Merge branch 'master' into improvement/lims-1564/remove-unused-depend…

…encies

api/config_sample.php

@@ -128,12 +128,12 @@
     $enabled_container_types = array();
 
     # Zocalo message broker credentials - Set to empty string to disable
-    $zocalo_server = 'tcp://activemq.server.ac.uk';
-    $zocalo_username = 'foo';
-    $zocalo_password = 'bar';
-
-    # Primary Zocalo entry point for recipe submission
-    $zocalo_mx_reprocess_queue = '/queue/zocolo.name';
+    $rabbitmq_zocalo_host = 'rabbitmq.server.ac.uk';
+    $rabbitmq_zocalo_port = 5672;
+    $rabbitmq_zocalo_username = 'foo';
+    $rabbitmq_zocalo_password = 'bar';
+    $rabbitmq_zocalo_vhost = 'zocalo';
+    $rabbitmq_zocalo_routing_key = 'processing_recipe';
 
     # This is used to trigger Zocalo recipes on adding new Protein sequences
     # Set to empty string to disable
@@ -381,4 +381,5 @@
     # Dials server values
     $dials_rest_url = "";
     $dials_rest_jwt = "";
+    $dials_rest_url_rings = false;
 ?>

api/index.php

@@ -71,7 +71,8 @@ function setupApplication($mode): Slim
             $facility_courier_countries, $facility_courier_countries_nde, $facility_courier_countries_link,
             $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $ifsummary, $synchweb_version, $redirects,
-            $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments;
+            $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments,
+            $dials_rest_url_rings;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -95,6 +96,7 @@ function setupApplication($mode): Slim
             'synchweb_version' => $synchweb_version,
             '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,
+            'dials_rest_url_rings' => $dials_rest_url_rings,
             'redirects' => $redirects
         )));
     });

api/scripts/mtz2map.sh

@@ -14,6 +14,14 @@ else
 	fi
 fi
 
+#export CCP4_MASTER=/dls_sw/apps/ccp4/<ccp4 version>
+export CCP4_MASTER=$5
+export CINCL=$CCP4_MASTER/include
+export CLIBD=$CCP4_MASTER/lib/data
+
+export CCP4_SCR=/tmp
+export root=$CCP4_MASTER/bin
+
 if [ $3 == 'dimple' -o $3 == 'mrbump' ]; then
 
 if [ -f $4 ]; then
@@ -28,14 +36,6 @@ else
 	fi
 fi
 
-#export CCP4_MASTER=/dls_sw/apps/ccp4/<ccp4 version>
-export CCP4_MASTER=$5
-export CINCL=$CCP4_MASTER/include
-export CLIBD=$CCP4_MASTER/lib/data
-
-export CCP4_SCR=/tmp
-export root=$CCP4_MASTER/bin
-
 if [ $3 == 'dimple' ]; then
 
 	if $root/mtzinfo $mtz | grep -q PH2FOFCWT; then

api/src/Controllers/UserController.php

@@ -275,13 +275,8 @@ function _update_user()
         $person = $this->userData->getUser($this->user->personId, $this->proposalid, $this->arg('PERSONID'));
         $person = $person[0];
         $this->_output((array) $person);
-        $laboratory = null;
-        if ($person['LABORATORYID'])
-        {
-            $laboratory = $this->userData->getLaboratory($person['LABORATORYID'])[0];
-        }
 
-        $this->userData->updateLaboratory(
+        $laboratoryId = $this->userData->updateLaboratory(
             $this->arg('PERSONID'),
             $this->argOrNull('LABNAME'),
             $this->argOrNull('ADDRESS'),
@@ -290,7 +285,7 @@ function _update_user()
             $this->argOrNull('COUNTRY'),
             $person['LABORATORYID']
         );
-        $laboratory = $this->userData->getLaboratory($person['LABORATORYID']);
+        $laboratory = $this->userData->getLaboratory($laboratoryId);
         $this->_output((array) $laboratory[0]);
     }
 
