<?php
/**
* @file
* Handles install, uninstall, disable and enable functionality including database tables.
*
* @ingroup tripal_contact
*/
/**
* Implements hook_disable().
* Disable default views when module is disabled
*
* @ingroup tripal_contact
*/
function tripal_contact_disable() {
// Disable all default views provided by this module
require_once("tripal_contact.views_default.inc");
$views = tripal_contact_views_default_views();
foreach (array_keys($views) as $view_name) {
tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
}
}
/**
* Implementation of hook_requirements().
*
* @ingroup tripal_contact
*/
function tripal_contact_requirements($phase) {
$requirements = array();
if ($phase == 'install') {
// make sure chado is installed
if (!$GLOBALS["chado_is_installed"]) {
$requirements ['tripal_contact'] = array(
'title' => "tripal_contact",
'value' => "ERROR: Chado must be installed before this module can be enabled",
'severity' => REQUIREMENT_ERROR,
);
}
}
return $requirements;
}
/**
* Implementation of hook_install().
*
* @ingroup tripal_contact
*/
function tripal_contact_install() {
// Add the contactprop table to Chado.
tripal_contact_add_custom_tables();
// Add loading of the the tripal contact ontology to the job queue.
$obo_path = '{tripal_contact}/files/tcontact.obo';
$obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
tripal_submit_obo_job(array('obo_id' => $obo_id));
// Add cvterms for relationship types.
tripal_contact_add_cvs();
tripal_contact_add_cvterms();
// Set the default vocabularies.
tripal_set_default_cv('contact', 'type_id', 'tripal_contact');
tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
tripal_set_default_cv('contact_relationship', 'type_id', 'contact_relationship');
}
/**
* Implementation of hook_uninstall().
*
* @ingroup tripal_contact
*/
function tripal_contact_uninstall() {
/*
// remove our custom block visibility settings per node type
db_delete('block_node_type')
->condition('module', 'chado_contact')
->condition('delta', 'contbase')
->execute();
*/
}
/**
* Adds any cvs needed by this module.
*
* @ingroup tripal_contact
*/
function tripal_contact_add_cvs() {
// Add the cv for contact properties. This is a default vocabulary in the event
// that a user does not want to use the tripal_contact vocabulary
tripal_insert_cv(
'contact_property',
'Contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
);
// add the cv for the contact type. This is a default vocabulary in the event
// that a user does not want to use the tripal_contact vocabulary
tripal_insert_cv(
'contact_type',
'Contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
);
// Add the cv for the tripal_contact vocabulary which is loaded via the OBO
tripal_insert_cv(
'tripal_contact',
'A heirarchical set of terms for describing a contact. It is intended to be used as the default vocabularies in Tripal for contact types and contact properties.'
);
// add the cv for contact relationships
tripal_insert_cv(
'contact_relationship',
'Contains types of relationships between contacts.'
);
}
/**
* Adds any cvterms needed by this module.
*
* @ingroup tripal_contact
*/
function tripal_contact_add_cvterms() {
}
/**
* Implementation of hook_schema().
*
* @ingroup tripal_contact
*/
function tripal_contact_schema() {
$schema['chado_contact'] = 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
),
'contact_id' => array(
'type' => 'int',
'not null' => TRUE,
'default' => 0
)
),
'indexes' => array(
'contact_id' => array('contact_id')
),
'unique keys' => array(
'nid_vid' => array('nid', 'vid'),
'vid' => array('vid')
),
'primary key' => array('nid'),
);
return $schema;
}
/**
* Add any custom tables needed by this module.
* - Contactprop: keep track of properties of contact
*
* @ingroup tripal_contact
*/
function tripal_contact_add_custom_tables(){
$schema = array (
'table' => 'contactprop',
'fields' => array (
'contactprop_id' => array (
'type' => 'serial',
'not null' => true,
),
'contact_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 => 'contactprop_id',
),
'unique keys' => array (
'contactprop_c1' => array (
0 => 'contact_id',
1 => 'type_id',
2 => 'rank',
),
),
'indexes' => array (
'contactprop_idx1' => array (
0 => 'contact_id',
),
'contactprop_idx2' => array (
0 => 'type_id',
),
),
'foreign keys' => array (
'cvterm' => array (
'table' => 'cvterm',
'columns' => array (
'type_id' => 'cvterm_id',
),
),
'contact' => array (
'table' => 'contact',
'columns' => array (
'contact_id' => 'contact_id',
),
),
),
);
chado_create_custom_table('contactprop', $schema, TRUE);
}
/**
* This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
*
*/
function tripal_contact_update_7200() {
// We cannot use the Tripal API calls in the 7200 update
// because during upgrade the tripal_core will be disabled
// add the contact_type CV
try {
$cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'tripal_contact'")->fetchField();
if (!$cv_id) {
// add the vocabulary
$cv_id = db_insert('chado.cv')
->fields(array(
'name' => 'tripal_contact',
'definition' => 'A heirarchical set of terms for describing a contact. It is intended to be used as the default vocabularies in Tripal for contact types and contact properties.'
