tripal/tripal_organism/tripal_organism.module

<?php

require_once "api/tripal_organism.api.inc";
require_once "includes/tripal_organism.admin.inc";
require_once "includes/organism_sync.inc";

/**
 * @file
 * @defgroup tripal_organism Organism Module
 * @ingroup tripal_modules
 */

/**
 *
 * @ingroup tripal_organism
 */
function tripal_organism_init() {

  // add the jGCharts JS and CSS
  drupal_add_css(drupal_get_path('module', 'tripal_organism') . '/theme/css/tripal_organism.css');
  drupal_add_js(drupal_get_path('module', 'tripal_organism') . '/theme/js/tripal_organism.js');
}

/**
 *  Provide information to drupal about the node types that we're creating
 *  in this module
 *
 * @ingroup tripal_organism
 */
function tripal_organism_node_info() {
  $nodes = array();
  $nodes['chado_organism'] = array(
    'name' => t('Organism'),
    'base' => 'chado_organism',
    'description' => t('An organism'),
    'has_title' => FALSE,
    'title_label' => t('Organism'),
    'locked' => TRUE
  );
  return $nodes;
}

/**
 *
 * @ingroup tripal_organism
 */
function tripal_organism_block_info() {

  $blocks['base']['info'] = t('Tripal Organism Details');
  $blocks['base']['cache'] = DRUPAL_NO_CACHE;

  $blocks['description']['info'] = t('Tripal Organism Description');
  $blocks['description']['cache'] = DRUPAL_NO_CACHE;

  $blocks['image']['info'] = t('Tripal Organism Image');
  $blocks['image']['cache'] = DRUPAL_NO_CACHE;

  return $blocks;

}
/**
 *
 * @ingroup tripal_organism
 */
function tripal_organism_block_view($delta = '') {

  if (user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
    $nid = arg(1);
    $node = node_load($nid);

    $block = array();
    switch ($delta) {
      case 'base':
        $block['subject'] = t('Organism Details');
        $block['content'] = theme('tripal_organism_base', $node);
        break;
      case 'description':
        $block['subject'] = t('Organism Description');
        $block['content'] = theme('tripal_organism_description', $node);
        break;
      case 'image':
        $block['subject'] = t('Organism Image');
        $block['content'] = theme('tripal_organism_image', $node);
        break;
      default:
    }
    return $block;
  }
}
/**
 *  Menu items are automatically added for the new node types created
 *  by this module to the 'Create Content' Navigation menu item.  This function
 *  adds more menu items needed for this module.
 *
 * @ingroup tripal_organism
 */
function tripal_organism_menu() {
  $items = array();

  // the administative settings menu
  $items['admin/tripal/chado/tripal_organism'] = array(
   'title' => 'Organisms',
   'description' => 'Any living biological entity, such as an animal, plant, fungus, or bacterium.',
   'page callback' => 'tripal_organism_admin_organism_view',
   'access arguments' => array('adminster tripal organism'),
   'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_organism/help'] = array(
   'title' => 'Help',
   'description' => "A description of the Tripal Organism module including a short description of it's usage.",
   'page callback' => 'theme',
   'page arguments' => array('tripal_organism_help'),
   'access arguments' => array('adminster tripal organism'),
   'type' => MENU_LOCAL_TASK,
  );

  $items['admin/tripal/chado/tripal_organism/configuration'] = array(
   'title' => 'Settings',
   'description' => 'Manage integration of Chado organisms including associated features',
   'page callback' => 'drupal_get_form',
   'page arguments' => array('tripal_organism_admin'),
   'access arguments' => array('adminster tripal organism'),
   'type' => MENU_LOCAL_TASK,
  );

  $items['admin/tripal/chado/tripal_organism/sync'] = array(
    'title' => 'Sync',
    'description' => 'Sync Chado organisms with Drupal',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_organism_sync'),
    'access arguments' => array('adminster tripal organism'),
    'type' => MENU_LOCAL_TASK,
  );

  $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
    'title' => 'Enable Organism Administrative View',
    'page callback' => 'tripal_views_admin_enable_view',
    'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/chado/tripal_organism'),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_organism_help ($path, $arg) {
  if ($path == 'admin/help#tripal_organism') {
    return theme('tripal_organism_help', array());
  }
}

