diff --git a/api/scripts/mtz2map.sh b/api/scripts/mtz2map.sh
index e6f1df143..04fb213c0 100755
--- a/api/scripts/mtz2map.sh
+++ b/api/scripts/mtz2map.sh
@@ -15,15 +15,35 @@ export CLIBD=$CCP4_MASTER/lib/data
export CCP4_SCR=/tmp
export root=$CCP4_MASTER/bin
+if [ -f $1 ]; then
+ mtz=$1
+else
+ if [ -f $1.gz ]; then
+ mtz=/tmp/$2_$3.mtz
+ gunzip -c $1.gz > $mtz
+ else
+ echo "No mtz file found"
+ exit
+ fi
+fi
+
if [ $3 == 'dimple' -o $3 == 'mrbump' ]; then
+if [ -f $4 ]; then
+ pdb=$4
+else
+ if [ -f $4.gz ]; then
+ pdb=/tmp/$2_$3.pdb
+ gunzip -c $4.gz > $pdb
+ else
+ echo "No pdb file found"
+ exit
+ fi
+fi
+
if [ $3 == 'dimple' ]; then
- # fofc2="F1=F SIG1=SIGF PHI=PH2FOFCWT W=FOM"
- # fofc="F1=F SIG1=SIGF PHI=PHFOFCWT W=FOM"
- # fofc2="F1=F SIG1=SIGF PHI=PHWT W=FOM"
- # fofc="F1=F SIG1=SIGF PHI=PHDELWT W=FOM"
- if $root/mtzinfo $1 | grep -q PH2FOFCWT; then
+ if $root/mtzinfo $mtz | grep -q PH2FOFCWT; then
fofc2="F1=2FOFCWT SIG1=SIGF PHI=PH2FOFCWT"
fofc="F1=F SIG1=SIGF PHI=PHFOFCWT W=FOM"
else
@@ -37,7 +57,7 @@ fi
# F SIGF FC PHIC FC_ALL PHIC_ALL FWT PHWT DELFWT PHDELWT FOM FC_ALL_LS PHIC_ALL_LS
-$root/fft HKLIN $1 MAPOUT "/tmp/$2_$3_2fofc.map.tmp" << eof
+$root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3_2fofc.map.tmp" << eof
title $2 2fofc
xyzlim asu
scale F1 1.0
@@ -46,11 +66,11 @@ $fofc2
end
eof
-$root/mapmask MAPIN "/tmp/$2_$3_2fofc.map.tmp" MAPOUT "/tmp/$2_$3_2fofc.map" XYZIN "$4" << eof
+$root/mapmask MAPIN "/tmp/$2_$3_2fofc.map.tmp" MAPOUT "/tmp/$2_$3_2fofc.map" XYZIN "$pdb" << eof
BORDER 5
eof
-$root/fft HKLIN $1 MAPOUT "/tmp/$2_$3_fofc.map.tmp" << eof
+$root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3_fofc.map.tmp" << eof
title $2 fofc
xyzlim asu
scale F1 1.0
@@ -60,16 +80,17 @@ end
eof
-$root/mapmask MAPIN "/tmp/$2_$3_fofc.map.tmp" MAPOUT "/tmp/$2_$3_fofc.map" XYZIN "$4" << eof
+$root/mapmask MAPIN "/tmp/$2_$3_fofc.map.tmp" MAPOUT "/tmp/$2_$3_fofc.map" XYZIN "$pdb" << eof
BORDER 5
eof
gzip "/tmp/$2_$3_2fofc.map"
gzip "/tmp/$2_$3_fofc.map"
+rm -f /tmp/$2_$3.pdb
else
-$root/fft HKLIN $1 MAPOUT "/tmp/$2_$3.map" << eof
+$root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3.map" << eof
title $2 fofc
xyzlim asu
scale F1 1.0
@@ -78,10 +99,8 @@ F1=F SIG1=SIGF PHI=PHI W=FOM
end
eof
-#$mm MAPIN "/tmp/$2_ep.map.tmp" MAPOUT "/tmp/$2_ep.map" XYZIN "$4" << eof
-#BORDER 5
-#eof
-
gzip "/tmp/$2_$3.map"
fi
+
+rm -f /tmp/$2_$3.mtz
diff --git a/api/src/Downstream/BigEPPhasing.php b/api/src/Downstream/BigEPPhasing.php
index 8a2068d8a..63458784f 100644
--- a/api/src/Downstream/BigEPPhasing.php
+++ b/api/src/Downstream/BigEPPhasing.php
@@ -25,13 +25,17 @@ function results() {
}
$image = $this->_get_image();
- $dat['IMAGE'] = file_exists($image);
+ $dat['IMAGE'] = file_exists($image) || file_exists($image.'.gz');
$model = $this->_get_attachments('big_ep_model_ispyb.json');
- $dat['HASMODEL'] = $model && file_exists($model['FILE']);
+ $dat['HASMODEL'] = $model && (file_exists($model['FILE']) || file_exists($model['FILE'].'.gz'));
if ($model) {
if (file_exists($model['FILE'])) {
$json_str = file_get_contents($model['FILE']);
+ } elseif (file_exists($model['FILE'].'.gz')) {
+ $json_str = gzdecode(file_get_contents($model['FILE'].'.gz'));
+ }
+ if (isset($json_str)) {
$json_data = json_decode($json_str, true);
foreach (
array(
diff --git a/api/src/Downstream/Type/FastEp.php b/api/src/Downstream/Type/FastEp.php
index 906a1e0e5..f6a3d54cc 100644
