LIMS-1785: Create 'Assign Sample' page for VMXm (#974)

* LIMS-1785: Create 'Assign Sample' page for VMXm

* LIMS-1785: Label link to Assign page correctly

* LIMS-1785: Use consts rather than vars

* LIMS-1785: Fix unassign dialog

---------

Co-authored-by: Mark Williams <[email protected]>

Author: ndg63276

api/config_sample.php

@@ -395,6 +395,12 @@
         'i04' => False,
     );
 
+    # puck capacity of beamlines which take pucks, sample capacity of those which take samples
+    $bl_capacity = array(
+        "i03" => array("pucks" => 37, "samples" => 0),
+        "i04" => array("pucks" => 37, "samples" => 0),
+    );
+
     # Dials server values
     $dials_rest_url = "";
     $dials_rest_jwt = "";

api/index.php

@@ -73,7 +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;
+            $only_staff_can_assign, $industrial_prop_codes, $prop_codes_data_deleted, $container_types_with_parents,
+            $bl_capacity;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -106,6 +107,7 @@ function setupApplication($mode): Slim
             'container_types_with_parents' => $container_types_with_parents,
             'industrial_prop_codes' => $industrial_prop_codes,
             'prop_codes_data_deleted' => $prop_codes_data_deleted ?? array(),
+            'bl_capacity' => $bl_capacity,
         )));
     });
     return $app;

api/src/Controllers/AssignController.php

@@ -11,7 +11,7 @@ class AssignController extends Page
 {
     private $assignData;
 
-    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+', 'sid' => '\d+', 'pos' => '\d+', 'bl' => '[\w\-]+');
 
     public static $dispatch = array(
             array('/assign', 'get', 'assignContainer'),
@@ -32,15 +32,24 @@ function __construct(Slim $app, $db, $user, AssignData $assignData)
     function assignContainer()
     {
         global $only_staff_can_assign;
-        $cs = $this->assignData->getContainer($this->arg('visit'), $this->arg('cid'));
+        if ($this->has_arg('cid')) {
+            $cs = $this->assignData->getContainer($this->arg('visit'), $this->arg('cid'));
+        } else if ($this->has_arg('sid')) {
+            $cs = $this->assignData->getSample($this->arg('visit'), $this->arg('sid'));
+        } else {
+            $cs = array();
+        }
         if (sizeof($cs) > 0)
         {
             $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) {
                 $this->_error("Only staff can assign containers on this beamline");
-            } else {
+            } else if ($this->has_arg('cid')) {
                 $this->assignData->assignContainer($cs[0], $this->arg('pos'));
                 $this->_output(1);
+            } else if ($this->has_arg('sid')) {
+                $this->assignData->assignSample($cs[0], $this->arg('pos'));
+                $this->_output(1);
             }
         }
         else
@@ -52,16 +61,25 @@ function assignContainer()
     function unassignContainer()
     {
         global $only_staff_can_assign;
-        $cs = $this->assignData->getContainer($this->arg('visit'), $this->arg('cid'));
+        if ($this->has_arg('cid')) {
+            $cs = $this->assignData->getContainer($this->arg('visit'), $this->arg('cid'));
+        } else if ($this->has_arg('sid')) {
+            $cs = $this->assignData->getSample($this->arg('visit'), $this->arg('sid'));
+        } else {
+            $cs = array();
+        }
 
         if (sizeof($cs) > 0)
         {
             $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) {
                 $this->_error("Only staff can unassign containers on this beamline");
-            } else {
+            } else if ($this->has_arg('cid')) {
                 $this->assignData->unassignContainer($cs[0]);
                 $this->_output(1);
+            } else if ($this->has_arg('sid')) {
+                $this->assignData->unassignSample($cs[0]);
+                $this->_output(1);
             }
         }
         else

api/src/Model/Services/AssignData.php

@@ -27,6 +27,18 @@ function getContainer($visitId, $containerId)
                                     AND c.containerid=:2", array($visitId, $containerId));
     }
 
+    function getSample($visitId, $sampleId)
+    {
+        return $this->db->pq("SELECT b.blsampleid,b.name,d.dewarid,bl.beamlinename,c.containerid,c.code FROM blsample b
+                                INNER JOIN container c ON c.containerid = b.containerid
+                                INNER JOIN dewar d ON d.dewarid = c.dewarid
+                                INNER JOIN shipping s ON s.shippingid = d.shippingid
+                                INNER JOIN blsession bl ON bl.proposalid = s.proposalid
+                                INNER JOIN proposal p ON s.proposalid = p.proposalid
+                                WHERE CONCAT(p.proposalcode, p.proposalnumber, '-', bl.visit_number) LIKE :1
+                                    AND b.blsampleid=:2", array($visitId, $sampleId));
+    }
+
     function assignContainer($container, $location)
     {
         $this->updateDewar($container['DEWARID'], 'processing');
@@ -36,11 +48,27 @@ function assignContainer($container, $location)
         $this->updateDewarHistory($container['DEWARID'], 'processing', $container['BEAMLINENAME'], $container['CODE'] . ' => ' . $location);
     }
 