/**
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 *
 * @ingroup tripal_organism
 */
function tripal_organism_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  $items = array(
    'node__chado_organism' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),
    'tripal_organism_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_base',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_description' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_description',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_image' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_image',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_teaser',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_help' => array(
      'template' => 'tripal_organism_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme",
    ),
  );
  return $items;
}
/**
 *
 * @ingroup tripal_feature
 */
function tripal_organism_node_view($node, $view_mode, $langcode) {
  switch ($node->type) {
  	case 'chado_organism':
  	  // Show feature browser and counts
  	  if ($view_mode == 'full') {
  	    $node->content['tripal_organism_base'] = array(
  	      '#value' => theme('tripal_organism_base', array('node' => $node)),
  	    );
  	  }
  	  if ($view_mode == 'teaser') {
        $node->content['tripal_organism_teaser'] = array(
          '#value' => theme('tripal_organism_teaser', array('node' => $node)),
        );
      }
  	  break;
  }
}
/**
  *  Set the permission types that the chado module uses.  Essentially we
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
  *
  *
  @ingroup tripal_organism
  */
function tripal_organism_permission() {
  return array(
    'access chado_organism content' => array(
      'title' => t('View Organisms'),
      'description' => t('Allow users to view organism pages.'),
    ),
    'create chado_organism content' => array(
      'title' => t('Create Organisms'),
      'description' => t('Allow users to create new organism pages.'),
    ),
    'delete chado_organism content' => array(
      'title' => t('Delete Organisms'),
      'description' => t('Allow users to delete organism pages.'),
    ),
    'edit chado_organism content' => array(
      'title' => t('Edit Organisms'),
      'description' => t('Allow users to edit organism pages.'),
    ),
    'adminster tripal organism' => array(
      'title' => t('Administer Organisms'),
      'description' => t('Allow users to administer all organisms.'),
    ),
  );
}
/**
 * Implements hook_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_organism
 */
function tripal_organism_views_api() {
  return array(
    'api' => 3.0,
  );
}
/**
 *
 *
 * @ingroup tripal_organism
 */
function tripal_organism_job_describe_args($callback, $args) {

  $new_args = array();
  if ($callback == 'tripal_organism_sync_organisms') {
    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0]));
    $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
  }
  return $new_args;
}
/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $op
 *  The operation to be performed
 *
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_organism
 */
function chado_organism_node_access($node, $op, $account) {
  if ($op == 'create') {
    if (!user_access('create chado_organism content', $account)) {
      return FALSE;
    }
    return TRUE;
  }
  if ($op == 'update') {
    if (!user_access('edit chado_organism content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_organism content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_organism content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}
/**
 * Implementation of hook_validate
 *
 * @param $node
 * @param $form
 * @param $form_state
 *
 *  @ingroup tripal_organism
 */
function chado_organism_validate($node, $form, &$form_state) {
  // remove any white space around values
  $node->genus        = trim($node->genus);
  $node->species      = trim($node->species);
  $node->abbreviation = trim($node->abbreviation);
  $node->common_name  = trim($node->common_name);
  $node->description  = trim($node->description);

  // if this is an update, we want to make sure that a different organism doesn't
  // already have this genus and speces
  if (property_exists($node, 'organism_id')) {
    $sql = "
      SELECT *
      FROM {organism} O
      WHERE
        genus = :genus AND
        species = :species AND NOT
        organism_id = :organism_id
    ";
    $args = array(':genus' => $node->genus, ':species' => $node->species, ':organism_id' => $node->organism_id);
    $result = chado_query($sql, $args)->fetchObject();
    if ($result) {
      form_set_error('genus', t("Update cannot proceed. The organism genus
        '$node->genus' and species '$node->species' is already present in the database."));
      watchdog('tripal_organism',
        'Update organism: genus and species already exists: %values',
        array('%values' => "genus = $node->genus, species = $node->species"),
        WATCHDOG_WARNING);
    }
  }
  // if this is an insert then check to make sure the genus and species are unique
  else {
    $values = array(
      'genus' => $node->genus,
      'species' => $node->species,
    );
    $organism = tripal_core_chado_select('organism', array('organism_id'), $values);
    if (sizeof($organism) > 0) {
      form_set_error('genus', 'Cannot add the organism with this genus and species.
        The organism already exists.');
      watchdog('tripal_organism',
        'Insert organism: genus and species already exists: %values',
        array('%values' => "genus = $node->genus, species = $node->species"),
        WATCHDOG_WARNING);
    }
  }
}
/**
 *  When a new chado_organism node is created we also need to add information
 *  to our chado_organism table.  This function is called on insert of a new node
 *  of type 'chado_organism' and inserts the necessary information.
 *
 * @ingroup tripal_organism
 */
function chado_organism_insert($node) {
  // remove any white space around values
  $node->genus        = trim($node->genus);
  $node->species      = trim($node->species);
  $node->abbreviation = trim($node->abbreviation);
  $node->common_name  = trim($node->common_name);
  $node->description  = trim($node->description);

