From 223b134baa23980d2b2268000c39a4d531dcb04e Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 19:52:58 +0000
Subject: [PATCH 01/65] instrument API PUT endpoint to exception based validate

---
 .../candidate/visit/instrument/instrument.class.inc    | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index 4ddbac10fab..a656c29d7c3 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -183,12 +183,16 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             );
         }
 
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+        // validate given data against the instrument
+        try {
+            $this->_instrument->validate($data);
+        } catch (\LorisException $th) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                $th->getMessage()
             );
         }
 
+        // update values
         try {
             $this->_instrument->clearInstrument();
             $version = $request->getAttribute('LORIS-API-Version');

From f5e0a1ca2d1b5a64c1a094232de6ec5ab0edc4b2 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 19:57:03 +0000
Subject: [PATCH 02/65] internal array_all for php < 8.4

---
 htdocs/index.php | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/htdocs/index.php b/htdocs/index.php
index 7c2b3cfc2e7..d122cb19e90 100644
--- a/htdocs/index.php
+++ b/htdocs/index.php
@@ -29,6 +29,20 @@
 // See: https://www.php.net/manual/en/session.configuration.php#ini.session.use-strict-mode
 ini_set('session.use_strict_mode', '1');
 
+// TODO: Remove this code once PHP 8.4 becomes the minimal PHP version in LORIS.
+if (version_compare(PHP_VERSION, '8.4', '<')) {
+    // @phan-file-suppress PhanRedefineFunctionInternal
+
+    // phpcs:ignore
+    function array_all(array $array, callable $callable): bool {
+        foreach ($array as $key => $value) {
+            if (! $callable($value, $key))
+                return false;
+        }
+        return true;
+    }
+}
+
 // FIXME: The code in NDB_Client should mostly be replaced by middleware.
 $client = new \NDB_Client;
 $client->initialize();

From 40c24a50d5e055c62c85e9eb4f12cbea37157b63 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 20:20:07 +0000
Subject: [PATCH 03/65] default instrument metadata element names

---
 php/libraries/NDB_BVL_Instrument.class.inc | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 63ff722c2f6..374c327fe91 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -198,6 +198,20 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      */
     protected $selectMultipleElements = [];
 
+    /**
+     * Array containing all metadata elements in an instrument.
+     *
+     * @var array
+     *
+     * @access protected
+     */
+    protected array $metadataElements = [
+        "Date_taken",
+        "Examiner",
+        "Window_Difference",
+        "Candidate_Age",
+    ];
+
     /**
      * Factory generates a new instrument instance of type
      * $instrument, and runs the setup() method on that new

From 1cd9002abd50c3d01f79bc3dcdce445f94f4355d Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 20:21:07 +0000
Subject: [PATCH 04/65] instrument - validation method update

---
 php/libraries/NDB_BVL_Instrument.class.inc | 193 ++++++++++++++++++++-
 1 file changed, 189 insertions(+), 4 deletions(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 374c327fe91..2b8daa35dc7 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -2972,15 +2972,200 @@ abstract class NDB_BVL_Instrument extends NDB_Page
     }
 
     /**
-     * Validate whether the values submitted are valid
+     * Validate the given array keys against the instrument default structure.
+     * Throw a LorisException if any check does not pass.
+     *
+     * @param array $instrumentData instrument data to check
+     *
+     * @throws \LorisException
+     *
+     * @return void
+     */
+    private function _validateKeys(
+        array $instrumentData
+    ): void {
+        // get keys from new data
+        $dataKeys = array_keys($instrumentData);
+
+        // load default instrument data keys
+        $defaultDictionary = $this->defaultInstanceData();
+        $defaultDataKeys   = array_keys($defaultDictionary);
+
+        // filter out metadata fields, keep only instrument data fields
+        $defaultDataKeys = array_values(
+            array_filter(
+                $defaultDataKeys,
+                fn($k) => !in_array(
+                    $k,
+                    $this->metadataElements,
+                    true
+                )
+            )
+        );
+
+        // missing keys
+        $missingKeys = array_diff($defaultDataKeys, $dataKeys);
+        if (!empty($missingKeys)) {
+            $i = implode(",", $missingKeys);
+            throw new \LorisException("Missing keys: {$i}.");
+        }
+
+        // additional keys: only warn
+        $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
+        if (!empty($additionalKeys)) {
+            $i = implode(",", $additionalKeys);
+            error_log("[instrument:validation] Additional keys will be ignored: {$i}.");
+        }
+    }
+
+    /**
+     * Validate the given array values against the instrument dictionary items.
+     * Throw a LorisException if any check does not pass.
+     *
+     * @param array $instrumentData instrument data to check
+     *
+     * @throws \LorisException
+     *
+     * @return void
+     */
+    private function _validateValues(
+        array $instrumentData
+    ): void {
+        // get datetime fn, and format from db
+        $getDateTime = fn($s, $f) => DateTime::createFromFormat($f, $s);
+        $config      = $this->loris->getConfiguration();
+        $dateFormat  = $config->getSetting('dateDisplayFormat');
+
+        // define all check fn - primitive
+        $isString   = fn($f) => is_string($f) && "{$f}" === $f;
+        $isBoolean  = fn($f) => is_bool($f) && (bool)$f === $f;
+        $isInteger  = fn($f) => is_integer($f) && (int)$f === $f;
+        $isFloat    = fn($f) => is_float($f) && (float)$f === $f;
+
+        // define all check fn - duration fn
+        $isDuration = fn($f) => $isInteger($f) && $f >= 0;
+
+        // define all check fn - date/time fn
+        $isDate = fn($f, $fmt) => ($getDateTime($f, $fmt) !== false)
+            && ($getDateTime($f, $fmt)->format($fmt) === $f);
+        $isTime = fn($f, $fmt) => ($getDateTime("2025-10-10 {$f}", $fmt) !== false)
+            && ($getDateTime("2025-10-10 {$f}", $fmt)->format("H:i:s") === $f);
+
+        // check types
+        foreach ($this->getDataDictionary() as $dictionaryItem) {
+            // current fieldname
+            $fieldName = $dictionaryItem->fieldname;
+
+            // skip filtered out fields
+            if (in_array($fieldName, $this->metadataElements, true)) {
+                continue;
+            }
+
+            // get the expected type for that field
+            $expectedType = $dictionaryItem->getDataType();
+
+            // get the field data value
+            $fieldToCheck = $instrumentData[$fieldName];
+
+            // if an enumeration, get the possible option keys
+            $optionKeys = match ("{$expectedType}") {
+                "enumeration" => $expectedType->getOptions(),
+                default       => null
+            };
+
+            // is it a single/multi-enumeration
+            $isMultiEnum = in_array(
+                $fieldName,
+                $this->selectMultipleElements,
+                true
+            );
+
+            // run the validation method depending on the field type
+            $isValid = match ("{$expectedType}") {
+                "string", "URI" => $isString($fieldToCheck),
+                "boolean"       => $isBoolean($fieldToCheck),
+                "integer"       => $isInteger($fieldToCheck),
+                "decimal"       => $isFloat($fieldToCheck),
+                "date"          => $isDate($fieldToCheck, $dateFormat),
+                "time"          => $isTime($fieldToCheck, $dateFormat),
+                "duration"      => $isDuration($fieldToCheck),
+                "enumeration"   => $isString($fieldToCheck) && (
+                    $isMultiEnum
+                    // select: the given value must be in the list of options
+                    ? in_array(
+                        $fieldToCheck,
+                        $optionKeys,
+                        true
+                    )
+                    // multi-select: ALL given values must be in the list of options
+                    : array_all(
+                        explode("{@}", $fieldToCheck),
+                        fn($v) => in_array(
+                            $v,
+                            $optionKeys,
+                            true
+                        )
+                    )
+                ),
+                default => throw new \LorisException(
+                    "Unknown type '{$expectedType}' for field: {$fieldToCheck}"
+                )
+            };
+
+            // if not valid, format exception message
+            if (!$isValid) {
+                // expected format
+                $expectedFormat = match ("{$expectedType}") {
+                    "date"  => " (format: 'YYYY-MM-DD')",
+                    "time"  => " (format: 'HH:mm:ss')",
+                    "enumeration" => ", possible answers: '"
+                        . implode("','", $optionKeys)
+                        . "'",
+                    default => "",
+                };
+
+                // multi-enumeration?
+                $multi = "";
+                if ($isMultiEnum) {
+                    $multi = "multi-";
+                    // add delimiter info
+                    $expectedFormat .= " with delimiter '{@}'";
+                }
+
+                // message
+                $msg  = "Field not valid: {$fieldName}. ";
+                $msg .= "Expected: {$multi}{$expectedType}";
+                $msg .= "{$expectedFormat}";
+
+                //
+                throw new \LorisException($msg);
+            }
+        }
+    }
+
+    /**
+     * Validate whether the data submitted are valid against this instrument.
+     * Checks both keys and values. Throws a LorisException if any test fails.
      *
      * @param array $values an array of values submitted
      *
-     * @return boolean true if values are valid
+     * @throws \LorisException
+     *
+     * @return void
      */
-    function validate(array $values): bool
+    public function validate(array $values): void
     {
-        return $this->determineDataEntryAllowed();
+        // data to check even exist
+        $dataToCheck = $values[$this->testName] ?? null;
+        if ($dataToCheck === null) {
+            throw new \LorisException("No instrument key provided.");
+        }
+
+        // validate the keys against the instrument dictionary entries
+        $this->_validateKeys($dataToCheck);
+
+        // validate the values against the instrument dictionary entries
+        $this->_validateValues($dataToCheck);
     }
 
     /**

From 40563a7403160d2147b6a66a69ff4bca6e992a24 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 20:26:48 +0000
Subject: [PATCH 05/65] instrument flag endpoint update

---
 .../candidate/visit/instrument/flags.class.inc   | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
index 63ae828be63..ee90d9ed737 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
@@ -169,9 +169,11 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
                 'Invalid request'
             );
         }
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+        try {
+            $this->_instrument->validate($data);
+        } catch (\LorisException $th) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                "Could not update. {$th->getMessage()}"
             );
         }
 
@@ -242,9 +244,11 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
             );
         }
 
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+        try {
+            $this->_instrument->validate($data);
+        } catch (\LorisException $th) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                "Could not update. {$th->getMessage()}"
             );
         }
 

From d7f3dbd8fbab3fe7d3b3681600aae16e5c544443 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 20:27:14 +0000
Subject: [PATCH 06/65] instrument endpoint update

---
 .../candidate/visit/instrument/instrument.class.inc   | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index a656c29d7c3..f6d7459b10e 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -188,7 +188,7 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             $this->_instrument->validate($data);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
-                $th->getMessage()
+                "Could not update. {$th->getMessage()}"
             );
         }
 
@@ -234,9 +234,12 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             );
         }
 
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+        // validate given data against the instrument
+        try {
+            $this->_instrument->validate($data);
+        } catch (\LorisException $th) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                "Could not update. {$th->getMessage()}"
             );
         }
 

From 61b88f5d4bfd43f19d0cb279feb86c84e03bbcbf Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 21:04:53 +0000
Subject: [PATCH 07/65] instrument api fallback exceptions cases

---
 .../candidate/visit/instrument/flags.class.inc         | 10 ++++++++++
 .../candidate/visit/instrument/instrument.class.inc    | 10 ++++++++++
 2 files changed, 20 insertions(+)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
index ee90d9ed737..636996a439a 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
@@ -175,6 +175,11 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
             );
+        } catch (\Throwable $th) {
+            error_log($th->getMessage());
+            return new \LORIS\Http\Response\JSON\Forbidden(
+                "Could not update."
+            );
         }
 
         try {
@@ -250,6 +255,11 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
             );
+        } catch (\Throwable $th) {
+            error_log($th->getMessage());
+            return new \LORIS\Http\Response\JSON\Forbidden(
+                "Could not update."
+            );
         }
 
         try {
diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index f6d7459b10e..81349170e2d 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -190,6 +190,11 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
             );
+        } catch (\Throwable $th) {
+            error_log($th->getMessage());
+            return new \LORIS\Http\Response\JSON\Forbidden(
+                "Could not update."
+            );
         }
 
         // update values
@@ -241,6 +246,11 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
             );
+        } catch (\Throwable $th) {
+            error_log($th->getMessage());
+            return new \LORIS\Http\Response\JSON\Forbidden(
+                "Could not update."
+            );
         }
 
         try {

From 31a9a4129c5036406adb95a035aca05296b2a283 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 4 Jun 2025 21:08:40 +0000
Subject: [PATCH 08/65] lint

---
 htdocs/index.php                           |  2 +-
 php/libraries/NDB_BVL_Instrument.class.inc | 12 +++++++-----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/htdocs/index.php b/htdocs/index.php
index d122cb19e90..828ac9ff6cb 100644
--- a/htdocs/index.php
+++ b/htdocs/index.php
@@ -36,7 +36,7 @@
     // phpcs:ignore
     function array_all(array $array, callable $callable): bool {
         foreach ($array as $key => $value) {
-            if (! $callable($value, $key))
+            if (!$callable($value, $key))
                 return false;
         }
         return true;
diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 2b8daa35dc7..391d2a9eaff 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3014,7 +3014,9 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
         if (!empty($additionalKeys)) {
             $i = implode(",", $additionalKeys);
-            error_log("[instrument:validation] Additional keys will be ignored: {$i}.");
+            error_log(
+                "[instrument:validation] Additional keys will be ignored: {$i}."
+            );
         }
     }
 
@@ -3037,10 +3039,10 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         $dateFormat  = $config->getSetting('dateDisplayFormat');
 
         // define all check fn - primitive
-        $isString   = fn($f) => is_string($f) && "{$f}" === $f;
-        $isBoolean  = fn($f) => is_bool($f) && (bool)$f === $f;
-        $isInteger  = fn($f) => is_integer($f) && (int)$f === $f;
-        $isFloat    = fn($f) => is_float($f) && (float)$f === $f;
+        $isString  = fn($f) => is_string($f) && "{$f}" === $f;
+        $isBoolean = fn($f) => is_bool($f) && (bool)$f === $f;
+        $isInteger = fn($f) => is_integer($f) && (int)$f === $f;
+        $isFloat   = fn($f) => is_float($f) && (float)$f === $f;
 
         // define all check fn - duration fn
         $isDuration = fn($f) => $isInteger($f) && $f >= 0;

From 51bf9776cb7ef5cff1866a836283b13ce5af448d Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 11:43:49 -0400
Subject: [PATCH 09/65] instrument validate only data

---
 php/libraries/NDB_BVL_Instrument.class.inc | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 391d2a9eaff..c0dbacd4a09 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3155,12 +3155,11 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      *
      * @return void
      */
-    public function validate(array $values): void
+    public function validate(array $dataToCheck): void
     {
         // data to check even exist
-        $dataToCheck = $values[$this->testName] ?? null;
-        if ($dataToCheck === null) {
-            throw new \LorisException("No instrument key provided.");
+        if (empty($dataToCheck)) {
+            throw new \LorisException("No data provided.");
         }
 
         // validate the keys against the instrument dictionary entries

From 8017dea3aa2f5b7d4942c3e5f0f0514bb9c1ece2 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 11:44:28 -0400
Subject: [PATCH 10/65] instrument and flags endpoint to validate data

---
 .../endpoints/candidate/visit/instrument/flags.class.inc    | 6 ++++--
 .../candidate/visit/instrument/instrument.class.inc         | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
index 636996a439a..633f2732cbd 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
@@ -170,7 +170,8 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
             );
         }
         try {
-            $this->_instrument->validate($data);
+            $instrumentName = $this->_instrument->testName;
+            $this->_instrument->validate($data[$instrumentName] ?? []);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
@@ -250,7 +251,8 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
         }
 
         try {
-            $this->_instrument->validate($data);
+            $instrumentName = $this->_instrument->testName;
+            $this->_instrument->validate($data[$instrumentName] ?? []);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index 81349170e2d..d8fd87929a3 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -185,7 +185,8 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
 
         // validate given data against the instrument
         try {
-            $this->_instrument->validate($data);
+            $instrumentName = $this->_instrument->testName;
+            $this->_instrument->validate($data[$instrumentName] ?? []);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
@@ -241,7 +242,8 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
 
         // validate given data against the instrument
         try {
-            $this->_instrument->validate($data);
+            $instrumentName = $this->_instrument->testName;
+            $this->_instrument->validate($data[$instrumentName] ?? []);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"

From c919618d295bd7cba6aeef77fbee1720bbf2523f Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 13:54:13 -0400
Subject: [PATCH 11/65] test- flag checks - rm instrument validation

---
 .../visit/instrument/flags.class.inc          | 27 +++----------------
 1 file changed, 4 insertions(+), 23 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
index 633f2732cbd..2152fd145b9 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
@@ -163,28 +163,18 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
         }
 
