<?php
/**
* @file
* Installation of the example module
*/
/**
* Implements hook_disable().
*
* Perform actions when the module is disabled by the site administrator
*
* @ingroup tripal_example
*/
function tripal_example_disable() {
// EXPLANATION: If you are using Drupal Views you want to ensure that any
// default views that your module provides are disabled when the module is
// disabled. Default views are specified in the
// [module name].views.default.inc file. The following code will disable these
// views. If your module does not create any default views you can remove the
// following code.
// Disable all default views provided by this module
require_once("tripal_example.views_default.inc");
$views = tripal_example_views_default_views();
foreach (array_keys($views) as $view_name) {
tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
}
}
/**
* Implements hook_requirements().
*
* Performs check to see if all required dependencies are met. Drupal will
* automatically check for module dependencies but here you can check for other
* requirements.
*
* @ingroup tripal_example
*/
function tripal_example_requirements($phase) {
$requirements = array();
if ($phase == 'install') {
// EXPLANATION: It is essential that Chado be installed for almost all
// Tripal modules. Therefore, the following code checks to ensure Chado is
// installed and available. If your module does not require that Chado be
// installed, you can remove the following check.
// make sure chado is installed
if (!$GLOBALS["chado_is_installed"]) {
$requirements ['tripal_example'] = array(
'title' => "tripal_example",
'value' => "ERROR: Chado must be installed before this module can be enabled",
'severity' => REQUIREMENT_ERROR,
);
}
}
return $requirements;
}
/**
* Implements hook_install().
*
* Performs actions when the modules is first installed.
*
* @ingroup tripal_example
*/
function tripal_example_install() {
// EXPLANATION: Here is a good place to add any materialized views, controlled
// vocabularies CV, databases or CV terms needed by your module.
// To keep this module code short, create functions to do each of those tasks
// add any materialized view
tripal_example_add_mviews();
// add any external databases used by the example module.
tripal_example_add_dbs();
// add any controlled vocabularies used by the example module. You may need
// to add a vocabulary if you to set it as default (see next lines of code).
// For example, the Sequence Ontology (SO) is used by the feature module as
// the default vocabulary for the feature type_id field. But, that vocabulary
// does not yet exist in Chado until after the SO is loaded using the Tripal
// OBO loader. But, we can add it here as a place-holder so that we can then
// set it as a default vocabulary (see below).
tripal_example_add_cvs();
// add any controlled vocabulary terms
tripal_example_add_cvterms();
// EXPLANATION: Many tables in Chado have a 'type_id' column which allows for
// association of controlled vocabularies to describe the record. Chado places
// no restrictions on which vocabularies can be used, but Tripal can be
// instructed to provide a default vocabulary for any given field. For
// example, the feature.type_id column will typically use the Sequence
// Ontology. In that case, we can use the tripal_set_default_cv() function to
// specify the Sequence Ontology (sequence) as the default vocabulary.
tripal_set_default_cv('example', 'type_id', 'example_type');
tripal_set_default_cv('exampleprop', 'type_id', 'example_property');
tripal_set_default_cv('example_relationship', 'type_id', 'example_relationship');
// add any custom tables. For this case we will add an 'example' table to the
// chado schema
tripal_example_add_custom_tables();
}
/**
* Implements hook_uninstall().
*
* Performs actions when the modules is uninstalled.
*
* @ingroup tripal_example
*/
function tripal_example_uninstall() {
}
/**
* Implementation of hook_schema().
*
* Provides a list of tables to be created inside of the Drupal schema (the
* 'public' schema by default). It uses the Drupal Schema API array structure to
* define the table, its indexes and constraints.
*
* Schema API documentation is here:
* https://api.drupal.org/api/drupal/includes%21database%21schema.inc/group/schemaapi/7
*
* @ingroup tripal_example
*/
function tripal_example_schema() {
// EXPLANATION: If your module creates a node type for data in the Chado
// database then you probably need to link Drupal nodes with a respective ID
// in the Chado table. The following is an example array for a table that will
// link the 'chado_example' node type (created by this example module) with a
// record in the fake Chado example table. This table will link the 'nid' of
// the node with the 'example_id' of the example record.
$schema['chado_example'] = array(
'fields' => array(
'vid' => array(
'type' => 'int',
'unsigned' => TRUE,
'not null' => TRUE,
'default' => 0
),
'nid' => array(
'type' => 'int',
'unsigned' => TRUE,
'not null' => TRUE,
'default' => 0
),
'example_id' => array(
'type' => 'int',
'not null' => TRUE,
'default' => 0
),
'sync_date' => array(
'type' => 'int',
'not null' => FALSE,
'description' => 'UNIX integer sync date/time'
),
),
'indexes' => array(
'chado_example_idx1' => array('example_id')
),
'unique keys' => array(
'chado_example_uq1' => array('nid', 'vid'),
'chado_example_uq2' => array('vid')
),
'primary key' => array('nid'),
);
return $schema;
};
/**
* Creates a materialized view that stores the type & number of examples per
* organism.
