tripal_chado/src/Form/ChadoManagerForm.php
<?php
namespace Drupal\tripal_chado\Form;
use Drupal\Core\Form\FormBase;
use Drupal\Core\Form\FormStateInterface;
use Drupal\Core\Link;
use Drupal\Core\Url;
use Drupal\tripal\TripalDBX\TripalDbx;
use Drupal\tripal_chado\Database\ChadoConnection;
use Drupal\tripal_chado\Task\ChadoInstaller;
/**
* Class ChadoManagerForm.
*/
class ChadoManagerForm extends FormBase {
/**
* @defgroup chado_manager_form_tasks Form task names.
* @{
* Names used to identify form tasks in Chado manager form.
*/
/**
* Rename Chado task identifier.
*/
public const RENAME_TASK = 'rename';
/**
* Set default Chado schema task identifier.
*/
public const SET_DEFAULT_TASK = 'set_default';
/**
* Integrate Chado task identifier.
*/
public const INTEGRATE_TASK = 'integrate';
/**
* Clone Chado task identifier.
*/
public const CLONE_TASK = 'clone';
/**
* Drop Chado task identifier.
*/
public const DROP_TASK = 'remove';
/**
* Upgrade Chado task identifier.
*/
public const UPGRADE_TASK = 'upgrade';
/**
* @} End of "defgroup chado_manager_form_tasks".
*/
/**
* {@inheritdoc}
*/
public function getFormId() {
return 'chado_manager_form';
}
/**
* {@inheritdoc}
*/
public function buildForm(array $form, FormStateInterface $form_state) {
// Get values from state.
$schema_name = $form_state->getValue('chado_schema');
$task = $form_state->getValue('task');
$confirm = $form_state->getValue('confirm');
if ($schema_name && $task) {
switch ($task) {
case static::RENAME_TASK:
$form = $this->buildRenameForm($form, $form_state);
break;
case static::CLONE_TASK:
$form = $this->buildCloneForm($form, $form_state);
break;
case static::UPGRADE_TASK:
$form = $this->buildUpgradeForm($form, $form_state);
break;
case static::DROP_TASK:
$form_state->set(
'confirm_message',
$this->t(
"Are you sure you want to remove schema '@schema_name'? This operation cannot be undone. We recommand you backup your data first.",
[
'@schema_name' => $schema_name,
]
)
);
$form = $this->buildConfirmForm($form, $form_state);
break;
case static::INTEGRATE_TASK:
case static::SET_DEFAULT_TASK:
default:
$form = $this->buildMainForm($form, $form_state);
}
}
else {
$form = $this->buildMainForm($form, $form_state);
}
return $form;
}
/**
* Builds default form with Chado instance table.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function buildMainForm(array $form, FormStateInterface $form_state) {
$tripal_dbx = \Drupal::service('tripal.dbx');
$chado = new ChadoConnection();
// Now that we support multiple chado instances, we need to list all the
// currently installed ones here since they may be different versions.
$rows = [];
$instances = $chado->getAvailableInstances();
$form['#attached']['library'][] = 'tripal_chado/tripal_chado.chado_table';
$form['chado_schema'] = [
'#type' => 'hidden',
'#name' => 'chado_schema',
'#default_value' => '',
];
$form['task'] = [
'#type' => 'hidden',
'#name' => 'task',
'#default_value' => '',
];
// Sort instances.
uasort($instances, function ($a, $b) {
$order = 0;
// Sort by test/reservation status first.
if ($a['is_test'] || $a['is_reserved']) {
if ($b['is_test'] || $b['is_reserved']) {
// Then sort by schema name.
$order = strcasecmp($a['schema_name'], $b['schema_name']);
}
else {
$order = 1;
}
}
else {
if ($b['is_test'] || $b['is_reserved']) {
$order = -1;
}
else {
// Then sort by Tripal integration.
if ($a['integration']) {
if ($b['integration']) {
// Then sort by schema name.
