Public Member Functions | |
| installChado ($options=['schema-name'=> 'chado', 'chado-version'=> 1.3]) | |
| migrateChado ($options=['schema-name'=> 'chado']) | |
| dropChado ($options=['schema-name'=> 'chado']) | |
| prepareChado ($options=['schema-name'=> 'chado']) | |
| setupTests () | |
| publish (string $bundle, array $options=['schema-name'=> '', 'datastore'=> 'chado_storage', 'batch-size'=> '1000', 'migration-file'=> '', 'lenient-migration'=> FALSE, 'republish'=> FALSE]) | |
| unpublish (string $bundle, array $options=['schema-name'=> '', 'datastore'=> 'chado_storage', 'all'=> FALSE,]) | |
| addToTripal ($options=['schema-name'=> 'chado']) | |
| setDefault ($options=['schema-name'=> 'chado']) | |
Detailed Description
Drush commands
Member Function Documentation
◆ addToTripal()
| Drupal\tripal_chado\Commands\ChadoManageCommands::addToTripal | ( | $options = ['schema-name' => 'chado'] | ) |
Add a Chado schema to Tripal. Does not set this schema as the default, as there can be more than one Chado schema added to Tripal. See the command tripal-chado:set_default for this functionality.
@command tripal-chado:add_to_tripal @aliases trp-add-chado @options schema-name The name of the chado schema to add to Tripal. @usage drush trp-add-chado –schema-name="chado" Adds the specified Chado to Tripal.
◆ dropChado()
| Drupal\tripal_chado\Commands\ChadoManageCommands::dropChado | ( | $options = ['schema-name' => 'chado'] | ) |
Drops the Chado schema.
@command tripal-chado:drop-chado @aliases trp-drop-chado @options schema-name The name of the schema to drop. @usage drush trp-drop-chado –schema-name='teapot' Removes the chado schema named "teapot".
◆ installChado()
| Drupal\tripal_chado\Commands\ChadoManageCommands::installChado | ( | $options = ['schema-name' => 'chado', 'chado-version' => 1.3] | ) |
Install the Chado schema.
@command tripal-chado:install-chado @aliases trp-install-chado @options schema-name The name of the schema to install chado in. @options chado-version The version of chado to install. Currently only 1.3 is supported. @usage drush trp-install-chado –schema-name='teapot' –version=1.3 Installs chado 1.3 in a schema named "teapot".
◆ migrateChado()
| Drupal\tripal_chado\Commands\ChadoManageCommands::migrateChado | ( | $options = ['schema-name' => 'chado'] | ) |
Apply migrations to an existing Chado schema.
@command tripal-chado:migrate-chado @aliases trp-migrate-chado @options schema-name The name of the schema to apply chado migrations to. @usage drush trp-migrate-chado –schema-name='teapot' Applies all pending migrations to a schema named "teapot".
◆ prepareChado()
| Drupal\tripal_chado\Commands\ChadoManageCommands::prepareChado | ( | $options = ['schema-name' => 'chado'] | ) |
Prepare the Tripal Chado system.
@command tripal-chado:prepare @aliases trp-prep-chado @options schema-name The name of the chado schema to prepare. Only a single chado schema should be prepared with Tripal and this will become the default chado schema. @usage drush trp-prep-chado –schema-name="chado" Prepare the Tripal Chado system and set the schema named "chado" as the default Chado instance to use with Tripal.
◆ publish()
| Drupal\tripal_chado\Commands\ChadoManageCommands::publish | ( | string | $bundle, |
| array | $options = [ 'schema-name' => '', 'datastore' => 'chado_storage', 'batch-size' => '1000', 'migration-file' => '', 'lenient-migration' => FALSE, 'republish' => FALSE] |
||
| ) |
Publish Chado Records as Tripal Content.
@command tripal-chado:publish @aliases trp-chado-publish @options schema-name The name of the chado schema to use.
- Parameters
-
string $bundle The id of the TripalContentType you would like to publish content for. array $options Publish options. Defaults are 'schema-name' => 'chado' 'datastore' => 'chado_storage' 'migration-file' => '' 'lenient-migration' => FALSE 'batch-size' => '1000' @usage drush trp-chado-publish organism Submits a standard chado publish job for the organism content type which publishes records in the default chado schema organism table. @usage drush trp-chado-publish organism –schema-name=prod Submits a chado publish job for the organism content type which publishes records in the prod.organism table.
◆ setDefault()
| Drupal\tripal_chado\Commands\ChadoManageCommands::setDefault | ( | $options = ['schema-name' => 'chado'] | ) |
Sets a specified Chado schema to be the default in Tripal. Only one schema may be set to default at a time.
@command tripal-chado:set_default_schema @aliases trp-set-default @options schema-name The name of the chado schema to be set to default in Tripal. @usage drush trp-set-default –schema-name="chado" Sets the specified Chado to be default in Tripal.
◆ setupTests()
| Drupal\tripal_chado\Commands\ChadoManageCommands::setupTests | ( | ) |
Set-up the Tripal Chado test environment.
@command tripal-chado:setup-tests @aliases trp-prep-tests @usage drush trp-prep-tests Sets up the standard Tripal Chado test environment.
◆ unpublish()
| Drupal\tripal_chado\Commands\ChadoManageCommands::unpublish | ( | string | $bundle, |
| array | $options = [ 'schema-name' => '', 'datastore' => 'chado_storage', 'all' => FALSE, ] |
||
| ) |
Unpublish previously published Tripal Content.
Chado records are not modified in any way by unpublish.
- Parameters
-
string $bundle The id of the TripalContentType you would like to unpublish content for. array $options Publish options, defaults are provided in the function declaration.
@command tripal-chado:unpublish @aliases trp-chado-unpublish @options schema-name The name of the chado schema to use. @options all Unpublish all records of the specified content type. Without this option, only orphaned records are unpublished.
@usage drush trp-chado-unpublish contact Submits a standard chado publish job to unpublish only orphaned records in the contact content type. @usage drush trp-chado-unpublish organism –all –schema-name=prod Submits a chado publish job for the organism content type which unpublishes ALL records based on the prod.organism table.
The documentation for this class was generated from the following file:
- tripal_chado/src/Commands/ChadoManageCommands.php
