Merge pre-release/2025-R5.3 into master (#1014)

* LIMS-1983: Update phpCAS and php-jwt (#1005)

* LIMS-1970: Fix Logs & Files view if filepath is null (#1004)

* LIMS-1962: Allow downloading of html files (#1006)

* LIMS-1431 - Display Metal Id downstream pipeline (#1003)

* LIMS-1854: Prevent submission of multiple reprocessing jobs (#1009)

* LIMS-1956: Add dewar names and serial nos to shipment requests (#1000)

* Fix unit tests (#1015)

Author: ndg63276

.github/workflows/ci.yml

@@ -19,7 +19,6 @@ defaults:
     shell: bash
     working-directory: ./api
 
-# Note, jobs do not share the same working environment, whereas steps do.  Also, jobs will run in parallel unless the 'needs' tag is used to flag a dependency    
 jobs:
   php-build:
     name: Checkout, build, test and lint PHP code
@@ -33,6 +32,9 @@ jobs:
         with:
           php-version: 7.3
           tools: psalm:4
+          # Added extensions and coverage here so they are ready for the native run
+          extensions: mysqli, zip, xdebug
+          coverage: xdebug
 
       - name: Validate composer.json and composer.lock
         run: composer validate
@@ -49,17 +51,12 @@ jobs:
       - name: Install dependencies
         run: composer install --prefer-dist --no-progress
 
+      # CHANGED: Replaced php-actions/phpunit with native execution
+      # This runs the PHPUnit located in your vendor folder, avoiding the PHAR crash
       - name: PHPUnit Tests
-        uses: php-actions/phpunit@v3
+        run: vendor/bin/phpunit --configuration tests/phpunit.xml --coverage-text
         env:
           XDEBUG_MODE: coverage
-        with:
-          bootstrap: api/vendor/autoload.php
-          configuration: api/tests/phpunit.xml
-          php_extensions: xdebug mysqli zip
-          args: --coverage-text
-          php_version: 7.3
-          version: 9
 
       - name: Run Psalm
         run: psalm --output-format=github
@@ -77,8 +74,7 @@ jobs:
           node-version: 18.x
       - name: JavaScript build, lint and test
         working-directory: ./client
-        # hack the output from the linting steps to avoid these stopping the builds - we are not going to get 
-        # to a clean output without considerable effort, but it's useful to see the output
+        # hack the output from the linting steps to avoid these stopping the builds
         run: |
               cp src/js/config_sample.json src/js/config.json
               node --version

api/composer.json

@@ -14,9 +14,9 @@
     }
   ],
   "require": {
-    "apereo/phpcas": "1.3.8",
+    "apereo/phpcas": "1.6.1",
     "ezyang/htmlpurifier": "4.12.0",
-    "firebase/php-jwt": "2.2.0",
+    "firebase/php-jwt": "6.0.0",
     "jdorn/sql-formatter": "1.2.9",
     "mpdf/mpdf": "8.1.2",
     "ralouphie/getallheaders": "2.0.5",

api/config_sample.php

@@ -264,7 +264,6 @@
     $use_shipping_service_incoming_shipments = null;
     $use_shipping_service_redirect = null;
     $use_shipping_service_redirect_incoming_shipments = null;
-    $shipping_service_api_url = null;
     $shipping_service_api_user = null;
     $shipping_service_api_password = null;
     $shipping_service_app_url = null;

api/src/Authentication/Type/CAS.php

@@ -27,7 +27,13 @@ function check()
         /**
          * @psalm-suppress UndefinedConstant define in CAS.php
          */
-        phpCAS::client(CAS_VERSION_2_0, $cas_url, 443, '/cas');
+        $protocol = 'http';
+        if (isset($_SERVER['HTTPS']) && $_SERVER['HTTPS'] === 'on') {
+            $protocol = 'https';
+        }
+        $hostname = $_SERVER['HTTP_HOST'];
+        $service_base_url = $protocol . '://' . $hostname;
+        phpCAS::client(CAS_VERSION_2_0, $cas_url, 443, '/cas', $service_base_url);
         phpCAS::setCasServerCACert($cacert);
 
         try {

api/src/Controllers/AuthenticationController.php

@@ -3,7 +3,8 @@
 namespace SynchWeb\Controllers;
 
 use Exception;
-use JWT;
+use Firebase\JWT\JWT;
+use Firebase\JWT\Key;
 use Slim\Slim;
 use SynchWeb\Model\User;
 
@@ -280,7 +281,7 @@ private function checkForAndValidateAuthenticationToken()
 
             try
             {
-                $token = JWT::decode($jwt, $jwt_key, array('HS512'));
+                $token = JWT::decode($jwt, new Key($jwt_key, 'HS512'), array('HS512'));
                 $this->loginId = $token->data->login;
             }
             catch (\Exception $e)

api/src/Downstream/Type/Dimple.php

@@ -22,22 +22,12 @@ function _get_blobs() {
         );
     }
 
-    # This will break if dimple is run more than once on the same scalingid
-    # TODO: Change structure of MXMRRun to link to autoprocprogram
-    # https://jira.diamond.ac.uk/browse/SCI-7941
     function _find_mrrun() {
-        if (!array_key_exists("scaling_id", $this->process['PARAMETERS'])) {
-            return;
-        }
-
         $mrrun = $this->db->pq(
-            "SELECT mxmrrunid, processingstatus, processingmessage, 
-            rvaluestart, rvalueend, rfreevaluestart, rfreevalueend
+            "SELECT m.mxmrrunid
             FROM mxmrrun m
-            INNER JOIN autoprocprogram app
-            ON m.autoprocprogramid = app.autoprocprogramid
-            WHERE autoprocscalingid=:1",
-            array($this->process['PARAMETERS']["scaling_id"])
+            WHERE m.autoprocprogramid=:1",
+            array($this->autoprocprogramid)
         );
 
