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
 *
 * Implements 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/chado/tripal_pub']= array(
    'title' => 'Publications',
    'description' => ('A documented provenance artefact - publications, documents, personal communication.'),
    'page callback' => 'tripal_pub_admin_pub_view',
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/chado/tripal_pub/help']= array(
    'title' => 'Help',
    '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_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_pub/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal publication module.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_admin'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_pub/sync'] = array(
    'title' => ' Sync',
    '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_LOCAL_TASK,
    'weight' => 2
  );

  $items['admin/tripal/chado/tripal_pub/citation'] = array(
    'title' => 'Citations',
    'description' => 'Update publication citations',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_citation_form'),
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 1
  );
  
  $items['admin/tripal/chado/tripal_pub/import_list'] = array(
    'title' => t('Importers'),
    'description' => t('List all publication importers'),
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );
  
  // add a second link for the importer on the data loaders page
  $items['admin/tripal/loaders/pub_import'] = array(
    'title' => 'Publications Importers',
    'description' => 'Create importers that can periodically import publications from remote online publication databases.',
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pubs'),
    'type' => MENU_NORMAL_ITEM,
  );
  
  $items['admin/tripal/chado/tripal_pub/import/new'] = array(
    'title' => t('Add an Importer'),
    'description' => t('Add a new publication importer.'),
    'page callback' => 'tripal_pub_importer_setup_page',
    'access arguments' => array('administer tripal pubs'),
    'type ' => MENU_CALLBACK,
  );

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

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

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

  return $items;
}


/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 *
 * @return
 *   An array of themeing functions to register
 *
 */
function tripal_pub_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');
  
  $items = array(
    'node__chado_pub' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),
    // node templates
    'tripal_pub_authors' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_authors',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_base',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_featuremaps' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_featuremaps',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_features' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_features',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_libraries' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_libraries',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_projects' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_projects',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_properties' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_properties',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_references' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_references',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_relationships' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_relationships',
      'path' => "$path/theme/tripal_pub",
    ),
    'tripal_pub_stocks' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_stocks',
      'path' => "$path/theme/tripal_pub",
    ),

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

    // themed forms
    'tripal_pub_importer_setup_form_elements' => array(
      'render element' => 'form',
    ),
    'tripal_pub_search_setup_form_elements' => array(
      'render element' => 'form',
    ),
    
    // teaser
    'tripal_pub_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_pub_teaser',
      'path' => "$path/theme/tripal_pub",
    ),
  );

  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());
  }
}

/**
 * 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_pub
 */
function tripal_pub_views_api() {
  return array(
    'api' => 3.0,
  );
}

/**
 * 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) {

  $title        = trim($node->pubtitle);
  $pyear        = trim($node->pyear);
  $uniquename   = trim($node->uniquename);
  $is_obsolete  = $node->is_obsolete;
  $type_id      = $node->type_id;
  
  // 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 there is an pub_id in the $node object then this must be a sync so
  // we can skip adding the pub as it is already there, although
  // we do need to proceed with the rest of the insert
  if (!property_exists($node, 'pub_id')) {
  
    $properties = array(); // stores all of the properties we need to add
    $cross_refs = array(); // stores any cross references for this publication

    // get the properties from the form
    $properties = tripal_core_properties_form_retreive($node, 'tripal_pub');
    
    // 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;
      }
    }

    // iterate through all of the properties and remove those that really are
    // part of the pub table fields
    $volume = '';
    $volumetitle = '';
    $issue = '';
    $pages = '';
    $publisher = '';
    $series_name = '';
    $pubplace = '';
    $miniref = '';
    $cross_refs = array();
    foreach ($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 == "Series Name" or $name == "Journal Name" or $name == "Conference Name") {
        $series_name = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Journal Country" or $name == "Published Location") {
        $pubplace = $value;
        // allow this property to go into the pubprop table so we don't loose info
        // so don't unset it. But it will also go into the pub.pubplace field
      }
      elseif ($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'       => $node->pubtitle,
      'series_name' => substr($series_name, 0, 255),
      'type_id'     => $node->type_id,
      'pyear'       => $node->pyear,
      'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
      'uniquename'  => $node->uniquename,
      'volumetitle' => $volumetitle,
      'volume'      => $volume,
      'issue'       => $issue,
      'pages'       => $pages,
      'miniref'     => substr($miniref, 0, 255),
      'publisher'   => substr($publisher, 0, 255),
      'pubplace'    => substr($pubplace, 0, 255),
    );
    $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;
    }
    $pub_id = $pub['pub_id'];

    // 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);
      }
    }
  }
  else {
    $pub_id = $node->pub_id;
  }

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

/*
 *
 * 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) {
  $title        = trim($node->pubtitle);
  $pyear        = trim($node->pyear);
  $uniquename   = trim($node->uniquename);
  $is_obsolete  = $node->is_obsolete;
  $type_id      = $node->type_id;

