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/Cell.php b/api/src/Page/Cell.php index 80fbcc071..e0e0b7d4b 100644 --- a/api/src/Page/Cell.php +++ b/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'])); diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php index 34e59f5f2..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 @@ -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']); diff --git a/api/src/Page/Download.php b/api/src/Page/Download.php index a1ed29bca..6333e6b0e 100644 --- a/api/src/Page/Download.php +++ b/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); } diff --git a/api/src/Page/Sample.php b/api/src/Page/Sample.php index d1a051493..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'), @@ -2062,6 +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 $pdb['CONTENTS']; + } + # ------------------------------------------------------------------------ # Add a new pdb function _add_pdb() diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php index fdb44b725..24fbeea13 100644 --- a/api/src/Page/Shipment.php +++ b/api/src/Page/Shipment.php @@ -484,10 +484,10 @@ function _add_history() if (!$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... diff --git a/client/src/js/models/protein.js b/client/src/js/models/protein.js index 8cafd4338..2ef5f4758 100644 --- a/client/src/js/models/protein.js +++ b/client/src/js/models/protein.js @@ -16,7 +16,7 @@ define(['backbone', 'markdown'], function(Backbone, markdown) { }, refreshOptions: function() { - if (this.get('SEQUENCE')) this.attributes.SEQUENCEMD = markdown.toHTML(this.get('SEQUENCE')) + if (this.get('SEQUENCE')) this.set('SEQUENCEMD', markdown.toHTML(this.get('SEQUENCE'))) }, validation: { diff --git a/client/src/js/models/visit.js b/client/src/js/models/visit.js index ef8a86874..f62f49407 100644 --- a/client/src/js/models/visit.js +++ b/client/src/js/models/visit.js @@ -51,10 +51,10 @@ define(['backbone', 'backbone-validation', 'luxon'], function(Backbone, BackBone addDate: function() { var { DateTime } = luxon - this.attributes.ENISO = DateTime.fromISO(this.get('ENISO'), { zone: this.dateTimeZone }) - this.attributes.STISO = DateTime.fromISO(this.get('STISO'), { zone: this.dateTimeZone }) - this.attributes.LEN = Number(this.attributes.ENISO.diff(this.attributes.STISO)/(3600*1000)).toFixed(2); - this.attributes.VISITDETAIL = this.get('VISIT')+' ('+this.get('BL')+': '+this.get('ST')+')' + this.set('ENISO', DateTime.fromISO(this.get('ENISO'), { zone: this.dateTimeZone })) + this.set('STISO', DateTime.fromISO(this.get('STISO'), { zone: this.dateTimeZone })) + this.set('LEN', Number(this.get('ENISO').diff(this.get('STISO'))/(3600*1000)).toFixed(2)) + this.set('VISITDETAIL', this.get('VISIT')+' ('+this.get('BL')+': '+this.get('ST')+')') }, dateTimeZone: 'Europe/London' diff --git a/client/src/js/modules/cell/views/beamlines.js b/client/src/js/modules/cell/views/beamlines.js index d5481b991..1fd4470af 100644 --- a/client/src/js/modules/cell/views/beamlines.js +++ b/client/src/js/modules/cell/views/beamlines.js @@ -30,28 +30,27 @@ define(['marionette', 'utils', }) var bl = [] + var data = {} _.each(bls, function(i, b) { + data[b] = {} bl.push(b) ticks.push([bl.length-1, b]) + _.each(years, function(x, y) { + data[b][y] = 0 + }) }) - _.each(this.model.get('data')[did], function(v, i) { - var y = yrs.indexOf(v.YEAR) - var b = bl.indexOf(v.BL) - //console.log('d', y, b) - d[y].data.push([b, v.COUNT]) - }) - - function