Fisharebest\Webtrees\Tree

Complexity

Total Complexity

70

Size/Duplication

Total Lines	731
Duplicated Lines	2.6 %

Importance

Changes

0

28 Methods

Rating	Name	Duplication	Size	Complexity
B	__construct()	0	29	4
A	findByName()	0	8	3
A	getNameList()	7	7	2
A	getNameHtml()	0	2	1
B	setUserPreference()	0	28	3
A	getTreeId()	0	2	1
A	getNewXref()	0	48	3
A	getPreference()	0	11	3
A	getFactPrivacy()	0	2	1
A	getName()	0	2	1
A	getTitleHtml()	0	2	1
B	exportGedcom()	0	30	3
A	delete()	0	21	2
A	findById()	0	7	3
A	canAcceptChanges()	0	2	1
A	getIdList()	7	7	2
C	importGedcomFile()	0	39	7
B	createRecord()	3	43	6
A	getIndividualPrivacy()	0	2	1
B	getAll()	0	27	3
C	create()	0	88	8
A	getIndividualFactPrivacy()	0	2	1
A	getTitle()	0	2	1
A	deleteGenealogyData()	0	17	2
A	setPreference()	0	17	2
A	getNameUrl()	0	2	1
A	hasPendingEdit()	0	6	1
A	getUserPreference()	0	13	3

<?php
/**
 * webtrees: online genealogy
 * Copyright (C) 2017 webtrees development team
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
namespace Fisharebest\Webtrees;

use Fisharebest\Webtrees\Functions\FunctionsExport;
use Fisharebest\Webtrees\Functions\FunctionsImport;
use PDOException;

/**
 * Provide an interface to the wt_gedcom table.
 */
class Tree {
	/** @var int The tree's ID number */
	private $tree_id;

	/** @var string The tree's name */
	private $name;

	/** @var string The tree's title */
	private $title;

	/** @var int[] Default access rules for facts in this tree */
	private $fact_privacy;

	/** @var int[] Default access rules for individuals in this tree */
	private $individual_privacy;

	/** @var integer[][] Default access rules for individual facts in this tree */
	private $individual_fact_privacy;

	/** @var Tree[] All trees that we have permission to see. */
	private static $trees;

	/** @var string[] Cached copy of the wt_gedcom_setting table. */
	private $preferences = [];

	/** @var string[][] Cached copy of the wt_user_gedcom_setting table. */
	private $user_preferences = [];

	/**
	 * Create a tree object. This is a private constructor - it can only
	 * be called from Tree::getAll() to ensure proper initialisation.
	 *
	 * @param int    $tree_id
	 * @param string $tree_name
	 * @param string $tree_title
	 */
	private function __construct($tree_id, $tree_name, $tree_title) {
		$this->tree_id                 = $tree_id;
		$this->name                    = $tree_name;
		$this->title                   = $tree_title;
		$this->fact_privacy            = [];
		$this->individual_privacy      = [];
		$this->individual_fact_privacy = [];

		// Load the privacy settings for this tree
		$rows = Database::prepare(
			"SELECT SQL_CACHE xref, tag_type, CASE resn WHEN 'none' THEN :priv_public WHEN 'privacy' THEN :priv_user WHEN 'confidential' THEN :priv_none WHEN 'hidden' THEN :priv_hide END AS resn" .
			" FROM `##default_resn` WHERE gedcom_id = :tree_id"
		)->execute([
			'priv_public' => Auth::PRIV_PRIVATE,
			'priv_user'   => Auth::PRIV_USER,
			'priv_none'   => Auth::PRIV_NONE,
			'priv_hide'   => Auth::PRIV_HIDE,
			'tree_id'     => $this->tree_id,
		])->fetchAll();

		foreach ($rows as $row) {
			if ($row->xref !== null) {
				if ($row->tag_type !== null) {
					$this->individual_fact_privacy[$row->xref][$row->tag_type] = (int) $row->resn;
				} else {
					$this->individual_privacy[$row->xref] = (int) $row->resn;
				}
			} else {
				$this->fact_privacy[$row->tag_type] = (int) $row->resn;
			}
		}
	}