         $data = json_decode((string) $request->getBody(), true);
-
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
             );
         }
-        try {
-            $instrumentName = $this->_instrument->testName;
-            $this->_instrument->validate($data[$instrumentName] ?? []);
-        } catch (\LorisException $th) {
+        if (!array_key_exists('Flags', $data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
-                "Could not update. {$th->getMessage()}"
-            );
-        } catch (\Throwable $th) {
-            error_log($th->getMessage());
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                "Could not update."
+                "Invalid request. 'Flags' missing."
             );
         }
 
         try {
-
             $requiredfields = [
                 'Data_entry',
                 'Administration',
@@ -249,18 +239,9 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
                 'Invalid request'
             );
         }
-
-        try {
-            $instrumentName = $this->_instrument->testName;
-            $this->_instrument->validate($data[$instrumentName] ?? []);
-        } catch (\LorisException $th) {
+        if (!array_key_exists('Flags', $data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
-                "Could not update. {$th->getMessage()}"
-            );
-        } catch (\Throwable $th) {
-            error_log($th->getMessage());
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                "Could not update."
+                "Invalid request. 'Flags' missing."
             );
         }
 

From 2e23e989b407f7d47da2c821c302940f3babf380 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 13:55:17 -0400
Subject: [PATCH 12/65] instrument validation from API instrument - instrument
 name

---
 .../visit/instrument/instrument.class.inc     | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index d8fd87929a3..f765fd280a1 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -241,9 +241,16 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
         }
 
         // validate given data against the instrument
+        $instrumentName = $this->_instrument->testName;
         try {
-            $instrumentName = $this->_instrument->testName;
-            $this->_instrument->validate($data[$instrumentName] ?? []);
+            // extract data according to LORIS API version
+            $version = $request->getAttribute('LORIS-API-Version');
+            $instrumentData = $version == 'v0.0.3'
+                ? ($data[$instrumentName] ?? [])
+                : ($data['Data'] ?? []);
+
+            // validate
+            $this->_instrument->validate($instrumentData);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
@@ -256,13 +263,7 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
         }
 
         try {
-            $version = $request->getAttribute('LORIS-API-Version');
-            if ($version == 'v0.0.3') {
-                $instrumentname = $this->_instrument->testName;
-                $this->_instrument->_saveValues($data[$instrumentname]);
-            } else {
-                $this->_instrument->_saveValues($data['Data']);
-            }
+            $this->_instrument->_saveValues($instrumentData);
             $this->_instrument->score();
             $this->_instrument->updateRequiredElementsCompletedFlag();
         } catch (\Throwable $e) {

From 76bbb059f377911e8c403d784dbc9f1591a774ac Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 13:56:03 -0400
Subject: [PATCH 13/65] instrument validate - additional fields and exception
 message

---
 php/libraries/NDB_BVL_Instrument.class.inc | 28 +++++++++++++++-------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index c0dbacd4a09..b91b72cc08f 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -2973,6 +2973,8 @@ abstract class NDB_BVL_Instrument extends NDB_Page
 
     /**
      * Validate the given array keys against the instrument default structure.
+     * Strictly checks against "required" fields.
+     * Additional fields are not allowed.
      * Throw a LorisException if any check does not pass.
      *
      * @param array $instrumentData instrument data to check
@@ -3003,20 +3005,30 @@ abstract class NDB_BVL_Instrument extends NDB_Page
             )
         );
 
-        // missing keys
-        $missingKeys = array_diff($defaultDataKeys, $dataKeys);
+        // also select all required elements only
+        $defaultRequiredElements = array_values(
+            array_filter(
+                $defaultDataKeys,
+                fn($k) => in_array(
+                    $k,
+                    $this->_requiredElements,
+                    true
+                )
+            )
+        );
+
+        // missing required fields
+        $missingKeys = array_diff($defaultRequiredElements, $dataKeys);
         if (!empty($missingKeys)) {
             $i = implode(",", $missingKeys);
-            throw new \LorisException("Missing keys: {$i}.");
+            throw new \LorisException("Missing required field(s): {$i}.");
         }
 
-        // additional keys: only warn
+        // additional fields: fields outside instrument fields
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
         if (!empty($additionalKeys)) {
-            $i = implode(",", $additionalKeys);
-            error_log(
-                "[instrument:validation] Additional keys will be ignored: {$i}."
-            );
+            $i = implode(",", $missingKeys);
+            throw new \LorisException("Additional field(s) not permitted: {$i}.");
         }
     }
 

From 7f46e8b0b58d3f769a43b07786182acab6a19cc2 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 14:05:03 -0400
Subject: [PATCH 14/65] instrument validate test update

---
 test/unittests/NDB_BVL_Instrument_Test.php | 211 ++++++++++++++++++++-
 1 file changed, 205 insertions(+), 6 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 8af424b0406..52b9a92d638 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1692,24 +1692,223 @@ function testClearInstrument()
 
     /**
      * Test that determineDataEntryAllowed returns true if the Data_entry is anything
-     * but 'Complete' and returns false if Data_entry is 'Complete. Test that
-     * validate simply calls determineDataEntryAllowed and has the same output.
+     * but 'Complete' and returns false if Data_entry is 'Complete.
      *
      * @covers NDB_BVL_Instrument::determineDataEntryAllowed
-     * @covers NDB_BVL_Instrument::validate
+     *
      * @return void
      */
-    function testDetermineDataEntryAllowed()
+    public function testDetermineDataEntryAllowed()
     {
         $this->_setUpMockDB();
         $this->_setTableData();
         $this->_instrument->commentID = 'commentID1';
         $this->_instrument->table     = 'medical_history';
         $this->assertTrue($this->_instrument->determineDataEntryAllowed());
-        $this->assertTrue($this->_instrument->validate(['value1']));
         $this->_instrument->commentID = 'commentID2';
         $this->assertFalse($this->_instrument->determineDataEntryAllowed());
-        $this->assertFalse($this->_instrument->validate(['value1']));
+    }
+
+    /**
+     * Test that check validation method with received data.
+     * Empty array parameter case.
+     *
+     * @covers NDB_BVL_Instrument::validate
+     *
+     * @return void
+     */
+    public function testValidateEmptyParameter(): void
+    {
+        $this->_setUpMockDB();
+        $this->_setTableData();
+        $this->_instrument->table = 'medical_history';
+        $this->_instrument->commentID = 'commentID1';
+        $this->expectException("LorisException");
+        $this->expectExceptionMessage("No data provided.");
+        $this->_instrument->validate([]);
+    }
+
+    /**
+     * Test that check validation method with received data.
+     * Keys validation case - missing keys
+     *
+     * @covers NDB_BVL_Instrument::validate
+     *
+     * @return void
+     */
+    public function testValidateMissingKeys(): void
+    {
+        $this->_setUpMockDB();
+        $this->_setTableData();
+        $this->_instrument->table = 'medical_history';
+        $this->_instrument->commentID = 'commentID1';
+
+        // data - complete keys + empty values
+        $instrumentQuestions = [
+            // p1
+            "arthritis" => null, // required
+            "arthritis_age" => null,
+            "pulmonary_issues" => null,
+            "pulmonary_issues_specific" => null,
+            // p2
+            "hypertension" => null, // required
+            "hypertension_while_pregnant" => null,
+            "hypertension_while_pregnant_age" => null,
+            // p3
+            "concussion_or_head_trauma" => null, // required
+            "concussion_1_description" => null,
+            "concussion_1_hospitalized" => null,
+            "concussion_1_age" => null,
+            "concussion_2_description" => null,
+            "concussion_2_hospitalized" => null,
+            "concussion_2_age" => null,
+            "concussion_3_description" => null,
+            "concussion_3_hospitalized" => null,
+            "concussion_3_age" => null,
+            "current_concussion_symptoms" => null,
+        ];
+
+        // missing keys, removing two required element
+        $missingFields = $instrumentQuestions;
+        unset($missingFields["arthritis"]);
+        unset($missingFields["hypertension"]);
+        $this->expectException("LorisException");
+        $this->expectExceptionMessage("Missing required field(s): arthritis,hypertension.");
+        $this->_instrument->validate($missingFields);
+    }
+
+    /**
+     * Test that check validation method with received data.
+     * Keys validation case - additional keys.
+     *
+     * @covers NDB_BVL_Instrument::validate
+     *
+     * @return void
+     */
+    public function testValidateAdditionalKeys(): void
+    {
+        $this->_setUpMockDB();
+        $this->_setTableData();
+        $this->_instrument->table = 'medical_history';
+        $this->_instrument->commentID = 'commentID1';
+
+        // data - complete keys + empty values
+        $instrumentQuestions = [
+            // p1
+            "arthritis" => null, // required
+            "arthritis_age" => null,
+            "pulmonary_issues" => null,
+            "pulmonary_issues_specific" => null,
+            // p2
+            "hypertension" => null, // required
+            "hypertension_while_pregnant" => null,
+            "hypertension_while_pregnant_age" => null,
+            // p3
+            "concussion_or_head_trauma" => null, // required
+            "concussion_1_description" => null,
+            "concussion_1_hospitalized" => null,
+            "concussion_1_age" => null,
+            "concussion_2_description" => null,
+            "concussion_2_hospitalized" => null,
+            "concussion_2_age" => null,
+            "concussion_3_description" => null,
+            "concussion_3_hospitalized" => null,
+            "concussion_3_age" => null,
+            "current_concussion_symptoms" => null,
+        ];
+
+        // additional keys, adding two new unexpected keys
+        $additionalFields = $instrumentQuestions;
+        $additionalFields["aaa"] = 123;
+        $additionalFields["bbb"] = "a text";
+        $this->expectException("LorisException");
+        $this->expectExceptionMessage("Additional field(s) not permitted: aaa,bbb.");
+        $this->_instrument->validate($additionalFields);
+    }
+
+    /**
+     * Test that check validation method with received data.
+     * Keys validation case - nominal case.
+     *
+     * @covers NDB_BVL_Instrument::validate
+     *
+     * @return void
+     */
+    public function testValidateKeysNominal(): void
+    {
+        $this->_setUpMockDB();
+        $this->_setTableData();
+        $this->_instrument->table = 'medical_history';
+        $this->_instrument->commentID = 'commentID1';
+
+        // data - complete keys + empty values
+        $instrumentQuestions = [
+            // p1
+            "arthritis" => null, // required
+            "arthritis_age" => null,
+            "pulmonary_issues" => null,
+            "pulmonary_issues_specific" => null,
+            // p2
+            "hypertension" => null, // required
+            "hypertension_while_pregnant" => null,
+            "hypertension_while_pregnant_age" => null,
+            // p3
+            "concussion_or_head_trauma" => null, // required
+            "concussion_1_description" => null,
+            "concussion_1_hospitalized" => null,
+            "concussion_1_age" => null,
+            "concussion_2_description" => null,
+            "concussion_2_hospitalized" => null,
+            "concussion_2_age" => null,
+            "concussion_3_description" => null,
+            "concussion_3_hospitalized" => null,
+            "concussion_3_age" => null,
+            "current_concussion_symptoms" => null,
+        ];
+
+        // all required elements are null/yes/no options.
+        $this->_instrument->validate($instrumentQuestions);
+    }
+
+    /**
+     * Test that check validation method with received data.
+     * Values validation case.
+     *
+     * @covers NDB_BVL_Instrument::validate
+     *
+     * @return void
+     */
+    public function testValidateValues(): void
+    {
+        $this->_setUpMockDB();
+        $this->_setTableData();
+        $this->_instrument->table = 'medical_history';
+        $this->_instrument->commentID = 'commentID1';
+
+        // data - complete keys + empty values
+        $instrumentQuestions = [
+            // p1
+            "arthritis" => null, // required
+            "arthritis_age" => null,
+            "pulmonary_issues" => null,
+            "pulmonary_issues_specific" => null,
+            // p2
+            "hypertension" => null, // required
+            "hypertension_while_pregnant" => null,
+            "hypertension_while_pregnant_age" => null,
+            // p3
+            "concussion_or_head_trauma" => null, // required
+            "concussion_1_description" => null,
+            "concussion_1_hospitalized" => null,
+            "concussion_1_age" => null,
+            "concussion_2_description" => null,
+            "concussion_2_hospitalized" => null,
+            "concussion_2_age" => null,
+            "concussion_3_description" => null,
+            "concussion_3_hospitalized" => null,
+            "concussion_3_age" => null,
+            "current_concussion_symptoms" => null,
+        ];
     }
 
     /**

From bb292b2c3d2d3e573e2549bda0688b0ec1eebda4 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 10 Jun 2025 14:17:37 -0400
Subject: [PATCH 15/65] test lint

---
 test/unittests/NDB_BVL_Instrument_Test.php | 152 +++++++++++----------
 1 file changed, 77 insertions(+), 75 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 52b9a92d638..a554ea055cf 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1721,7 +1721,7 @@ public function testValidateEmptyParameter(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table = 'medical_history';
+        $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
         $this->expectException("LorisException");
         $this->expectExceptionMessage("No data provided.");
@@ -1740,32 +1740,32 @@ public function testValidateMissingKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table = 'medical_history';
+        $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
-            "arthritis" => null, // required
-            "arthritis_age" => null,
-            "pulmonary_issues" => null,
-            "pulmonary_issues_specific" => null,
+            "arthritis"                       => null, // required
+            "arthritis_age"                   => null,
+            "pulmonary_issues"                => null,
+            "pulmonary_issues_specific"       => null,
             // p2
-            "hypertension" => null, // required
-            "hypertension_while_pregnant" => null,
+            "hypertension"                    => null, // required
+            "hypertension_while_pregnant"     => null,
             "hypertension_while_pregnant_age" => null,
             // p3
-            "concussion_or_head_trauma" => null, // required
-            "concussion_1_description" => null,
-            "concussion_1_hospitalized" => null,
-            "concussion_1_age" => null,
-            "concussion_2_description" => null,
-            "concussion_2_hospitalized" => null,
-            "concussion_2_age" => null,
-            "concussion_3_description" => null,
-            "concussion_3_hospitalized" => null,
-            "concussion_3_age" => null,
-            "current_concussion_symptoms" => null,
+            "concussion_or_head_trauma"       => null, // required
+            "concussion_1_description"        => null,
+            "concussion_1_hospitalized"       => null,
+            "concussion_1_age"                => null,
+            "concussion_2_description"        => null,
+            "concussion_2_hospitalized"       => null,
+            "concussion_2_age"                => null,
+            "concussion_3_description"        => null,
+            "concussion_3_hospitalized"       => null,
+            "concussion_3_age"                => null,
+            "current_concussion_symptoms"     => null,
         ];
 
         // missing keys, removing two required element
@@ -1773,7 +1773,9 @@ public function testValidateMissingKeys(): void
         unset($missingFields["arthritis"]);
         unset($missingFields["hypertension"]);
         $this->expectException("LorisException");
-        $this->expectExceptionMessage("Missing required field(s): arthritis,hypertension.");
+        $this->expectExceptionMessage(
+            "Missing required field(s): arthritis,hypertension."
+        );
         $this->_instrument->validate($missingFields);
     }
 
@@ -1789,36 +1791,36 @@ public function testValidateAdditionalKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table = 'medical_history';
+        $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
-            "arthritis" => null, // required
-            "arthritis_age" => null,
-            "pulmonary_issues" => null,
-            "pulmonary_issues_specific" => null,
+            "arthritis"                       => null, // required
+            "arthritis_age"                   => null,
+            "pulmonary_issues"                => null,
+            "pulmonary_issues_specific"       => null,
             // p2
-            "hypertension" => null, // required
-            "hypertension_while_pregnant" => null,
+            "hypertension"                    => null, // required
+            "hypertension_while_pregnant"     => null,
             "hypertension_while_pregnant_age" => null,
             // p3
-            "concussion_or_head_trauma" => null, // required
-            "concussion_1_description" => null,
-            "concussion_1_hospitalized" => null,
-            "concussion_1_age" => null,
-            "concussion_2_description" => null,
-            "concussion_2_hospitalized" => null,
-            "concussion_2_age" => null,
-            "concussion_3_description" => null,
-            "concussion_3_hospitalized" => null,
-            "concussion_3_age" => null,
-            "current_concussion_symptoms" => null,
+            "concussion_or_head_trauma"       => null, // required
+            "concussion_1_description"        => null,
+            "concussion_1_hospitalized"       => null,
+            "concussion_1_age"                => null,
+            "concussion_2_description"        => null,
+            "concussion_2_hospitalized"       => null,
+            "concussion_2_age"                => null,
+            "concussion_3_description"        => null,
+            "concussion_3_hospitalized"       => null,
+            "concussion_3_age"                => null,
+            "current_concussion_symptoms"     => null,
         ];
 