--- a/api/src/Downstream/Type/FastEp.php
+++ b/api/src/Downstream/Type/FastEp.php
@@ -16,83 +16,95 @@ function results() {
$pdb = $this->_get_attachments("sad_fa.pdb");
if ($pdb) {
if (file_exists($pdb["FILE"])) {
- $pdb = file_get_contents($pdb["FILE"]);
- foreach (explode("\n", $pdb) as $l) {
- if (strpos($l, 'HETATM') !== false) {
- $parts = preg_split('/\s+/', $l);
- array_push($ats, array(
- $parts[1],
- $parts[5],
- $parts[6],
- $parts[7],
- $parts[8],
- ));
- }
- }
+ $pdb_cont = file_get_contents($pdb["FILE"]);
+ } elseif (file_exists($pdb['FILE'].'.gz')) {
+ $pdb_cont = gzdecode(file_get_contents($pdb['FILE'].'.gz'));
+ }
+ }
- $dat['ATOMS'] = array_slice($ats, 0, 5);
+ if (isset($pdb_cont)) {
+ foreach (explode("\n", $pdb_cont) as $l) {
+ if (strpos($l, 'HETATM') !== false) {
+ $parts = preg_split('/\s+/', $l);
+ array_push($ats, array(
+ $parts[1],
+ $parts[5],
+ $parts[6],
+ $parts[7],
+ $parts[8],
+ ));
+ }
}
+
+ $dat['ATOMS'] = array_slice($ats, 0, 5);
+
}
$lst = $this->_get_attachments("sad.lst");
if ($lst) {
if (file_exists($lst['FILE'])) {
- $p1 = array();
- $p2 = array();
-
- $lst = file_get_contents($lst['FILE']);
- $graph_vals = 0;
- $gvals = array();
- foreach (explode("\n", $lst) as $l) {
- if (
- strpos(
- $l,
- 'Estimated mean FOM and mapCC as a function of resolution'
- ) !== false
- ) {
- $graph_vals = 1;
- }
-
- if ($graph_vals && $graph_vals < 5) {
- array_push($gvals, $l);
- $graph_vals++;
- }
-
- if (
- preg_match(
- '/ Estimated mean FOM = (\d+.\d+)\s+Pseudo-free CC = (\d+.\d+)/',
- $l,
- $mat
- )
- ) {
- $dat['FOM'] = floatval($mat[1]);
- $dat['CC'] = floatval($mat[2]);
- }
+ $lst_cont = file_get_contents($lst['FILE']);
+ } elseif (file_exists($lst['FILE'].'.gz')) {
+ $lst_cont = gzdecode(file_get_contents($lst['FILE'].'.gz'));
+ }
+ }
+
+ if (isset($lst_cont)) {
+ $p1 = array();
+ $p2 = array();
+
+ $graph_vals = 0;
+ $gvals = array();
+ foreach (explode("\n", $lst_cont) as $l) {
+ if (
+ strpos(
+ $l,
+ 'Estimated mean FOM and mapCC as a function of resolution'
+ ) !== false
+ ) {
+ $graph_vals = 1;
}
- if (sizeof($gvals) > 0) {
- $x = array_map(
- 'floatval',
- array_slice(explode(' - ', $gvals[1]), 1)
- );
- $y = array_map(
- 'floatval',
- array_slice(preg_split('/\s+/', $gvals[2]), 2)
- );
- $y2 = array_map(
- 'floatval',
- array_slice(preg_split('/\s+/', $gvals[3]), 2)
- );
-
- foreach ($x as $i => $v) {
- array_push($p1, array(1.0 / pow($v, 2), $y[$i]));
- array_push($p2, array(1.0 / pow($v, 2), $y2[$i]));
- }
+ if ($graph_vals && $graph_vals < 5) {
+ array_push($gvals, $l);
+ $graph_vals++;
}
- $dat['PLOTS']['FOM'] = $p1;
- $dat['PLOTS']['CC'] = $p2;
+ if (
+ preg_match(
+ '/ Estimated mean FOM = (\d+.\d+)\s+Pseudo-free CC = (\d+.\d+)/',
+ $l,
+ $mat
+ )
+ ) {
+ $dat['FOM'] = floatval($mat[1]);
+ $dat['CC'] = floatval($mat[2]);
+ }
}
+
+ if (sizeof($gvals) > 0) {
+ $x = array_map(
+ 'floatval',
+ array_slice(explode(' - ', $gvals[1]), 1)
+ );
+ $y = array_map(
+ 'floatval',
+ array_slice(preg_split('/\s+/', $gvals[2]), 2)
+ );
+ $y2 = array_map(
+ 'floatval',
+ array_slice(preg_split('/\s+/', $gvals[3]), 2)
+ );
+
+ foreach ($x as $i => $v) {
+ array_push($p1, array(1.0 / pow($v, 2), $y[$i]));
+ array_push($p2, array(1.0 / pow($v, 2), $y2[$i]));
+ }
+ }
+
+ $dat['PLOTS']['FOM'] = $p1;
+ $dat['PLOTS']['CC'] = $p2;
+
}
$results = new DownstreamResult($this);
diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php
index 7879d0615..31056572a 100644
