Integrate/imca shipments

README.md

@@ -23,6 +23,8 @@ $ git clone https://github.com/DiamondLightSource/SynchWeb
 ### Customise front end - config.json
 An example configuration is provided in client/src/js/config_sample.json
 This file should be copied to create a client/src/js/config.json file and edited to customise the application for your site.
+To create your own logo at the top of the page, update the tailwind.config.js header-site-logo.
+The footer logo (ispyb logo image) can also be customised by setting the tailwind.config.js footer-site-logo before building the client.
 
 | Parameter | Description |
 | ------ | ------ |
@@ -35,9 +37,11 @@ This file should be copied to create a client/src/js/config.json file and edited
 | maintenance_message | Can be used so app serves static page under maintenance periods |
 | maintenance | Flag to indicate if client is in maintenance mode|
 | ga_ident | Google Analytics id|
-| site_name | Site Name to display in footer |
-| site_link | URL to site home page |
 | data_catalogue | Object that includes name and url property for a link to a data catalogue - displayed on the landing page |
+| csv_profile | The csv profile for importing shipments, currently only imca, see src/js/csv/imca.js |
+| enable_exp_plan | Whether to enable editing of experimental plan fields when creating samples |
+| auto_collect_label | Customise the auto collect label from the default 'Automated' |
+| queue_shipment | Allow entire shipment to be queued for automated / mail-in collection |
 
 Site Image can be customised via the tailwind.config.js header-site-logo and footer-site-logo values.
 

api/docs/definitions/sample-new.yaml

@@ -31,6 +31,11 @@ properties:
     description: Sample comments
     example: in 25% PEG4000 50um
 
+  STAFFCOMMENTS:
+    type: string
+    description: Sample staff comments
+    example: no crystal in loop
+
   SPACEGROUP:
     type: string
     description: Spacegroup

api/docs/dist/spec.json

@@ -3714,6 +3714,11 @@
           "description": "Sample comments",
           "example": "in 25% PEG4000 50um"
         },
+        "STAFFCOMMENTS": {
+          "type": "string",
+          "description": "Sample staff comments",
+          "example": "no crystal in loop"
+        },
         "SPACEGROUP": {
           "type": "string",
           "description": "Spacegroup",
@@ -4018,6 +4023,11 @@
               "description": "Sample comments",
               "example": "in 25% PEG4000 50um"
             },
+            "STAFFCOMMENTS": {
+              "type": "string",
+              "description": "Sample staff comments",
+              "example": "no crystal in loop"
+            },
             "SPACEGROUP": {
               "type": "string",
               "description": "Spacegroup",

api/src/Page/Assign.php

@@ -7,7 +7,7 @@
 class Assign extends Page
 {
 
-        public static $arg_list = array('visit' => '\w+\d+-\d+', 'cid' => '\d+', 'did' => '\d+', 'pos' => '\d+', 'bl' => '[\w-]+');
+        public static $arg_list = array('visit' => '\w+\d+-\d+', 'cid' => '\d+', 'did' => '\d+', 'pos' => '\d+', 'bl' => '[\w-]+', 'nodup' => '\d');
 
         public static $dispatch = array(array('/visits(/:visit)', 'get', '_blsr_visits'),
                               array('/assign', 'get', '_assign'),
@@ -23,54 +23,107 @@ class Assign extends Page
         # ------------------------------------------------------------------------
         # Assign a container
         function _assign() {
-            if (!$this->has_arg('visit')) $this->_error('No visit specified');
+            if (!$this->has_arg('visit') && !$this->has_arg('prop')) $this->_error('No visit or prop specified');
             if (!$this->has_arg('cid')) $this->_error('No container id specified');
             if (!$this->has_arg('pos')) $this->_error('No position specified');
-
+
+            $where = 'c.containerid=:1';
+            $args = array($this->arg('cid'));
+
+            if ($this->has_arg('visit')) {
+                $where .= " AND CONCAT(p.proposalcode, p.proposalnumber, '-', bl.visit_number) LIKE :".(sizeof($args)+1);
+                array_push($args, $this->arg('visit'));
+            } else {
+                $where .= " AND CONCAT(p.proposalcode, p.proposalnumber) LIKE :".(sizeof($args)+1);
+                array_push($args, $this->arg('prop'));
+            }
+
             $cs = $this->db->pq("SELECT d.dewarid,bl.beamlinename,c.containerid,c.code FROM container c
                                 INNER JOIN dewar d ON d.dewarid = c.dewarid
                                 INNER JOIN shipping s ON s.shippingid = d.shippingid
                                 INNER JOIN blsession bl ON bl.proposalid = s.proposalid
                                 INNER JOIN proposal p ON s.proposalid = p.proposalid
-                                WHERE CONCAT(CONCAT(CONCAT(p.proposalcode, p.proposalnumber), '-'), bl.visit_number) LIKE :1 AND c.containerid=:2", array($this->arg('visit'), $this->arg('cid')));
+                                WHERE $where", $args);
 
