diff --git a/api/composer.json b/api/composer.json index 8101fed18..8ec82129d 100644 --- a/api/composer.json +++ b/api/composer.json @@ -21,12 +21,13 @@ "mpdf/mpdf": "8.1.2", "ralouphie/getallheaders": "2.0.5", "slim/slim": "2.6.2", - "stomp-php/stomp-php": "3.0.6", + "php-amqplib/php-amqplib": "^2.0", "symfony/http-foundation": "^5.4", "symfony/filesystem": "^5.4", "mpdf/qrcode": "^1.2", "mtcmedia/dhl-api": "dev-master#9b4b6315", - "maennchen/zipstream-php": "2.1.0" + "maennchen/zipstream-php": "2.1.0", + "phpseclib/bcmath_compat": "^2.0" }, "autoload": { "psr-4": { diff --git a/api/scripts/mtz2map.sh b/api/scripts/mtz2map.sh index 00542447d..1d25a72a4 100755 --- a/api/scripts/mtz2map.sh +++ b/api/scripts/mtz2map.sh @@ -14,6 +14,14 @@ else fi fi +#export CCP4_MASTER=/dls_sw/apps/ccp4/ +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/ -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 $mtz | grep -q PH2FOFCWT; then diff --git a/api/src/Page.php b/api/src/Page.php index c9f293507..f098868f9 100644 --- a/api/src/Page.php +++ b/api/src/Page.php @@ -1109,14 +1109,16 @@ function _submit_zocalo_recipe($recipe, $parameters, $error_code = 500) } - function _send_zocalo_message($zocalo_queue, $zocalo_message, $error_code = 500) + function _send_zocalo_message($rabbitmq_zocalo_vhost, $zocalo_message, $error_code = 500) { global - $zocalo_server, - $zocalo_username, - $zocalo_password; + $rabbitmq_zocalo_host, + $rabbitmq_zocalo_port, + $rabbitmq_zocalo_username, + $rabbitmq_zocalo_password, + $rabbitmq_zocalo_routing_key; - if (empty($zocalo_server) || empty($zocalo_queue)) + if (empty($rabbitmq_zocalo_host) || empty($rabbitmq_zocalo_vhost)) { $message = 'Zocalo server or queue not specified.'; error_log($message); @@ -1129,8 +1131,8 @@ function _send_zocalo_message($zocalo_queue, $zocalo_message, $error_code = 500) try { error_log("Sending message" . var_export($zocalo_message, true)); - $queue = new Queue($zocalo_server, $zocalo_username, $zocalo_password); - $queue->send($zocalo_queue, $zocalo_message, true, $this->user->loginId); + $queue = new Queue($rabbitmq_zocalo_host, $rabbitmq_zocalo_port, $rabbitmq_zocalo_username, $rabbitmq_zocalo_password, $rabbitmq_zocalo_vhost); + $queue->send($zocalo_message, $rabbitmq_zocalo_routing_key); } catch (Exception $e) { diff --git a/api/src/Page/Contact.php b/api/src/Page/Contact.php index 2136b5f00..3b1159550 100644 --- a/api/src/Page/Contact.php +++ b/api/src/Page/Contact.php @@ -9,8 +9,8 @@ class Contact extends Page { public static $arg_list = array('CARDNAME' => '([\w\s\-])+', - 'FAMILYNAME' => '([\w\-])+', - 'GIVENNAME' => '([\w\-])+', + 'FAMILYNAME' => '([\w\s\-])+', + 'GIVENNAME' => '([\w\s\-])+', 'PHONENUMBER' => '.*', 'EMAILADDRESS' => '.*', 'LABNAME' => '([\w\s\-])+', diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php index 33f259721..165e53c6d 100644 --- a/api/src/Page/DC.php +++ b/api/src/Page/DC.php @@ -62,6 +62,8 @@ class DC extends Page array('/dat/:id', 'get', '_plot'), ); + const EVTOA = 12398.4198; + # ------------------------------------------------------------------------ # Data Collection AJAX Requests # This is pretty crazy, it will return unioned data collections, energy @@ -121,11 +123,11 @@ function _data_collections($single = null) $where = ''; if ($this->arg('t') == 'sc') - $where = ' AND (dc.overlap != 0 OR ifnull(et.name, dcg.experimenttype) = "Screening")'; + $where = ' AND (dc.overlap != 0 OR ifnull(et.name, dcg.experimenttype) in ("Screening", "Characterization"))'; else if ($this->arg('t') == 'gr') $where = ' AND dc.axisrange = 0'; else if ($this->arg('t') == 'fc') - $where = ' AND dc.overlap = 0 AND dc.axisrange > 0 AND dc.numberOfImages > 1 AND ifnull(et.name, dcg.experimenttype) != "Screening"'; + $where = ' AND dc.overlap = 0 AND dc.axisrange > 0 AND dc.numberOfImages > 1 AND ifnull(et.name, dcg.experimenttype) not in ("Screening", "Characterization")'; } else if ($this->arg('t') == 'edge') { $where2 = ''; } else if ($this->arg('t') == 'mca') { @@ -139,11 +141,11 @@ function _data_collections($single = null) $where2 = " AND es.comments LIKE '%_FLAG_%'"; $where4 = " AND xrf.comments LIKE '%_FLAG_%'"; } else if ($this->arg('t') == 'ap') { - $where = ' AND app.processingstatus = 1'; + $where = " AND ifnull(et.name, dcg.experimenttype) not in ('Screening', 'Characterization') AND app.processingstatus = 1"; $extj[0] .= "INNER JOIN autoprocintegration ap ON dc.datacollectionid = ap.datacollectionid INNER JOIN autoprocprogram app ON app.autoprocprogramid = ap.autoprocprogramid"; } else if ($this->arg('t') == 'ph') { - $where = " AND app.processingstatus = 1 AND app.processingprograms in ('big_ep', 'fast_ep')"; + $where = " AND ifnull(et.name, dcg.experimenttype) not in ('Screening', 'Characterization') AND app.processingstatus = 1 AND app.processingprograms in ('big_ep', 'fast_ep')"; $extj[0] .= "INNER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid INNER JOIN autoprocprogram app ON app.processingjobid = pj.processingjobid"; } else if ($this->arg('t') == 'err') { @@ -368,13 +370,14 @@ function _data_collections($single = null) $s = str_replace('_', '$_', $this->arg('s')); $st = sizeof($args) + 1; - $where .= " AND (lower(dc.filetemplate) LIKE lower(CONCAT(CONCAT('%',:$st),'%')) ESCAPE '$' OR lower(dc.imagedirectory) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 1) . "), '%')) ESCAPE '$' OR lower(smp.name) LIKE lower(CONCAT(CONCAT('%', :" . ($st + 2) . "), '%')) ESCAPE '$')"; - $where2 .= " AND (lower(es.comments) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 3) . "), '%')) ESCAPE '$' OR lower(es.element) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 4) . "), '%')) ESCAPE '$' OR lower(smp.name) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 5) . "), '%')) ESCAPE '$')"; + $where .= " AND (dc.filetemplate LIKE CONCAT('%',:$st,'%') ESCAPE '$' OR dc.imagedirectory LIKE CONCAT('%',:" . ($st + 1) . ",'%') ESCAPE '$' OR smp.name LIKE CONCAT('%', :" . ($st + 2) . ",'%') ESCAPE '$')"; + $where2 .= " AND (es.comments LIKE CONCAT('%',:" . ($st + 3) . ",'%') ESCAPE '$' OR es.element LIKE CONCAT('%',:" . ($st + 4) . ",'%') ESCAPE '$' OR smp.name LIKE CONCAT('%',:" . ($st + 5) . ",'%') ESCAPE '$')"; $where3 .= ' AND r.robotactionid < 0'; - $where4 .= " AND (lower(xrf.filename) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 6) . "), '%')) ESCAPE '$' OR lower(smp.name) LIKE lower(CONCAT(CONCAT('%',:" . ($st + 7) . "), '%')) ESCAPE '$')"; + $where4 .= " AND (xrf.filename LIKE CONCAT('%',:" . ($st + 6) . ",'%') ESCAPE '$' OR smp.name LIKE CONCAT('%',:" . ($st + 7) . ",'%') ESCAPE '$')"; for ($i = 0; $i < 8; $i++) array_push($args, $s); + } # Set Count field @@ -421,9 +424,12 @@ function _data_collections($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, @@ -440,7 +446,7 @@ function _data_collections($single = null) dc.c2lens, dc.objaperture, dc.magnification, - dc.totalexposeddose as totaldose, + dose.total as totaldose, CAST(dc.totalabsorbeddose AS DECIMAL(5, 2)) as totalabsdose, d.detectorpixelsizehorizontal, d.detectorpixelsizevertical, @@ -511,9 +517,9 @@ function _data_collections($single = null) // $this->db->set_debug(True); // will want to support these too at some point - $where2 = ' AND es.energyscanid < 0'; - $where3 = ' AND r.robotactionid < 0'; - $where4 = ' AND xrf.xfefluorescencespectrumid < 0'; + $where2 .= ' AND es.energyscanid < 0'; + $where3 .= ' AND r.robotactionid < 0'; + $where4 .= ' AND xrf.xfefluorescencespectrumid < 0'; if ($this->has_arg('dcg')) { $where .= ' AND dc.datacollectiongroupid=:' . (sizeof($args) + 1); @@ -555,9 +561,12 @@ function _data_collections($single = null) min(dc.transmission) as transmission, min(dc.axisrange) as axisrange, min(dc.wavelength) as wavelength, + ".self::EVTOA."/min(dc.wavelength) as energy, min(dc.comments) as comments, 1 as epk, 1 as ein, + 1 as wpk, + 1 as win, min(dc.xtalsnapshotfullpath1) as x1, min(dc.xtalsnapshotfullpath2) as x2, min(dc.xtalsnapshotfullpath3) as x3, @@ -574,7 +583,7 @@ function _data_collections($single = null) max(dc.c2lens) as c2lens, max(dc.objaperture) as objaperture, max(dc.magnification) as magnification, - sum(dc.totalabsorbeddose) as totaldose, + dose.total as totaldose, CAST(dc.totalabsorbeddose AS DECIMAL(5, 2)) as totalabsdose, max(d.detectormanufacturer) as detectormanufacturer, max(d.detectormodel) as detectormodel, @@ -660,6 +669,9 @@ function _data_collections($single = null) SELECT $extcg $fields FROM datacollection dc INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid + INNER JOIN ( + select datacollectiongroupid, sum(totalabsorbeddose) as total from datacollection group by datacollectiongroupid) dose + ON dc.datacollectiongroupid = dose.datacollectiongroupid INNER JOIN blsession ses ON ses.sessionid = dcg.sessionid LEFT OUTER JOIN experimenttype et on dcg.experimenttypeid = et.experimenttypeid $sample_joins[0] @@ -701,17 +713,20 @@ function _data_collections($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', @@ -801,10 +816,13 @@ function _data_collections($single = null) TO_CHAR(xrf.starttime, 'DD-MM-YYYY HH24:MI:SS') as st, xrf.beamtransmission, 1, - xrf.energy, + ".self::EVTOA."/xrf.energy as wavelength, + xrf.energy as energy, xrf.comments, 1, 1, + 1 as wpk, + 1 as win, 'A', 'A', 'A', @@ -895,9 +913,12 @@ function _data_collections($single = null) 1, 1, 1, + 1 as energy, 'A', 1, 1, + 1 as wpk, + 1 as win, r.xtalsnapshotbefore, r.xtalsnapshotafter, 'A', @@ -970,7 +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'] . '\//', '', $dc['DIR']); @@ -989,9 +1010,10 @@ function _data_collections($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'); @@ -1006,12 +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']); diff --git a/api/src/Page/Download.php b/api/src/Page/Download.php index debeaeb45..6333e6b0e 100644 --- a/api/src/Page/Download.php +++ b/api/src/Page/Download.php @@ -56,6 +56,7 @@ class Download extends Page array('/ap/attachments(/:AUTOPROCPROGRAMATTACHMENTID)(/dl/:download)', 'get', '_get_autoproc_attachments'), array('/ap/archive/:AUTOPROCPROGRAMID', 'get', '_get_autoproc_archive'), + array('/ap/log/:AUTOPROCPROGRAMID', 'get', '_get_autoproc_log'), ); @@ -91,9 +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) @@ -220,7 +219,7 @@ function __get_autoproc_attachments() INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid INNER JOIN blsession s ON s.sessionid = dcg.sessionid WHERE s.proposalid=:1 $where - ORDER BY importancerank" + ORDER BY importancerank, filename" ), $args); return $rows; @@ -413,6 +412,48 @@ function _get_attachment() } } + # ------------------------------------------------------------------------ + # Get the most important log of an autoprocessing job + function _get_autoproc_log() + { + + if (!