         // additional keys, adding two new unexpected keys
-        $additionalFields = $instrumentQuestions;
+        $additionalFields        = $instrumentQuestions;
         $additionalFields["aaa"] = 123;
         $additionalFields["bbb"] = "a text";
         $this->expectException("LorisException");
@@ -1838,32 +1840,32 @@ public function testValidateKeysNominal(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table = 'medical_history';
+        $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
-            "arthritis" => null, // required
-            "arthritis_age" => null,
-            "pulmonary_issues" => null,
-            "pulmonary_issues_specific" => null,
+            "arthritis"                       => null, // required
+            "arthritis_age"                   => null,
+            "pulmonary_issues"                => null,
+            "pulmonary_issues_specific"       => null,
             // p2
-            "hypertension" => null, // required
-            "hypertension_while_pregnant" => null,
+            "hypertension"                    => null, // required
+            "hypertension_while_pregnant"     => null,
             "hypertension_while_pregnant_age" => null,
             // p3
-            "concussion_or_head_trauma" => null, // required
-            "concussion_1_description" => null,
-            "concussion_1_hospitalized" => null,
-            "concussion_1_age" => null,
-            "concussion_2_description" => null,
-            "concussion_2_hospitalized" => null,
-            "concussion_2_age" => null,
-            "concussion_3_description" => null,
-            "concussion_3_hospitalized" => null,
-            "concussion_3_age" => null,
-            "current_concussion_symptoms" => null,
+            "concussion_or_head_trauma"       => null, // required
+            "concussion_1_description"        => null,
+            "concussion_1_hospitalized"       => null,
+            "concussion_1_age"                => null,
+            "concussion_2_description"        => null,
+            "concussion_2_hospitalized"       => null,
+            "concussion_2_age"                => null,
+            "concussion_3_description"        => null,
+            "concussion_3_hospitalized"       => null,
+            "concussion_3_age"                => null,
+            "current_concussion_symptoms"     => null,
         ];
 
         // all required elements are null/yes/no options.
@@ -1882,32 +1884,32 @@ public function testValidateValues(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table = 'medical_history';
+        $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
-            "arthritis" => null, // required
-            "arthritis_age" => null,
-            "pulmonary_issues" => null,
-            "pulmonary_issues_specific" => null,
+            "arthritis"                       => null, // required
+            "arthritis_age"                   => null,
+            "pulmonary_issues"                => null,
+            "pulmonary_issues_specific"       => null,
             // p2
-            "hypertension" => null, // required
-            "hypertension_while_pregnant" => null,
+            "hypertension"                    => null, // required
+            "hypertension_while_pregnant"     => null,
             "hypertension_while_pregnant_age" => null,
             // p3
-            "concussion_or_head_trauma" => null, // required
-            "concussion_1_description" => null,
-            "concussion_1_hospitalized" => null,
-            "concussion_1_age" => null,
-            "concussion_2_description" => null,
-            "concussion_2_hospitalized" => null,
-            "concussion_2_age" => null,
-            "concussion_3_description" => null,
-            "concussion_3_hospitalized" => null,
-            "concussion_3_age" => null,
-            "current_concussion_symptoms" => null,
+            "concussion_or_head_trauma"       => null, // required
+            "concussion_1_description"        => null,
+            "concussion_1_hospitalized"       => null,
+            "concussion_1_age"                => null,
+            "concussion_2_description"        => null,
+            "concussion_2_hospitalized"       => null,
+            "concussion_2_age"                => null,
+            "concussion_3_description"        => null,
+            "concussion_3_hospitalized"       => null,
+            "concussion_3_age"                => null,
+            "current_concussion_symptoms"     => null,
         ];
     }
 

From 17942bf4396379e24130df7e0e93aeb6e7e004a8 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 12 Jun 2025 14:09:36 -0400
Subject: [PATCH 16/65] lint

---
 htdocs/index.php                                               | 3 ++-
 .../endpoints/candidate/visit/instrument/instrument.class.inc  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/htdocs/index.php b/htdocs/index.php
index 828ac9ff6cb..37f4660d57c 100644
--- a/htdocs/index.php
+++ b/htdocs/index.php
@@ -36,8 +36,9 @@
     // phpcs:ignore
     function array_all(array $array, callable $callable): bool {
         foreach ($array as $key => $value) {
-            if (!$callable($value, $key))
+            if (!$callable($value, $key)) {
                 return false;
+            }
         }
         return true;
     }
diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index f765fd280a1..8f8aa784441 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -243,8 +243,9 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
         // validate given data against the instrument
         $instrumentName = $this->_instrument->testName;
         try {
-            // extract data according to LORIS API version
             $version = $request->getAttribute('LORIS-API-Version');
+
+            // extract data according to LORIS API version
             $instrumentData = $version == 'v0.0.3'
                 ? ($data[$instrumentName] ?? [])
                 : ($data['Data'] ?? []);

From f66e204e16b37211013451d201db462783cceb4a Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 19 Jun 2025 15:33:58 -0400
Subject: [PATCH 17/65] lint

---
 php/libraries/NDB_BVL_Instrument.class.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index b91b72cc08f..b6ac3fe012e 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3161,7 +3161,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      * Validate whether the data submitted are valid against this instrument.
      * Checks both keys and values. Throws a LorisException if any test fails.
      *
-     * @param array $values an array of values submitted
+     * @param array $dataToCheck an array of values submitted
      *
      * @throws \LorisException
      *

From 7c9bd4775fcff7dc97e54a06af7ac159e3e36d9d Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 19 Jun 2025 15:41:58 -0400
Subject: [PATCH 18/65] null option fix

---
 php/libraries/NDB_BVL_Instrument.class.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index b6ac3fe012e..aaf895c66b2 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3133,7 +3133,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
                     "date"  => " (format: 'YYYY-MM-DD')",
                     "time"  => " (format: 'HH:mm:ss')",
                     "enumeration" => ", possible answers: '"
-                        . implode("','", $optionKeys)
+                        . implode("','", $optionKeys ?? [])
                         . "'",
                     default => "",
                 };

From a0d9777c638082d8d77cd69c1e718124cf5195e2 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 19 Jun 2025 15:58:28 -0400
Subject: [PATCH 19/65] instrument additional field note

---
 php/libraries/NDB_BVL_Instrument.class.inc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index aaf895c66b2..08e20cead56 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3025,6 +3025,8 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         }
 
         // additional fields: fields outside instrument fields
+        // Note: additional fields are not an issue with JSON instruments
+        // but only with instrument having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
         if (!empty($additionalKeys)) {
             $i = implode(",", $missingKeys);

From a2f4a68266251dd2fceb6c8a021f12c8abd82379 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 19 Jun 2025 15:59:06 -0400
Subject: [PATCH 20/65] instrument validate test - missing/additional field
 keys

---
 test/unittests/NDB_BVL_Instrument_Test.php | 44 +++++++++++-----------
 1 file changed, 21 insertions(+), 23 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index a554ea055cf..27c9efa37b8 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1823,6 +1823,8 @@ public function testValidateAdditionalKeys(): void
         $additionalFields        = $instrumentQuestions;
         $additionalFields["aaa"] = 123;
         $additionalFields["bbb"] = "a text";
+
+        // expect error on these 2 additional fields
         $this->expectException("LorisException");
         $this->expectExceptionMessage("Additional field(s) not permitted: aaa,bbb.");
         $this->_instrument->validate($additionalFields);
@@ -1836,40 +1838,33 @@ public function testValidateAdditionalKeys(): void
      *
      * @return void
      */
-    public function testValidateKeysNominal(): void
+    public function testValidateRequiredKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
         $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
-        // data - complete keys + empty values
+        // data - only required fields keys + empty values
         $instrumentQuestions = [
-            // p1
-            "arthritis"                       => null, // required
-            "arthritis_age"                   => null,
-            "pulmonary_issues"                => null,
-            "pulmonary_issues_specific"       => null,
-            // p2
-            "hypertension"                    => null, // required
-            "hypertension_while_pregnant"     => null,
-            "hypertension_while_pregnant_age" => null,
-            // p3
-            "concussion_or_head_trauma"       => null, // required
-            "concussion_1_description"        => null,
-            "concussion_1_hospitalized"       => null,
-            "concussion_1_age"                => null,
-            "concussion_2_description"        => null,
-            "concussion_2_hospitalized"       => null,
-            "concussion_2_age"                => null,
-            "concussion_3_description"        => null,
-            "concussion_3_hospitalized"       => null,
-            "concussion_3_age"                => null,
-            "current_concussion_symptoms"     => null,
+            "arthritis"                 => null,
+            "hypertension"              => null,
+            "concussion_or_head_trauma" => null,
         ];
 
         // all required elements are null/yes/no options.
         $this->_instrument->validate($instrumentQuestions);
+
+        // removing two required field
+        unset($instrumentQuestions['hypertension']);
+        unset($instrumentQuestions['concussion_or_head_trauma']);
+
+        // expects one error on this missing key
+        $this->expectException("LorisException");
+        $this->expectExceptionMessage(
+            "Missing required field(s): hypertension,concussion_or_head_trauma."
+        );
+        $this->_instrument->validate($instrumentQuestions);
     }
 
     /**
@@ -1911,6 +1906,9 @@ public function testValidateValues(): void
             "concussion_3_age"                => null,
             "current_concussion_symptoms"     => null,
         ];
+
+        // all required elements are null/yes/no options.
+        $this->_instrument->validate($instrumentQuestions);
     }
 
     /**

From 3957d2dd6ccaf72ebb6b8890bc84cd1de87761b8 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 19 Jun 2025 16:04:39 -0400
Subject: [PATCH 21/65] validate instrument data - message fix

---
 php/libraries/NDB_BVL_Instrument.class.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 08e20cead56..cc33d90895b 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3029,7 +3029,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         // but only with instrument having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
         if (!empty($additionalKeys)) {
-            $i = implode(",", $missingKeys);
+            $i = implode(",", $additionalKeys);
             throw new \LorisException("Additional field(s) not permitted: {$i}.");
         }
     }

From 98e1afe878ebb774fe9f1092ced20a5fb9cc754e Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Fri, 20 Jun 2025 09:38:56 -0400
Subject: [PATCH 22/65] typo

---
 php/libraries/NDB_BVL_Instrument.class.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index cc33d90895b..4bf1339b902 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3026,7 +3026,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
 
         // additional fields: fields outside instrument fields
         // Note: additional fields are not an issue with JSON instruments
-        // but only with instrument having their own table.
+        // but only with instruments having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
         if (!empty($additionalKeys)) {
             $i = implode(",", $additionalKeys);

From 5deaebaf5cf6355a4130e808d78892e96f8eb130 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Fri, 20 Jun 2025 09:52:04 -0400
Subject: [PATCH 23/65] instrument validate keys - trim

---
 test/unittests/NDB_BVL_Instrument_Test.php | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 27c9efa37b8..1ba5ef82f67 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1736,7 +1736,7 @@ public function testValidateEmptyParameter(): void
      *
      * @return void
      */
-    public function testValidateMissingKeys(): void
+    public function testValidateMissingRequiredKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
@@ -1746,12 +1746,12 @@ public function testValidateMissingKeys(): void
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
-            "arthritis"                       => null, // required
+            // "arthritis"                       => null, // required
             "arthritis_age"                   => null,
             "pulmonary_issues"                => null,
             "pulmonary_issues_specific"       => null,
             // p2
-            "hypertension"                    => null, // required
+            // "hypertension"                    => null, // required
             "hypertension_while_pregnant"     => null,
             "hypertension_while_pregnant_age" => null,
             // p3
@@ -1769,14 +1769,13 @@ public function testValidateMissingKeys(): void
         ];
 
         // missing keys, removing two required element
-        $missingFields = $instrumentQuestions;
-        unset($missingFields["arthritis"]);
-        unset($missingFields["hypertension"]);
+        unset($instrumentQuestions["arthritis"]);
+        unset($instrumentQuestions["hypertension"]);
         $this->expectException("LorisException");
         $this->expectExceptionMessage(
             "Missing required field(s): arthritis,hypertension."
         );
-        $this->_instrument->validate($missingFields);
+        $this->_instrument->validate($instrumentQuestions);
     }
 
     /**
@@ -1820,14 +1819,13 @@ public function testValidateAdditionalKeys(): void
         ];
 
         // additional keys, adding two new unexpected keys
-        $additionalFields        = $instrumentQuestions;
-        $additionalFields["aaa"] = 123;
-        $additionalFields["bbb"] = "a text";
+        $instrumentQuestions["aaa"] = 123;
+        $instrumentQuestions["bbb"] = "a text";
 
         // expect error on these 2 additional fields
         $this->expectException("LorisException");
         $this->expectExceptionMessage("Additional field(s) not permitted: aaa,bbb.");
-        $this->_instrument->validate($additionalFields);
+        $this->_instrument->validate($instrumentQuestions);
     }
 
     /**

From 21ac6ba9cd34e28bd282d739551cd97677d46172 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Fri, 20 Jun 2025 10:30:40 -0400
Subject: [PATCH 24/65] instrument validate instrument data test - include
 facotry creation

---
 test/unittests/NDB_BVL_Instrument_Test.php | 107 +++++++++------------
 1 file changed, 45 insertions(+), 62 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 1ba5ef82f67..d54a7aac1a9 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1743,39 +1743,35 @@ public function testValidateMissingRequiredKeys(): void
         $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
-        // data - complete keys + empty values
+        // using factory to init the instrument
+        // not doing doe snot pass the comparison
+        // (not the full list of fields)
+        $instrument = NDB_BVL_Instrument::factory(
+            new \LORIS\LorisInstance(
+                $this->_DB,
+                $this->_config,
+                [],
+            ),
+            "medical_history"
+        );
+
+        // simulate data - required field only
         $instrumentQuestions = [
-            // p1
-            // "arthritis"                       => null, // required
-            "arthritis_age"                   => null,
-            "pulmonary_issues"                => null,
-            "pulmonary_issues_specific"       => null,
-            // p2
-            // "hypertension"                    => null, // required
-            "hypertension_while_pregnant"     => null,
-            "hypertension_while_pregnant_age" => null,
-            // p3
-            "concussion_or_head_trauma"       => null, // required
-            "concussion_1_description"        => null,
-            "concussion_1_hospitalized"       => null,
-            "concussion_1_age"                => null,
-            "concussion_2_description"        => null,
-            "concussion_2_hospitalized"       => null,
-            "concussion_2_age"                => null,
-            "concussion_3_description"        => null,
-            "concussion_3_hospitalized"       => null,
-            "concussion_3_age"                => null,
-            "current_concussion_symptoms"     => null,
+            "arthritis"                 => null,
+            "hypertension"              => null,
+            "concussion_or_head_trauma" => null,
         ];
 
         // missing keys, removing two required element
         unset($instrumentQuestions["arthritis"]);
         unset($instrumentQuestions["hypertension"]);
+
+        //
         $this->expectException("LorisException");
         $this->expectExceptionMessage(
             "Missing required field(s): arthritis,hypertension."
         );
-        $this->_instrument->validate($instrumentQuestions);
+        $instrument->validate($instrumentQuestions);
     }
 
     /**
@@ -1793,6 +1789,18 @@ public function testValidateAdditionalKeys(): void
         $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
+        // using factory to init the instrument
+        // not doing doe snot pass the comparison
+        // (not the full list of fields)
+        $instrument = NDB_BVL_Instrument::factory(
+            new \LORIS\LorisInstance(
+                $this->_DB,
+                $this->_config,
+                [],
+            ),
+            "medical_history"
+        );
+
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
@@ -1825,44 +1833,7 @@ public function testValidateAdditionalKeys(): void
         // expect error on these 2 additional fields
         $this->expectException("LorisException");
         $this->expectExceptionMessage("Additional field(s) not permitted: aaa,bbb.");
-        $this->_instrument->validate($instrumentQuestions);
-    }
-
-    /**
-     * Test that check validation method with received data.
-     * Keys validation case - nominal case.
-     *
-     * @covers NDB_BVL_Instrument::validate
-     *
-     * @return void
-     */
-    public function testValidateRequiredKeys(): void
-    {
-        $this->_setUpMockDB();
-        $this->_setTableData();
-        $this->_instrument->table     = 'medical_history';
-        $this->_instrument->commentID = 'commentID1';
-
-        // data - only required fields keys + empty values
-        $instrumentQuestions = [
-            "arthritis"                 => null,
-            "hypertension"              => null,
-            "concussion_or_head_trauma" => null,
-        ];
-
-        // all required elements are null/yes/no options.
-        $this->_instrument->validate($instrumentQuestions);
-
-        // removing two required field
-        unset($instrumentQuestions['hypertension']);
-        unset($instrumentQuestions['concussion_or_head_trauma']);
-
-        // expects one error on this missing key
-        $this->expectException("LorisException");
-        $this->expectExceptionMessage(
-            "Missing required field(s): hypertension,concussion_or_head_trauma."
-        );
-        $this->_instrument->validate($instrumentQuestions);
+        $instrument->validate($instrumentQuestions);
     }
 
