add working geo_downloader

diff --git a/geo_downloader b/geo_downloader
index 541d319aec2e1b37e0e71fdeffa7ac9f1809b781..a1c3953140b24bcdf262cf009c4363dde7cc6974 100755 (executable)
--- a/geo_downloader
+++ b/geo_downloader
@@ -52,6 +52,8 @@ geo_downloader GSE20400
 
 use vars qw($DEBUG);
 use Net::FTP;
+use Cwd;
+use Data::Printer;
 
 my %options = (debug           => 0,
                help            => 0,
@@ -91,18 +93,55 @@ print STDERR "logged in\n" if $DEBUG;
 $ftp->binary();
 print STDERR "binary\n" if $DEBUG;
 
-
+use Data::Printer;
 
 for my $geo_acc (@ARGV) {
     my $geo_directory = geo_directory($geo_acc);
-    $ftp->cwd($geo_directory);
-    print STDERR "changed to $geo_directory\n" if $DEBUG;
-    print STDERR "(really) changed to ".$ftp->pwd()."\n" if $DEBUG;
-    my @files = $ftp->ls();
-    print map {$_."\n"} @files;
-    print STDERR "transferred listing\n" if $DEBUG;
+    my $listing = recursive_file_listing($ftp,$geo_directory);
+    p($listing) if $DEBUG;
+    my $orig_dir = getcwd;
+    mkdir($geo_acc) unless -d $geo_acc;
+    chdir($geo_acc);
+    for my $dir (qw(matrix miniml suppl)) {
+        # we want all of the raw files, the xml file, and the matrix file
+        if (exists $listing->{$dir} and ref($listing->{$dir})) {
+            for my $file (keys %{$listing->{$dir}}) {
+                next if ref($listing->{$dir}{$file});
+                $ftp->get($listing->{$dir}{$file});
+            }
+        }
+    }
+    chdir($orig_dir);
 }
 
+
+sub recursive_file_listing {
+    my ($ftp,$dir) = @_;
+    my $listing;
+    my $orig_dir = $ftp->pwd();
+    eval {
+        $ftp->cwd($dir) or die "Not a directory $dir";
+        $listing = {};
+        my @files = $ftp->ls();
+        p @files if $DEBUG;
+        for my $file (@files) {
+            print STDERR "file: $file\n";
+            my $subdirs = recursive_file_listing($ftp,$file);
+            print STDERR  "subdirs is :";
+            print STDERR p($subdirs);
+            if (defined $subdirs) {
+                $listing->{$file} = $subdirs;
+            } else {
+                $listing->{$file} = $orig_dir.'/'.$dir.'/'.$file;
+            }
+        }
+    };
+    $ftp->cwd($orig_dir);
+    return $listing;
+}
+
+
+
 sub geo_directory {
     my $geo_acc = shift;
     $geo_acc = uc($geo_acc);