Merge pre-release/2026-R2.1 into master

api/src/Authentication/Type/OIDC.php

@@ -132,8 +132,13 @@ function authenticateByCode($code)
             'samesite' => 'Strict'
         );
 
-        setcookie($cookie_key, $token, $cookieOpts);
-        return $this->getUser($token);
+        $user = $this->getUser($token);
+
+        if ($user) {
+            setcookie($cookie_key, $token, $cookieOpts);
+        }
+
+        return $user;
     }
 
     function logout()

api/src/Controllers/AuthenticationController.php

@@ -84,6 +84,8 @@ function check()
             {
                 $this->returnResponse(200, $this->generateJwtToken($userId));
             }
+        } else if ($userId === null) {
+            $this->returnError(403, 'User not recognised');
         }
         $this->returnError(400, 'No previous session');
     }
@@ -358,7 +360,7 @@ function authorise()
 
         if ($cas_sso) {
             header('Location: ' . $this->authenticateByType()->authorise());
-            $this->returnResponse(302, array('status' => "Redirecting to CAS"));
+            $this->returnResponse(302, array('status' => "Redirecting to provider"));
         } else {
             $this->returnError(501, "SSO not configured");
         }
@@ -379,7 +381,7 @@ function authenticateByCode()
             }
             $this->returnResponse(200, $this->generateJwtToken($fedid));
         } else {
-            $this->returnError(401, 'Invalid Credentials');
+            $this->returnError(403, 'User not recognised');
         }
     }
 

api/src/Page/DC.php

@@ -1212,24 +1212,6 @@ function _mca($id)
         $this->db->close();
 
         $data = array(array(), array());
-        if (file_exists($info['DAT'])) {
-            $dat = explode("\n", file_get_contents($info['DAT']));
-
-            foreach ($dat as $i => $d) {
-                if ($i > 2 && $d) {
-                    list($e, $v) = preg_split('/\s+/', trim($d));
-                    if ($i % 2 == 1) {
-                        if (floatval($e) <= $info['ENERGY']) {
-                            if (floatval($e) > ($info['ENERGY'] - 1100))
-                                array_push($data[1], array(floatval($e), floatval($v)));
-                            else
-                                array_push($data[0], array(floatval($e), floatval($v)));
-                        }
-                    }
-                }
-            }
-        }
-
 
         # pymca
         $results = str_replace('.mca', '.results.dat', preg_replace('/(data\/\d\d\d\d\/\w\w\d+-\d+)/', '\1/processed/pymca', $info['DIR']));
@@ -1238,22 +1220,56 @@ function _mca($id)
         $elements = array();
         $el_no_match = array();
         $max_counts = 0;
+        $line_number = 0;
+        $max_elements = 5;
+        $compton_cutoff = $info['ENERGY'] - 1100;
 
         if (file_exists($results)) {
             $dat = explode("\n", file_get_contents($results));
-            foreach ($dat as $i => $d) {
-                if ($i < 5) {
+            foreach ($dat as $d) {
+                if (empty($d) || strpos($d, '#') === 0) {
+                    if (strpos($d, 'COMPTON_CUTOFF_EV') !== false) {
+                        $parts = explode('COMPTON_CUTOFF_EV', $d);
+                        $compton_cutoff = floatval(trim($parts[1]));
+                    }
+                    continue;
+                }
+                if ($line_number < $max_elements) {
                     $l = explode(' ', $d);
-                    if ($i == 0)
+                    if ($line_number == 0) {
                         $max_counts = floatval($l[1]);
+                    }
                     if (array_key_exists($l[0], $el_to_en)) {
                         $els = $el_to_en[$l[0]];
                         $elements[$l[0]] = array(array_map('floatval', $els), floatval($l[1]), floatval($l[2]));
-                    } else
+                    } else {
                         array_push($el_no_match, $l[0]);
+                    }
+                    $line_number++;
+                } else {
+                    break;
                 }
             }
         }
+
+        if (file_exists($info['DAT'])) {
+            $dat = explode("\n", file_get_contents($info['DAT']));
+
+            foreach ($dat as $i => $d) {
+                if ($i > 2 && $d) {
+                    list($e, $v) = preg_split('/\s+/', trim($d));
+                    if ($i % 2 == 1) {
+                        if (floatval($e) <= $info['ENERGY']) {
+                            if (floatval($e) > $compton_cutoff)
+                                array_push($data[1], array(floatval($e), floatval($v)));
+                            else
+                                array_push($data[0], array(floatval($e), floatval($v)));
+                        }
+                    }
+                }
+            }
+        }
+
         array_push($data, $elements);
         array_push($data, $el_no_match);
         array_push($data, $max_counts);