@@ -362,4 +357,4 @@ function _update_permission()
         );
         $this->_output(array('TYPE' => $this->arg('TYPE'), 'DESCRIPTION' => $desc));
     }
-}
+}

api/src/Model/Services/UserData.php

@@ -340,6 +340,7 @@ function updateLaboratory($personId, $labName, $labAddress, $city, $postcode, $c
                 ->whereIdEquals("personid", $personId)
                 ->update("person");
         }
+        return $laboratoryId;
     }
 
     function addGroupUser($personId, $gid)

api/src/Page.php

@@ -222,7 +222,6 @@ function auth($require_staff)
         {
             $auth = $this->staff;
 
-            // Beamline Sample Registration
         }
         // Barcode Scanners
         else if ($this->bcr() && !$this->user->loginId)
@@ -1037,9 +1036,9 @@ function get_visit_processed_dir($dc, $location)
 
     function _submit_zocalo_recipe($recipe, $parameters, $error_code = 500)
     {
-        global $zocalo_mx_reprocess_queue;
+        global $rabbitmq_zocalo_vhost;
 
-        if (isset($zocalo_mx_reprocess_queue))
+        if (isset($rabbitmq_zocalo_vhost))
         {
             // Send job to processing queue
             $zocalo_message = array(
@@ -1048,7 +1047,7 @@ function _submit_zocalo_recipe($recipe, $parameters, $error_code = 500)
                 ),
                 'parameters' => $parameters,
             );
-            $this->_send_zocalo_message($zocalo_mx_reprocess_queue, $zocalo_message, $error_code);
+            $this->_send_zocalo_message($rabbitmq_zocalo_vhost, $zocalo_message, $error_code);
         }
     }
 
@@ -1074,7 +1073,6 @@ function _send_zocalo_message($rabbitmq_zocalo_vhost, $zocalo_message, $error_co
 
         try
         {
-            error_log("Sending message" . var_export($zocalo_message, true));
             $queue = new Queue($rabbitmq_zocalo_host, $rabbitmq_zocalo_port, $rabbitmq_zocalo_username, $rabbitmq_zocalo_password, $rabbitmq_zocalo_vhost);
             $queue->send($zocalo_message, $rabbitmq_zocalo_routing_key);
         }

api/src/Page/Cell.php

@@ -274,8 +274,8 @@ function _beamlines()
         $pdb = $this->db->pq("SELECT TO_CHAR(p.pdbdate, 'YYYY') as year, $replace as bl, count(p.pdbentryid) as count
                 FROM pdbentry p
                 WHERE p.pdbdate > TO_DATE('2010-05', 'YYYY-MM')
-                GROUP BY $replace, TO_CHAR(p.pdbdate, 'YYYY')
-                ORDER BY TO_CHAR(p.pdbdate, 'YYYY')");
+                GROUP BY bl, year
+                ORDER BY year, bl");
 
         $isp = $this->db->pq("SELECT TO_CHAR(p.pdbdate, 'YYYY') as year, CASE WHEN p.autoprocprogramid > 0 THEN UPPER(s.beamlinename) ELSE $replace END as bl, count(p.pdbentryid) as count
                 FROM pdbentry p
@@ -284,8 +284,8 @@ function _beamlines()
                 INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
                 INNER JOIN blsession s ON s.sessionid = dcg.sessionid
                 WHERE p.pdbdate > TO_DATE('2010-05', 'YYYY-MM')
-                GROUP BY CASE WHEN p.autoprocprogramid > 0 THEN UPPER(s.beamlinename) ELSE $replace END, TO_CHAR(p.pdbdate, 'YYYY')
-                ORDER BY TO_CHAR(p.pdbdate, 'YYYY')");
+                GROUP BY bl, year
+                ORDER BY year, bl");
 
         foreach ($pdb as $i => &$s) {
             $s['COUNT'] = intval(($s['COUNT']));

api/src/Page/DC.php

@@ -62,6 +62,8 @@ class DC extends Page
         array('/dat/:id', 'get', '_plot'),
     );
 