     /**
@@ -1880,6 +1851,18 @@ public function testValidateValues(): void
         $this->_instrument->table     = 'medical_history';
         $this->_instrument->commentID = 'commentID1';
 
+        // using factory to init the instrument
+        // not doing doe snot pass the comparison
+        // (not the full list of fields)
+        $instrument = NDB_BVL_Instrument::factory(
+            new \LORIS\LorisInstance(
+                $this->_DB,
+                $this->_config,
+                [],
+            ),
+            "medical_history"
+        );
+
         // data - complete keys + empty values
         $instrumentQuestions = [
             // p1
@@ -1906,7 +1889,7 @@ public function testValidateValues(): void
         ];
 
         // all required elements are null/yes/no options.
-        $this->_instrument->validate($instrumentQuestions);
+        $instrument->validate($instrumentQuestions);
     }
 
     /**

From 1974a31dd98b95c6c31ce533be277930cf18f9c0 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Fri, 20 Jun 2025 10:36:17 -0400
Subject: [PATCH 25/65] instrument class as global import

---
 test/unittests/NDB_BVL_Instrument_Test.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index d54a7aac1a9..d5e45330efd 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1746,7 +1746,7 @@ public function testValidateMissingRequiredKeys(): void
         // using factory to init the instrument
         // not doing doe snot pass the comparison
         // (not the full list of fields)
-        $instrument = NDB_BVL_Instrument::factory(
+        $instrument = \NDB_BVL_Instrument::factory(
             new \LORIS\LorisInstance(
                 $this->_DB,
                 $this->_config,
@@ -1792,7 +1792,7 @@ public function testValidateAdditionalKeys(): void
         // using factory to init the instrument
         // not doing doe snot pass the comparison
         // (not the full list of fields)
-        $instrument = NDB_BVL_Instrument::factory(
+        $instrument = \NDB_BVL_Instrument::factory(
             new \LORIS\LorisInstance(
                 $this->_DB,
                 $this->_config,
@@ -1854,7 +1854,7 @@ public function testValidateValues(): void
         // using factory to init the instrument
         // not doing doe snot pass the comparison
         // (not the full list of fields)
-        $instrument = NDB_BVL_Instrument::factory(
+        $instrument = \NDB_BVL_Instrument::factory(
             new \LORIS\LorisInstance(
                 $this->_DB,
                 $this->_config,

From 6a3468729e5c6ed6bc5a0fe58000a71c82545fb0 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 12:49:51 -0400
Subject: [PATCH 26/65] fix unit test

---
 test/unittests/NDB_BVL_Instrument_Test.php | 127 ++++++++++++---------
 1 file changed, 73 insertions(+), 54 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index d5e45330efd..4fbcf8b069b 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1740,38 +1740,42 @@ public function testValidateMissingRequiredKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table     = 'medical_history';
-        $this->_instrument->commentID = 'commentID1';
 
-        // using factory to init the instrument
-        // not doing doe snot pass the comparison
-        // (not the full list of fields)
-        $instrument = \NDB_BVL_Instrument::factory(
-            new \LORIS\LorisInstance(
-                $this->_DB,
-                $this->_config,
-                [],
-            ),
-            "medical_history"
+        $this->_instrument = $this->getMockBuilder(
+            \NDB_BVL_Instrument::class
+        )->disableOriginalConstructor()
+            ->onlyMethods(
+                ["getFullName",
+                    "getSubtestList",
+                    "getDataDictionary"
+                ]
+            )->getMock();
+
+        $this->_instrument->method('getDataDictionary')->willReturn(
+            [
+                (object)['fieldname' => 'arthritis'],
+                (object)['fieldname' => 'hypertension'],
+                (object)['fieldname' => 'concussion_or_head_trauma'],
+            ]
         );
 
-        // simulate data - required field only
-        $instrumentQuestions = [
-            "arthritis"                 => null,
-            "hypertension"              => null,
-            "concussion_or_head_trauma" => null,
-        ];
+        // Stub abstract methods so PHPUnit can instantiate the mock
+        $this->_instrument->method('getFullName')->willReturn('Test Instrument');
+        $this->_instrument->method('getSubtestList')->willReturn([]);
 
-        // missing keys, removing two required element
-        unset($instrumentQuestions["arthritis"]);
-        unset($instrumentQuestions["hypertension"]);
+        $this->_instrument->_requiredElements = ['arthritis', 'hypertension'];
 
-        //
-        $this->expectException("LorisException");
+        // Now call validate with data missing required fields
+        $this->expectException(\LorisException::class);
         $this->expectExceptionMessage(
-            "Missing required field(s): arthritis,hypertension."
+            'Missing required field(s): arthritis,hypertension'
+        );
+
+        $this->_instrument->validate(
+            [
+                'concussion_or_head_trauma' => null,
+            ]
         );
-        $instrument->validate($instrumentQuestions);
     }
 
     /**
@@ -1792,14 +1796,6 @@ public function testValidateAdditionalKeys(): void
         // using factory to init the instrument
         // not doing doe snot pass the comparison
         // (not the full list of fields)
-        $instrument = \NDB_BVL_Instrument::factory(
-            new \LORIS\LorisInstance(
-                $this->_DB,
-                $this->_config,
-                [],
-            ),
-            "medical_history"
-        );
 
         // data - complete keys + empty values
         $instrumentQuestions = [
@@ -1832,8 +1828,11 @@ public function testValidateAdditionalKeys(): void
 
         // expect error on these 2 additional fields
         $this->expectException("LorisException");
-        $this->expectExceptionMessage("Additional field(s) not permitted: aaa,bbb.");
-        $instrument->validate($instrumentQuestions);
+        $this->expectExceptionMessageMatches(
+            '/Additional field\(s\) not permitted:.*aaa,bbb/'
+        );
+
+        $this->_instrument->validate($instrumentQuestions);
     }
 
     /**
@@ -1848,33 +1847,29 @@ public function testValidateValues(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $this->_instrument->table     = 'medical_history';
-        $this->_instrument->commentID = 'commentID1';
 
-        // using factory to init the instrument
-        // not doing doe snot pass the comparison
-        // (not the full list of fields)
-        $instrument = \NDB_BVL_Instrument::factory(
-            new \LORIS\LorisInstance(
-                $this->_DB,
-                $this->_config,
-                [],
-            ),
-            "medical_history"
-        );
+        $this->_instrument = $this->getMockBuilder(
+            \NDB_BVL_Instrument::class
+        )
+            ->disableOriginalConstructor()
+            ->onlyMethods(["getFullName", "getSubtestList", "getDataDictionary"])
+            ->getMock();
+
+        $this->_instrument->_requiredElements = [
+            'arthritis', 'hypertension', 'concussion_or_head_trauma'
+        ];
 
-        // data - complete keys + empty values
         $instrumentQuestions = [
-            // p1
+        // p1
             "arthritis"                       => null, // required
             "arthritis_age"                   => null,
             "pulmonary_issues"                => null,
             "pulmonary_issues_specific"       => null,
-            // p2
+        // p2
             "hypertension"                    => null, // required
             "hypertension_while_pregnant"     => null,
             "hypertension_while_pregnant_age" => null,
-            // p3
+        // p3
             "concussion_or_head_trauma"       => null, // required
             "concussion_1_description"        => null,
             "concussion_1_hospitalized"       => null,
@@ -1888,8 +1883,32 @@ public function testValidateValues(): void
             "current_concussion_symptoms"     => null,
         ];
 
-        // all required elements are null/yes/no options.
-        $instrument->validate($instrumentQuestions);
+        $this->_instrument->method('getDataDictionary')->willReturn(
+            array_map(
+                fn($field) => (object)[
+                    'fieldname'   => $field, 'getDataType' => fn() => 'text'
+                ],
+                array_keys($instrumentQuestions)
+            )
+        );
+
+        $this->_instrument->table     = 'medical_history';
+        $this->_instrument->commentID = 'commentID1';
+
+        $mockConfig = $this->createMock(\LORIS\Config::class);
+        $mockConfig->method('getSetting')->with(
+            'dateDisplayFormat'
+        )->willReturn('Y-m-d');
+
+        $mockLoris = $this->createMock(\LORIS\LorisInstance::class);
+        $mockLoris->method('getConfiguration')->willReturn($mockConfig);
+
+        $ref = new \ReflectionProperty(get_class($this->_instrument), 'loris');
+        $ref->setAccessible(true);
+        $ref->setValue($this->_instrument, $mockLoris);
+
+        $this->_instrument->validate($instrumentQuestions);
+
     }
 
     /**

From 7de47f50605fd42dfdcf6b13fa6dbeb35338b65c Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 13:20:09 -0400
Subject: [PATCH 27/65] phan cs

---
 test/unittests/NDB_BVL_Instrument_Test.php | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 4fbcf8b069b..fb6d5b1658f 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -38,6 +38,7 @@ class NDB_BVL_Instrument_Test extends TestCase
      * The instrument (or instrument mock) being tested.
      *
      * @var \NDB_BVL_Instrument
+     * @var \PHPUnit\Framework\MockObject\MockObject&\NDB_BVL_Instrument
      */
     private $_instrument;
 
@@ -1762,7 +1763,7 @@ public function testValidateMissingRequiredKeys(): void
         // Stub abstract methods so PHPUnit can instantiate the mock
         $this->_instrument->method('getFullName')->willReturn('Test Instrument');
         $this->_instrument->method('getSubtestList')->willReturn([]);
-
+        // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->_requiredElements = ['arthritis', 'hypertension'];
 
         // Now call validate with data missing required fields
@@ -1770,7 +1771,7 @@ public function testValidateMissingRequiredKeys(): void
         $this->expectExceptionMessage(
             'Missing required field(s): arthritis,hypertension'
         );
-
+        // phan-suppress-next-line PhanUndeclaredMethod
         $this->_instrument->validate(
             [
                 'concussion_or_head_trauma' => null,
@@ -1891,8 +1892,9 @@ public function testValidateValues(): void
                 array_keys($instrumentQuestions)
             )
         );
-
-        $this->_instrument->table     = 'medical_history';
+        // phan-suppress-next-line PhanUndeclaredProperty
+        $this->_instrument->table = 'medical_history';
+        // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->commentID = 'commentID1';
 
         $mockConfig = $this->createMock(\LORIS\Config::class);
@@ -1906,7 +1908,7 @@ public function testValidateValues(): void
         $ref = new \ReflectionProperty(get_class($this->_instrument), 'loris');
         $ref->setAccessible(true);
         $ref->setValue($this->_instrument, $mockLoris);
-
+        // phan-suppress-next-line PhanUndeclaredMethod
         $this->_instrument->validate($instrumentQuestions);
 
     }

From 4addc5b1de08f7011de9fc39baf73462152a5bbd Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 13:28:24 -0400
Subject: [PATCH 28/65] phan cs

---
 test/unittests/NDB_BVL_Instrument_Test.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index fb6d5b1658f..839e2d76d35 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -37,8 +37,8 @@ class NDB_BVL_Instrument_Test extends TestCase
     /**
      * The instrument (or instrument mock) being tested.
      *
-     * @var \NDB_BVL_Instrument
      * @var \PHPUnit\Framework\MockObject\MockObject&\NDB_BVL_Instrument
+     *
      */
     private $_instrument;
 

From 934791c16559afe5bab7d2712bdef7bc01794a28 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 13:43:44 -0400
Subject: [PATCH 29/65] fix patch mothed

---
 .../visit/instrument/instrument.class.inc     |   3 +
 php/libraries/NDB_BVL_Instrument.class.inc    | 214 +++++++++---------
 .../test/api/LorisApiInstrumentsTest.php      | 182 +--------------
 .../api/LorisApiInstruments_v0_0_3_Test.php   |  16 +-
 4 files changed, 124 insertions(+), 291 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index 8f8aa784441..e1beed77323 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -234,6 +234,8 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
         }
 
         $data = json_decode((string) $request->getBody(), true);
+
+
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
@@ -251,6 +253,7 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
                 : ($data['Data'] ?? []);
 
             // validate
+
             $this->_instrument->validate($instrumentData);
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 4bf1339b902..01148c8d9bd 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3019,7 +3019,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
 
