Merge Master into Prerelease

api/config_sample.php

@@ -247,6 +247,7 @@
 
     # Shipping service details
     $use_shipping_service = null;
+    $use_shipping_service_incoming_shipments = null;
     $shipping_service_url = null;
     $shipping_service_links_in_emails = null;
 

api/src/Database/DatabaseFactory.php

@@ -22,25 +22,26 @@ function __construct($databaseConnectionFactory)
 
     public function get($databaseType = null)
     {   
+        global $dbtype;
+
         if ( $databaseType == null) {
             // Global variable is named $dbtype in config.php.
-            global $dbtype;
             $databaseType = $dbtype;
         }
 
         if (!$databaseType) {
             error_log('Database type variable, dbtype, is not specified in config.php - defaulting to MySql.');
-            $database_type = 'MySQL';
+            $databaseType = 'MySQL';
         }
 
         // Determine fully-qualified class name of database class corresponding to $database_type.
         if (key_exists(strtolower($databaseType), $this->database_types)) {
-            $dbType = $this->database_types[strtolower($databaseType)];
+            $selectedDBConfig = $this->database_types[strtolower($databaseType)];
 
-            $full_class_name = 'SynchWeb\\Database\\Type\\' . $dbType["dbClassName"];;
+            $full_class_name = 'SynchWeb\\Database\\Type\\' . $selectedDBConfig["dbClassName"];
 
             if (class_exists($full_class_name)) {
-                $conn = $this->databaseConnectionFactory->get($dbType["dataConnectionName"]);
+                $conn = $this->databaseConnectionFactory->get($selectedDBConfig["dataConnectionName"]);
                 return new $full_class_name($conn);
             }
             else {

api/src/Page/Shipment.php

@@ -951,7 +951,9 @@ function _dispatch_dewar_in_shipping_service($dispatch_info, $dewar)
             "shipper_contact_email" => $facility_email,
             "internal_contact_name" => $this->has_arg('LOCALCONTACT') ? $this->args['LOCALCONTACT'] : null,
             "shipment_reference" =>  $dispatch_info['VISIT'],
-            "external_id" => (int) $dispatch_info['DEWARID']
+            "external_id" => (int) $dispatch_info['DEWARID'],
+            "journey_type" => ShippingService::JOURNEY_FROM_FACILITY,
+            "packages" => array(array("external_id" => (int) $dispatch_info['DEWARID']))
         );
 
         # Split up address. Necessary as address is a single field in ispyb
@@ -968,15 +970,16 @@ function _dispatch_dewar_in_shipping_service($dispatch_info, $dewar)
 
         try {
             if ($create === true) {
+                $shipment_data["proposal"] = $dewar["PROPOSAL"];
                 $response = $this->shipping_service->create_shipment($shipment_data);
             } else {
-                $this->shipping_service->update_shipment($dispatch_info['DEWARID'], $shipment_data);
-                $response = $this->shipping_service->get_shipment($dispatch_info['DEWARID']);
+                $this->shipping_service->update_shipment($dispatch_info['DEWARID'], $shipment_data, ShippingService::JOURNEY_FROM_FACILITY);
+                $response = $this->shipping_service->get_shipment($dispatch_info['DEWARID'], ShippingService::JOURNEY_FROM_FACILITY);
             }
             $shipment_id = $response['shipmentId'];
-            $this->shipping_service->dispatch_shipment($shipment_id);
+            $this->shipping_service->dispatch_shipment($shipment_id, false);
         } catch (Exception $e) {
-            throw new Exception("Error returned from shipping service: " . $e . "\nShipment data: " . $shipment_data);
+            throw new Exception("Error returned from shipping service: " . $e . "\nShipment data: " . json_encode($shipment_data));
         }
 
         return $shipment_id;
@@ -1004,7 +1007,7 @@ function _dispatch_dewar()
         }
 
         $dew = $this->db->pq(
-            "SELECT d.dewarid, d.barcode, d.storagelocation, d.dewarstatus, s.shippingid
+            "SELECT d.dewarid, d.barcode, d.storagelocation, d.dewarstatus, s.shippingid, CONCAT(p.proposalcode, p.proposalnumber) as proposal
                 FROM dewar d 
                 INNER JOIN shipping s ON s.shippingid = d.shippingid 
                 INNER JOIN proposal p ON p.proposalid = s.proposalid
@@ -2646,9 +2649,66 @@ function _get_default_dewar()
     }
 