$order = strcasecmp($a['schema_name'], $b['schema_name']);
}
else {
$order = -1;
}
}
else {
if ($b['integration']) {
$order = 1;
}
else {
// Then sort by schema name.
$order = strcasecmp($a['schema_name'], $b['schema_name']);
}
}
}
}
return $order;
});
$default_chado = '';
foreach ($instances as $schema_name => $details) {
// Schema name.
$schema_name = $details['schema_name'];
if ($details['is_default']) {
$default_chado = $schema_name;
}
// Version.
$version = $details['version'];
// Integration.
$integrated = $details['integration']
? $this->t('Yes')
: (
$details['is_test']
? $this->t('Test')
: $this->t('No')
)
;
// Adds integration data.
$created = '';
$updated = '';
if ($details['integration']) {
// @todo: row style should highlight it is integrated.
// @todo: add a "check" sign in front of default Chado schema.
$created =
\Drupal::service('date.formatter')->format(
$details['integration']['created']
)
;
$updated =
\Drupal::service('date.formatter')->format(
$details['integration']['updated']
)
;
}
// Set available operations.
$operations = [];
// Check if renamable, dropable.
if (!$tripal_dbx->isSchemaReserved($schema_name)) {
// Rename.
$operations['rename_button'] = [
'#type' => 'button',
'#value' => $this->t('Rename'),
'#attributes' => [
'class' => ['chadoTableButton'],
'data-chado-task' => static::RENAME_TASK,
'data-chado-schema' => $schema_name,
],
];
if ($details['integration']) {
if (!$details['is_default']) {
// Default instance.
$operations['set_default_button'] = [
'#type' => 'button',
'#value' => $this->t('Set default'),
'#attributes' => [
'class' => ['chadoTableButton'],
'data-chado-task' => static::SET_DEFAULT_TASK,
'data-chado-schema' => $schema_name,
],
];
}
}
else {
// Integrate.
$operations['integrate_button'] = [
'#type' => 'button',
'#value' => $this->t('Add to Tripal'),
'#attributes' => [
'class' => ['chadoTableButton'],
'data-chado-task' => static::INTEGRATE_TASK,
'data-chado-schema' => $schema_name,
],
];
}
}
// Clone.
$operations['clone_button'] = [
'#type' => 'button',
'#value' => $this->t('Clone'),
'#attributes' => [
'class' => ['chadoTableButton'],
'data-chado-task' => static::CLONE_TASK,
'data-chado-schema' => $schema_name,
],
];
// Drop.
$operations['drop_button'] = [
'#type' => 'button',
'#value' => $this->t('Drop'),
'#attributes' => [
'class' => ['chadoTableButton'],
'data-chado-task' => static::DROP_TASK,
'data-chado-schema' => $schema_name,
],
];
$default_version = (float) ChadoInstaller::DEFAULT_CHADO_VERSION;
if ((float)$details['version'] < $default_version) {
// Upgrade.
$operations['upgrade_button'] = [
'#type' => 'button',
'#value' => $this->t(
'Upgrade to @default_version',
['@default_version' => $default_version, ]
),
'#attributes' => [
'class' => ['chadoTableButton'],
'data-chado-task' => static::UPGRADE_TASK,
'data-chado-schema' => $schema_name,
],
];
}
$rows[$schema_name] = [
$schema_name . ($default_chado == $schema_name ? $this->t(' (default)') : ''),
$version,
$details['has_data'] ? $this->t('Yes') : $this->t('No'),
$integrated,
$created,
$updated,
['data' => [$operations]],
];
}
if (!empty($rows)) {
$form['existing_instances'] = [
'#type' => 'table',
'#multiple' => FALSE,
'#header' => ['Schema Name', 'Chado Version', 'Has data', 'In Tripal', 'Created', 'Updated', 'Operations'],
'#rows' => $rows,
];
}
else {
\Drupal::messenger()->addError(t('No Chado installations are found. @install.', [
'@install' => Link::fromTextAndUrl('Please install a new Chado schema', Url::fromUri('internal:/admin/tripal/storage/chado/install'))->toString(),
]));
}
// Table buttons cannot submit the form without a submit button.