	/**
	 * The ID of this tree
	 *
	 * @return int
	 */
	public function getTreeId() {
		return $this->tree_id;
	}

	/**
	 * The name of this tree
	 *
	 * @return string
	 */
	public function getName() {
		return $this->name;
	}

	/**
	 * The name of this tree
	 *
	 * @return string
	 */
	public function getNameHtml() {
		return Html::escape($this->name);
	}

	/**
	 * The name of this tree
	 *
	 * @return string
	 */
	public function getNameUrl() {
		return rawurlencode($this->name);
	}

	/**
	 * The title of this tree
	 *
	 * @return string
	 */
	public function getTitle() {
		return $this->title;
	}

	/**
	 * The title of this tree, with HTML markup
	 *
	 * @return string
	 */
	public function getTitleHtml() {
		return '<span dir="auto">' . Html::escape($this->title) . '</span>';
	}

	/**
	 * The fact-level privacy for this tree.
	 *
	 * @return int[]
	 */
	public function getFactPrivacy() {
		return $this->fact_privacy;
	}

	/**
	 * The individual-level privacy for this tree.
	 *
	 * @return int[]
	 */
	public function getIndividualPrivacy() {
		return $this->individual_privacy;
	}

	/**
	 * The individual-fact-level privacy for this tree.
	 *
	 * @return integer[][]
	 */
	public function getIndividualFactPrivacy() {
		return $this->individual_fact_privacy;
	}

	/**
	 * Get the tree’s configuration settings.
	 *
	 * @param string $setting_name
	 * @param string $default
	 *
	 * @return string
	 */
	public function getPreference($setting_name, $default = '') {
		if (empty($this->preferences)) {
			$this->preferences = Database::prepare(
				"SELECT SQL_CACHE setting_name, setting_value FROM `##gedcom_setting` WHERE gedcom_id = ?"
			)->execute([$this->tree_id])->fetchAssoc();
		}

		if (array_key_exists($setting_name, $this->preferences)) {
			return $this->preferences[$setting_name];
		} else {
			return $default;
		}
	}

	/**
	 * Set the tree’s configuration settings.
	 *
	 * @param string $setting_name
	 * @param string $setting_value
	 *
	 * @return $this
	 */
	public function setPreference($setting_name, $setting_value) {
		if ($setting_value !== $this->getPreference($setting_name)) {
			Database::prepare(
				"REPLACE INTO `##gedcom_setting` (gedcom_id, setting_name, setting_value)" .
				" VALUES (:tree_id, :setting_name, LEFT(:setting_value, 255))"
			)->execute([
				'tree_id'       => $this->tree_id,
				'setting_name'  => $setting_name,
				'setting_value' => $setting_value,
			]);

			$this->preferences[$setting_name] = $setting_value;

			Log::addConfigurationLog('Tree preference "' . $setting_name . '" set to "' . $setting_value . '"', $this);
		}

		return $this;
	}

	/**
	 * Get the tree’s user-configuration settings.
	 *
	 * @param User        $user
	 * @param string      $setting_name
	 * @param string|null $default
	 *
	 * @return string
	 */
	public function getUserPreference(User $user, $setting_name, $default = null) {
		// There are lots of settings, and we need to fetch lots of them on every page
		// so it is quicker to fetch them all in one go.
		if (!array_key_exists($user->getUserId(), $this->user_preferences)) {
			$this->user_preferences[$user->getUserId()] = Database::prepare(
				"SELECT SQL_CACHE setting_name, setting_value FROM `##user_gedcom_setting` WHERE user_id = ? AND gedcom_id = ?"
			)->execute([$user->getUserId(), $this->tree_id])->fetchAssoc();
		}

		if (array_key_exists($setting_name, $this->user_preferences[$user->getUserId()])) {
			return $this->user_preferences[$user->getUserId()][$setting_name];
		} else {
			return $default;
		}
	}

