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api.php
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<?php
/***********************************************************
* ASM Species database API target
*
* Find the full API description here:
*
* https://github.com/tigerhawkvok/asm-mammal-database/blob/master/README.md
*
* @param boolean fuzzy
* @param boolean loose
* @param int limit
* @param string order (comma-seperated values)
* @param string only (comma-seperated values)
* @param string include (comma-seperated values)
* @param string type
* @param JSON filter
* @param boolean dwc_only
*
* @author Philip Kahn / [email protected]
* @date January 2017
*
* Forked from
* https://github.com/SSARHERPS/SSAR-species-database/blob/v1.2.5/commonnames_api.php
*
* @url https://github.com/tigerhawkvok/asm-mammal-database
**********************************************************/
/*****************
* Setup
*****************/
#$show_debug = true;
if ($show_debug === true) {
error_reporting(E_ALL);
ini_set('display_errors', 1);
error_log('API is running in debug mode!');
$debug = true; # compat
} else {
# Rigorously avoid errors in production
ini_set('display_errors', 0);
$debug = false;
}
require dirname(__FILE__)."/CONFIG.php";
require_once(dirname(__FILE__)."/core/core.php");
# This is a public API
header("Access-Control-Allow-Origin: *");
$db = new DBHelper($default_database, $default_sql_user, $default_sql_password, $default_sql_url, $default_table, $db_cols);
if (isset($_SERVER['QUERY_STRING'])) {
parse_str($_SERVER['QUERY_STRING'], $_REQUEST);
}
$start_script_timer = microtime_float();
$_REQUEST = array_merge($_REQUEST, $_GET, $_POST);
if (!function_exists('elapsed')) {
function elapsed($start_time = null)
{
/***
* Return the duration since the start time in
* milliseconds.
* If no start time is provided, it'll try to use the global
* variable $start_script_timer
*
* @param float $start_time in unix epoch. See http://us1.php.net/microtime
***/
if (!is_numeric($start_time)) {
global $start_script_timer;
if (is_numeric($start_script_timer)) {
$start_time = $start_script_timer;
} else {
return false;
}
}
return 1000*(microtime_float() - (float)$start_time);
}
}
function utf8ize($d)
{
if (is_array($d)) {
foreach ($d as $k => $v) {
$d[$k] = utf8ize($v);
}
} elseif (is_string($d)) {
return utf8_encode($d);
}
return $d;
}
if (!function_exists("returnAjax")) {
function returnAjax($data)
{
/***
* Return the data as a JSON object
*
* @param array $data
*
***/
if (!is_array($data)) {
$data=array($data);
}
$data = utf8ize($data);
$data["execution_time"] = elapsed();
header('Cache-Control: no-cache, must-revalidate');
header('Expires: Mon, 26 Jul 1997 05:00:00 GMT');
header('Content-type: application/json; charset=utf-8');
$json = json_encode($data, JSON_FORCE_OBJECT | JSON_PARTIAL_OUTPUT_ON_ERROR | JSON_UNESCAPED_UNICODE);
if ($json === false) {
$json = json_last_error();
}
//print_r(json_last_error());
$replace_array = array(""",""");
print str_replace($replace_array, "\\\"", $json);
exit();
}
}
function checkColumnExists($column_list)
{
/***
* Check if a comma-seperated list of columns exists in the
* database.
* @param string $column_list (comma-sep)
* @return array
***/
if (empty($column_list)) {
return true;
}
global $db;
$cols = $db->getCols();
foreach (explode(",", $column_list) as $column) {
if (strtolower($column) == "count(*)" || $column == "*") {
continue;
}
if (!array_key_exists($column, $cols)) {
try {
returnAjax(array("status"=>false,"error"=>"Invalid column '$column'. If it exists, it may be an illegal lookup column.","human_error"=>"Sorry, you specified a lookup criterion that doesn't exist. Please try again.","columns"=>$column_list,"bad_column"=>$column));
} catch (Exception $e) {
returnAjax(array("status"=>false,"error"=>"Invalid column. If it exists, it may be an illegal lookup column.","human_error"=>"Sorry, you specified a lookup criterion that doesn't exist. Please try again.","columns"=>$column_list,"bad_column"=>$column));
}
}
}
return true;
}
if (toBool($_REQUEST["missing"]) || toBool($_REQUEST["fetch_missing"])) {
$save = isset($_REQUEST["prefetch"]) ? toBool($_REQUEST["prefetch"]) : false;
returnAjax(getTaxonIucnData($_REQUEST), $save);
}
if (toBool($_REQUEST["get_unique"])) {
returnAjax(getUniqueVals($_REQUEST["col"]));
}
if (toBool($_REQUEST["random"])) {
$hasImage = false;
$query = "SELECT `genus`, `species`, `subspecies` from `".$db->getTable()."` ORDER BY RAND() LIMIT 1";