// We add a submit button in order to fix that.
$form['submit'] = [
'#type' => 'submit',
'#name' => 'action',
'#value' => t('Refresh'),
];
$form['#prefix'] = '<div id="tripal_chado_manage_form">';
$form['#suffix'] = '</div>';
return $form;
}
/**
* {@inheritdoc}
*/
public function submitForm(array &$form, FormStateInterface $form_state) {
// Get values from form first and then from state.
$schema_name =
$form_state->getValue('chado_schema')
?: $form_state->get('chado_schema')
;
$form_state->set('chado_schema', $schema_name);
$task =
$form_state->getValue('task')
?: $form_state->get('task')
;
$form_state->set('task', $task);
$confirm = $form_state->getValue('confirm');
switch ($task) {
case static::SET_DEFAULT_TASK:
$this->setDefaultSchema($schema_name);
break;
case static::INTEGRATE_TASK:
$this->integrateSchema($schema_name);
break;
case static::DROP_TASK:
if ($confirm) {
$this->dropSchema($schema_name);
$this->goBackForm($form, $form_state);
break;
}
case static::UPGRADE_TASK:
case static::RENAME_TASK:
case static::CLONE_TASK:
default:
// A second form page should be provided.
$form_state->setRebuild(TRUE);
}
}
/**
* Go back submission.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function goBackForm(array &$form, FormStateInterface $form_state) {
$form_state
->set('task', '')
->set('schema_name', '')
->set('confirm_message', '')
->setValues([])
->setRebuild(TRUE);
}
/**
* Validates forms that create a new schema.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function validateNewSchemaForm(array &$form, FormStateInterface $form_state) {
$old_schema_name = $form_state->getValue('chado_schema');
$new_schema_name = $form_state->getValue('new_schema_name');
$tripal_dbx = \Drupal::service('tripal.dbx');
// Check new schame name is valid.
$issue = $tripal_dbx->isInvalidSchemaName($new_schema_name);
if ($issue) {
$form_state->setErrorByName(
'new_schema_name',
$issue
);
}
// Make sure new schema does not exist.
if ($tripal_dbx->schemaExists($new_schema_name)) {
$form_state->setErrorByName(
'new_schema_name',
$this->t(
'New schema name is already in use. Please choose a different name.'
)
);
}
parent::validateForm($form, $form_state);
}
/**
* Sets default Chado schema.
*
* @param string $schema_name
* The schema name that will be used as default Chado schema. It should
* correspond to an existing Chado instance integrated in Tripal.
*/
protected function setDefaultSchema(string $schema_name) {
// Edit current config.
$config = \Drupal::service('config.factory')
->getEditable('tripal_chado.settings')
;
$config->set('default_schema', $schema_name)->save();
\Drupal::messenger()->addStatus(
$this->t(
'Default Chado schema set to @schema_name.',
['@schema_name' => $schema_name, ]
)
);
}
/**
* Live-runs a task on a Chado schema.
*
* @param string $task_service
* The name of the task service to use.
* @param array $parameters
* Task parameters.
*/
protected function runTask(string $task_service, array $parameters, $success_message) {
$task = \Drupal::service($task_service);
$task->setParameters($parameters);
try {
$success = $task->performTask();
}
catch (\Drupal\tripal\TripalDBX\Exceptions\TripalDbxException $e) {
$success = FALSE;
}
if (!$success) {
$error = "Failed to perform task."
. ($e ? $e->getMessage() : " See previous log messages for details.")
;
if ($e) {
\Drupal::logger('tripal_chado')->error($e);
}
else {
\Drupal::logger('tripal_chado')->error($error);
}
\Drupal::messenger()->addError($error);
}
else {
\Drupal::messenger()->addStatus($success_message);
}
}
/**
* Integrates a Chado schema into Tripal.
