tripal/tripal_pub/tripal_pub.module

<?php

require_once "api/tripal_pub.api.inc";
require_once "includes/tripal_pub.admin.inc";
require_once "includes/pub_sync.inc";
require_once "includes/pub_form.inc";
require_once "includes/pub_importers.inc";
require_once "includes/pub_search.inc";
require_once "includes/pub_citation.inc";
require_once "includes/importers/PMID.inc";
require_once "includes/importers/AGL.inc";
/**
 * @file
 *
 * The Tripal Publication module allows you to search the PubMed databse for academic articles,
 * that relate to user specified tpoic\s. As well, it allows management of publications so that
 * a user can enter specified details regarding a desired publication. This allows all of the important
 * information that is unique to a Academic Publication to be stored for access.
 */


/**
 *
 * @ingroup tripal_pub
 */
function tripal_pub_init() {
  drupal_add_css(drupal_get_path('module', 'tripal_pub') . '/theme/css/tripal_pub.css');
  drupal_add_js(drupal_get_path('module', 'tripal_pub') . '/theme/js/tripal_pub.js');
}


/**
 * Implementation of hook_tripal_pub_node_info().
 *
 * This node_info, is a simple node that describes the functionallity of the module.
 *
 */
function tripal_pub_node_info() {

  return array(
    'chado_pub' => array(
      'name' => t('Publication'),
      'base' => 'chado_pub',
      'description' => t('A publication from the Chado database'),
      'title_label' => t('Article Title'),
      'body_label' => t('Abstract'),
      'has_title' => TRUE,
      'has_body' => FALSE,
  ),
  );
}

/**
 * Tripal-Publication-Menu
 *
 * Implemets hook_menu(): Adds menu items for the tripal_pub module menu. This section
 * gives the outline for the main menu of the Tripal-Publication module
 *
 * @return
 *   An array of menu items that is visible within the Drupal Menu, returned as soon
 *   as the program is ran
 */
function tripal_pub_menu() {
  $items = array();


  $items['find/publications' ]= array(
    'title' => 'Publication Search',
    'description' => ('Search for publications'),
    'page callback' => 'tripal_pub_search_page',
    'access arguments' => array('access chado_pub content'),
    'type' => MENU_CALLBACK
  );

  $items['find/publications/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_search_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('access chado_pub content'),    
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub']= array(
    'title' => 'Publications',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_pub_help'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/tripal_pub/configuration'] = array(
    'title' => 'Configuration',
    'description' => 'Configure the Tripal publication module.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_help'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/tripal_pub/sync'] = array(
    'title' => ' Sync Publications',
    'description' => 'Sync publications in Chado with Drupal',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_sync_form'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM,
  );


  $items['admin/tripal/tripal_pub/import_list'] = array(
    'title' => t('Importers List'),
    'description' => t('List all publication importers'),
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub/import/new'] = array(
    'title' => t('Add an Importer'),
    'description' => t('Add a new publication importer.'),
    'page callback' => 'tripal_pub_importer_setup',
    'page arguments' => array(4, NULL),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub/import/raw/%'] = array(
    'page callback' => 'tripal_pub_get_raw_data',
    'page arguments' => array(5),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub/import/edit/%'] = array(
    'page callback' => 'tripal_pub_importer_setup',
    'page arguments' => array(4, 5),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub/import/delete/%'] = array(
    'page callback' => 'tripal_pub_importer_delete',
    'page arguments' => array(5),
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );
  $items['admin/tripal/tripal_pub/import/changedb'] = array(
    'page callback' => 'tripal_pub_importer_setup_page_update_remotedb',
    'page arguments' => array(),
    'access arguments' => array('administer tripal pubs'),    
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub/import/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_importer_setup_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('administer tripal pubs'),    
    'type ' => MENU_CALLBACK,
  );