             if (sizeof($cs) > 0) {
                 $c = $cs[0];
+
+                $bl = $c['BEAMLINENAME'];
+                if ($this->staff) {
+                    if ($this->has_arg('bl')) {
+                        $bl = $this->arg('bl');
+                    }
+                }
+
+                if ($this->has_arg(('nodup'))) {
+                    $existing = $this->db->pq("SELECT c.containerid, c.name, CONCAT(p.proposalcode, p.proposalnumber) as prop
+                        FROM container c
+                        INNER JOIN dewar d ON d.dewarid = c.dewarid
+                        INNER JOIN shipping s ON s.shippingid = d.shippingid
+                        INNER JOIN proposal p ON s.proposalid = s.proposalid
+                        WHERE beamlinelocation=1 AND samplechangerlocation:2", array($bl, $this->arg('pos')));
+
+                    if (sizeof($existing)) {
+                        $ex = $existing[0];
+                        return $this->_error('A container is already a assigned that position: '+$ex[0]['NAME'] + '('+$ex['PROP']+')');
+                    }
+                }
+
+
                 $this->db->pq("UPDATE dewar SET dewarstatus='processing' WHERE dewarid=:1", array($c['DEWARID']));
 
-                $this->db->pq("UPDATE container SET beamlinelocation=:1,samplechangerlocation=:2,containerstatus='processing' WHERE containerid=:3", array($c['BEAMLINENAME'], $this->arg('pos'), $c['CONTAINERID']));
-                $this->db->pq("INSERT INTO containerhistory (containerid,status,location,beamlinename) VALUES (:1,:2,:3,:4)", array($c['CONTAINERID'], 'processing', $this->arg('pos'), $c['BEAMLINENAME']));
-                $this->_update_history($c['DEWARID'], 'processing', $c['BEAMLINENAME'], $c['CODE'].' => '.$this->arg('pos'));
+                $this->db->pq("UPDATE container SET beamlinelocation=:1,samplechangerlocation=:2,containerstatus='processing' WHERE containerid=:3", array($bl, $this->arg('pos'), $c['CONTAINERID']));
+                $this->db->pq("INSERT INTO containerhistory (containerid,status,location,beamlinename) VALUES (:1,:2,:3,:4)", array($c['CONTAINERID'], 'processing', $this->arg('pos'), $bl));
+                $this->_update_history($c['DEWARID'], 'processing', $bl, $c['CODE'].' => '.$this->arg('pos'));
 
                 $this->_output(1);
+            } else {
+                $this->_error('No such container');
             }
-
-            $this->_output(0);
         }
 
         # ------------------------------------------------------------------------
         # Unassign a container
         function _unassign() {
-            if (!$this->has_arg('visit')) $this->_error('No visit specified');
+            if (!$this->has_arg('visit') && !$this->has_arg('prop')) $this->_error('No visit or prop specified');
             if (!$this->has_arg('cid')) $this->_error('No container id specified');
-
+
+            $where = 'c.containerid=:1';
+            $args = array($this->arg('cid'));
+
+            if ($this->has_arg('visit')) {
+                $where .= " AND CONCAT(p.proposalcode, p.proposalnumber, '-', bl.visit_number) LIKE :".(sizeof($args)+1);
+                array_push($args, $this->arg('visit'));
+            } else {
+                $where .= " AND CONCAT(p.proposalcode, p.proposalnumber) LIKE :".(sizeof($args)+1);
+                array_push($args, $this->arg('prop'));
+            }
+
             $cs = $this->db->pq("SELECT d.dewarid,bl.beamlinename,c.containerid FROM container c
                                 INNER JOIN dewar d ON d.dewarid = c.dewarid
                                 INNER JOIN shipping s ON s.shippingid = d.shippingid
                                 INNER JOIN blsession bl ON bl.proposalid = s.proposalid
                                 INNER JOIN proposal p ON s.proposalid = p.proposalid
-                                WHERE CONCAT(CONCAT(CONCAT(p.proposalcode, p.proposalnumber), '-'), bl.visit_number) LIKE :1 AND c.containerid=:2", array($this->arg('visit'), $this->arg('cid')));
+                                WHERE $where", $args);
 
             if (sizeof($cs) > 0) {
                 $c = $cs[0];
+
+                $bl = $c['BEAMLINENAME'];
+                if ($this->staff) {
+                    if ($this->has_arg('bl')) {
+                        $bl = $this->arg('bl');
+                    }
+                }
 
                 $this->db->pq("UPDATE container SET samplechangerlocation='',beamlinelocation='',containerstatus='at facility' WHERE containerid=:1",array($c['CONTAINERID']));
-                $this->db->pq("INSERT INTO containerhistory (containerid,status,beamlinename) VALUES (:1,:2,:3)", array($c['CONTAINERID'], 'at facility', $c['BEAMLINENAME']));                
+                $this->db->pq("INSERT INTO containerhistory (containerid,status,beamlinename) VALUES (:1,:2,:3)", array($c['CONTAINERID'], 'at facility', $bl));
                 //$this->_update_history($c['DEWARID'], 'unprocessing');
 
                 $this->_output(1);
+            } else {
+                $this->_error('No such container');
             }
-            $this->_output(0);
         }
 
 
@@ -102,10 +155,10 @@ function _deactivate() {
                     $this->db->pq("UPDATE container SET containerstatus='at facility', samplechangerlocation='', beamlinelocation='' WHERE containerid=:1", array($c['ID']));
                     $this->db->pq("INSERT INTO containerhistory (containerid,status) VALUES (:1,:2)", array($c['ID'], 'at facility'));
                 }
-                $this->_output(1);
-
+                $this->_output(1);     
+            } else {
+                $this->_error('No such dewar');
             }
-            $this->_output(0);
         }