*
* @param string $schema_name
* The schema name to integrate to Tripal.
*/
protected function integrateSchema(string $schema_name) {
$this->runTask(
'tripal_chado.integrator',
['input_schemas' => [$schema_name], ],
$this->t(
'Chado schema @schema_name has been integrated into Tripal.',
['@schema_name' => $schema_name, ]
)
);
}
/**
* Drops the given Chado schema.
*
* @param string $schema_name
* The schema name to drop.
*/
protected function dropSchema(string $schema_name) {
$this->runTask(
'tripal_chado.remover',
['output_schemas' => [$schema_name], ],
$this->t(
'Chado schema @schema_name has been dropped.',
['@schema_name' => $schema_name, ]
)
);
}
/**
* Builds a confirmation form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function buildConfirmForm(array $form, FormStateInterface $form_state) {
$schema_name = $form_state->get('chado_schema');
$message = $form_state->get('confirm_message');
if (empty($message)) {
$message = $this->t('Are you sure you want to continue?');
}
$form['confirm_message'] = [
'#type' => 'item',
'#markup' => $message,
];
$form['confirm'] = [
'#type' => 'hidden',
'#name' => 'confirm',
'#value' => '1',
];
$form['cancel'] = [
'#type' => 'submit',
'#name' => 'back',
'#value' => t('Cancel'),
'#submit' => ['::goBackForm'],
'#limit_validation_errors' => [],
];
$form['submit'] = [
'#type' => 'submit',
'#name' => 'action',
'#value' => t('Confirm'),
'#submit' => ['::submitForm'],
];
return $form;
}
/**
* Builds rename form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function buildRenameForm(array $form, FormStateInterface $form_state) {
$schema_name = $form_state->getValue('chado_schema');
$form['task'] = [
'#type' => 'item',
'#markup' => t(
'<h2>Rename "@schema_name" schema</h2>',
['@schema_name' => $schema_name, ]
),
];
$form['chado_schema'] = [
'#type' => 'hidden',
'#name' => 'chado_schema',
'#value' => $schema_name,
];
$form['new_schema_name'] = [
'#type' => 'textfield',
'#title' => t('New Schema Name'),
'#required' => TRUE,
'#description' => t('Enter the new schema name to use.'),
'#default_value' => '',
'#attributes' => ['autocomplete' => 'off'],
];
$form['cancel'] = [
'#type' => 'submit',
'#name' => 'back',
'#value' => t('Cancel'),
'#submit' => ['::goBackForm'],
'#limit_validation_errors' => [],
];
$form['submit'] = [
'#type' => 'submit',
'#name' => 'action',
'#value' => t('Rename'),
'#submit' => ['::submitRenameForm'],
'#validate' => ['::validateNewSchemaForm'],
];
return $form;
}
/**
* Submit rename form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function submitRenameForm(array &$form, FormStateInterface $form_state) {
$old_schema_name = $form_state->getValue('chado_schema');
$new_schema_name = $form_state->getValue('new_schema_name');
$this->runTask(
'tripal_chado.renamer',
[
'output_schemas' => [
$old_schema_name,
$new_schema_name,
],
],
$this->t(
'Chado schema @old_schema_name has been renamed into @new_schema_name.',
[
'@old_schema_name' => $old_schema_name,
'@new_schema_name' => $new_schema_name,
]
)
);
// Go back.