 
+    function _book_shipment_in_shipping_service($user, $shipment, $dewars, $journey_type) {
+        $address_lines = explode(PHP_EOL, rtrim($user["address"]));
+        $contact = array(
+            "company_name" => $user["company"],
+            "address_line1" => isset($address_lines[0]) ? $address_lines[0] : null,
+            "address_line2" => isset($address_lines[1]) ? $address_lines[1] : null,
+            "address_line3" => isset($address_lines[2]) ? $address_lines[2] : null,
+            "city" => $user["city"],
+            "country" => $user["country"],
+            "post_code" => rtrim($user["postcode"]),
+            "contact_name" => $user["name"],
+            "contact_phone_number" => $user["phone"],
+            "contact_email" => rtrim($user["email"])
+        );
+        $shipment_data = array(
+            "shipment_reference" => $shipment["PROP"],
+            "external_id" => $shipment['SHIPPINGID'],
+            "packages" => array_map(
+                function($dewar) {return array("external_id" => $dewar["DEWARID"]);},
+                $dewars
+            )
+        );
+
+        // Create or update shipment in shipping service
+        try {
+            $response = $this->shipping_service->get_shipment($shipment['SHIPPINGID'], $journey_type);
+            $user_shipment_role = $this->has_arg('RETURN') ? "consignee" : "shipper";
+            $relabelled_contact = array_combine(
+                array_map(function($key) use ($user_shipment_role) {return $user_shipment_role."_".$key;}, 
+                    array_keys($contact)), 
+                $contact);
+            $shipment_update_data = array_merge($response, $shipment_data, $relabelled_contact);
+            $this->shipping_service->update_shipment($shipment["SHIPPINGID"], $shipment_update_data, ShippingService::JOURNEY_TO_FACILITY);
+        } catch (\Exception $e) {
+            $shipment_data["proposal"] = $shipment["PROP"];
+            $shipment_data["contact"] = $contact;
+            $response = $this->shipping_service->create_shipment_by_journey_type($shipment_data, $journey_type);
+        }
+
+        // Dispatch shipment in shipping service
+        $shipmentId = $response["shipmentId"];
+        $dispatch_details = $this->shipping_service->dispatch_shipment($shipmentId, false);
+
+        $awb_pieces = array_map(
+            function($package, $index) {return array("piecenumber" => $index+1, "licenseplate" => $package["tracking_number"]);},
+            $dispatch_details["packages"],
+            array_keys($dispatch_details["packages"])
+        );
+
+        return array(
+            "awb" => $dispatch_details["tracking_number"],
+            "label" => $dispatch_details["air_waybill"],
+            "pieces" => $awb_pieces
+        );
+    }
+
+
     function _create_awb()
     {
-        global $dhl_service, $dhl_service_eu, $dhl_acc, $dhl_acc_import, $facility_courier_countries, $facility_courier_countries_nde;
+        global $dhl_service, $dhl_service_eu, $dhl_acc, $dhl_acc_import, $facility_courier_countries, $facility_courier_countries_nde, $use_shipping_service_incoming_shipments;
 
