EDIT

<?php

/**

 * @file

 * Provides external links for sources to taxa information.

 *

 * @copyright

 *   (C) 2007-2012 EDIT

 *   European Distributed Institute of Taxonomy

 *   http://www.e-taxonomy.eu

 *

 *   The contents of this module are subject to the Mozilla

 *   Public License Version 1.1.

 * @see http://www.mozilla.org/MPL/MPL-1.1.html

 *

 * @author

 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>

 *   - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)

 */

/**

 * Display help and module information.

 *

 * @param string $path

 *   For which path of the site we're displaying help.

 * @param array $arg

 *   Array that holds the current path as would be returned from arg() function.

 *

 * @return string

 *   Help text for the path.

 */

function ext_links_help($path, $arg) {

  switch ($path) {

    case 'admin/help#ext_links':

      $output = '<p>' . t("Link to external sources like ## for taxa.") . '</p>';

    case 'admin/config/cdm_dataportal/ext_links':

      $output = '<p>' . t('The external links module allows to configure URL templates for links to external data sources.');

      return $output;

    case 'admin/config/cdm_dataportal/ext_links/%':

      $output = '<p>' . t('An external link template.');

      return $output;

/**

 * Implements hook_menu().

 */

function ext_links_menu() {

    'access arguments' => ['access administration pages'],

    'file' => 'ext_links.admin.inc'

  ];

  $items['admin/config/cdm_dataportal/ext_links/list'] = [

    'title' => 'List',

    'type' => MENU_DEFAULT_LOCAL_TASK,

  ];

  $items['admin/config/cdm_dataportal/ext_links/add'] = [

    'title' => 'Add external link',

    'page callback' => 'ext_links_admin_link_template_page',

    'access arguments' => ['access administration pages'],

    'type' => MENU_LOCAL_ACTION,

    'weight' => 1,

    'file' => 'ext_links.admin.inc',

  ];

    'title' => 'Appearance',

    'page callback' => 'drupal_get_form',

    'page arguments' => ['ext_links_admin_appearance_page'],

    'access arguments' => ['access administration pages'],

    'type' => MENU_LOCAL_TASK,

    'weight' => 2,

    'file' => 'ext_links.admin.inc',

  ];

    'title' => 'Edit external link',

    'page arguments' => [4],

    'access arguments' => ['access administration pages'],

    'file' => 'ext_links.admin.inc',

  ];

    'title' => 'Enable or disable external link',

    'page callback' => 'ext_links_admin_link_template_set_status',

    'page arguments' => [4, 6],

    'access arguments' => ['access administration pages'],

 //   'type' => MENU_CALLBACK,

    'file' => 'ext_links.admin.inc',

  ];

/**

 * Retrieves a list of External Link templates, ordered by weight.

 *

 *

 * @see ext_links_template_defaults()

 *

 *   When TRUE external link templates with status != null are excluded from the list.

 *   weight.

 *

 */

  $link_templates = &drupal_static(__FUNCTION__, array());

  // cache_clear_all("ext_links_templates:{$language->language}");

  // All available link_templates are cached for performance.

  if (!is_array($link_templates) || !count($link_templates)) {

    }

    else {

        $link_templates = [];

        $link_templates_arrays = ext_links_template_defaults();

        foreach($link_templates_arrays as $a){

          $link_templates[] = (object)$a;

        }

      } else {

        if($enabled_only){

          $query = $query->condition('status', '1');

        }

        $link_templates =

          $query->orderBy('category')

          ->fetchAllAssoc('id');

      }

      if(!count($link_templates)) {

        $link_templates_arrays = ext_links_template_defaults();

        $query = db_insert('ext_links')

          ->fields(array_keys(array_values($link_templates_arrays)[0]));

        foreach($link_templates_arrays as $a){

          $query->values($a);

        }

        try {

          $query->execute();

        } catch (Exception $e) {

          drupal_set_message("Error while initializing ext_links database: " . $e->getMessage(), "error");

        }

        $link_templates = [];

        foreach($link_templates_arrays as $a){

          $link_templates[] = (object)$a;

        }

  }

  return $link_templates;

}

 * Resets the text format caches.

 *

 * @see filter_formats()

 */

function ext_links_templates_reset() {

  drupal_static_reset('ext_links');

/**

 * Loads a text format object from the database.