$this->has_arg('prop')) { + $this->_error('No proposal specified'); + } + $args = array($this->proposalid, $this->arg('AUTOPROCPROGRAMID')); + + $rows = $this->db->union(array( + "SELECT app.autoprocprogramid, appa.filename, appa.filepath + FROM autoprocintegration api + INNER JOIN autoprocprogram app ON api.autoprocprogramid = app.autoprocprogramid + INNER JOIN autoprocprogramattachment appa ON appa.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 + AND appa.importancerank=1 + AND appa.filetype='Log'", + "SELECT app.autoprocprogramid, appa.filename, appa.filepath + FROM autoprocprogram app + INNER JOIN processingjob pj on pj.processingjobid = app.processingjobid + INNER JOIN autoprocprogramattachment appa ON appa.autoprocprogramid = app.autoprocprogramid + INNER JOIN datacollection dc ON dc.datacollectionid = pj.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 + AND appa.importancerank=1 + AND appa.filetype='Log'" + ), $args); + + if (!sizeof($rows)) { + return $this->_error('No log file found'); + } + $this->_get_file($rows[0]['AUTOPROCPROGRAMID'], $rows[0]); + + } + # ------------------------------------------------------------------------ # Get an archive of an autoproc @@ -425,14 +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 @@ -454,7 +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); } diff --git a/api/src/Page/Imaging.php b/api/src/Page/Imaging.php index 43c480859..fa19544ad 100644 --- a/api/src/Page/Imaging.php +++ b/api/src/Page/Imaging.php @@ -376,6 +376,11 @@ function _get_inspections() $where .= " AND i.state='Completed'"; } + if ($this->has_arg('s')) { + $where .= " AND (CONCAT(p.proposalcode, p.proposalnumber) LIKE CONCAT('%', :" . (sizeof($args) + 1) . ", '%') OR c.code LIKE CONCAT('%', :" . (sizeof($args) + 2) . ", '%'))"; + array_push($args, $this->arg('s'), $this->arg('s')); + } + $tot = $this->db->pq("SELECT count(i.containerinspectionid) as tot FROM containerinspection i INNER JOIN container c ON c.containerid = i.containerid INNER JOIN dewar d ON d.dewarid = c.dewarid @@ -422,12 +427,6 @@ function _get_inspections() $order = $cols[$this->arg('sort_by')] . ' ' . $dir; } - if ($this->has_arg('s')) { - $where .= " AND (LOWER(CONCAT(p.proposalcode, p.proposalnumber)) LIKE LOWER(CONCAT(CONCAT('%', :" . (sizeof($args) + 1) . "), '%')) OR LOWER(c.code) LIKE LOWER(CONCAT(CONCAT('%', :" . (sizeof($args) + 2) . "), '%')))"; - array_push($args, $this->arg('s')); - array_push($args, $this->arg('s')); - } - if ($this->has_arg('ty')) { if ($this->arg('ty') == 'COMPLETED') $where .= " AND i.state = 'Completed' AND i.manual=0"; diff --git a/api/src/Page/Process.php b/api/src/Page/Process.php index 70fadb66d..d26ccd61b 100644 --- a/api/src/Page/Process.php +++ b/api/src/Page/Process.php @@ -355,7 +355,7 @@ function _add_reprocessing_sweep($args) { function _enqueue() { - global $zocalo_mx_reprocess_queue; + global $rabbitmq_zocalo_vhost; if (!$this->has_arg('PROCESSINGJOBID')) $this->_error('No processing job specified'); @@ -379,7 +379,7 @@ function _enqueue() 'ispyb_process' => intval($this->arg('PROCESSINGJOBID')), ) ); - $this->_send_zocalo_message($zocalo_mx_reprocess_queue, $message); + $this->_send_zocalo_message($rabbitmq_zocalo_vhost, $message); $this->_output(new \stdClass); } diff --git a/api/src/Page/Processing.php b/api/src/Page/Processing.php index 20546718c..098d77b26 100644 --- a/api/src/Page/Processing.php +++ b/api/src/Page/Processing.php @@ -141,7 +141,7 @@ function _autoproc_status($where, $ids) { INNER JOIN processingjob pj ON pj.datacollectionid = dc.datacollectionid INNER JOIN autoprocprogram app ON pj.processingjobid = app.processingjobid LEFT OUTER JOIN autoprocintegration api ON api.autoprocprogramid = app.autoprocprogramid - WHERE $where AND api.autoprocintegrationid IS NULL AND pj.automatic = 1 + WHERE $where AND api.autoprocintegrationid IS NULL AND app.processingprograms NOT IN ('$filter')", ), $ids @@ -697,11 +697,17 @@ private function _autoprocessing_query_builder($where, $group, $order = '') { ap.refinedcell_alpha as cell_al, ap.refinedcell_beta as cell_be, ap.refinedcell_gamma as cell_ga, - (SELECT COUNT(api1.autoprocintegrationid) FROM autoprocintegration api1 WHERE api1.autoprocprogramid = app.autoprocprogramid) as imagesweepcount, + (SELECT COUNT(api1.autoprocintegrationid) FROM autoprocintegration api1 WHERE api1.autoprocprogramid = app.autoprocprogramid) as imagesweepcount, app.processingstatus, app.processingmessage, count(distinct pjis.datacollectionid) as dccount, max(pjis.processingjobid) as processingjobid, + (SELECT IFNULL(blsg.name, bls.name) FROM processingjobparameter pjp + LEFT OUTER JOIN blsample bls ON pjp.parametervalue = bls.blsampleid + LEFT OUTER JOIN blsamplegroup blsg ON pjp.parametervalue = blsg.blsamplegroupid + WHERE pjp.processingjobid = pj.processingjobid + AND pjp.parameterkey in ('sample_id', 'sample_group_id') + ) as groupname, pj.automatic"; $from = "FROM autoprocintegration api"; @@ -751,7 +757,7 @@ private function _format_auto_processing_result($table_rows, $messages_result) { 'cell_ga', ); $resolution_data = array('rlow', 'rhigh'); - $returned_keys = array('PROCESSINGJOBID', 'IMAGESWEEPCOUNT', 'DCCOUNT', 'TYPE', 'PROCESSINGSTATUS', 'PROCESSINGMESSAGE'); + $returned_keys = array('PROCESSINGJOBID', 'IMAGESWEEPCOUNT', 'DCCOUNT', 'TYPE', 'PROCESSINGSTATUS', 'PROCESSINGMESSAGE', 'GROUPNAME'); foreach($table_rows as &$row) { if (!array_key_exists($row['AUTOPROCPROGRAMID'], $formatted_result)) { @@ -772,6 +778,9 @@ private function _format_auto_processing_result($table_rows, $messages_result) { $prefix = preg_match('/multi/', $value) ? '' : 'multi-'; $value = $row['DCCOUNT'] . 'x ' . $prefix . $value; } + if ($row['GROUPNAME']) { + $value .= ' ('.$row['GROUPNAME'].')'; + } } diff --git a/api/src/Page/Proposal.php b/api/src/Page/Proposal.php index ab719e2e7..fcc019322 100644 --- a/api/src/Page/Proposal.php +++ b/api/src/Page/Proposal.php @@ -393,7 +393,8 @@ function _get_visits($visit = null, $output = true) } if ($this->has_arg('s')) { - $where .= " AND s.visit_number LIKE :" . (sizeof($args) + 1); + $where .= " AND (s.visit_number LIKE :" . (sizeof($args) + 1) . " OR s.beamlinename LIKE :" . (sizeof($args) + 2) . ")"; + array_push($args, $this->arg('s')); array_push($args, $this->arg('s')); } @@ -435,7 +436,9 @@ function _get_visits($visit = null, $output = true) $order = 's.startdate DESC'; if ($this->has_arg('sort_by')) { - $cols = array('ST' => 's.startdate', 'EN' => 's.enddate', 'VIS' => 's.visit_number', 'BL' => 's.beamlinename', 'LC' => 's.beamlineoperator', 'COMMENT' => 's.comments'); + $cols = array('ST' => 's.startdate', 'EN' => 's.enddate', 'VIS' => 's.visit_number', 'BL' => 's.beamlinename', + 'LC' => 's.beamlineoperator', 'COMMENT' => 's.comments', 'ERA' => 's.riskrating', + 'SESSIONTYPE' => 'sessiontype', 'DCCOUNT' => 'dccount'); $dir = $this->has_arg('order') ? ($this->arg('order') == 'asc' ? 'ASC' : 'DESC') : 'ASC'; if (array_key_exists($this->arg('sort_by'), $cols)) $order = $cols[$this->arg('sort_by')] . ' ' . $dir; @@ -456,6 +459,7 @@ function _get_visits($visit = null, $output = true) s.beamlineoperator AS lc, s.comments, s.scheduled, + s.riskrating, st.typename AS sessiontype, DATE_FORMAT(s.startdate, '%d-%m-%Y %H:%i') AS startdate, DATE_FORMAT(s.enddate, '%d-%m-%Y %H:%i') AS enddate, @@ -468,6 +472,7 @@ function _get_visits($visit = null, $output = true) s.beamcalendarid, CONCAT(p.proposalcode, p.proposalnumber) AS proposal, COUNT(shp.personid) AS persons, + COUNT(distinct dc.datacollectionid) AS dccount, s.proposalid FROM BLSession s INNER JOIN proposal p ON p.proposalid = s.proposalid @@ -475,35 +480,14 @@ function _get_visits($visit = null, $output = true) LEFT OUTER JOIN session_has_person shp ON shp.sessionid = s.sessionid LEFT OUTER JOIN beamlinesetup bls on bls.beamlinesetupid = s.beamlinesetupid LEFT OUTER JOIN beamcalendar bc ON bc.beamcalendarid = s.beamcalendarid + LEFT OUTER JOIN datacollectiongroup dcg ON dcg.sessionid = s.sessionid + LEFT OUTER JOIN datacollection dc ON dcg.datacollectiongroupid = dc.datacollectiongroupid $where GROUP BY s.sessionid ORDER BY $order", $args); - $ids = array(); - $wcs = array(); - foreach ($rows as $r) { - array_push($ids, $r['SESSIONID']); - array_push($wcs, 'dcg.sessionid=:' . sizeof($ids)); - } - - $dcs = array(); - if (sizeof($ids)) { - $where = implode(' OR ', $wcs); - $tdcs = $this->db->pq("SELECT count(dc.datacollectionid) as c, dcg.sessionid - FROM datacollection dc - INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid - WHERE $where GROUP BY dcg.sessionid", $ids); - foreach ($tdcs as $t) - $dcs[$t['SESSIONID']] = $t['C']; - } - foreach ($rows as &$r) { - $dc = array_key_exists($r['SESSIONID'], $dcs) ? $dcs[$r['SESSIONID']] : 0; - $r['COMMENT'] = $r['COMMENTS']; - $r['DCCOUNT'] = $dc; - $bl_type = $this->_get_type_from_beamline($r['BL']); - $r['TYPE'] = $bl_type ? $bl_type : 'gen'; } diff --git a/api/src/Page/Sample.php b/api/src/Page/Sample.php index eb8850184..4d2093fff 100644 --- a/api/src/Page/Sample.php +++ b/api/src/Page/Sample.php @@ -195,6 +195,7 @@ class Sample extends Page array('/pdbs(/pid/:pid)', 'get', '_get_pdbs'), array('/pdbs', 'post', '_add_pdb'), array('/pdbs(/:pdbid)', 'delete', '_remove_pdb'), + array('/pdbs/download/:pdbid', 'get', '_download_pdb'), array('/concentrationtypes', 'get', '_concentration_types'), array('/componenttypes', 'get', '_component_types'), @@ -1819,12 +1820,17 @@ function _distinct_proteins() $where .= ' AND pr.externalid IS NOT NULL'; } - $has_safety_level = $this->has_arg('SAFETYLEVEL'); - if ($has_safety_level && $this->arg('SAFETYLEVEL') === 'ALL') { - $where .= ' AND pr.safetyLevel IS NOT NULL'; - } else if ($has_safety_level && $this->arg('SAFETYLEVEL') !== 'ALL') { - $where .= ' AND pr.safetyLevel=:' . (sizeof($args) + 1); - array_push($args, $this->arg('SAFETYLEVEL')); + if ($this->has_arg('SAFETYLEVEL')) { + if ($this->arg('SAFETYLEVEL') === 'ALL') { + $where .= ' AND pr.safetyLevel IS NOT NULL'; + } else if (strtolower($this->arg('SAFETYLEVEL')) === 'yellow') { + $where .= " AND pr.safetyLevel in ('green','yellow')"; + } else if (strtolower($this->arg('SAFETYLEVEL')) === 'red') { + $where .= " AND pr.safetyLevel in ('green','yellow','red')"; + } else { + $where .= ' AND pr.safetyLevel=:' . (sizeof($args) + 1); + array_push($args, $this->arg('SAFETYLEVEL')); + } } if ($this->has_arg('term')) { @@ -2057,6 +2063,21 @@ function _get_pdbs() $this->_output($rows); } + # ------------------------------------------------------------------------ + # Download a pdb file + function _download_pdb() + { + if (!$this->has_arg('pdbid')) + $this->_error('No PDB id specified'); + + $pdb = $this->db->pq("SELECT name, contents FROM pdb WHERE pdbid = :1", array($this->arg('pdbid'))); + $pdb = $pdb[0]; + + header('Content-Type:text/plain'); + header('Content-Disposition:attachment;filename='.$pdb['NAME']); + print $pdb['CONTENTS']; + } + # ------------------------------------------------------------------------ # Add a new pdb function _add_pdb() diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php index 6b3f16f4a..24fbeea13 100644 --- a/api/src/Page/Shipment.php +++ b/api/src/Page/Shipment.php @@ -484,10 +484,10 @@ function _add_history() if (!