         if (!$this->has_arg('prop'))
             $this->_error('No proposal specified');
@@ -2764,22 +2824,28 @@ function _create_awb()
         $awb = null;
         if (!$ship['DELIVERYAGENT_FLIGHTCODE']) {
             try {
-                $awb = $this->dhl->create_awb(array(
-                    'payee' => $payee,
-                    'accountnumber' => $accno,
-                    'shipperid' => $ship['PROP'],
-                    'service' => $product,
-                    'date' => $ship['DELIVERYAGENT_SHIPPINGDATE'],
-                    'declaredvalue' => $this->arg('DECLAREDVALUE'),
-                    'description' => $this->arg('DESCRIPTION'),
-
-                    'sender' => $this->has_arg('RETURN') ? $facility : $user,
-                    'receiver' => $this->has_arg('RETURN') ? $user : $facility,
-
-                    'pieces' => $pieces,
-                    'notification' => implode(';', $emails),
-                    'message' => $facility_company . ': Shipment booked from ISPyB for ' . $ship['PROP'] . ' ' . $ship['SHIPPINGNAME'] . ' containing ' . implode(',', $names)
-                ));
+                if (Utils::getValueOrDefault($use_shipping_service_incoming_shipments) && $accno === $dhl_acc) {
+                    $journey_type = $this->has_arg('RETURN') ? ShippingService::JOURNEY_FROM_FACILITY : ShippingService::JOURNEY_TO_FACILITY;
+                    $awb = $this->_book_shipment_in_shipping_service($user, $ship, $dewars, $journey_type);
+                } else {
+                    error_log("Not using shipping service for: {$ship['SHIPPINGID']}");
+                    $awb = $this->dhl->create_awb(array(
+                        'payee' => $payee,
+                        'accountnumber' => $accno,
+                        'shipperid' => $ship['PROP'],
+                        'service' => $product,
+                        'date' => $ship['DELIVERYAGENT_SHIPPINGDATE'],
+                        'declaredvalue' => $this->arg('DECLAREDVALUE'),
+                        'description' => $this->arg('DESCRIPTION'),
+
+                        'sender' => $this->has_arg('RETURN') ? $facility : $user,
+                        'receiver' => $this->has_arg('RETURN') ? $user : $facility,
+
+                        'pieces' => $pieces,
+                        'notification' => implode(';', $emails),
+                        'message' => $facility_company . ': Shipment booked from ISPyB for ' . $ship['PROP'] . ' ' . $ship['SHIPPINGNAME'] . ' containing ' . implode(',', $names)
+                    ));
+                }
 
                 $this->db->pq("UPDATE shipping 
                     SET deliveryagent_flightcode=:1, deliveryagent_flightcodetimestamp=CURRENT_TIMESTAMP, deliveryagent_label=:2, deliveryagent_productcode=:3, deliveryagent_flightcodepersonid=:4, shippingstatus='awb created', deliveryagent_agentname='DHL'

api/src/Shipment/ShippingService.php

@@ -10,6 +10,8 @@ class ShippingService
 {
     private $shipping_api_url;
     private $headers;
+    public const JOURNEY_TO_FACILITY = "TO_FACILITY";
+    public const JOURNEY_FROM_FACILITY = "FROM_FACILITY";
 
     function __construct()
     {
@@ -77,34 +79,46 @@ function create_shipment($shipment_data)
     }
 
 
-    function get_shipment($external_id)
+    function create_shipment_by_journey_type($shipment_data, $journey_type)
     {
         return $this->_send_request(
-            $this->shipping_api_url . '/shipments/external_id/' . $external_id,
+            $this->shipping_api_url . '/shipments/' . $journey_type,
+            "POST",
+            $shipment_data,
+            201
+        );
+    }
+
+
+    function get_shipment($external_id, $journey_type)
+    {
+        return $this->_send_request(
+            $this->shipping_api_url . '/shipments/external_id/' . $external_id . '?journey_type=' . $journey_type,
             "GET",
             null,
             200
         );
     }
 
 
-    function update_shipment($external_id, $shipment_data)
+    function update_shipment($external_id, $shipment_data, $journey_type)
     {
         return $this->_send_request(
-            $this->shipping_api_url . '/shipments/external_id/' . $external_id,
+            $this->shipping_api_url . '/shipments/external_id/' . $external_id . '?journey_type=' . $journey_type,
             "PUT",
             $shipment_data,
             204
         );
     }
 