	/**
	 * Set the tree’s user-configuration settings.
	 *
	 * @param User    $user
	 * @param string  $setting_name
	 * @param string  $setting_value
	 *
	 * @return $this
	 */
	public function setUserPreference(User $user, $setting_name, $setting_value) {
		if ($this->getUserPreference($user, $setting_name) !== $setting_value) {
			// Update the database
			if ($setting_value === null) {
				Database::prepare(
					"DELETE FROM `##user_gedcom_setting` WHERE gedcom_id = :tree_id AND user_id = :user_id AND setting_name = :setting_name"
				)->execute([
					'tree_id'      => $this->tree_id,
					'user_id'      => $user->getUserId(),
					'setting_name' => $setting_name,
				]);
			} else {
				Database::prepare(
					"REPLACE INTO `##user_gedcom_setting` (user_id, gedcom_id, setting_name, setting_value) VALUES (:user_id, :tree_id, :setting_name, LEFT(:setting_value, 255))"
				)->execute([
					'user_id'       => $user->getUserId(),
					'tree_id'       => $this->tree_id,
					'setting_name'  => $setting_name,
					'setting_value' => $setting_value,
				]);
			}
			// Update our cache
			$this->user_preferences[$user->getUserId()][$setting_name] = $setting_value;
			// Audit log of changes
			Log::addConfigurationLog('Tree preference "' . $setting_name . '" set to "' . $setting_value . '" for user "' . $user->getUserName() . '"', $this);
		}

		return $this;
	}

	/**
	 * Can a user accept changes for this tree?
	 *
	 * @param User $user
	 *
	 * @return bool
	 */
	public function canAcceptChanges(User $user) {
		return Auth::isModerator($this, $user);
	}

	/**
	 * Fetch all the trees that we have permission to access.
	 *
	 * @return Tree[]
	 */
	public static function getAll() {
		if (self::$trees === null) {
			self::$trees = [];
			$rows        = Database::prepare(
				"SELECT SQL_CACHE g.gedcom_id AS tree_id, g.gedcom_name AS tree_name, gs1.setting_value AS tree_title" .
				" FROM `##gedcom` g" .
				" LEFT JOIN `##gedcom_setting`      gs1 ON (g.gedcom_id=gs1.gedcom_id AND gs1.setting_name='title')" .
				" LEFT JOIN `##gedcom_setting`      gs2 ON (g.gedcom_id=gs2.gedcom_id AND gs2.setting_name='imported')" .
				" LEFT JOIN `##gedcom_setting`      gs3 ON (g.gedcom_id=gs3.gedcom_id AND gs3.setting_name='REQUIRE_AUTHENTICATION')" .
				" LEFT JOIN `##user_gedcom_setting` ugs ON (g.gedcom_id=ugs.gedcom_id AND ugs.setting_name='canedit' AND ugs.user_id=?)" .
				" WHERE " .
				"  g.gedcom_id>0 AND (" . // exclude the "template" tree
				"    EXISTS (SELECT 1 FROM `##user_setting` WHERE user_id=? AND setting_name='canadmin' AND setting_value=1)" . // Admin sees all
				"   ) OR (" .
				"    (gs2.setting_value = 1 OR ugs.setting_value = 'admin') AND (" . // Allow imported trees, with either:
				"     gs3.setting_value <> 1 OR" . // visitor access
				"     IFNULL(ugs.setting_value, 'none')<>'none'" . // explicit access
				"   )" .
				"  )" .
				" ORDER BY g.sort_order, 3"
			)->execute([Auth::id(), Auth::id()])->fetchAll();
			foreach ($rows as $row) {
				self::$trees[] = new self((int) $row->tree_id, $row->tree_name, $row->tree_title);
			}
		}

		return self::$trees;
	}

	/**
	 * Find the tree with a specific ID.
	 *
	 * @param int $tree_id
	 *
	 * @throws \DomainException
	 *
	 * @return Tree
	 */
	public static function findById($tree_id) {
		foreach (self::getAll() as $tree) {
			if ($tree->tree_id == $tree_id) {
				return $tree;
			}
		}
		throw new \DomainException;
	}

	/**
	 * Find the tree with a specific name.
	 *
	 * @param string $tree_name
	 *
	 * @return Tree|null
	 */
	public static function findByName($tree_name) {
		foreach (self::getAll() as $tree) {
			if ($tree->name === $tree_name) {
				return $tree;
			}
		}

		return null;
	}

	/**
	 * Create arguments to select_edit_control()
	 * Note - these will be escaped later
	 *
	 * @return string[]
	 */
	public static function getIdList() {

This method seems to be duplicated in your project.