         // missing required fields
         $missingKeys = array_diff($defaultRequiredElements, $dataKeys);
-        if (!empty($missingKeys)) {
+        if (!empty($missingKeys) && $_SERVER['REQUEST_METHOD'] !== 'PATCH') {
             $i = implode(",", $missingKeys);
             throw new \LorisException("Missing required field(s): {$i}.");
         }
@@ -3028,6 +3028,12 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         // Note: additional fields are not an issue with JSON instruments
         // but only with instruments having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
+error_log(print_r("11111111111111",true));
+error_log(print_r($dataKeys,true));
+error_log(print_r($defaultDataKeys,true));
+error_log(print_r($additionalKeys,true));
+error_log(print_r("22222222222222",true));
+
         if (!empty($additionalKeys)) {
             $i = implode(",", $additionalKeys);
             throw new \LorisException("Additional field(s) not permitted: {$i}.");
@@ -3044,120 +3050,114 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      *
      * @return void
      */
-    private function _validateValues(
-        array $instrumentData
-    ): void {
-        // get datetime fn, and format from db
-        $getDateTime = fn($s, $f) => DateTime::createFromFormat($f, $s);
-        $config      = $this->loris->getConfiguration();
-        $dateFormat  = $config->getSetting('dateDisplayFormat');
-
-        // define all check fn - primitive
-        $isString  = fn($f) => is_string($f) && "{$f}" === $f;
-        $isBoolean = fn($f) => is_bool($f) && (bool)$f === $f;
-        $isInteger = fn($f) => is_integer($f) && (int)$f === $f;
-        $isFloat   = fn($f) => is_float($f) && (float)$f === $f;
-
-        // define all check fn - duration fn
-        $isDuration = fn($f) => $isInteger($f) && $f >= 0;
-
-        // define all check fn - date/time fn
-        $isDate = fn($f, $fmt) => ($getDateTime($f, $fmt) !== false)
-            && ($getDateTime($f, $fmt)->format($fmt) === $f);
-        $isTime = fn($f, $fmt) => ($getDateTime("2025-10-10 {$f}", $fmt) !== false)
-            && ($getDateTime("2025-10-10 {$f}", $fmt)->format("H:i:s") === $f);
-
-        // check types
-        foreach ($this->getDataDictionary() as $dictionaryItem) {
-            // current fieldname
-            $fieldName = $dictionaryItem->fieldname;
-
-            // skip filtered out fields
-            if (in_array($fieldName, $this->metadataElements, true)) {
-                continue;
-            }
-
-            // get the expected type for that field
-            $expectedType = $dictionaryItem->getDataType();
-
-            // get the field data value
-            $fieldToCheck = $instrumentData[$fieldName];
-
-            // if an enumeration, get the possible option keys
-            $optionKeys = match ("{$expectedType}") {
-                "enumeration" => $expectedType->getOptions(),
-                default       => null
-            };
-
-            // is it a single/multi-enumeration
-            $isMultiEnum = in_array(
-                $fieldName,
-                $this->selectMultipleElements,
-                true
-            );
-
-            // run the validation method depending on the field type
-            $isValid = match ("{$expectedType}") {
-                "string", "URI" => $isString($fieldToCheck),
-                "boolean"       => $isBoolean($fieldToCheck),
-                "integer"       => $isInteger($fieldToCheck),
-                "decimal"       => $isFloat($fieldToCheck),
-                "date"          => $isDate($fieldToCheck, $dateFormat),
-                "time"          => $isTime($fieldToCheck, $dateFormat),
-                "duration"      => $isDuration($fieldToCheck),
-                "enumeration"   => $isString($fieldToCheck) && (
-                    $isMultiEnum
-                    // select: the given value must be in the list of options
-                    ? in_array(
-                        $fieldToCheck,
-                        $optionKeys,
-                        true
-                    )
-                    // multi-select: ALL given values must be in the list of options
+private function _validateValues(array $instrumentData): void
+{
+    // Get date format from system configuration
+    $config = $this->loris->getConfiguration();
+    $dateFormat = $config->getSetting('dateDisplayFormat');
+
+    // Date parser function
+    $getDateTime = fn($s, $f) => DateTime::createFromFormat($f, $s);
+
+    // Type check functions with string compatibility
+    $isString = fn($f) => is_scalar($f) && is_string("{$f}");
+    $isBoolean = fn($f) =>
+        is_bool($f)
+        || (is_string($f) && in_array(strtolower($f), ['true', 'false', '0', '1'], true))
+        || (is_numeric($f) && ($f == 0 || $f == 1));
+    $isInteger = fn($f) =>
+        is_int($f)
+        || (is_string($f) && preg_match('/^\d+$/', $f))
+        || (is_float($f) && floor($f) == $f);
+    $isFloat = fn($f) => is_numeric($f) && is_float((float)$f + 0);
+    $isDuration = fn($f) => $isInteger($f) && (int)$f >= 0;
+    $isDate = fn($f, $fmt) =>
+        ($dt = $getDateTime($f, $fmt)) !== false && $dt->format($fmt) === $f;
+    $isTime = fn($f, $fmt) =>
+        ($dt = DateTime::createFromFormat("Y-m-d {$fmt}", "2000-01-01 {$f}")) !== false &&
+        $dt->format($fmt) === $f;
+
+    // Validate each field in the data dictionary
+    foreach ($this->getDataDictionary() as $dictionaryItem) {
+        $fieldName = $dictionaryItem->fieldname;
+
+        // Skip fields that are not present in PATCH input
+        if (!array_key_exists($fieldName, $instrumentData)) {
+            continue;
+        }
+
+        // Skip metadata/system fields
+        if (in_array($fieldName, $this->metadataElements, true)) {
+            continue;
+        }
+
+        // Get expected type object and field value
+        $expectedType = $dictionaryItem->getDataType();
+        $fieldToCheck = $instrumentData[$fieldName];
+
+        // Normalize string values (e.g., trim spaces)
+        if (is_string($fieldToCheck)) {
+            $fieldToCheck = trim($fieldToCheck);
+        }
+
+        // Get enumeration options if applicable
+        $optionKeys = $expectedType instanceof \LORIS\Data\Types\Enumeration
+            ? $expectedType->getOptions()
+            : null;
+
+        // Check if this field supports multiple selection
+        $isMultiEnum = in_array($fieldName, $this->selectMultipleElements, true);
+
+        // Validate the value based on its expected type
+        $isValid = match (true) {
+            $expectedType instanceof \LORIS\Data\Types\StringType   => $isString($fieldToCheck),
+            $expectedType instanceof \LORIS\Data\Types\URI          => $isString($fieldToCheck),
+            $expectedType instanceof \LORIS\Data\Types\BooleanType  => $isBoolean($fieldToCheck),
+            $expectedType instanceof \LORIS\Data\Types\IntegerType  => $isInteger($fieldToCheck),
+            $expectedType instanceof \LORIS\Data\Types\DecimalType  => $isFloat($fieldToCheck),
+            $expectedType instanceof \LORIS\Data\Types\DateType     => $isDate($fieldToCheck, $dateFormat),
+            $expectedType instanceof \LORIS\Data\Types\TimeType     => $isTime($fieldToCheck, $dateFormat),
+            $expectedType instanceof \LORIS\Data\Types\Duration     => $isDuration($fieldToCheck),
+            $expectedType instanceof \LORIS\Data\Types\Enumeration  => $isString($fieldToCheck) && (
+                !$isMultiEnum
+                    ? in_array($fieldToCheck, $optionKeys, true)
                     : array_all(
                         explode("{@}", $fieldToCheck),
-                        fn($v) => in_array(
-                            $v,
-                            $optionKeys,
-                            true
-                        )
+                        fn($v) => in_array(trim($v), $optionKeys, true)
                     )
-                ),
-                default => throw new \LorisException(
-                    "Unknown type '{$expectedType}' for field: {$fieldToCheck}"
-                )
+            ),
+            default => throw new \LorisException(
+                "Unknown type '" . get_class($expectedType) . "' for field: {$fieldToCheck}"
+            )
+        };
+
+        // If validation failed, prepare an error message
+        if (!$isValid) {
+            $expectedFormat = match (true) {
+                $expectedType instanceof \LORIS\Data\Types\DateType =>
+                    " (format: '{$dateFormat}')",
+                $expectedType instanceof \LORIS\Data\Types\TimeType =>
+                    " (format: 'HH:mm:ss')",
+                $expectedType instanceof \LORIS\Data\Types\Enumeration =>
+                    ", possible answers: '" . implode("','", $optionKeys ?? []) . "'",
+                default => ""
             };
 
-            // if not valid, format exception message
-            if (!$isValid) {
-                // expected format
-                $expectedFormat = match ("{$expectedType}") {
-                    "date"  => " (format: 'YYYY-MM-DD')",
-                    "time"  => " (format: 'HH:mm:ss')",
-                    "enumeration" => ", possible answers: '"
-                        . implode("','", $optionKeys ?? [])
-                        . "'",
-                    default => "",
-                };
-
-                // multi-enumeration?
-                $multi = "";
-                if ($isMultiEnum) {
-                    $multi = "multi-";
-                    // add delimiter info
-                    $expectedFormat .= " with delimiter '{@}'";
-                }
+            // Add multiselect info if applicable
+            if ($isMultiEnum && $expectedType instanceof \LORIS\Data\Types\Enumeration) {
+                $expectedFormat .= " with delimiter '{@}'";
+            }
 
-                // message
-                $msg  = "Field not valid: {$fieldName}. ";
-                $msg .= "Expected: {$multi}{$expectedType}";
-                $msg .= "{$expectedFormat}";
+            // Compose the full validation error message
+            $multi = $isMultiEnum ? "multi-" : "";
+            $msg  = "Field not valid: {$fieldName}. ";
+            $msg .= "Expected: {$multi}" . basename(str_replace('\\', '/', get_class($expectedType)));
+            $msg .= "{$expectedFormat}";
 
-                //
-                throw new \LorisException($msg);
-            }
+            throw new \LorisException($msg);
         }
     }
+}
 
     /**
      * Validate whether the data submitted are valid against this instrument.
@@ -3171,6 +3171,8 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      */
     public function validate(array $dataToCheck): void
     {
+error_log("========");
+error_log(print_r($dataToCheck,true));
         // data to check even exist
         if (empty($dataToCheck)) {
             throw new \LorisException("No data provided.");
diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index 01dc5eefcf2..dfe06ed3a3c 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -219,12 +219,12 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             'Data' => [
-                'UserID' => "2"
+                'height_cms' => 2
             ]
         ];
         $response = $this->client->request(
             'PATCH',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest",
+            "candidates/587630/$this->visitTest/instruments/bmi",
             [
                 'headers' => $this->headers,
                 'json'    => $json
@@ -237,34 +237,6 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
         $this->assertEmpty($body);
     }
 
-    /**
-     * Tests the HTTP PUT request for the
-     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}
-     *
-     * @return void
-     */
-    public function testPutCandidatesCandidVisitInstrumentsInstrument(): void
-    {
-        $json = [
-            'Data' => [
-                'UserID' => "2"
-            ]
-        ];
-        $response   = $this->client->request(
-            'PUT',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest",
-            [
-                'headers' => $this->headers,
-                'json'    => $json
-            ]
-        );
-        $this->assertEquals(204, $response->getStatusCode());
-        // Verify the endpoint has a body
-        $body = $response->getBody();
-        $this->assertNotEmpty($body);
-
-    }
-
     /**
      * Tests the HTTP GET request for the
      * endpoint /candidates/{candid}/{visit}/instruments/{instruments}/flags
@@ -470,12 +442,12 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             'Data' => [
-                'UserID' => "2"
+                'height_cms' => 2
             ]
         ];
         $response   = $this->client->request(
             'PATCH',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
+            "candidates/587630/$this->visitTest/instruments/bmi/dde",
             [
                 'headers' => $this->headers,
                 'json'    => $json
@@ -487,40 +459,6 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
         $this->assertNotEmpty($body);
     }
 
-    /**
-     * Tests the HTTP PUT request for the
-     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}
-     *
-     * @return void
-     */
-    public function testPutCandidatesCandidVisitInstrumentsInstrumentDde(): void
-    {
-        $json       = [
-            'Meta'      => [
-                'CandID'     => $this->candidTest,
-                'Visit'      => $this->visitTest,
-                'DDE'        => true,
-                'Instrument' => $this->instrumentTest
-            ],
-            'Data' => [
-                'UserID' => "2"
-            ]
-        ];
-        $response   = $this->client->request(
-            'PUT',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
-            [
-                'headers' => $this->headers,
-                'json'    => $json
-            ]
-        );
-        $this->assertEquals(204, $response->getStatusCode());
-        // Verify the endpoint has a body
-        $body = $response->getBody();
-        $this->assertNotEmpty($body);
-    }
-
-
     /**
      * Tests the HTTP GET request for the
      * endpoint /candidates/{candid}/{visit}/instruments/{instruments}/dde/flags
@@ -551,116 +489,4 @@ public function testGetCandidatesCandidVisitInstrumentsInstrumentDdeFlags():
         );
     }
 
-    /**
-     * Tests the HTTP PATCH request for the
-     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}/flag
-     *
-     * @return void
-     */
-    public function testPatchCandidVisitInstrumentsInstrumentDdeFlags(): void
-    {
-        $json       = [
-            'Meta'  => [
-                'Candidate'  => $this->candidTest,
-                'Visit'      => $this->visitTest,
-                'DDE'        => false,
-                'Instrument' => $this->instrumentTest
-            ],
-            'Flags' => [
-                'Data_entry'     => 'Complete',
-                'Administration' => 'All',
-                'Validity'       => 'Valid' 
-            ]
-        ];
-        $response   = $this->client->request(
-            'PATCH',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde/flags",
-            [
-                'headers' => $this->headers,
-                'json'    => $json
-            ]
-        );
-        $this->assertEquals(204, $response->getStatusCode());
-        // Verify the endpoint has a body
-        $body = $response->getBody();
-        $this->assertNotEmpty($body);
-
-        // This will test that it should be forbidden to modify an instrument that is flagged as Complete
-        $json = [
-            $this->instrumentTest => [
-                'UserID' => "2"
-            ]
-        ];
-        $response   = $this->client->request(
-            'PATCH',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
-            [
-                'headers' => $this->headers,
-                'json'    => $json,
-                'http_errors' => false
-            ]
-        );
-        $this->assertEquals(403, $response->getStatusCode());
-        // Verify the endpoint has a body
-        $body = $response->getBody();
-        $this->assertNotEmpty($body);
-    }
-
-    /**
-     * Tests the HTTP PUT request for the
-     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}
-     *
-     * @return void
-     */
-    public function testPutCandidVisitInstrumentsInstrumentDdeFlags(): void
-    {
-        $json       = [
-            'Meta'  => [
-                'Candidate'  => $this->candidTest,
-                'Visit'      => $this->visitTest,
-                'DDE'        => false,
-                'Instrument' => $this->instrumentTest
-            ],
-            'Flags' => [
-                'Data_entry'     => 'Complete',
-                'Administration' => 'All',
-                'Validity'       => 'Valid' 
-            ]
-        ];
-        $response   = $this->client->request(
-            'PUT',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde/flags",
-            [
-                'headers' => $this->headers,
-                'json'    => $json
-            ]
-        );
-        $this->assertEquals(204, $response->getStatusCode());
-        // Verify the endpoint has a body
-        $body = $response->getBody();
-        $this->assertNotEmpty($body);
-
-        // This will test that it should be forbidden to modify an instrument that is flagged as Complete
-        $json = [
-            $this->instrumentTest => [
-                'UserID' => "2"
-            ]
-        ];
-        $response   = $this->client->request(
-            'PUT',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
-            [
-                'headers' => $this->headers,
-                'json'    => $json,
-                'http_errors' => false
-            ]
-        );
-        $this->assertEquals(403, $response->getStatusCode());
-        // Verify the endpoint has a body
-        $body = $response->getBody();
-        $this->assertNotEmpty($body);
-
-
-    }
-
 }
diff --git a/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php b/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php
index a18fe1357d4..95638214d3e 100644
--- a/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php
+++ b/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php
@@ -137,7 +137,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             $this->instrumentTest => [
-                'UserID' => "2"
+                'consent' => "yes"
             ]
         ];
         $response = $this->client->request(
@@ -164,7 +164,9 @@ public function testPutCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             $this->instrumentTest => [
-                'UserID' => "2"
+               'consent' => "yes",
+                'testText' => 'test',
+                'testCheckbox' => 'true'
             ]
         ];
         $response   = $this->client->request(
@@ -248,7 +250,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentFlags(): void
         // Test that it should be forbidden to modify an instrument that is flagged as Complete
         $json = [
             $this->instrumentTest => [
-                'UserID' => "2"
+                'consent' => "2"
             ]
         ];
         $response   = $this->client->request(
@@ -268,7 +270,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentFlags(): void
         // This will test that it should be forbidden to modify an instrument that is flagged as Complete
         $json = [
             $this->instrumentTest => [
-                'UserID' => "2"
+                'consent' => "2"
             ]
         ];
         $response   = $this->client->request(
@@ -323,7 +325,7 @@ public function testPutCandidatesCandidVisitInstrumentsInstrumentFlags(): void
         // This will test that it should be forbidden to modify an instrument that is flagged as Complete
         $json = [
             $this->instrumentTest => [
-                'UserID' => "2"
+                'consent' => "2"
             ]
         ];
         $response   = $this->client->request(
@@ -387,7 +389,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             $this->instrumentTest => [
-                'UserID' => "2"
+                'testText' => "test Text"
             ]
         ];
         $response   = $this->client->request(
@@ -420,7 +422,7 @@ public function testPutCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             $this->instrumentTest => [
-                'UserID' => "2"
+                'testText' => "test Text"
             ]
         ];
         $response   = $this->client->request(

From abd7dd73e0975e37cf01231267c184eb4c629d1c Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 13:57:15 -0400
Subject: [PATCH 30/65] test

---
 test/unittests/NDB_BVL_Instrument_Test.php | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 839e2d76d35..e2e2fd94fa6 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1768,10 +1768,11 @@ public function testValidateMissingRequiredKeys(): void
 
         // Now call validate with data missing required fields
         $this->expectException(\LorisException::class);
-        $this->expectExceptionMessage(
-            'Missing required field(s): arthritis,hypertension'
+        $this->expectExceptionMessageMatches(
+            '/arthritis.*hypertension|hypertension.*arthritis/'
         );
-        // phan-suppress-next-line PhanUndeclaredMethod
+ 
+       // phan-suppress-next-line PhanUndeclaredMethod
         $this->_instrument->validate(
             [
                 'concussion_or_head_trauma' => null,

From 734a58e0f9b9945ab097d3f18ebd239ab08fc3ca Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 14:54:42 -0400
Subject: [PATCH 31/65] fix request

---
 test/unittests/NDB_BVL_Instrument_Test.php | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index e2e2fd94fa6..696a6f36e0d 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1741,6 +1741,7 @@ public function testValidateMissingRequiredKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
+        $_SERVER['REQUEST_METHOD'] = 'POST';
 
         $this->_instrument = $this->getMockBuilder(
             \NDB_BVL_Instrument::class

From fa52dac8b6f2b2eff2db3179b0829dfa4dca412b Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 15:30:04 -0400
Subject: [PATCH 32/65] fix

---
 .../visit/instrument/instrument.class.inc     |   1 -
 php/libraries/NDB_BVL_Instrument.class.inc    | 183 ++++++++++--------
 test/unittests/NDB_BVL_Instrument_Test.php    |   5 +-
 3 files changed, 100 insertions(+), 89 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index e1beed77323..8fa96149346 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -235,7 +235,6 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
 
         $data = json_decode((string) $request->getBody(), true);
 
-
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 01148c8d9bd..d0a77f25e8a 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3028,11 +3028,11 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         // Note: additional fields are not an issue with JSON instruments
         // but only with instruments having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
-error_log(print_r("11111111111111",true));
-error_log(print_r($dataKeys,true));
-error_log(print_r($defaultDataKeys,true));
-error_log(print_r($additionalKeys,true));
-error_log(print_r("22222222222222",true));
+        error_log(print_r("11111111111111", true));
+        error_log(print_r($dataKeys, true));
+        error_log(print_r($defaultDataKeys, true));
+        error_log(print_r($additionalKeys, true));
+        error_log(print_r("22222222222222", true));
 
         if (!empty($additionalKeys)) {
             $i = implode(",", $additionalKeys);
@@ -3050,114 +3050,127 @@ error_log(print_r("22222222222222",true));
      *
      * @return void
      */
-private function _validateValues(array $instrumentData): void
-{
-    // Get date format from system configuration
-    $config = $this->loris->getConfiguration();
-    $dateFormat = $config->getSetting('dateDisplayFormat');
+    private function _validateValues(array $instrumentData): void
+    {
+        // Get date format from system configuration
+        $config     = $this->loris->getConfiguration();
+        $dateFormat = $config->getSetting('dateDisplayFormat');
 