--- a/api/src/Page/DC.php
+++ b/api/src/Page/DC.php
@@ -1605,6 +1605,10 @@ function _rd($aid, $id)
$rows = array();
if (file_exists($file)) {
$log = file_get_contents($file);
+ } elseif (file_exists($file.'.gz')) {
+ $log = gzdecode(file_get_contents($file.'.gz'));
+ }
+ if (isset($log)) {
$start = 0;
foreach (explode("\n", $log) as $l) {
diff --git a/api/src/Page/Download.php b/api/src/Page/Download.php
index b86188db5..8b24a186b 100644
--- a/api/src/Page/Download.php
+++ b/api/src/Page/Download.php
@@ -9,6 +9,7 @@
use Symfony\Component\HttpFoundation\BinaryFileResponse;
use Symfony\Component\HttpFoundation\ResponseHeaderBag;
use Symfony\Component\HttpFoundation\StreamedResponse;
+use Symfony\Component\HttpFoundation\Response;
use ZipStream\Option\Archive;
use ZipStream\ZipStream;
@@ -84,10 +85,7 @@ function _download_visit()
if ($filesystem->exists($data)) {
$response = new BinaryFileResponse($data);
$response->headers->set("Content-Type", "application/octet-stream");
- $response->setContentDisposition(
- ResponseHeaderBag::DISPOSITION_ATTACHMENT,
- $this->arg('visit') . '_download.zip'
- );
+ $this->_set_disposition_attachment($response, $this->arg('visit') . '_download.zip');
$response->send();
} else
$this->_error('There doesnt seem to be a data archive available for this visit');
@@ -137,6 +135,11 @@ function _auto_processing_plots()
$r['PLOTS'] = array();
if (file_exists($json)) {
$cont = file_get_contents($json);
+ } elseif (file_exists($json.'.gz')) {
+ $cont = gzdecode(file_get_contents($json.'.gz'));
+ }
+
+ if (isset($cont)) {
$plotData = json_decode($cont);
$r['PLOTS'] = $plotData;
@@ -260,25 +263,25 @@ function _get_file($id, $file)
// Do the check first, if no file quit early
if ($filesystem->exists($filename)) {
-
$response = new BinaryFileResponse($filename);
-
- # Set mime / content type
- $this->set_mime_content($response, $file['FILENAME'], $id);
-
- // All OK - send it
- // We were getting out of memory errors - switch off output buffer to fix
- if (ob_get_level()) {
- ob_end_clean();
- }
- // Setting content length means browser can indicate how long is left
+ $this->set_mime_content($response, $filename, $id);
$response->headers->set("Content-Length", filesize($filename));
-
- $response->send();
- exit();
+ } elseif ($filesystem->exists($filename.'.gz')) {
+ $filename = $filename.'.gz';
+ if ($this->arg('download') == 1) {
+ // View log file, so unzip and serve
+ $response = new Response(readgzfile($filename));
+ $this->set_mime_content($response, $file['FILENAME'], $id);
+ } else {
+ // Download gzipped file
+ $response = new BinaryFileResponse($filename);
+ $this->set_mime_content($response, $filename, $id);
+ $response->headers->set("Content-Length", filesize($filename));
+ }
} else {
$this->_error("No such file, the specified file " . $filename . " doesn't exist");
}
+ $response->send();
}
@@ -306,7 +309,7 @@ function _csv_report()
WHERE dcg.sessionid=:1 ORDER BY dc.starttime", array($vis['SESSIONID']));
$this->app->response->headers->set("Content-type", "application/vnd.ms-excel");
- $this->app->response->headers->set("Content-disposition", "attachment; filename=" . $vis['ST'] . "_" . $vis['BEAMLINENAME'] . "_" . $this->arg('visit') . ".csv");
+ $this->_set_disposition_attachment($this->app->response, $vis['ST'] . "_" . $vis['BEAMLINENAME'] . "_" . $this->arg('visit') . ".csv");
