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>';

      return $output;

    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() {

  $items = [];

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

    'title' => 'External links',

    'description' => 'Configure external links templates.',

    'page callback' => 'drupal_get_form',

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

    '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',

  ];

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

    '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',

  ];

  $items['admin/config/cdm_dataportal/ext_links/%ext_links'] = [ // %ext_links refers to ext_links_load

    'title' => 'Edit external link',

    'page callback' => 'ext_links_admin_link_template_page',

    'page arguments' => [4],

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

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

  ];

  $items['admin/config/cdm_dataportal/ext_links/%ext_links/status/%'] = [

    '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',

  ];

  $items['ext_links/category/autocomplete'] = [

    'title' => 'Autocomplete for external link categories',

    'page callback' => 'ext_links_category_autocomplete',

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

    'type' => MENU_CALLBACK

  ];

  return $items;

}

/**

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

 *

 * Empty 'ext_links' tables will be initialized with the default templates.

 *

 * @see ext_links_template_defaults()

 *

 * @param $enabled_only boolean

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

 * @return array

 *   An array of external link template objects, keyed by the format ID and ordered by

 *   weight.

 *

 */

function ext_links_templates($enabled_only = FALSE) {

  global $language;

  $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)) {

    if ($cache = cache_get("ext_links:{$language->language}")) {

      $link_templates = $cache->data;

    }

    else {

      $test = false;

      if($test){

        $link_templates = [];

        $link_templates_arrays = ext_links_template_defaults();

        foreach($link_templates_arrays as $a){

          $link_templates[] = (object)$a;

        }

      } else {

        $query = db_select('ext_links', 'elt')

          ->addTag('translatable')

          ->fields('elt');

        if($enabled_only){

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

        }

        $link_templates =

          $query->orderBy('weight')

          ->execute()

          ->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;

        }

      }

      // cache_set("ext_links:{$language->language}", $link_templates);

    }

  }

  return $link_templates;

}

/**

 * Resets the text format caches.

 *

 * @see filter_formats()

 */

function ext_links_templates_reset() {

  cache_clear_all('ext_links', 'cache', TRUE);

  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) {

  $test = false;

  if($test) {

    $defaults = ext_links_template_defaults();

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

  }

  else {

   $link_templates = ext_links_templates();

    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.

 *   - 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) {

  $link_template->title = trim($link_template->title);

  $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')

    ->key(array('id' => $link_template->id))

    ->fields(array(

      'id' => $link_template->id,

      'title' => $link_template->title,

      'link' => $link_template->link,

      'category' => $link_template->category,

      '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 id = :id', 0, 1, array(':id' => $ext_link_name))->fetchField();

}

/**

 * Autocomplete function called via the menu hook ext_links/category/autocomplete

 *

 * @param $query_string

 *  the string to search for

 */

function ext_links_category_autocomplete($query_string){

  $matches = array();

  $sql = 'SELECT * FROM {ext_links} WHERE category LIKE :category';

  $args = [':category' => '%' . db_like($query_string) . '%'];

  $result = db_query($sql, $args);

  foreach ($result as $row) {

    $matches[$row->category] = check_plain($row->category);

  }

  // Return the result to the form in json

  drupal_json_output($matches);

}

/**

 * 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) {

    $block[0]["info"] = t("CDM - External Links");

    $block[0]["visibility"] = BLOCK_VISIBILITY_LISTED;

    $block[0]["pages"] = "cdm_dataportal/taxon/*\ncdm_dataportal/name/*";

    return $block;

  }

}

/**

 * Implements hook_block_view().

 */

function ext_links_block_view($delta) {

  switch ($delta) {

    case '0':

      $block['subject'] = t('Search name in') . ' ...';

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

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

        $block['content'] = render_ext_links_list_grouped();

      } else {

        $block['content'] = render_ext_links_list_plain();

      }

    }

      return $block;

}

/**

 * Applies the name tokens to the external link templates.

 *

 * @param $ext_link_template

 *

 * @return array

 *  Array with the keys:

 *     - title: the title of the link

 *     - url: the url of the link

 */

function ext_links_apply_template($ext_link_template) {

      $ext_link_array = [

        'title' => $ext_link_template->title,

        'url' => token_replace($ext_link_template->link, [],

          [

            'callback' => 'ext_links_token_replacement_urlencode',

            'clear' => true

          ])

      ];

  return $ext_link_array;

}

/**

 * Callback function to be passed to token_replace() to urlencode the token replacements.