$this->goBackForm($form, $form_state);
}
/**
* Builds clone schema form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function buildCloneForm(array $form, FormStateInterface $form_state) {
$schema_name = $form_state->getValue('chado_schema');
$form['task'] = [
'#type' => 'item',
'#markup' => t(
'<h2>Clone "@schema_name" schema</h2>',
['@schema_name' => $schema_name, ]
),
];
$form['chado_schema'] = [
'#type' => 'hidden',
'#name' => 'chado_schema',
'#value' => $schema_name,
];
$form['new_schema_name'] = [
'#type' => 'textfield',
'#title' => t('Clone Name'),
'#required' => TRUE,
'#description' => t('Enter the new schema name to use for the clone.'),
'#default_value' => '',
'#attributes' => ['autocomplete' => 'off'],
];
$form['cancel'] = [
'#type' => 'submit',
'#name' => 'back',
'#value' => t('Cancel'),
'#submit' => ['::goBackForm'],
'#limit_validation_errors' => [],
];
$form['submit'] = [
'#type' => 'submit',
'#name' => 'action',
'#value' => t('Clone'),
'#submit' => ['::submitCloneForm'],
'#validate' => ['::validateNewSchemaForm'],
];
return $form;
}
/**
* Submit clone form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function submitCloneForm(array &$form, FormStateInterface $form_state) {
$source_schema_name = $form_state->getValue('chado_schema');
$new_schema_name = $form_state->getValue('new_schema_name');
$current_user = \Drupal::currentUser();
$args = [$source_schema_name, $new_schema_name];
tripal_add_job(
t('Clone Chado schema'),
'tripal_chado',
'tripal_chado_clone_schema',
$args,
$current_user->id(),
10
);
// Go back.
$this->goBackForm($form, $form_state);
}
/**
* Builds upgrade schema form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function buildUpgradeForm(array $form, FormStateInterface $form_state) {
$schema_name = $form_state->getValue('chado_schema');
$form['task'] = [
'#type' => 'item',
'#markup' => t(
'<h2>Upgrade "@schema_name" schema</h2>',
['@schema_name' => $schema_name, ]
),
];
$form['chado_schema'] = [
'#type' => 'hidden',
'#name' => 'chado_schema',
'#value' => $schema_name,
];
$form['cleanup'] = [
'#type' => 'checkbox',
'#title' => t('Remove database objects and table columns not existing in the official Chado schema.'),
'#description' => t(
"Checking this box will perform a database cleanup. If you didn't customize your Chado schema, leave this checked. If you uncheck it, be aware that there are more chances the update process may fail du to database object dependencies related to non-chado objects."
),
'#default_value' => TRUE,
];
$form['sql_file'] = [
'#type' => 'textfield',
'#title' => t('Generate an update SQL file instead (optional)'),
'#required' => FALSE,
'#description' => t(
'If you specify a file, your schema will <strong>not</strong> be upgraded. You can leave this field empty if you want the upgrader to upgrade your schema. Otherwise, you can provide a file name relative to your Drupal public folder "files" (or private folder if set as default) or an absolute file name starting with "/". The target file must not exist. You can later execute that SQL file to mnually upgrade your schema and deal with issues (advanced users).'
),
'#default_value' => '',
];
$form['cancel'] = [
'#type' => 'submit',
'#name' => 'back',
'#value' => t('Cancel'),
'#submit' => ['::goBackForm'],
'#limit_validation_errors' => [],
];
$form['submit'] = [
'#type' => 'submit',
'#name' => 'action',
'#value' => t('Upgrade'),
'#submit' => ['::submitUpgradeForm'],
];
return $form;
}
/**
* Submit upgrade form.
*
* @param array $form
* An associative array containing the structure of the form.
* @param \Drupal\Core\Form\FormStateInterface $form_state
* The current state of the form.
*/
public function submitUpgradeForm(array &$form, FormStateInterface $form_state) {
$schema_name = $form_state->getValue('chado_schema');
$sql_file = $form_state->getValue('sql_file');
$cleanup = $form_state->getValue('cleanup');
$current_user = \Drupal::currentUser();
$args = [$schema_name, '1.3', $sql_file, $cleanup];
tripal_add_job(
t('Upgrade Chado schema'),
'tripal_chado',
'tripal_chado_upgrade_schema',
$args,
$current_user->id(),
10
);
// Go back.
$this->goBackForm($form, $form_state);
}
}