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Merge pull request #7060 from JakubOnderka/galaxy-cluster-tag-name-ci 

chg: [schema] Convert GalaxyCluster tag name to case insensitive
pull/7104/head
Jakub Onderka 2021-03-03 09:07:05 +01:00 committed by GitHub
parent 956a45c34b e3b2a0a40c
commit 8c316b7245
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 20 additions and 13 deletions
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5
INSTALL/MYSQL.sql
View File

@ -243,7 +243,8 @@ CREATE TABLE IF NOT EXISTS event_reports (
`deleted` tinyint(1) NOT NULL DEFAULT 0,
PRIMARY KEY (id),
CONSTRAINT u_uuid UNIQUE (uuid),
INDEX `name` (`name`)
INDEX `name` (`name`),
INDEX `event_id` (`event_id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
-- --------------------------------------------------------
@ -455,7 +456,7 @@ CREATE TABLE IF NOT EXISTS `galaxy_clusters` (
`collection_uuid` varchar(255) COLLATE utf8_bin NOT NULL,
`type` varchar(255) COLLATE utf8_bin NOT NULL,
`value` text COLLATE utf8_bin NOT NULL,
`tag_name` varchar(255) COLLATE utf8_bin NOT NULL DEFAULT '',
`tag_name` varchar(255) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
`description` text COLLATE utf8_bin NOT NULL,
`galaxy_id` int(11) NOT NULL,
`source` varchar(255) COLLATE utf8_bin NOT NULL DEFAULT '',

15
app/Model/AppModel.php
View File

@ -1568,6 +1568,10 @@ class AppModel extends Model
INDEX `value` (`value`(255))
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;";
break;
case 66:
$sqlArray[] = "ALTER TABLE `galaxy_clusters` MODIFY COLUMN `tag_name` varchar(255) COLLATE utf8_unicode_ci NOT NULL DEFAULT '';";
$indexArray[] = ['event_reports', 'event_id'];
break;
case 'fixNonEmptySharingGroupID':
$sqlArray[] = 'UPDATE `events` SET `sharing_group_id` = 0 WHERE `distribution` != 4;';
$sqlArray[] = 'UPDATE `attributes` SET `sharing_group_id` = 0 WHERE `distribution` != 4;';
@ -1821,18 +1825,19 @@ class AppModel extends Model
}
}
private function __addIndex($table, $field, $length = false)
private function __addIndex($table, $field, $length = null, $unique = false)
{
$dataSourceConfig = ConnectionManager::getDataSource('default')->config;
$dataSource = $dataSourceConfig['datasource'];
$this->Log = ClassRegistry::init('Log');
$index = $unique ? 'UNIQUE INDEX' : 'INDEX';
if ($dataSource == 'Database/Postgres') {
$addIndex = "CREATE INDEX idx_" . $table . "_" . $field . " ON " . $table . " (" . $field . ");";
$addIndex = "CREATE $index idx_" . $table . "_" . $field . " ON " . $table . " (" . $field . ");";
} else {
if (!$length) {
$addIndex = "ALTER TABLE `" . $table . "` ADD INDEX `" . $field . "` (`" . $field . "`);";
$addIndex = "ALTER TABLE `" . $table . "` ADD $index `" . $field . "` (`" . $field . "`);";
} else {
$addIndex = "ALTER TABLE `" . $table . "` ADD INDEX `" . $field . "` (`" . $field . "`(" . $length . "));";
$addIndex = "ALTER TABLE `" . $table . "` ADD $index `" . $field . "` (`" . $field . "`(" . $length . "));";
}
}
$result = true;
@ -1841,7 +1846,7 @@ class AppModel extends Model
try {
$this->query($addIndex);
} catch (Exception $e) {
$duplicate = (strpos($e->getMessage(), '1061') !== false);
$duplicate = strpos($e->getMessage(), '1061') !== false;
$errorMessage = $e->getMessage();
$result = false;
}

8
app/Model/GalaxyCluster.php
View File

@ -915,7 +915,7 @@ class GalaxyCluster extends AppModel
if (!$isGalaxyTag) {
return null;
}
$conditions = array('LOWER(GalaxyCluster.tag_name)' => strtolower($name));
$conditions = array('GalaxyCluster.tag_name' => $name);
}
$cluster = $this->fetchGalaxyClusters($user, array(
'conditions' => $conditions,
@ -943,7 +943,7 @@ class GalaxyCluster extends AppModel
if (count(array_filter($namesOrIds, 'is_numeric')) === count($namesOrIds)) { // all elements are numeric
$conditions = array('GalaxyCluster.id' => $namesOrIds);
} else {
$conditions = array('LOWER(GalaxyCluster.tag_name)' => array_map('strtolower', $namesOrIds));
$conditions = array('GalaxyCluster.tag_name' => $namesOrIds);
}
$options = ['conditions' => $conditions];
@ -1470,7 +1470,7 @@ class GalaxyCluster extends AppModel
foreach ($events as $event) {
foreach ($event['EventTag'] as $eventTag) {
if ($eventTag['Tag']['is_galaxy']) {
$clusterTagNames[$eventTag['Tag']['id']] = strtolower($eventTag['Tag']['name']);
$clusterTagNames[$eventTag['Tag']['id']] = $eventTag['Tag']['name'];
}
}
}
@ -1480,7 +1480,7 @@ class GalaxyCluster extends AppModel
}
$options = [
'conditions' => ['LOWER(GalaxyCluster.tag_name)' => $clusterTagNames],
'conditions' => ['GalaxyCluster.tag_name' => $clusterTagNames],
'contain' => ['Galaxy', 'GalaxyElement'],
];
$clusters = $this->fetchGalaxyClusters($user, $options);

5
db_schema.json
View File

@ -2356,7 +2356,7 @@
"data_type": "varchar",
"character_maximum_length": "255",
"numeric_precision": null,
"collation_name": "utf8_bin",
"collation_name": "utf8_unicode_ci",
"column_type": "varchar(255)",
"column_default": "",
"extra": ""
@ -7654,7 +7654,8 @@
"event_reports": {
"id": true,
"uuid": true,
"name": false
"name": false,
"event_id": false
},
"event_tags": {
"id": true,