config.php

<?php

// configuration variables used across the scripts and applications
require_once('../vendor/autoload.php');
include_once("../../backbone_secrets.php");

// backbone_secrets contains $db_hidden_dir as well.

session_name($session_name); // set in secrets to differentiate sandbox from live site.
session_start();

// create and initialise the database connection
$mysqli = new mysqli($db_host, $db_user, $db_password, $db_database);  

// connect to the database
if ($mysqli->connect_error) {
  echo $mysqli->connect_error;
}

if (!$mysqli->set_charset("utf8mb4")) {
  echo printf("Error loading character set utf8: %s\n", $mysqli->error);
}

// ORCID Connection details
// client id and secret are loaded in the secret file
define('ORCID_CLIENT_ID', $orcid_client_id);
define('ORCID_CLIENT_SECRET', $orcid_client_secret);
define('ORCID_REDIRECT_URI', $orcid_redirect_uri);
define('ORCID_LOG_OUT_URI', $orcid_log_out_uri);
define('ORCID_TOKEN_URI', 'https://orcid.org/oauth/token');

// the login uri is constructed from variables above
define('ORCID_LOG_IN_URI', 'https://orcid.org/oauth/authorize?client_id='. ORCID_CLIENT_ID .'&response_type=code&scope=/authenticate&redirect_uri=' . ORCID_REDIRECT_URI);

// gbif web services (end in slash)
define('GBIF_WEB_SERVICE_URI', 'https://api.gbif.org/v1/');

// webservices for accessing the plant list API
define('PLANT_LIST_URI_LIVE', 'https://list.worldfloraonline.org/');
define('PLANT_LIST_URI_STAGING', 'https://rhakhis.rbge.info/');

// status flags
define("WFO_INTEGRITY_OK", 1); // when the integrity of a name or taxon checks out
define("WFO_INTEGRITY_FAIL", 2); // when the integrity of a name or taxon does not check out
define("WFO_INTEGRITY_WARN", 3); // when the integrity is OK but there are information messages
define("WFO_AUTONYM", 4); // returned when this is the autonym
define("WFO_AUTONYM_EXISTS", 5); // returned when this isn't the autonym - but one exists
define("WFO_AUTONYM_REQUIRED", 6); // returned when this isn't the autonym and no autonym exists at this rank
define("WFO_AUTONYM_NA", 7); // returned when this isn't the autonym and no autonym exists at this rank
define("WFO_RANK_REBALANCE", 8); // the ranks at this point are out of balance and need fixing.

// the rank table - having this in code saves a lot of sql queries and joins because
// it is used everywhere.
// -- READ -- THIS --
// this should be kept in syn with the enumeration values in the db
// ALSO IN THE WFO-PLANT-LIST repository
$ranks_table = array(

  "code" => array(
    "children" => array("kingdom", "phylum"), // permissible ranks for child taxa
    "abbreviation" => "ICN", // official abbreviation
    "plural" => "Code",
    "aka" => array() // alternative representations for import
  ),

  "kingdom" => array(
    "children" => array("subkingdom", "phylum"), // permissible ranks for child taxa
    "abbreviation" => "King.", // official abbreviation
    "plural" => "Kingdoms",
    "aka" => array() // alternative representations for import
  ),

  "subkingdom" => array(
    "children" => array("phylum", "class", "order","family", "superorder"), // permissible ranks for child taxa
    "abbreviation" => "subking.", // official abbreviation
    "plural" => "Subkingdoms",
    "aka" => array() // alternative representations for import
  ),

  "phylum" => array(
    "children" => array("class", "order", "family", "superorder"), // permissible ranks for child taxa
    "abbreviation" => "phyllum", // official abbreviation
    "plural" => "Phyla",
    "aka" => array() // alternative representations for import
  ),

  "class" => array(
    "children" => array("subclass", "order", "family","superorder"), // permissible ranks for child taxa
    "abbreviation" => "class", // official abbreviation
    "plural" => "Classes",
    "aka" => array() // alternative representations for import
  ),

  "subclass" => array(
    "children" => array("order", "family", "superorder"), // permissible ranks for child taxa
    "abbreviation" => "subclass.", // official abbreviation
    "plural" => "Subclasses",
    "aka" => array() // alternative representations for import
  ),

  "superorder" => array(
    "children" => array("order"), // permissible ranks for child taxa
    "abbreviation" => "superord.", // official abbreviation
    "plural" => "Superorders",
    "aka" => array() // alternative representations for import
  ),

  "order" => array(
    "children" => array("suborder", "family"), // permissible ranks for child taxa
    "abbreviation" => "ord.", // official abbreviation
    "plural" => "Orders",
    "aka" => array() // alternative representations for import
  ),

  "suborder" => array(
    "children" => array("family"), // permissible ranks for child taxa
    "abbreviation" => "subord.", // official abbreviation
    "plural" => "Suborders",
    "aka" => array() // alternative representations for import
  ),