api/src/Page/Process.php

@@ -435,9 +435,15 @@ function _pipelines() {
         $status = $this->has_arg('pipelinestatus') ? $this->arg('pipelinestatus') : null;
         $category = $this->has_arg('category') ? $this->arg('category') : null;
 
+        // allow more than one status
         if ($status) {
-            $where .= ' AND pp.pipelinestatus=:'.(sizeof($args)+1);
-            array_push($args, $this->arg('pipelinestatus'));
+            $status_queries = array();
+            $status_array = is_array($status) ? $status : array($status);
+            foreach ($status_array as $s) {
+                array_push($args, $s);
+                array_push($status_queries, 'pp.pipelinestatus=:' . count($args));
+            }
+            $where .= ' AND (' . implode(' OR ', $status_queries) . ')';
         }
         if ($category) {
             $where .= ' AND ppc.name=:'.(sizeof($args)+1);

api/src/Page/Processing.php

@@ -32,7 +32,7 @@ class Processing extends Page {
         'n' => '\d+',
         'sampleGroupId' => '\d+',
         'resultCount' => '\d+',
-        'pipeline' => '[\w\s\+]+',
+        'pipeline' => '\d+',
         'spacegroup' => '(\w|\s|\-|\/)+',
         'resolution' => '[\d\.]+',
         'completeness' => '[\d\.]+',
@@ -403,7 +403,7 @@ function _results_for_visit() {
 
         if ($this->has_arg('pipeline')) {
             $st = sizeof($args);
-            $where .= " AND app.processingprograms = :" . ($st + 1);
+            $where .= " AND app.processingpipelineid = :" . ($st + 1);
             array_push($args, $this->arg('pipeline'));
         }
 

api/src/Page/Proposal.php

@@ -156,7 +156,9 @@ function _get_proposals($id = null)
             array_push($args, $id);
         }
 
-        if ($this->staff) {
+        if ($this->user->hasPermission('all_dewars')) {
+            // allow to see shipments on all proposals
+        } else if ($this->staff) {
             if (!$this->user->hasPermission('super_admin')) {
                 $bls = array();
                 foreach ($this->user->perms as $p) {
@@ -172,8 +174,6 @@ function _get_proposals($id = null)
                 $where .= " AND (shp.personid=:" . (sizeof($args) + 1) . " OR s.beamlinename in ('" . implode("','", $bls) . "'))";
                 array_push($args, $this->user->personId);
             }
-        } else if ($this->user->hasPermission('all_dewars')) {
-            // allow to see shipments on all proposals
         } else {
             $where = " INNER JOIN session_has_person shp ON shp.sessionid = s.sessionid  " . $where;
             $where .= " AND shp.personid=:" . (sizeof($args) + 1);
@@ -919,7 +919,9 @@ function _lookup()
         $args = array();
 
 
-        if ($this->staff) {
+        if ($field == 'SHIPPINGID' && $this->user->hasPermission('all_dewars')) {
+            // allow to see shipments
+        } else if ($this->staff) {
             if (!$this->user->hasPermission('super_admin')) {
                 $bls = array();
                 foreach ($this->user->perms as $p) {
@@ -933,8 +935,6 @@ function _lookup()
 