ascsort(a,b) { - if (a[0] == b[0]) return 0 - else return (a[0] < b[0]) ? -1 : 1 - } - - _.each(d, function(d,i) { - d.data.sort(ascsort) - }) + _.each(this.model.get('data')[did], function(v, i) { + data[v.BL][v.YEAR] = v.COUNT + }) - console.log(d) + _.each(data, function(el, beamline) { + _.each(el, function(count, year) { + var y = yrs.indexOf(year) + var b = bl.indexOf(beamline) + d[y].data.push([b, count]) + }) + }) var options = { series: { diff --git a/client/src/js/modules/dc/models/autointegration.js b/client/src/js/modules/dc/models/autointegration.js index 6bf2df8e5..b47510ea2 100644 --- a/client/src/js/modules/dc/models/autointegration.js +++ b/client/src/js/modules/dc/models/autointegration.js @@ -13,13 +13,13 @@ define(['backbone'], function(Backbone){ var shells = this.get('SHELLS') if (!shells) return - this.attributes.CLASS = { RMERGE: {}, RMEAS: {}, COMPLETENESS: {} } + this.set('CLASS', { RMERGE: {}, RMEAS: {}, COMPLETENESS: {} }) _.each(['overall', 'innerShell', 'outerShell'], function(k) { var c = shells[k] ? shells[k].COMPLETENESS : null - this.attributes.CLASS.COMPLETENESS[k] = c > 95 ? 'active' : (c > 80 ? 'minor' : 'inactive') + this.set('CLASS[COMPLETENESS[k]]', c > 95 ? 'active' : (c > 80 ? 'minor' : 'inactive')) var r = shells[k] ? shells[k].RMEAS : null - this.attributes.CLASS.RMEAS[k] = r < 0.5 ? 'active' : (r < 0.6 ? 'minor' : 'inactive') + this.set('CLASS[RMEAS[k]]', r < 0.5 ? 'active' : (r < 0.6 ? 'minor' : 'inactive')) }, this) }, diff --git a/client/src/js/modules/dc/models/dccomment.js b/client/src/js/modules/dc/models/dccomment.js index 2a7913eee..41e8bc75b 100644 --- a/client/src/js/modules/dc/models/dccomment.js +++ b/client/src/js/modules/dc/models/dccomment.js @@ -27,11 +27,11 @@ define(['backbone', 'markdown'], function(Backbone, markdown) { }, addDate: function() { - this.attributes.CREATETIMEISO = new Date(this.get('CREATETIME')) - this.attributes.MODTIMEISO = new Date(this.get('MODTIME')) - if (this.get('COMMENTS')) this.attributes.COMMENTSMD = markdown.toHTML(this.get('COMMENTS')) + this.set('CREATETIMEISO', new Date(this.get('CREATETIME'))) + this.set('MODTIMEISO', new Date(this.get('MODTIME'))) + if (this.get('COMMENTS')) this.set('COMMENTSMD', markdown.toHTML(this.get('COMMENTS'))) } }) -}) \ 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 6dee03148..0b1b13aff 100644 --- a/client/src/js/modules/dc/views/reprocess2.js +++ b/client/src/js/modules/dc/views/reprocess2.js @@ -162,8 +162,8 @@ define(['backbone', 'marionette', 'views/dialog', if (e) e.preventDefault() if (this.aps.length) { - var e = this.aps.at(0) - var c = e.get('CELL') + const a = this.aps.at(0) + const c = a.get('CELL') this.ui.a.val(c['CELL_A']).trigger('change') this.ui.b.val(c['CELL_B']).trigger('change') @@ -172,7 +172,7 @@ define(['backbone', 'marionette', 'views/dialog', this.ui.be.val(c['CELL_BE']).trigger('change') this.ui.ga.val(c['CELL_GA']).trigger('change') - this.ui.sg.val(e['SG']).trigger('change') + this.ui.sg.val(a['SG']).trigger('change') } }, @@ -300,11 +300,11 @@ define(['backbone', 'marionette', 'views/dialog', } var self = this + var reqs = [] // Integrate individually if (this.ui.ind.is(':checked')) { var jobs = 0 - var reqs = [] var rps = [] _.each(s, function(sw) { var p = this.pipelines.findWhere({ VALUE: sw.get('PIPELINE') }) @@ -405,7 +405,6 @@ define(['backbone', 