		$list = [];
		foreach (self::getAll() as $tree) {
			$list[$tree->tree_id] = $tree->title;
		}

		return $list;
	}

	/**
	 * Create arguments to select_edit_control()
	 * Note - these will be escaped later
	 *
	 * @return string[]
	 */
	public static function getNameList() {

This method seems to be duplicated in your project.

		$list = [];
		foreach (self::getAll() as $tree) {
			$list[$tree->name] = $tree->title;
		}

		return $list;
	}

	/**
	 * Create a new tree
	 *
	 * @param string $tree_name
	 * @param string $tree_title
	 *
	 * @return Tree
	 */
	public static function create($tree_name, $tree_title) {
		try {
			// Create a new tree
			Database::prepare(
				"INSERT INTO `##gedcom` (gedcom_name) VALUES (?)"
			)->execute([$tree_name]);
			$tree_id = Database::prepare("SELECT LAST_INSERT_ID()")->fetchOne();
		} catch (PDOException $ex) {
			DebugBar::addThrowable($ex);

			// A tree with that name already exists?
			return self::findByName($tree_name);
		}

		// Update the list of trees - to include this new one
		self::$trees = null;
		$tree        = self::findById($tree_id);

It seems like $tree_id can also be of type string; however, parameter $tree_id of Fisharebest\Webtrees\Tree::findById() does only seem to accept integer, maybe add an additional type check?

		$tree->setPreference('imported', '0');
		$tree->setPreference('title', $tree_title);

		// Module privacy
		Module::setDefaultAccess($tree_id);

It seems like $tree_id can also be of type string; however, parameter $tree_id of Fisharebest\Webtrees\Module::setDefaultAccess() does only seem to accept integer, maybe add an additional type check?

		// Set preferences from default tree
		Database::prepare(
			"INSERT INTO `##gedcom_setting` (gedcom_id, setting_name, setting_value)" .
			" SELECT :tree_id, setting_name, setting_value" .
			" FROM `##gedcom_setting` WHERE gedcom_id = -1"
		)->execute([
			'tree_id' => $tree_id,
		]);

		Database::prepare(
			"INSERT INTO `##default_resn` (gedcom_id, tag_type, resn)" .
			" SELECT :tree_id, tag_type, resn" .
			" FROM `##default_resn` WHERE gedcom_id = -1"
		)->execute([
			'tree_id' => $tree_id,
		]);

		Database::prepare(
			"INSERT INTO `##block` (gedcom_id, location, block_order, module_name)" .
			" SELECT :tree_id, location, block_order, module_name" .
			" FROM `##block` WHERE gedcom_id = -1"
		)->execute([
			'tree_id' => $tree_id,
		]);

		// Gedcom and privacy settings
		$tree->setPreference('CONTACT_USER_ID', Auth::id());
		$tree->setPreference('WEBMASTER_USER_ID', Auth::id());
		$tree->setPreference('LANGUAGE', WT_LOCALE); // Default to the current admin’s language
		switch (WT_LOCALE) {
		case 'es':
			$tree->setPreference('SURNAME_TRADITION', 'spanish');
			break;
		case 'is':
			$tree->setPreference('SURNAME_TRADITION', 'icelandic');
			break;
		case 'lt':
			$tree->setPreference('SURNAME_TRADITION', 'lithuanian');
			break;
		case 'pl':
			$tree->setPreference('SURNAME_TRADITION', 'polish');
			break;
		case 'pt':
		case 'pt-BR':
			$tree->setPreference('SURNAME_TRADITION', 'portuguese');
			break;
		default:
			$tree->setPreference('SURNAME_TRADITION', 'paternal');
			break;
		}

