
db = rfam
| query=sequences <!-- which prepared statement? -->
| parameters=10116 <!-- substitutes ?'s in prepared statement -->
| data=account=rfam_acc,sec=rfamseq_acc,start=seq_start,end=seq_end
}}
If prepared SQL statements are defined for a database connection,
arbitrary SQL queries are effectively disallowed.
Changes to the class hierarchy:
* EDConnectorBase
...
** EDConnectorDb
...
*** EDConnectorComposed (new, abstract)
**** EDConnectorRelational (abstract)
***** EDConnectorRdbms (new, for DBs handled by Wikimedia\Rdbms\Database)
...
**** EDConnectorMongoDb
...
*** EDConnectorPrepared (new, abstract)
**** EDConnectorPreparedMysql (new)
The new classes EDConnectorComposed and EDConnectorPrepared are contraposed.
In addition, some property names are brought to camelCase, some methods
are renamed and some unnecessary contructors are removed;
the class ParsesParams now handles warning suppression.
Bug: T287328
Change-Id: Ibf7593eff63074bda86cdaf3b0a6e7a2fc2708bd- Loading branch information
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