'marionette', 'views/dialog', return } - var reqs = [] reqs.push(reprocessing.save({}, { success: function() { var reprocessingparams = new ReprocessingParameters() diff --git a/client/src/js/modules/dc/views/reprocessoverview.js b/client/src/js/modules/dc/views/reprocessoverview.js index 50970dc61..1f78946e1 100644 --- a/client/src/js/modules/dc/views/reprocessoverview.js +++ b/client/src/js/modules/dc/views/reprocessoverview.js @@ -53,14 +53,14 @@ define(['marionette', }, render: function() { - var columns = [ + var pcolumns = [ { name: 'PARAMETERKEY', label: 'Key', cell: 'string', editable: false }, { name: 'PARAMETERVALUE', label: 'Value', cell: 'string', editable: false }, ] var ptable = new TableView({ collection: this.params, - columns: columns, + columns: pcolumns, loading: false, pages: false, backgrid: { emptyText: 'No parameters found' }, @@ -68,14 +68,14 @@ define(['marionette', this.$el.html(ptable.render().$el) - var columns = [ + var scolumns = [ { label: 'Files', cell: table.TemplateCell, editable: false, template: '<%-IMAGEDIRECTORY%><%-IMAGEPREFIX%>_<%-DATACOLLECTIONNUMBER%>' }, { label: 'Image #', cell: table.TemplateCell, editable: false, template: '<%-STARTIMAGE%> - <%-ENDIMAGE%>' }, ] var stable = new TableView({ collection: this.sweeps, - columns: columns, + columns: scolumns, loading: false, pages: false, backgrid: { emptyText: 'No image sweeps found' }, diff --git a/client/src/js/modules/dc/views/samplechanger.js b/client/src/js/modules/dc/views/samplechanger.js index a76a7c267..2ab1e9fd3 100644 --- a/client/src/js/modules/dc/views/samplechanger.js +++ b/client/src/js/modules/dc/views/samplechanger.js @@ -162,11 +162,11 @@ define(['marionette', 'utils/canvas', 'utils', // Draw Grid this.ctx.clearRect(0, 0, this.canvas.width, this.canvas.height) //this.ctx.drawImage(this.numbers, 0, 0, this.canvas.width, this.canvas.height) - for (var j = 0; j < this.sc; j++) { + for (var n = 0; n < this.sc; n++) { this.ctx.fillStyle = '#000' this.ctx.font = "11px Arial" this.ctx.lineWidth = 1 - this.ctx.fillText(j+1,10,this.sh*j+this.tpad+4); + this.ctx.fillText(n+1,10,this.sh*n+this.tpad+4); } for (var i = 0; i < this.positions; i++) { 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/fault/models/component.js b/client/src/js/modules/fault/models/component.js index 7f4a66ab7..54b26121d 100644 --- a/client/src/js/modules/fault/models/component.js +++ b/client/src/js/modules/fault/models/component.js @@ -8,15 +8,15 @@ define(['backbone'], function(Backbone) { }, initialize: function(options) { this.on('change', this._add_id, this) - this._add_id() + this._add_id() }, urlRoot: '/fault/com', idAttribute: 'COMPONENTID', _add_id: function() { - this.attributes.ID = this.get('COMPONENTID') + this.set('ID', this.get('COMPONENTID')) }, }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/fault/models/fault.js b/client/src/js/modules/fault/models/fault.js index 9d9c94d1d..acf9dfd05 100644 --- a/client/src/js/modules/fault/models/fault.js +++ b/client/src/js/modules/fault/models/fault.js @@ -22,11 +22,11 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi }, refreshOptions: function() { - this.attributes.RESOLVEDTEXT = this.resolvedOptions[this.get('RESOLVED')] - this.attributes.BEAMTIMELOSTTEXT = this.btlOptions[this.get('BEAMTIMELOST')] + this.set('RESOLVEDTEXT', this.resolvedOptions[this.get('RESOLVED')]) + this.set('BEAMTIMELOSTTEXT', this.btlOptions[this.get('BEAMTIMELOST')]) - if (this.get('DESCRIPTION')) this.attributes.DESCRIPTIONMD = markdown.toHTML(this.get('DESCRIPTION')) - if (this.get('RESOLUTION')) this.attributes.RESOLUTIONMD = markdown.toHTML(this.get('RESOLUTION')) + if (this.get('DESCRIPTION')) this.set('DESCRIPTIONMD', markdown.toHTML(this.get('DESCRIPTION'))) + if (this.get('RESOLUTION')) this.set('RESOLUTIONMD', markdown.toHTML(this.get('RESOLUTION'))) }, validation: { diff --git a/client/src/js/modules/fault/models/subcomponent.js b/client/src/js/modules/fault/models/subcomponent.js index f96e950af..1c6856212 100644 --- a/client/src/js/modules/fault/models/subcomponent.js +++ b/client/src/js/modules/fault/models/subcomponent.js @@ -8,12 +8,12 @@ define(['backbone'], function(Backbone) { }, initialize: function(options) { this.on('change', this._add_id, this) - this._add_id() + this._add_id() }, urlRoot: '/fault/scom', idAttribute: 'SUBCOMPONENTID', _add_id: function() { - this.attributes.ID = this.get('SUBCOMPONENTID') + this.set('ID', this.get('SUBCOMPONENTID')) }, }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/fault/models/system.js b/client/src/js/modules/fault/models/system.js index bd4f02f6c..5a59cd5be 100644 --- a/client/src/js/modules/fault/models/system.js +++ b/client/src/js/modules/fault/models/system.js @@ -13,8 +13,8 @@ define(['backbone'], function(Backbone) { urlRoot: '/fault/sys', idAttribute: 'SYSTEMID', _add_id: function() { - this.attributes.ID = this.get('SYSTEMID') + this.set('ID', this.get('SYSTEMID')) }, }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/imaging/views/queuecontainer.js b/client/src/js/modules/imaging/views/queuecontainer.js index 9de3e613f..49c2dd2ef 100644 --- a/client/src/js/modules/imaging/views/queuecontainer.js +++ b/client/src/js/modules/imaging/views/queuecontainer.js @@ -692,10 +692,11 @@ define(['marionette', }, applyModel: function(modelParameter, isLimitedToSelected) { + var models = null if (isLimitedToSelected) { - var models = this.qsubsamples.where({ isGridSelected: true }) + models = this.qsubsamples.where({ isGridSelected: true }) } else { - var models = this.qsubsamples.fullCollection.toArray() + models = this.qsubsamples.fullCollection.toArray() } _.each(models, function(model) { if (modelParameter.get('EXPERIMENTKIND') !== model.get('EXPERIMENTKIND')) return @@ -773,7 +774,7 @@ define(['marionette', }, refreshSubSamples: function() { - this.subsamples.fetch() + this.subsamples.fetch().done(this.onSubsamplesReady.bind(this)) }, initialize: function() { 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/containerreport.js b/client/src/js/modules/shipment/models/containerreport.js index 29d7c8085..33cf734f3 100644 --- a/client/src/js/modules/shipment/models/containerreport.js +++ b/client/src/js/modules/shipment/models/containerreport.js @@ -14,7 +14,7 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi }, refreshOptions: function() { - if (this.get('REPORT')) this.attributes.REPORTMD = markdown.toHTML(this.get('REPORT')) + if (this.get('REPORT')) this.set('REPORTMD', markdown.toHTML(this.get('REPORT'))) }, validation: { diff --git a/client/src/js/modules/shipment/models/dewarreport.js b/client/src/js/modules/shipment/models/dewarreport.js index b167c0c6d..6ace09e45 100644 --- a/client/src/js/modules/shipment/models/dewarreport.js +++ b/client/src/js/modules/shipment/models/dewarreport.js @@ -14,7 +14,7 