 *

 * @param $extlink_id

 *   The external link ID. ($link->id)

 *

 * @return

 *   A fully-populated text format object, if the requested format exists and

 *   is enabled. If the format does not exist, or exists in the database but

 *   has been marked as disabled, FALSE is returned.

 *

 * @see ext_links_exists()

 */

function ext_links_load($extlink_id) {

    $defaults = ext_links_template_defaults();

    return isset($defaults[$extlink_id]) ? (object)$defaults[$extlink_id] : FALSE;

  }

  else {

    return isset($link_templates[$extlink_id]) ? $link_templates[$extlink_id] : FALSE;

/**

 * Saves a text format object to the database.

 *

 * @param $link_template

 *   A link template object having the properties:

 *   - id: The machine name of the external link. If this corresponds

 *     to an existing external link, this one will be updated;

 *     otherwise, a new external link will be created.

 *   - title: The link title

 *   - link: The link url template.

 *   - glue: The string to concatenate name parts in the URL query string.

 *   - status: (optional) An integer indicating whether the ext link is

 *     enabled (1) or not (0). Defaults to 1.

 *   - weight: (optional) The weight of the external link, which controls its

 *     placement in external link block. If omitted, the weight is set to 0.

 *     Defaults to NULL.

 *

 * @return

 *   SAVED_NEW or SAVED_UPDATED.

 */

function ext_links_save($link_template) {

  $link_template->cache = true;

  if (!isset($link_template->status)) {

    $link_template->status = 1;

  }

  if (!isset($link_template->weight)) {

    $link_template->weight = 0;

  }

  // Insert or update the text format.

  $return = db_merge('ext_links')

      'id' => $link_template->id,

      'title' => $link_template->title,

      'link' => $link_template->link,

      'glue' => $link_template->glue,

      'status' => (int) $link_template->status,

      'weight' => (int) $link_template->weight,

    ))

    ->execute();

  ext_links_templates_reset();

  return $return;

}

/**

 * Determines if a external link exists.

 *

 * @param $ext_link_name

 *   The ID of the external link to check.

 *

 * @return

 *   TRUE if the external link exists, FALSE otherwise.

 *

 * @see ext_links_load()

 */

function ext_links_exists($ext_link_name) {

  return (bool) db_query_range('SELECT 1 FROM {ext_links} WHERE name = :name', 0, 1, array(':name' => $ext_link_name))->fetchField();

}

/**

 * Returns the genus and the first epithet from the object taxon.

 *

 * @param $taxon

 *   A CDM Taxon instance object

 * @return array

 *  An associate array with two elements:

 *     - genus: the uninomial

 *     - species: the species epithet

 */

function ext_link_species_name($taxon) {

  $speciesName = array();

  $i = 0;

  while (isset($taxon->name->taggedName[$i]) && !isset($speciesName['species'])) {

    if ($taxon->name->taggedName[$i]->type == "name") {

      if (!isset($speciesName['genus'])) {

        $speciesName['genus'] = $taxon->name->taggedName[$i]->text;

      }

      else {

        $speciesName['species'] = $taxon->name->taggedName[$i]->text;

      }

    }

    $i++;

  }

  return $speciesName;

}

 * Implements hook_block_info().

 */

function ext_links_block_info() {

  if (TRUE) {

  }

}

/**

 * Implements hook_block_view().

 */

function ext_links_block_view($delta) {

  // TODO Rename block deltas (e.g. '0') to readable strings.

  switch ($delta) {

    case '0':

      $block['subject'] = 'External links';

      if ($uuid) {

        // $taxon->titleCache;

        // var_export()

        if (!empty($taxon)) {

          drupal_add_js(drupal_get_path('module', 'ext_links') . '/ext_links.js');

          $genus = $taxon->name->taggedName[0]->text;

          if(isset($taxon->name->taggedName[1])){

            $species = $taxon->name->taggedName[1]->text;

          }

          if ($grouped) {

          }

          else {

            $block['content'] = theme('ext_links_list_plain', array('speciesName' => $speciesName, 'genus' => $genus, 'species' => $species ));

          }

          // if(variable_get('ext_links_gbif_check', TRUE)) {

          // $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_gbif_link', $ext_links_default[gbif][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_gbif_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_gbif_text', $ext_links_default[gbif][text_default_value]).'</a><br />';

          /*

           $block_content .=

           /* TODO

           Please manually fix the parameters on the l() or url() function on the next line.