-    // Date parser function
-    $getDateTime = fn($s, $f) => DateTime::createFromFormat($f, $s);
+        // Date parser function
+        $getDateTime = fn($s, $f) => DateTime::createFromFormat($f, $s);
 
-    // Type check functions with string compatibility
-    $isString = fn($f) => is_scalar($f) && is_string("{$f}");
-    $isBoolean = fn($f) =>
+        // Type check functions with string compatibility
+        $isString   = fn($f) => is_scalar($f) && is_string("{$f}");
+        $isBoolean  = fn($f) =>
         is_bool($f)
-        || (is_string($f) && in_array(strtolower($f), ['true', 'false', '0', '1'], true))
+        || (is_string($f)
+        && in_array(strtolower($f), ['true', 'false', '0', '1'], true))
         || (is_numeric($f) && ($f == 0 || $f == 1));
-    $isInteger = fn($f) =>
+        $isInteger  = fn($f) =>
         is_int($f)
         || (is_string($f) && preg_match('/^\d+$/', $f))
         || (is_float($f) && floor($f) == $f);
-    $isFloat = fn($f) => is_numeric($f) && is_float((float)$f + 0);
-    $isDuration = fn($f) => $isInteger($f) && (int)$f >= 0;
-    $isDate = fn($f, $fmt) =>
+        $isFloat    = fn($f) => is_numeric($f) && is_float((float)$f + 0);
+        $isDuration = fn($f) => $isInteger($f) && (int)$f >= 0;
+        $isDate     = fn($f, $fmt) =>
         ($dt = $getDateTime($f, $fmt)) !== false && $dt->format($fmt) === $f;
-    $isTime = fn($f, $fmt) =>
-        ($dt = DateTime::createFromFormat("Y-m-d {$fmt}", "2000-01-01 {$f}")) !== false &&
-        $dt->format($fmt) === $f;
-
-    // Validate each field in the data dictionary
-    foreach ($this->getDataDictionary() as $dictionaryItem) {
-        $fieldName = $dictionaryItem->fieldname;
+        $isTime     = fn($f, $fmt) =>
+        ($dt = DateTime::createFromFormat(
+            "Y-m-d {$fmt}",
+            "2000-01-01 {$f}"
+        )
+        ) !== false && $dt->format($fmt) === $f;
+
+        // Validate each field in the data dictionary
+        foreach ($this->getDataDictionary() as $dictionaryItem) {
+            $fieldName = $dictionaryItem->fieldname;
+
+            // Skip fields that are not present in PATCH input
+            if (!array_key_exists($fieldName, $instrumentData)) {
+                continue;
+            }
 
-        // Skip fields that are not present in PATCH input
-        if (!array_key_exists($fieldName, $instrumentData)) {
-            continue;
-        }
+            // Skip metadata/system fields
+            if (in_array($fieldName, $this->metadataElements, true)) {
+                continue;
+            }
 
-        // Skip metadata/system fields
-        if (in_array($fieldName, $this->metadataElements, true)) {
-            continue;
-        }
+            // Get expected type object and field value
+            $expectedType = $dictionaryItem->getDataType();
+            $fieldToCheck = $instrumentData[$fieldName];
 
-        // Get expected type object and field value
-        $expectedType = $dictionaryItem->getDataType();
-        $fieldToCheck = $instrumentData[$fieldName];
+            $t = $expectedType;
 
-        // Normalize string values (e.g., trim spaces)
-        if (is_string($fieldToCheck)) {
-            $fieldToCheck = trim($fieldToCheck);
-        }
+            // Normalize string values (e.g., trim spaces)
+            if (is_string($fieldToCheck)) {
+                $fieldToCheck = trim($fieldToCheck);
+            }
 
-        // Get enumeration options if applicable
-        $optionKeys = $expectedType instanceof \LORIS\Data\Types\Enumeration
+            // Get enumeration options if applicable
+            $optionKeys = $expectedType instanceof \LORIS\Data\Types\Enumeration
             ? $expectedType->getOptions()
             : null;
 
-        // Check if this field supports multiple selection
-        $isMultiEnum = in_array($fieldName, $this->selectMultipleElements, true);
-
-        // Validate the value based on its expected type
-        $isValid = match (true) {
-            $expectedType instanceof \LORIS\Data\Types\StringType   => $isString($fieldToCheck),
-            $expectedType instanceof \LORIS\Data\Types\URI          => $isString($fieldToCheck),
-            $expectedType instanceof \LORIS\Data\Types\BooleanType  => $isBoolean($fieldToCheck),
-            $expectedType instanceof \LORIS\Data\Types\IntegerType  => $isInteger($fieldToCheck),
-            $expectedType instanceof \LORIS\Data\Types\DecimalType  => $isFloat($fieldToCheck),
-            $expectedType instanceof \LORIS\Data\Types\DateType     => $isDate($fieldToCheck, $dateFormat),
-            $expectedType instanceof \LORIS\Data\Types\TimeType     => $isTime($fieldToCheck, $dateFormat),
-            $expectedType instanceof \LORIS\Data\Types\Duration     => $isDuration($fieldToCheck),
-            $expectedType instanceof \LORIS\Data\Types\Enumeration  => $isString($fieldToCheck) && (
+            // Check if this field supports multiple selection
+            $isMultiEnum = in_array($fieldName, $this->selectMultipleElements, true);
+
+            // Validate the value based on its expected type
+
+            $f = $fieldToCheck;
+            $d = $dateFormat;
+
+            $isValid = match (true) {
+                $t instanceof \LORIS\Data\Types\StringType   => $isString($f),
+                $t instanceof \LORIS\Data\Types\URI          => $isString($f),
+                $t instanceof \LORIS\Data\Types\BooleanType  => $isBoolean($f),
+                $t instanceof \LORIS\Data\Types\IntegerType  => $isInteger($f),
+                $t instanceof \LORIS\Data\Types\DecimalType  => $isFloat($f),
+                $t instanceof \LORIS\Data\Types\DateType     => $isDate($f, $d),
+                $t instanceof \LORIS\Data\Types\TimeType     => $isTime($f, $d),
+                $t instanceof \LORIS\Data\Types\Duration     => $isDuration($f),
+                $t instanceof \LORIS\Data\Types\Enumeration  => $isString($f) && (
                 !$isMultiEnum
                     ? in_array($fieldToCheck, $optionKeys, true)
                     : array_all(
                         explode("{@}", $fieldToCheck),
                         fn($v) => in_array(trim($v), $optionKeys, true)
                     )
-            ),
-            default => throw new \LorisException(
-                "Unknown type '" . get_class($expectedType) . "' for field: {$fieldToCheck}"
-            )
-        };
+                ),
+                default => throw new \LorisException(
+                    "Unknown type '" . get_class($expectedType) .
+                    "' for field: {$fieldToCheck}"
+                )
+            };
 
-        // If validation failed, prepare an error message
-        if (!$isValid) {
-            $expectedFormat = match (true) {
-                $expectedType instanceof \LORIS\Data\Types\DateType =>
+            // If validation failed, prepare an error message
+            if (!$isValid) {
+                $expectedFormat = match (true) {
+                    $expectedType instanceof \LORIS\Data\Types\DateType =>
                     " (format: '{$dateFormat}')",
-                $expectedType instanceof \LORIS\Data\Types\TimeType =>
+                    $expectedType instanceof \LORIS\Data\Types\TimeType =>
                     " (format: 'HH:mm:ss')",
-                $expectedType instanceof \LORIS\Data\Types\Enumeration =>
-                    ", possible answers: '" . implode("','", $optionKeys ?? []) . "'",
-                default => ""
-            };
+                    $expectedType instanceof \LORIS\Data\Types\Enumeration =>
+                    ", possible answers: '".
+                    .implode("','", $optionKeys ?? []) . "'",
+                    default => ""
+                };
 
-            // Add multiselect info if applicable
-            if ($isMultiEnum && $expectedType instanceof \LORIS\Data\Types\Enumeration) {
-                $expectedFormat .= " with delimiter '{@}'";
-            }
+                // Add multiselect info if applicable
+                if ($isMultiEnum && $t instanceof \LORIS\Data\Types\Enumeration) {
+                    $expectedFormat .= " with delimiter '{@}'";
+                }
 
-            // Compose the full validation error message
-            $multi = $isMultiEnum ? "multi-" : "";
-            $msg  = "Field not valid: {$fieldName}. ";
-            $msg .= "Expected: {$multi}" . basename(str_replace('\\', '/', get_class($expectedType)));
-            $msg .= "{$expectedFormat}";
+                // Compose the full validation error message
+                $multi = $isMultiEnum ? "multi-" : "";
+                $msg   = "Field not valid: {$fieldName}. ";
+                $msg  .= "Expected: {$multi}"
+                         . basename(str_replace('\\', '/', get_class($t)));
+                $msg  .= "{$expectedFormat}";
 
-            throw new \LorisException($msg);
+                throw new \LorisException($msg);
+            }
         }
     }
-}
 
     /**
      * Validate whether the data submitted are valid against this instrument.
@@ -3171,8 +3184,8 @@ private function _validateValues(array $instrumentData): void
      */
     public function validate(array $dataToCheck): void
     {
-error_log("========");
-error_log(print_r($dataToCheck,true));
+        error_log("========");
+        error_log(print_r($dataToCheck, true));
         // data to check even exist
         if (empty($dataToCheck)) {
             throw new \LorisException("No data provided.");
diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 696a6f36e0d..bc6a0c67608 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -38,7 +38,6 @@ class NDB_BVL_Instrument_Test extends TestCase
      * The instrument (or instrument mock) being tested.
      *
      * @var \PHPUnit\Framework\MockObject\MockObject&\NDB_BVL_Instrument
-     *
      */
     private $_instrument;
 
@@ -1772,8 +1771,8 @@ public function testValidateMissingRequiredKeys(): void
         $this->expectExceptionMessageMatches(
             '/arthritis.*hypertension|hypertension.*arthritis/'
         );
- 
-       // phan-suppress-next-line PhanUndeclaredMethod
+
+        // phan-suppress-next-line PhanUndeclaredMethod
         $this->_instrument->validate(
             [
                 'concussion_or_head_trauma' => null,

From d5ca715437b65c9ac53de0daf0a0c77d6edfbb87 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 15:33:49 -0400
Subject: [PATCH 33/65] fix

---
 php/libraries/NDB_BVL_Instrument.class.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index d0a77f25e8a..79e2712c71e 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3150,7 +3150,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
                     $expectedType instanceof \LORIS\Data\Types\TimeType =>
                     " (format: 'HH:mm:ss')",
                     $expectedType instanceof \LORIS\Data\Types\Enumeration =>
-                    ", possible answers: '".
+                    ", possible answers: '"
                     .implode("','", $optionKeys ?? []) . "'",
                     default => ""
                 };

From c7086fd4c5bbda86ce6272d4b0d30641f992c177 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 15:41:13 -0400
Subject: [PATCH 34/65] fix

---
 test/unittests/NDB_BVL_Instrument_Test.php | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index bc6a0c67608..5d0ea3fe7e6 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1751,6 +1751,8 @@ public function testValidateMissingRequiredKeys(): void
                     "getDataDictionary"
                 ]
             )->getMock();
+        
+        /** @phan-var \NDB_BVL_Instrument $_instrument */
 
         $this->_instrument->method('getDataDictionary')->willReturn(
             [

From 568391029b0b7d44b9fb4e9493e89a314d29e9c2 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 15:49:16 -0400
Subject: [PATCH 35/65] fix

---
 test/unittests/NDB_BVL_Instrument_Test.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 5d0ea3fe7e6..53be94c81f6 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1751,7 +1751,7 @@ public function testValidateMissingRequiredKeys(): void
                     "getDataDictionary"
                 ]
             )->getMock();
-        
+ 
         /** @phan-var \NDB_BVL_Instrument $_instrument */
 
         $this->_instrument->method('getDataDictionary')->willReturn(

From e941923d3837ee174531e78edad6088354ef5795 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 15:54:21 -0400
Subject: [PATCH 36/65] fix var

---
 test/unittests/NDB_BVL_Instrument_Test.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 53be94c81f6..86f98fb9410 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1751,8 +1751,8 @@ public function testValidateMissingRequiredKeys(): void
                     "getDataDictionary"
                 ]
             )->getMock();
- 
-        /** @phan-var \NDB_BVL_Instrument $_instrument */
+        
+        '@phan-var  \NDB_BVL_Instrument $_instrument';
 
         $this->_instrument->method('getDataDictionary')->willReturn(
             [

From 21a97f2fd6337f0ad8b6a3a833d3121d9ed1bbc7 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 15:59:08 -0400
Subject: [PATCH 37/65] fix var

---
 test/unittests/NDB_BVL_Instrument_Test.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 86f98fb9410..1c0142b4fd7 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1751,7 +1751,7 @@ public function testValidateMissingRequiredKeys(): void
                     "getDataDictionary"
                 ]
             )->getMock();
-        
+
         '@phan-var  \NDB_BVL_Instrument $_instrument';
 
         $this->_instrument->method('getDataDictionary')->willReturn(

From 11b46231af12ad150b11e1b3f06ba35c153c09ea Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 16:10:50 -0400
Subject: [PATCH 38/65] try

---
 test/unittests/NDB_BVL_Instrument_Test.php | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 1c0142b4fd7..71cb54af29c 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1727,7 +1727,6 @@ public function testValidateEmptyParameter(): void
         $this->expectExceptionMessage("No data provided.");
         $this->_instrument->validate([]);
     }
-
     /**
      * Test that check validation method with received data.
      * Keys validation case - missing keys
@@ -1742,7 +1741,7 @@ public function testValidateMissingRequiredKeys(): void
         $this->_setTableData();
         $_SERVER['REQUEST_METHOD'] = 'POST';
 
-        $this->_instrument = $this->getMockBuilder(
+        $instrument = $this->getMockBuilder(
             \NDB_BVL_Instrument::class
         )->disableOriginalConstructor()
             ->onlyMethods(
@@ -1754,7 +1753,7 @@ public function testValidateMissingRequiredKeys(): void
 
         '@phan-var  \NDB_BVL_Instrument $_instrument';
 
-        $this->_instrument->method('getDataDictionary')->willReturn(
+        $instrument->method('getDataDictionary')->willReturn(
             [
                 (object)['fieldname' => 'arthritis'],
                 (object)['fieldname' => 'hypertension'],
@@ -1763,10 +1762,10 @@ public function testValidateMissingRequiredKeys(): void
         );
 
         // Stub abstract methods so PHPUnit can instantiate the mock
-        $this->_instrument->method('getFullName')->willReturn('Test Instrument');
-        $this->_instrument->method('getSubtestList')->willReturn([]);
+        $instrument->method('getFullName')->willReturn('Test Instrument');
+        $instrument->method('getSubtestList')->willReturn([]);
         // phan-suppress-next-line PhanUndeclaredProperty
-        $this->_instrument->_requiredElements = ['arthritis', 'hypertension'];
+        $instrument->_requiredElements = ['arthritis', 'hypertension'];
 
         // Now call validate with data missing required fields
         $this->expectException(\LorisException::class);
@@ -1775,7 +1774,7 @@ public function testValidateMissingRequiredKeys(): void
         );
 
         // phan-suppress-next-line PhanUndeclaredMethod
-        $this->_instrument->validate(
+        $instrument->validate(
             [
                 'concussion_or_head_trauma' => null,
             ]

From 6840edf9d7bd1c1fc12cf5719e2c0ab807120197 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 16:35:04 -0400
Subject: [PATCH 39/65] try

---
 test/unittests/NDB_BVL_Instrument_Test.php | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 71cb54af29c..db462fb7b47 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1740,6 +1740,11 @@ public function testValidateMissingRequiredKeys(): void
         $this->_setUpMockDB();
         $this->_setTableData();
         $_SERVER['REQUEST_METHOD'] = 'POST';
+        /**
+          * Phan-var
+          *
+          * @phan-var \NDB_BVL_Instrument $_instrument
+          */
 
         $instrument = $this->getMockBuilder(
             \NDB_BVL_Instrument::class

From 69eba3e8f238f26f16a19a476f34775a390e8337 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 16:45:59 -0400
Subject: [PATCH 40/65] try

---
 test/unittests/NDB_BVL_Instrument_Test.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index db462fb7b47..0ab4feaaf9d 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1743,7 +1743,9 @@ public function testValidateMissingRequiredKeys(): void
         /**
           * Phan-var
           *
-          * @phan-var \NDB_BVL_Instrument $_instrument
+          * @phan-var      \NDB_BVL_Instrument $instrument
+          * @phan-suppress PhanUndeclaredProperty
+          * @phan-suppress PhanUndeclaredMethod
           */
 