 *

 * @param array $replacements

 *   The replacements for the tokens

 * @param array $data

 *    Unused, see token_replace()

 * @param array $options

 *    Unused, see token_replace()

 *

 * @see token_replace()

 */

function ext_links_token_replacement_urlencode(array &$replacements, array $data = [], array $options = []){

  foreach ($replacements as &$repl){

    $repl = rawurlencode($repl);

  }

}

/**

 * Creates html markup of ext_links grouped by category

 */

function render_ext_links_list_grouped() {

  $ext_links = ext_links_templates(true);

  $ext_links_by_category = [];

  foreach ($ext_links as $ext_link) {

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

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

    }

    $ext_link_render_array = ext_links_apply_template($ext_link);

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

  }

  $block_content = '';

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

    $block_content .= "<label class=\"category-label\">" . $category . "</label><div class=\"category category-$category\">";

    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;

}

/**

 * Creates html markup of ext_links as plain list

 */

function render_ext_links_list_plain() {

  $ext_links_templates = ext_links_templates(true);

  $block_content = '';

  foreach ($ext_links_templates as $ext_link) {

    $ext_link = ext_links_apply_template($ext_link);

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

  }

  return $block_content;

}

/**

 * Implements hook_theme()

 */

function ext_links_theme() {

  return array(

    // theme_ext_links_admin_overview

    'ext_links_admin_overview' => array(

      'render element' => 'form',

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

    )

  );

}

/**

 * Get the default external links.

 *

 * @return array

 *   Returns an array with default external links values.

 */

function ext_links_template_defaults() {

  // --- General ---

  $ext_links_default["eol"] = array(

    'id' => "eol",

    'link' => 'http://eol.org/search/?q=[cdm:taxon_name]',

    'title' => 'Encyclopaedia of Life',

    'weight' => 0,

    'status' => 1,

    'category' => 'General',

  );

  $ext_links_default["jstor"] = array(

    'id' => "jstor",

    'link' => 'https://plants.jstor.org/search?filter=name&so=ps_group_by_genus_species+asc&Query=[cdm:taxon_name]',

    'title' => 'JSTOR Plant Science',

    'weight' => 0,

    'status' => 1,

    'category' => 'General',

  );

  // --- Classification/Nomenclature ---

  $ext_links_default["col"] = array(

    'id' => "col",

    'link' => 'https://www.catalogueoflife.org/data/search?facet=rank&facet=issue&facet=status&facet=nomStatus&facet=nameType&facet=field&limit=50&offset=0&q=[cdm:taxon_name]&sortBy=taxonomic&type=EXACT',

    'title' => 'Catalogue of Life',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification/Nomenclature',

  );

  $ext_links_default["ipni"] = array(

    'id' => "ipni",

    'link' => 'https://www.ipni.org/?q=[cdm:taxon_name]',

    'title' => 'IPNI',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification/Nomenclature',

  );

  $ext_links_default["tpl"] = array(

    'id' => "tpl",

    'link' => 'http://www.theplantlist.org/tpl/search?q=[cdm:taxon_name]',

    'title' => 'The Plant List',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification/Nomenclature',

  );

  $ext_links_default["wcsp"] = array(

    'id' => "wcsp",

    'link' => 'http://wcsp.science.kew.org/qsearch.do?plantName=[cdm:taxon_name]',

    'title' => 'World Checklist Monocots',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification/Nomenclature',

  );

  $ext_links_default["wfo"] = array(

    'id' => "wfo",

    'link' => 'http://www.worldfloraonline.org/search?query=[cdm:taxon_name]',

    'title' => 'World Flora Online',

    'weight' => 0,

    'status' => 1,

    'category' => 'Classification/Nomenclature',

  );

  // --- Specimens/Occurrences ---

  $ext_links_default["biocase"] = array(

    'id' => "biocase",

    'link' => 'http://search.biocase.org/edit/search/units/simpleSearch/query1?unitName=[cdm:taxon_name]',

    'title' => 'BioCASE',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  );

  $ext_links_default["fairchild"] = array(

    //disabled since Fairchild Guide To Palms seems to be down

    'id' => "fairchild",

    'link' => 'http://palmguide.org/palmsearch.php?query=',

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

    'weight' => 0,

    'status' => 0,

    'category' => 'Specimens/Occurrences',

  );

  $ext_links_default["gbif"] = array(

    'id' => "gbif",

    'link' => 'http://www.gbif.org/species/search?q=[cdm:taxon_name]',

    'title' => 'GBIF',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  );

  $ext_links_default["herbcat"] = array(

    'id' => "herbcat",

    'link' => 'http://apps.kew.org/herbcat/getSearchPageResults.do?typeSpecimen=false&imageSpecimen=false&currentName=false&typeOfCollection=all_collection&&genus=[cdm:taxon_name:genus_or_uninomial]&&species=[cdm:taxon_name:epithet]&infraspecificName=[cdm:taxon_name:infraspecific_epithet]',