           Typically, this was not changed because of a function call inside an array call like

           array('title' => t('View user profile.')).

           l(variable_get('ext_links_gbif_text', $ext_links_default[gbif][text_default_value]),

           'JavaScript:popupExternalLinks('.variable_get('ext_links_gbif_link', $ext_links_default[gbif][link_default_value]).$speciesName[genus].variable_get('ext_links_gbif_concat', ' ').$speciesName[species],

           array(), null, null, true);

           */

          /*}

           if(variable_get('ext_links_biocase_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_biocase_link', $ext_links_default[biocase][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_biocase_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_biocase_text', $ext_links_default[biocase][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_nybg_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_nybg_link', $ext_links_default[nybg][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_nybg_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_nybg_text', $ext_links_default[nybg][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_tropicos_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_tropicos_link', $ext_links_default[tropicos][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_tropicos_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_tropicos_text', $ext_links_default[tropicos][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_ncbi_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_ncbi_link', $ext_links_default[ncbi][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_ncbi_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_ncbi_text', $ext_links_default[ncbi][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_google_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_google_link', $ext_links_default[google][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_google_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_google_text', $ext_links_default[google][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_flickr_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_flickr_link', $ext_links_default[flickr][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_flickr_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_flickr_text', $ext_links_default[flickr][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_scholar_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_scholar_link', $ext_links_default[scholar][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_scholar_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_scholar_text', $ext_links_default[scholar][text_default_value]).'</a><br />';

           }

           if(variable_get('ext_links_bhl_check', 1)) {

           $block_content .= '<a href="JavaScript:popupExternalLinks(\''.variable_get('ext_links_bhl_link', $ext_links_default[bhl][link_default_value]).str_replace('"','%22',$speciesName[genus]).variable_get('ext_links_bhl_concat', ' ').str_replace('"','%22',$speciesName[species]).'\')">'.variable_get('ext_links_bhl_text', $ext_links_default[bhl][text_default_value]).'</a><br />';

           }

           $block['content'] = $block_content;

           $block['content'] = theme('ext_links_list_plain');

           }

           }*/

          // if taxon

        }

      }

      // If path.

      return $block;

  } /* switch */

}

 * Applies the name tokens to the external link templates.

 *

 * @param $ext_link

 * @param $species_name

 *

 * @return array

 *  Array with the keys:

 *     - title: the title of the link

 *     - url: the url of the link

 */

function make_ext_link($ext_link, $species_name) {

  switch ($ext_link->id) {

    case 'nybg':

      if ($species_name['genus'] != NULL) {

        $query = 'DetFiledAsGenusLocal+%3D+\%27' . $species_name['genus'] . '\%27';

      }

      if ($species_name['species'] != NULL) {

        $query .= $ext_link->glue . 'DetFiledAsSpeciesLocal+%3D+\%27' . $species_name['species'] . '\%27';

      }

      break;

    case 'arkive':

      $postURL = '&output=xml_no_dtd&client=arkive-images&site=arkive-images&ie=utf8&oe=utf8&num=20&proxystylesheet=tng-search&filter=0&getfields=*';

      $query = str_replace('"', '%22', $species_name['genus']) . variable_get('ext_links_arkive_concat', '+') . str_replace('"', '%22', $species_name['species']) . $postURL;

      break;

    case 'herbcat':

      $postURL = '&x=11&y=13&homePageSearchOption=scientific_name&nameOfSearchPage=home_page';

      $query = str_replace('"', '%22', $species_name['genus']) . variable_get('ext_links_herbcat_concat', '+') . str_replace('"', '%22', $species_name['species']) . $postURL;

      break;

    case 'iucn':

    case 'wcsp':

      // apparently no search api, thus plain link without genus and species

      $query = '';

      break;

    case 'ipni':

      $query = 'find_genus=' . $species_name['genus'] . '&find_species=' . $species_name['species'];

      break;

    default:

      $query = str_replace('"', '%22', $species_name['genus']) . $ext_link->glue . str_replace('"', '%22', $species_name['species']);

  }

  $ext_link_array = [

    'title' => $ext_link->title,

    'url' => $ext_link->link . $query

  ];

  return $ext_link_array;

}

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function theme_ext_links_list_grouped($variables) {

  if(!isset($species_name['genus'])) {

    $species_name['genus'] = '';

    $species_name['species'] = '';

    if(!array_key_exists($ext_link->category, $ext_links_by_category)){

      $ext_links_by_category[$ext_link->category] = [];

    }

    $ext_link_render_array = make_ext_link($ext_link, $species_name);