while (!$hasImage) {
if (!isset($_REQUEST["require_image"]) || !toBool($_REQUEST["require_image"])) {
# We don't care if it really has an image. Pretend it
# does.
$hasImage = true;
} else {
# We need to test the presence of an image
$query = "SELECT `genus`, `species`, `subspecies`, `image` from `".$db->getTable()."` ORDER BY RAND() LIMIT 1";
}
$result = mysqli_query($db->getLink(), $query);
$row = mysqli_fetch_assoc($result);
if (!$hasImage) {
/***
* As per
* https://github.com/tigerhawkvok/asm-mammal-database/issues/56
***/
if (!function_exists("getCanonicalSpecies")) {
function getCanonicalSpecies($speciesRow, $short = false)
{
$output = ucwords($speciesRow["genus"]);
$short = ucwords(substr($speciesRow["genus"], 0, 1)) . ". ";
$output .= " " . $speciesRow["species"];
if (!empty($speciesRow["subspecies"])) {
$output .= " " . $speciesRow["subspecies"];
$short .= substr($speciesRow["species"], 0, 1) . ". " . $speciesRow["subspecies"];
} else {
$short .= $speciesRow["species"];
}
if (!empty($speciesRow["canonical_sciname"])) {
$output = $speciesRow["canonical_sciname"];
}
return $short === true ? $short : $output;
}
}
$imgPath = preg_replace('/species_photos/im', 'species_photos', $row["image"]);
# Does it exist?
if (!empty($imgPath) && file_exists(dirname(__FILE__)."/".$imgPath)) {
$hasImage = true;
} else {
# Check for other available ones
try {
include_once dirname(__FILE__) . "/phpquery/phpQuery/phpQuery.php";
if (!class_exists("phpQuery")) {
throw(new Exception("BadPHPQuery"));
}
$url = $mammalDomain . "/search/asm_custom_search/" . urlencode(getCanonicalSpecies($row));
$images .= "<!-- Image from search $url -->";
$html = file_get_contents($url);
phpQuery::newDocumentHTML($html);
$imgElement = pq("#imageLibraryContent #current_image img");
$imgRelPath = $imgElement->attr("src");
if (!empty($imgRelPath) && !toBool($_REQUEST["skip_mil"])) {
$hasImage = true;
} else {
# We couldn't find a picture in the mammal library. Try
# iNaturalist.
#
# Sample:
# https://www.inaturalist.org/observations.json?taxon_name=ursus+arctos&quality_grade=research&photo_license=any&iconic_taxa[]=Mammalia&has[]=photos
$endpoint = "https://www.inaturalist.org/observations.json";
$postArgs = array(
"taxon_name" => urlencode(getCanonicalSpecies($row)),
"quality_grade" => "research",
"photo_license" => "any",
"iconic_taxa[]" => "Mammalia",
"has[]" => "photos",
);
$result = do_post_request($endpoint, $postArgs, "GET");
$response = json_decode($result["response"], true);
$textArgs = http_build_query($postArgs);
# Some stupid replacements
$search = array(
"%2B",
"%5B",
"%5D",
);
$replace = array(
"+",
"[",
"]",
);
$textArgs = str_replace($search, $replace, $textArgs);
$inat = 0;
if (sizeof($response) > 0 && !toBool($_REQUEST["skip_inat"])) {
shuffle($response);
$useObservation = $response[0];
# First, we have to check that there was a match, and
# iNat didn't return an unhelpful blob
$obsTaxon = explode(" ", $useObservation["taxon"]["name"]);
$refMatchGenus = strlen(substr($row["genus"], 0, -3)) < 3 ? $row["genus"] : substr($row["genus"], 0, -3);
$refMatchSpecies = strlen(substr($row["species"], 0, -3)) < 3 ? $row["species"] : substr($row["species"], 0, -3);
$obsMatchGenus = strlen(substr($obsTaxon[0], 0, -3)) < 3 ? strtolower($obsTaxon[0]) : substr(strtolower($obsTaxon[0]), 0, -3);
$obsMatchSpecies = strlen(substr($obsTaxon[1], 0, -3)) < 3 ? $obsTaxon[1] : substr($obsTaxon[1], 0, -3);
if ($refMatchGenus == $obsMatchGenus || $refMatchSpecies == $obsMatchSpecies) {
$hasImage = true;