$this->has_arg('BARCODE')) $this->_error('No barcode specified'); - if (!$this->has_arg('LOCATION')) - $this->_error('No location specified'); + if (!$this->has_arg('LOCATION') && !$this->has_arg('STATUS')) + $this->_error('No location or status specified'); - $dew = $this->db->pq("SELECT CONCAT(pe.givenname, ' ', pe.familyname) as lcout, pe.emailaddress as lcoutemail, CONCAT(CONCAT(pe2.givenname, ' '), pe2.familyname) as lcret, pe2.emailaddress as lcretemail, CONCAT(p.proposalcode, p.proposalnumber, '-', e.visit_number) as firstexp, TO_CHAR(e.startdate, 'DD-MM-YYYY HH24:MI') as firstexpst, e.beamlinename, e.beamlineoperator, d.dewarid, d.trackingnumberfromsynchrotron, s.shippingid, s.shippingname, p.proposalcode, CONCAT(p.proposalcode, p.proposalnumber) as prop, d.barcode, d.facilitycode, d.firstexperimentid, d.dewarstatus + $dew = $this->db->pq("SELECT CONCAT(pe.givenname, ' ', pe.familyname) as lcout, pe.emailaddress as lcoutemail, CONCAT(CONCAT(pe2.givenname, ' '), pe2.familyname) as lcret, pe2.emailaddress as lcretemail, CONCAT(p.proposalcode, p.proposalnumber, '-', e.visit_number) as firstexp, TO_CHAR(e.startdate, 'DD-MM-YYYY HH24:MI') as firstexpst, e.beamlinename, e.beamlineoperator, d.dewarid, d.trackingnumberfromsynchrotron, s.shippingid, s.shippingname, p.proposalcode, CONCAT(p.proposalcode, p.proposalnumber) as prop, d.barcode, d.facilitycode, d.firstexperimentid, d.dewarstatus, d.storagelocation FROM dewar d INNER JOIN shipping s ON s.shippingid = d.shippingid LEFT OUTER JOIN labcontact c ON s.sendinglabcontactid = c.labcontactid @@ -505,15 +505,9 @@ function _add_history() $track = $this->has_arg('TRACKINGNUMBERFROMSYNCHROTRON') ? $this->arg('TRACKINGNUMBERFROMSYNCHROTRON') : $dew['TRACKINGNUMBERFROMSYNCHROTRON']; - // What was the last history entry for this dewar? - // If it's come from a beamline, register flag so we can e-mail further down... - $last_history_results = $this->db->pq("SELECT storageLocation FROM dewartransporthistory WHERE dewarId = :1 ORDER BY DewarTransportHistoryId DESC LIMIT 1", array($dew['DEWARID'])); - - if (sizeof($last_history_results)) { - $last_history = $last_history_results[0]; - // We only add data to dewar history in lower case from this method. - // If that ever changes, update this to become case insensitive search - $last_location = $last_history['STORAGELOCATION']; + if ($this->has_arg('LOCATION')) { + // If it's come from a beamline, register flag so we can e-mail further down... + $last_location = $dew['STORAGELOCATION']; if (!isset($dewar_complete_email_locations) || !is_array($dewar_complete_email_locations)) { $bls = $this->_get_beamlines_from_type('all'); $send_return_email = in_array($last_location, $bls); @@ -521,99 +515,103 @@ function _add_history() $email_location = $dewar_complete_email_locations[$last_location]; $send_return_email = preg_match($email_location, strtolower($this->arg('LOCATION'))); } + // If dewar status is dispatch-requested - don't change it. + // This way the dewar can be moved between storage locations and keep the record that a user requested the dispatch + // Default status is 'at-facility' + $dewarstatus = strtolower($dew['DEWARSTATUS']) == 'dispatch-requested' ? 'dispatch-requested' : 'at facility'; + $dewarlocation = $this->arg('LOCATION'); + } else { - // No history - could be a new dewar, so not necessarily an error... - if ($this->debug) - error_log("No previous dewar transport history for DewarId " . $dew['DEWARID']); + // just a status given + $dewarstatus = $this->arg('STATUS'); + $dewarlocation = $dew['STORAGELOCATION']; } - // If dewar status is dispatch-requested - don't change it. - // This way the dewar can be moved between storage locations and keep the record that a user requested the dispatch - // Default status is 'at-facility' - $dewarstatus = strtolower($dew['DEWARSTATUS']) == 'dispatch-requested' ? 'dispatch-requested' : 'at facility'; - $this->db->pq("INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate) VALUES (s_dewartransporthistory.nextval,:1,lower(:2),lower(:3),CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id", array($dew['DEWARID'], $dewarstatus, $this->arg('LOCATION'))); + $this->db->pq("INSERT INTO dewartransporthistory (dewartransporthistoryid,dewarid,dewarstatus,storagelocation,arrivaldate) VALUES (s_dewartransporthistory.nextval,:1,lower(:2),lower(:3),CURRENT_TIMESTAMP) RETURNING dewartransporthistoryid INTO :id", array($dew['DEWARID'], $dewarstatus, $dewarlocation)); $dhid = $this->db->id(); - $this->db->pq("UPDATE dewar set dewarstatus=lower(:4), storagelocation=lower(:2), trackingnumberfromsynchrotron=:3 WHERE dewarid=:1", array($dew['DEWARID'], $this->arg('LOCATION'), $track, $dewarstatus)); - $this->db->pq("UPDATE shipping set shippingstatus=lower(:2) WHERE shippingid=:1", array($dew['SHIPPINGID'], $dewarstatus)); - - $containers = $this->db->pq("SELECT containerid - FROM container - WHERE dewarid=:1", array($dew['DEWARID'])); - foreach ($containers as $c) { - $this->db->pq("INSERT INTO containerhistory (containerid,status) VALUES (:1,:2)", array($c['CONTAINERID'], 'at facility')); - } - - // Email - // EHCs, local contact(s), labcontact, dh, pa - $dew['NOW'] = strftime('%d-%m-%Y %H:%M'); - $dew['INCONTACTS'] = $in_contacts; - $dew['TRACKINGNUMBERFROMSYNCHROTRON'] = $track; - - if (strtolower($this->arg('LOCATION')) == 'stores-in' && $dew['LCOUTEMAIL']) { - $lcs = $this->db->pq("SELECT p.login - FROM person p - INNER JOIN session_has_person shp ON shp.personid = p.personid - WHERE shp.sessionid=:1 AND (shp.role = 'Local Contact' OR shp.role = 'Local Contact 2')", array($dew['FIRSTEXPERIMENTID'])); - $emails = array($dew['LCOUTEMAIL'], $arrival_email); - foreach ($lcs as $lc) { - array_push($emails, $this->_get_email($lc['LOGIN'])); - } + if ($this->has_arg('LOCATION')) { + $this->db->pq("UPDATE dewar set dewarstatus=lower(:4), storagelocation=lower(:2), trackingnumberfromsynchrotron=:3 WHERE dewarid=:1", array($dew['DEWARID'], $this->arg('LOCATION'), $track, $dewarstatus)); + $this->db->pq("UPDATE shipping set shippingstatus=lower(:2) WHERE shippingid=:1", array($dew['SHIPPINGID'], $dewarstatus)); - $email = new Email($dew['PROPOSALCODE'] == 'in' ? 'dewar-stores-in-in' : 'dewar-stores-in', '*** Dewar Received for ' . $dew['PROP'] . ' at ' . $dew['NOW'] . ' ***'); - $email->data = $dew; - $email->send(implode(', ', $emails)); - } + $containers = $this->db->pq("SELECT containerid + FROM container + WHERE dewarid=:1", array($dew['DEWARID'])); + foreach ($containers as $c) { + $this->db->pq("INSERT INTO containerhistory (containerid,status) VALUES (:1,:2)", array($c['CONTAINERID'], 'at facility')); + } - if (strtolower($this->arg('LOCATION')) == 'stores-out' && $dew['LCRETEMAIL']) { - $email = new Email('dewar-stores-out', '*** Dewar ready to leave Synchrotron ***'); - $email->data = $dew; - $email->send($dew['LCRETEMAIL']); - } + // Email + // EHCs, local contact(s), labcontact, dh, pa + $dew['NOW'] = strftime('%d-%m-%Y %H:%M'); + $dew['INCONTACTS'] = $in_contacts; + $dew['TRACKINGNUMBERFROMSYNCHROTRON'] = $track; + + if (strtolower($this->arg('LOCATION')) == 'stores-in' && $dew['LCOUTEMAIL']) { + $lcs = $this->db->pq("SELECT p.login + FROM person p + INNER JOIN session_has_person shp ON shp.personid = p.personid + WHERE shp.sessionid=:1 AND (shp.role = 'Local Contact' OR shp.role = 'Local Contact 2')", array($dew['FIRSTEXPERIMENTID'])); + $emails = array($dew['LCOUTEMAIL'], $arrival_email); + foreach ($lcs as $lc) { + array_push($emails, $this->_get_email($lc['LOGIN'])); + } - if (strpos(strtolower($this->arg('LOCATION')), '-rack') !== false && $dew['LCRETEMAIL']) { - $dew['LOCATION'] = $this->arg('LOCATION'); + $email = new Email($dew['PROPOSALCODE'] == 'in' ? 'dewar-stores-in-in' : 'dewar-stores-in', '*** Dewar Received for ' . $dew['PROP'] . ' at ' . $dew['NOW'] . ' ***'); + $email->data = $dew; + $email->send(implode(', ', $emails)); + } - $email = new Email('dewar-rack', '*** Dewar now outside Beamline ***'); - $email->data = $dew; - $email->send($dew['LCRETEMAIL']); - } + if (strtolower($this->arg('LOCATION')) == 'stores-out' && $dew['LCRETEMAIL']) { + $email = new Email('dewar-stores-out', '*** Dewar ready to leave Synchrotron ***'); + $email->data = $dew; + $email->send($dew['LCRETEMAIL']); + } - if ($dew['LCRETEMAIL'] && $send_return_email) { - // Any data collections for this dewar's containers? - // Note this counts data collection ids for containers and uses the DataCollection.SESSIONID to determine the session/visit - // Should work for UDC (where container.sessionid is set) as well as any normal scheduled session (where container.sessionid is not set) - $rows = $this->db->pq("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', ses.visit_number) as visit, dc.sessionid, count(dc.datacollectionid) as dccount - FROM Dewar d - INNER JOIN Container c on c.dewarid = d.dewarid - INNER JOIN BLSample bls ON bls.containerid = c.containerid - INNER JOIN DataCollection dc ON dc.blsampleid = bls.blsampleid - INNER JOIN BLSession ses ON dc.sessionid = ses.sessionid - INNER JOIN Proposal p ON p.proposalid = ses.proposalid - WHERE d.dewarid = :1 - GROUP BY dc.sessionid", array($dew['DEWARID'])); + if (strpos(strtolower($this->arg('LOCATION')), '-rack') !== false && $dew['LCRETEMAIL']) { + $dew['LOCATION'] = $this->arg('LOCATION'); - if (sizeof($rows)) - $dew['DC'] = $rows; + $email = new Email('dewar-rack', '*** Dewar now outside Beamline ***'); + $email->data = $dew; + $email->send($dew['LCRETEMAIL']); + } - $cc = array($dewar_complete_email ? $dewar_complete_email : null); + if ($dew['LCRETEMAIL'] && $send_return_email) { + // Any data collections for this dewar's containers? + // Note this counts data collection ids for containers and uses the DataCollection.SESSIONID to determine the session/visit + // Should work for UDC (where container.sessionid is set) as well as any normal scheduled session (where container.sessionid is not set) + $rows = $this->db->pq("SELECT CONCAT(p.proposalcode, p.proposalnumber, '-', ses.visit_number) as visit, dc.sessionid, count(dc.datacollectionid) as dccount + FROM Dewar d + INNER JOIN Container c on c.dewarid = d.dewarid + INNER JOIN BLSample bls ON bls.containerid = c.containerid + INNER JOIN DataCollection dc ON dc.blsampleid = bls.blsampleid + INNER JOIN BLSession ses ON dc.sessionid = ses.sessionid + INNER JOIN Proposal p ON p.proposalid = ses.proposalid + WHERE d.dewarid = :1 + GROUP BY dc.sessionid", array($dew['DEWARID'])); + + if (sizeof($rows)) + $dew['DC'] = $rows; + + $cc = array($dewar_complete_email ? $dewar_complete_email : null); + + $owners = $this->db->pq("SELECT p.emailaddress + FROM Container c + INNER JOIN Person p ON c.ownerId = p.personId + WHERE c.dewarId = :1 + GROUP BY p.emailaddress", array($dew['DEWARID'])); + + foreach ($owners as $owner) { + if ($owner['EMAILADDRESS'] != '') array_push($cc, $owner['EMAILADDRESS']); + } - $owners = $this->db->pq("SELECT p.emailaddress - FROM Container c - INNER JOIN Person p ON c.ownerId = p.personId - WHERE c.dewarId = :1 - GROUP BY p.emailaddress", array($dew['DEWARID'])); + // Log the event if debugging + if ($this->debug) error_log("Dewar " . $dew['DEWARID'] . " back from beamline..."); - foreach ($owners as $owner) { - if ($owner['EMAILADDRESS'] != '') array_push($cc, $owner['EMAILADDRESS']); + $email = new Email('storage-rack', '*** Visit finished, dewar awaiting instructions ***'); + $email->data = $dew; + $email->send($dew['LCRETEMAIL'], implode(', ', $cc)); } - - // Log the event if debugging - if ($this->debug) error_log("Dewar " . $dew['DEWARID'] . " back from beamline..."); - - $email = new Email('storage-rack', '*** Visit finished, dewar awaiting instructions ***'); - $email->data = $dew; - $email->send($dew['LCRETEMAIL'], implode(', ', $cc)); } $this->_output(array('DEWARHISTORYID' => $dhid)); @@ -1147,6 +1145,7 @@ function _dispatch_dewar() global $facility_country; global $facility_courier_countries; global $dispatch_email; + global $dispatch_email_regex; global $dispatch_email_intl; global $use_shipping_service; global $shipping_service_links_in_emails; @@ -1315,6 +1314,14 @@ function _dispatch_dewar() $local_contact_email = $this->has_arg('LCEMAIL') ? $this->args['LCEMAIL'] : ''; if ($local_contact_email) $recpts .