From 3a033232d30cfd4e7f87a85f2c4fb72f37f594db Mon Sep 17 00:00:00 2001
From: Gael Yvert <Gael.Yvert@ens-lyon.fr>
Date: Mon, 19 Apr 2021 11:14:34 +0200
Subject: [PATCH] plasmid maps now stored in tmp dirs with id as their name
(issue #96)
---
.../Controllers/PlasmidBaseController.php | 2 +-
app/Http/Controllers/lib/Seq.php | 20 ++++++++++++-------
storage/app/public/tmp/.gitignore | 3 ---
3 files changed, 14 insertions(+), 11 deletions(-)
delete mode 100644 storage/app/public/tmp/.gitignore
diff --git a/app/Http/Controllers/PlasmidBaseController.php b/app/Http/Controllers/PlasmidBaseController.php
index ee8ceb4..1f81155 100755
--- a/app/Http/Controllers/PlasmidBaseController.php
+++ b/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, $id);
}
// prepare to return the view
diff --git a/app/Http/Controllers/lib/Seq.php b/app/Http/Controllers/lib/Seq.php
index baf1b50..f7055ed 100755
--- a/app/Http/Controllers/lib/Seq.php
+++ b/app/Http/Controllers/lib/Seq.php
@@ -74,14 +74,20 @@ function blast2cirdna($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;
}
diff --git a/storage/app/public/tmp/.gitignore b/storage/app/public/tmp/.gitignore
deleted file mode 100644
index a5baada..0000000
--- a/storage/app/public/tmp/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*
-!.gitignore
-
--
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