}
}
if ($inat == 0) {
# iNaturalist failed us too.
# Last attempt: calPhotos
# Queries of format: http://calphotos.berkeley.edu/cgi/img_query?getthumbinfo=1&num=all&taxon=ursus+arctos&format=xml
$endpoint = "http://calphotos.berkeley.edu/cgi/img_query";
$postArgs = array(
"getthumbinfo" => 1,
"cconly" => 1,
"num" => "all",
"taxon" => getCanonicalSpecies($row),
"format" => "xml",
);
$dest = $endpoint."?".http_build_query($postArgs);
$xmlContent = file_get_contents($dest);
$xml = new Xml();
$xml->setXml($xmlContent);
$imgArr = $xml->getAllTagContents("enlarge_jpeg_url");
if (sizeof($imgArr) > 0 && !toBool($_REQUEST["skip_calphotos"])) {
$hasImage = true;
}
}
}
} catch (Exception $e) {
# Somethign went wrong with that image
$hasImage = false;
}
}
}
}
$row["specificEpithet"] = $row["species"];
$row["subspecificEpithet"] = $row["subspecies"];
returnAjax($row);
}
switch (strtolower($_REQUEST["action"])) {
case "taxonomy":
returnAjax(getOrderedTaxonomy($_REQUEST));
die();
break;
case "query":
returnAjax(doLiveQuery($_REQUEST));
die();
break;
case "getAccount":
case "getaccount":
case "get-account":
case "get_account":
try {
$endpoint = "http://www.science.smith.edu/departments/Biology/VHAYSSEN/msi/msiaccounts.html";
$opts = array(
'http' => array(
'method' => 'GET',
#'request_fulluri' => true,
'ignore_errors' => true,
'timeout' => 3.5, # Seconds
),
);
$context = stream_context_create($opts);
$htmlPage = file_get_contents($endpoint, false, $context);
include_once dirname(__FILE__) . "/phpquery/phpQuery/phpQuery.php";
if (!class_exists("phpQuery")) {
throw(new Exception("BadPHPQuery"));
}
phpQuery::newDocumentHTML($htmlPage);
$body = pq("body");
returnAjax(array(
"status" => !empty($body),
"body_content" => encode64($body),
"endpoint" => $endpoint,
));
} catch (Exception $e) {
returnAjax(array(
"status" => false,
"error" => "EXCEPTION_PROCESSING_ENDPOINT",
"exception" => $e->getMessage(),
));
}
die();
break;
case "iucn":
$iucnBase = "http://apiv3.iucnredlist.org/api/v3/";
$validIucnApis = array(
"species/common_names/",
"species/countries/name/",
);
$iucnEndpoint = decode64($_REQUEST["iucn_endpoint"]);
if (empty($iucnEndpoint)) {
$iucnEndpoint = $_REQUEST["iucn_endpoint"];
}
if (!in_array($iucnEndpoint, $validIucnApis)) {
returnAjax(array(
"status" => false,
"error" => "INVALID_API_TARGET",
"human_error" => "You specified an invalid IUCN endpoint",
"valid_endpoints" => $validIucnApis,
"parsed_endpoint" => $iucnEndpoint,
"provided" => $_REQUEST,
));
}
$iucnApiHit = $iucnBase . $iucnEndpoint;
$iucnTaxonLookup = decode64($_REQUEST["taxon"]);
if (empty($iucnTaxonLookup)) {
$iucnTaxonLookup = $_REQUEST["taxon"];
}
$canonicalVerify = $db->sanitize(urldecode($iucnTaxonLookup));
# Verify the taxon exists in our database
if (!$db->isEntry($canonicalVerify, "canonical_sciname", true)) {
$response = array(
"status" => false,
"error" => "INVALID_TAXON",
"human_error" => "You specified a taxon we don't recognize",
"parsed_taxon" => $canonicalVerify,
"provided" => $_REQUEST,
);
if ($show_debug === true) {
$response["verification"] = $db->isEntry($canonicalVerify, "canonical_species", true, true);
}
returnAjax($response);
}
$endpoint = $iucnApiHit . $iucnTaxonLookup . "?token=" . $iucnToken;
$opts = array(
'http' => array(
'method' => 'GET',
#'request_fulluri' => true,
'ignore_errors' => true,
'timeout' => 3.5, # Seconds
),
);
$context = stream_context_create($opts);
$response = file_get_contents($endpoint, false, $context);
$decoded = json_decode($response, true);
$status = !empty($decoded) && empty($decoded["error"]);
$response = array(
"status" => $status,
"response" => $decoded,
"target" => $iucnEndpoint,
"taxon" => $canonicalVerify,
);
if ($show_debug === true) {
$response["iucn_token"] = $iucnToken;
if (!$status) {
$response["endpoint"] = $endpoint;
}
}
returnAjax($response);
die();
break;
default:
break;
}
function doLiveQuery($get)
{
/***
* Handles directly querying the database with an SQL string.
