Merge pre-release/2025-R2.5 into master (#940)

* LIMS-1648: Only display auto proc program attachment files where deleted column is 0 (#921)

* LIMS-1400: Remove logon stats page (#916)

* LIMS-1702: Rename Archive button to Download Zip (#930)

* LIMS-1719: Fix data collection comments button (#931)

* LIMS-1694: Allow beamlines to disable user assignment of pucks (#925)

* LIMS-1687: Remove references to GridInfo.pixelsPerMicronX/Y (#926)

Author: ndg63276

api/config_sample.php

@@ -142,6 +142,8 @@
 
     # Visit directory on disk
     $visit_directory = '/dls/<%=BEAMLINENAME%>/data/<%=YEAR%>/<%=VISIT%>';
+    # If found ANYWHERE in a visit filePath the system will assume that any files there exist indefinitely
+    $visit_persist_storage_dir_segment = 'persistent/dir/name';
 
     # Diffraction image snapshots
     $jpeg_location = '<%=VISITDIR%>/jpegs/<%=IMDIRECTORY%>/<%=IMFILE%>.jpeg';
@@ -220,6 +222,8 @@
     $facility_contact = "A person";
     $facility_phone = "01234 567890";
     $facility_email = "stores@facility.co.uk";
+    # Append to find logs/files etc once they have been moved to cold storage
+    $icat_base_url = "https://icat.yourFacility.ac.uk";
 
     // List of domestic free countries
     $facility_courier_countries = array('United Kingdom');
@@ -375,6 +379,11 @@
         'i03' => "BL03I-MO-ROBOT-01:PUCK_%02d_NAME"
     );
 
+    $only_staff_can_assign = array(
+        'i03' => False,
+        'i04' => False,
+    );
+
     # Dials server values
     $dials_rest_url = "";
     $dials_rest_jwt = "";

api/docs/db/DataCollections.md

@@ -89,8 +89,8 @@ steps_x | int | Number of steps in x in the grid scan
 steps_y | int | Number of steps in y in the grid scan
 snapshot_offsetxpixel | int | Number of pixels from top left of the snapshot image in x to where the top left of the grid starts
 snapshot_offsetypixel | int | Number of pixels from top left of the snapshot image in y to where the top left of the grid starts
-pixelspermicronx | float | Confusingly, microns per pixel. Physical size of the pixel in x in microns
-pixelspermicrony | float | Confusingly, microns per pixel. Physical size of the pixel in y in microns
+micronsperpixelx | float | Physical size of the pixel in x in microns
+micronsperpixely | float | Physical size of the pixel in y in microns
 
 This allows the snapshot to be cropped to the correct location and the grid to be navigatable by click to show an resulting diffraction image. The results from Per Image Analysis are then merged on top as a heatmap.
 

api/docs/definitions/gridinfo.yaml

@@ -40,13 +40,13 @@ properties:
     type: string
     description: Number of steps in x
     example: 10
-  PIXELSPERMICRONX:
+  MICRONSPERPIXELX:
     type: string
-    description: Pixels per micron in x for snapshot
+    description: Microns per pixel in x for snapshot
     example: 1.2200000286102
-  PIXELSPERMICRONY:
+  MICRONSPERPIXELX:
     type: string
-    description: Pixels per micron in y for snapshot
+    description: Microns per pixel in y for snapshot
     example: 1.1900000572205
   SNAPSHOT_OFFSETXPIXEL:
     type: string
@@ -62,4 +62,4 @@ properties:
     example: horizontal
     enum:
       - horizontal
-      - vertical
+      - vertical

api/docs/dist/spec.json

@@ -5947,14 +5947,14 @@
           "description": "Number of steps in x",
           "example": 10
         },
-        "PIXELSPERMICRONX": {
+        "MICRONSPERPIXELX": {
           "type": "string",
-          "description": "Pixels per micron in x for snapshot",
+          "description": "Microns per pixel in x for snapshot",
           "example": 1.2200000286102
         },
-        "PIXELSPERMICRONY": {
+        "MICRONSPERPIXELY": {
           "type": "string",
-          "description": "Pixels per micron in y for snapshot",
+          "description": "Microns per pixel in y for snapshot",
           "example": 1.1900000572205
         },
         "SNAPSHOT_OFFSETXPIXEL": {