*
* @ingroup tripal_example
*/
function tripal_example_add_mviews() {
// EXPLANATION: use the tripal_add_mview() function to add a materialized view
// needed by your module. If you have more than one materialized view it is
// best to create a single function for each one and call each function here.
// Otherwise this function can become quite long.
}
/**
* Add cvs related to publications
*
* @ingroup tripal_example
*/
function tripal_example_add_dbs() {
// EXPLANATION: use the tripal_insert_db() function to add any external
// databases needed by your module. If the database already exists then the
// function will gracefully return.
tripal_insert_db(array(
'name' => 'example_db',
'description' => 'An example database.'
));
}
/**
* Add cvs related to publications
*
* @ingroup tripal_example
*/
function tripal_example_add_cvs() {
// EXPLANATION: use the tripal_insert_cv() function to add any controlled
// vocabularies needed by your module. If the vocabulary already exists then
// the function will gracefully return. Chado conventions use a singular name
// for CV names (not plural).
tripal_insert_cv(
'example_property',
'Contains property terms for examples.'
);
tripal_insert_cv(
'example_type',
'Contains terms describing types of examples.'
);
tripal_insert_cv(
'example_relationship',
'Contains terms for describing relationship types between examples.'
);
}
/**
* Adds controlled vocabulary terms needed by this module.
*
* @ingroup tripal_example
*/
function tripal_example_add_cvterms() {
// EXPLANATION: for our test module to work we need to add some terms to our
// example_type controlled vocabulary. Ideally we should have a full OBO file
// for loading but sometimes we just have a small list that won't really
// change so we can add those terms here.
tripal_insert_cvterm(array(
'id' => 'test', // the term accession
'name' => 'Test type', // the human readable term name
'cv_name' => 'example_type', // the CV name this term belongs to.
'definition' => 'A test type for the example module.',
'db_name' => 'example_db', // the database in which the term is found.
));
}
/**
* Add custom tables to Chado that are required by this module
*
* @ingroup tripal_example
*/
function tripal_example_add_custom_tables() {
// EXPLANATION: for this example module we will create a set of example tables
// that mimic Chado tables. These tables are:
//
// 1) example (for storing the primary example records)
// 2) exampleprop (for sorting properties about the example)
// 3) example_relationship (for storing relationships about examples)
// 4) example_dbxref (for storing cross-references about an example)
//
// To make the code easier to read, each table is created by a separate
// function called here:
tripal_example_add_example_table();
tripal_example_add_exampleprop_table();
tripal_example_add_example_relationship_table();
tripal_example_add_example_dbxref_table();
}
/**
* Adds the 'example' custom table to Chado.
*
* @ingroup tripal_example
*/
function tripal_example_add_example_table() {
// EXPLANATION: use the Drupal Schema API to describe the custom table. Then
// add the table using the chado_create_custom_table() function.
$schema = array(
'table' => 'example',
'fields' => array(
'example_id' => array(
'type' => 'serial',
'not null' => true,
),
'uniquename' => array(
'type' => 'varchar',
'length' => '255',
'not null' => TRUE,
),
'type_id' => array(
'type' => 'int',
'not null' => true,
),
'organism_id' => array(
'type' => 'int',
'not null' => true,
),
'description' => array(
'type' => 'text',
),
),
'primary key' => array(
0 => 'example_id',
),
'unique keys' => array(
'example_uq1' => array(
0 => 'uniquename',
1 => 'type_id',
2 => 'organism_id',
),
),
'indexes' => array(
'example_idx1' => array(
0 => 'example_id',
),
'example_idx2' => array(
0 => 'uniquename',
),
),
'foreign keys' => array(
'cvterm' => array(
'table' => 'cvterm',
'columns' => array(
'type_id' => 'cvterm_id',
),
),
'organism' => array(
'table' => 'organism',
'columns' => array(
'organism_id' => 'organism_id',
),
),
),
// EXPLANATION: the 'referring_tables' array is the list of tables that have
// a foreign key relationships with this table. This information is required
// for the Tripal API to be able to expand tables in templates.
'referring_tables' => array(
0 => 'example_relationship',
1 => 'exampleprop',
2 => 'example_dbxref',
),
);
chado_create_custom_table('example', $schema, TRUE);
}
/**
* Adds the 'example_relationship' custom table to Chado.
*
* @ingroup tripal_example
*/
function tripal_example_add_exampleprop_table() {
// EXPLANATION: use the Drupal Schema API to describe the custom table. Then
// add the table using the chado_create_custom_table() function.