  $items['tripal_pub/properties/add'] = array(
    'page callback' => 'tripal_pub_property_add',
    'access arguments' => array('edit chado_pub content'),
    'type ' => MENU_CALLBACK,
  );
  $items['tripal_pub/properties/description'] = array(
    'page callback' => 'tripal_pub_property_get_description',
    'access arguments' => array('edit chado_pub content'),
    'type ' => MENU_CALLBACK,
  );
  $items['tripal_pub/properties/minus/%/%'] = array(
    'page callback' => 'tripal_pub_property_delete',
    'page arguments' => array(3, 4),
    'access arguments' => array('edit chado_pub content'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/tripal_pub/citation'] = array(
      'title' => ' Create Citations',
      'description' => 'Create citations in Chado with Drupal',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_pub_citation_form'),
      'access arguments' => array('administer tripal pubs'),
      'type' => MENU_NORMAL_ITEM,
  );

  return $items;
}


/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 *
 * @return
 *   An array of themeing functions to register
 *
 */
function tripal_pub_theme() {
  $theme_path = drupal_get_path('module', 'tripal_pub') . '/theme';
  $items = array(
    // node templates
    'tripal_pub_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_properties' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_authors' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_references' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_relationships' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_featuremaps' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_features' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_libraries' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_projects' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),
    'tripal_pub_stocks' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_project_base',
      'path' => "$theme_path/tripal_pub",
    ),

    // instructions page for the pub module
    'tripal_pub_help' => array(
      'template' => 'tripal_pub_help',  
      'arguments' =>  array(NULL),  
      'path' => $theme_path, 
    ),

    // themed forms
    'tripal_pub_importer_setup_form' => array(
      'arguments' => array('form'),
    ),
    'tripal_pub_search_form' => array(
      'arguments' => array('form'),
    ),
    'chado_pub_node_form' => array(
      'arguments' => array('form'),
    ),
  );

  return $items;
}

/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_pub_help ($path, $arg) {
  if ($path == 'admin/help#tripal_pub') {
    return theme('tripal_pub_help', array());
  }
}
/**
 * Implement hook_permissions().
 */
function tripal_pub_permissions() {
  return array(
    'access chado_pub content' => array(
      'title' => t('View Publications'),
      'description' => t('Allow users to view publication pages.'),
    ),
    'create chado_pub content' => array(
      'title' => t('Create Publication'),
      'description' => t('Allow users to create new publication pages.'),
    ),
    'delete chado_pub content' => array(
      'title' => t('Delete Publication'),
      'description' => t('Allow users to delete publication pages.'),
    ),
    'edit chado_pub content' => array(
      'title' => t('Edit Publications'),
      'description' => t('Allow users to edit publication pages.'),
    ),
    'adminster tripal pub' => array(
      'title' => t('Administer Publications'),
      'description' => t('Allow users to administer all publications.'),
    ),
  );
}


/**
 * 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 $op == 'create'.  We will always 
 *  return TRUE if the permission is set.
 *
 */
function chado_pub_node_access($node, $op, $account ) {
  if ($op == 'create') {
    if (!user_access('create chado_pub content', $account)) {
      return FALSE;
    }
    return TRUE;
  }

  if ($op == 'update') {
    if (!user_access('edit chado_pub content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_pub content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_pub content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}





/**
 * Implementation of tripal_pub_insert().
 *
 * This function inserts user entered information pertaining to the Publication instance into the
 * 'pubauthor', 'pubprop', 'chado_pub', 'pub' talble of the database.
 *
 *  @parm $node
 *    Then node which contains the information stored within the node-ID
 *
 *
 */
function chado_pub_insert($node) {

	// we need an array suitable for the tripal_pub_create_citation() function
	// to automatically generate a citation if a uniquename doesn't already exist
	$pub_arr = array();
	
  // if a pub_id already exists for this node then it already exists in Chado and
  // we get here because we are syncing the node.  Therefore, we can skip the insert
  // but we always want to set the URL path alias to be the Chado pub ID
  if ($node->pub_id) {
    $pub['pub_id'] = $node->pub_id;
  }
  else {
    $properties = array(); // stores all of the properties we need to add
    $cross_refs = array(); // stores any cross references for this publication

    // get the list of properties for easy lookup (without doing lots of database queries
    $properties_list = array();
    $sql = "
      SELECT CVTS.cvterm_id, CVTS.name, CVTS.definition
      FROM {cvtermpath} CVTP
        INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
        INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
        INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
      WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Details' and 
        NOT CVTS.is_obsolete = 1
      ORDER BY CVTS.name ASC 
    ";
    $prop_types = chado_query($sql);
    while ($prop = $prop_types->fetchObject()) {
      $properties_list[$prop->cvterm_id] = $prop->name;
      // The 'Citation' term is special because it serves
      // both as a property and as the uniquename for the
      // pub and we want it stored in both the pub table and the pubprop table
      if ($prop->name == 'Citation') {
        $properties[$prop->name][0] = $node->uniquename;
      }
    }

