DiamondLightSource · ndg63276 · Oct 22, 2025 · Oct 14, 2025 · Oct 14, 2025 · Oct 14, 2025
diff --git a/api/config_sample.php b/api/config_sample.php
@@ -406,6 +406,34 @@
     $dials_rest_jwt = "";
     $dials_rest_url_rings = false;
 
+    # Upstream reprocessing pipelines, by beamline type
+    $upstream_reprocessing_pipelines = array(
+        'sm' => array(
+            array('NAME' => 'Xia2 DIALS', 'VALUE' => 'xia2-dials'),
+            array('NAME' => 'Xia2 DIALS aimless', 'VALUE' => 'xia2-dials-aimless'),
+        ),
+        'default' => array(
+            array('NAME' => 'Xia2 DIALS', 'VALUE' => 'xia2-dials'),
+            array('NAME' => 'Xia2 3dii', 'VALUE' => 'xia2-3dii'),
+            array('NAME' => 'Fast DP', 'VALUE' => 'fast_dp'),
+            array('NAME' => 'autoPROC', 'VALUE' => 'autoPROC'),
+        ),
+    );
+
+    # Downstream reprocessing pipelines, by beamline type
+    $downstream_reprocessing_pipelines = array(
+        'sm' => array(
+            array('NAME' => 'shelxt', 'VALUE' => 'trigger-shelxt'),
+        ),
+        'default' => array(
+            array('NAME' => 'Dimple', 'VALUE' => 'trigger-dimple'),
+            array('NAME' => 'Fast EP', 'VALUE' => 'trigger-fastep'),
+            array('NAME' => 'Big EP', 'VALUE' => 'trigger-bigep'),
+            array('NAME' => 'MrBUMP', 'VALUE' => 'trigger-mrbump'),
+        ),
+    );
+
+
     # Add a button to upload file to CCP4 cloud
     #$ccp4_cloud_upload_url = 'https://data.cloud.ccp4.ac.uk/api/data/<%=USERNAME%>/<%=FACILITYNAME%>/<%=IMAGEPREFIX%>_<%=DATACOLLECTIONNUMBER%>/upload';
 ?>
diff --git a/api/index.php b/api/index.php
@@ -73,8 +73,8 @@ function setupApplication($mode): Slim
             $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,
-            $only_staff_can_assign, $industrial_prop_codes, $prop_codes_data_deleted, $container_types_with_parents,
-            $bl_capacity;
+            $only_staff_can_assign, $industrial_prop_codes, $upstream_reprocessing_pipelines, $downstream_reprocessing_pipelines,
+            $prop_codes_data_deleted, $container_types_with_parents, $bl_capacity;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -97,16 +97,18 @@ function setupApplication($mode): Slim
             'valid_components' => $valid_components,
             'enabled_container_types' => $enabled_container_types,
             'synchweb_version' => $synchweb_version,
+            'redirects' => $redirects,
             'shipping_service_app_url' => $use_shipping_service_redirect || $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
             'shipping_service_app_url_incoming' => $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
-            'closed_proposal_link' => $closed_proposal_link,
             'dials_rest_url_rings' => $dials_rest_url_rings,
+            'closed_proposal_link' => $closed_proposal_link,
             'ccp4_cloud_upload_url' => $ccp4_cloud_upload_url,
-            'redirects' => $redirects,
             'only_staff_can_assign' => $only_staff_can_assign,
-            'container_types_with_parents' => $container_types_with_parents,
             'industrial_prop_codes' => $industrial_prop_codes,
+            'upstream_reprocessing_pipelines' => $upstream_reprocessing_pipelines,
+            'downstream_reprocessing_pipelines' => $downstream_reprocessing_pipelines,
             'prop_codes_data_deleted' => $prop_codes_data_deleted ?? array(),
+            'container_types_with_parents' => $container_types_with_parents,
             'bl_capacity' => $bl_capacity,
         )));
     });

diff --git a/api/src/Downstream/Type/FastEp.php b/api/src/Downstream/Type/FastEp.php
@@ -16,6 +16,15 @@ function results() {
             'ATOMS' => array(array('sad_fa.pdb file not found'))
         );
 
