plasmid maps now stored in tmp dirs with id as their name (issue #96)

app/Http/Controllers/PlasmidBaseController.php

@@ -247,7 +247,7 @@ class PlasmidBaseController extends BaseController
              $plasmidmap_imgurl=NULL; //todo: put a default image telling that there is no seq
         } else {
              // draw the map and store its address
-             $plasmidmap_imgurl=seq2png($seq);
+             $plasmidmap_imgurl=drawplasmidmap($seq, $id);
         }
 	
 	// prepare to return the view

app/Http/Controllers/lib/Seq.php

@@ -74,14 +74,20 @@ function blast2cirdna($infile, $outfile, $start, $end){
 }
 
 
-function seq2png($seq){
+function drawplasmidmap($seq, $id){
    // -------------------------
    // blast it on dna-features
    // -------------------------
    
-   // create a tmp dir with a random name
-   $tmpdir = 'storage/tmp/' . sha1( microtime() ) . '/';
-   system(mkdir($tmpdir));
+   // create a tmp dir with name the plasmid id
+   $tmpdir = 'storage/tmp/plasmidmaps/' . $id . '/';
+   $cmd_mktmpdir = 'mkdir -p ' . $tmpdir; 
+   system($cmd_mktmpdir, $retval0);
+   if ($retval0 != 0){
+        return "Error in drawplasmidmap() when running " . $cmd_mktmpdir;
+        exit;
+   }
+
 
    $blastdb = 'storage/blast/dnafeatures';
    $blastoutfile = $tmpdir . 'blastout.tab';
@@ -95,7 +101,7 @@ function seq2png($seq){
    $cmd_blast = "blastn -query ". $qryfasta . " -db ". $blastdb . " -out ". $blastoutfile . " -outfmt 6";
    system($cmd_blast, $retval1);
    if ($retval1 != 0){
-        return "Error in seq2png() when running " . $cmd_blast;
+        return "Error in drawplasmidmap() when running " . $cmd_blast;
         exit;
    }
 
@@ -115,14 +121,14 @@ function seq2png($seq){
    $cmd_cirdna = "cirdna -posblocks Out -posticks Out -blocktype Outline -blockheight 2.5 -postext 1 -textheight 2 -textlength 3.2 -intercolour 7 -graphout pdf -ruler Y -gtitle ' ' -infile ". $cirdnainfile . " -goutfile " . $cirdnaoutfile . " >/dev/null";
    system($cmd_cirdna, $retval2);
    if ($retval2 != 0){
-        return "Error in seq2png() when running " . $cmd_cirdna;
+        return "Error in drawplasmidmap() when running " . $cmd_cirdna;
         exit;
    }
    // convert it to svg format
    $cmd_convert2svg = "pdf2svg " . $cirdnaoutfile . ".pdf " . $cirdnaoutfile . ".svg";
    system($cmd_convert2svg, $retval3);
    if ($retval3 != 0){
-        return "Error in seq2png() when running " . $cmd_convert2svg;
+        return "Error in drawplasmidmap() when running " . $cmd_convert2svg;
         exit;
    }
 

storage/app/public/tmp/.gitignore

-*
-!.gitignore
-