api/index.php

@@ -68,11 +68,12 @@ function setupApplication($mode): Slim
 
     $app->get('/options', function () use ($app) {
         global $motd, $authentication_type, $cas_url, $cas_sso, $sso_url, $package_description,
-            $facility_courier_countries, $facility_courier_countries_nde, $facility_courier_countries_link,
-            $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
+            $facility_courier_countries, $facility_courier_countries_nde, $facility_courier_countries_link, $icat_base_url,
+            $visit_persist_storage_dir_segment, $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $synchweb_version, $redirects,
             $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments,
-            $dials_rest_url_rings, $closed_proposal_link, $ccp4_cloud_upload_url;
+            $dials_rest_url_rings, $closed_proposal_link, $ccp4_cloud_upload_url,
+            $only_staff_can_assign;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -85,6 +86,8 @@ function setupApplication($mode): Slim
             'facility_courier_countries' => $facility_courier_countries,
             'facility_courier_countries_nde' => $facility_courier_countries_nde,
             'facility_courier_countries_link' => $facility_courier_countries_link,
+            'icat_base_url' => $icat_base_url,
+            'visit_persist_storage_dir_segment' => $visit_persist_storage_dir_segment,
             'dhl_enable' => $dhl_enable,
             'scale_grid' => $scale_grid,
             'scale_grid_end_date' => $scale_grid_end_date,
@@ -98,7 +101,8 @@ function setupApplication($mode): Slim
             'closed_proposal_link' => $closed_proposal_link,
             'dials_rest_url_rings' => $dials_rest_url_rings,
             'ccp4_cloud_upload_url' => $ccp4_cloud_upload_url,
-            'redirects' => $redirects
+            'redirects' => $redirects,
+            'only_staff_can_assign' => $only_staff_can_assign
         )));
     });
     return $app;

api/src/Controllers/AssignController.php

@@ -31,12 +31,17 @@ function __construct(Slim $app, $db, $user, AssignData $assignData)
 
     function assignContainer()
     {
+        global $only_staff_can_assign;
         $cs = $this->assignData->getContainer($this->arg('visit'), $this->arg('cid'));
-
         if (sizeof($cs) > 0)
         {
-            $this->assignData->assignContainer($cs[0], $this->arg('pos'));
-            $this->_output(1);
+            $bl = $cs[0]['BEAMLINENAME'];
+            if (is_array($only_staff_can_assign) && array_key_exists($bl, $only_staff_can_assign) && $only_staff_can_assign[$bl] == true && !$this->staff) {
+                $this->_error("Only staff can assign containers on this beamline");
+            } else {
+                $this->assignData->assignContainer($cs[0], $this->arg('pos'));
+                $this->_output(1);
+            }
         }
         else
         {
@@ -46,12 +51,18 @@ function assignContainer()
 
     function unassignContainer()
     {
+        global $only_staff_can_assign;
         $cs = $this->assignData->getContainer($this->arg('visit'), $this->arg('cid'));
 
         if (sizeof($cs) > 0)
         {
-            $this->assignData->unassignContainer($cs[0]);
-            $this->_output(1);
+            $bl = $cs[0]['BEAMLINENAME'];
+            if (is_array($only_staff_can_assign) && array_key_exists($bl, $only_staff_can_assign) && $only_staff_can_assign[$bl] == true && !$this->staff) {
+                $this->_error("Only staff can unassign containers on this beamline");
+            } else {
+                $this->assignData->unassignContainer($cs[0]);
+                $this->_output(1);
+            }
         }
         else
         {

api/src/Database/Type/MySQL.php

@@ -80,16 +80,6 @@ class MySQL extends DatabaseParent {
         'Protein_has_PDB',
         'ExperimentType',
 
-        // Stat Views
-        'v_logonByHour',
-        'v_logonByMonthDay',
-        'v_logonByWeek',
-        'v_logonByWeekDay',
-        'v_logonByHour2',
-        'v_logonByMonthDay2',
-        'v_logonByWeek2',
-        'v_logonByWeekDay2',
-
         // Projects
         'Project',
         'Project_has_User',

