Merge branch 'master' into improvement/LIMS-1528/fix-sorting-on-old-s…

…ummary-page

api/scripts/mtz2map.sh

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

api/src/Page/Cell.php

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

api/src/Page/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\-])+',

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

api/src/Page/Download.php

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

api/src/Page/Processing.php

@@ -152,7 +152,7 @@ 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')",
             ),
             $ids
@@ -900,11 +900,17 @@ private function _autoprocessing_query_builder($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";
 
         $from = "FROM autoprocintegration api";
@@ -954,7 +960,7 @@ private function _format_auto_processing_result($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'], $formatted_result)) {
@@ -975,6 +981,9 @@ private function _format_auto_processing_result($table_rows, $messages_result) {
                             $prefix = preg_match('/multi/', $value) ? '' : 'multi-';
                             $value = $row['DCCOUNT'] . 'x ' . $prefix . $value;
                         }
+                        if ($row['GROUPNAME']) {
+                            $value .= ' ('.$row['GROUPNAME'].')';
+                        }
                     }
 
 

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()