 
-    function dispatch_shipment($shipment_id)
+    function dispatch_shipment($shipment_id, $pickup_requested)
     {
+        $pickup_requested_str = ($pickup_requested) ? "true" : "false";
         return $this->_send_request(
-            $this->shipping_api_url . '/shipments/' . $shipment_id . '/dispatch',
+            $this->shipping_api_url . '/shipments/' . $shipment_id . '/dispatch?pickup_requested=' . $pickup_requested_str,
             "POST",
-            array(),
+            null,
             201
         );
     }

api/tests/Database/DatabaseFactoryTest.php

@@ -64,7 +64,7 @@ public function testErrorIsLoggedForDatabaseTypeClassThatDoesNotExist(): void
     {
         global $dbtype;
         $dbtype = "obscure-db2";
-        $this->dbFactory->database_types[$dbtype] = $dbtype;
+        $this->dbFactory->database_types[$dbtype] = ["dbClassName" =>$dbtype, "dataConnectionName" => 'MySQL'];        
 
         $log = $this->getFunctionMock(__NAMESPACE__, "error_log");
         $log->expects($this->once())->with("Database class 'SynchWeb\Database\Type\obscure-db2' does not exist.");

client/src/css/main.scss

@@ -23,7 +23,7 @@
 @import "partials/_mc.scss";
 @import "partials/_imaging.scss";
 
-@import "partials/_summary.scss";
+
 
 
 // Third-party

client/src/js/modules/shipment/views/createawb.js

@@ -314,11 +314,19 @@ define(['backbone',
         },
 
         checkAvailability: function() {
-            if (this.shipment.get('DELIVERYAGENT_AGENTNAME').toLowerCase() != 'dhl' && (
-                    !(app.options.get('facility_courier_countries').indexOf(this.lc.get('COUNTRY')) > -1) &&
-                    !(app.options.get('facility_courier_countries_nde').indexOf(this.lc.get('COUNTRY')) > -1)
-                ))
-                app.message({ title: 'Service Not Available', message: 'This service is only available for shipments from '+app.options.get('facility_courier_countries').concat(app.options.get('facility_courier_countries_nde')).join(',')+', or for user with DHL accounts. Please either update your labcontact or the shipment courier'})
+            const agent_name = this.shipment.get('DELIVERYAGENT_AGENTNAME')
+            const facility_courier_countries = app.options.get('facility_courier_countries')
+            const facility_courier_countries_nde = app.options.get('facility_courier_countries_nde')
+            if ((agent_name==null || agent_name.toLowerCase() != 'dhl') && (
+                    !(facility_courier_countries.indexOf(this.lc.get('COUNTRY')) > -1) &&
+                    !(facility_courier_countries_nde.indexOf(this.lc.get('COUNTRY')) > -1)
+                )) {
+                    const valid_countries = facility_courier_countries.concat(facility_courier_countries_nde).join(', ')
+                    app.message({ 
+                        title: 'Service Not Available', 
+                        message: 'This service is only available for shipments from ' + valid_countries +
+                            ', or for user with DHL accounts. Please either update your labcontact or the shipment courier'})
+                }
         },
 
         populateLC: function() {            
@@ -435,7 +443,7 @@ define(['backbone',
                     PRODUCTCODE: prod,
                 },
                 success: function(resp) {
-                    app.alert({ message: 'Air Waybill Successfully Created'})
+                    app.message({ message: 'Air Waybill Successfully Created'})
                     setTimeout(function() {
                         app.trigger('shipment:show', self.shipment.get('SHIPPINGID'))
                     }, 1000)
@@ -452,7 +460,8 @@ define(['backbone',
                             console.error("Error parsing response: ", err)
                         }
                     }
-                    app.alert({ message: json.message })
+                    app.alert({ message: json.message, persist:true })
+                    app.alert({ message: json.message})
                     self.ui.submit.prop('disabled', false)
                     self.$el.removeClass('loading')
                 }