= ', ' . $local_contact_email; + if (!is_null($dispatch_email_regex)) { + foreach ($dispatch_email_regex as $address => $pattern) { + if (preg_match($pattern, $data['BARCODE'])) { + $recpts .= ', ' . $address; + } + } + } + $email->send($recpts); // Update the dewar status and storage location @@ -1343,6 +1350,7 @@ function _dispatch_dewar() function _dispatch_dewar_confirmation() { global $dispatch_email; + global $dispatch_email_regex; global $shipping_service_app_url; if (!$this->has_arg('did')) @@ -1405,6 +1413,14 @@ function _dispatch_dewar_confirmation() $local_contact_email = $this->has_arg('LCEMAIL') ? $this->args['LCEMAIL'] : ''; if ($local_contact_email) $recpts .= ', ' . $local_contact_email; + if (!is_null($dispatch_email_regex)) { + foreach ($dispatch_email_regex as $address => $pattern) { + if (preg_match($pattern, $data['BARCODE'])) { + $recpts .= ', ' . $address; + } + } + } + $email->send($recpts); // Also update the dewar status and storage location to keep it in sync with history... @@ -1626,7 +1642,7 @@ function _get_dewars() $order = $cols[$this->arg('sort_by')] . ' ' . $dir; } - $dewars = $this->db->paginate("SELECT CONCAT(p.proposalcode, p.proposalnumber) as prop, CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number) as firstexperiment, r.labcontactid, se.beamlineoperator as localcontact, se.beamlinename, TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY') as firstexperimentst, d.firstexperimentid, s.shippingid, s.shippingname, d.facilitycode, count(c.containerid) as ccount, (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end) as exp, d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid, d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, d.externalShippingIdFromSynchrotron, s.deliveryagent_agentname, d.weight, d.deliveryagent_barcode, GROUP_CONCAT(c.code SEPARATOR ', ') as containers, s.sendinglabcontactid, s.returnlabcontactid, pe.givenname, pe.familyname + $dewars = $this->db->paginate("SELECT CONCAT(p.proposalcode, p.proposalnumber) as prop, CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number) as firstexperiment, r.labcontactid, se.beamlineoperator as localcontact, se.beamlinename, TO_CHAR(se.startdate, 'HH24:MI DD-MM-YYYY') as firstexperimentst, d.firstexperimentid, s.shippingid, s.shippingname, d.facilitycode, count(c.containerid) as ccount, (case when se.visit_number > 0 then (CONCAT(p.proposalcode, p.proposalnumber, '-', se.visit_number)) else '' end) as exp, d.code, d.barcode, d.storagelocation, d.dewarstatus, d.dewarid, d.trackingnumbertosynchrotron, d.trackingnumberfromsynchrotron, d.externalShippingIdFromSynchrotron, s.deliveryagent_agentname, d.weight, d.deliveryagent_barcode, GROUP_CONCAT(c.code SEPARATOR ', ') as containers, s.sendinglabcontactid, s.returnlabcontactid, pe.givenname, pe.familyname, s.safetylevel as shippingsafetylevel FROM dewar d LEFT OUTER JOIN container c ON c.dewarid = d.dewarid INNER JOIN shipping s ON d.shippingid = s.shippingid @@ -1700,6 +1716,39 @@ function _add_dewar() $this->_output(array('DEWARID' => $id)); } + # Check new safety level is ok + function _check_safety_level() + { + $ship = $this->db->pq("SELECT cq.containerqueueid, p.safetylevel FROM dewar d + LEFT OUTER JOIN container c on c.dewarid = d.dewarid + LEFT OUTER JOIN containerqueue cq on cq.containerid = c.containerid + LEFT OUTER JOIN blsample b ON b.containerid = c.containerid + LEFT OUTER JOIN crystal cr ON cr.crystalid = b.crystalid + LEFT OUTER JOIN protein p ON p.proteinid = cr.proteinid + WHERE d.shippingid = :1", array($this->arg('sid'))); + if (strtolower($this->arg('SAFETYLEVEL')) == 'green') { + foreach ($ship as $s) { + if (strtolower($s['SAFETYLEVEL']) == 'yellow') + $this->_error('Cannot set safety level to green as one or more samples are yellow.'); + if (strtolower($s['SAFETYLEVEL']) == 'red') + $this->_error('Cannot set safety level to green as one or more samples are red.'); + } + } else if (strtolower($this->arg('SAFETYLEVEL')) == 'yellow') { + foreach ($ship as $s) { + if ($s['CONTAINERQUEUEID'] != null) + $this->_error('Cannot set safety level to yellow as one or more containers are queued.'); + if (strtolower($s['SAFETYLEVEL']) == 'red') + $this->_error('Cannot set safety level to yellow as one or more samples are red.'); + } + } else { + foreach ($ship as $s) { + if ($s['CONTAINERQUEUEID'] != null) + $this->_error('Cannot set safety level to red as one or more containers are queued.'); + } + } + } + + # Update shipment function _update_shipment() { @@ -1721,6 +1770,9 @@ function _update_shipment() if (in_array($f, array('DELIVERYAGENT_DELIVERYDATE', 'DELIVERYAGENT_SHIPPINGDATE'))) { $fl = "TO_DATE(:1, 'DD-MM-YYYY')"; } + if ($f == 'SAFETYLEVEL') { + $this->_check_safety_level(); + } $this->db->pq("UPDATE shipping SET $f=$fl WHERE shippingid=:2", array($this->arg($f), $this->arg('sid'))); @@ -2120,6 +2172,7 @@ function _get_all_containers() } // $this->db->set_debug(True); $rows = $this->db->paginate("SELECT round(TIMESTAMPDIFF('HOUR', min(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as age, case when count(ci2.containerinspectionid) > 1 then 0 else 1 end as allow_adhoc, c.scheduleid, c.screenid, sc.name as screen, c.imagerid, i.temperature as temperature, i.name as imager, TO_CHAR(max(ci.bltimestamp), 'HH24:MI DD-MM-YYYY') as lastinspection, round(TIMESTAMPDIFF('HOUR', max(ci.bltimestamp), CURRENT_TIMESTAMP)/24,1) as lastinspectiondays, count(distinct ci.containerinspectionid) as inspections, CONCAT(p.proposalcode, p.proposalnumber) as prop, c.bltimestamp, c.samplechangerlocation, c.beamlinelocation, d.dewarstatus, c.containertype, c.capacity, c.containerstatus, c.containerid, c.code as name, d.code as dewar, sh.shippingname as shipment, d.dewarid, sh.shippingid, count(distinct s.blsampleid) as samples, cq.containerqueueid, TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp, CONCAT(p.proposalcode, p.proposalnumber, '-', ses.visit_number) as visit, ses.beamlinename, c.requestedreturn, c.requestedimagerid, c.comments, c.experimenttype, c.storagetemperature, c.barcode, reg.barcode as registry, reg.containerregistryid, + sh.safetylevel as shippingsafetylevel, (SELECT sch.name FROM schedule sch WHERE sch.scheduleid = c.scheduleid) as schedule, (SELECT i2.name FROM imager i2 WHERE i2.imagerid = c.requestedimagerid) as requestedimager, (SELECT count(distinct ss.blsubsampleid) FROM blsubsample ss RIGHT OUTER JOIN blsample s2 ON s2.blsampleid = ss.blsampleid WHERE s2.containerid = c.containerid AND ss.source='manual') as subsamples, diff --git a/api/src/Queue.php b/api/src/Queue.php index 44b334099..4440d45a7 100644 --- a/api/src/Queue.php +++ b/api/src/Queue.php @@ -2,42 +2,34 @@ namespace SynchWeb; -use Stomp\Exception\StompException; -use Stomp\Stomp; +use PhpAmqpLib\Connection\AMQPStreamConnection; +use PhpAmqpLib\Message\AMQPMessage; class Queue { - private $server, $username, $password; + private $host, $port, $username, $password, $vhost; - function __construct($server, $username, $password) + function __construct($host, $port, $username, $password, $vhost) { - $this->server = $server; + $this->host = $host; + $this->port = $port; $this->username = $username; $this->password = $password; + $this->vhost = $vhost; } - function send($queue, array $message, $persistent = false, $login = null) + function send(array $message, $routing_key) { - try { - $connection = new Stomp($this->server); - - $connection->connect($this->username, $this->password); - - $connection->send( - $queue, - json_encode($message, JSON_UNESCAPED_SLASHES), - array( - 'persistent' => ($persistent === true), - 'synchweb.host' => gethostname(), - 'synchweb.user' => $login, - ) - ); - - $connection->disconnect(); - } catch (StompException $e) { - /** @noinspection PhpUnhandledExceptionInspection */ - - throw $e; - } + $connection = new AMQPStreamConnection($this->host, $this->port, $this->username, $this->password, $this->vhost); + $channel = $connection->channel(); + + $msg = new AMQPMessage( + json_encode($message, JSON_UNESCAPED_SLASHES) + ); + + $channel->basic_publish($msg, null, $routing_key); + + $channel->close(); + $connection->close(); } } diff --git a/client/src/js/models/labcontact.js b/client/src/js/models/labcontact.js index b2eff310d..9a56f9923 100644 --- a/client/src/js/models/labcontact.js +++ b/client/src/js/models/labcontact.js @@ -14,11 +14,11 @@ define(['backbone'], function(Backbone) { }, FAMILYNAME: { required: true, - pattern: 'wwdash', + pattern: 'wwsdash', }, GIVENNAME: { required: true, - pattern: 'wwdash', + pattern: 'wwsdash', }, PHONENUMBER: { required: true, diff --git a/client/src/js/models/shipment.js b/client/src/js/models/shipment.js index e1849b9bf..eccef8c27 100644 --- a/client/src/js/models/shipment.js +++ b/client/src/js/models/shipment.js @@ -18,6 +18,11 @@ define(['backbone'], function (Backbone) { pattern: 'fcode', }, + FIRSTEXPERIMENTID: { + required: false, + pattern: 'number', + }, + REMOTEORMAILIN: { required: false, }, diff --git a/client/src/js/modules/calendar/views/components/calendar-day-events.vue b/client/src/js/modules/calendar/views/components/calendar-day-events.vue index 7c2b70a20..319978312 100644 --- a/client/src/js/modules/calendar/views/components/calendar-day-events.vue +++ b/client/src/js/modules/calendar/views/components/calendar-day-events.vue @@ -21,7 +21,12 @@ class="tw-no-underline tw-text-content-page-color" > {{ session['VISIT'] }} - ({{ session['LEN'] }}) + + 🟢 + 🟡 + 🔴 + + ({{ session['LEN'] }})

