Merge pre-release/2024-R4.2 into master

api/assets/emails/html/dewar-dispatch-lite.html

@@ -1,4 +1,4 @@
-<h1 style="font-size: 16px; font-weight: normal; border-bottom: 1px solid #000; margin: 1%; margin-bottom: 1.5%">Dewar ready to leave diamond</h1>
+<h1 style="font-size: 16px; font-weight: normal; border-bottom: 1px solid #000; margin: 1%; margin-bottom: 1.5%">Dewar ready to leave Diamond</h1>
 
 <div class="inset" style="margin: 1%; padding: 1%; margin-bottom: 2%; border-radius: 5px; background: #82d180">
 	Goods Handling, please arrange dispatch of the following Dewar.

api/config_sample.php

@@ -155,6 +155,9 @@
     # Server log location
     $server_log = '/dls_sw/<%=BEAMLINENAME%>/logs/gda-server.log';
 
+    # Path to ccp4 location
+    $ccp4_location = '/dls_sw/apps/ccp4/latest/ccp4-9';
+
     # Email addresses, comma separate for multiple recepients
     # - Email templates in assets/emails in plain and html/ format
 
@@ -239,6 +242,8 @@
     $facility_courier_countries = array('United Kingdom');
     // List of non dom eu free countries
     $facility_courier_countries_nde = array('France', 'Italy', 'Spain');
+    // Link to help with international shipments
+    $facility_courier_countries_link = '';
     $package_description = 'Dry shipper containing frozen crystals';
     $dewar_weight = 18;
 

api/index.php

@@ -68,7 +68,7 @@ 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, $facility_courier_countries_nde, $facility_courier_countries_link,
             $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $ifsummary, $synchweb_version, $redirects,
             $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments;
@@ -83,6 +83,7 @@ function setupApplication($mode): Slim
             'package_description' => $package_description,
             'facility_courier_countries' => $facility_courier_countries,
             'facility_courier_countries_nde' => $facility_courier_countries_nde,
+            'facility_courier_countries_link' => $facility_courier_countries_link,
             'dhl_enable' => $dhl_enable,
             'scale_grid' => $scale_grid,
             'scale_grid_end_date' => $scale_grid_end_date,

api/scripts/mtz2map.sh

@@ -2,19 +2,6 @@
 
 cd /tmp
 
-# If you are running with the module system, load ccp4
-#. /etc/profile.d/modules.sh
-#module load ccp4
-
-# If not, define the environment variables required below
-#export CCP4_MASTER=/dls_sw/apps/ccp4/<ccp4 version>
-export CCP4_MASTER=/dls_sw/apps/ccp4/latest/ccp4-8.0
-export CINCL=$CCP4_MASTER/include
-export CLIBD=$CCP4_MASTER/lib/data
-
-export CCP4_SCR=/tmp
-export root=$CCP4_MASTER/bin
-
 if [ -f $1 ]; then
 	mtz=$1
 else
@@ -41,6 +28,14 @@ else
 	fi
 fi
 
+#export CCP4_MASTER=/dls_sw/apps/ccp4/<ccp4 version>
+export CCP4_MASTER=$5
+export CINCL=$CCP4_MASTER/include
+export CLIBD=$CCP4_MASTER/lib/data
+
+export CCP4_SCR=/tmp
+export root=$CCP4_MASTER/bin
+
 if [ $3 == 'dimple' ]; then
 
 	if $root/mtzinfo $mtz | grep -q PH2FOFCWT; then

api/src/Authentication/AuthenticationParent.php

@@ -16,4 +16,6 @@ public function check();
     public function authorise();
 
     public function authenticateByCode($code);
+
+    public function logout();
 }

api/src/Authentication/Type/CAS.php

@@ -122,5 +122,10 @@ function validate($service, $ticket)
 
         return rtrim($resp);
     }
+
+    function logout()
+    {
+        return false;
+    }
 }
 

api/src/Authentication/Type/Combined.php

@@ -36,4 +36,9 @@ public function authorise() {
     public function authenticateByCode($code){
         return $this->OIDCAuth->authenticateByCode($code);
     }
+
+    public function logout()
+    {
+        return $this->OIDCAuth->logout();
+    }
 }

api/src/Authentication/Type/Dummy.php

@@ -26,4 +26,9 @@ function authenticate($login, $password)
     {
         return true;
     }
+
+    function logout()
+    {
+        return false;
+    }
 }

api/src/Authentication/Type/LDAP.php

@@ -66,4 +66,9 @@ function authenticate($login, $password)
             }
         }
     }
+
+    function logout()
+    {
+        return false;
+    }
 }

api/src/Authentication/Type/OIDC.php

@@ -135,4 +135,9 @@ function authenticateByCode($code)
         setcookie($cookie_key, $token, $cookieOpts);
         return $this->getUser($token);
     }
+
+    function logout()
+    {
+        return $this->getProviderConfig()->end_session_endpoint;
+    }
 }