                 $where .= " AND ses.beamlinename in ('" . implode("','", $bls) . "')";
             }
-        } else if ($field == 'SHIPPINGID' && $this->user->hasPermission('all_dewars')) {
-            // allow to see shipments
         } else {
             $where = " INNER JOIN session_has_person shp ON shp.sessionid = ses.sessionid  " . $where;
             $where .= " AND shp.personid=:" . (sizeof($args) + 1);

api/tests/Controllers/AuthenticationControllerTest.php

@@ -159,7 +159,7 @@ public function testCodeAuthenticationInitiallyFailsWhenAuthenticationTypeReturn
         });
 
         $this->assertContains('Content-Type: application/json', Output::$headers);
-        $this->assertContains('X-PHP-Response-Code: 401', Output::$headers);
+        $this->assertContains('X-PHP-Response-Code: 403', Output::$headers);
     }
 
     public function testCodeAuthenticationWhenGetValidFedIdReturnsSuccess(): void

client/src/js/app/store/modules/store.auth.js

@@ -125,7 +125,7 @@ const auth = {
           },
           error: function(req, status, error) {
             commit('authError')
-            reject(error)
+            reject(req)
           }, 
           complete: function() {
             commit('loading', false, { root: true })

client/src/js/app/views/login.vue

@@ -199,7 +199,7 @@ export default {
             .dispatch("auth/getToken", token)
             .then(() => this.$router.push(actualRedirectUrl))
             .catch((e) => {
-              if (e === "Forbidden") {
+              if (e.status === 403) {
                 this.authError = "not-recognised";
               }
             });

client/src/js/modules/dc/views/dcbase.js

@@ -87,6 +87,7 @@ define(['marionette',
             console.log('updateDCC', this.ui.dcglink, this.model)
             if (this.model.get('DCC') > 1) {
                 this.$el.find('li.group').show()
+                this.$el.find('.gridsize2').show()
                 this.$el.find('.dcglink').show()
                 this.$el.find('.dclink').hide()
                 this.$el.find('.reprocess').hide()
@@ -95,6 +96,7 @@ define(['marionette',
                 }
             } else {
                 this.$el.find('li.group').hide()
+                this.$el.find('.gridsize2').hide()
                 this.$el.find('.dcglink').hide()
                 this.$el.find('.dclink').show()
                 this.$el.find('.reprocess').show()

client/src/js/modules/dc/views/grid.js

@@ -46,6 +46,7 @@ define(['marionette',
       xrcholder: '.holder h1.xrc',
       apholder: '.holder h1.ap',
       gridsize: '.gridsize',
+      gridsize2: '.gridsize2',
     },
 
     toggleZoom: function(e) {
@@ -126,9 +127,8 @@ define(['marionette',
         if (this.ui.bx.text) this.ui.by.text((gi.get('DY_MM')*1000).toFixed(0))
 
         if (gi.get('STEPS_Y') > 10 && this.ui.zoom.show) this.ui.zoom.show()
-        var gridsize = gi.get('STEPS_X') + ' x ' + gi.get('STEPS_Y')
-        if (gi.get('STEPS_Z')) { gridsize += ' x ' + gi.get('STEPS_Z') }
-        this.ui.gridsize.html(gridsize)
+        this.ui.gridsize.html(gi.get('STEPS_X') + ' x ' + gi.get('STEPS_Y'))
+        if (gi.get('STEPS_Z')) { this.ui.gridsize2.html(' x ' + gi.get('STEPS_Z')) }
     },
 
     checkXRCandAP: function() {

client/src/js/modules/dc/views/summary.js

@@ -6,12 +6,14 @@ define(['backbone',
     'utils/table',
     'utils/kvcollection',
     'collections/spacegroups',
+    'collections/processingpipelines',
     'templates/dc/summary.html'], 
     function(Backbone, Marionette, Backgrid, TableView,
         utils,
         table,
         KVCollection,
         Spacegroups,
+        ProcessingPipelines,
         template) {
 
     var Pipelines = Backbone.Collection.extend(_.extend({
@@ -186,19 +188,20 @@ define(['backbone',
             this.updateData()
         },
 
+        updatePipelines: function() {
+            this.ui.pipeline.html('<option value="">All pipelines</option>'+this.processing_pipelines.opts())
+        },
+
         onRender: function() {
             this.showSpaceGroups()
 