// Add the exampleprop table
$schema = array(
'table' => 'exampleprop',
'fields' => array(
'exampleprop_id' => array(
'type' => 'serial',
'not null' => TRUE,
),
'example_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'type_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'value' => array(
'type' => 'text',
'not null' => FALSE,
),
'rank' => array(
'type' => 'int',
'not null' => TRUE,
),
),
'primary key' => array(
0 => 'exampleprop_id',
),
'unique keys' => array(
'example_id_type_id_rank' => array(
0 => 'example_id',
1 => 'type_id',
2 => 'rank',
),
),
'foreign keys' => array(
'cvterm' => array(
'table' => 'cvterm',
'columns' => array(
'type_id' => 'cvterm_id',
),
),
'example' => array(
'table' => 'example',
'columns' => array(
'example_id' => 'example_id',
),
),
),
);
chado_create_custom_table('exampleprop', $schema, TRUE);
}
/**
* Adds the 'example_relationship' custom table to Chado.
*
* @ingroup tripal_example
*/
function tripal_example_add_example_relationship_table() {
// EXPLANATION: use the Drupal Schema API to describe the custom table. Then
// add the table using the chado_create_custom_table() function.
$schema = array(
'table' => 'example_relationship',
'fields' => array(
'example_relationship_id' => array(
'type' => 'serial',
'not null' => TRUE,
),
'subject_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'object_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'type_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'value' => array(
'type' => 'text',
'not null' => FALSE,
),
'rank' => array(
'type' => 'int',
'not null' => TRUE,
'default' => 0,
),
),
'primary key' => array(
0 => 'example_relationship_id',
),
'unique keys' => array(
'example_relationship_c1' => array(
0 => 'subject_id',
1 => 'object_id',
2 => 'type_id',
3 => 'rank',
),
),
'indexes' => array(
'example_relationship_idx1' => array(
0 => 'subject_id',
),
'example_relationship_idx2' => array(
0 => 'object_id',
),
'example_relationship_idx3' => array(
0 => 'type_id',
),
),
'foreign keys' => array(
'cvterm' => array(
'table' => 'cvterm',
'columns' => array(
'type_id' => 'cvterm_id',
),
),
'example' => array(
'table' => 'example',
'columns' => array(
'subject_id' => 'example_id',
'object_id' => 'example_id',
),
),
),
);
chado_create_custom_table('example_relationship', $schema, TRUE);
}
/**
* Adds the 'example_dbxref' custom table to Chado.
*
* @ingroup tripal_example
*/
function tripal_example_add_example_dbxref_table() {
// EXPLANATION: use the Drupal Schema API to describe the custom table. Then
// add the table using the chado_create_custom_table() function.
$schema = array(
'table' => 'example_dbxref',
'fields' => array(
'example_dbxref_id' => array(
'type' => 'serial',
'not null' => TRUE,
),
'example_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'dbxref_id' => array(
'type' => 'int',
'not null' => TRUE,
),
'is_current' => array(
'type' => 'int',
'size' => 'tiny',
'not null' => TRUE,
'default' => 1,
),
),
'primary key' => array(
0 => 'example_dbxref_id',
),
'unique keys' => array(
'example_dbxref_unq1' => array(
0 => 'example_id',
1 => 'dbxref_id',
),
),
'indexes' => array(
'example_dbxref_idx1' => array(
0 => 'example_id',
),
'example_dbxref_idx2' => array(
0 => 'dbxref_id',
),
),
'foreign keys' => array(
'dbxref' => array(
'table' => 'dbxref',
'columns' => array(
'dbxref_id' => 'dbxref_id',
),
),
'example' => array(
'table' => 'example',
'columns' => array(
'example_id' => 'example_id',
),
),
),
);
chado_create_custom_table('example_dbxref', $schema, TRUE);
}
/**
* This is the required update for tripal_example.
*/
function tripal_example_update_7200() {
// EXPLANATION: as you create new releases of your module you may find that
// tables your module created, or data may need to be adjusted. This function
// allows you to do that. This function is executed using the
// http://[your site]/update.php URL or using the drush command 'updatedb'.
// This function should be named according to the instructions provided here:
// https://api.drupal.org/api/drupal/modules%21system%21system.api.php/function/hook_update_N/7
//
// It is best not to use Tripal API calls inside of this function because an
// upgrade from Drupal 6 to Drupal 7 requires that all modules be disabled
// which means the Tripal API is not available. This is an unfortunate
// requirement, but will prevent errors during a major upgrade.
// it is good to wrap any database changes inside of a try catch block:
try {
// perform database changes
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Could not apply updates: '. $error);
}
}
/**
* Implementation of hook_update_dependencies(). It specifies a list of other
* modules whose updates must be run prior to this one.
*/
function tripal_example_update_dependencies() {
$dependencies = array();
// EXPLANATION: here we can specify which modules must be updated prior to
// applying the updates in this module. This is useful because it prevents
// updates from being executed out of order. The following example code shows
// that the 'tripal_example' module update number 7200 must be executed after
// the 'tripal_cv' module's 7200 update.
$dependencies['tripal_example'][7200] = array(
'tripal_cv' => 7200
);
return $dependencies;
}