tripal_file.module

<?php

/**
 * @file
 * This file contains all Drupal hooks for the module other than any
 * node hooks and block hooks. Those go in the [module name].chado_node.inc file
 * and [module_name].blocks.inc respectively
 *
 */

// EXPLANATION: include any files needed for this module.  That includes any
// API file, the theme file, or include files.
require_once('api/tripal_file.api.inc');
require_once('theme/tripal_file.theme.inc');
require_once('includes/tripal_file.admin.inc');

/**
 * Implements hook_menu().
 */
function tripal_file_menu() {

  // tripal file administration page
  $items['admin/tripal/extension/tripal_file'] = [
    'title' => 'Tripal File User Interface',
    'description' => 'A module for associating files with Tripal content and for accessing files via web services.',
    'page callback' => 'drupal_get_form',
    'page arguments' => ['tripal_file_admin_form'],
    'access arguments' => ['administer tripal'],
    'type' => MENU_NORMAL_ITEM,
  ];
  $items['admin/tripal/extension/tripal_file/config'] = [
    'title' => 'Configuration',
    'type' => MENU_DEFAULT_LOCAL_TASK,
  ];
  $items['admin/tripal/extension/tripal_file/help'] = [
    'title' => 'Help',
    'page callback' => 'theme',
    'page arguments' => ['tripal_file_help'],
    'access arguments' => ['administer tripal'],
    'type' => MENU_LOCAL_TASK,
  ];
  // Autocomplete for e.g. sbo__relationship widget.
  $items['admin/tripal/storage/chado/auto_name/file/%'] = [
    'page callback' => 'chado_autocomplete_file',
    'page arguments' => [6],
    'access arguments' => ['access content'],
    'file' => 'api/tripal_file.api.inc',
    'file path' => drupal_get_path('module', 'tripal_file'),
    'type' => MENU_CALLBACK,
  ];

  return $items;
}

/**
 * Implements hook_theme().
 */
function tripal_file_theme() {

  // Module Help
  $path = drupal_get_path('module', 'tripal_file');
  $items['tripal_file_help'] = [
    'template' => 'tripal_file_help',
    'path' => "$path/theme",
  ];

  return $items;
}

/**
 * Implements hook_help().
 */
function tripal_file_help($path, $arg) {
  if ($path == 'admin/help#tripal_file') {
    return theme('tripal_file_help', []);
  }
}

/**
 * Implements hook_views_api()
 *
 * This hook tells drupal that there is views support for
 * this module which then automatically includes the tripal_db.views.inc
 * where all the views integration code is found.
 *
 * @ingroup tripal_file
 */
function tripal_file_views_api() {
  return [
    'api' => 3.0,
  ];
}

/**
 * Implements hook_bundle_fields_info().
 *
 * This is a Tripal defined hook that supports integration with the
 * TripalEntity field.
 */
function tripal_file_bundle_fields_info($entity_type, $bundle) {
  $info = [];
  $chado_bundle = db_select('chado_bundle', 'cb')
    ->fields('cb')
    ->condition('bundle_id', $bundle->id)
    ->execute()
    ->fetchObject();

  if ($chado_bundle->data_table == 'file') {
    $info['schema__itemlocation'] = [
      'field_name' => 'schema__itemlocation',
      'type' => 'schema__itemlocation',
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => [
        'type' => 'field_chado_storage',
      ],
    ];

    $info['schema__license'] = [
      'field_name' => 'schema__license',
      'type' => 'schema__license',
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => [
        'type' => 'field_chado_storage',
      ],
    ];

    $info['sio__references_file'] = [
      'field_name' => 'sio__references_file',
      'type' => 'sio__references_file',
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => [
        'type' => 'field_chado_storage',
      ],
    ];
  }

  // If a _file linker table exists for the base data table.
  if (chado_table_exists($chado_bundle->data_table . '_file')) {
    $info['sio__file'] = [
      'field_name' => 'sio__file',
      'type' => 'sio__file',
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => [
        'type' => 'field_chado_storage',
      ],
    ];
  }
  return $info;
}

/**
 * Implements hook_create_tripalfield_instance().
 *
 * This is a Tripal defined hook that supports integration with the
 * TripalEntity field.
 */
function tripal_file_bundle_instances_info($entity_type, $bundle) {
  $info = [];
  $chado_bundle = db_select('chado_bundle', 'cb')
    ->fields('cb')
    ->condition('bundle_id', $bundle->id)
    ->execute()
    ->fetchObject();

  if ($chado_bundle->data_table == 'file') {
    $info['schema__itemlocation'] = [
      'field_name' => 'schema__itemlocation',
      'entity_type' => 'TripalEntity',
      'bundle' => $bundle->name,
      'label' => 'Download',
      'description' => 'The download location of the file.',
      'required' => TRUE,
      'settings' => [
        'auto_attach' => TRUE,
        'chado_table' => 'fileloc',
        'chado_column' => 'file_id',
        'base_table' => 'file',
        'term_accession' => 'itemLocation',
        'term_vocabulary' => 'schema',
        'term_name' => 'itemLocation',
      ],
      'widget' => [
        'type' => 'schema__itemlocation_widget',
        'settings' => [
          'display_label' => 1,
        ],
      ],
      'display' => [
        'default' => [
          'label' => 'inline',
          'type' => 'schema__itemlocation_formatter',
          'settings' => [],
        ],
      ],
    ];