    'title' => 'Kew Herbarium Catalogue',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  );

  $ext_links_default["nybg"] = array(

    'id' => "nybg",

    'link' => 'http://sweetgum.nybg.org/science/vh/specimen_list.php?SummaryData=[cdm:taxon_name]',

    'title' => 'NYBG',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  );

  $ext_links_default["tropicos"] = array(

    'id' => "tropicos",

    'link' => 'http://www.tropicos.org/NameSearch.aspx?name=[cdm:taxon_name]',

    'title' => 'Tropicos',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  );

  $ext_links_default["wfo-specimens"] = array(

    'id' => "wfo-specimens",

    'link' => 'http://wfospecimens.cybertaxonomy.org/search/result?fullScientificName=[cdm:taxon_name]',

    'title' => 'World Flora Online - Specimens',

    'weight' => 0,

    'status' => 1,

    'category' => 'Specimens/Occurrences',

  );

  // --- Molecular Resources ---

  $ext_links_default["ggbn"] = array(

    'id' => "ggbn",

    'link' => 'http://www.ggbn.org/ggbn_portal/search/result?fullScientificName=[cdm:taxon_name]',

    'title' => 'GGBN',

    'weight' => 0,

    'status' => 1,

    'category' => 'Molecular Resources',

  );

  $ext_links_default["ncbi"] = array(

    'id' => "ncbi",

    'link' => 'http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=%22[cdm:taxon_name]%22',

    'title' => 'NCBI',

    'weight' => 0,

    'status' => 1,

    'category' => 'Molecular Resources',

  );

  // --- Images ---

  $ext_links_default["europeana"] = array(

    'id' => "europeana",

    'link' => 'https://www.europeana.eu/en/search?query=[cdm:taxon_name]',

    'title' => 'Europeana',

    'weight' => 0,

    'status' => 1,

    'category' => 'Images',

  );

  $ext_links_default["flickr"] = array(

    'id' => "flickr",

    'link' => 'http://www.flickr.com/search/?w=all&q=%22[cdm:taxon_name]%22',

    'title' => 'flickr',

    'weight' => 0,

    'status' => 1,

    'category' => 'Images',

  );

  $ext_links_default["google"] = array(

    'id' => "google",

    'link' => 'http://images.google.com/images?q=%22[cdm:taxon_name]%22',

    'title' => 'Google Images',

    'weight' => 0,

    'status' => 1,

    'category' => 'Images',

  );

  $ext_links_default["morphbank"] = array(

    'id' => "morphbank",

    'link' => 'https://www.morphbank.net/Browse/ByImage/index.php?keywords=&tsnKeywords=[cdm:taxon_name]',

    'title' => 'Morphbank',

    'weight' => 0,

    'status' => 1,

    'category' => 'Images',

  );

  // --- Conservation ---

  $ext_links_default["iucn"] = array(

    'id' => "iucn",

    'link' => 'https://www.iucnredlist.org/search?query=[cdm:taxon_name]',

    'title' => 'IUCN Red List',

    'weight' => 0,

    'status' => 1,

    'category' => 'Conservation',

  );

  // --- Literature ---

  $ext_links_default["scholar"] = array(

    'id' => "scholar",

    'link' => 'http://scholar.google.de/scholar?q=%22[cdm:taxon_name]%22',

    'title' => 'Google scholar',

    'weight' => 0,

    'status' => 1,

    'category' => 'Literature',

  );

  $ext_links_default["bhl"] = array(

    'id' => "bhl",

    // BHL does not normalize rank terms, ssp., sub., subsp. are not unified, therefore we skip that part:

    'link' => 'https://www.biodiversitylibrary.org/search?searchTerm=[cdm:taxon_name:genus_or_uninomial]+[cdm:taxon_name:epithet]+[cdm:taxon_name:infraspecific_epithet]&stype=F#/names',

    'title' => 'BHL',

    'weight' => 0,

    'status' => 1,

    'category' => 'Literature',

  );

  $ext_links_default["pubmed"] = array(

    'id' => "pubmed",

    'link' => 'https://pubmed.ncbi.nlm.nih.gov/?term=[cdm:taxon_name]',

    'title' => 'PubMed',

    'weight' => 0,

    'status' => 1,

    'category' => 'Literature',

  );

  $weight = -10;

  foreach($ext_links_default as &$template){

    $template['weight'] = $weight++;

  }

  return $ext_links_default;

}