api/src/Page/DC.php

@@ -474,6 +474,7 @@ function _data_collections($single = null)
                     d.numberofpixelsx as detectornumberofpixelsx,
                     d.numberofpixelsy as detectornumberofpixelsy,
                     ses.archived,
+                    ses.purgedProcessedData,
                     IFNULL(dc.rotationaxis, 'Omega') as rotationaxis,
                     dc.detector2theta";
             $groupby = 'GROUP BY smp.name,
@@ -611,6 +612,7 @@ function _data_collections($single = null)
                     max(d.numberofpixelsx) as detectornumberofpixelsx,
                     max(d.numberofpixelsy) as detectornumberofpixelsy,
                     max(ses.archived) as archived,
+                    max(ses.purgedProcessedData) as purgedProcessedData,
                     IFNULL(max(dc.rotationaxis), 'Omega') as rotationaxis,
                     dc.detector2theta";
             $groupby = "GROUP BY dc.datacollectiongroupid";
@@ -771,6 +773,7 @@ function _data_collections($single = null)
                     '',
                     '',
                     ses.archived,
+                    ses.purgedProcessedData,
                     '',
                     ''
                 FROM energyscan es
@@ -867,6 +870,7 @@ function _data_collections($single = null)
                 '',
                 '',
                 ses.archived,
+                ses.purgedProcessedData,
                 '',
                 ''
             FROM xfefluorescencespectrum xrf
@@ -963,6 +967,7 @@ function _data_collections($single = null)
                 '',
                 '',
                 ses.archived,
+                ses.purgedProcessedData,
                 '',
                 ''
             FROM robotaction r
@@ -1461,7 +1466,7 @@ function _null_or($field, $conversion)
     # Grid Scan Info
     function _grid_info()
     {
-        $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid, dc.axisstart, p.posx as x, p.posy as y, p.posz as z, g.dx_mm, g.dy_mm, g.steps_x, g.steps_y, g2.steps_y as steps_z, IFNULL(g.micronsperpixelx,g.pixelspermicronx) as micronsperpixelx, IFNULL(g.micronsperpixely,g.pixelspermicrony) as micronsperpixely, g.snapshot_offsetxpixel, g.snapshot_offsetypixel, g.orientation, g.snaked, DATE_FORMAT(dc.starttime, '%Y%m%d') as startdate, xrc.status as xrcstatus, xrcr.xraycentringresultid
+        $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid, dc.axisstart, p.posx as x, p.posy as y, p.posz as z, g.dx_mm, g.dy_mm, g.steps_x, g.steps_y, g2.steps_y as steps_z, g.micronsperpixelx, g.micronsperpixely, g.snapshot_offsetxpixel, g.snapshot_offsetypixel, g.orientation, g.snaked, DATE_FORMAT(dc.starttime, '%Y%m%d') as startdate, xrc.status as xrcstatus, xrcr.xraycentringresultid
                 FROM gridinfo g
                 INNER JOIN datacollection dc on (dc.datacollectionid = g.datacollectionid) or (dc.datacollectiongroupid = g.datacollectiongroupid)
                 LEFT OUTER JOIN position p ON dc.positionid = p.positionid

api/src/Page/Stats.php

@@ -16,7 +16,6 @@ class Stats extends Page
 
         public static $dispatch = array(array('/online', 'get', '_online_users'),
                               array('/last', 'get', '_last_actions'),
-                              array('/logon(/:t)', 'get', '_logons'),
                               array('/bl(/:t)', 'get', '_beamline'),
                               array('/pl(/:t)', 'get', '_pipelines'),
                               array('/pc', 'get', '_processing'),
@@ -45,46 +44,8 @@ function _last_actions() {
 
             $this->_output($rows);            
         }
-        
-        
-        function _logons() {
-            $days = array('Mon', 'Tue', 'Wed', 'Thu', 'Fri', 'Sat', 'Sun');
-            
-            $ty = $this->has_arg('t') ? $this->arg('t') : 'hour';
-            
-            $types = array('hour' => array('hour', 'hour'), 'wd' => array('day', 'weekday'), 'week' => array('week', 'week'), 'md' => array('day', 'monthday'));
-            
-            $k = array_key_exists($ty, $types) ? $ty : 'hour';
-            $t = $types[$k];
-            
-            $rows = $this->db->pq("SELECT $t[0] as k, \"Total logins\" as t, \"Distinct logins\" as d FROM v_logonby${t[1]}2");
-            
-            $out = array(array('label' => 'Total (ISPyB)', 'color' => 'red', 'data' => array()), array('label' => 'Unique (ISPyB)', 'color' => 'orange', 'data' => array()),
-                         array('label' => 'Total (ISPyB2)', 'color' => 'blue', 'data' => array()), array('label' => 'Unique (ISPyB2)', 'color' => 'cyan', 'data' => array())
-                         );
-            
-            foreach ($rows as $r) {
-                if ($k == 'wd') $r['K'] = array_search($r['K'], $days);
-                
-                array_push($out[2]['data'], array(intval($r['K']), intval($r['T'])));
-                array_push($out[3]['data'], array(intval($r['K']), intval($r['D'])));
-            }
-            
-            // $rows = $this->db->pq("SELECT $t[0] as k, \"Total logins\" as t, \"Distinct logins\" as d FROM v_logonby${t[1]}");
-            // foreach ($rows as $r) {
-            //     if ($k == 'wd') $r['K'] = array_search($r['K'], $days);
-                
-            //     array_push($out[0]['data'], array(intval($r['K']), intval($r['T'])));
-            //     array_push($out[1]['data'], array(intval($r['K']), intval($r['D'])));
-            // }
-            
-            $this->_output($out);
-            
-        }
-        
-        
-        
-        
+
+
         // Dispatch to beamline stats
         function _beamline() {
             $types = array('dc' => '_all_dcs',

api/tests/Controllers/AssignControllerTest.php

@@ -51,6 +51,8 @@ protected function setUp(): void
         );
         global $bl_pv_env;
         $bl_pv_env = 'EPICS_CA_ADDR_LIST_TEST=666.45.678.9';
+        global $only_staff_can_assign;
+        $only_staff_can_assign = array();
     }
 
     protected function tearDown(): void