+    const EVTOA = 12398.4198;
+
     # ------------------------------------------------------------------------
     # Data Collection AJAX Requests
     #   This is pretty crazy, it will return unioned data collections, energy
@@ -422,9 +424,12 @@ function _data_collections($single = null)
                     dc.transmission,
                     dc.axisrange,
                     dc.wavelength,
+                    ".self::EVTOA."/dc.wavelength as energy,
                     dc.comments,
                     1 as epk,
                     1 as ein,
+                    1 as wpk,
+                    1 as win,
                     dc.xtalsnapshotfullpath1 as x1,
                     dc.xtalsnapshotfullpath2 as x2,
                     dc.xtalsnapshotfullpath3 as x3,
@@ -556,9 +561,12 @@ function _data_collections($single = null)
                     min(dc.transmission) as transmission,
                     min(dc.axisrange) as axisrange,
                     min(dc.wavelength) as wavelength,
+                    ".self::EVTOA."/min(dc.wavelength) as energy,
                     min(dc.comments) as comments,
                     1 as epk,
                     1 as ein,
+                    1 as wpk,
+                    1 as win,
                     min(dc.xtalsnapshotfullpath1) as x1,
                     min(dc.xtalsnapshotfullpath2) as x2,
                     min(dc.xtalsnapshotfullpath3) as x3,
@@ -705,17 +713,20 @@ function _data_collections($single = null)
                     es.energyscanid,
                     1,
                     es.element,
-                    es.peakfprime,
+                    es.peakfprime as resolution,
                     es.exposuretime,
                     es.axisposition,
-                    es.peakfdoubleprime,
+                    es.peakfdoubleprime as numimg,
                     es.starttime as st,
                     es.transmissionfactor,
-                    es.inflectionfprime,
-                    es.inflectionfdoubleprime,
+                    es.inflectionfprime as axisrange,
+                    es.inflectionfdoubleprime as wavelength,
+                    1 as energy,
                     es.comments,
                     es.peakenergy,
                     es.inflectionenergy,
+                    ".self::EVTOA."/es.peakenergy as wpk,
+                    ".self::EVTOA."/es.inflectionenergy as win,
                     'A',
                     'A',
                     'A',
@@ -805,10 +816,13 @@ function _data_collections($single = null)
                 TO_CHAR(xrf.starttime, 'DD-MM-YYYY HH24:MI:SS') as st,
                 xrf.beamtransmission,
                 1,
-                xrf.energy,
+                ".self::EVTOA."/xrf.energy as wavelength,
+                xrf.energy as energy,
                 xrf.comments,
                 1,
                 1,
+                1 as wpk,
+                1 as win,
                 'A',
                 'A',
                 'A',
@@ -899,9 +913,12 @@ function _data_collections($single = null)
                 1,
                 1,
                 1,
+                1 as energy,
                 'A',
                 1,
                 1,
+                1 as wpk,
+                1 as win,
                 r.xtalsnapshotbefore,
                 r.xtalsnapshotafter,
                 'A',
@@ -974,7 +991,7 @@ function _data_collections($single = null)
 
             // Data collections
             if ($dc['TYPE'] == 'data') {
-                $nf = array(1 => array('AXISSTART', 'CHISTART', 'PHI', 'OVERLAP'), 2 => array('RESOLUTION', 'TRANSMISSION', 'AXISRANGE', 'TOTALDOSE'), 4 => array('WAVELENGTH', 'EXPOSURETIME'));
+                $nf = array(0 => array('ENERGY'), 1 => array('AXISSTART', 'CHISTART', 'PHI', 'OVERLAP'), 2 => array('RESOLUTION', 'TRANSMISSION', 'AXISRANGE', 'TOTALDOSE'), 4 => array('WAVELENGTH', 'EXPOSURETIME'));
 
                 $dc['DIRFULL'] = $dc['DIR'];
                 $dc['DIR'] = preg_replace('/.*\/' . $this->arg('prop') . '-' . $dc['VN'] . '\//', '', $dc['DIR']);
@@ -993,9 +1010,10 @@ function _data_collections($single = null)
                         $dc['DCT'] = 'Data Collection';
                 }
 