    // get the properties that should be added. Properties are in one of two forms:
    //  1) prop_value-[type id]-[index]
    //  2) new_value-[type id]-[index]
    //  3) new_id, new_value
    foreach ($node as $name => $value) {
      if (preg_match('/^new_value-(\d+)-(\d+)/', $name, $matches)) {
        $type_id = $matches[1];
        $index = $matches[2];
        $name = $properties_list[$type_id];
        $properties[$name][$index] = trim($value);
      }
    }
    if ($node->new_id and $node->new_value) {
      $type_id = $node->new_id;
      $index = count($properties[$name]);
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($node->new_value);
    }

    // iterate through all of the properties and remove those that really are
    // part of the pub table fields
    foreach ($properties as $name => $element) {    	    
      $value = trim($element[0]);
      
    	// populate our $pub_array for building a citation
    	$pub_arr[$name] = $value;
    	
      // remove properties that are stored in the pub table
      if ($name == "Volume") {
        $volume = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Volume Title") {
        $volumetitle = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Issue") {
        $issue = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Pages") {
        $pages = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Publisher") {
        $publisher = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Journal Name" or $name == "Conference Name") {
        $node->series_name = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Journal Country" or $name == "Published Location") {
        $pubplace = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Publication Dbxref") {
        // we will add the cross-references to the pub_dbxref table
        // but we also want to keep the property in the pubprop table so don't unset it
        $cross_refs[] = $value;
      }
    }
    // generate a citation for this pub if one doesn't already exist 
    if (!$node->uniquename and array_key_exists('Citation', $properties)) {
    	$pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
    	$pub_arr['Title'] = $node->pubtitle;
      $pub_arr['Publication Type'][0] = $pub_type->name;
      $pub_arr['Year'] = $node->pyear;
      $node->uniquename = tripal_pub_create_citation($pub_arr);
      $properties['Citation'][0] = $node->uniquename;
    }
    
    // insert the pub record
    $values = array(
      'title'       => trim($node->pubtitle),
      'series_name' => trim($node->series_name),
      'type_id'     => trim($node->type_id),
      'pyear'       => trim($node->pyear),
      'is_obsolete' => $node->is_obsolete ? 'true' : 'false', 
      'uniquename'  => trim($node->uniquename),
      'volumetitle' => $volumetitle,
      'volume'      => $volume,    
      'issue'       => $issue,    
      'pages'       => $pages,
      'miniref'     => $miniref,        
      'publisher'   => $publisher,
      'pubplace'    => $pubplace,
    );
    $pub = tripal_core_chado_insert('pub', $values);
    if (!$pub) {
      drupal_set_message("Error inserting publication", "error");
      watchdog('tripal_pub', "Error inserting publication", array(), WATCHDOG_ERROR);
      return;
    }

    // now add in the properties
    foreach ($properties as $property => $elements) {
      foreach ($elements as $rank => $value) {
         
        $status = tripal_pub_insert_property($pub['pub_id'], $property, $value, FALSE);
        if (!$status) {
          drupal_set_message("Error cannot add property: $property", "error");
          watchdog('tripal_pub', "Error cannot add property: %prop",
          array('%property' => $property), WATCHDOG_ERROR);
        }
      }
    }

    // add in any database cross-references
    foreach ($cross_refs as $index => $ref) {
      $pub_dbxref = tripal_pub_add_pub_dbxref($pub['pub_id'], trim($ref));
      if (!$pub_dbxref) {
        drupal_set_message("Error cannot add publication cross reference: $ref", "error");
        watchdog('tripal_pub', "Error cannot add publication cross reference: %ref",
        array('%ref' => $ref), WATCHDOG_ERROR);
      }
    }
  } // if ($node->pub_id) {} else

  if ($pub) {
    // make sure the entry for this feature doesn't already exist in the chado_pub table
    // if it doesn't exist then we want to add it.
    $pub_id = chado_get_id_for_node('pub', $node->nid) ;
    if (!$pub_id) {
      // next add the item to the drupal table
      $sql = "INSERT INTO {chado_pub} (nid, vid, pub_id) ".
             "VALUES (:nid, :vid, :pub_id)";
      db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':pub_id' => $pub['pub_id']));
    }
  }
  else {
    drupal_set_message(t('Unable to add publication.', 'warning'));
    watchdog('tripal_pub', 'Insert publication: Unable to create pub where values: %values',
      array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
  }
}

