add a function to download all log files.

includes/class/job/mcl_job.class.inc

@@ -123,21 +123,19 @@ class MCL_JOB extends PUBLIC_MCL_JOB {
     // Insert a new job.
     if (parent::insert()) {
 
-      // If $this->working_dir is empty, assigns the default working directory.
-      if (empty($this->working_dir)) {
-        $this->working_dir = mcl_get_config_setting('mcl_working_dir');
-      }
+      // Get MCL user directory.
+      $mcl_user_directory = mcl_get_config_setting('mcl_working_dir') . '/user';
 
-      // Creates the user directory if not exists.
-      if (empty($this->user_dir)) {
-        $drupal_user = MCL_USER::getDrupalUser($this->user_id);
-        $this->user_dir  = $this->working_dir . '/' . $drupal_user->name;
-      }
+      // Gets username.
+      $drupal_user = MCL_USER::getDrupalUser($this->user_id);
+      $username = $drupal_user->name;
 
+      // Updates MCL directories.
+      $this->user_dir = "$mcl_user_directory/$username";
       $this->job_dir  = $this->user_dir . '/' . $this->job_id;
       $this->log_dir  = $this->job_dir . '/logs';
       $this->file_dir = $this->job_dir . '/files';
-      $this->setPropByKey('working_dir', $this->working_dir);
+      $this->setPropByKey('working_dir', $this->user_dir);
       $this->setPropByKey('user_dir', $this->user_dir);
       $this->setPropByKey('job_dir', $this->job_dir);
       $this->setPropByKey('log_dir', $this->log_dir);

includes/class/template/module/mcl_template_marker.class.inc

@@ -127,7 +127,9 @@ class MCL_TEMPLATE_MARKER extends MCL_TEMPLATE {
     MCL_CHADO_ORGANISM::checkOrganism($this, $line['genus'], $line['species']);
 
     // Checks SNP_chip_name.
-//    MCL_CHADO_LIBRARY::checkLibrary($this, $line['snp_chip']);
+    $organism = MCL_CHADO_ORGANISM::getOrganism($line['genus'], $line['species']);
+    $type_id  = $this->cvterms['SITE_CV']['SNP_chip'];
+    MCL_CHADO_LIBRARY::checkLibrary($this, $line['snp_chip_name'], $type_id. $organism->getOrganismID());
 
     // Checks contacts.
     MCL_CHADO_CONTACT::checkContact($this, $line['contact'], '[;,]');

includes/form/mcl.job_view.form.inc

@@ -345,7 +345,7 @@ function _mcl_get_detail_table(MCL_JOB_UPLOAD $mcl_job) {
   $rows []= array('<b>Data Template File</b>', $link_template);
   $rows []= array('<b>Submit Date</b>', $mcl_job->getSubmitDate());
   $rows []= array('<b>Complete Date</b>', $complete_date);
-//  $rows []= array('<b>Log Files</b>', $link_log);
+  $rows []= array('<b>Log Files</b>', $link_log);
 
   // Table variables.
   $table_vars = array(

includes/mcl.inc

@@ -161,20 +161,23 @@ function mcl_download_log($job_id) {
   $log_root_dir = dirname($mcl_job->getLogDir());
 
   // Sets zip path and name.
-  $filename = "mcl-$job_id-" . date("Y-m-d-G-i-s") . '.zip';
-  $filepath = file_directory_temp() . "/$filename";
-
-  // Zips the folder.
-  $cmd = "cd $log_root_dir;zip -rq $filepath logs";
-  exec("which zip", $output, $return_var);
-  if ($return_var) {
-    drupal_set_message("Failed to zip the folder");
-
-//    return FALSE;
+  $filename = "mcl-$job_id-logs.zip";
+  $filepath = $mcl_job->getLogDir() . "/$filename";
+
+  // Create a zip file.
+  $zip = new ZipArchive;
+  $zip->open($filepath, ZipArchive::OVERWRITE);
+
+  $files = mcl_retrive_files($mcl_job->getLogDir(), '/.*\.log$/');
+  foreach ($files as $file) {
+    $file_name = basename($file);
+    $rel_path = str_replace($log_root_dir, '', dirname($file));
+    $zip->addFile($file, "$rel_path/$file_name");
   }
+  $zip->close();
 
   // Attaches the zip file.
-  header("Content-Type: text/plain");
+  header("Content-Type: application/zip");
   header("Content-Disposition: attachment; filename=$filename");
   readfile($filepath);
   exit();