Update to 3.1.5 (#42)

* 3.1.1 Release: Merge Hotfix branch into Master (BioKIC#1747)

* Occurrence Mapping: Adjust SQL to relax enforcement of link to taxon thesaurus, thus to include records with coordinates but lacking thesaurus relationship 
* Styling: Various styling, spacing, and display adjustments 
* Occurrence search: add type attribute to buttons to avoid defaulting as submit buttons 
* Occurrence Profile: Fix error triggered when otherCatalogNumbers are used to create backlink to original snapshot record within external institution web resource
* Occurrence editing functions  
-- Fix fatal error triggered by cloning an occurrence record with the create association option selected
-- Fix fatal error triggered when quick association feature is activated within occurrence editor
-- Fix fatal error when deleting an occurrence when the occurrence was previously deleted (e.g. record already in omoccurarchive)
-- Adjust occurrence restore option to dynamically determine associationType when restoring a record that was deleted prior to this field being added as a required input
-- If resource association does not have an objectID, use url as the display text
* Taxonomy editor: bug fix triggered by adding a child directly to the root node of the thesaurus (e.g. kingdom)
* Scientific name parsing utility functions: Integrate cleanInfra function directly into code. It served no purpose being separate, and was also causing a bug where parent authors were being incorrectly merged with insfraspecific authors

---------

Co-authored-by: Katie Pearson <[email protected]>
Co-authored-by: Mark <[email protected]>
Co-authored-by: MuchQuak <[email protected]>
Co-authored-by: Logan Wilt <[email protected]>

* 3.1.2 Release: Merge Hotfix branch into Master (BioKIC#1770)

* Hotfix v.3.1.3  (BioKIC#1821)

* Hotfix v3.1.3 
- Adjusted hotfix merge instructions
- Inventory Management: Bug fix interfering with adding new editors to an inventory project
- Image migration modifications
-- Add option to copy over existing target files
-- Add checks and error handling for non-existent source files and already existing target files
-- Direct log files to be written to /content/logs/
- fix misspelled log directory name, with support still maintained for portals that already have the misspelled directory
- Fix jquery selector to be correct so button is enabled when trait is changed
- Misc language file and wording adjustments

* Hotfix 3.1.4  (BioKIC#1858)

- Checklist voucher link bug 
-- Resolves issue where checklist link PK is not passed to link function. 
-- Resolves issue: BioKIC#1828
- Specimen upload bug
-- Add IGNORE to avoid complete failure of insert statement
-- Capture and display warnings to user
-- Fix display of final record process count
- Occurrence Search breadcrumb bug fix 
-- Add comingFrom variable to pagination links within the list and tablelist pages
-- If comingFrom variable is not set, or set to anything other than "newsearch" or "harvestparams", set the variable to what is defined as the default within the symbini file. If default action is not defined within symbini, default to new search form.
-- Add comingFrom variable to harvestparams.php form
-- Resolves issue: BioKIC#1840
- Occurrence Association Form Validation bug
-- Fix issue with internal association form validation failing and allowing for creation of an association without an internal occurrence being defined
-- Add form validation for external resource and general observation
-- Addresses issue: BioKIC#1852
-- Add guid omoassociations RecordID on insert within occurrence editor
- Vendor library updates via composer 
-- update phpoffice/phpspreadsheet to v3.3.0
-- updated phpseclib/phpseclib explicitly to v3.0.42
-- update phpoffice/phpword to v1.3.0
- Fix data binding bug associated with searching occurrence via GUID within Occurrence Profile pages 
- Misc language translation issues

* Hotfix 3.1.5 (BioKIC#1956)