print "Image prefix,Beamline,Run no,Start Time,Sample Name,Protein Acronym,# images, Wavelength (angstrom), Distance (mm), Exp. Time (sec), Phi start (deg), Phi range (deg), Xbeam (mm), Ybeam (mm), Detector resol. (angstrom), Comments\n";
foreach ($rows as $r) {
$r['COMMENTS'] = '"' . $r['COMMENTS'] . '"';
@@ -474,7 +477,11 @@ function _streamZipFile($files, $zipName)
$zip = new ZipStream($zipName . '.zip', $options);
foreach ($files as $file) {
$filename = $file['FILEPATH'] . '/' . $file['FILENAME'];
- $zip->addFileFromPath(basename($filename), $filename);
+ if (file_exists($filename)) {
+ $zip->addFileFromPath(basename($filename), $filename);
+ } elseif (file_exists($filename.'.gz')) {
+ $zip->addFileFromPath(basename($filename).'.gz', $filename.'.gz');
+ }
}
$zip->finish();
@@ -499,28 +506,37 @@ function set_mime_content($response, $filename, $prefix = null)
if (in_array($path_ext, array('html', 'htm'))) {
$response->headers->set("Content-Type", "text/html");
- $response->setContentDisposition(ResponseHeaderBag::DISPOSITION_INLINE);
+ $this->_set_disposition_inline($response);
} elseif ($path_ext == 'pdf') {
$response->headers->set("Content-Type", "application/pdf");
- $response->setContentDisposition(ResponseHeaderBag::DISPOSITION_ATTACHMENT, $saved_filename);
+ $this->_set_disposition_attachment($response, $saved_filename);
} elseif ($path_ext == 'png') {
$response->headers->set("Content-Type", "image/png");
- $response->setContentDisposition(ResponseHeaderBag::DISPOSITION_ATTACHMENT, $saved_filename);
+ $this->_set_disposition_attachment($response, $saved_filename);
} elseif (in_array($path_ext, array('jpg', 'jpeg'))) {
$response->headers->set("Content-Type", "image/jpeg");
- $response->setContentDisposition(ResponseHeaderBag::DISPOSITION_ATTACHMENT, $saved_filename);
+ $this->_set_disposition_attachment($response, $saved_filename);
} elseif (in_array($path_ext, array('log', 'txt', 'error', 'LP', 'json', 'lsa'))) {
$response->headers->set("Content-Type", "text/plain");
- $response->setContentDisposition(ResponseHeaderBag::DISPOSITION_INLINE);
+ $this->_set_disposition_inline($response);
} else {
$response->headers->set("Content-Type", "application/octet-stream");
- $response->setContentDisposition(
- ResponseHeaderBag::DISPOSITION_ATTACHMENT,
- $saved_filename
- );
+ $this->_set_disposition_attachment($response, $saved_filename);
}
}
+ function _set_disposition_attachment($response, $filename) {
+ $response->headers->set("Content-Disposition",
+ ResponseHeaderBag::makeDisposition(ResponseHeaderBag::DISPOSITION_ATTACHMENT, $filename)
+ );
+ }
+
+ function _set_disposition_inline($response) {
+ $response->headers->set("Content-Disposition",
+ ResponseHeaderBag::makeDisposition(ResponseHeaderBag::DISPOSITION_INLINE, '')
+ );
+ }
+
# ------------------------------------------------------------------------
# Download Data
@@ -551,25 +567,11 @@ function _download()
if ($filesystem->exists($data)) {
$response = new BinaryFileResponse($data);
$response->headers->set("Content-Type", "application/octet-stream");
- $response->setContentDisposition(
- ResponseHeaderBag::DISPOSITION_ATTACHMENT,
- $this->arg('id') . '_download.zip'
- );
+ $this->_set_disposition_attachment($response, $this->arg('id') . '_download.zip');
$response->send();
} else {
error_log("Download file " . $data . " not found");
$this->_error('File not found on filesystem', 404);
}
}
-
-
- # ------------------------------------------------------------------------