    $ext_links_by_category[$ext_link->category][] = $ext_link_render_array;

  foreach ($ext_links_by_category as $categoryTitle => $ext_links) {

    $block_content .= "<div class=\"category\"><h5>" . $categoryTitle . "</h5>\n";

    foreach($ext_links as $ext_link){

      $block_content .= l($ext_link['title'], 'JavaScript:popupExternalLinks(\'' . $ext_link['url'] . '\')', ['external' => TRUE]) .'<br />';

    $block_content .= "</div>";

  }

  return $block_content;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function theme_ext_links_list_plain($variables) {

  $speciesName = $variables['speciesName'];

  if (!isset($speciesName['genus'])) {

    $speciesName['genus'] = '';

  }

  if (!isset($speciesName['species'])) {

    $speciesName['species'] = '';

  }

  $block_content = '';

  foreach ($ext_links_templates as $ext_link) {

    $ext_link = make_ext_link($ext_link, $speciesName);

    $block_content .= l($ext_link['title'], 'JavaScript:popupExternalLinks(\'' . $ext_link['url'] . '\')', ['external' => TRUE]) .'<br />';

  return $block_content;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function ext_links_theme() {

  return array(

    'ext_links_list_grouped' => array('variables' => array(

      'speciesName' => NULL,

      'genus' => NULL,

      'species' => NULL,

      )),

    'ext_links_list_plain' => array('variables' => array(

      'speciesName' => NULL,

      'genus' => NULL,

      'species' => NULL,

      )),

    'ext_links_admin_overview' => array(

      'render element' => 'form',

      'file' => 'ext_links.admin.inc',

    ),

//    'ext_links_link_template_filter_order' => array(

//      'render element' => 'element',

//      'file' => 'ext_links.admin.inc',

//    ),

}

/**

 * Get the default external links.

 *

 * @return array

 *   Returns an array with default external links values.

 */

    'title' => 'Search GBIF...',

    'glue' => ' ',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  $ext_links_default["biocase"] = array(

    'title' => 'Search BioCASE...',

    'glue' => ' ',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  $ext_links_default["nybg"] = array(

    'title' => 'Search NYBG...',

    'glue' => '+AND+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  $ext_links_default["tropicos"] = array(

    'title' => 'Search Tropicos...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  $ext_links_default["ncbi"] = array(

    'title' => 'Search NCBI...',

    'glue' => '+AND+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Molecular Resources',

  $ext_links_default["google"] = array(

    'title' => 'Search Google Images...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Images',

  $ext_links_default["flickr"] = array(

    'title' => 'Search flickr...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Images',

  $ext_links_default["scholar"] = array(

    'title' => 'Search Google scholar...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Literature',

  $ext_links_default["bhl"] = array(

    'title' => 'Search BHL...',

    'glue' => ' ',

    'weight' => 0,

    'status' => 1,

    'category' => 'Literature',

  $ext_links_default["arkive"] = array(

    'title' => 'Search ARKive...',

    'glue' => '+',

    'weight' => 0,

  $ext_links_default["herbcat"] = array(

    'title' => 'Search Kew Herbarium Catalogue...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  $ext_links_default["iucn"] = array(

    'title' => 'Go to IUCN Red List...',

    'glue' => ' ',

    'weight' => 0,

    'status' => 1,

    'category' => 'Conservation',

  $ext_links_default["ipni"] = array(

    'title' => 'Search IPNI...',

    'glue' => '&',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification',

  $ext_links_default["wcsp"] = array(

    'title' => 'Search World Checklist Monocots...',

    'glue' => ' ',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification',

  $ext_links_default["tpl"] = array(

    'title' => 'Search The Plant List...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification',

  $ext_links_default["eol"] = array(

    'title' => 'Search Encyclopaedia of Life...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'General',

  $ext_links_default["jstor"] = array(

    'title' => 'Search JSTOR Plant Science...',

    'glue' => ' ',

    'weight' => 0,

    'status' => 1,

    'category' => 'General',

  $ext_links_default["epic"] = array(

    'title' => 'Search ePIC...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'General',

  $ext_links_default["fairchild"] = array(

    'title' => 'Search Fairchild Guide To Palms...',

    'glue' => '+',

    'weight' => 0,

    'title' => 'Search GGBN...',

    'glue' => '+',

    'weight' => 0,

    'status' => 1,

    'category' => 'Molecular Resources',

}