  // 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 properties from the form
  $properties = tripal_core_properties_form_retreive($node, 'tripal_pub');
  
  // 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;
    }
  }

  // iterate through all of the properties and remove those that really are
  // part of the pub table fields
  $volume = '';
  $volumetitle = '';
  $issue = '';
  $pages = '';
  $publisher = '';
  $series_name = '';
  $pubplace = '';
  $miniref = '';
  $cross_refs = array();
  foreach ($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") {
        $series_name = $value;
        unset($properties[$name]);
      }
      elseif ($name == "Journal Country" or $name == "Published Location") {
        $pubplace = $value;
        // allow this property to go into the pubprop table so we don't loose info
        // so don't unset it. But it will also go into the pub.pubplace field
      }
      elseif ($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'       => $node->pubtitle,
    'type_id'     => $node->type_id,
    'pyear'       => $node->pyear,
    'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
    'uniquename'  => $node->uniquename,
    'series_name' => substr($series_name, 0, 255),
    'volumetitle' => $volumetitle,
    'volume'      => $volume,
    'issue'       => $issue,
    'pages'       => $pages,
    'miniref'     => substr($miniref, 0, 255),
    'publisher'   => substr($publisher, 0, 255),
    'pubplace'    => substr($pubplace, 0, 255),
  );
  $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 $node
 *   The node with the information to be loaded into the database
 *
 */
function chado_pub_load($nodes) {
  
  foreach ($nodes as $nid => $node) {
    // find the pub and add in the details
    $pub_id = chado_get_id_for_node('pub', $nid);
  
    // get the pub
    $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
    $pub = tripal_core_expand_chado_vars($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
    $nodes[$nid]->path = "pub/$pub_id";
    $nodes[$nid]->pub = $pub;
  }
}

/**
 * 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));
}

/**
 *
 *
 * @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'][] = $params['message'];
        break;
  }
}
/**
 *
 * @ingroup tripal_feature
 */
function tripal_pub_node_view($node, $view_mode, $langcode) {
  switch ($node->type) {
    case 'chado_pub':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_pub_authors'] = array(
          '#value' => theme('tripal_pub_authors', array('node' => $node)),
        );
        $node->content['tripal_pub_base'] = array(
          '#value' => theme('tripal_pub_base', array('node' => $node)),
        );
        $node->content['tripal_pub_featuremaps'] = array(
          '#value' => theme('tripal_pub_featuremaps', array('node' => $node)),
        );
        $node->content['tripal_pub_features'] = array(
          '#value' => theme('tripal_pub_features', array('node' => $node)),
        );
        $node->content['tripal_pub_libraries'] = array(
          '#value' => theme('tripal_pub_libraries', array('node' => $node)),
        );
        $node->content['tripal_pub_projects'] = array(
          '#value' => theme('tripal_pub_projects', array('node' => $node)),
        );
        $node->content['tripal_pub_properties'] = array(
          '#value' => theme('tripal_pub_properties', array('node' => $node)),
        );
        $node->content['tripal_pub_references'] = array(
          '#value' => theme('tripal_pub_references', array('node' => $node)),
        );
        $node->content['tripal_pub_relationships'] = array(
          '#value' => theme('tripal_pub_relationships', array('node' => $node)),
        );
        $node->content['tripal_pub_stocks'] = array(
          '#value' => theme('tripal_pub_stocks', array('node' => $node)),
        );
      }
      if ($view_mode == 'teaser') {
        $node->content['tripal_pub_teaser'] = array(
          '#value' => theme('tripal_pub_teaser', array('node' => $node)),
        );
      }
      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 $types
 */
function tripal_pub_node_load($nodes, $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 (count(array_intersect(array('chado_pub'), $types))) {
    foreach ($nodes as $nid => $node) {
      if ($node->type == 'chado_pub' and !property_exists($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);
  }
}

/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_pub_node_form") {
    $form['actions']['preview']['#access'] = FALSE;
  }
  if ($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 (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'edit') {
      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
    }
    if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'new') {
      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
    }
    */
  }
  if ($form_id == "tripal_pub_search_form") {
    $form['#action'] = url("find/publications");
  }
  if ($form_id == "chado_pub_node_form") {
  }
}

/**
 * 
 * @param $callback
 * @param $args
 */
function tripal_pub_job_describe_args($callback, $args) {

  $new_args = array();
  if ($callback == 'tripal_pub_import_publications_by_import_id') {
    // get all of the loaders
    $qargs = array(':import_id' => $args[0]);
    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";
    $import = db_query($sql, $qargs)->fetchObject();
    
    $new_args['Importer'] = $import->name;
  }
  return $new_args;
}