*
* @param array $get -> an array containing keys:
* - @key sql_query: a base64-encoded string for an SQL statement
* - @key (opt) bool dwc: If true, only return DarwinCore values
***/
global $show_debug, $db;
$sqlQuery = decode64($get['sql_query'], true);
if (empty($sqlQuery)) {
$sqlQuery = base64_decode(urldecode($get["sql_query"]));
}
$originalQuery = $sqlQuery;
$dwcOnly = isset($get["dwc"]) ? toBool($get["dwc"]) : false;
# If it's a "SELECT" style statement, make sure the accessing user
# has permissions to read this dataset
$searchSql = strtolower($sqlQuery);
# We're going to check against well-formed selects
$queryPattern = '/^SELECT +((?:(?:(`?)[a-zA-Z_\-]+\g{2}|count\(\*\))(?: +as +[a-zA-Z\_]+)?(?:, *)?)+|\*)(?<!,) +FROM +(`?)'.$db->getTable().'\g{3}( +\(?where +((?:(?:\(?(`?)[a-zA-Z_\-]+\g{6} *(?:=|!=| is | is not | like ) *([\'"]?)[^\'"`;]+\g{7})(?:(?: +AND| +OR| *,| *\)(?: +AND| +OR| *,)) +)?)+|false)\)?)?( +GROUP BY +(?:(`?)[a-zA-Z_\-]+\g{9}(?:, *)?)+(?<!,))?( +ORDER BY +(?:(`?)[a-zA-Z_\-]+\g{11}(?:, *)?)+(?<!,))? *; *$/im';
# Purely for emacs not liking the thing above meaning it has to be
#commented out in dev
if (!isset($queryPattern)) {
return array(
"error" => "Please uncomment \$queryPattern before using"
);
}
$statements = explode(';', $sqlQuery);
$effectiveKey = 0;
$statementsSize = sizeof($statements);
$statementResponse = array();
$status = true;
foreach ($statements as $k => $statement) {
$queryInfo = array();
$statement = trim($statement);
if (empty($statement)) {
unset($statements[$k]);
continue;
} else {
$statement .= ";";
}
$effectiveKey++;
$safePreflight = false;
if (preg_match($queryPattern, $statement)) {
$safePreflight = true;
$sqlAction = "SELECT";
} elseif (preg_match('/\A(?i)SELECT +\* +(?:FROM)?[ `]*'.$db->getTable().'[ `]* +(WHERE FALSE)[;]?\Z/m', $statement) || preg_match('/^show +columns +from +(`?)'.$db->getTable().'\g{1} *;?$/im', $statement)) {
# Looking up the columns is a safe action
$safePreflight = true;
$sqlAction = "LOOKUP_COLS";
# We'll just do this now
$query = "SHOW COLUMNS FROM `".$db->getTable()."`";
$r = mysqli_query($db->getLink(), $query);
$cols = array();
while ($row = mysqli_fetch_row($r)) {
$cols[] = $row[0];
}
$statementResult = array(
"result" => $cols,
"action" => $sqlAction,
);
$statementResponse[] = $statementResult;
continue;
} else {
# Unverified action
$safePreflight = false;
$sqlAction = "UNVERIFIED";
}
if ($safePreflight === true) {
try {
# Split up statements into chunks and prep for a safe
# query
global $db, $default_database, $readonly_sql_user, $readonly_sql_password, $default_sql_url, $default_sql_user, $default_sql_password;
# We're going ito use peices of PDO since this is more
# or less arbitrarily specifiable by users
$dsn = "mysql:host=$default_sql_url;dbname=$default_database;charset=utf8";
$opt = array(
PDO::ATTR_ERRMODE => PDO::ERRMODE_EXCEPTION,
PDO::ATTR_DEFAULT_FETCH_MODE => PDO::FETCH_ASSOC,
PDO::ATTR_EMULATE_PREPARES => false,
);
$pdo = new PDO($dsn, $readonly_sql_user, $readonly_sql_password, $opt);
#$pdo = new PDO($dsn, $default_sql_user, $default_sql_password, $opt);
$select = preg_replace($queryPattern, '$1', $statement);
$selectCols = explode(",", $select);
$realSelect = array();