		// Genealogy data
		// It is simpler to create a temporary/unimported GEDCOM than to populate all the tables...
		$john_doe = /* I18N: This should be a common/default/placeholder name of an individual. Put slashes around the surname. */ I18N::translate('John /DOE/');
		$note     = I18N::translate('Edit this individual and replace their details with your own.');
		Database::prepare("INSERT INTO `##gedcom_chunk` (gedcom_id, chunk_data) VALUES (?, ?)")->execute([
			$tree_id,
			"0 HEAD\n1 CHAR UTF-8\n0 @I1@ INDI\n1 NAME {$john_doe}\n1 SEX M\n1 BIRT\n2 DATE 01 JAN 1850\n2 NOTE {$note}\n0 TRLR\n",
		]);

		// Update our cache
		self::$trees[$tree->tree_id] = $tree;

		return $tree;
	}

	/**
	 * Are there any pending edits for this tree, than need reviewing by a moderator.
	 *
	 * @return bool
	 */
	public function hasPendingEdit() {
		return (bool) Database::prepare(
			"SELECT 1 FROM `##change` WHERE status = 'pending' AND gedcom_id = :tree_id"
		)->execute([
			'tree_id' => $this->tree_id,
		])->fetchOne();
	}

	/**
	 * Delete all the genealogy data from a tree - in preparation for importing
	 * new data. Optionally retain the media data, for when the user has been
	 * editing their data offline using an application which deletes (or does not
	 * support) media data.
	 *
	 * @param bool $keep_media
	 */
	public function deleteGenealogyData($keep_media) {
		Database::prepare("DELETE FROM `##gedcom_chunk` WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##individuals`  WHERE i_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##families`     WHERE f_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##sources`      WHERE s_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##other`        WHERE o_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##places`       WHERE p_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##placelinks`   WHERE pl_file   = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##name`         WHERE n_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##dates`        WHERE d_file    = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##change`       WHERE gedcom_id = ?")->execute([$this->tree_id]);

		if ($keep_media) {
			Database::prepare("DELETE FROM `##link` WHERE l_file =? AND l_type<>'OBJE'")->execute([$this->tree_id]);
		} else {
			Database::prepare("DELETE FROM `##link`  WHERE l_file =?")->execute([$this->tree_id]);
			Database::prepare("DELETE FROM `##media` WHERE m_file =?")->execute([$this->tree_id]);
		}
	}

	/**
	 * Delete everything relating to a tree
	 */
	public function delete() {
		// If this is the default tree, then unset it
		if (Site::getPreference('DEFAULT_GEDCOM') === $this->name) {
			Site::setPreference('DEFAULT_GEDCOM', '');
		}

		$this->deleteGenealogyData(false);

		Database::prepare("DELETE `##block_setting` FROM `##block_setting` JOIN `##block` USING (block_id) WHERE gedcom_id=?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##block`               WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##user_gedcom_setting` WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##gedcom_setting`      WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##module_privacy`      WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##hit_counter`         WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##default_resn`        WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##gedcom_chunk`        WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##log`                 WHERE gedcom_id = ?")->execute([$this->tree_id]);
		Database::prepare("DELETE FROM `##gedcom`              WHERE gedcom_id = ?")->execute([$this->tree_id]);

		// After updating the database, we need to fetch a new (sorted) copy
		self::$trees = null;
	}