/*
 *
 * Implements hook_update
 *
 * The purpose of the function is to allow the module to take action when an edited node is being
 * updated. It updates any name changes to the database tables that werec reated upon registering a Publication.
 * As well, the database will be changed, so the user changed information will be saved to the database.
 *
 * @param $node
 *   The node being updated
 *
 * @ingroup tripal_pub
 */
function chado_pub_update($node) {
  if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }
  
  // we need an array suitable for the tripal_pub_create_citation() function
  // to automatically generate a citation if a uniquename doesn't already exist
  $pub_arr = array();

  // get the publication ID for this publication
  $pub_id = chado_get_id_for_node('pub', $node->nid) ;

  $properties = array(); // stores all of the properties we need to add
  $cross_refs = array(); // stores any cross references for this publication
   
  // get the list of properties for easy lookup (without doing lots of database queries
  $properties_list = array();
  $sql = "
    SELECT DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
    FROM {cvtermpath} CVTP
      INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
      INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
      INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
    WHERE CV.name = 'tripal_pub' and 
      (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and 
      NOT CVTS.is_obsolete = 1
    ORDER BY CVTS.name ASC 
  ";
  $prop_types = chado_query($sql);
  while ($prop = $prop_types->fetchObject()) {
    $properties_list[$prop->cvterm_id] = $prop->name;
    // The 'Citation' term is special because it serves
    // both as a property and as the uniquename for the
    // pub and we want it stored in both the pub table and the pubprop table
    if ($prop->name == 'Citation') {
      $properties[$prop->name][0] = $node->uniquename;
    }
  }

  // get the properties that should be added. Properties are in one of three forms:
  //  1) prop_value-[type id]-[index]
  //  2) new_value-[type id]-[index]
  //  3) new_id, new_value
  //  dpm($node);
  foreach ($node as $key => $value) {
    if (preg_match('/^prop_value-(\d+)-(\d+)/', $key, $matches)) {
      $type_id = $matches[1];
      $index = $matches[2];
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($value);
    }
    if (preg_match('/^new_value-(\d+)-(\d+)/', $key, $matches)) {
      $type_id = $matches[1];
      $index = $matches[2];
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($value);
    }
  }
  if ($node->new_id and $node->new_value) {
    $type_id = $node->new_id;
    $name = $properties_list[$type_id];
    $index = count($properties[$name]);
    $properties[$name][$index] = trim($node->new_value);
  }

  // iterate through all of the properties and remove those that really are
  // part of the pub table fields
  foreach ($properties as $name => $element) {
    foreach ($element as $index => $value) {
    	// populate our $pub_array for building a citation
      $pub_arr[$name] = $value;
      
      // remove properties that are stored in the pub table
      if ($name == "Volume") {
        $volume = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Volume Title") {
        $volumetitle = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Issue") {
        $issue = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Pages") {
        $pages = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Publisher") {
        $publisher = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Journal Name" or $name == "Conference Name") {
        $node->series_name = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Journal Country" or $name == "Published Location") {
        $pubplace = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Publication Dbxref") {
        // we will add the cross-references to the pub_dbxref table
        // but we also want to keep the property in the pubprop table so don't unset it
        $cross_refs[] = $value;
      }
    }
  }
  // generate a citation for this pub if one doesn't already exist 
  if (!$node->uniquename) {
    $pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
    $pub_arr['Title'] = $node->pubtitle;
    $pub_arr['Publication Type'][0] = $pub_type->name;
    $pub_arr['Year'] = $node->pyear;
    $node->uniquename = tripal_pub_create_citation($pub_arr);
    $properties['Citation'][0] = $node->uniquename;
  }

  // update the pub record
  $match = array(
    'pub_id' => $pub_id,
  );
  $values = array(
    'title'       => trim($node->pubtitle),
    'type_id'     => trim($node->type_id),
    'pyear'       => trim($node->pyear),
    'is_obsolete' => $node->is_obsolete ? 'true' : 'false', 
    'uniquename'  => trim($node->uniquename),
    'series_name' => trim($node->series_name),
    'volumetitle' => $volumetitle,
    'volume'      => $volume,    
    'issue'       => $issue,    
    'pages'       => $pages,
    'miniref'     => $miniref,        
    'publisher'   => $publisher,
    'pubplace'    => $pubplace,
  );
  $status = tripal_core_chado_update('pub', $match, $values);
  if (!$status) {
    drupal_set_message("Error updating publication", "error");
    watchdog('tripal_pub', "Error updating publication", array(), WATCHDOG_ERROR);
    return;
  }

