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api updates: caching update, notebook POST to shock #229

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merged 2 commits into from
Jan 16, 2013
Merged

api updates: caching update, notebook POST to shock #229

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773dce9
added post of notebook file for loading to shock
Jan 15, 2013
fb4060b
updated caching to use master function in resource.pm
Jan 15, 2013
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13 changes: 4 additions & 9 deletions src/MGRAST/lib/resources2/matrix.pm
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Expand Up @@ -226,14 +226,9 @@ sub instance {
$self->return_data( {"ERROR" => "no valid ids submitted and/or found: ".join(", ", @ids)}, 401 );
}

# get cached if exists
my $cached = $self->memd->get($self->url_id);
if ($cached) {
# do a runaround on ->return_data
print $self->header;
print $cached;
exit 0;
}
# return cached if exists
$self->return_cached();

# prepare data
my $data = $self->prepare_data([keys %$mgids], $type);
$self->return_data($data, undef, 1); # cache this!
Expand All @@ -257,7 +252,7 @@ sub prepare_data {
my $leaf_node = 0;
my $matrix_id = join("_", sort @$data).'_'.join("_", ($type, $glvl, $source, $rtype, $eval, $ident, $alen));
if (@filter > 0) {
$matrix_id .= join("_", sort map { $_ =~ s/\s+/_/ } @filter)."_".$fsrc;
$matrix_id .= join("_", sort map { $_ =~ s/\s+/_/g } @filter)."_".$fsrc;
}

# initialize analysis obj with mgids
Expand Down
11 changes: 3 additions & 8 deletions src/MGRAST/lib/resources2/metagenome.pm
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Expand Up @@ -123,14 +123,9 @@ sub instance {
$self->return_data( {"ERROR" => "insufficient permissions to view this data"}, 401 );
}

# get cached if exists
my $cached = $self->memd->get($self->url_id);
if ($cached) {
# do a runaround on ->return_data
print $self->header;
print $cached;
exit 0;
}
# return cached if exists
$self->return_cached();

# prepare data
my $data = $self->prepare_data( [$job] );
$data = $data->[0];
Expand Down
66 changes: 64 additions & 2 deletions src/MGRAST/lib/resources2/notebook.pm
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Expand Up @@ -93,7 +93,16 @@ sub info {
},
'required' => { "id" => ["string", "unique shock object identifier"],
"nbid" => ["string", "unique notebook object identifier"] },
'body' => {} } }
'body' => {} } },
{ 'name' => "upload",
'request' => $self->cgi->url."/".$self->name."/upload",
'description' => "Upload a notebook to shock.",
'method' => "POST",
'type' => "synchronous",
'attributes' => $self->attributes,
'parameters' => { 'options' => {},
'required' => {},
'body' => { "ipynb" => ["file", ".pynb file in JSON format"] } } },
]
};
$self->return_data($content);
Expand All @@ -102,6 +111,11 @@ sub info {
# the resource is called with an id parameter
sub instance {
my ($self) = @_;

# possible upload
if (($self->rest->[0] eq 'upload') && ($self->method eq 'POST')) {
$self->upload_notebook();
}

# get data
my $data = [];
Expand All @@ -128,7 +142,7 @@ sub instance {
created => strftime("%Y-%m-%dT%H:%M:%S", localtime)
};
$file->{'metadata'} = $attr;
my $clone = $self->set_shock_node($node->{id}.'ipynb', $file, $attr);
my $clone = $self->set_shock_node($node->{id}.'.ipynb', $file, $attr);
$data = $self->prepare_data( [$clone] );
} else {
$data = $self->prepare_data( [$node] );
Expand Down Expand Up @@ -189,4 +203,52 @@ sub prepare_data {
return $objects;
}

# upload notebook file to shock / create metadata
sub upload_notebook {
my ($self) = @_;

# get notebook file
my $tmp_dir = "$Conf::temp";
my $fname = $self->cgi->param('upload');

# error check
unless ($fname) {
$self->return_data({"ERROR" => "Invalid parameters, requires filename and data"}, 400);
}
if ($fname =~ /\.\./) {
$self->return_data({"ERROR" => "Invalid parameters, trying to change directory with filename, aborting"}, 400);
}
if ($fname !~ /^[\w\d_\.]+$/) {
$self->return_data({"ERROR" => "Invalid parameters, filename allows only word, underscore, . and number characters"}, 400);
}

my $fhdl = $self->cgi->upload('upload');
unless ($fhdl) {
$self->return_data({"ERROR" => "Storing object failed - could not obtain filehandle"}, 507);
}
my $nb_string = "";
my $io_handle = $fhdl->handle;
my ($bytesread, $buffer);
while ($bytesread = $io_handle->read($buffer,4096)) {
$nb_string .= $buffer;
}

# get notebook object and attribute object
my $nb_obj = $self->json->decode($nb_string);
my $nb_attr = { type => 'ipynb',
name => $nb_obj->{metadata}{name} ? $nb_obj->{metadata}{name} : 'Untitled',
user => $self->user ? $self->user->login : 'public',
uuid => $self->uuidv4(),
created => strftime("%Y-%m-%dT%H:%M:%S", localtime)
};
$nb_obj->{'metadata'} = $nb_attr;

# add to shock
my $name = $nb_attr->{name};
$name =~ s/\s+/_/g;
my $node = $self->set_shock_node($name.'.ipynb', $nb_obj, $nb_attr);
my $data = $self->prepare_data( [$node] );
$self->return_data($data->[0]);
}

1;
11 changes: 3 additions & 8 deletions src/MGRAST/lib/resources2/project.pm
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Expand Up @@ -117,14 +117,9 @@ sub instance {
$self->return_data( {"ERROR" => "insufficient permissions to view this data"}, 401 );
}

# get cached if exists
my $cached = $self->memd->get($self->url_id);
if ($cached) {
# do a runaround on ->return_data
print $self->header;
print $cached;
exit 0;
}
# return cached if exists
$self->return_cached();

# prepare data
my $data = $self->prepare_data( [$project] );
$data = $data->[0];
Expand Down
21 changes: 21 additions & 0 deletions src/MGRAST/lib/resources2/resource.pm
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Expand Up @@ -235,6 +235,19 @@ sub check_pagination {
}
}

# return cached data if exists
sub return_cached {
my ($self) = @_;

my $cached = $self->memd->get($self->url_id);
if ($cached) {
# do a runaround on ->return_data
print $self->header;
print $cached;
exit 0;
}
}

# print the actual data output
sub return_data {
my ($self, $data, $error, $cache_me) = @_;
Expand Down Expand Up @@ -468,6 +481,14 @@ sub get_shock_query {
}
}

# I can't find a perl library that gives me random UUID !
sub uuidv4 {
my ($self) = @_;
my $uuid = `python -c "import uuid; print uuid.uuid4()"`;
chomp $uuid;
return $uuid;
}

sub toFloat {
my ($self, $x) = @_;
return $x * 1.0;
Expand Down