-                if ($dc['DCT'] == 'Mesh')
+                if ($dc['DCT'] == 'Mesh' || $dc['DCT'] == 'Mesh3D' ||
+                    ($dc['DCT'] != 'Serial Fixed' && $dc['DCT'] != 'Serial Jet' && $dc['AXISRANGE'] == 0 && $dc['NI'] > 1)
+                ) {
                     $dc['DCT'] = 'Grid Scan';
-                if ($dc['DCT'] != 'Serial Fixed' && $dc['DCT'] != 'Serial Jet' && $dc['AXISRANGE'] == 0 && $dc['NI'] > 1) {
                     $dc['TYPE'] = 'grid';
                 }
                 //$this->profile('dc');
@@ -1010,12 +1028,12 @@ function _data_collections($single = null)
 
                 $dc['FILETEMPLATE'] = preg_replace('/.*\/' . $this->arg('prop') . '-' . $dc['VN'] . '\//', '', $dc['FILETEMPLATE']);
 
-                $nf = array(2 => array('EXPOSURETIME', 'AXISSTART', 'RESOLUTION', 'TRANSMISSION'));
+                $nf = array(1 => array('EPK', 'EIN'), 2 => array('AXISRANGE', 'WAVELENGTH', 'EXPOSURETIME', 'AXISSTART', 'RESOLUTION', 'TRANSMISSION', 'NUMIMG'), 5 => array('WPK', 'WIN'));
                 $this->profile('edge');
 
                 // MCA Scans
             } else if ($dc['TYPE'] == 'mca') {
-                $nf = array(2 => array('EXPOSURETIME', 'WAVELENGTH', 'TRANSMISSION'));
+                $nf = array(0 => array('ENERGY'), 2 => array('EXPOSURETIME', 'TRANSMISSION'), 4 => array('WAVELENGTH'));
                 $dc['DIRFULL'] = $dc['DIR'];
                 $dc['DIR'] = preg_replace('/.*\/\d\d\d\d\/\w\w\d+-\d+\//', '', $dc['DIR']);
 

api/src/Page/Download.php

@@ -92,9 +92,7 @@ function _download_visit()
             $this->_error('There doesnt seem to be a data archive available for this visit');
     }
 
-    # ------------------------------------------------------------------------
-    # Download mtz/log file for Fast DP / XIA2
-    #   TODO: Delete me
+
     # This method either returns a list of plots from MX auto processing tools (n_obs, n_uniq, completeness etc.)
     # Or returns a specific plot based on auto processing attachment id (aid).
     # Individual plotly format Graphs can be returned via an aid, but will not be included in the list of plots (as their format is different)
@@ -468,14 +466,14 @@ function _get_autoproc_archive()
 
         $aps = $this->db->union(
             array(
-                "SELECT app.autoprocprogramid, app.processingprograms, app.processingstatus
+                "SELECT app.autoprocprogramid, app.processingprograms, app.processingstatus, dc.imageprefix, dc.datacollectionnumber
                     FROM autoprocintegration api 
                     INNER JOIN autoprocprogram app ON api.autoprocprogramid = app.autoprocprogramid 
                     INNER JOIN datacollection dc ON dc.datacollectionid = api.datacollectionid
                     INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid
                     INNER JOIN blsession s ON s.sessionid = dcg.sessionid
                     WHERE s.proposalid=:1 AND app.autoprocprogramid=:2",
-                "SELECT app.autoprocprogramid, app.processingprograms, app.processingstatus
+                "SELECT app.autoprocprogramid, app.processingprograms, app.processingstatus, dc.imageprefix, dc.datacollectionnumber
                     FROM autoprocprogram app
                     INNER JOIN processingjob pj on pj.processingjobid = app.processingjobid
                     INNER JOIN datacollection dc ON dc.datacollectionid = pj.datacollectionid
@@ -497,7 +495,7 @@ function _get_autoproc_archive()
         }
 
