Merge master into prerelease

api/src/Database/Type/MySQL.php

@@ -458,8 +458,6 @@ function pq($query, $args = array(), $upperCaseKeys = true)
                         {
                             if ($val !== null)
                             {
-                                if (gettype($val) == gettype(0.1))
-                                    $val = round($val, 5);
                                 $val = strval($val);
                             }
                             if ($upperCaseKeys)

api/src/Page/DC.php

@@ -151,7 +151,7 @@ function _data_collections($single = null)
                 $where = " AND appm.autoprocprogrammessageid IS NOT NULL AND (appm.severity = 'WARNING' OR appm.severity = 'ERROR')";
                 $extj[0] .= "LEFT OUTER JOIN autoprocintegration api ON dc.datacollectionid = api.datacollectionid
                         LEFT OUTER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
-                        LEFT OUTER JOIN autoprocprogram app ON (app.autoprocprogramid = api.autoprocprogramid OR dc.datacollectionid = pj.datacollectionid)
+                        LEFT OUTER JOIN autoprocprogram app ON app.autoprocprogramid = api.autoprocprogramid
                         INNER JOIN autoprocprogrammessage appm ON appm.autoprocprogramid = app.autoprocprogramid";
             } else if ($this->arg('t') == "scrystal" || $this->arg('t') == "nscrystal") {
                 // Single crystal or explicitly non-single-crystal fields
@@ -615,6 +615,7 @@ function _data_collections($single = null)
             $groupby = "GROUP BY dc.datacollectiongroupid";
         }
 
+        // We don't want to remove duplicates, since if two counts are equal, one might go uncounted
         $total_query = "SELECT sum(tot) as t FROM (
                 $with
                 SELECT count($count_field) as tot
@@ -625,21 +626,21 @@ function _data_collections($single = null)
                     $extj[0]
                     WHERE $sess[0] $where
 
-                UNION SELECT count(es.energyscanid) as tot
+                UNION ALL SELECT count(es.energyscanid) as tot
                     FROM energyscan es
                     INNER JOIN blsession ses ON ses.sessionid = es.sessionid
                     $sample_joins[1]
                     $extj[1]
                     WHERE $sess[1] $where2
 
-                UNION SELECT count(xrf.xfefluorescencespectrumid) as tot
+                UNION ALL SELECT count(xrf.xfefluorescencespectrumid) as tot
                     FROM xfefluorescencespectrum xrf
                     INNER JOIN blsession ses ON ses.sessionid = xrf.sessionid
                     $sample_joins[3]
                     $extj[3]
                     WHERE $sess[3] $where4
 
-                UNION SELECT count(r.robotactionid) as tot
+                UNION ALL SELECT count(r.robotactionid) as tot
                     FROM robotaction r
                     INNER JOIN blsession ses ON ses.sessionid = r.blsessionid
                     $sample_joins[2]

api/src/Page/Sample.php

@@ -355,7 +355,7 @@ function _add_simple_sample()
                 $isCapillary = sizeof($crystals) > 1 ? true : false;
 
                 foreach ($crystals as $sample) {
-                    $c = array('NAME' => $phase->ACRONYM . '-sample');
+                    $c = $isCapillary ? array('NAME' => $sample->NAME) : array('NAME' => $phase->ACRONYM . '-sample');
                     foreach (array('SPACEGROUP', 'COMMENTS') as $f)
                         $c[$f] = array_key_exists($f, $sample) ? $sample->$f : '';
                     foreach (array('ABUNDANCE', 'THEORETICALDENSITY') as $f)
@@ -412,7 +412,7 @@ function _add_simple_sample()
                 if (array_key_exists('CAPILLARYID', $ids[$model]) && $capillary->CRYSTALID == null && !$capillary->CONTAINERLESS)
                     $blSamples['capillary'] = array('CONTAINERID' => $ids[$model]['CONTAINERID'], 'CRYSTALID' => $ids[$model]['CAPILLARYID'], 'PROTEINID' => $ids[$model]['CAPILLARYPHASEID'], 'LOCATION' => ++$maxLocation, 'NAME' => $capillary->NAME, 'PACKINGFRACTION' => 1, 'COMMENTS' => array_key_exists('COMMENTS', $capillary) ? $capillary->COMMENTS : '', 'DIMENSION1' => $capillary->OUTERDIAMETER, 'DIMENSION2' => $capillary->INNERDIAMETER, 'DIMENSION3' => $capillary->LENGTH, 'SHAPE' => $capillary->SHAPE, 'LOOPTYPE' => 1);
 