))
->execute();
}
// make this CV the defaults for the contact properties and contact types
db_insert('tripal_cv_defaults')
->fields(array(
'table_name' => 'contact',
'field_name' => 'type_id',
'cv_id' => $cv_id
))
->execute();
db_insert('tripal_cv_defaults')
->fields(array(
'table_name' => 'contactprop',
'field_name' => 'type_id',
'cv_id' => $cv_id
))
->execute();
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Failed to add tripal_contact vocabulary: '. $error);
}
// add the contact_relationship CV
try {
$cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_relationship'")->fetchField();
if (!$cv_id) {
// add the vocabulary
$cv_id = db_insert('chado.cv')
->fields(array(
'name' => 'contact_relationship',
'definition' => 'Contains types of relationships between contacts.'
))
->execute();
}
// add the default
db_insert('tripal_cv_defaults')
->fields(array(
'table_name' => 'contact_relationship',
'field_name' => 'type_id',
'cv_id' => $cv_id
))
->execute();
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Failed to add contact_type vocabulary: '. $error);
}
// add the contact_type CV
try {
$cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_type'")->fetchField();
if (!$cv_id) {
// add the vocabulary
$cv_id = db_insert('chado.cv')
->fields(array(
'name' => 'contact_type',
'definition' => 'Contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
))
->execute();
}
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Failed to add contact_type vocabulary: '. $error);
}
// add the contact_property CV
try {
$cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_property'")->fetchField();
if (!$cv_id) {
// add the vocabulary
$cv_id = db_insert('chado.cv')
->fields(array(
'name' => 'contact_property',
'definition' => 'Contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
))
->execute();
}
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Failed to add contact_property vocabulary: '. $error);
}
}
/**
* Implementation of hook_update_dependencies(). It specifies a list of
* other modules whose updates must be run prior to this one.
*/
function tripal_contact_update_dependencies() {
$dependencies = array();
// the tripal_cv update 7200 must run prior to update 7200 of this module
$dependencies['tripal_contact'][7200] = array(
'tripal_cv' => 7200
);
return $dependencies;
}
/**
* Adds missing foreign key constraints
*
*/
function tripal_contact_update_7201() {
// there was a bug in the function for creating a custom table that
// kept foreign key constraints from being added. So, we need to add those
// to keep from error messages appear, we will drop the FK if it already
// exists and then re-add it.
try {
$fkey_exists = db_query('SELECT TRUE FROM pg_constraint WHERE conname = :constraint', array(':constraint' => 'contactprop_type_id_fkey'))->fetchField();
if ($fkey_exists) {
db_query('
ALTER TABLE chado.contactprop
DROP CONSTRAINT contactprop_type_id_fkey CASCADE
');
db_query('
ALTER TABLE chado.contactprop
DROP CONSTRAINT contactprop_contact_id_fkey CASCADE
');
}
db_query('
ALTER TABLE chado.contactprop
ADD CONSTRAINT contactprop_type_id_fkey
FOREIGN KEY (type_id) REFERENCES chado.cvterm (cvterm_id)
ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
');
db_query('
ALTER TABLE chado.contactprop
ADD CONSTRAINT contactprop_contact_id_fkey
FOREIGN KEY (contact_id) REFERENCES chado.contact (contact_id)
ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
');
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Failed to update foriegn key: '. $error);
}
}
/**
* Updates path of tripal_contact OBO to be relative.
*/
function tripal_contact_update_7202() {
try {
// Remove duplicates.
db_delete('tripal_cv_obo')
->condition('name', 'Tripal Contacts')
->execute();
// Add in the updated path.
$obo_path = '{tripal_contact}/files/tcontact.obo';
$obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
}
catch (\PDOException $e) {
$error = $e->getMessage();
throw new DrupalUpdateException('Failed to update tripal_contact OBO path: '. $error);
}
}