client/src/js/modules/shipment/views/dispatch.js

@@ -148,6 +148,8 @@ define(['marionette', 'views/form',
             this.ui.exp.html(this.visits.opts()).val(this.model.get('VISIT'))
             this.updateLC()
             this.populateCountries()
+            this.stripPostCode()
+            this.formatAddress()
         },
 
         populateCountries: function() {

client/src/js/modules/summary/views/summary.vue

@@ -31,7 +31,7 @@
                             <h> Filter </h>
                         </div>
                         <div class="tw-flex tw-col-span-2 tw-col-start-2 tw-mt-3 tw-ml-3">
-                            <p class="tw-mt-2 tw-text-sm">Select Proposals </p>
+                            <p class="tw-mt-2 tw-text-sm tw-whitespace-no-wrap">Select Proposals </p>
                             <combo-box v-if="filters[0].inputtype == 'combo-box'"
                                 class="tw-w-7/12 tw-text-sm tw-ml-2 tw-mr-1 tw-mb-2"
                                 :data="filters[0].data"
@@ -45,12 +45,12 @@
                                 :valueArray="filters[0].selectedArr"
                                 :searchArray="filters[0].selectedArr"
                                 ></combo-box>
-                                <button class="sidebar-button tw-mr-1 tw-mb-2" @click="getStarted()">Get Started</button>
+                                <button class="sidebar-button tw-mr-1 tw-mb-3 tw-whitespace-no-wrap" @click="getStarted()">Get Started</button>
                         </div>
-                        <div class="tw-col-span-1 tw-col-start-6 tw-mt-2 tw-mr-3 ">
+                        <div class="tw-col-span-1 tw-col-start-6 tw-mr-3 ">
 
-                            <div class="tw-flex tw-mb-2">
-                                <button class="sidebar-button tw-mr-1" @click="toggleSidebar()">Advanced Filter</button>
+                            <div class="tw-flex tw-mb-3 tw-mt-3">
+                                <button class="sidebar-button tw-mr-1 " @click="toggleSidebar()">Advanced Filter</button>
                                 <button class="sidebar-button" @click="searchFilterParams" >
                                 Search
                                 </button>
@@ -1351,6 +1351,7 @@ export default {
 </style>
 
 <style scoped>
+    @import "../styles/_summary.scss";
 
     .search-icon {
         font-size: 12px;

client/src/js/modules/types/mx/samples/tabbed-columns-view.vue

@@ -388,7 +388,7 @@
       <extended-validation-provider
         :ref="`sample_${sampleIndex}_required_resolution`"
         class-names="tw-px-2 tw-w-24"
-        :rules="sample['PROTEINID'] > -1 ? `required_if:sample ${sampleIndex + 1} screening method,none|positive_decimal:6` : ''"
+        :rules="sample['PROTEINID'] > -1 && queueForUDC ? `required_if:sample ${sampleIndex + 1} screening method,none,|positive_decimal:6` : ''"
         :name="`Sample ${sampleIndex + 1} Required Resolution`"
         :vid="`sample ${sampleIndex + 1} required resolution`"
       >

client/src/js/templates/contact/contactview.html

@@ -42,7 +42,7 @@ <h1>View Home Lab Contact</h1>
         </li>
 
         <li class="clearfix">
-            <span class="label">Street Address <br />(excluding post code, city)</span>
+            <span class="label">Street Address <br />(Max 3 lines, excluding post code, city)</span>
             <div class="ADDRESS text editable tw-block"><%-ADDRESS%></div>
         </li>
 

client/src/js/templates/shipment/createawb.html

@@ -64,7 +64,7 @@ <h2>Laboratory Details</h2>
         </li>
 
         <li class="clearfix">
-            <span class="label">Laboratory Address <br /><span class="small">(excluding post code)</span></span>
+            <span class="label">Laboratory Address <br /><span class="small">(Max 3 lines, excluding post code, city)</span></span>
             <div class="ADDRESS text"></div>
         </li>