-                $blSamples['sample'] = array('CONTAINERID' => $ids[$model]['CONTAINERID'], 'CRYSTALID' => $ids[$model]['CRYSTALID'], 'PROTEINID' => $ids[$model]['PHASEID'], 'LOCATION' => ++$maxLocation, 'NAME' => $phase->ACRONYM, 'PACKINGFRACTION' => $attrs->PACKINGFRACTION ? $attrs->PACKINGFRACTION : null, 'COMMENTS' => array_key_exists('COMMENTS', $crystal) ? $crystal->COMMENTS : '');
+                $blSamples['sample'] = array('CONTAINERID' => $ids[$model]['CONTAINERID'], 'CRYSTALID' => $ids[$model]['CRYSTALID'], 'PROTEINID' => $ids[$model]['PHASEID'], 'LOCATION' => ++$maxLocation, 'NAME' => $crystal->NAME, 'PACKINGFRACTION' => $attrs->PACKINGFRACTION ? $attrs->PACKINGFRACTION : null, 'COMMENTS' => array_key_exists('COMMENTS', $crystal) ? $crystal->COMMENTS : '');
 
                 foreach ($blSamples as $key => $blSample) {
                     $a = $this->_prepare_sample_args($blSample);

api/src/Page/Shipment.php

@@ -2685,10 +2685,10 @@ function _book_shipment_in_shipping_service($user, $shipment, $dewars, $journey_
             "address_line3" => isset($address_lines[2]) ? $address_lines[2] : null,
             "city" => $user["city"],
             "country" => $user["country"],
-            "post_code" => rtrim($user["postcode"]),
+            "post_code" => trim($user["postcode"]),
             "contact_name" => $user["name"],
             "contact_phone_number" => $user["phone"],
-            "contact_email" => rtrim($user["email"])
+            "contact_email" => trim($user["email"])
         );
         $shipment_data = array(
             "shipment_reference" => $shipment["PROP"],

client/src/js/app/layouts/main.vue

@@ -20,7 +20,7 @@
       Main panel to store proposal menu, messages and content
       Sets the main width of the content area on screen
     -->
-    <div class="tw-w-full tw-px-2 lg:tw-w-10/12 lg:tw-mx-auto">
+    <div class="tw-w-full tw-px-2 lg:tw-w-11/12 lg:tw-mx-auto">
       <navbar-menu
         :proposal-menu="proposalMenu"
         :extras-menu="extraMenu"

client/src/js/app/layouts/maintenance.vue

@@ -5,7 +5,7 @@
       class="tw-flex tw-justify-between tw-items-center tw-h-10 tw-bg-header-background"
     />
 
-    <div class="tw-w-10/12 tw-mx-auto">
+    <div class="tw-w-11/12 tw-mx-auto">
       <!-- Sets the main width of the content on screen -->
       <h1 class="tw-mt-4 tw-py-4 tw-text-xl">
         The site is currently undergoing maintenance

client/src/js/modules/types/xpdf/samples/views/vue-simplesample.vue

@@ -533,7 +533,7 @@
                     })
 
                     let crystal = new Crystal({
-                        NAME: self.name,
+                        NAME: item.acronym,
                         COMMENTS: item.comments,
                         THEORETICALDENSITY: item.density,
                         ABUNDANCE: 1
@@ -611,7 +611,7 @@
                 })
 
                 let crystal = new Crystal({
-                    NAME: this.name,
+                    NAME: this.acronym,
                     COMMENTS: this.comments,
                     THEORETICALDENSITY: this.density,
                     ABUNDANCE: 1