- # Force browser to download file
- # Deprecated function now we are using symfony filesystem
- function _header($f)
- {
- header("Content-Type: application/octet-stream");
- header("Content-Transfer-Encoding: Binary");
- header("Content-disposition: attachment; filename=\"$f\"");
- }
}
diff --git a/api/src/Page/Processing.php b/api/src/Page/Processing.php
index ab1c792fc..bfe1bd9d2 100644
--- a/api/src/Page/Processing.php
+++ b/api/src/Page/Processing.php
@@ -424,8 +424,10 @@ function _get_downstreams($dcid = null, $aid = null) {
if ($downstream["PARAMETERS"]) {
$str_params = explode(',', $downstream["PARAMETERS"]);
foreach ($str_params as $str_param) {
- list($key, $value) = explode('=', $str_param);
- $params[$key] = $value;
+ if (str_contains($str_param, '=')) {
+ list($key, $value) = explode('=', $str_param);
+ $params[$key] = $value;
+ }
}
}
$downstream['PARAMETERS'] = $params;
@@ -518,20 +520,27 @@ function _downstream_images($aid) {
$im = $plugin->images($this->has_arg('n') ? $this->arg("n") : 0);
if ($im) {
if (file_exists($im)) {
- $ext = pathinfo($im, PATHINFO_EXTENSION);
- if (in_array($ext, array('png', 'jpg', 'jpeg', 'gif'))) {
- $head = 'image/' . $ext;
- }
-
+ $this->_set_content_type_header($im);
$this->_browser_cache();
- $this->app->contentType($head);
readfile($im);
+ } elseif (file_exists($im.'.gz')) {
+ $this->_set_content_type_header($im);
+ $this->_browser_cache();
+ readgzfile($im.'.gz');
} else {
$this->_error("No such image");
}
}
}
+ function _set_content_type_header($im) {
+ $ext = pathinfo($im, PATHINFO_EXTENSION);
+ if (in_array($ext, array('png', 'jpg', 'jpeg', 'gif'))) {
+ $head = 'image/' . $ext;
+ $this->app->contentType($head);
+ }
+ }
+
function _browser_cache() {
$expires = 60 * 60 * 24 * 14;
$this->app->response->headers->set('Pragma', 'public');
@@ -589,6 +598,8 @@ function _downstream_mapmodel($aid) {
filesize($mapmodel)
);
readfile($mapmodel);
+ } elseif (file_exists($mapmodel.'.gz')) {
+ readgzfile($mapmodel.'.gz');
} else {
$this->_error('Could not find map / model');
}
diff --git a/client/src/js/modules/dc/views/autoprocattachments.js b/client/src/js/modules/dc/views/autoprocattachments.js
index f114cd171..c962098fa 100644
--- a/client/src/js/modules/dc/views/autoprocattachments.js
+++ b/client/src/js/modules/dc/views/autoprocattachments.js
@@ -18,7 +18,7 @@ define(['marionette',
},
render: function() {
- this.$el.html(' Download')
+ this.$el.html(' Download')
if (this.model.get('FILETYPE') == 'Log' || this.model.get('FILETYPE') == 'Logfile') {
this.$el.append(' View')
@@ -115,4 +115,4 @@ define(['marionette',
},
})
-})
\ No newline at end of file
+})
diff --git a/client/src/js/templates/dc/dc_autoproc.html b/client/src/js/templates/dc/dc_autoproc.html
index 0ae0a1f91..6969b9ebd 100644
--- a/client/src/js/templates/dc/dc_autoproc.html
+++ b/client/src/js/templates/dc/dc_autoproc.html
@@ -8,7 +8,7 @@
Logs & Files
- This procesing job failed: <%-PROCESSINGMESSAGE%>
+ This processing job failed: <%-PROCESSINGMESSAGE%>
<% } else { %>
diff --git a/client/src/js/templates/dc/downstreamerror.html b/client/src/js/templates/dc/downstreamerror.html
index 625f8d7c1..784f3b6ef 100644
--- a/client/src/js/templates/dc/downstreamerror.html
+++ b/client/src/js/templates/dc/downstreamerror.html
@@ -3,4 +3,4 @@
Logs & Files
-This procesing job failed: <%-PROCESS.PROCESSINGMESSAGE%>
+This processing job failed: <%-PROCESS.PROCESSINGMESSAGE%>