         $clean_program = preg_replace('/[^A-Za-z0-9\-]/', '', $ap['PROCESSINGPROGRAMS']);
-        $zipName = $this->arg('AUTOPROCPROGRAMID')  . '_' . $clean_program;
+        $zipName = $this->arg('AUTOPROCPROGRAMID') . '_' . $ap['IMAGEPREFIX'] . '_' . $ap['DATACOLLECTIONNUMBER'] . '_' . $clean_program;
         $this->_streamZipFile($files, $zipName);
     }
 

api/src/Page/Image.php

@@ -20,11 +20,13 @@ class Image extends Page
             'aid' => '\d+', 
             'visit' => '\w+\d+-\d+',
             'thresh' => '\d',
+            'res' => '\d',
+            'ice' => '\d',
         );
 
         public static $dispatch = array(array('/id/:id(/n/:n)', 'get', '_xtal_image'),
                               array('/diff/id/:id(/f/:f)(/n/:n)', 'get', '_diffraction_image'),
-                              array('/di/id/:id(/thresh/:thresh)(/n/:n)', 'get', '_diffraction_viewer'),
+                              array('/di/id/:id(/thresh/:thresh)(/res/:res)(/ice/:ice)(/n/:n)', 'get', '_diffraction_viewer'),
                               array('/cam/bl/:bl(/n/:n)', 'get', '_forward_webcam'),
                               array('/oav/bl/:bl(/n/:n)', 'get', '_forward_oav'),
                               array('/fa/fid/:id', 'get', '_fault_attachment'),
@@ -192,7 +194,7 @@ function _diffraction_viewer() {
             }
 
             $im = $info['LOC'] . '/' . $info['FT'];
-            $out = '/tmp/' . $this->arg('id') . '_' . $n . ($this->has_arg('thresh') ? '_th' : '') . '.jpg';
+            $out = '/tmp/' . $this->arg('id') . '_' . $n . ($this->has_arg('thresh') ? '_th' : '') . ($this->has_arg('res') ? '_res' : '') . ($this->has_arg('ice') ? '_ice' : '') . '.jpg';
             global $dials_rest_url, $dials_rest_jwt;
             if (!file_exists($out)) {                
                 if (!empty($dials_rest_url) && !empty($dials_rest_jwt)) {
@@ -212,6 +214,8 @@ function _diffraction_viewer() {
                             'colour_scheme' => 'greyscale',
                             'brightness' => $this->has_arg('thresh') ? 1000 : 10,
                             'format' => 'png',
+                            'resolution_rings' => array('show' => $this->has_arg('res')),
+                            'ice_rings' => array('show' => $this->has_arg('ice')),
                         )
                     ));
                 } else {

api/src/Page/Proposal.php

@@ -1205,8 +1205,8 @@ function _update_autocollect_session($sessionId, $uasSessionId, $containerId, $t
             $uas = new UAS($auto_user, $auto_pass);
             $code = $uas->update_session($uasSessionId, $data);
 
-            if ($code == 200) {
-                // Update ISPyB records
+            if ($code == 200 || $code == 404) {
+                // Update ISPyB records, even if UAS says session not found
                 $this->db->pq("UPDATE container SET sessionid=:1 WHERE containerid=:2", array($sessionId, $containerId));
                 // For debugging - actually just want to return Success!
                 $result = array(
@@ -1216,13 +1216,11 @@ function _update_autocollect_session($sessionId, $uasSessionId, $containerId, $t
                 );
             } else if ($code == 403) {
                 $this->_error('UAS Error - samples and/or investigators not valid. ISPyB/UAS Session ID: ' . $sessionId . ' / ' . $uasSessionId);
-            } else if ($code == 404) {
-                $this->_error('UAS Error - session not found in UAS, Session ID: ' . $sessionId . ' UAS Session ID: ' . $uasSessionId);
             } else {
-                $this->_error('UAS Error - something wrong creating a session for that container ' . $containerId . ', response code was: ' . $code);
+                $this->_error('UAS Error - something went wrong updating a session for that container ' . $containerId . ', response code was: ' . $code);
             }
         } else {
-            error_log("Something wrong - an Auto Collect session exists but with no containers " . $sessionId);
+            error_log("Something went wrong - an Auto Collect session exists but with no containers " . $sessionId);
 
             $this->_error('No valid containers on the existing Auto Collect Session id:', $sessionId);
         }