+        $integrator = $this->_lookup_autoproc(
+            null,
+            $this->process['PARAMETERS']['scaling_id']
+        );
+        if ($integrator) {
+            $dat['PARENTAUTOPROCPROGRAM'] = $integrator['PROCESSINGPROGRAMS'];
+            $dat['PARENTAUTOPROCPROGRAMID'] = $integrator['AUTOPROCPROGRAMID'];
+        }
+
         $ats = array();
         $pdb = $this->_get_attachments("sad_fa.pdb");
         if ($pdb) {

diff --git a/api/src/Downstream/Type/LigandFit.php b/api/src/Downstream/Type/LigandFit.php
@@ -42,12 +42,13 @@ function _get_model_appaid() {
     }
 
     function results() {
+        $json_data = "[]";
         $json_filepath = $this->_get_ligandfit_results_json();
         if (sizeof($json_filepath)) {
-            $json_path = $json_filepath[0]["FILEPATH"] . "/" . $json_filepath[0]["FILENAME"] ;
-            $json_data = file_get_contents($json_path);
-        } else {
-            $json_data = "[]";
+            $json_path = $json_filepath[0]["FILEPATH"] . "/" . $json_filepath[0]["FILENAME"];
+            if (file_exists($json_path)) {
+                $json_data = file_get_contents($json_path);
+            }
         }
         $dat = array();
         $appaid = $this->_get_model_appaid();

diff --git a/api/src/Downstream/Type/Shelxt.php b/api/src/Downstream/Type/Shelxt.php
@@ -42,12 +42,13 @@ function _get_pdb() {
     }
 
     function results() {
+        $json_data = "[]";
         $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 = "[]";
+            $json_path = $json_filepath[0]["FILEPATH"] . "/shelxt_results.json";
+            if (file_exists($json_path)) {
+                $json_data = file_get_contents($json_path);
+            }
         }
         $dat = array();
         $dat['BLOBS'] = 1;

diff --git a/api/src/Page/Fault.php b/api/src/Page/Fault.php
@@ -308,19 +308,14 @@ function _update_fault()
     # Return a list of beamlines with ids
     function _get_beamlines()
     {
-        $row_tmp = $this->db->pq("SELECT distinct beamlinename as name FROM blsession WHERE beamlinename NOT LIKE 'i04 1' ORDER BY beamlinename");
+        $row_tmp = $this->db->pq("SELECT distinct beamlinename as name FROM blsession WHERE beamlinename != '' ORDER BY beamlinename");
         $rows = array();
         foreach ($row_tmp as $r)
         {
             array_push($rows, array('NAME' => $r['NAME']));
         }
 
-        // $rows = array(array('NAME' => 'i02'), array('NAME' => 'i03'), array('NAME' => 'i04'), array('NAME' => 'i04-1'), array('NAME' => 'i24'));
-
-        $bls = array();
-        foreach ($rows as $r)
-            $bls[$r['NAME']] = $r['NAME'];
-        $this->_output($this->has_arg('array') ? $bls : $rows);
+        $this->_output($rows);
     }
 
     # ------------------------------------------------------------------------
@@ -348,19 +343,18 @@ function _get_systems()
 
         $rows = $this->db->pq("SELECT s.systemid, s.name, s.description, string_agg(hs.beamlinename) as beamlines FROM bf_system s INNER JOIN bf_system_beamline hs ON s.systemid = hs.systemid " . $where . " GROUP BY s.systemid, s.name, s.description ORDER BY s.name", $args);
 
-        $sys = array();
-        foreach ($rows as $s)
-            $sys[$s['SYSTEMID']] = $s['NAME'];
-
-        $this->_output($this->has_arg('array') ? $sys : $rows);
+        $this->_output($rows);
     }
 