         if (!sizeof($mrrun)) {

api/src/Downstream/Type/MetalId.php

@@ -0,0 +1,80 @@
+<?php
+
+namespace SynchWeb\Downstream\Type;
+
+use SynchWeb\Downstream\DownstreamPlugin;
+use SynchWeb\Downstream\DownstreamResult;
+
+class MetalId extends DownstreamPlugin {
+    var $has_images = true;
+    var $friendlyname = 'Metal Id';
+    var $has_mapmodel = array(0, 0);
+    var $_mrrun;
+
+    function results() {
+        $blobs = $this->_get_blobs();
+        if (sizeof($blobs)) {
+            $headings = array('Peak', 'Height', 'XYZ');
+        } else {
+            $headings = array('No peaks found');
+        }
+        $peaks = array($headings);
+        foreach($blobs as $n => $blob) {
+            $peak = array($n+1, $blob['HEIGHT'], '('.$blob['X'].', '.$blob['Y'].', '.$blob['Z'].')');
+            array_push($peaks, $peak);
+        }
+        $dat = array();
+        $dat['BLOBS'] = sizeof($blobs);
+        $dat['PEAKS'] = $peaks;
+
+        $integrator = $this->_lookup_autoproc(
+            null,
+            $this->process['PARAMETERS']['scaling_id']
+        );
+        if ($integrator) {
+            $dat['PARENTAUTOPROCPROGRAM'] = $integrator['PROCESSINGPROGRAMS'];
+            $dat['PARENTAUTOPROCPROGRAMID'] = $integrator['AUTOPROCPROGRAMID'];
+        }
+
+        $results = new DownstreamResult($this);
+        $results->data = $dat;
+
+        return $results;
+    }
+
+    function _find_mrrun() {
+        $mrrun = $this->db->pq(
+            "SELECT m.mxmrrunid
+            FROM mxmrrun m
+            WHERE m.autoprocprogramid=:1",
+            array($this->autoprocprogramid)
+        );
+
+        if (!sizeof($mrrun)) {
+            return;
+        }
+
+        $this->_mrrun = $mrrun[0];
+        return true;
+    }
+
+    function _get_blobs() {
+        if (!$this->_find_mrrun()) {
+            return array();
+        }
+        return $this->db->pq(
+            "SELECT view1, filepath, x, y, z, height
+            FROM mxmrrunblob
+            WHERE mxmrrunid = :1
+            AND filepath is not NULL",
+            array($this->_mrrun["MXMRRUNID"])
+        );
+    }
+
+    function images($n = 0) {
+        $blobs = $this->_get_blobs();
+        if ($n < sizeof($blobs)) {
+            return $blobs[$n]["FILEPATH"] . '/' . $blobs[$n]["VIEW1"];
+        }
+    }
+}

api/src/Page/Download.php

@@ -268,8 +268,8 @@ function _get_file($id, $file)
             $response->headers->set("Content-Length", filesize($filename));
         } elseif ($filesystem->exists($filename.'.gz')) {
             $filename = $filename.'.gz';
-            if ($this->arg('download') == 1) {
-                // View log file, so unzip and serve
+            if ($this->has_arg('download') && $this->arg('download') < 3) {
+                // View/open file, so unzip and serve
                 $response = new Response(readgzfile($filename));
                 $this->set_mime_content($response, $file['FILENAME'], $id);
             } else {
@@ -549,21 +549,20 @@ function set_mime_content($response, $filename, $prefix = null)
 
         if (in_array($path_ext, array('html', 'htm'))) {
             $response->headers->set("Content-Type", "text/html");
-            $this->_set_disposition_inline($response);
         } elseif ($path_ext == 'pdf') {
             $response->headers->set("Content-Type", "application/pdf");
-            $this->_set_disposition_attachment($response, $saved_filename);
         } elseif ($path_ext == 'png') {
             $response->headers->set("Content-Type", "image/png");
-            $this->_set_disposition_attachment($response, $saved_filename);
         } elseif (in_array($path_ext, array('jpg', 'jpeg'))) {
             $response->headers->set("Content-Type", "image/jpeg");
-            $this->_set_disposition_attachment($response, $saved_filename);
-        } elseif (in_array($path_ext, array('log', 'txt', 'error', 'LP', 'json', 'lsa'))) {
+        } elseif (in_array($path_ext, array('log', 'txt', 'error', 'LP', 'json', 'lsa', 'lst'))) {
             $response->headers->set("Content-Type", "text/plain");
-            $this->_set_disposition_inline($response);
         } else {
             $response->headers->set("Content-Type", "application/octet-stream");
+        }
+        if ($this->has_arg('download') && $this->arg('download') < 3) {
+            $this->_set_disposition_inline($response);
+        } else {
             $this->_set_disposition_attachment($response, $saved_filename);
         }
     }

api/src/Page/Process.php

@@ -383,7 +383,7 @@ function _enqueue()
         );
         $this->_send_zocalo_message($rabbitmq_zocalo_vhost, $message);
 
-        $this->_output(new \stdClass);
+        $this->_output('Job successfully submitted');
     }
 
     function _enqueue_downstream()
@@ -413,7 +413,7 @@ function _enqueue_downstream()
 
         $this->_submit_zocalo_recipe($this->arg('RECIPE'), $parameters);
 
-        $this->_output(new \stdClass);
+        $this->_output('Job successfully submitted');
     }
 
     /*