- {{ session['BEAMLINEOPERATOR'] }} @@ -105,4 +110,4 @@ export default { } } - \ No newline at end of file + diff --git a/client/src/js/modules/dc/views/distl.js b/client/src/js/modules/dc/views/distl.js index e21dd9bd4..76496c70f 100644 --- a/client/src/js/modules/dc/views/distl.js +++ b/client/src/js/modules/dc/views/distl.js @@ -27,7 +27,7 @@ define(['marionette', 'modules/dc/models/distl', 'utils', }, plotSelected: function(e, ranges) { - this.trigger('plot:select', Math.floor(ranges.xaxis.from), Math.ceil(ranges.xaxis.to)) + this.trigger('plot:select', Math.round(ranges.xaxis.from), Math.round(ranges.xaxis.to)) }, plotUnselected: function(e) { @@ -112,4 +112,4 @@ define(['marionette', 'modules/dc/models/distl', 'utils', } }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/dc/views/reprocess2.js b/client/src/js/modules/dc/views/reprocess2.js index 4ffb2d81c..0b1b13aff 100644 --- a/client/src/js/modules/dc/views/reprocess2.js +++ b/client/src/js/modules/dc/views/reprocess2.js @@ -110,13 +110,19 @@ define(['backbone', 'marionette', 'views/dialog', var si = parseInt(this.model.get('SI')) var ni = parseInt(this.model.get('NUMIMG')) - if (this.ui.st.val() > (si+ni-1)) this.ui.st.val(si+ni-1) - if (this.ui.st.val() < si) this.ui.st.val(si) + if (this.ui.st.val()) { + if (this.ui.st.val() > (si+ni-1)) this.ui.st.val(si+ni-1) + if (this.ui.st.val() < si) this.ui.st.val(si) + } - if (this.ui.en.val() > (si+ni-1)) this.ui.en.val(si+ni-1) - if (this.ui.en.val() < si) this.ui.en.val(si) + if (this.ui.en.val()) { + if (this.ui.en.val() > (si+ni-1)) this.ui.en.val(si+ni-1) + if (this.ui.en.val() < si) this.ui.en.val(si) + } - this.plotview.setSelection(parseInt(this.ui.st.val()), parseInt(this.ui.en.val())) + if (this.ui.st.val() && this.ui.en.val()) { + this.plotview.setSelection(parseInt(this.ui.st.val()), parseInt(this.ui.en.val())) + } }, initialize: function(options) { @@ -377,7 +383,7 @@ define(['backbone', 'marionette', 'views/dialog', }, this) $.when.apply($, reqs).done(function() { - app.alert({ message: jobs+' reprocessing job(s) successfully submitted'}) + app.message({ message: jobs+' reprocessing job(s) successfully submitted'}) _.each(rps, function(rp) { self._enqueue({ PROCESSINGJOBID: rp.get('PROCESSINGJOBID') }) }) @@ -462,7 +468,7 @@ define(['backbone', 'marionette', 'views/dialog', reqs.push(reprocessingsweeps.save()) $.when.apply($, reqs).done(function() { - app.alert({ message: '1 reprocessing job successfully submitted'}) + app.message({ message: '1 reprocessing job successfully submitted'}) self._enqueue({ PROCESSINGJOBID: reprocessing.get('PROCESSINGJOBID') }) }) }, diff --git a/client/src/js/modules/dc/views/summary.js b/client/src/js/modules/dc/views/summary.js index bf7116830..670ad84b4 100644 --- a/client/src/js/modules/dc/views/summary.js +++ b/client/src/js/modules/dc/views/summary.js @@ -125,7 +125,7 @@ define(['marionette', { label: 'Resolution', cell: APCell, template: '<%-SHELLS.overall.RLOW%> - <%-SHELLS.overall.RHIGH%>
<%-SHELLS.innerShell.RLOW%> - <%-SHELLS.innerShell.RHIGH%>
<%-SHELLS.outerShell.RLOW%> - <%-SHELLS.outerShell.RHIGH%>', editable: false }, { label: 'Rmeas', cell: APCell, template: '<%-SHELLS.overall.RMEAS%>
<%-SHELLS.innerShell.RMEAS%>
<%-SHELLS.outerShell.RMEAS%>', editable: false }, { label: 'Completeness', cell: APCell, template: '<%-SHELLS.overall.COMPLETENESS%>
<%-SHELLS.innerShell.COMPLETENESS%>
<%-SHELLS.outerShell.COMPLETENESS%>', editable: false }, - { label: '', cell: APCell, template: ' Download MTZ file', editable: false }, + { label: '', cell: APCell, template: ' Download autoprocessing archive', editable: false }, ] diff --git a/client/src/js/modules/imaging/views/queuecontainer.js b/client/src/js/modules/imaging/views/queuecontainer.js index e21707af5..49c2dd2ef 100644 --- a/client/src/js/modules/imaging/views/queuecontainer.js +++ b/client/src/js/modules/imaging/views/queuecontainer.js @@ -99,7 +99,7 @@ define(['marionette', var self = this p.save({}, { success: function() { - app.alert({ message: 'Preset successfully saved' }) + app.message({ message: 'Preset successfully saved' }) self.column.get('plans').add(p) }, error: function() { @@ -128,8 +128,7 @@ define(['marionette', render: function() { this.$el.empty() - if (!this.model.get('CONTAINERQUEUEID')) - this.$el.html('\ + this.$el.html('\ \ ') @@ -539,6 +538,9 @@ define(['marionette', xtal: '.xtalpreview', nodata: 'input[name=nodata]', notcompleted: 'input[name=notcompleted]', + queuebutton: '.queuebutton', + unqueuebutton: '.unqueuebutton', + queuelength: '.queuelength', }, @@ -634,7 +636,7 @@ define(['marionette', }, success: function(resp) { _.each(resp, function (r) { - let ss = self.qsubsamples.fullCollection.findWhere({ BLSUBSAMPLEID: r.BLSUBSAMPLEID }) + let ss = self.typeselector.shadowCollection.findWhere({ BLSUBSAMPLEID: r.BLSUBSAMPLEID }) ss.set({ READYFORQUEUE: '0' }) }) }, @@ -650,12 +652,13 @@ define(['marionette', e.preventDefault() utils.confirm({ title: 'Unqueue Container?', - content: 'Are you sure you want to remove this container from the queue? You will loose your current place', + content: 'Are you sure you want to remove this container from the queue? You will lose your current place', callback: this.doUnqueueContainer.bind(this) }) }, doUnqueueContainer: function() { + var self = this Backbone.ajax({ url: app.apiurl+'/shipment/containers/queue', data: { @@ -663,7 +666,10 @@ define(['marionette', UNQUEUE: 1, }, success: function() { - app.alert({ message: 'Container Successfully Unqueued' }) + app.message({ message: 'Container Successfully Unqueued' }) + self.ui.unqueuebutton.hide() + self.ui.queuebutton.show() + self.model.set('CONTAINERQUEUEID', null) }, error: function() { app.alert({ message: 'Something went wrong unqueuing this container' }) @@ -711,12 +717,12 @@ define(['marionette', queueContainer: function(e) { e.preventDefault() - if (!this.qsubsamples.fullCollection.length) { + if (!this.typeselector.shadowCollection.length) { app.alert({ message: 'Please add some samples before queuing this container' }) return } - // need to validate all models here again incase they havnt been rendered + // need to validate all models here again in case they haven't been rendered this.qsubsamples.fullCollection.each(function(qs) { if (qs.get('_valid') !== undefined) return @@ -725,7 +731,7 @@ define(['marionette', console.log({ experimentCell: val }) }, this) - var invalid = this.qsubsamples.fullCollection.where({ '_valid': false }) + var invalid = this.typeselector.shadowCollection.where({ '_valid': false }) console.log('queue', invalid, invalid.length > 0) if (invalid.length > 0) { app.alert({ message: 'There are '+invalid.length+' sub samples with invalid experimental plans, please either correct or remove these from the queue' }) @@ -733,13 +739,17 @@ define(['marionette', if (inv) inv.set({ isSelected: true }) } else { + var self = this Backbone.ajax({ url: app.apiurl+'/shipment/containers/queue', data: { CONTAINERID: this.model.get('CONTAINERID') }, - success: function() { - app.alert({ message: 'Container Successfully Queued' }) + success: function(json) { + app.message({ message: 'Container Successfully Queued' }) + self.ui.unqueuebutton.show() + self.ui.queuebutton.hide() + self.model.set('CONTAINERQUEUEID', json.CONTAINERQUEUEID) }, error: function() { app.alert({ message: 'Something went wrong queuing this container' }) @@ -764,26 +774,30 @@ define(['marionette', }, refreshSubSamples: function() { - this.subsamples.fetch() + this.subsamples.fetch().done(this.onSubsamplesReady.bind(this)) }, initialize: function() { this._lastSample = null + this._subsamples_ready = [] this.platetypes = new PlateTypes() this.type = this.platetypes.findWhere({ name: this.model.get('CONTAINERTYPE') }) + this.unfilteredSubsamples = null this.subsamples = new SubSamples() this.subsamples.queryParams.cid = this.model.get('CONTAINERID') this.subsamples.state.pageSize = 10 - this.listenTo(this.subsamples, 'change:isSelected', this.selectSubSample, this) - this.listenTo(this.subsamples, 'sync add remove change:READYFORQUEUE', this.refreshQSubSamples, this) - this.subsamples.fetch() + + this._subsamples_ready.push(this.subsamples.fetch()) this.inspections = new ContainerInspections() this.inspections.queryParams.cid = this.model.get('CONTAINERID') this.inspections.setSorting('BLTIMESTAMP', 1) - this.inspections.fetch().done(this.getInspectionImages.bind(this)) + + this._subsamples_ready.push(this.inspections.fetch()) + + $.when.apply($, this._subsamples_ready).done(this.onSubsamplesReady.bind(this)) this.inspectionimages = new InspectionImages() @@ -833,6 +847,31 @@ define(['marionette', this.ui.preset.html(this.plans.opts()) }, + onSubsamplesReady: function() { + this.unfilteredSubsamples = this.subsamples.fullCollection.clone() + this.getInspectionImages() + this.refreshQSubSamples() + this.listenTo(this.subsamples, 'change:isSelected', this.selectSubSample, this) + this.listenTo(this.unfilteredSubsamples, 'sync add remove change:READYFORQUEUE', this.refreshQSubSamples, this) + this.listenTo(this.unfilteredSubsamples, 'change', this.updateQueueLength) + this.listenTo(this.model, 'change:CONTAINERQUEUEID', this.onContainerQueueIdChange) + }, + + updateQueueLength: function() { + var n = this.typeselector.shadowCollection.length + this.ui.queuelength.html(`(${n} data collection${n===1 ? '' : 's'})`) + }, + + onContainerQueueIdChange: function() { + if (!this.model.get('CONTAINERQUEUEID')) { + var models = this.unfilteredSubsamples.filter(function(m) { return m.get('CONTAINERQUEUEID') }) + _.each(models, function(model) { + model.set('READYFORQUEUE', '1') + }, this) + } + this.doOnRender() + }, + getInspectionImages: function() { this.inspectionimages.queryParams.iid = this.inspections.at(0).get('CONTAINERINSPECTIONID') this.inspectionimages.fetch().done(this.selectSample.bind(this)) @@ -844,8 +883,8 @@ define(['marionette', refreshQSubSamples: function() { if (this.model.get('CONTAINERQUEUEID')) { - this.qsubsamples.fullCollection.reset(this.subsamples.fullCollection.where({ CONTAINERQUEUEID: this.model.get('CONTAINERQUEUEID') })) - } else this.qsubsamples.fullCollection.reset(this.subsamples.fullCollection.where({ READYFORQUEUE: '1' })) + this.qsubsamples.fullCollection.reset(this.unfilteredSubsamples.where({ CONTAINERQUEUEID: this.model.get('CONTAINERQUEUEID') })) + } else this.qsubsamples.fullCollection.reset(this.unfilteredSubsamples.where({ READYFORQUEUE: '1' })) }, selectSubSample: function() { @@ -860,6 +899,7 @@ define(['marionette', onRender: function() { + this.ui.unqueuebutton.hide() this.subsamples.queryParams.nodata = this.getNoData.bind(this) this.subsamples.queryParams.notcompleted = this.getNotCompleted.bind(this) this._ready.done(this.doOnRender.bind(this)) @@ -905,7 +945,6 @@ define(['marionette', { name: '_valid', label: 'Valid', cell: table.TemplateCell, editable: false, test: '_valid', template: '' }, { name: '', cell: table.StatusCell, editable: false }, { label: '', cell: SnapshotCell, editable: false, inspectionimages: this.inspectionimages }, - { label: '', cell: ActionsCell, editable: false, plans: this.plans }, ] if (app.mobile()) { @@ -929,8 +968,15 @@ define(['marionette', if (this.model.get('CONTAINERQUEUEID')) { this.ui.rpreset.hide() + this.ui.queuebutton.hide() + this.ui.unqueuebutton.show() queuedSubSamples.push({ label: '', cell: table.StatusCell, editable: false }) queuedSubSamples.push({ label: '', cell: table.TemplateCell, editable: false, template: '' }) + } else { + this.ui.rpreset.show() + this.ui.queuebutton.show() + this.ui.unqueuebutton.hide() + queuedSubSamples.push({ label: '', cell: ActionsCell, editable: false, plans: this.plans }) } this.table2 = new TableView({ diff --git a/client/src/js/modules/samples/views/pdbs.js b/client/src/js/modules/samples/views/pdbs.js index 28708ce93..bbbd52b22 100644 --- a/client/src/js/modules/samples/views/pdbs.js +++ b/client/src/js/modules/samples/views/pdbs.js @@ -1,15 +1,28 @@ -define(['marionette'], function(Marionette) { +define(['marionette', 'utils'], function(Marionette, utils) { var UserItem = Marionette.ItemView.extend({ - template: _.template('<%-NAME%> <% if (CODE) { %>[CODE]<% } else { %>[File]<% } %> Delete'), + template: _.template(''), tagName: 'li', attributes: { 'data-testid': 'protein-pdb-list-item' }, events: { - 'click a.delete': 'deleteUser', + 'click a.delete': 'deletePDB', + 'click a.download': utils.signHandler, }, - deleteUser: function(e) { + render: function() { + UserItem.__super__.render.call(this) + const linkButton = ' EBI' + const deleteButton = ' Delete' + const downloadButton = ' Download' + if (this.model.get('CODE')) { + this.$el.append(this.model.get('NAME')+' [Code] '+linkButton+' '+deleteButton+'') + } else { + this.$el.append(this.model.get('NAME')+' [File] '+downloadButton+' '+deleteButton+'') + } + }, + + deletePDB: function(e) { this.model.destroy() }, }) @@ -30,4 +43,4 @@ define(['marionette'], function(Marionette) { }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/shipment/models/dispatch.js b/client/src/js/modules/shipment/models/dispatch.js index 195045bf3..bfbc37c60 100644 --- a/client/src/js/modules/shipment/models/dispatch.js +++ b/client/src/js/modules/shipment/models/dispatch.js @@ -24,12 +24,12 @@ define(['backbone'], function(Backbone) { GIVENNAME: { required: function () {return this.dispatchDetailsRequired}, - pattern: 'wwdash', + pattern: 'wwsdash', }, FAMILYNAME: { required: function () {return this.dispatchDetailsRequired}, - pattern: 'wwdash', + pattern: 'wwsdash', }, PHONENUMBER: { diff --git a/client/src/js/modules/shipment/views/dispatch.js b/client/src/js/modules/shipment/views/dispatch.js index 113415195..416375168 100644 --- a/client/src/js/modules/shipment/views/dispatch.js +++ b/client/src/js/modules/shipment/views/dispatch.js @@ -276,6 +276,7 @@ define(['marionette', 'views/form', this.dispatchCountry = this.ui.country.val() this.ui.courierSection.show(); this.ui.dispatchDetails.show(); + this.model.visitRequired = true this.model.dispatchDetailsRequired = true this.ui.submit.show(); if ( @@ -334,6 +335,7 @@ define(['marionette', 'views/form', ){ this.model.visitRequired = false this.ui.dispatchDetails.hide() + this.model.dispatchDetailsRequired = false this.ui.submit.text("Proceed") this.ui.shippingadvice.html("On clicking 'Proceed' you will be redirected to the new Diamond shipping service to book the shipment. Please ensure all stages of the form are completed.