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi }, refreshOptions: function() { - if (this.get('REPORT')) this.attributes.REPORTMD = markdown.toHTML(this.get('REPORT')) + if (this.get('REPORT')) this.set('REPORTMD', markdown.toHTML(this.get('REPORT'))) }, validation: { @@ -37,4 +37,4 @@ define(['backbone', 'markdown', 'models/wfile'], function(Backbone, markdown, Fi } } }, File)) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/shipment/views/containerregistry.js b/client/src/js/modules/shipment/views/containerregistry.js index 4bfc20f89..e350702c7 100644 --- a/client/src/js/modules/shipment/views/containerregistry.js +++ b/client/src/js/modules/shipment/views/containerregistry.js @@ -116,7 +116,7 @@ define(['marionette', this.listenTo(this.proposals, 'backgrid:selected', this.selectModel, this) this.proposals.fetch() - var columns = [ + var columns2 = [ { label: '', cell: 'select-row', headerCell: 'select-all', editable: false }, { name: 'PROPOSALCODE', label: 'Code', cell: 'string', editable: false }, { name: 'PROPOSALNUMBER', label: 'Number', cell: 'string', editable: false }, @@ -126,7 +126,7 @@ define(['marionette', this.table2 = new TableView({ collection: this.proposals, - columns: columns, tableClass: 'proposals', filter: 's', search: options.params.s, loading: true, noPageUrl: true, noSearchUrl: true, + columns: columns2, tableClass: 'proposals', filter: 's', search: options.params.s, loading: true, noPageUrl: true, noSearchUrl: true, backgrid: { emptyText: 'No proposals found' } }) @@ -175,4 +175,4 @@ define(['marionette', } }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/shipment/views/manifest.js b/client/src/js/modules/shipment/views/manifest.js index ff40fd8db..748df41bc 100644 --- a/client/src/js/modules/shipment/views/manifest.js +++ b/client/src/js/modules/shipment/views/manifest.js @@ -57,14 +57,14 @@ define(['marionette', var d = new Date() _.each([d.getFullYear(), d.getFullYear()-1], function(y) { _.each(_.range(1,13), function(m) { - var m = (m < 10 ? ('0'+m) : m)+'-'+y + m = (m < 10 ? ('0'+m) : m)+'-'+y this.ui.month.append('') }, this) }, this) - var m = d.getMonth() +1 - var cur = (m < 10 ? ('0'+m) : m)+'-'+d.getFullYear() + var mon = d.getMonth() +1 + var cur = (mon < 10 ? ('0'+mon) : mon)+'-'+d.getFullYear() this.ui.month.val(cur) var columns = [ @@ -95,4 +95,4 @@ define(['marionette', }) -}) \ No newline at end of file +}) diff --git a/client/src/js/modules/shipment/views/migrate.js b/client/src/js/modules/shipment/views/migrate.js index a2fda3305..4710668e0 100644 --- a/client/src/js/modules/shipment/views/migrate.js +++ b/client/src/js/modules/shipment/views/migrate.js @@ -232,20 +232,20 @@ define(['marionette', var validOnly = app.options.get('valid_components') - if (!validOnly) { - this.rprots.show(new TableView({ + if (!validOnly) { + this.rprots.show(new TableView({ collection: this.proteins, - columns: columns, + columns: columns, tableClass: 'proteins', filter: 's', loading: true, noSearchUrl: false, backgrid: { emptyText: 'No proteins found' } - })) + })) } - var columns = [ + var columns2 = [ { label: '', cell: 'select-row', headerCell: 'select-all', editable: false }, { name: 'CARDNAME', label: 'Card Name', cell: 'string', editable: false }, { name: 'GIVENNAME', label: 'First Name', cell: 'string', editable: false }, @@ -260,7 +260,7 @@ define(['marionette', this.rconts.show(new TableView({ collection: this.contacts, - columns: columns, + columns: columns2, tableClass: 'labcontacts', filter: 's', loading: true, diff --git a/client/src/js/modules/shipment/views/plate.js b/client/src/js/modules/shipment/views/plate.js index f0bb321f5..b29f44f2f 100644 --- a/client/src/js/modules/shipment/views/plate.js +++ b/client/src/js/modules/shipment/views/plate.js @@ -192,9 +192,9 @@ define(['marionette', 'backbone', 'utils', 'backbone-validation'], function(Mari var sampleid = i*this.pt.dropTotal()+did+1 var sample = this.collection.findWhere({ LOCATION: sampleid.toString() }) + var im = null - if (sample && (this.showImageStatus || this.showMaxScore) && this.inspectionimages) var im = this.inspectionimages.findWhere({ BLSAMPLEID: sample.get('BLSAMPLEID') }) - else var im = null + if (sample && (this.showImageStatus || this.showMaxScore) && this.inspectionimages) im = this.inspectionimages.findWhere({ BLSAMPLEID: sample.get('BLSAMPLEID') }) this.ctx.beginPath() this.ctx.lineWidth = 1; @@ -273,10 +273,12 @@ define(['marionette', 'backbone', 'utils', 'backbone-validation'], function(Mari } } + var isc = null + // Show image score if (sample && this.showImageStatus) { if (im) { - var isc = im.get('SCORECOLOUR') + isc = im.get('SCORECOLOUR') if (isc){ this.ctx.fillStyle = isc this.ctx.fill() @@ -287,7 +289,7 @@ define(['marionette', 'backbone', 'utils', 'backbone-validation'], function(Mari // Show max image score if (sample && this.showMaxScore) { if (im) { - var isc = im.get('MAXSCORECOLOUR') + isc = im.get('MAXSCORECOLOUR') if (isc){ this.ctx.fillStyle = isc this.ctx.fill() diff --git a/client/src/js/modules/shipment/views/regdewar.js b/client/src/js/modules/shipment/views/regdewar.js index 76252e088..69a2e053c 100644 --- a/client/src/js/modules/shipment/views/regdewar.js +++ b/client/src/js/modules/shipment/views/regdewar.js @@ -99,7 +99,7 @@ define(['marionette', this.dewars.queryParams.all = 1 this.dewars.fetch().done(this.getHistory.bind(this)) - var columns = [ + var columns2 = [ { name: 'CODE', label: 'Name', cell: 'string', editable: false }, { label: 'Shipment', cell: table.TemplateCell, editable: false, template: '<%-SHIPPINGNAME%>' }, { name: 'EXP', label: 'First Exp', cell: 'string', editable: false }, @@ -113,12 +113,12 @@ define(['marionette', if (app.mobile()) { _.each([0,1,3,6,7], function(v) { - columns[v].renderable = false + columns2[v].renderable = false }) } this.dewtable = new TableView({ collection: this.dewars, - columns: columns, tableClass: 'dewars', loading: true, + columns: columns2, tableClass: 'dewars', loading: true, backgrid: { emptyText: 'No dewars found' } }) @@ -126,14 +126,14 @@ define(['marionette', this.listenTo(this.reports, 'sync', this.setupPopups, this) this.reports.fetch() - var columns = [ + var columns3 = [ { name: 'BLTIMESTAMP', label: 'Time / Date', cell: 'string', editable: false }, { name: 'REPORT', label: 'Report', cell: 'string', editable: false }, { label: 'Image', cell: ImageCell, editable: false }, ] this.reptable = new TableView({ collection: this.reports, - columns: columns, tableClass: 'samples', loading: true, + columns: columns3, tableClass: 'samples', loading: true, backgrid: { emptyText: 'No reports found' } }) @@ -141,7 +141,7 @@ define(['marionette', this.proposals.queryParams.DEWARREGISTRYID = this.model.get('DEWARREGISTRYID') this.proposals.fetch() - var columns = [ + var columns4 = [ { name: 'PROPOSAL', label: 