     # ------------------------------------------------------------------------
     # Return a list of components for a system on a beamline
     function _get_components()
     {
-        if (!$this->has_arg('sid'))
-            $this->_error('No systemid specified');
+        if (!$this->has_arg('sid')) {
+            $this->_output(array());
+            return;
+        }
+
         $args = array($this->arg('sid'));
 
         if ($this->has_arg('bl'))
@@ -381,19 +375,18 @@ function _get_components()
 
         $rows = $this->db->pq('SELECT c.componentid, c.name, c.description, string_agg(hc.beamlinename) as beamlines FROM bf_component c INNER JOIN bf_component_beamline hc ON c.componentid = hc.componentid WHERE c.systemid=:1' . $where . ' GROUP BY c.componentid, c.name, c.description ORDER BY beamlines,c.name', $args);
 
-        $com = array();
-        foreach ($rows as $c)
-            $com[$c['COMPONENTID']] = $c['NAME'];
-
-        $this->_output($this->has_arg('array') ? $com : $rows);
+        $this->_output($rows);
     }
 
     # ------------------------------------------------------------------------
     # Return a list of subcomponents for a component on a beamline
     function _get_subcomponents()
     {
-        if (!$this->has_arg('cid'))
-            $this->_error('No componentid specified');
+        if (!$this->has_arg('cid')) {
+            $this->_output(array());
+            return;
+        }
+
         $args = array($this->arg('cid'));
 
         if ($this->has_arg('bl'))
@@ -414,11 +407,7 @@ function _get_subcomponents()
 
         $rows = $this->db->pq('SELECT s.subcomponentid, s.name, s.description, string_agg(hs.beamlinename) as beamlines FROM bf_subcomponent s INNER JOIN bf_subcomponent_beamline hs ON s.subcomponentid = hs.subcomponentid WHERE s.componentid=:1' . $where . ' GROUP BY s.subcomponentid, s.name, s.description ORDER BY s.name', $args);
 
-        $scom = array();
-        foreach ($rows as $s)
-            $scom[$s['SUBCOMPONENTID']] = $s['NAME'];
-
-        $this->_output($this->has_arg('array') ? $scom : $rows);
+        $this->_output($rows);
     }
 
 

diff --git a/api/src/Page/Sample.php b/api/src/Page/Sample.php
@@ -17,8 +17,8 @@ class Sample extends Page
         's' => '\w+',
         'prop' => '\w+\d+',
         'term' => '\w+',
-        'pid' => '\d+',
-        'sid' => '\d+',
+        'pid' => '-?\d+',
+        'sid' => '-?\d+',
         'ssid' => '\d+',
         'cid' => '\d+',
         'crid' => '\d+',

diff --git a/client/src/js/modules/dc/views/autointegration.js b/client/src/js/modules/dc/views/autointegration.js
@@ -184,6 +184,11 @@ define(['marionette',
             }
 
             this.$el.slideDown()
+
+            if (typeof this.getOption('onReady') === 'function') {
+                this.getOption('onReady')(this)
+            }
+
         }
 
     })

diff --git a/client/src/js/modules/dc/views/dc.js b/client/src/js/modules/dc/views/dc.js
@@ -167,15 +167,20 @@ define(['marionette',
       } else this.strat.$el.slideToggle()
     },
 
-    loadAP: function(e) {
+    loadAP: function(e, callback) {
       if (!this.ap) {
         this.ap = new DCAutoIntegrationView({ 
-            id: this.model.get('ID'), 
-            dcPurgedProcessedData: this.model.get('PURGEDPROCESSEDDATA'),
-            el: this.$el.find('div.autoproc'),
-            parent: this.model
-          })
-      } else this.ap.$el.slideToggle()
+          id: this.model.get('ID'),
+          dcPurgedProcessedData: this.model.get('PURGEDPROCESSEDDATA'),
+          el: this.$el.find('div.autoproc'),
+          parent: this.model,
+          onReady: callback
+        })
+      } else {
+        this.ap.$el.slideToggle(() => {
+          if (callback) callback(this.ap);
+        });
+      }
     },
 