  // if there is an organism_id in the $node object then this must be a sync so
  // we can skip adding the organism as it is already there, although
  // we do need to proceed with the rest of the insert
  if (!property_exists($node,'organism_id')) {
    $values = array(
      'genus'        => $node->genus,
      'species'      => $node->species,
      'abbreviation' => $node->abbreviation,
      'common_name'  => $node->common_name,
      'comment'      => $node->description
    );
    $organism = tripal_core_chado_insert('organism', $values);
    if (!$organism) {
      drupal_set_message(t('Unable to add organism.', 'warning'));
      watchdog('tripal_organism', 'Insert Organism: Unable to create organism where values:%values',
        array('%values' => print_r($values, TRUE)), WATCHDOG_ERROR);
      return;
    }
    $organism_id = $organism['organism_id'];
  }
  else {
    $organism_id = $node->organism_id;
  }

  // Make sure the entry for this organism doesn't already exist in the
  // chado_organism table if it doesn't exist then we want to add it.
  $check_org_id = chado_get_id_for_node('organism', $node->nid);
  if (!$check_org_id) {
    $record = new stdClass();
    $record->nid = $node->nid;
    $record->vid = $node->vid;
    $record->organism_id = $organism_id;
    drupal_write_record('chado_organism', $record);
  }

  // set the title for the node
  $record = new stdClass();
  $record->title = "$node->genus $node->species";
  $record->nid = $node->nid;
  drupal_write_record('node', $record, 'nid');
  drupal_write_record('node_revisions', $record, 'nid');

  // add the image
  chado_organism_add_image($node);
}
/**
 * Update organisms
 *
 * @ingroup tripal_organism
 */
function chado_organism_update($node) {
  // remove any white space around values
  $node->genus        = trim($node->genus);
  $node->species      = trim($node->species);
  $node->abbreviation = trim($node->abbreviation);
  $node->common_name  = trim($node->common_name);
  $node->description  = trim($node->description);

  if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }
  $match = array(
    'organism_id' => chado_get_id_for_node('organism', $node->nid),
  );
  $values = array(
    'genus' => $node->genus,
    'species' => $node->species,
    'abbreviation' => $node->abbreviation,
    'common_name' => $node->common_name,
    'comment' => $node->description
  );
  $org_status = tripal_core_chado_update('organism', $match, $values);

  // set the title for the node
  $record = new stdClass();
  $record->title = "$node->genus $node->species";
  $record->nid = $node->nid;
  drupal_write_record('node', $record, 'nid');
  drupal_write_record('node_revisions', $record, 'nid');

  // add the image
  chado_organism_add_image($node);
}
/**
 * Delete organism from both drupal and chado databases. Check dependency before
 * deleting from chado.
 *
 * @ingroup tripal_organism
 */
function chado_organism_delete($node) {
  $organism_id = chado_get_id_for_node('organism', $node->nid);

  // if we don't have an organism id for this node then this isn't a node of
  // type chado_organism or the entry in the chado_organism table was lost.
  if (!$organism_id) {
    return;
  }

  // Remove data from the {chado_organism}, {node}, and {node_revisions} tables
  $sql_del = "DELETE FROM {chado_organism} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node_revision} WHERE nid = ':nid' AND vid = ':vid'";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));

  // Test dependency before deleting from chado database. If a library or
  // feature depends on this organism, don't delete it

  $sql = "SELECT feature_id FROM {feature} WHERE organism_id = :organism_id";
  $check_feature = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
  $sql = "SELECT library_id FROM {library} WHERE organism_id = :organism_id";
  $check_lib = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();

  if (!$check_lib && !$check_feature) {
    tripal_core_chado_delete('organism', array('organism_id' => $organism_id));
  }
  else {
    drupal_set_message(t("Organism deleted from drupal. Warning: at least one " .
      "library or feature depends on this organism. It was not removed from chado."));
  }
}

/**
 *
 *
 * @ingroup tripal_organism
 */
function chado_organism_add_image($node) {
  // check to see if a file was uploaded. If so then copy it to the images
  // directory for display with the organism
  if (isset($_FILES['files']) &&
      $_FILES['files']['name']['organism_image'] &&
      is_uploaded_file($_FILES['files']['tmp_name']['organism_image'])) {