  "family" => array(
    "children" => array("supertribe", "subfamily", "tribe", "genus"), // permissible ranks for child taxa
    "abbreviation" => "fam.", // official abbreviation
    "plural" => "Families",
    "aka" => array() // alternative representations for import
  ),

  "subfamily" => array(
    "children" => array("supertribe", "tribe", "genus"), // permissible ranks for child taxa
    "abbreviation" => "subfam.", // official abbreviation
    "plural" => "Subfamilies",
    "aka" => array() // alternative representations for import
  ),

  "supertribe" => array(
    "children" => array("tribe"), // permissible ranks for child taxa
    "abbreviation" => "suptr.", // official abbreviation
    "plural" => "Supertribes",
    "aka" => array('supertrib.') // alternative representations for import
  ),

  "tribe" => array(
    "children" => array("subtribe", "genus"), // permissible ranks for child taxa
    "abbreviation" => "tr.", // official abbreviation
    "plural" => "Tribes",
    "aka" => array('trib.') // alternative representations for import
  ),

  "subtribe" => array(
    "children" => array("genus"), // permissible ranks for child taxa
    "abbreviation" => "subtr.", // official abbreviation
    "plural" => "Subtribes",
    "aka" => array('subtrib.', 'subtrib') // alternative representations for import
  ),

  "genus" => array(
    "children" => array("subgenus", "section", "series", "species"), // permissible ranks for child taxa
    "abbreviation" => "gen.", // official abbreviation
    "plural" => "Genera",
    "aka" => array() // alternative representations for import
  ),

  "subgenus" => array(
    "children" => array("section", "series", "species"), // permissible ranks for child taxa
    "abbreviation" => "subg.", // official abbreviation
    "plural" => "Subgenera",
    "aka" => array('subgen.') // alternative representations for import
  ),

  "section" => array(
    "children" => array("subsection", "series", "species"), // permissible ranks for child taxa
    "abbreviation" => "sect.", // official abbreviation
    "plural" => "Sections",
    "aka" => array("sect",  "nothosect.") // alternative representations for import
  ),
  
  "subsection" => array(
    "children" => array("series", "species"), // permissible ranks for child taxa
    "abbreviation" => "subsect.", // official abbreviation
    "plural" => "Subsections",
    "aka" => array() // alternative representations for import
  ),

  "series" => array(
    "children" => array("subseries", "species"), // permissible ranks for child taxa
    "abbreviation" => "ser.", // official abbreviation
    "plural" => "Series",
    "aka" => array() // alternative representations for import
  ),

  "subseries" => array(
    "children" => array("species"), // permissible ranks for child taxa
    "abbreviation" => "subser.", // official abbreviation
    "plural" => "Subseries",
    "aka" => array() // alternative representations for import
  ),

  "species" => array(
    "children" => array("subspecies", "variety", "form", "prole", "lusus"), // permissible ranks for child taxa
    "abbreviation" => "sp.", // official abbreviation
    "plural" => "Species",
    "aka" => array("nothospecies", "spec.") // alternative representations for import
  ),

  "subspecies" => array(
    "children" => array("variety", "form", "prole", "lusus"), // permissible ranks for child taxa
    "abbreviation" => "subsp.", // official abbreviation
    "plural" => "Subspecies",
    "aka" => array("nothosubspecies", "nothosubsp.", "subsp.", "subsp", "ssp", "ssp.", "subspec.") // alternative representations for import
  ),

  "prole" => array(
    "children" => array(), // permissible ranks for child taxa
    "abbreviation" => "prol.", // official abbreviation
    "plural" => "Proles",
    "aka" => array("race", "proles") // alternative representations for import
  ),

  "variety" => array(
    "children" => array("subvariety", "form", "prole", "lusus"), // permissible ranks for child taxa
    "abbreviation" => "var.", // official abbreviation
    "plural" => "Varieties",
    "aka" => array("nothovar.", "var.", "var") // alternative representations for import
  ),

  "subvariety" => array(
    "children" => array("form"), // permissible ranks for child taxa
    "abbreviation" => "subvar.", // official abbreviation
    "plural" => "Subvarieties",
    "aka" => array("subvar") // alternative representations for import
  ),

  "form" => array(
    "children" => array("subform"), // permissible ranks for child taxa
    "abbreviation" => "f.", // official abbreviation
    "plural" => "Forms",
    "aka" => array("forma", "f") // alternative representations for import
  ),

  "subform" => array(
    "children" => array(), // permissible ranks for child taxa
    "abbreviation" => "subf.", // official abbreviation
    "plural" => "Subforms",
    "aka" => array("subforma") // alternative representations for import
  ),

  "lusus" => array(
    "children" => array(), // permissible ranks for child taxa
    "abbreviation" => "lus.", // official abbreviation
    "plural" => "Lusus",
    "aka" => array("lus", "lusus naturae") // alternative representations for import
  ),

  "unranked" => array(
    "children" => array(), // permissible ranks for child taxa = none
    "abbreviation" => "unr.", // official abbreviation
    "plural" => "Unranked",
    "aka" => array() // alternative representations for import
  )

);