") } diff --git a/client/src/js/modules/shipment/views/plate.js b/client/src/js/modules/shipment/views/plate.js index 7bc45777c..b29f44f2f 100644 --- a/client/src/js/modules/shipment/views/plate.js +++ b/client/src/js/modules/shipment/views/plate.js @@ -250,7 +250,7 @@ define(['marionette', 'backbone', 'utils', 'backbone-validation'], function(Mari this.ctx.fillStyle = sample.get(this.rankOption.value) ? utils.rainbow(val/4) - : (sample.get(this.rankOption.check) > 0 ? 'yellow' : '#dfdfdf') + : '#dfdfdf' this.ctx.fill() } else { diff --git a/client/src/js/modules/shipment/views/shipment.js b/client/src/js/modules/shipment/views/shipment.js index 6932f8645..bbde464f3 100644 --- a/client/src/js/modules/shipment/views/shipment.js +++ b/client/src/js/modules/shipment/views/shipment.js @@ -200,7 +200,7 @@ define(['marionette', var edit = new Editable({ model: this.model, el: this.$el }) edit.create('SHIPPINGNAME', 'textlong') - edit.create('SAFETYLEVEL', 'select', { data: {'Green': 'Green', 'Yellow':'Yellow', 'Red': 'Red'} }) + edit.create('SAFETYLEVEL', 'select', { data: {'Green': 'Green', 'Yellow':'Yellow', 'Red': 'Red'}, alert: true, revert: true }) edit.create('COMMENTS', 'textarea') edit.create('DELIVERYAGENT_AGENTNAME', 'text') edit.create('DELIVERYAGENT_AGENTCODE', 'text') diff --git a/client/src/js/modules/shipment/views/shipmentadd.js b/client/src/js/modules/shipment/views/shipmentadd.js index a5fea270b..602e33487 100644 --- a/client/src/js/modules/shipment/views/shipmentadd.js +++ b/client/src/js/modules/shipment/views/shipmentadd.js @@ -63,6 +63,7 @@ define(['marionette', 'views/form', 'click a.add_lc': 'addLC', 'click @ui.noexp': 'updateFirstExp', 'click @ui.dynamic': 'updateDynamicSchedule', + 'change select[name^=SAFETYLEVEL]': 'changeSafetyLevel', }, ui: { @@ -73,6 +74,8 @@ define(['marionette', 'views/form', noexp: 'input[name=noexp]', dynamic: 'input[name=DYNAMIC]', // A checkbox to indicate dynamic/remote mail-in scheduling comments: 'textarea[name=COMMENTS]', // We need this so we can prefill comments to aid users + safetylevel: 'select[name^=SAFETYLEVEL]', + udcresponsive: '.udcresponsive', }, addLC: function(e) { @@ -97,12 +100,24 @@ define(['marionette', 'views/form', app.alert({ message: 'Something went wrong registering this shipment, please try again'}) }, + changeSafetyLevel: function() { + if (this.ui.safetylevel.val() === 'Green') { + this.ui.udcresponsive.show() + } else { + this.ui.noexp.prop('checked', false) + this.updateFirstExp() + this.ui.dynamic.prop('checked', false) + this.updateDynamicSchedule() + this.ui.udcresponsive.hide() + } + }, + updateFirstExp: function() { if (this.ui.noexp.is(':checked')) { this.ui.first.html('') this.ui.dynamic.prop('checked', false) } else { - this.ui.first.html(this.visits.opts()) + this.ui.first.html(''+this.visits.opts()) } }, @@ -121,7 +136,7 @@ define(['marionette', 'views/form', } } else { this.model.validation.REMOTEORMAILIN.required = false - this.ui.first.html(this.visits.opts()) + this.ui.first.html(''+this.visits.opts()) this.$el.find(".remoteform").hide() if (industrial_visit) { this.$el.find(".remoteormailin").hide() diff --git a/client/src/js/modules/summary/views/summary.vue b/client/src/js/modules/summary/views/summary.vue index e57f83fed..9eb3ebcae 100644 --- a/client/src/js/modules/summary/views/summary.vue +++ b/client/src/js/modules/summary/views/summary.vue @@ -397,8 +397,8 @@