$dontQuote = array(
"count(*)",
"*",
);
foreach ($selectCols as $colStatement) {
$col = preg_replace('/^([`]?)([a-zA-Z_\-]+)\g{1}$/im', '$2', $colStatement);
$col = trim($col);
$realCol = getDarwinCore($col, true, true);
checkColumnExists($realCol);
$realSelect[] = in_array($realCol, $dontQuote) ? $realCol : "`$realCol`";
}
$query = "SELECT ".implode(",", $realSelect)." FROM `".$db->getTable()."`";
$where = preg_replace($queryPattern, '${4}', $statement);
if (!empty($where)) {
# Extract parameters from the where
$buildWhere = array();
$buildWhereVals = array();
$where = trim($where);
$whereStatements = preg_replace('/ *where *(.*) *$/im', '$1', $where);
$groups = explode(")", $whereStatements);
$buildGroup = array();
$orConds = array();
$andConds = array();
foreach ($groups as $k => $group) {
# Trim any leading parens or spaces
if (empty($group)) {
continue;
}
if (preg_match('/^ *(and|or) +.*$/im', $group)) {
$glue = preg_replace('/^ *(and|or) +.*$/im', '$1', $group);
$group = preg_replace('/^ *(and|or) +(.*)$/im', '$2', $group);
$buildGroup[$k] = " $glue (";
} else {
$buildGroup[$k] = "(";
}
$group = preg_replace('/^\(? *(.*)$/im', '$1', $group);
if (preg_match('/(?: |^)and /im', $group)) {
# AND statements
if (preg_match('/^and /im', $group)) {
# The group leads with an and
$buildGroup[$k] = " AND (";
}
$conds = preg_split('/(?: |^)and */im', $group);
$andConds = $conds;
$ands = array();
foreach ($conds as $cond) {
if (!empty(trim($cond))) {
$condParts = preg_split('/ *(=|!=| is | is not | like ) */im', $cond, -1, PREG_SPLIT_NO_EMPTY);
$glue = preg_replace('/.*?(=|!=| is | is not | like ).*/im', '$1', $cond);
$col = preg_replace('/^([`]?)([a-zA-Z_\-]+)\g{1}$/im', '$2', $condParts[0]);
$realCol = getDarwinCore($col, true, true);
checkColumnExists($realCol);
$ands[] = "`$realCol`" . $glue . " ? ";
$buildWhereVals[] = preg_replace('/^([\'"]?)([^\'"]+)\g{1}$/im', '$2', $condParts[1]);
}
}
$buildGroup[$k] .= implode(" AND ", $ands);
} elseif (preg_match('/(?: |^)or /im', $group)) {
# OR statements
if (preg_match('/^or /im', $group)) {
# The group leads with an or
$buildGroup[$k] = " OR (";
}
$conds = preg_split('/(?: |^)or */im', $group);
$orConds = $conds;
$ors = array();
foreach ($conds as $cond) {
if (!empty(trim($cond))) {
$condParts = preg_split('/ *(=|!=| is | is not | like ) */im', $cond, -1, PREG_SPLIT_NO_EMPTY);
$glue = preg_replace('/.*?(=|!=| is | is not | like ).*/im', '$1', $cond);
$col = preg_replace('/^([`]?)([a-zA-Z_\-]+)\g{1}$/im', '$2', $condParts[0]);
$realCol = getDarwinCore($col, true, true);
checkColumnExists($realCol);
$ors[] = "`$realCol`" . $glue . " ? ";
$buildWhereVals[] = preg_replace('/^([\'"]?)([^\'"]+)\g{1}$/im', '$2', $condParts[1]);
}
}
$buildGroup[$k] .= implode(" or ", $ors);
} else {
if (sizeof($groups) === 1) {
$condParts = preg_split('/ *(=|!=| is | is not | like ) */im', $group, -1, PREG_SPLIT_NO_EMPTY);
$glue = preg_replace('/.*?(=|!=| is | is not | like ).*/im', '$1', $group);
$col = preg_replace('/^([`]?)([a-zA-Z_\-]+)\g{1}$/im', '$2', $condParts[0]);
$realCol = getDarwinCore($col, true, true);
checkColumnExists($realCol);
$buildGroup[$k] = "(`$realCol` $glue ?";
$buildWhereVals[] = preg_replace('/^([\'"]?)([^\'"]+)\g{1}$/im', '$2', $condParts[1]);