-            this.pipelines = new Pipelines([
-                { NAME: 'Any', VALUE: '' },
-                { NAME: 'Xia2 DIALS', VALUE: 'xia2 dials' },
-                { NAME: 'Xia2 3dii', VALUE: 'xia2 3dii' },
-                { NAME: 'Fast DP', VALUE: 'fast_dp' },
-                { NAME: 'autoPROC', VALUE: 'autoPROC' },
-                { NAME: 'autoPROC+STARANISO', VALUE: 'autoPROC+STARANISO' },
-            ])
-
-            this.ui.pipeline.html(this.pipelines.opts())
+            this.processing_pipelines = new ProcessingPipelines()
+            this.processing_pipelines.fetch({
+                data: {
+                    category: 'processing',
+                    pipelinestatus: ['automatic', 'optional'],
+                }
+            }).done(this.updatePipelines.bind(this));
 
             var columns = [
                 { label: '', cell: table.TemplateCell, editable: false, template: '<a href="/dc/visit/'+this.visit+'/id/<%-ID%>" class="button button-notext"><i class="fa fa-search"></i> <span>View Data Collection</span></a>' },

client/src/js/modules/shipment/views/shipments.js

@@ -40,10 +40,12 @@ define(['marionette',
 
   return Marionette.LayoutView.extend({
     className: 'content',
-    template: '<div><h1>Shipments</h1><p class="help">This page shows a list of shipments associated with the currently selected proposal</p><p class="help">In order to register your samples you need to create a shipment. Shipments contain dewars, dewars contain containers, and containers individual samples. These can be created sequentially by viewing a particular shipment</p><div class="ra"><a class="button add" href="/shipments/add" data-testid="add-shipment-button"><i class="fa fa-plus"></i> Add Shipment</a></div><div class="wrapper"></div></div>',
+    template: '<div><h1>Shipments</h1><div id="ebic-banner" class="tw-hidden tw-my-4 tw-p-4 tw-bg-content-active tw-rounded tw-flex tw-justify-between"> <p class="tw-text-md"> eBIC is switching to SCAUP for shipments. <a id="ebic-link" href="">Click here to select a session and create a new shipment.</a></p></div><p class="help">This page shows a list of shipments associated with the currently selected proposal</p><p class="help">In order to register your samples you need to create a shipment. Shipments contain dewars, dewars contain containers, and containers individual samples. These can be created sequentially by viewing a particular shipment</p><div class="ra"><a class="button add" href="/shipments/add" data-testid="add-shipment-button"><i class="fa fa-plus"></i> Add Shipment</a></div><div class="wrapper"></div></div>',
     regions: { 'wrap': '.wrapper' },
     ui: {
       add: 'a.add',
+      ebicBanner: 'div#ebic-banner',
+      ebicLink: 'a#ebic-link'
     },
 
     initialize: function(options) {
@@ -71,6 +73,10 @@ define(['marionette',
     onRender: function() {
       if (app.proposal && app.proposal.get('ACTIVE') != 1) this.ui.add.hide()
 
+      if (app.proposal.get("TYPES").includes("em") && "em" in app.options.get("redirects")) {
+        this.ui.ebicBanner.show();
+        this.ui.ebicLink.prop("href", `${app.options.get("redirects").em }/proposals/${app.proposal.get("PROPOSAL")}`);
+      }
       this.wrap.show(this.table)
     }
   })

client/src/js/templates/dc/grid.html

@@ -13,7 +13,7 @@ <h1 class="title"></h1>
         <li>Transmission: <%-TRANSMISSION%>%</li>
         <li>Beamsize: <%-BSX%>x<%-BSY%>&mu;m</li>
         <li>Boxsize: <span class="boxx"></span>x<span class="boxy"></span>&mu;m</li>
-        <li>Grid scan size: <span class="gridsize"></span></li>
+        <li>Grid scan size: <span class="gridsize"></span><span class="gridsize2"></span></li>
         <li class="comment">Comment: <span class="COMMENTS"><%-COMMENTS%></span></li>
         <% if (!STATE) { %><li>Status: <span class="b">Stopped</span></li><% } %>