+    function assignSample($sample, $location)
+    {
+        $this->updateSample($sample['BLSAMPLEID'], $location);
+
+        $this->updateDewar($sample['DEWARID'], 'processing');
+
+        $this->updateContainerAndHistory($sample['CONTAINERID'], 'processing', $sample['BEAMLINENAME'], null);
+
+        $this->updateDewarHistory($sample['DEWARID'], 'processing', $sample['BEAMLINENAME'], $sample['NAME'] . ' => ' . $location);
+    }
+
     function unassignContainer($container)
     {
         $this->updateContainerAndHistory($container['CONTAINERID'], 'at facility', '', '');
     }
 
+    function unassignSample($sample)
+    {
+        $this->updateSample($sample['BLSAMPLEID'], null);
+    }
+
     function updateContainerAndHistory($containerId, $status, $beamlineName, $location)
     {
         $this->updateContainer($containerId, $status, $beamlineName, $location);
@@ -61,6 +89,12 @@ function updateContainer($containerId, $status, $beamlineName, $location)
                             WHERE containerid=:4", array($beamlineName, $location, $status, $containerId));
     }
 
+    function updateSample($sampleId, $location)
+    {
+        $this->db->pq("UPDATE blsample SET isinsamplechanger=:1
+                            WHERE blsampleid=:2", array($location, $sampleId));
+    }
+
     function getDewar($dewarId, $proposalId, $visitId)
     {
         $where = "p.proposalid=:1";

api/src/Page/Sample.php

@@ -120,6 +120,8 @@ class Sample extends Page
         'BEAMLINENAME' => '[\w\-]+',
         'SOURCE' => '[\w\-]+',
 
+        'assigned' => '[\w\-]+',
+        'unassigned' => '[\w\-]+',
         'queued' => '\d',
         'UNQUEUE' => '\d',
         'nodata' => '\d',
@@ -1145,6 +1147,16 @@ function _samples()
             array_push($args, $sessionid);
         }
 
+        if ($this->has_arg('assigned')) {
+            $where .= " AND d.dewarstatus LIKE 'processing' AND b.isinsamplechanger > 0 AND c.beamlinelocation LIKE :" . (sizeof($args) + 1);
+            array_push($args, $this->arg('assigned'));
+        }
+
+        if ($this->has_arg('unassigned')) {
+            $where .= " AND b.isinsamplechanger is null AND d.storagelocation=:" . (sizeof($args) + 1);
+            array_push($args, $this->arg('unassigned'));
+        }
+
         // Search
         if ($this->has_arg('s')) {
             $st = sizeof($args) + 1;
@@ -1219,7 +1231,7 @@ function _samples()
                                   , TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp, b.smiles
                                   , $cseq $sseq string_agg(cpr.name) as componentnames, string_agg(cpr.density) as componentdensities
                                   , string_agg(cpr.proteinid) as componentids, string_agg(cpr.acronym) as componentacronyms, string_agg(cpr.global) as componentglobals, string_agg(chc.abundance) as componentamounts, string_agg(ct.symbol) as componenttypesymbols, b.volume, pct.symbol,ROUND(cr.abundance,3) as abundance, TO_CHAR(b.recordtimestamp, 'DD-MM-YYYY') as recordtimestamp, dp.radiationsensitivity, dp.energy, dp.userpath, dp.strategyoption, dp.minimalresolution as minimumresolution
-                                  , count(distinct dc.dataCollectionId) as dcc            
+                                  , count(distinct dc.dataCollectionId) as dcc, b.isinsamplechanger
                                   
                                   FROM blsample b
 

client/src/js/config_sample.json

@@ -6,12 +6,7 @@
     "production": false,
 
     "pucks": { 
-        "i02": 10,
-        "i03": 23,
-        "i04": 37,
-        "i04-1": 9,
-        "i24": 9,
-        "i23": 4
+        "moved to": "config.php"
     },
 
     "_gsMajorAxisOrientation" : "Determines whether the major grid scan axis determines the orientation of the view",