  // now add in the properties by first removing any the publication
  // already has and adding the ones we have
  tripal_core_chado_delete('pubprop', array('pub_id' => $pub_id));
  foreach ($properties as $property => $elements) {
    foreach ($elements as $rank => $value) {
      $status = tripal_pub_insert_property($pub_id, $property, $value, FALSE);
      if (!$status) {
        drupal_set_message("Error cannot add property: '$property'", "error");
        watchdog('tripal_pub', "Error cannot add property: '%prop'",
        array('%prop' => $property), WATCHDOG_ERROR);
      }
    }
  }

  // add in any database cross-references after first removing
  tripal_core_chado_delete('pub_dbxref', array('pub_id' => $pub_id));
  foreach ($cross_refs as $index => $ref) {
    $pub_dbxref = tripal_pub_add_pub_dbxref($pub_id, trim($ref));
    if (!$pub_dbxref) {
      drupal_set_message("Error cannot add publication cross reference: $ref", "error");
      watchdog('tripal_pub', "Error cannot add publication cross reference: %ref",
      array('%ref' => $ref), WATCHDOG_ERROR);
    }
  }
}


/**
 * Implementation of tripal_pub_load().
 *
 *
 * @param $node
 *   The node that is to be accessed from the database
 *
 * @return $node
 *   The node with the information to be loaded into the database
 *
 */
function chado_pub_load($node) {
  // get the feature details from chado
  $pub_id = chado_get_id_for_node('pub', $node->nid);

  $values = array('pub_id' => $pub_id);
  $pub = tripal_core_generate_chado_var('pub', $values);

  // expand the 'text' fields as those aren't included by default
  // and they really shouldn't be so large to cause problems
  if (is_array($pub) or is_object($pub)) {
    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.volumetitle');
    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.uniquename');
  }

  // set the URL path
  $path = "pub/$pub_id";

  $additions = new stdClass();
  $additions->pub = $pub;
  return $additions;

}

/**
 * Implementation of tripal_pub_delete().
 *
 * This function takes a node and if the delete button has been chosen by the user, the publication
 * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
 * the 'chado_pub' table.
 *
 *  @parm $node
 *    Then node which contains the information stored within the node-ID
 *
 */
function chado_pub_delete(&$node) {

  $pub_id = chado_get_id_for_node('pub', $node->nid);

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

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

  // Remove data from pub and pubprop tables of chado database as well
  chado_query("DELETE FROM {pubprop} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
  chado_query("DELETE FROM {pub} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
}

/*
 *
 */

function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  if ($form_id == "tripal_pub_importer_setup_form") {
    // updating the form through the ahah callback sets the action of
    // the form to the ahah callback URL. We need to set it back
    // to the normal form URL
    if ($form_state['values']['action'] == 'edit') {
      $form['#action'] = url("admin/tripal/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
    }
    if ($form_state['values']['action'] == 'new') {
      $form['#action'] = url("admin/tripal/tripal_pub/import/new");
    }
  }
  if ($form_id == "tripal_pub_search_form") {
    $form['#action'] = url("find/publications");
  }
  if ($form_id == "chado_pub_node_form") {
  }
}

/**
 *
 *
 * @ingroup tripal_pub
 */
function tripal_pub_preprocess_tripal_pub_relationships(&$variables) {
  // we want to provide a new variable that contains the matched pubs.
  $pub = $variables['node']->pub;

  // normally we would use tripal_core_expand_chado_vars to expand our
  // organism object and add in the relationships, however whan a large
  // number of relationships are present this significantly slows the
  // query, therefore we will manually perform the query
  $sql = "
    SELECT P.title, P.pub_id, CP.nid, CVT.name as rel_type
    FROM pub_relationship PR
      INNER JOIN {pub} P            ON PR.object_id = P.pub_id
      INNER JOIN {cvterm} CVT       ON PR.type_id   = CVT.cvterm_id
      LEFT JOIN public.chado_pub CP ON P.pub_id     = CP.pub_id
    WHERE PR.subject_id = :subject_id
  ";
  $as_subject = chado_query($sql, array(':subject_id' => $pub->pub_id));
  $sql = "
    SELECT P.title, P.pub_id, CP.nid, CVT.name as rel_type
    FROM pub_relationship PR
      INNER JOIN {pub} P            ON PR.subject_id = P.pub_id
      INNER JOIN {cvterm} CVT       ON PR.type_id    = CVT.cvterm_id
      LEFT JOIN public.chado_pub CP ON P.pub_id      = CP.pub_id
    WHERE PR.object_id = :object_id
  ";
  $as_object = chado_query($sql, array(':object_id' => $pub->pub_id));