- +

--> diff --git a/client/src/js/modules/types/mx/shipment/views/container-mixin.js b/client/src/js/modules/types/mx/shipment/views/container-mixin.js index f622ac683..e29c60b4d 100644 --- a/client/src/js/modules/types/mx/shipment/views/container-mixin.js +++ b/client/src/js/modules/types/mx/shipment/views/container-mixin.js @@ -128,7 +128,7 @@ export default { proteinsCollection.queryParams.external = 1 } - proteinsCollection.queryParams.SAFETYLEVEL = 'ALL' + proteinsCollection.queryParams.SAFETYLEVEL = this.shippingSafetyLevel const result = await this.$store.dispatch('getCollection', proteinsCollection) this.proteins = result.toJSON() diff --git a/client/src/js/modules/types/mx/shipment/views/mx-container-add.vue b/client/src/js/modules/types/mx/shipment/views/mx-container-add.vue index f08642bef..865384a38 100644 --- a/client/src/js/modules/types/mx/shipment/views/mx-container-add.vue +++ b/client/src/js/modules/types/mx/shipment/views/mx-container-add.vue @@ -90,9 +90,16 @@
+ + Cannot queue container until shipment safety level is set + + + Cannot queue containers in {{ shippingSafetyLevel }} shipments +
@@ -461,6 +468,7 @@ export default { // The dewar that this container will belong to dewar: null, + shippingSafetyLevel: null, processingPipeline: '', processingPipelines: [], @@ -542,23 +550,6 @@ export default { } } }, - AUTOMATED: { - immediate: true, - handler: function(newVal) { - const proteinsCollection = new DistinctProteins() - // If now on, add safety level to query - // Automated collections limited to GREEN Low risk samples - if (newVal) { - proteinsCollection.queryParams.SAFETYLEVEL = 'GREEN'; - } else { - proteinsCollection.queryParams.SAFETYLEVEL = 'ALL'; - } - this.$store.dispatch('getCollection', proteinsCollection).then( (result) => { - this.proteins = result.toJSON() - }) - app.trigger('samples:automated', newVal) - } - }, CONTAINERREGISTRYID: { immediate: true, handler: function(newVal) { @@ -593,6 +584,7 @@ export default { created: function() { this.containerType = INITIAL_CONTAINER_TYPE this.dewar = this.options.dewar.toJSON() + this.shippingSafetyLevel = this.dewar.SHIPPINGSAFETYLEVEL this.DEWARID = this.dewar.DEWARID this.resetSamples(this.containerType.CAPACITY) @@ -674,7 +666,7 @@ export default { await this.$store.dispatch('samples/save', containerId) this.$store.commit('notifications/addNotification', { - message: `New Container created, click here to view it`, + message: `New Container created, click here to view it. Remember to add sequences and PDBs if needed.`, level: 'info', persist: true }) diff --git a/client/src/js/modules/types/mx/shipment/views/mx-container-view.vue b/client/src/js/modules/types/mx/shipment/views/mx-container-view.vue index 20c5b46ac..fcd97ec9a 100644 --- a/client/src/js/modules/types/mx/shipment/views/mx-container-view.vue +++ b/client/src/js/modules/types/mx/shipment/views/mx-container-view.vue @@ -106,24 +106,28 @@ @click="onUnQueueContainer" > Unqueue + + Cannot queue container until shipment safety level is set + + + Cannot queue containers in {{ shippingSafetyLevel }} shipments + + + There was an error submitting the container to the queue. Please fix any errors in the samples table. + Try again + Cancel + - - There was an error submitting the container to the queue. Please fix any errors in the samples table. - Try again - Cancel - - - Queue this container for Auto Collect - + Queue this container for Auto Collect @@ -324,6 +328,7 @@ export default { dewarsCollection: null, selectedDewarId: null, selectedShipmentId: null, + shippingSafetyLevel: null, editingSampleLocation: null } }, @@ -354,6 +359,7 @@ export default { loadContainerData() { this.container = Object.assign({}, this.containerModel.toJSON()) this.containerId = this.containerModel.get('CONTAINERID') + this.shippingSafetyLevel = this.containerModel.get('SHIPPINGSAFETYLEVEL') this.containerQueueId = this.containerModel.get('CONTAINERQUEUEID') if (this.containerQueueId) this.QUEUEFORUDC = true }, @@ -477,6 +483,7 @@ export default { }) this.$nextTick(() => { this.loadContainerData() + this.getProteins() // TODO: Toggle Auto in the samples table }) } catch (error) { @@ -497,6 +504,7 @@ export default { this.$emit('update-container-state', { CONTAINERQUEUEID: null }) this.$nextTick(() => { this.loadContainerData() + this.getProteins() // TODO: Toggle Auto in the samples table }) } catch (error) { diff --git a/client/src/js/modules/visits/views/visit_list.vue b/client/src/js/modules/visits/views/visit_list.vue index 5b1abbf84..26c019ee9 100644 --- a/client/src/js/modules/visits/views/visit_list.vue +++ b/client/src/js/modules/visits/views/visit_list.vue @@ -16,15 +16,16 @@
@@ -57,7 +58,10 @@ - + 🟢 + 🟡 + 🔴 +
@@ -117,30 +121,39 @@ export default { visits: [], dewars: [], searchVisit : '', + orderBy: '', + order: 1, headers: [ { key: "STARTDATE", - title: 'Start' + title: 'Start', + order: 'ST' }, { key: "ENDDATE", - title: 'End' + title: 'End', + order: 'EN' }, { key: "VIS", title: 'Number' }, { - key: "BEAMLINENAME", + key: "BL", title: 'Beamline' }, + { + key: "ERA", + title: 'ERA' + }, { key: "DEWARS", title: 'Dewar(s)' }, { key: "UNIQUELCS", - title: 'Local Contact' + title: 'Local Contact', + order: 'LC' }, { key: "COMMENTS", @@ -171,6 +184,7 @@ export default { window.location.href = '/proposals/'; } this.fetchData() + this.fetchData = _.debounce(this.fetchData, 500) }, methods: { async fetchData() { @@ -181,8 +195,18 @@ export default { page: this.currentPage, per_page: this.pageSize, prop: this.proposal, - s: this.searchVisit, + order: 'order', + directions: { + '-1': 'asc', + '1': 'desc', + }, + }; + this.visitCollection.state = { + sortKey: 'sort_by', + order: this.order, }; + if (this.searchVisit) this.visitCollection.queryParams.s = this.searchVisit; + if (this.orderBy) this.visitCollection.queryParams.sort_by = this.orderBy; const results = await this.$store.dispatch('getCollection', this.visitCollection); this.visits = results.toJSON().map((e) => { @@ -252,6 +276,15 @@ export default { window.location.href = 'dc/visit/' + this.proposal + '-' + visit.VIS; } }, + headerClick(event) { + if (this.orderBy === event.target.id) { + this.order = -this.order; + } else { + this.order = 1; + } + this.orderBy = event.target.id; + this.fetchData(); + }, handleFocusOut(visit) { // if click outside of active input box then input returns to text if(visit.clicked) { diff --git a/client/src/js/templates/dc/dc.html b/client/src/js/templates/dc/dc.html index 4237f4515..b23bb657a 100644 --- a/client/src/js/templates/dc/dc.html +++ b/client/src/js/templates/dc/dc.html @@ -24,7 +24,7 @@