 
@@ -185,7 +190,8 @@ define(['marionette',
           id: this.model.get('ID'),
           dcPurgedProcessedData: this.model.get('PURGEDPROCESSEDDATA'),
           el: this.$el.find('div.downstream'),
-          holderWidth: this.$el.find('.holder').width() 
+          holderWidth: this.$el.find('.holder').width(),
+          upstreamLink: true,
         })
       } else this.dp.$el.slideToggle()
     },

diff --git a/client/src/js/modules/dc/views/downstream.js b/client/src/js/modules/dc/views/downstream.js
@@ -9,18 +9,17 @@ define(['backbone', 'marionette',
     'modules/dc/views/bigep',
     'modules/dc/views/shelxt',
     'modules/dc/views/ligandfit',
-    'templates/dc/downstreamerror.html'
 
     ], function(Backbone, Marionette, TabView, DownStreams, DownstreamWrapper, 
         TableView, 
-        FastEP, DIMPLE, MrBUMP, BigEP, Shelxt, LigandFit, downstreamerror) {
+        FastEP, DIMPLE, MrBUMP, BigEP, Shelxt, LigandFit) {
 
     var dcPurgedProcessedData = "0"; // dataCollection.PURGEDPROCESSEDDATA via options from DC.js
 
     var DownstreamsCollection = Backbone.Collection.extend()
 
     var DownStreamError = Marionette.ItemView.extend({
-        template: downstreamerror
+        template: _.template('<p>This processing job failed: <%-PROCESS.PROCESSINGMESSAGE%></p>')
     })
 
     var DownStreamRunning = Marionette.ItemView.extend({
@@ -69,12 +68,17 @@ define(['backbone', 'marionette',
                 'LigandFit': LigandFit,
             }
 
-            if (model.get('PROCESS').PROCESSINGSTATUS != 1) {
+            if (model.get('PROCESS').PROCESSINGSTATUS == null) {
                 return DownstreamWrapper.extend({
                     links: false,
                     dcPurgedProcessedData,
-                    childView: model.get('PROCESS').PROCESSINGSTATUS == null
-                        ?  DownStreamRunning : DownStreamError
+                    childView: DownStreamRunning
+                })
+            } else if (model.get('PROCESS').PROCESSINGSTATUS != 1) {
+                return DownstreamWrapper.extend({
+                    mapLink: false,
+                    dcPurgedProcessedData,
+                    childView: DownStreamError
                 })
             }
 
@@ -106,6 +110,7 @@ define(['backbone', 'marionette',
                     }
                 },
                 DCID: this.getOption('DCID'),
+                upstreamLink: this.getOption('upstreamLink'),
             }
         },
 
@@ -128,6 +133,7 @@ define(['backbone', 'marionette',
                 downstreams: this.getOption('downstreams'),
                 DCID: this.getOption('id'),
                 mapButton: this.getOption('mapButton'),
+                upstreamLink: this.getOption('upstreamLink'),
             }
         },
 
@@ -175,7 +181,8 @@ define(['backbone', 'marionette',
                     downstreams: this.collection,
                     id: this.getOption('id'),
                     el: this.$el.find('.res'),
-                    holderWidth: this.$el.parent().width()
+                    holderWidth: this.$el.parent().width(),
+                    upstreamLink: this.getOption('upstreamLink'),
                 }))
             } else {
                 this.$el.addClass('ui-tabs')
-Original file line number
+Diff line change
@@ Expand Up / @@ -184,6 +184,11 @@ define(['marionette', @@
                 }
                 this.$el.slideDown()
+                if (typeof this.getOption('onReady') === 'function') {
+                    this.getOption('onReady')(this)
+                }
             }
         })
@@ Expand Down @@