    // make sure the destination directory exists
    $dest = tripal_file_directory_path() . "/tripal_organism/images";
    file_prepare_directory($dest, FILE_CREATE_DIRECTORY);

    // now move the file
    $validators = array('file_validate_is_image' => array());
    $destination = "public://tripal/tripal_organism/images/";
    $file = file_save_upload('organism_image', $validators, $destination);
    if (!$file) {
      drupal_set_message(t("Organism image was not uploaded."));
    }
    else {
      file_move($file, $destination . "/" . $node->nid . ".jpg", FILE_EXISTS_REPLACE);
    }
  }
}


/**
 *  When editing or creating a new node of type 'chado_organism' we need
 *  a form.  This function creates the form that will be used for this.
 *
 * @ingroup tripal_organism
 */
function chado_organism_form($node, $form_state) {
  $form = array();

  // we have a file upload element on the form soe we need the multipart encoding type
  $form['#attributes']['enctype'] = 'multipart/form-data';

  // if the organism is part of the node object then we are editing. If not we are inserting
  if (property_exists($node, 'organism')) {
    $organism = $node->organism;

    // add in the comment since it is a text field and may not be included if too big
    $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');

    // get form defaults
    $abbreviation   = property_exists($node, 'abbreviation')   ? property_exists($node, 'abbreviation')   : $organism->abbreviation;
    $genus          = property_exists($node, 'genus')          ? property_exists($node, 'genus')          : $organism->genus;
    $species        = property_exists($node, 'species')        ? property_exists($node, 'species')        : $organism->species;
    $common_name    = property_exists($node, 'common_name')    ? property_exists($node, 'common_name')    : $organism->common_name;
    $description    = property_exists($node, 'description')    ? property_exists($node, 'description')    : $organism->comment;
    $organism_image = property_exists($node, 'organism_image') ? property_exists($node, 'organism_image') : '';

    // set the organism_id in the form
    $form['organism_id'] = array(
      '#type' => 'value',
      '#value' => $organism->organism_id,
    );
  }
  else {
    // get form defaults
    $abbreviation   = property_exists($node, 'abbreviation')   ? property_exists($node, 'abbreviation')   : '';
    $genus          = property_exists($node, 'genus')          ? property_exists($node, 'genus')          : '';
    $species        = property_exists($node, 'species')        ? property_exists($node, 'species')        : '';
    $common_name    = property_exists($node, 'common_name')    ? property_exists($node, 'common_name')    : '';
    $description    = property_exists($node, 'description')    ? property_exists($node, 'description')    : '';
    $organism_image = property_exists($node, 'organism_image') ? property_exists($node, 'organism_image') : '';
  }

  $form['abbreviation']= array(
    '#type' => 'textfield',
    '#title' => t('Abbreviation'),
    '#required' => TRUE,
    '#default_value' => $abbreviation,
  );
  $form['genus']= array(
    '#type' => 'textfield',
    '#title' => t('Genus'),
    '#required' => TRUE,
    '#default_value' => $genus,
  );
  $form['species']= array(
    '#type' => 'textfield',
    '#title' => t('Species'),
    '#required' => TRUE,
    '#default_value' => $species,
  );
  $form['common_name']= array(
    '#type' => 'textfield',
    '#title' => t('Common Name'),
    '#required' => TRUE,
    '#default_value' => $common_name,
  );
  $form['description']= array(
    '#type' => 'textarea',
    '#rows' => 15,
    '#title' => t('Description'),
    '#default_value' => $description,
  );
  $form['organism_image']= array(
    '#type' => 'file',
    '#title' => t('Organism Image'),
    '#description' => 'Add an image for this organism',
    '#progress_indicator' => 'bar',
  );
  return $form;
}

/**
 *  When a node is requested by the user this function is called to allow us
 *  to add auxiliary data to the node object.
 *
 * @ingroup tripal_organism
 */
function chado_organism_load($nodes) {

  foreach ($nodes as $nid => $node) {
    // find the organism and add in the details
    $organism_id = chado_get_id_for_node('organism', $nid);

    // build the organism variable
    $values = array('organism_id' => $organism_id);
    $organism = tripal_core_generate_chado_var('organism', $values);


    // add in the description field
    $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
    $nodes[$nid]->organism = $organism;
  }
}