<% if (SI != 1 ) { %>
  • First Image: <%-SI%>
  • <% } %> <% if ((KAPPA && KAPPA !=0) || (PHI && PHI != 0) || (CHISTART && CHISTART !=0)) { %>
  • <% if (KAPPA != null) { %>κ: <%-KAPPA%>°<% } %> <% if (PHI != null) { %>φ: <%-PHI%>°<% } %> <% if (CHISTART != null) { %>χ: <%-CHISTART%>°<% } %>
  • <% } %>
  • Resolution: <%-RESOLUTION%>Å
  • -
  • Wavelength: <%-WAVELENGTH%>Å
  • +
  • Wavelength: <%-WAVELENGTH%>Å (<%-ENERGY%>eV)
  • Exposure: <%-EXPOSURETIME%>s
  • <%if (DCC > 1 && TOTALDOSE) { %>
  • Total Dose: <%-TOTALDOSE%>MGy
  • diff --git a/client/src/js/templates/dc/dc_autoproc.html b/client/src/js/templates/dc/dc_autoproc.html index cde85c1f9..94c69e5d9 100644 --- a/client/src/js/templates/dc/dc_autoproc.html +++ b/client/src/js/templates/dc/dc_autoproc.html @@ -22,6 +22,7 @@ <% } %> + Processing Log Plots Archive Logs & Files diff --git a/client/src/js/templates/dc/edge.html b/client/src/js/templates/dc/edge.html index 1349e0ba5..4e2697a12 100644 --- a/client/src/js/templates/dc/edge.html +++ b/client/src/js/templates/dc/edge.html @@ -9,11 +9,11 @@

      -
    • Scan File: <%-FILETEMPLATE%>
    • -
    • E(Peak): <%-EPK.toFixed(1) %>eV (<% print ((12398.4193/EPK).toFixed(4)) %>Å)
    • -
    • f’’: <%-NUMIMG%> / f’: <%-RESOLUTION%>e
    • -
    • E(Inf): <%-EIN.toFixed(1) %>eV (<% print((12398.4193/EIN).toFixed(4)) %>Å)
    • -
    • f’’: <%-WAVELENGTH%> / f’: <%-AXISRANGE%>e
    • +
    • Scan File: <%-FILETEMPLATE%>
    • +
    • E(Peak): <%-EPK%>eV (<%-WPK%>Å)
    • +
    • f’’: <%-NUMIMG%>e- / f’: <%-RESOLUTION%>e-
    • +
    • E(Inf): <%-EIN%>eV (<%-WIN%>Å)
    • +
    • f’’: <%-WAVELENGTH%>e- / f’: <%-AXISRANGE%>e-
    • Exposure: <%-EXPOSURETIME%>s
    • Transmission: <%-TRANSMISSION%>%
    • Beamsize: <%-BSX%>x<%-BSY%>μm
    • diff --git a/client/src/js/templates/dc/grid.html b/client/src/js/templates/dc/grid.html index 4232c7392..996258409 100644 --- a/client/src/js/templates/dc/grid.html +++ b/client/src/js/templates/dc/grid.html @@ -8,7 +8,7 @@

    • &<%-ROTATIONAXIS%>; Start: <%-AXISSTART%>°
    • <% if ((KAPPA && KAPPA !=0) || (PHI && PHI != 0) || (CHISTART && CHISTART !=0)) { %>
    • <% if (KAPPA != null) { %>κ: <%-KAPPA%>°<% } %> <% if (PHI != null) { %>φ: <%-PHI%>°<% } %> <% if (CHISTART != null) { %>χ: <%-CHISTART%>°<% } %>
    • <% } %>
    • Resolution: <%-RESOLUTION%>Å
    • -
    • Wavelength: <%-WAVELENGTH%>Å
    • +
    • Wavelength: <%-WAVELENGTH%>Å (<%-ENERGY%>eV)
    • Exposure: <%-EXPOSURETIME%>s
    • Transmission: <%-TRANSMISSION%>%
    • Beamsize: <%-BSX%>x<%-BSY%>μm
    • diff --git a/client/src/js/templates/dc/mca.html b/client/src/js/templates/dc/mca.html index 69da71439..9bea88fde 100644 --- a/client/src/js/templates/dc/mca.html +++ b/client/src/js/templates/dc/mca.html @@ -10,11 +10,11 @@

        -
      • Energy: <%-WAVELENGTH%>eV
      • +
      • Energy: <%-ENERGY%>eV (<%-WAVELENGTH%>Å)
      • Exposure: <%-EXPOSURETIME%>s
      • Transmission: <%-TRANSMISSION%>%
      • Beamsize: <%-BSX%>x<%-BSY%>μm
      • Axis Position: <%-AXISSTART%>°
      • Comment: <%-COMMENTS%>
      - \ No newline at end of file + diff --git a/client/src/js/templates/imaging/queuecontainer.html b/client/src/js/templates/imaging/queuecontainer.html index cff3c820b..4c84d99c9 100644 --- a/client/src/js/templates/imaging/queuecontainer.html +++ b/client/src/js/templates/imaging/queuecontainer.html @@ -2,8 +2,7 @@

      Prepare Container for Data Collection

      This pages allows you to queue samples in a container for data collection

      -<% if (CONTAINERQUEUEID) { %> -

      +

      <% if (['disposed', 'in_storage', null].indexOf(CONTAINERSTATUS) > -1) { %> This container is queued for data collection, you can not modify it without unqueuing it Unqueue @@ -11,7 +10,6 @@

      Prepare Container for Data Collection

      This container is en route for data collection, it cannot be unqueued. <% } %>

      -<% } %>
      @@ -65,10 +63,12 @@

      Queued Samples

      -<% if (!CONTAINERQUEUEID) { %> +

      Queue Plate

      Queuing the container will make the queued items immutable, please make sure you have added all sub samples, and that they have valid experimental plans

      +
      -<% } %> +
      + diff --git a/client/src/js/templates/shipment/containerli.html b/client/src/js/templates/shipment/containerli.html index b3f73d39a..c93be9f2b 100644 --- a/client/src/js/templates/shipment/containerli.html +++ b/client/src/js/templates/shipment/containerli.html @@ -1,10 +1,13 @@ <%- NAME %> (<%-SAMPLES%> samples) <% if (REQUESTEDIMAGERID) { %> - [Req: <%-REQUESTEDIMAGER%>] + [Req: <%-REQUESTEDIMAGER%>] <% } %> <% if (IMAGERID) { %> - [Img: <%-IMAGER%>] + [Img: <%-IMAGER%>] + <% } %> + <% if (VISIT) { %> + (<%-VISIT%>) <% } %> Print Container Report diff --git a/client/src/js/templates/shipment/shipmentadd.html b/client/src/js/templates/shipment/shipmentadd.html index 3866fe012..927b68a39 100644 --- a/client/src/js/templates/shipment/shipmentadd.html +++ b/client/src/js/templates/shipment/shipmentadd.html @@ -52,12 +52,14 @@

      Add New Shipment

      - - + + + +
      diff --git a/client/src/js/utils/editable.js b/client/src/js/utils/editable.js index 90221df24..a33d32027 100644 --- a/client/src/js/utils/editable.js +++ b/client/src/js/utils/editable.js @@ -158,10 +158,13 @@ define(['marionette', */ create: function(attr, type, options, refetch) { var submit = function(value, settings) { + prevValue = this.model.get(attr) this.model.set(attr, value) console.log('valid', this.model.isValid(true), attr, 'changed', this.model.changedAttributes()) var self = this + toReturn = refetch ? '' : _.escape(value) this.model.save(this.model.changedAttributes(), { patch: true, validate: false, + async: !(options && options.revert), success: function() { if (refetch) self.model.fetch() }, @@ -179,10 +182,14 @@ define(['marionette', if (json.message) app.alert({ message: json.message }) else app.alert({ message: 'Something went wrong' }) } + if(options && options.revert) { + self.model.set(attr, prevValue) + toReturn = prevValue + } } }) - return refetch ? 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