* Add login form button to prevent circular links
* Bump symfony/process from 5.4.19 to 5.4.46 in /api
* Bump symfony/http-foundation from 5.4.20 to 5.4.46 in /api
* Remove non-template contacts and aboutproject files (BioKIC#1864)
* Add condition for elevation type number in searchform.js, fixed typo for maximum elevation
* Fix typos
* Unify top/northern, bottom/southern usage
* Fix image alignment and button names in flashcards (BioKIC#1881)
* Fix image alignment and button names
* Add stylesheet, removed in-line styling, added flex classes for games in main.css
* Fix over-translated lang tags (BioKIC#1911)
* closes BioKIC#1916 by removing union return type
* Fix parsing issue
* Fix (BioKIC#1920)
* Resolve editor lock bug
* Resolves issue: BioKIC#1923
* Collection Profile issue
* Add form value interpolation for EW NS and units values so sessions is loaded correctly
* Update API Vendor Libraries
* Closes BioKIC#1942 Adjust Language Tags of Cross Portal Results
* Improve Sign-in and Contact Us button layout on <768px wide devices.

---------
Co-authored-by: Edward Gilbert <[email protected]>
Co-authored-by: Katie Pearson <[email protected]>
Co-authored-by: Nikita Salikov <[email protected]>
Co-authored-by: MuchQuak <[email protected]>

---------

Co-authored-by: Edward Gilbert <[email protected]>
Co-authored-by: Mark <[email protected]>
Co-authored-by: MuchQuak <[email protected]>
Co-authored-by: Logan Wilt <[email protected]>
Co-authored-by: Greg Post <[email protected]>
Co-authored-by: Greg Post <[email protected]>

api/vendor/autoload.php

@@ -2,6 +2,24 @@
 
 // autoload.php @generated by Composer
 
+if (PHP_VERSION_ID < 50600) {
+    if (!headers_sent()) {
+        header('HTTP/1.1 500 Internal Server Error');
+    }
+    $err = 'Composer 2.3.0 dropped support for autoloading on PHP <5.6 and you are running '.PHP_VERSION.', please upgrade PHP or use Composer 2.2 LTS via "composer self-update --2.2". Aborting.'.PHP_EOL;
+    if (!ini_get('display_errors')) {
+        if (PHP_SAPI === 'cli' || PHP_SAPI === 'phpdbg') {
+            fwrite(STDERR, $err);
+        } elseif (!headers_sent()) {
+            echo $err;
+        }
+    }
+    trigger_error(
+        $err,
+        E_USER_ERROR
+    );
+}
+
 require_once __DIR__ . '/composer/autoload_real.php';
 
 return ComposerAutoloaderInite18bd6b57182fc88f4b9d0452696caaa::getLoader();

api/vendor/bin/carbon

@@ -4,21 +4,116 @@
 /**
  * Proxy PHP file generated by Composer
  *
- * This file includes the referenced bin path (../nesbot/carbon/bin/carbon) using eval to remove the shebang if present
+ * This file includes the referenced bin path (../nesbot/carbon/bin/carbon)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
  *
  * @generated
  */
 
-$binPath = realpath(__DIR__ . "/" . '../nesbot/carbon/bin/carbon');
-$contents = file_get_contents($binPath);
-$contents = preg_replace('{^#!/.+\r?\n<\?(php)?}', '', $contents, 1, $replaced);
-if ($replaced) {
-    $contents = strtr($contents, array(
-        '__FILE__' => var_export($binPath, true),
-        '__DIR__' => var_export(dirname($binPath), true),
-    ));
-
-    eval($contents);
-    exit(0);
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/nesbot/carbon/bin/carbon');
+    }
 }
-include $binPath;
+
+return include __DIR__ . '/..'.'/nesbot/carbon/bin/carbon';

api/vendor/bin/carbon.bat

@@ -1,4 +1,5 @@
 @ECHO OFF
 setlocal DISABLEDELAYEDEXPANSION
-SET BIN_TARGET=%~dp0/../nesbot/carbon/bin/carbon
+SET BIN_TARGET=%~dp0/carbon
+SET COMPOSER_RUNTIME_BIN_DIR=%~dp0
 php "%BIN_TARGET%" %*

api/vendor/bin/patch-type-declarations

@@ -4,21 +4,116 @@
 /**
  * Proxy PHP file generated by Composer
  *
- * This file includes the referenced bin path (../symfony/error-handler/Resources/bin/patch-type-declarations) using eval to remove the shebang if present
+ * This file includes the referenced bin path (../symfony/error-handler/Resources/bin/patch-type-declarations)
+ * using a stream wrapper to prevent the shebang from being output on PHP<8
  *
  * @generated
  */
 