	/**
	 * Export the tree to a GEDCOM file
	 *
	 * @param resource $stream
	 */
	public function exportGedcom($stream) {
		$stmt = Database::prepare(
			"SELECT i_gedcom AS gedcom, i_id AS xref, 1 AS n FROM `##individuals` WHERE i_file = :tree_id_1" .
			" UNION ALL " .
			"SELECT f_gedcom AS gedcom, f_id AS xref, 2 AS n FROM `##families`    WHERE f_file = :tree_id_2" .
			" UNION ALL " .
			"SELECT s_gedcom AS gedcom, s_id AS xref, 3 AS n FROM `##sources`     WHERE s_file = :tree_id_3" .
			" UNION ALL " .
			"SELECT o_gedcom AS gedcom, o_id AS xref, 4 AS n FROM `##other`       WHERE o_file = :tree_id_4 AND o_type NOT IN ('HEAD', 'TRLR')" .
			" UNION ALL " .
			"SELECT m_gedcom AS gedcom, m_id AS xref, 5 AS n FROM `##media`       WHERE m_file = :tree_id_5" .
			" ORDER BY n, LENGTH(xref), xref"
		)->execute([
			'tree_id_1' => $this->tree_id,
			'tree_id_2' => $this->tree_id,
			'tree_id_3' => $this->tree_id,
			'tree_id_4' => $this->tree_id,
			'tree_id_5' => $this->tree_id,
		]);

		$buffer = FunctionsExport::reformatRecord(FunctionsExport::gedcomHeader($this));
		while (($row = $stmt->fetch()) !== false) {
			$buffer .= FunctionsExport::reformatRecord($row->gedcom);
			if (strlen($buffer) > 65535) {
				fwrite($stream, $buffer);
				$buffer = '';
			}
		}
		fwrite($stream, $buffer . '0 TRLR' . WT_EOL);
		$stmt->closeCursor();
	}

	/**
	 * Import data from a gedcom file into this tree.
	 *
	 * @param string  $path       The full path to the (possibly temporary) file.
	 * @param string  $filename   The preferred filename, for export/download.
	 *
	 * @throws \Exception
	 */
	public function importGedcomFile($path, $filename) {
		// Read the file in blocks of roughly 64K. Ensure that each block
		// contains complete gedcom records. This will ensure we don’t split
		// multi-byte characters, as well as simplifying the code to import
		// each block.

		$file_data = '';
		$fp        = fopen($path, 'rb');

		// Don’t allow the user to cancel the request. We do not want to be left with an incomplete transaction.
		ignore_user_abort(true);

true of type true is incompatible with the type string expected by parameter $value of ignore_user_abort().

		Database::beginTransaction();
		$this->deleteGenealogyData($this->getPreference('keep_media'));

$this->getPreference('keep_media') of type string is incompatible with the type boolean expected by parameter $keep_media of Fisharebest\Webtrees\Tree::deleteGenealogyData().

		$this->setPreference('gedcom_filename', $filename);
		$this->setPreference('imported', '0');

		while (!feof($fp)) {

It seems like $fp can also be of type false; however, parameter $handle of feof() does only seem to accept resource, maybe add an additional type check?

			$file_data .= fread($fp, 65536);

It seems like $fp can also be of type false; however, parameter $handle of fread() does only seem to accept resource, maybe add an additional type check?

			// There is no strrpos() function that searches for substrings :-(
			for ($pos = strlen($file_data) - 1; $pos > 0; --$pos) {
				if ($file_data[$pos] === '0' && ($file_data[$pos - 1] === "\n" || $file_data[$pos - 1] === "\r")) {
					// We’ve found the last record boundary in this chunk of data
					break;
				}
			}
			if ($pos) {
				Database::prepare(
					"INSERT INTO `##gedcom_chunk` (gedcom_id, chunk_data) VALUES (?, ?)"
				)->execute([$this->tree_id, substr($file_data, 0, $pos)]);
				$file_data = substr($file_data, $pos);
			}
		}
		Database::prepare(
			"INSERT INTO `##gedcom_chunk` (gedcom_id, chunk_data) VALUES (?, ?)"
		)->execute([$this->tree_id, $file_data]);

		Database::commit();
		fclose($fp);

It seems like $fp can also be of type false; however, parameter $handle of fclose() does only seem to accept resource, maybe add an additional type check?

