importer: fix files handling

tripal/includes/TripalImporter.inc

@@ -415,15 +415,15 @@ class TripalImporter {
     }
 
     try {
-      for($i = 0; $i < count($this->arguments['file']); $i++) {
-        if (!empty($this->arguments['file'][$i]['file_remote'])) {
-          $file_remote = $this->arguments['file'][$i]['file_remote'];
+      for($i = 0; $i < count($this->arguments['files']); $i++) {
+        if (!empty($this->arguments['files'][$i]['file_remote'])) {
+          $file_remote = $this->arguments['files'][$i]['file_remote'];
           $this->logMessage('Download file: !file_remote...', array('!file_remote' => $file_remote));
 
           // If this file is compressed then keepthe .gz extension so we can
           // uncompress it.
           $ext = '';
-          if (preg_match('/^(.*?)\.gz$/', $this->arguments['file']['file_remote'])) {
+          if (preg_match('/^(.*?)\.gz$/', $file_remote)) {
             $ext = '.gz';
           }
           // Create a temporary file.
@@ -442,17 +442,17 @@ class TripalImporter {
             fwrite($tmp_fh, fread($url_fh, 255), 255);
           }
           // Set the path to the file for the importer to use.
-          $this->arguments['file']['file_path'] = $temp;
+          $this->arguments['files'][$i]['file_path'] = $temp;
           $this->is_prepared = TRUE;
         }
 
         // Is this file compressed?  If so, then uncompress it
         $matches = array();
-        if (preg_match('/^(.*?)\.gz$/', $this->arguments['file']['file_path'], $matches)) {
-          $this->logMessage("Uncompressing: !file", array('!file' => $this->arguments['file']['file_path']));
+        if (preg_match('/^(.*?)\.gz$/', $this->arguments['files'][$i]['file_path'], $matches)) {
+          $this->logMessage("Uncompressing: !file", array('!file' => $this->arguments['files'][$i]['file_path']));
           $buffer_size = 4096;
           $new_file_path = $matches[1];
-          $gzfile = gzopen($this->arguments['file']['file_path'], 'rb');
+          $gzfile = gzopen($this->arguments['files'][$i]['file_path'], 'rb');
           $out_file = fopen($new_file_path, 'wb');
           if (!$out_file) {
             throw new Exception("Cannot uncompress file: new temporary file, '$new_file_path', cannot be created.");
@@ -471,8 +471,8 @@ class TripalImporter {
 
           // Now remove the .gz file and reset the file_path to the new
           // uncompressed version.
-          unlink($this->arguments['file'][$i]['file_path']);
-          $this->arguments['file'][$i]['file_path'] = $new_file_path;
+          unlink($this->arguments['files'][$i]['file_path']);
+          $this->arguments['files'][$i]['file_path'] = $new_file_path;
         }
       }
     }
@@ -490,11 +490,13 @@ class TripalImporter {
   public function cleanFile() {
     try {
       // If a remote file was downloaded then remove it.
-      if (!empty($this->arguments['file']['file_remote']) and
-          file_exists($this->arguments['file']['file_path'])) {
-        $this->logMessage('Removing downloaded file...');
-        unlink($this->arguments['file']['file_path']);
-        $this->is_prepared = FALSE;
+      for($i = 0; $i < count($this->arguments['files']); $i++) {
+          if (!empty($this->arguments['files'][$i]['file_remote']) and
+              file_exists($this->arguments['files'][$i]['file_path'])) {
+            $this->logMessage('Removing downloaded file...');
+            unlink($this->arguments['files'][$i]['file_path']);
+            $this->is_prepared = FALSE;
+          }
       }
     }
     catch (Exception $e){