} elseif (!empty($group)) {
# What?
$buildGroup[$k] = "ILLEGAL_GROUP::>>>$group<<<";
}
}
}
$buildWhere = " WHERE ".implode(") ", $buildGroup).")";
$query .= $buildWhere;
# Generate some values now, in case we need to debug
$queryInfo = array(
"where" => $buildWhere,
"values" => $buildWhereVals,
"full_query" => $query,
"used_statement" => $statement,
);
$debugInfo = array(
"raw_where" => $where,
"cleaned_where" => $whereStatements,
"groups" => $groups,
"build_group" => $buildGroup,
"last_and" => $ands,
"select" => $select,
"conds" => array(
"or" => $orConds,
"and" => $andConds,
),
);
//return array_merge($queryInfo, $debugInfo);
$stmt = $pdo->prepare($query);
$stmt->execute($buildWhereVals);
$data = array();
foreach ($stmt as $row) {
$tmp = array(
"result" => array($row),
);
$dwc = getDarwinCore($tmp);
$dwcRow = $dwc["result"][0];
if ($dwcOnly) {
$dwcRow = $dwcRow["dwc"];
}
$data[] = $dwcRow;
}
# Set a statement
$statementResult = array(
"result" => $data,
"action" => $sqlAction,
"query" => $queryInfo,
);
if ($show_debug === true) {
$statementResult["debug"] = $debugInfo;
}
}
} catch (Exception $e) {
$exceptionMessage = $e->getMessage();
if (strpos(strtolower($exceptionMessage), "sql syntax") !== false) {
$sqlResponse = false;
} else {
$sqlResponse = null;
}
$statementResult = array(
"result" => "ERROR",
"error" => array(
"safety_check" => $safePreflight,
"sql_response" => $sqlResponse,
"was_server_exception" => true,
),
"action" => $sqlAction,
"original_results" => $statementResult,
"provided" => $originalQuery,
"query" => $queryInfo,
);
if ($show_debug === true) {
$statementResult["dev_error"] = array(
"exception" => $exceptionMessage,
"debug" => $debugInfo,
);
}
# TODO log to error log
$status = false;
}
} else {
$sqlAction = preg_replace('/^([a-z-A-Z]+).*$/im', '$1', $statement);
$statementResult = array(
"result" => "ERROR",
"error" => array(
"safety_check" => $safePreflight,
"sql_response" => null,
"was_server_exception" => false,
),
"action" => $sqlAction,
"original_results" => $statementResult,
"provided" => $originalQuery,
"query" => $queryInfo,
);
$status = false;
}
$statementResponse[] = $statementResult;
if ($status !== true) {
break;
}
}
return array(
"status" => $status,
"statements" => $statementResponse,
"statement_count" => sizeof($statements),
"provided" => $originalQuery,
);
}
function getOrderedTaxonomy($get)
{
/***
* Just a duplicate of what goes on in
* summary.php -- except async and order-able.
