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graphHandler.php
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<?php
/***
*
*
* Connection docs:
* https://github.com/graphaware/neo4j-php-client
*
* @author Philip Kahn
* @date 2017.11.22
***/
# Setup graph connection
require_once __DIR__ . '/vendor/autoload.php';
use GraphAware\Neo4j\Client\ClientBuilder;
/*****************
* 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);
}
}
$client = ClientBuilder::create()
->addConnection('default', $graphProtocol . "://" . $graphUser . ":" . $graphPassword . "@" . $graphUrl . ":" .$graphPorts[$graphProtocol])
->setDefaultTimeout(60)
->build();
switch ($_REQUEST["action"]) {
case "id_details":
getTaxonDetailsFromID($_REQUEST["id"]);
case "children":
getChildNodes($_REQUEST["taxon"]);
case "load":
# Authenticate
require_once(dirname(__FILE__)."/admin/async_login_handler.php");
$login_status = getLoginState($_REQUEST);
if ($login_status !== true) {
returnAjax(array(
"status" => false,
"error" => "You need to be logged in with admin credentials to perform this action"
));
}
returnAjax($login_status);
# Check flag
returnAjax(loadDatabase());
default:
getRelatedness();
}
function resultToGraphJSON($resultObj, $asNode = false) {
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');
$graphJson = array(
"nodes" => array(),
"edges" => array()
);
$treeRank = array(
"Species" => 0,
"Genus" => 1,
"Family" => 2,
"Order" => 3,
"Superorder" => 4,
"Magnaorder" => 5,
"Cohort" => 6,
);
$highestRank = 0;
$rootIndex = 0;
foreach($resultObj->records() as $recordBase) {
foreach ($recordBase->values() as $record) {
$i = 0;
if (!$asNode) {
foreach ($record->nodes() as $node) {
$type = $node->labels()[0];
$graphJson["nodes"][] = array(
"root" => False,
"id" => $node->identity(),
"type" => $type,
"label" => $node->value("label"),
"caption" => $type != "Species" ? $node->value("label") : $node->value("binomial"),
"values" => $node->values(),
"x" => $i,
"y" => $i,
"size" => 1,
"color" => "#58e",
);
try {
if ($treeRank[$node->value("rank")] > $highestRank) {
$highestRank = $treeRank[$node->value("rank")];
$rootIndex = $i;
}
} catch (Exception $e) {
$rootIndex = $i;
$highestRank = 999;
}
$i++;
}
foreach ($record->relationships() as $relationship) {
$graphJson["edges"][] = array(
"source" => $relationship->startNodeIdentity(),
"target" => $relationship->endNodeIdentity(),
"caption" => $relationship->type(),
"label" => $relationship->type(),
"type" => $relationship->type(),
"values" => $relationship->values(),
"id" => $relationship->identity(),
"color" => "#999",
);
}
} else {
$node = $record;
$type = $node->labels()[0];
$graphJson["nodes"][] = array(
"root" => False,
"id" => $node->identity(),
"type" => $type,
"label" => $node->value("label"),
"caption" => $type != "Species" ? $node->value("label") : $node->value("binomial"),
"values" => $node->values(),
);
if ($treeRank[$node->value("rank")] > $highestRank) {
$highestRank = $treeRank[$node->value("rank")];
$rootIndex = $i;
}
$i++;
}
}
}
$graphJson["nodes"][$rootIndex]["root"] = True;
$json = json_encode($graphJson, JSON_PARTIAL_OUTPUT_ON_ERROR | JSON_UNESCAPED_UNICODE);
if ($json === false) {
$json = json_last_error();
}
$replace_array = array(""",""");
print str_replace($replace_array, "\\\"", $json);
exit();
}
function loadDatabase() {
global $db, $client;
# Create nodes for the high level taxa
$looper = array(
"simple_linnean_group" => "Cohort",
"major_type" => "Magnaorder",
"major_subtype" => "Superorder",
"linnean_order" => "Order",
"linnean_family" => "Family",
);
$l = $db->getLink();
$errors = array();
$i = 0;
$dbKeys = array_keys($looper);
reset($looper);
try {
$client->run("MATCH (n) DETACH DELETE n");
$client->run("CREATE (:Mammals {label: 'mammalia'})");
while ($nodeLabel = current($looper)) {
# Create an array of parameters to pass to the graph database
$dbKey = $dbKeys[$i];
$query = "SELECT DISTINCT `$dbKey` FROM `".$db->getTable()."` ORDER BY id";
$r = mysqli_query($l, $query);
if ($r === false) {
$errors[] = mysqli_error($l);
continue;
}
# Build the parameters
$data = array();
while($row = mysqli_fetch_row($r)) {
if (empty($row[0])) {
continue;
}
$data[] = array($row[0]);
}
# Start the cypher query
$cypher = "
UNWIND {data} AS attr
MERGE (:Clade {label: attr[0], rank: '$nodeLabel'})
";
$client->run($cypher, array("data"=>$data));
$i++;
# If we have defineable children, let's specify them
$childNodeLabel = next($looper);
if ($childNodeLabel !== False) {
$childDBKey = $dbKeys[$i];
$origData = $data;
foreach ($origData as $dataSet) {
$parentClade = $dataSet[0];
$query = "SELECT DISTINCT `$childDBKey` FROM `".$db->getTable()."` WHERE lower(`$dbKey`)=lower('$parentClade') ORDER BY id";
