LIMS-1074: Deploy suggestions from code review

DiamondLightSource · Nov 1, 2023 · 6d98705 · 6d98705
1 parent 929b4bd
commit 6d98705
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Showing 3 changed files with 25 additions and 23 deletions.
diff --git a/api/scripts/mtz2map.sh b/api/scripts/mtz2map.sh
@@ -21,25 +21,27 @@ 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' -o $3 == 'mrbump' ]; then
-
 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 $mtz | grep -q PH2FOFCWT; then
 		fofc2="F1=2FOFCWT SIG1=SIGF PHI=PH2FOFCWT"
@@ -85,6 +87,7 @@ eof
 gzip "/tmp/$2_$3_2fofc.map"
 gzip "/tmp/$2_$3_fofc.map"
 
+rm -f /tmp/$2_$3.pdb
 
 else
 $root/fft HKLIN $mtz MAPOUT "/tmp/$2_$3.map" << eof
@@ -96,10 +99,8 @@ F1=F SIG1=SIGF PHI=PHI W=FOM
 end
 eof
 
-#$mm MAPIN "/tmp/$2_ep.map.tmp" MAPOUT "/tmp/$2_ep.map" XYZIN "$pdb" << eof
-#BORDER 5
-#eof
-
 gzip "/tmp/$2_$3.map"
 
 fi
+
+rm -f /tmp/$2_$3.mtz
diff --git a/api/src/Downstream/Type/FastEp.php b/api/src/Downstream/Type/FastEp.php
@@ -16,14 +16,14 @@ function results() {
         $pdb = $this->_get_attachments("sad_fa.pdb");
         if ($pdb) {
             if (file_exists($pdb["FILE"])) {
-                $pdb = file_get_contents($pdb["FILE"]);
+                $pdb_cont = file_get_contents($pdb["FILE"]);
             } elseif (file_exists($pdb['FILE'].'.gz')) {
-                $pdb = gzdecode(file_get_contents($pdb['FILE'].'.gz'));
-            } else {
-                $this->_error('Could not find sad_fa.pdb file');
+                $pdb_cont = gzdecode(file_get_contents($pdb['FILE'].'.gz'));
             }
+        }
 
-            foreach (explode("\n", $pdb) as $l) {
+        if (isset($pdb_cont)) {
+            foreach (explode("\n", $pdb_cont) as $l) {
                 if (strpos($l, 'HETATM') !== false) {
                     $parts = preg_split('/\s+/', $l);
                     array_push($ats, array(
@@ -43,19 +43,19 @@ function results() {
         $lst = $this->_get_attachments("sad.lst");
         if ($lst) {
             if (file_exists($lst['FILE'])) {
-                $lst = file_get_contents($lst['FILE']);
+                $lst_cont = file_get_contents($lst['FILE']);
             } elseif (file_exists($lst['FILE'].'.gz')) {
-                $lst = gzdecode(file_get_contents($lst['FILE'].'.gz'));
-            } else {
-                $this->_error('Could not find sad.lst file');
+                $lst_cont = gzdecode(file_get_contents($lst['FILE'].'.gz'));
             }
+        }
 
+        if (isset($lst_cont)) {
             $p1 = array();
             $p2 = array();
 
             $graph_vals = 0;
             $gvals = array();
-            foreach (explode("\n", $lst) as $l) {
+            foreach (explode("\n", $lst_cont) as $l) {
                 if (
                     strpos(
                         $l,

diff --git a/api/src/Page/Download.php b/api/src/Page/Download.php
@@ -257,15 +257,16 @@ function _get_file($id, $file)
     {
         // We don't want to allow unlimited file sizes
         ini_set('memory_limit', '512M');
+        $filesystem = new Filesystem();
 
         $filename = $file['FILEPATH'] . '/' . $file['FILENAME'];
 
         // Do the check first, if no file quit early
-        if (file_exists($filename)) {
+        if ($filesystem->exists($filename)) {
             $response = new BinaryFileResponse($filename);
             $this->set_mime_content($response, $filename, $id);
             $response->headers->set("Content-Length", filesize($filename));
-        } elseif (file_exists($filename.'.gz')) {
+        } elseif ($filesystem->exists($filename.'.gz')) {
             $filename = $filename.'.gz';
             if ($this->arg('download') == 1) {
                 // View log file, so unzip and serve
@@ -479,7 +480,7 @@ function _streamZipFile($files, $zipName)
                 if (file_exists($filename)) {
                     $zip->addFileFromPath(basename($filename), $filename);
                 } elseif (file_exists($filename.'.gz')) {
-                    $zip->addFileFromPath(basename($filename), $filename.'.gz');
+                    $zip->addFileFromPath(basename($filename).'.gz', $filename.'.gz');
                 }
             }