*
* @param array $get -> the args from a GET or POST request;
* expects:
* - str $sort -> the column to sort by for both order and genus (validates)
* - str $genus_sort -> the column to sort genera (validates)
* - str $order_sort -> the column to sort Linnean "orders" (validates)
* - bool $reverse -> sort by DESC rather than ASC if true
***/
global $db;
if (isset($get["sort"])) {
# Set them to the same thing
$orderOrderBy = $get["sort"];
$genusOrderBy = $get["sort"];
} else {
# Set them independently
$orderOrderBy = isset($get["order_sort"]) ? $get["order_sort"] : "linnean_order";
$genusOrderBy = isset($get["genus_sort"]) ? $get["genus_sort"] : "genus";
}
$reverse = isset($get["reverse"]) ? toBool($get["reverse"]) : false;
$response = array(
"status" => true,
"taxonomy" => array(
"order" => null,
"genus" => null,
),
"provided" => $get,
);
if ($orderOrderBy != "count") {
checkColumnExists($orderOrderBy);
# Errors out on its own on fail
}
if ($genusOrderBy != "count") {
checkColumnExists($genusOrderBy);
# Errors out on its own on fail
}
if ($reverse) {
$orderOrderBy .= " DESC";
$genusOrderBy .= " DESC";
}
$linneanOrderBinQuery = "select distinct `linnean_order`, count(*) as count from `".$db->getTable()."` group by `linnean_order` ORDER BY `$orderOrderBy`";
$r = mysqli_query($db->getLink(), $linneanOrderBinQuery);
$labels = array();
$data = array();
$speciesTotal = 0;
while ($row = mysqli_fetch_assoc($r)) {
$labels[] = ucwords($row["linnean_order"]);
$data[] = $row["count"];
$speciesTotal += $row["count"];
}
$genusBreakdown = array();
$genusTotal = 0;
foreach ($labels as $taxon) {
$genusBinQuery = "select distinct `genus`, count(*) as count from `".$db->getTable()."` where `linnean_order`='$taxon' group by `genus` ORDER BY `$genusOrderBy`";
$tmpLabels = array();
$tmpData = array();
$r = mysqli_query($db->getLink(), $genusBinQuery);
while ($row = mysqli_fetch_assoc($r)) {
$tmpLabels[] = ucwords($row["genus"]);
$tmpData[] = $row["count"];
$genusTotal++;
}
$genusBreakdown[$taxon] = array(
"data" => $tmpData,
"labels" => $tmpLabels,
);
}
$response["taxonomy"]["order"] = array(
"labels" => $labels,
"data" => $data,
"params" => array(
#"query" => $linneanOrderBinQuery,
"order" => $orderOrderBy,
),
);
$response["taxonomy"]["genus"] = array(
"data" => $genusBreakdown,
"params" => array(
#"query" => null,
"order" => $genusOrderBy,
),
);
returnAjax($response);
}
/*****************************
* Setup flags
*****************************/
$flag_fuzzy = toBool($_REQUEST['fuzzy']);
$loose = toBool($_REQUEST['loose']);
$strictSearchOnly = toBool($_REQUEST["strict"]);
# Default limit is specified in CONFIG
$limit = is_numeric($_REQUEST['limit']) && $_REQUEST['limit'] >= 1 ? intval($_REQUEST['limit']):$default_limit;
checkColumnExists($_REQUEST['only']);
checkColumnExists($_REQUEST['include']);
checkColumnExists($_REQUEST['order']);
$order_by = isset($_REQUEST['order']) ? $_REQUEST['order']:"genus,species,subspecies,common_name";
$params = array();
$boolean_type = false;
# This is always set by the filter
$filter_params = null;
$extra_deprecated_params = null;
if (isset($_REQUEST['filter'])) {
$params = smart_decode64($_REQUEST['filter']);
if (empty($params)) {
# Not base 64 encoded
$params_temp = json_decode($_REQUEST['filter'], true);
if (!empty($params_temp)) {
$params = array();
foreach ($params_temp as $col => $lookup) {
# Smart_decode takes care of this for us
$params[$db->sanitize(deEscape($col))] = $db->sanitize(deEscape($lookup));
}
}
}
if (!empty($params)) {
# De-escape the columns, since they'll be checked for
# existence anyway
$params_temp = $params;
$params = array();
foreach ($params_temp as $col => $lookup) {
$params[deEscape($col)] = $lookup;
}
$filter_params = $params;
# Does the "BOOLEAN_TYPE" key exist?
if (isset($params["boolean_type"])) {
$params["BOOLEAN_TYPE"] = $params["boolean_type"];
unset($params["boolean_type"]);
}
if (!array_key_exists("BOOLEAN_TYPE", $params)) {
returnAjax(array(
"status"=>false,
"error"=>"Missing required parameter",
"human_error"=>"The key 'BOOLEAN_TYPE' must exist and be either 'AND' or 'OR' when the \"filter\" parameter is specified.",
"given"=>$params));