api/src/Authentication/Type/Simple.php

@@ -22,6 +22,11 @@ function check()
         return false;
     }
 
+    function logout()
+    {
+        return false;
+    }
+
     function authenticate($login, $password)
     {
         $person = $this->db->pq("SELECT password FROM person WHERE login=:1", array($login));

api/src/Controllers/AuthenticationController.php

@@ -116,7 +116,10 @@ private function checkAuthRequiredForSpecificSituations($parts): bool
             ($parts[0] == 'shipment' && $parts[1] == 'containers' && $parts[2] == 'notify' && in_array($_SERVER["REMOTE_ADDR"], $auto)) ||
 
                 # Allow barcode reader ips unauthorised access to add container history
-            ($parts[0] == 'shipment' && $parts[1] == 'containers' && $parts[2] == 'history' && in_array($_SERVER["REMOTE_ADDR"], $bcr))
+            ($parts[0] == 'shipment' && $parts[1] == 'containers' && $parts[2] == 'history' && in_array($_SERVER["REMOTE_ADDR"], $bcr)) ||
+
+                # Allow shipping service to update dewar status
+            ($parts[0] == 'shipment' && $parts[1] == 'dewars' && $parts[2] == 'confirmdispatch')
             )
             {
                 $need_auth = false;
@@ -391,17 +394,24 @@ function authenticateByCode()
     // Logout
     function logout()
     {
-        global $cookie_key;
-        if (isset($_COOKIE[$cookie_key])) {
-            $cookieOpts = array (
-                'expires' => time() - 3600,
-                'path' => '/',
-                'secure' => true,
-                'httponly' => true,
-                'samesite' => 'Strict'
-            );
-
-            setcookie($cookie_key, null, $cookieOpts);
+        global $cookie_key, $cas_sso;
+        if($cas_sso) {
+            if (isset($_COOKIE[$cookie_key])) {
+                $cookieOpts = array (
+                    'expires' => time() - 3600,
+                    'path' => '/',
+                    'secure' => true,
+                    'httponly' => true,
+                    'samesite' => 'Strict'
+                );
+
+                setcookie($cookie_key, null, $cookieOpts);
+            }
+
+            header('Location: ' . $this->authenticateByType()->logout());
+            $this->returnResponse(302, array('status' => "Redirecting to SSO provider"));
+        } else {
+            $this->returnError(501, "SSO not configured");
         }
     }
 

api/src/Downstream/DownstreamProcessing.php

@@ -217,15 +217,14 @@ function _lookup_autoproc($aid, $scalingid = null) {
      * @param string $pdb The input pdb file to generate the map around
      */
     function convert_mtz($mtz, $aid, $program, $pdb, $map = 0) {
+        global $ccp4_location;
         exec(
             '/bin/bash ./scripts/mtz2map.sh ' .
-                $mtz .
-                ' ' .
-                $aid .
-                ' ' .
-                $program .
-                ' ' .
-                $pdb,
+                $mtz . ' ' .
+                $aid . ' ' .
+                $program . ' ' .
+                $pdb . ' ' .
+                $ccp4_location,
             $output,
             $res
         );

api/src/Downstream/Type/Shelxt.php

@@ -0,0 +1,91 @@
+<?php
+
+namespace SynchWeb\Downstream\Type;
+
+use SynchWeb\Downstream\DownstreamPlugin;
+use SynchWeb\Downstream\DownstreamResult;
+
+class Shelxt extends DownstreamPlugin {
+    var $has_images = true;
+    var $friendlyname = 'Shelxt';
+    var $has_mapmodel = array(1, 0);
+
+    function _get_shelxt_results_json() {
+        $appid = array($this->autoprocprogramid);
+        $filepath = $this->db->pq(
+            "SELECT app.filePath from autoprocprogramattachment app where autoprocprogramid = :1 and filename = 'shelxt_results.json' ", 
+            $appid
+        );
+        return $filepath;
+    }
+
+    function _get_shelxt_results_png() {
+        $appid = array($this->autoprocprogramid);
+        $filepath = $this->db->pq(
+            "SELECT app.filepath, app.filename from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.png%' ", 
+            $appid
+        );
+        return $filepath;
+    }
+
+    function _get_pdb() {
+        $appid = array($this->autoprocprogramid);
+        $filepath = $this->db->pq(
+            "SELECT app.filepath, app.filename from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.pdb%' ", 
+            $appid
+        );
+        if (sizeof($filepath)) {
+            return $filepath[0]["FILEPATH"] . "/" . $filepath[0]["FILENAME"];
+        } else {
+            return;
+        }
+    }
+
+    function results() {
+        $json_filepath = $this->_get_shelxt_results_json();
+        if (sizeof($json_filepath)) {
+            $json_path = $json_filepath[0]["FILEPATH"] . "/shelxt_results.json" ;
+            $json_data = file_get_contents($json_path);
+        } else {
+            $json_data = "[]";
+        }
+        $dat = array();
+        $dat['BLOBS'] = 1;
+        $dat['SOLUTIONS'] = json_decode($json_data);
+
+        // scaling_id should always be present, but just in case...
+        if (array_key_exists('scaling_id', $this->process['PARAMETERS'])) {
+            $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 $results;
+    }
+
+    function images($n = 0) {
+        $png = $this->_get_shelxt_results_png();
+        if (sizeof($png)) {
+            return $png[0]["FILEPATH"] . "/" . $png[0]["FILENAME"];
+        } else {
+            return;
+        }
+
+    }
+
+    function mapmodel($n = 0, $map = false) {
+        $pdb = $this->_get_pdb();
+        if (!$pdb) {
+            return;
+        } else {
+            return $pdb;
+        }
+    }
+}