'Proposal', cell: 'string', editable: false }, { name: 'GIVENNAME', label: 'Given Name', cell: 'string', editable: false }, { name: 'FAMILYNAME', label: 'Family Name', cell: 'string', editable: false }, @@ -150,12 +150,12 @@ define(['marionette', ] if (app.staff) { - columns.push({ name: '', label: '', cell: DeleteCell, editable: false }) + columns4.push({ name: '', label: '', cell: DeleteCell, editable: false }) } this.proptable = new TableView({ collection: this.proposals, - columns: columns, + columns: columns4, }) }, diff --git a/client/src/js/modules/shipment/views/registeredcontainer.js b/client/src/js/modules/shipment/views/registeredcontainer.js index c8779c2d2..3d30a56bb 100644 --- a/client/src/js/modules/shipment/views/registeredcontainer.js +++ b/client/src/js/modules/shipment/views/registeredcontainer.js @@ -175,7 +175,7 @@ define(['marionette', this.containers.queryParams.all = 1 this.containers.fetch().done(this.getHistory.bind(this)) - var columns = [ + var columns2 = [ // { label: 'Name', cell: table.TemplateCell, editable: false, template: '<%-NAME%>' }, { name: 'NAME', label: 'Name', cell: 'string', editable: false }, { name: 'BLTIMESTAMP', label: 'Created', cell: 'string', editable: false }, @@ -189,12 +189,12 @@ define(['marionette', if (app.mobile()) { _.each([4,6], function(v) { - columns[v].renderable = false + columns2[v].renderable = false }) } this.conttable = new TableView({ collection: this.containers, - columns: columns, tableClass: 'containers', loading: true, + columns: columns2, tableClass: 'containers', loading: true, backgrid: { row: ClickableRow, emptyText: 'No containers found' } }) @@ -202,7 +202,7 @@ define(['marionette', this.listenTo(this.reports, 'sync', this.setupPopups, this) this.reports.fetch() - var columns = [ + var columns3 = [ { name: 'RECORDTIMESTAMP', label: 'Time / Date', cell: 'string', editable: false }, { name: 'REPORTER', label: 'Reporter', cell: 'string', editable: false }, { name: 'REPORT', label: 'Report', cell: 'string', editable: false }, @@ -210,7 +210,7 @@ define(['marionette', ] this.reptable = new TableView({ collection: this.reports, - columns: columns, tableClass: 'reports', loading: true, + columns: columns3, tableClass: 'reports', loading: true, backgrid: { emptyText: 'No reports found' } }) @@ -248,4 +248,4 @@ define(['marionette', }) -}) \ No newline at end of file +}) 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/xpdf/views/plan.js b/client/src/js/modules/types/xpdf/views/plan.js index b5e6c9819..9fb017219 100644 --- a/client/src/js/modules/types/xpdf/views/plan.js +++ b/client/src/js/modules/types/xpdf/views/plan.js @@ -558,7 +558,7 @@ define(['marionette', this.asmps.show(this.table) - var columns = [ + var columns2 = [ { label: '', cell: CollapseExpandCell, editable: false, template: '' }, { label: '#', cell: table.TemplateCell, editable: false, template: '<%-parseInt(PLANORDER)+1%>' }, { label: 'Instance', cell: table.TemplateCell, editable: false, template: '<%-SAMPLE%>' }, @@ -570,7 +570,7 @@ define(['marionette', this.table2 = new SortableTableView({ collection: this.datacollectionplans, - columns: columns, + columns: columns2, tableClass: 'subsamples', loading: true, // Below overrides the SortableRow in the SortableTableView which breaks drag and drop events 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/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 @@