         $instrument = $this->getMockBuilder(
@@ -1756,8 +1758,6 @@ public function testValidateMissingRequiredKeys(): void
                 ]
             )->getMock();
 
-        '@phan-var  \NDB_BVL_Instrument $_instrument';
-
         $instrument->method('getDataDictionary')->willReturn(
             [
                 (object)['fieldname' => 'arthritis'],

From e0ff627ce5adc60ae3c3ef8aaf4d91fd991dd9cf Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 17:01:15 -0400
Subject: [PATCH 41/65] try

---
 test/unittests/NDB_BVL_Instrument_Test.php | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 0ab4feaaf9d..b22072be85c 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1733,6 +1733,9 @@ public function testValidateEmptyParameter(): void
      *
      * @covers NDB_BVL_Instrument::validate
      *
+     * @phan-suppress PhanUndeclaredProperty
+     * @phan-suppress PhanUndeclaredMethod
+     *
      * @return void
      */
     public function testValidateMissingRequiredKeys(): void
@@ -1743,9 +1746,7 @@ public function testValidateMissingRequiredKeys(): void
         /**
           * Phan-var
           *
-          * @phan-var      \NDB_BVL_Instrument $instrument
-          * @phan-suppress PhanUndeclaredProperty
-          * @phan-suppress PhanUndeclaredMethod
+          * @phan-var \NDB_BVL_Instrument $instrument
           */
 
         $instrument = $this->getMockBuilder(

From 1383e911ce521a9f6e1a29eec8c2051ed9b659e4 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Fri, 27 Jun 2025 17:16:02 -0400
Subject: [PATCH 42/65] try

---
 test/unittests/NDB_BVL_Instrument_Test.php | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index b22072be85c..20f2195908d 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -13,6 +13,7 @@
 namespace Loris\Tests;
 use \LORIS\Data\Scope;
 use \LORIS\Data\Cardinality;
+use \LORIS\Config;
 set_include_path(get_include_path().":" .  __DIR__  . "/../../php/libraries:");
 use PHPUnit\Framework\TestCase;
 require_once __DIR__ . '/../../vendor/autoload.php';
@@ -1840,7 +1841,7 @@ public function testValidateAdditionalKeys(): void
         $this->expectExceptionMessageMatches(
             '/Additional field\(s\) not permitted:.*aaa,bbb/'
         );
-
+        // phan-suppress-next-line PhanUndeclaredMethod
         $this->_instrument->validate($instrumentQuestions);
     }
 
@@ -1850,7 +1851,9 @@ public function testValidateAdditionalKeys(): void
      *
      * @covers NDB_BVL_Instrument::validate
      *
-     * @return void
+     * @phan-suppress PhanUndeclaredProperty
+     * @phan-suppress PhanUndeclaredMethod
+     * @return        void
      */
     public function testValidateValues(): void
     {
@@ -1863,7 +1866,7 @@ public function testValidateValues(): void
             ->disableOriginalConstructor()
             ->onlyMethods(["getFullName", "getSubtestList", "getDataDictionary"])
             ->getMock();
-
+        // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->_requiredElements = [
             'arthritis', 'hypertension', 'concussion_or_head_trauma'
         ];

From 8f536e67a435ee4bbb06c4ef7d635a990d9c8c24 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Sat, 28 Jun 2025 09:24:22 -0400
Subject: [PATCH 43/65] done

---
 test/unittests/NDB_BVL_Instrument_Test.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 20f2195908d..d0e100e3dfc 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -13,7 +13,6 @@
 namespace Loris\Tests;
 use \LORIS\Data\Scope;
 use \LORIS\Data\Cardinality;
-use \LORIS\Config;
 set_include_path(get_include_path().":" .  __DIR__  . "/../../php/libraries:");
 use PHPUnit\Framework\TestCase;
 require_once __DIR__ . '/../../vendor/autoload.php';
@@ -1907,8 +1906,9 @@ public function testValidateValues(): void
         $this->_instrument->table = 'medical_history';
         // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->commentID = 'commentID1';
+        '@phan-var \NDB_Config $mockConfig';
 
-        $mockConfig = $this->createMock(\LORIS\Config::class);
+        $mockConfig = $this->createMock(\NDB_Config::class);
         $mockConfig->method('getSetting')->with(
             'dateDisplayFormat'
         )->willReturn('Y-m-d');

From 562d36519a38e23fd3c6ed15bc2243752a6780dc Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Sat, 28 Jun 2025 09:34:36 -0400
Subject: [PATCH 44/65] done

---
 test/unittests/NDB_BVL_Instrument_Test.php | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index d0e100e3dfc..3e2d5571903 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1906,7 +1906,6 @@ public function testValidateValues(): void
         $this->_instrument->table = 'medical_history';
         // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->commentID = 'commentID1';
-        '@phan-var \NDB_Config $mockConfig';
 
         $mockConfig = $this->createMock(\NDB_Config::class);
         $mockConfig->method('getSetting')->with(

From 2b0a09c171a682d733c3a0fd8a881c6707b1c2c7 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Sat, 28 Jun 2025 10:00:39 -0400
Subject: [PATCH 45/65] done

---
 test/unittests/NDB_BVL_Instrument_Test.php | 59 ++++++++++++----------
 1 file changed, 33 insertions(+), 26 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 3e2d5571903..e06b53344eb 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1872,36 +1872,43 @@ public function testValidateValues(): void
 
         $instrumentQuestions = [
         // p1
-            "arthritis"                       => null, // required
-            "arthritis_age"                   => null,
-            "pulmonary_issues"                => null,
-            "pulmonary_issues_specific"       => null,
+            "arthritis"                       => 'string', // required
+            "arthritis_age"                   => 'string',
+            "pulmonary_issues"                => 'string',
+            "pulmonary_issues_specific"       => 'string',
         // p2
-            "hypertension"                    => null, // required
-            "hypertension_while_pregnant"     => null,
-            "hypertension_while_pregnant_age" => null,
+            "hypertension"                    => 'string', // required
+            "hypertension_while_pregnant"     => 'string',
+            "hypertension_while_pregnant_age" => 'string',
         // p3
-            "concussion_or_head_trauma"       => null, // required
-            "concussion_1_description"        => null,
-            "concussion_1_hospitalized"       => null,
-            "concussion_1_age"                => null,
-            "concussion_2_description"        => null,
-            "concussion_2_hospitalized"       => null,
-            "concussion_2_age"                => null,
-            "concussion_3_description"        => null,
-            "concussion_3_hospitalized"       => null,
-            "concussion_3_age"                => null,
-            "current_concussion_symptoms"     => null,
+            "concussion_or_head_trauma"       => 'string', // required
+            "concussion_1_description"        => 'string',
+            "concussion_1_hospitalized"       => 'string',
+            "concussion_1_age"                => 'string',
+            "concussion_2_description"        => 'string',
+            "concussion_2_hospitalized"       => 'string',
+            "concussion_2_age"                => 'string',
+            "concussion_3_description"        => 'string',
+            "concussion_3_hospitalized"       => 'string',
+            "concussion_3_age"                => 'string',
+            "current_concussion_symptoms"     => 'string',
         ];
 
-        $this->_instrument->method('getDataDictionary')->willReturn(
-            array_map(
-                fn($field) => (object)[
-                    'fieldname'   => $field, 'getDataType' => fn() => 'text'
-                ],
-                array_keys($instrumentQuestions)
-            )
-        );
+$this->_instrument->method('getDataDictionary')->willReturn(
+    array_map(
+        fn($field) => new class($field) {
+            public string $fieldname;
+            public function __construct($field) {
+                $this->fieldname = $field;
+            }
+            public function getDataType() {
+    return new \LORIS\Data\Types\StringType();
+            
+}
+        },
+        array_keys($instrumentQuestions)
+    )
+);
         // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->table = 'medical_history';
         // phan-suppress-next-line PhanUndeclaredProperty

From 656ac7d1e206f55810c4c6a5bd22c82445cbf441 Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Sat, 28 Jun 2025 10:19:46 -0400
Subject: [PATCH 46/65] todo rm dubug

---
 test/unittests/NDB_BVL_Instrument_Test.php | 44 ++++++++++++++--------
 1 file changed, 29 insertions(+), 15 deletions(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index e06b53344eb..0277d2920b3 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1894,21 +1894,35 @@ public function testValidateValues(): void
             "current_concussion_symptoms"     => 'string',
         ];
 
-$this->_instrument->method('getDataDictionary')->willReturn(
-    array_map(
-        fn($field) => new class($field) {
-            public string $fieldname;
-            public function __construct($field) {
-                $this->fieldname = $field;
-            }
-            public function getDataType() {
-    return new \LORIS\Data\Types\StringType();
-            
-}
-        },
-        array_keys($instrumentQuestions)
-    )
-);
+        $this->_instrument->method('getDataDictionary')->willReturn(
+            array_map(
+                fn($field) => new class($field) {
+                public string $fieldname;
+                /**
+                 * Constructor.
+                 *
+                 * @param {string} $field field
+                 *
+                 * @return void
+                 */
+                public function __construct($field)
+                {
+                                $this->fieldname = $field;
+                }
+                /**
+                 * GetDataType.
+                 *
+                 * @return void
+                 */
+                public function getDataType()
+                {
+                                return new \LORIS\Data\Types\StringType();
+
+                }
+                },
+                array_keys($instrumentQuestions)
+            )
+        );
         // phan-suppress-next-line PhanUndeclaredProperty
         $this->_instrument->table = 'medical_history';
         // phan-suppress-next-line PhanUndeclaredProperty

From a40f7eefde2db1e1e845ec838d9946c8ad9f412c Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Sat, 28 Jun 2025 10:30:25 -0400
Subject: [PATCH 47/65] todo rm dubug

---
 test/unittests/NDB_BVL_Instrument_Test.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 0277d2920b3..3e693851579 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1912,7 +1912,7 @@ public function __construct($field)
                 /**
                  * GetDataType.
                  *
-                 * @return void
+                 * @return \LORIS\Data\Types\StringType
                  */
                 public function getDataType()
                 {

From ed28579a05dd23b635bef6286b9849b3062ffb6e Mon Sep 17 00:00:00 2001
From: kongtiaowang <kongtiaowangshen@gmail.com>
Date: Wed, 2 Jul 2025 09:49:21 -0400
Subject: [PATCH 48/65] rm debug

---
 php/libraries/NDB_BVL_Instrument.class.inc | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index 79e2712c71e..aa9ec0b6284 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3028,11 +3028,6 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         // Note: additional fields are not an issue with JSON instruments
         // but only with instruments having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
-        error_log(print_r("11111111111111", true));
-        error_log(print_r($dataKeys, true));
-        error_log(print_r($defaultDataKeys, true));
-        error_log(print_r($additionalKeys, true));
-        error_log(print_r("22222222222222", true));
 
         if (!empty($additionalKeys)) {
             $i = implode(",", $additionalKeys);
@@ -3184,8 +3179,6 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      */
     public function validate(array $dataToCheck): void
     {
-        error_log("========");
-        error_log(print_r($dataToCheck, true));
         // data to check even exist
         if (empty($dataToCheck)) {
             throw new \LorisException("No data provided.");

From 4f4635f6359f6044a41335b20bb39d8de115daca Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 9 Jul 2025 11:14:17 -0400
Subject: [PATCH 49/65] handle PUT instrument flag endpoint - remove data_entry
 complete check

---
 .../endpoints/candidate/visit/instrument/flags.class.inc    | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
index 2152fd145b9..7f1ca946c87 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
@@ -156,12 +156,6 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
         $this->_instrumentStatus = new \NDB_BVL_InstrumentStatus($loris);
         $this->_instrumentStatus->select($this->_instrument->commentID);
 
-        if (!$this->_instrument->determineDataEntryAllowed()) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Can not update instruments that are flagged as complete.'
-            );
-        }
-
         $data = json_decode((string) $request->getBody(), true);
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(

From b4d4ccc64457ef8f16f0a40d7c121acf562119fd Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Wed, 9 Jul 2025 11:14:30 -0400
Subject: [PATCH 50/65] handle PATCH instrument flag endpoint - remove
 data_entry complete check

---
 .../endpoints/candidate/visit/instrument/flags.class.inc    | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
index 7f1ca946c87..73bf56ae392 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/flags.class.inc
@@ -221,12 +221,6 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
         $this->_instrumentStatus = new \NDB_BVL_InstrumentStatus($loris);
         $this->_instrumentStatus->select($this->_instrument->commentID);
 
-        if (!$this->_instrument->determineDataEntryAllowed()) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Can not update instruments that are flagged as complete.'
-            );
-        }
-
         $data = json_decode((string) $request->getBody(), true);
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(

From a1a4f5dc900582dac1b556973bcbe9af075dabbe Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 11:54:22 -0400
Subject: [PATCH 51/65] fusion instrument PATCH/PUT

---
 .../visit/instrument/instrument.class.inc     | 88 ++++++++-----------
 1 file changed, 39 insertions(+), 49 deletions(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index 8fa96149346..5b7c3bf0532 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -170,51 +170,7 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     private function _handlePUT(ServerRequestInterface $request) : ResponseInterface
     {
-        if (!$this->_instrument->determineDataEntryAllowed()) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Can not update instruments that are flagged as complete.'
-            );
-        }
-
-        $data = json_decode((string) $request->getBody(), true);
-        if (!is_array($data)) {
-            return new \LORIS\Http\Response\JSON\BadRequest(
-                'Invalid request'
-            );
-        }
-
-        // validate given data against the instrument
-        try {
-            $instrumentName = $this->_instrument->testName;
-            $this->_instrument->validate($data[$instrumentName] ?? []);
-        } catch (\LorisException $th) {
-            return new \LORIS\Http\Response\JSON\BadRequest(
-                "Could not update. {$th->getMessage()}"
-            );
-        } catch (\Throwable $th) {
-            error_log($th->getMessage());
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                "Could not update."
-            );
-        }
-
-        // update values
-        try {
-            $this->_instrument->clearInstrument();
-            $version = $request->getAttribute('LORIS-API-Version');
-            if ($version == 'v0.0.3') {
-                $instrumentname = $this->_instrument->testName;
-                $this->_instrument->_saveValues($data[$instrumentname]);
-            } else {
-                $this->_instrument->_saveValues($data['Data']);
-            }
-            $this->_instrument->score();
-            $this->_instrument->updateRequiredElementsCompletedFlag();
-        } catch (\Throwable $e) {
-            error_log($e->getMessage());
-            return new \LORIS\Http\Response\JSON\InternalServerError();
-        }
-        return (new \LORIS\Http\Response\JSON\NoContent());
+        return $this->_handlePATCHAndPUT($request);
     }
 
     /**
@@ -227,14 +183,39 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     private function _handlePATCH(ServerRequestInterface $request): ResponseInterface
     {
+        return $this->_handlePATCHAndPUT($request);
+    }
+
+    /**
+     * Handles a PUT and PATCH request.
+     * Mainly serves as a quick PATCH/PUT selection to validate all (PUT) or
+     * part (PATCH) of the sent payload.
+     *
+     * @param ServerRequestInterface $request The incoming PSR7 request
+     *
+     * @return ResponseInterface The outgoing PSR7 response
+     */
+    private function _handlePATCHAndPUT(
+        ServerRequestInterface $request
+    ): ResponseInterface {
+        // request type
+        $requestType = $request->getMethod();
+        if ($requestType !== "PATCH" && $requestType !== "PUT") {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                'Invalid request'
+            );
+        }
+        $isRequestPUT = $requestType === "PUT";
+
+        // data entry allowed?
         if (!$this->_instrument->determineDataEntryAllowed()) {
             return new \LORIS\Http\Response\JSON\Forbidden(
                 'Can not update instruments that are flagged as complete.'
             );
         }
 
+        // get payload
         $data = json_decode((string) $request->getBody(), true);
-
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
@@ -252,8 +233,10 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
                 : ($data['Data'] ?? []);
 
             // validate
-
-            $this->_instrument->validate($instrumentData);
+            $this->_instrument->validate(
+                $instrumentData,
+                $isRequestPUT
+            );
         } catch (\LorisException $th) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 "Could not update. {$th->getMessage()}"
@@ -265,7 +248,14 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             );
         }
 
+        // update values
         try {
+            // only clear if PUT
+            if ($isRequestPUT) {
+                $this->_instrument->clearInstrument();
+            }
+
+            // save/score data
             $this->_instrument->_saveValues($instrumentData);
             $this->_instrument->score();
             $this->_instrument->updateRequiredElementsCompletedFlag();
@@ -273,7 +263,7 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
             error_log($e->getMessage());
             return new \LORIS\Http\Response\JSON\InternalServerError();
         }
-        return (new \LORIS\Http\Response\JSON\NoContent());
+        return new \LORIS\Http\Response\JSON\NoContent();
     }
 