  // combine both object and subject relationshisp into a single array
  $relationships = array();
  $relationships['object'] = array();
  $relationships['subject'] = array();

  // iterate through the object relationships
  while ($relationship = $as_object->fetchObject()) {

    // get the relationship and child types
    $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
    $sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));

    if (!array_key_exists($rel_type, $relationships['object'])) {
      $relationships['object'][$rel_type] = array();
    }
    if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
      $relationships['object'][$rel_type][$sub_type] = array();
    }
    $relationships['object'][$rel_type][$sub_type][] = $relationship;
  }

  // now add in the subject relationships
  while ($relationship = $as_subject->fetchObject()) {

    // get the relationship and child types
    $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
    $obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));

    if (!array_key_exists($rel_type, $relationships['subject'])) {
      $relationships['subject'][$rel_type] = array();
    }
    if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
      $relationships['subject'][$rel_type][$obj_type] = array();
    }
    $relationships['subject'][$rel_type][$obj_type][] = $relationship;
  }

  $pub->all_relationships = $relationships;
}
/**
 *
 */
function tripal_pub_mail($key, &$message, $params) {
  $language = $message['language'];
  $variables = user_mail_tokens($params['account'], $language);
  switch($key) {
    case 'import_report':
      $headers = array(
        'MIME-Version' => '1.0',
        'Content-Type' => 'text/html; charset=UTF-8; format=flowed',
        'Content-Transfer-Encoding' => '8Bit',
        'X-Mailer' => 'Drupal'
        );
        foreach ($headers as $key => $value) {
          $message['headers'][$key] = $value;
        }
        $message['subject'] = t('Publication import from !site', $variables, $language->language);
        $message['body'][] = $params['message'];
        break;
  }
}

/**
 * 
 * @param $node
 */
function tripal_pub_node_insert($node) {
  // we want the publications to always have a URL of http://[base url]/pub/[pub id]
  // where [pub id] is the Chado publication ID.  This will allow for easy linking
  // into the publication without needing to know the node.  Of course if you know the
  // node that will still work too (e.g. http://[base url]/node/[node id]
  // so the nodeapi function ensures that the URL path is set after insert or update
  // of the node and when the node is loaded if it hasn't yet been set.
  if ($node->type == 'chado_pub') {
    $pub_id = chado_get_id_for_node('pub', $node->nid);
    tripal_pub_set_pub_url($node, $pub_id);
  }
}
/**
 * 
 * @param $node
 * @param $types
 */
function tripal_pub_node_load($node, $types) {
  // we want the publications to always have a URL of http://[base url]/pub/[pub id]
  // where [pub id] is the Chado publication ID.  This will allow for easy linking
  // into the publication without needing to know the node.  Of course if you know the
  // node that will still work too (e.g. http://[base url]/node/[node id]
  // so the nodeapi function ensures that the URL path is set after insert or update
  // of the node and when the node is loaded if it hasn't yet been set.
  if ($node->type == 'chado_pub') {
    if (!$node->path) {
      $pub_id = chado_get_id_for_node('pub', $node->nid);
      $path = tripal_pub_set_pub_url($node, $pub_id);
    }
  }
}
/**
 *
 * @param $node
 */
function tripal_pub_node_update($node) {
  // we want the publications to always have a URL of http://[base url]/pub/[pub id]
  // where [pub id] is the Chado publication ID.  This will allow for easy linking
  // into the publication without needing to know the node.  Of course if you know the
  // node that will still work too (e.g. http://[base url]/node/[node id]
  // so the nodeapi function ensures that the URL path is set after insert or update
  // of the node and when the node is loaded if it hasn't yet been set.
  if ($node->type == 'chado_pub') {  
    $pub_id = chado_get_id_for_node('pub', $node->nid);
    tripal_pub_set_pub_url($node, $pub_id);
  }
}