-$binPath = realpath(__DIR__ . "/" . '../symfony/error-handler/Resources/bin/patch-type-declarations');
-$contents = file_get_contents($binPath);
-$contents = preg_replace('{^#!/.+\r?\n<\?(php)?}', '', $contents, 1, $replaced);
-if ($replaced) {
-    $contents = strtr($contents, array(
-        '__FILE__' => var_export($binPath, true),
-        '__DIR__' => var_export(dirname($binPath), true),
-    ));
-
-    eval($contents);
-    exit(0);
+namespace Composer;
+
+$GLOBALS['_composer_bin_dir'] = __DIR__;
+$GLOBALS['_composer_autoload_path'] = __DIR__ . '/..'.'/autoload.php';
+
+if (PHP_VERSION_ID < 80000) {
+    if (!class_exists('Composer\BinProxyWrapper')) {
+        /**
+         * @internal
+         */
+        final class BinProxyWrapper
+        {
+            private $handle;
+            private $position;
+            private $realpath;
+
+            public function stream_open($path, $mode, $options, &$opened_path)
+            {
+                // get rid of phpvfscomposer:// prefix for __FILE__ & __DIR__ resolution
+                $opened_path = substr($path, 17);
+                $this->realpath = realpath($opened_path) ?: $opened_path;
+                $opened_path = $this->realpath;
+                $this->handle = fopen($this->realpath, $mode);
+                $this->position = 0;
+
+                return (bool) $this->handle;
+            }
+
+            public function stream_read($count)
+            {
+                $data = fread($this->handle, $count);
+
+                if ($this->position === 0) {
+                    $data = preg_replace('{^#!.*\r?\n}', '', $data);
+                }
+
+                $this->position += strlen($data);
+
+                return $data;
+            }
+
+            public function stream_cast($castAs)
+            {
+                return $this->handle;
+            }
+
+            public function stream_close()
+            {
+                fclose($this->handle);
+            }
+
+            public function stream_lock($operation)
+            {
+                return $operation ? flock($this->handle, $operation) : true;
+            }
+
+            public function stream_seek($offset, $whence)
+            {
+                if (0 === fseek($this->handle, $offset, $whence)) {
+                    $this->position = ftell($this->handle);
+                    return true;
+                }
+
+                return false;
+            }
+
+            public function stream_tell()
+            {
+                return $this->position;
+            }
+
+            public function stream_eof()
+            {
+                return feof($this->handle);
+            }
+
+            public function stream_stat()
+            {
+                return array();
+            }
+
+            public function stream_set_option($option, $arg1, $arg2)
+            {
+                return true;
+            }
+
+            public function url_stat($path, $flags)
+            {
+                $path = substr($path, 17);
+                if (file_exists($path)) {
+                    return stat($path);
+                }
+
+                return false;
+            }
+        }
+    }
+
+    if (
+        (function_exists('stream_get_wrappers') && in_array('phpvfscomposer', stream_get_wrappers(), true))
+        || (function_exists('stream_wrapper_register') && stream_wrapper_register('phpvfscomposer', 'Composer\BinProxyWrapper'))
+    ) {
+        return include("phpvfscomposer://" . __DIR__ . '/..'.'/symfony/error-handler/Resources/bin/patch-type-declarations');
+    }
 }
-include $binPath;
+
+return include __DIR__ . '/..'.'/symfony/error-handler/Resources/bin/patch-type-declarations';

api/vendor/bin/patch-type-declarations.bat

@@ -1,4 +1,5 @@
 @ECHO OFF
 setlocal DISABLEDELAYEDEXPANSION
-SET BIN_TARGET=%~dp0/../symfony/error-handler/Resources/bin/patch-type-declarations
+SET BIN_TARGET=%~dp0/patch-type-declarations
+SET COMPOSER_RUNTIME_BIN_DIR=%~dp0
 php "%BIN_TARGET%" %*