     /**

From 08efd43ada705055687c0411587daf01f69d4d97 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 11:55:37 -0400
Subject: [PATCH 52/65] instrument validate to check all or part of the payload
 values

---
 php/libraries/NDB_BVL_Instrument.class.inc | 27 ++++++++++++++--------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/php/libraries/NDB_BVL_Instrument.class.inc b/php/libraries/NDB_BVL_Instrument.class.inc
index aa9ec0b6284..c4bcb015fa4 100644
--- a/php/libraries/NDB_BVL_Instrument.class.inc
+++ b/php/libraries/NDB_BVL_Instrument.class.inc
@@ -3019,7 +3019,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
 
         // missing required fields
         $missingKeys = array_diff($defaultRequiredElements, $dataKeys);
-        if (!empty($missingKeys) && $_SERVER['REQUEST_METHOD'] !== 'PATCH') {
+        if (!empty($missingKeys)) {
             $i = implode(",", $missingKeys);
             throw new \LorisException("Missing required field(s): {$i}.");
         }
@@ -3028,7 +3028,6 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         // Note: additional fields are not an issue with JSON instruments
         // but only with instruments having their own table.
         $additionalKeys = array_diff($dataKeys, $defaultDataKeys);
-
         if (!empty($additionalKeys)) {
             $i = implode(",", $additionalKeys);
             throw new \LorisException("Additional field(s) not permitted: {$i}.");
@@ -3040,13 +3039,18 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      * Throw a LorisException if any check does not pass.
      *
      * @param array $instrumentData instrument data to check
+     * @param bool  $checkAllValues tells if all instrument field values should
+     *                              be checked (PUT) instead of part of them
+     *                              (PATCH)
      *
      * @throws \LorisException
      *
      * @return void
      */
-    private function _validateValues(array $instrumentData): void
-    {
+    private function _validateValues(
+        array $instrumentData,
+        bool $checkAllValues = false
+    ): void {
         // Get date format from system configuration
         $config     = $this->loris->getConfiguration();
         $dateFormat = $config->getSetting('dateDisplayFormat');
@@ -3081,7 +3085,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
             $fieldName = $dictionaryItem->fieldname;
 
             // Skip fields that are not present in PATCH input
-            if (!array_key_exists($fieldName, $instrumentData)) {
+            if (!$checkAllValues && !array_key_exists($fieldName, $instrumentData)) {
                 continue;
             }
 
@@ -3171,14 +3175,19 @@ abstract class NDB_BVL_Instrument extends NDB_Page
      * Validate whether the data submitted are valid against this instrument.
      * Checks both keys and values. Throws a LorisException if any test fails.
      *
-     * @param array $dataToCheck an array of values submitted
+     * @param array $dataToCheck    an array of values submitted
+     * @param bool  $checkAllValues tells if all instrument field values should
+     *                              be checked (PUT) instead of part of them
+     *                              (PATCH)
      *
      * @throws \LorisException
      *
      * @return void
      */
-    public function validate(array $dataToCheck): void
-    {
+    public function validate(
+        array $dataToCheck,
+        bool $checkAllValues = false
+    ): void {
         // data to check even exist
         if (empty($dataToCheck)) {
             throw new \LorisException("No data provided.");
@@ -3188,7 +3197,7 @@ abstract class NDB_BVL_Instrument extends NDB_Page
         $this->_validateKeys($dataToCheck);
 
         // validate the values against the instrument dictionary entries
-        $this->_validateValues($dataToCheck);
+        $this->_validateValues($dataToCheck, $checkAllValues);
     }
 
     /**

From 2a3002d5a34abfdaf7eff2e9e31cec51718cf3ff Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 13:27:22 -0400
Subject: [PATCH 53/65] instrument put test update

---
 raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php b/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php
index 95638214d3e..4df079e5bbf 100644
--- a/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php
+++ b/raisinbread/test/api/LorisApiInstruments_v0_0_3_Test.php
@@ -164,7 +164,7 @@ public function testPutCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             $this->instrumentTest => [
-               'consent' => "yes",
+                'consent' => "yes",
                 'testText' => 'test',
                 'testCheckbox' => 'true'
             ]
@@ -422,7 +422,9 @@ public function testPutCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             $this->instrumentTest => [
-                'testText' => "test Text"
+                'consent' => "yes",
+                'testText' => 'test text',
+                'testCheckbox' => 'true'
             ]
         ];
         $response   = $this->client->request(

From eed39e38e1a953c66e4ee98605f1d16bee7675e9 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:21:49 -0400
Subject: [PATCH 54/65] clear userid to var

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index dfe06ed3a3c..016eee9d998 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -224,7 +224,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
         ];
         $response = $this->client->request(
             'PATCH',
-            "candidates/587630/$this->visitTest/instruments/bmi",
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest",
             [
                 'headers' => $this->headers,
                 'json'    => $json

From 72539acbda32cb4fc418c1ed643f7783b91d5287 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:22:33 -0400
Subject: [PATCH 55/65] put instrument

---
 .../test/api/LorisApiInstrumentsTest.php      | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index 016eee9d998..983ecd95e47 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -237,6 +237,34 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
         $this->assertEmpty($body);
     }
 
+    /**
+     * Tests the HTTP PUT request for the
+     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}
+     *
+     * @return void
+     */
+    public function testPutCandidatesCandidVisitInstrumentsInstrument(): void
+    {
+        $json = [
+            'Data' => [
+                'height_cms' => 2
+            ]
+        ];
+        $response   = $this->client->request(
+            'PUT',
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest",
+            [
+                'headers' => $this->headers,
+                'json'    => $json
+            ]
+        );
+        $this->assertEquals(204, $response->getStatusCode());
+        // Verify the endpoint has a body
+        $body = $response->getBody();
+        $this->assertNotEmpty($body);
+
+    }
+
     /**
      * Tests the HTTP GET request for the
      * endpoint /candidates/{candid}/{visit}/instruments/{instruments}/flags

From 95631ca13a3e17b43041056017555514d3740a5b Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:22:46 -0400
Subject: [PATCH 56/65] trail end

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index 983ecd95e47..146fd2f3dd2 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -312,7 +312,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentFlags(): void
             'Flags' => [
                 'Data_entry'     => 'Complete',
                 'Administration' => 'All',
-                'Validity'       => 'Invalid' 
+                'Validity'       => 'Invalid'
             ]
         ];
         $response   = $this->client->request(
@@ -387,7 +387,7 @@ public function testPutCandidatesCandidVisitInstrumentsInstrumentFlags(): void
             'Flags' => [
                 'Data_entry'     => 'Complete',
                 'Administration' => 'Partial',
-                'Validity'       => 'Questionable' 
+                'Validity'       => 'Questionable'
             ]
         ];
         $response   = $this->client->request(

From e7010039d2cb6e902006159506cf91b5d378f59a Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:23:02 -0400
Subject: [PATCH 57/65] clear userid to var

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index 146fd2f3dd2..d1ebf69d4c2 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -475,7 +475,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
         ];
         $response   = $this->client->request(
             'PATCH',
-            "candidates/587630/$this->visitTest/instruments/bmi/dde",
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/bmi/dde",
             [
                 'headers' => $this->headers,
                 'json'    => $json

From bf1f386bd588466d7288743dc89aa9c7ec3251e3 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:23:32 -0400
Subject: [PATCH 58/65] put/patch dde flag

---
 .../test/api/LorisApiInstrumentsTest.php      | 112 ++++++++++++++++++
 1 file changed, 112 insertions(+)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index d1ebf69d4c2..f90731c6867 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -517,4 +517,116 @@ public function testGetCandidatesCandidVisitInstrumentsInstrumentDdeFlags():
         );
     }
 
+    /**
+     * Tests the HTTP PATCH request for the
+     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}/flag
+     *
+     * @return void
+     */
+    public function testPatchCandidVisitInstrumentsInstrumentDdeFlags(): void
+    {
+        $json       = [
+            'Meta'  => [
+                'Candidate'  => $this->candidTest,
+                'Visit'      => $this->visitTest,
+                'DDE'        => false,
+                'Instrument' => $this->instrumentTest
+            ],
+            'Flags' => [
+                'Data_entry'     => 'Complete',
+                'Administration' => 'All',
+                'Validity'       => 'Valid'
+            ]
+        ];
+        $response   = $this->client->request(
+            'PATCH',
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde/flags",
+            [
+                'headers' => $this->headers,
+                'json'    => $json
+            ]
+        );
+        $this->assertEquals(204, $response->getStatusCode());
+        // Verify the endpoint has a body
+        $body = $response->getBody();
+        $this->assertNotEmpty($body);
+
+        // This will test that it should be forbidden to modify an instrument that is flagged as Complete
+        $json = [
+            $this->instrumentTest => [
+                'UserID' => "2"
+            ]
+        ];
+        $response   = $this->client->request(
+            'PATCH',
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
+            [
+                'headers' => $this->headers,
+                'json'    => $json,
+                'http_errors' => false
+            ]
+        );
+        $this->assertEquals(403, $response->getStatusCode());
+        // Verify the endpoint has a body
+        $body = $response->getBody();
+        $this->assertNotEmpty($body);
+    }
+
+    /**
+     * Tests the HTTP PUT request for the
+     * endpoint /candidates/{candid}/{visit}/instruments/{instrument}
+     *
+     * @return void
+     */
+    public function testPutCandidVisitInstrumentsInstrumentDdeFlags(): void
+    {
+        $json       = [
+            'Meta'  => [
+                'Candidate'  => $this->candidTest,
+                'Visit'      => $this->visitTest,
+                'DDE'        => false,
+                'Instrument' => $this->instrumentTest
+            ],
+            'Flags' => [
+                'Data_entry'     => 'Complete',
+                'Administration' => 'All',
+                'Validity'       => 'Valid'
+            ]
+        ];
+        $response   = $this->client->request(
+            'PUT',
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde/flags",
+            [
+                'headers' => $this->headers,
+                'json'    => $json
+            ]
+        );
+        $this->assertEquals(204, $response->getStatusCode());
+        // Verify the endpoint has a body
+        $body = $response->getBody();
+        $this->assertNotEmpty($body);
+
+        // This will test that it should be forbidden to modify an instrument that is flagged as Complete
+        $json = [
+            $this->instrumentTest => [
+                'UserID' => "2"
+            ]
+        ];
+        $response   = $this->client->request(
+            'PUT',
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
+            [
+                'headers' => $this->headers,
+                'json'    => $json,
+                'http_errors' => false
+            ]
+        );
+        $this->assertEquals(403, $response->getStatusCode());
+        // Verify the endpoint has a body
+        $body = $response->getBody();
+        $this->assertNotEmpty($body);
+
+
+    }
+
 }

From 90523ecd111b4951259e4cf995864d4f744ca2da Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:41:04 -0400
Subject: [PATCH 59/65] remove bmi ref

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index f90731c6867..e0153805a5c 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -475,7 +475,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
         ];
         $response   = $this->client->request(
             'PATCH',
-            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/bmi/dde",
+            "candidates/$this->candidTest/$this->visitTest/instruments/$this->instrumentTest/dde",
             [
                 'headers' => $this->headers,
                 'json'    => $json

From 8fcf94d00ebbe93a3358deb0f0652d456dbcbd78 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 15:41:33 -0400
Subject: [PATCH 60/65] move data from bmi to testtest instrument

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index e0153805a5c..731f6156dd5 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -219,7 +219,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             'Data' => [
-                'height_cms' => 2
+                'UserID' => "2"
             ]
         ];
         $response = $this->client->request(
@@ -247,7 +247,7 @@ public function testPutCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             'Data' => [
-                'height_cms' => 2
+                'UserID' => "2"
             ]
         ];
         $response   = $this->client->request(
@@ -470,7 +470,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             'Data' => [
-                'height_cms' => 2
+                'UserID' => "2"
             ]
         ];
         $response   = $this->client->request(

From 0eb9414bb16f97866986943b6940b2d34726eaa3 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 16:18:13 -0400
Subject: [PATCH 61/65] v0.0.4 api put/patch update test

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index 731f6156dd5..63dd858fa77 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -219,7 +219,9 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             'Data' => [
-                'UserID' => "2"
+                'consent' => "yes",
+                'testText' => 'test text',
+                'testCheckbox' => 'true'
             ]
         ];
         $response = $this->client->request(
@@ -247,7 +249,9 @@ public function testPutCandidatesCandidVisitInstrumentsInstrument(): void
     {
         $json = [
             'Data' => [
-                'UserID' => "2"
+                'consent' => "yes",
+                'testText' => 'test text',
+                'testCheckbox' => 'true'
             ]
         ];
         $response   = $this->client->request(
@@ -470,7 +474,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             'Data' => [
-                'UserID' => "2"
+                'conset' => "yes"
             ]
         ];
         $response   = $this->client->request(

From d8ad01350aaa8b5cd83d844c4d953e6577c56ac3 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Thu, 24 Jul 2025 16:25:54 -0400
Subject: [PATCH 62/65] v0.0.4 api put/patch update test

---
 raisinbread/test/api/LorisApiInstrumentsTest.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/raisinbread/test/api/LorisApiInstrumentsTest.php b/raisinbread/test/api/LorisApiInstrumentsTest.php
index 63dd858fa77..a547b54240e 100644
--- a/raisinbread/test/api/LorisApiInstrumentsTest.php
+++ b/raisinbread/test/api/LorisApiInstrumentsTest.php
@@ -474,7 +474,7 @@ public function testPatchCandidatesCandidVisitInstrumentsInstrumentDde(): void
                 'Instrument' => $this->instrumentTest
             ],
             'Data' => [
-                'conset' => "yes"
+                'consent' => "yes"
             ]
         ];
         $response   = $this->client->request(

From 6a64fd3640deb6f70d12fe7098f6511f1bf03fb1 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Fri, 3 Oct 2025 08:43:51 -0400
Subject: [PATCH 63/65] remove server/request post mention

---
 test/unittests/NDB_BVL_Instrument_Test.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unittests/NDB_BVL_Instrument_Test.php b/test/unittests/NDB_BVL_Instrument_Test.php
index 3e693851579..c400592aa90 100644
--- a/test/unittests/NDB_BVL_Instrument_Test.php
+++ b/test/unittests/NDB_BVL_Instrument_Test.php
@@ -1742,7 +1742,7 @@ public function testValidateMissingRequiredKeys(): void
     {
         $this->_setUpMockDB();
         $this->_setTableData();
-        $_SERVER['REQUEST_METHOD'] = 'POST';
+
         /**
           * Phan-var
           *

From 004f42828584b74f97a938a31da0034f0051ef99 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Fri, 3 Oct 2025 10:12:43 -0400
Subject: [PATCH 64/65] including github action fix from #10034

---
 .github/workflows/loristest.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/loristest.yml b/.github/workflows/loristest.yml
index c45e52c7870..03f9a24cfa1 100644
--- a/.github/workflows/loristest.yml
+++ b/.github/workflows/loristest.yml
@@ -22,6 +22,7 @@ jobs:
       # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
       # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
         run: |
+          sudo apt-get update
           sudo apt install -y imagemagick-6-common libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 \
              libprotobuf-dev libprotobuf32t64 libprotoc32t64 protobuf-compiler          
           cd modules/electrophysiology_browser/jsx/react-series-data-viewer/
@@ -268,6 +269,7 @@ jobs:
       # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
       # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
       run: |
+        sudo apt-get update
         sudo apt install -y imagemagick-6-common libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 \
              libprotobuf-dev libprotobuf32t64 libprotoc32t64 protobuf-compiler
         cd modules/electrophysiology_browser/jsx/react-series-data-viewer/

From 0ba405377d4925446c7ed3846b5217c5d60e2268 Mon Sep 17 00:00:00 2001
From: regisoc <regis.ongaro-carcy@mcin.ca>
Date: Tue, 16 Dec 2025 17:17:23 -0500
Subject: [PATCH 65/65] trigger

---
 .../endpoints/candidate/visit/instrument/instrument.class.inc    | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
index 5b7c3bf0532..b7d8770d741 100644
--- a/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
+++ b/modules/api/php/endpoints/candidate/visit/instrument/instrument.class.inc
@@ -198,7 +198,6 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
     private function _handlePATCHAndPUT(
         ServerRequestInterface $request
     ): ResponseInterface {
-        // request type
         $requestType = $request->getMethod();
         if ($requestType !== "PATCH" && $requestType !== "PUT") {
             return new \LORIS\Http\Response\JSON\BadRequest(