Merge pull request #20 from s-andrews/master

Fix GEO data lookups
ewels · Nov 16, 2018 · 233758f · 233758f
2 parents d7c181b + 6653aa3
commit 233758f
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/ajax/sra_get_datasets.php b/ajax/sra_get_datasets.php
diff --git a/ajax/write_bash.php b/ajax/write_bash.php
@@ -46,9 +46,11 @@
 
 	// Check the directory exists
 	if(!is_dir($dir)){
-		if(!mkdir($dir, 0775)){
+		$old_umask = umask(0);
+		if(!mkdir($dir, 0777)){
 			die("can't create directory $dir");
 		}
+		umask($old_umask);
 	}
 
 	// Write file

diff --git a/js/datasets.js b/js/datasets.js
@@ -35,6 +35,9 @@ $('#sra-links-modal').on('show', function () {
 		var acc = $(this).text();
 		file += "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/"+acc.substring(0,3)+"/"+acc.substring(0,6)+"/"+acc+"/"+acc+".sra";
 		var name = $(this).closest('tr').find('.dataset_name').text();
+	        name = name.replace(/[\s:\?\/]+/g,'_');
+	        name = name.replace(/[\(\)]+/g,'');
+
 		file += "\t"+name+"_"+acc+".sra <br>\n";
 	});
 	$('#sra-links-modal .modal-body pre').html(file);