Skip to content

Commit

Permalink
Merge pull request #149 from wtsi-npg/devel
Browse files Browse the repository at this point in the history 
prep for release 2.8.1
  • Loading branch information
@dozy
dozy authored Jun 26, 2017
2 parents e487b0b + 89294de commit 6406103
Show file tree
Hide file tree
Showing 2 changed files with 19 additions and 158 deletions.
151 changes: 5 additions & 146 deletions lib/WTSI/NPG/iRODS.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1353,15 +1353,7 @@ sub add_object {

$self->debug("Adding '$file' as new object '$target'");

my $staging_path = $self->_find_staging_path($target);
if (not $staging_path) {
$self->logcroak("Failed to obtain a clear staging path for '$file' ",
" at '$target'");
}

$staging_path = $self->_stage_object($file, $staging_path, $checksum_action);

return $self->_unstage_object($staging_path, $target);
return $self->baton_client->put_object($file, $target, $checksum_action);
}

=head2 replace_object
Expand Down Expand Up @@ -1405,15 +1397,7 @@ sub replace_object {
$target = $self->ensure_object_path($target);
$self->debug("Replacing object '$target' with '$file'");

my $staging_path = $self->_find_staging_path($target);
if (not $staging_path) {
$self->logcroak("Failed to obtain a clear staging path for '$file' ",
" at '$target'");
}

$staging_path = $self->_stage_object($file, $staging_path, $checksum_action);

return $self->_unstage_object($staging_path, $target);
return $self->baton_client->put_object($file, $target, $checksum_action);
}

=head2 copy_object
Expand Down Expand Up @@ -1507,7 +1491,9 @@ sub move_object {
$self->debug("Moving object from '$source' to '$target'");
$self->_clear_caches($source);

$self->baton_client->move_object($source, $target);
WTSI::DNAP::Utilities::Runnable->new(executable => $IMV,
arguments => [$source, $target],
environment => $self->environment)->run;
return $target
}

Expand Down Expand Up @@ -2411,133 +2397,6 @@ sub _clear_caches {
return;
}

sub _stage_object {
my ($self, $file, $staging_path, @arguments) = @_;

defined $file or
$self->logconfess('A defined file argument is required');
defined $staging_path or
$self->logconfess('A defined staging_path argument is required');

my $num_errors = 0;
my $stage_error = q[];

try {
$self->debug("Staging '$file' to '$staging_path'");
$self->baton_client->put_object($file, $staging_path, @arguments);
# Tag staging file for easy location with a query
$self->add_object_avu($staging_path, $STAGING, 1);
} catch {
$num_errors++;
my @stack1 = split /\n/msx; # Chop up the stack trace
$stage_error = pop @stack1;

try {
# A failed iput may still leave orphaned replicates
if ($self->is_object($staging_path)) {
$self->debug("Cleaning up (deleting) staging file '$staging_path'");
$self->remove_object($staging_path);
}
} catch {
my @stack2 = split /\n/msx;
$self->error("Failed to remove failed staging file '$staging_path': ",
pop @stack2);
};
};

if ($num_errors > 0) {
$self->logconfess("Failed to stage '$file' to '$staging_path': ",
$stage_error);
}

return $staging_path;
}

sub _unstage_object {
my ($self, $staging_path, $target) = @_;

defined $staging_path or
$self->logconfess('A defined staging_path argument is required');
defined $target or
$self->logconfess('A defined target argument is required');

if (not $self->is_object($staging_path)) {
$self->logconfess("Staging path '$staging_path' is not a data object");
}

my $num_errors = 0;
my $unstage_error = q[];

try {
# imv will not overwrite an existing data object so we must copy
# all its metadata to the staged file and then remove it
if ($self->is_object($target)) {
my @target_meta = $self->get_object_meta($target);

# This includes target=1 so we are accepting a race condition
# between customer queries and the file move below
foreach my $avu (@target_meta) {
if ($avu->{attribute} eq $STAGING) {
$self->warn("Found $STAGING AVU on published file '$target'");
}
else {
$self->add_object_avu($staging_path, $avu->{attribute},
$avu->{value}, $avu->{units});
}
}
$self->remove_object($target);
}

$self->debug("Unstaging '$staging_path' to '$target'");
$self->move_object($staging_path, $target);

# Untag the unstaged file
$self->remove_object_avu($target, $STAGING, 1);
} catch {
$num_errors++;
my @stack1 = split /\n/msx;
$unstage_error = pop @stack1;

try {
$self->debug("Cleaning up (deleting) staging file '$staging_path'");
$self->remove_object($staging_path);
} catch {
my @stack2 = split /\n/msx;
$self->error("Failed to remove failed staging file '$staging_path': ",
pop @stack2);
};
};

if ($num_errors > 0) {
$self->logconfess("Failed to unstage '$staging_path' to '$target': ",
$unstage_error);
}

return $target;
}

sub _find_staging_path {
my ($self, $target) = @_;

defined $target or
$self->logconfess('A defined target argument is required');

my $staging_path;

foreach my $try (1 .. $STAGING_MAX_TRIES) {
my $path = sprintf "%s.%d", $target, int rand $STAGING_RAND_MAX;
if ($self->is_object($path)) {
$self->warn("Path $try '$path' for '$target' is not free");
}
else {
$self->debug("Path $try available '$path' for '$target'");
$staging_path = $path;
}
}

return $staging_path;
}

sub _build_irods_major_version {
my ($self) = @_;

Expand Down
26 changes: 14 additions & 12 deletions lib/WTSI/NPG/iRODS/BatonClient.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -122,22 +122,24 @@ sub put_object {
return $remote_path;
}

sub move_object {
my ($self, $source_path, $dest_path) = @_;
# This is affected by https://github.com/wtsi-npg/baton/issues/189

my ($data_object, $collection) = fileparse($source_path);
# sub move_object {
# my ($self, $source_path, $dest_path) = @_;

my $spec = {operation => 'move',
arguments => {path => $dest_path},
target => {collection => $collection,
data_object => $data_object}};
# my ($data_object, $collection) = fileparse($source_path);

my $response = $self->communicate($spec);
$self->validate_response($response);
$self->report_error($response);
# my $spec = {operation => 'move',
# arguments => {path => $dest_path},
# target => {collection => $collection,
# data_object => $data_object}};

return $dest_path
}
# my $response = $self->communicate($spec);
# $self->validate_response($response);
# $self->report_error($response);

# return $dest_path
# }

=head2 list_collection
Expand Down

0 comments on commit 6406103

Please sign in to comment.