api/src/Page/Sample.php

@@ -631,13 +631,15 @@ function _sub_samples()
         $where = '';
         $first_inner_select_where = '';
         $second_inner_select_where = '';
+        $third_inner_select_where = '';
         $args = array($this->proposalid);
 
         if ($this->has_arg('sid')) {
             $where .= ' AND s.blsampleid=:' . (sizeof($args) + 1);
             $first_inner_select_where .= ' AND s.blsampleid=:' . (sizeof($args) + 2);
             $second_inner_select_where .= ' AND s.blsampleid=:' . (sizeof($args) + 3);
-            array_push($args, $this->arg('sid'), $this->arg('sid'), $this->arg('sid'));
+            $third_inner_select_where .= ' AND s.blsampleid=:' . (sizeof($args) + 4);
+            array_push($args, $this->arg('sid'), $this->arg('sid'), $this->arg('sid'), $this->arg('sid'));
         }
 
         if ($this->has_arg('cid')) {
@@ -648,7 +650,7 @@ function _sub_samples()
         }
 
         $this->db->wait_rep_sync(true);
-        $ss_query_string = $this->get_sub_samples_query($where, $first_inner_select_where, $second_inner_select_where);
+        $ss_query_string = $this->get_sub_samples_query($where, $first_inner_select_where, $second_inner_select_where, $third_inner_select_where);
         $subs = $this->db->pq($ss_query_string, $args);
 
         $this->db->wait_rep_sync(false);
@@ -683,7 +685,7 @@ function _get_sub_sample()
         }
     }
 
-    private function get_sub_samples_query($where, $first_inner_select_where = '', $second_inner_select_where = '')
+    private function get_sub_samples_query($where, $first_inner_select_where = '', $second_inner_select_where = '', $third_inner_select_where = '')
     {
         $group_by = "";
         $order_by = "";
@@ -707,22 +709,34 @@ private function get_sub_samples_query($where, $first_inner_select_where = '', $
             $from_query = "FROM (
                     SELECT ss.blsubsampleid
                     FROM (
-                        SELECT s.blsampleid, max(si.blsampleimageid) AS blsampleimageid
+                      SELECT s.blsampleid, max(si.blsampleimageid) AS blsampleimageid
                       FROM blsample s
                           INNER JOIN blsampleimage si ON si.blsampleid = s.blsampleid
                       WHERE 1=1 $first_inner_select_where
                       GROUP BY s.blsampleid
                     ) qq
                     JOIN blsubsample ss ON ss.blsampleimageid = qq.blsampleimageid
                     WHERE ss.source = 'auto'
-            
+
                     UNION ALL
 
                     SELECT ss.blsubsampleid
                     FROM blsubsample ss
                         LEFT JOIN blsample s on ss.blsampleid = s.blsampleid
-                    WHERE ss.source = 'manual' $second_inner_select_where
-                ) q JOIN blsubsample ss ON ss.blsubsampleid = q.blsubsampleid";
+                    WHERE ss.source = 'manual' $second_inner_select_where";
+
+            // show auto generated subsamples with data collections
+            if ($third_inner_select_where != '') {
+                $from_query .= "
+                    UNION ALL
+                    SELECT ss.blsubsampleid
+                    FROM blsubsample ss
+                        LEFT JOIN blsample s on ss.blsampleid = s.blsampleid
+                        INNER JOIN datacollection dc ON ss.blsubsampleid = dc.blsubsampleid
+                    WHERE ss.source = 'auto' $third_inner_select_where";
+            }
+
+            $from_query .= ") q JOIN blsubsample ss ON ss.blsubsampleid = q.blsubsampleid";
 
             $group_by = "GROUP BY pr.acronym,
                     s.name,