    $info['schema__license'] = [
      'field_name' => 'schema__license',
      'entity_type' => 'TripalEntity',
      'bundle' => $bundle->name,
      'label' => 'License',
      'description' => 'The license for the file.',
      'required' => TRUE,
      'settings' => [
        'auto_attach' => TRUE,
        'chado_table' => 'file_license',
        'chado_column' => 'file_license_id',
        'base_table' => 'file',
        'term_accession' => 'license',
        'term_vocabulary' => 'schema',
        'term_name' => 'license',
      ],
      'widget' => [
        'type' => 'schema__license_widget',
        'settings' => [
          'display_label' => 1,
        ],
      ],
      'display' => [
        'default' => [
          'label' => 'inline',
          'type' => 'schema__license_formatter',
          'settings' => [],
        ],
      ],
    ];

    $info['sio__references_file'] = [
      'field_name' => 'sio__references_file',
      'entity_type' => 'TripalEntity',
      'bundle' => $bundle->name,
      'label' => 'References',
      'description' => 'Content that references this file.',
      'required' => FALSE,
      'settings' => [
        'auto_attach' => FALSE,
        'chado_table' => 'file',
        'chado_column' => 'file_id',
        'base_table' => 'file',
        'term_accession' => '000631',
        'term_vocabulary' => 'SIO',
        'term_name' => 'references',
      ],
      'widget' => [
        'type' => 'sio__references_file_widget',
        'settings' => [
          'display_label' => 1,
        ],
      ],
      'display' => [
        'default' => [
          'label' => 'inline',
          'type' => 'sio__references_file_formatter',
          'settings' => [],
        ],
      ],
    ];
  }

  // If a _file linker table exists for the base data table.
  if (chado_table_exists($chado_bundle->data_table . '_file')) {
    $base_table = $chado_bundle->data_table;
    $chado_table = $chado_bundle->data_table . '_file';
    $info['sio__file'] = [
      'field_name' => 'sio__file',
      'entity_type' => 'TripalEntity',
      'bundle' => $bundle->name,
      'label' => 'File',
      'description' => 'A file.',
      'required' => FALSE,
      'settings' => [
        'auto_attach' => FALSE,
        'chado_table' => $chado_table,
        'chado_column' => $chado_table . '_id',
        'base_table' => $base_table,
        'term_accession' => '000396',
        'term_vocabulary' => 'SIO',
        'term_name' => 'file',
      ],
      'widget' => [
        'type' => 'sio__file_widget',
        'settings' => [
          'display_label' => 1,
        ],
      ],
      'display' => [
        'default' => [
          'label' => 'inline',
          'type' => 'sio__file_formatter',
          'settings' => [],
        ],
      ],
    ];
  }
  return $info;
}

/**
 * Implements hook_bundle_fields_info_alter().
 */
function tripal_file_bundle_fields_info_alter(&$info, $bundle, $term) {

}

/**
 * Implements hook_bundle_fields_info_alter().
 */
function tripal_file_bundle_instances_info_alter(&$info, $bundle, $term) {
  if (!$info) {
    return;
  }

  if (array_key_exists('file_contact', $info)) {
    $info['file_contact']['label'] = 'File Source';
  }

  // Fields for the File content type.
  if ($bundle->accession == 'SIO:000396') {
    $info['schema__name']['widget']['type'] = 'text_textfield';
    $info['schema__name']['settings']['text_processing'] = '0';

  }

  // Fields for the License content type.
  if ($bundle->accession == 'schema:license') {
    // We don't want the URL to be a textfield:
    $info['data__uri']['label'] = 'URI';
    $info['data__uri']['widget']['type'] = 'text_textfield';
    $info['data__uri']['settings']['text_processing'] = '0';
  }
}

/**
 * Implements hook_tripal_default_title_format().
 *
 * Overrides the default titles.
 */
function tripal_file_tripal_default_title_format($bundle, $available_tokens) {
  $format = [];

  $table = $bundle->data_table;

  if ($table == 'file') {
    $format[] = [
      'format' => '[schema__name]',
      'weight' => -5,
    ];
  }
  if ($table == 'license') {
    $format[] = [
      'format' => '[schema__name]',
      'weight' => -5,
    ];
  }
  return $format;
}