}
# Is it valid?
if (strtoupper($params['BOOLEAN_TYPE']) != "AND" && strtoupper($params['BOOLEAN_TYPE']) != "OR") {
returnAjax(array("status"=>false,"error"=>"Missing required parameter","human_error"=>"The key 'BOOLEAN_TYPE' must be either 'AND' or 'OR'.","given"=>$params));
}
$boolean_type = strtoupper($params['BOOLEAN_TYPE']);
unset($params['BOOLEAN_TYPE']);
if ($boolean_type == "OR") {
# If the params include an authority, check the deprecated
if (isset($params["genus_authority"]) || isset($param["species_authority"])) {
if (!isset($params["deprecated_scientific"])) {
$params["deprecated_scientific"] = isset($params["genus_authority"]) ? $params["genus_authority"]:$params["species_authority"];
}
}
} else {
# AND search. If the params include an authority, check the deprecated
if (isset($params["genus_authority"]) || isset($param["species_authority"])) {
$deprecated_params = isset($params["genus_authority"]) ? $params["genus_authority"]:$params["species_authority"];
$extra_deprecated_params = "LOWER(`deprecated_scientific`) LIKE '%".$deprecated_params."%'";
}
}
if (isset($params["major_type"])) {
# We want to search all the higherClassification
$extra_deprecated_params = "`major_type`='".$params["major_type"]."' OR `major_subtype`='".$params["major_type"]."' OR `simple_linnean_group`='".$params["major_type"]."'";
}
//print_r($params);
//print_r($extra_deprecated_params);
# Do all the columns exist?
foreach ($params as $col => $lookup) {
checkColumnExists($col);
}
}
}
$search = strtolower($db->sanitize(deEscape(urldecode($_REQUEST['q']))));
$search = trim($search);
/*****************************
* The actual handlers
*****************************/
function fetchMajorMinorGroups($scientific = false)
{
global $db;
$sciMajor = array(
"eutheria"=>"eutheria",
"metatheria"=>"metatheria",
"prototheria"=>"prototheria",
);
$commonMajor = array(
"eutheria"=>"placental mammals",
"metatheria"=>"marsupials",
"prototheria"=>"monotremes",
);
$majorGroups = toBool($scientific) ? $sciMajor : $commonMajor;
$minorCol = toBool($scientific) ? "linnean_order":"simple_linnean_subgroup";
$query = "SELECT DISTINCT `$minorCol`, `linnean_order` FROM `".$db->getTable()."`";
$result = mysqli_query($db->getLink(), $query);
if ($result === false) {
return array(
"status" => false,
"error" => mysqli_error($db->getLink()),
"human_error" => "DATABASE_ERROR",
);
}
$minorGroups = array();
while ($row = mysqli_fetch_row($result)) {
$minorGroups[] = $row[0];
}
return array(
"status" => true,
"major" => $majorGroups,
"minor" => $minorGroups,
);
}
/***
* Break out early for these special cases
***/
if (toBool($_REQUEST["fetch-groups"])) {
returnAjax(fetchMajorMinorGroups($_REQUEST["scientific"]));
}
function areSimilar($string1, $string2, $distance = 70, $depth = 3)
{
/*
* Returns a TRUE if $string2 is similar to $string1,
* FALSE otherwise.
*/
# Is it a substring?
$i = 1;
if (metaphone($string1) == metaphone($string2) && $i<=$depth) {
return true;
}
$i++;
if (soundex($string1) == soundex($string2) && $i<=$depth) {
return true;
}
$i++;
$similar_difference = similar_text($string1, $string2, $percent);
if ($percent >= $distance && $i <=$depth) {
return true;
}
$i++;
$max_distance = strlen($string1)*($distance/100);
if (levenshtein($string1, $string2) < $max_distance && $i<=$depth) {
return true;
}
$i++;
return false;
}
function handleParamSearch($filter_params, $loose = false, $boolean_type = "AND", $extra_params = false)
{
/***
* Handle the searches when they're using advanced options
*
* @param extra_params a literal query
* @return array the result vector
***/
if (!is_array($filter_params) || sizeof($filter_params) === 0) {
global $method;
returnAjax(array("status"=>false,"error"=>"Invalid filter","human_error"=>"You cannot perform a parameter/filter search without setting the primary filters.","method"=>$method,"given"=>$filter_params));
}
global $db;
$query = "SELECT * FROM `".$db->getTable()."` WHERE ";
$where_arr = array();
foreach ($filter_params as $col => $crit) {
$where_arr[] = $loose ? "LOWER(`".$col."`) LIKE '%".$crit."%'":"`".$col."`='".$crit."'";
}
$where = "".implode(" ".strtoupper($boolean_type)." ", $where_arr)."";
if (!empty($extra_params)) {
global $extra_deprecated_params;
if (!empty($extra_deprecated_params)) {
$where = "(".$where." OR " . $extra_deprecated_params .")";
}
$where .= " AND (".$extra_params.")";
# $where .= " " . strtoupper($boolean_type) . " (".$extra_params.")";
} elseif (!empty($extra_deprecated_params)) {
$where .= " OR (".$extra_deprecated_params.")";
}
$where = "(".$where.")";
$query .= $where;
global $order_by;