	}

	/**
	 * Generate a new XREF, unique across all family trees
	 *
	 * @return string
	 */
	public function getNewXref() {
		$prefix = 'X';

		$increment = 1.0;
		do {
			// Use LAST_INSERT_ID(expr) to provide a transaction-safe sequence. See
			// http://dev.mysql.com/doc/refman/5.6/en/information-functions.html#function_last-insert-id
			$statement = Database::prepare(
				"UPDATE `##site_setting` SET setting_value = LAST_INSERT_ID(setting_value + :increment) WHERE setting_name = 'next_xref'"
			);
			$statement->execute([
				'increment'   => (int) $increment,
			]);

			if ($statement->rowCount() === 0) {
				// First time we've used this record type.
				Site::setPreference('next_xref', '1');
				$num = 1;
			} else {
				$num = Database::prepare("SELECT LAST_INSERT_ID()")->fetchOne();
			}

			$xref = $prefix . $num;

			// Records may already exist with this sequence number.
			$already_used = Database::prepare(
				"SELECT" .
				" EXISTS (SELECT 1 FROM `##individuals` WHERE i_id = :i_id) OR" .
				" EXISTS (SELECT 1 FROM `##families` WHERE f_id = :f_id) OR" .
				" EXISTS (SELECT 1 FROM `##sources` WHERE s_id = :s_id) OR" .
				" EXISTS (SELECT 1 FROM `##media` WHERE m_id = :m_id) OR" .
				" EXISTS (SELECT 1 FROM `##other` WHERE o_id = :o_id) OR" .
				" EXISTS (SELECT 1 FROM `##change` WHERE xref = :xref)"
			)->execute([
				'i_id' => $xref,
				'f_id' => $xref,
				's_id' => $xref,
				'm_id' => $xref,
				'o_id' => $xref,
				'xref' => $xref,
			])->fetchOne();

			// This exponential increment allows us to scan over large blocks of
			// existing data in a reasonable time.
			$increment *= 1.01;
		} while ($already_used !== '0');

		return $xref;
	}

	/**
	 * Create a new record from GEDCOM data.
	 *
	 * @param string $gedcom
	 *
	 * @throws \Exception
	 *
	 * @return GedcomRecord|Individual|Family|Note|Source|Repository|Media
	 */
	public function createRecord($gedcom) {
		if (preg_match('/^0 @(' . WT_REGEX_XREF . ')@ (' . WT_REGEX_TAG . ')/', $gedcom, $match)) {
			$xref = $match[1];
			$type = $match[2];
		} else {
			throw new \Exception('Invalid argument to GedcomRecord::createRecord(' . $gedcom . ')');
		}
		if (strpos("\r", $gedcom) !== false) {
			// MSDOS line endings will break things in horrible ways
			throw new \Exception('Evil line endings found in GedcomRecord::createRecord(' . $gedcom . ')');
		}

		// webtrees creates XREFs containing digits. Anything else (e.g. “new”) is just a placeholder.
		if (!preg_match('/\d/', $xref)) {
			$xref   = $this->getNewXref();
			$gedcom = preg_replace('/^0 @(' . WT_REGEX_XREF . ')@/', '0 @' . $xref . '@', $gedcom);
		}

		// Create a change record, if not already present
		if (!preg_match('/\n1 CHAN/', $gedcom)) {
			$gedcom .= "\n1 CHAN\n2 DATE " . date('d M Y') . "\n3 TIME " . date('H:i:s') . "\n2 _WT_USER " . Auth::user()->getUserName();

Are you sure date('H:i:s') of type false|string can be used in concatenation?

Are you sure date('d M Y') of type false|string can be used in concatenation?

		}

		// Create a pending change
		Database::prepare(
			"INSERT INTO `##change` (gedcom_id, xref, old_gedcom, new_gedcom, user_id) VALUES (?, ?, '', ?, ?)"
		)->execute([
			$this->tree_id,
			$xref,
			$gedcom,
			Auth::id(),
		]);

		Log::addEditLog('Create: ' . $type . ' ' . $xref);

		// Accept this pending change
		if (Auth::user()->getPreference('auto_accept')) {
			FunctionsImport::acceptAllChanges($xref, $this->tree_id);
		}
		// Return the newly created record. Note that since GedcomRecord
		// has a cache of pending changes, we cannot use it to create a
		// record with a newly created pending change.
		return GedcomRecord::getInstance($xref, $this, $gedcom);
	}
}