$r2 = mysqli_query($l, $query);
if ($r2 !== false) {
$data = array();
$j = 0;
while ($childRow = mysqli_fetch_row($r2)) {
if (empty($childRow[0])) {
continue;
}
$data[] = array(
$parentClade,
$childRow[0]
);
}
$cypher = "
UNWIND {data} AS attr
MATCH (c:Clade {label: attr[0]})
MERGE (c)-[:CONTAINS_CLADE]->(:Clade {label: attr[1], rank: '$childNodeLabel', parent: '$parentClade'})-[:DESCENDANT_OF]->(c)";
$client->run($cypher, array("data"=>$data));
} else {
$errors[] = "No children found for child: ".$query;
}
}
} else {
# No children
$cypher = "
MATCH c WHERE NOT (c:Clade)<-[:CONTAINS_CLADE]-(:Clade)
";
}
}
# Link the top level back
$client->run("MATCH (m:Mammals) WITH m AS m MATCH (c:Clade {rank:'Cohort'}) MERGE (m)-[:CONTAINS_CLADE]->(c)-[:DESCENDANT_OF]->(m)");
} catch (\GraphAware\Neo4j\Client\Exception\Neo4jException $e) {
return array(
"status" => False,
"error" => $e->getMessage(),
"data" => $data
);
}
# Tag out genus and species
$query = "SELECT DISTINCT `genus`, `linnean_family` FROM `".$db->getTable()."`";
$r = mysqli_query($l, $query);
if ($r === false) {
$errors[] = mysqli_error($l);
return array(
"status" => False,
"error" => "Unable to assign genera"
);
}
# Build the parameters
$data = array();
while($row = mysqli_fetch_row($r)) {
if (empty($row[0])) {
continue;
}
$data[] = array($row[0], $row[1]);
}
# Start the cypher query
$cypher = "
UNWIND {data} AS attr
CREATE (g:Genus {label: attr[0], rank: 'Genus'})
WITH g AS g, attr as attr
MATCH (c:Clade {label: attr[1]})
MERGE (g)<-[:CONTAINS_CLADE]-(c)<-[:DESCENDANT_OF]-(g)
";
$client->run($cypher, array("data"=>$data));
$query = "SELECT DISTINCT `species`, `genus`, CONCAT(genus, ' ', species) FROM `".$db->getTable()."`";
$r = mysqli_query($l, $query);
if ($r === false) {
$errors[] = mysqli_error($l);
return array(
"status" => False,
"error" => "Unable to assign species"
);
}
# Build the parameters
$data = array();
while($row = mysqli_fetch_row($r)) {
if (empty($row[0])) {
continue;
}
$data[] = array($row[0], $row[1], $row[2]);
}
# Start the cypher query
$cypher = "
UNWIND {data} AS attr
CREATE (g:Species {label: attr[0], rank: 'Species', binomial: attr[2] })
WITH g AS g, attr as attr
MATCH (c:Genus {label: attr[1]})
MERGE (g)<-[:CONTAINS_CLADE]-(c)<-[:DESCENDANT_OF]-(g)
";
$client->run($cypher, array("data"=>$data));
return array(
"status" => True,
"errors" => $errors
);
}
function updateTaxonomy($changeDetails, $taxonomyLevel = "clade") {
/***
* Update a taxon changed on the main site.
*
* @param array $changeType -> Details the change type.
* array(
* "type" => [RENAME, MOVE]
* "update" => For rename, a string of the new name. For move, string of the new parent (must be of same rank of previous parent)
* )
* @param str $taxonomyLevel -> controlled vocabulary. "genus", "species", or null/"clade"
***/
global $db, $client;
if(empty($taxonomyLevel)) {
$taxonomyLevel = "clade";
}
$taxonomyLevel = ucwords($taxonomyLevel);
$validLevels = array(
"Genus",
"Species",
"Clade"
);
if(!in_array($taxonomyLevel, $validLevels, True)) {
return array(
"status" => False,
"error" => "Invalid taxonomy level '".$taxonomyLevel."'"
);
}
# Operations
}
function getChildNodes($taxonLabel) {
/***
* From a given taxon label, find all the children and return
* a graphJSON
***/
global $db, $client;
$cypher = "MATCH path = (t {label:'$taxonLabel'})-[:CONTAINS_CLADE]->(r) RETURN path";
$neo4jResults = $client->run($cypher);
resultToGraphJSON($neo4jResults);
}
function getTaxonDetailsFromID($nodeID) {
/***
*
*/
$cleanNodeID = intval($nodeID);
if (!is_numeric($cleanNodeID)) {
return False;
}
global $client;
$cypher = "MATCH (c) WHERE ID(c) = $cleanNodeID RETURN c.label, c.rank";
# Do the thing
$result = $client->run($cypher);
$recordBase = $result->records();
$resultDetails = $recordBase[0]->values();
# Return it
returnAjax(array(
"label" => $resultDetails[0],
"rank" => $resultDetails[1]
));
}
function getRelatedness($taxon1, $taxon2) {
/***
*
***/
global $client, $db;
$taxon1 = empty($taxon1) ? $_REQUEST["taxon1"] : $taxon1;
$taxon2 = empty($taxon2) ? $_REQUEST["taxon2"] : $taxon2;
/**
* Sample:
*
* match (start:Species {binomial: 'rhinoceros unicornis'}), (end:Species {binomial: 'bradypus tridactylus'})
* call apoc.algo.dijkstraWithDefaultWeight(start, end, 'CLADE_CONTAINS|DESCENDANT_OF', 'distance', 1) YIELD path, weight
* return path
*
*/
# Do a regex check on the taxa
# execute query
$cypher = "
MATCH (start:Species {binomial: '$taxon1'}), (end:Species {binomial: '$taxon2'})
CALL apoc.algo.dijkstraWithDefaultWeight(start, end, 'CLADE_CONTAINS|DESCENDANT_OF', 'distance', 1) YIELD path, weight
RETURN path
";
$result = $client->run($cypher);
resultToGraphJSON($result);
}
?>