grab status (a single value for the GI now), now retrievable using ge…

…t_status()
bioperl · Dec 15, 2011 · 9fc9df5 · 9fc9df5
1 parent 48bf5f6
commit 9fc9df5
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Showing 2 changed files with 40 additions and 5 deletions.
diff --git a/Bio/DB/SeqVersion/gi.pm b/Bio/DB/SeqVersion/gi.pm
@@ -168,6 +168,25 @@ sub get_recent {
     $ref->[0]->[0];
 }
 
+=head2 get_status
+
+ Title   : get_status
+ Usage   : my $newest_gi = $q->get_status(2)
+ Function: Get most recent GI given a single GI
+ Returns : String
+ Args    : A single GI number (string)
+
+=cut
+
+sub get_status {
+    my ( $self, $id ) = @_;
+    $self->throw("Must pass an ID") if !defined $id;
+    if ($id ne $self->{_last_id} ) {
+        $self->get_history($id);
+    }
+    $self->{_last_status};
+}
+
 =head2 get_history
 
  Title   : get_history
@@ -180,7 +199,6 @@ sub get_recent {
            0      GI number
            1      Version
            2      Update Date
-           3      Status
 
            For example, to get the GI number of the first version:
 
@@ -191,6 +209,10 @@ sub get_recent {
            $ref->[0]->[2]
 
  Args    : One identifier (string)
+ Note    : Status of the GI was returned here previously as the last element in
+           the row of elemnts above; however the status is currently only
+           returned for the GI requested (e.g. a single value).  One can get
+           the status for this using the get_status() method above
 
 =cut
 
@@ -203,6 +225,7 @@ sub get_history {
     # are called using the same identifier
     $self->{_last_result} = $ref;
     $self->{_last_id}     = $id;
+    $self->{_last_status} = $status;
     $ref;
 }
 
@@ -219,7 +242,7 @@ sub get_history {
 sub _get_request {
     my ( $self, $id ) = @_;
 
-    $self->throw("Must specify a single id to query") if ( !$id || ref($id) );
+    $self->throw("Must specify a single id to query") if ( !defined($id) || ref($id) );
 
     my $url = sprintf( $URL, $id );
     my $response = $self->get($url);
@@ -244,16 +267,23 @@ sub _get_request {
 sub _process_data {
     my ( $self, $html ) = @_;
 
-    # TODO: this is a quick patch, the status is not currently captured as
-    # it lies outside the table
+    # Only one status is returned (not one per revision).  Setting once
+    my $status;
+    if ($html =~ /<div class="status">Current status:\s+(\S+)<\/div>/) {
+        $status = $1;
+    } else {
+        $self->warn("No current status found, setting to 'unknown'");
+        $status = 'unknown';
+    }
+
     my $te = HTML::TableExtract->new(
         headers => ['Gi', 'Version', 'Update Date'] ,
         depth   => 0);
     $te->parse($html);
     my $table = $te->first_table_found;
     $self->throw("No table found") unless defined $table;
     my $t = [$table->rows];
-    ($t, 1);  # the prior version never returned a status...
+    ($t, $status);
 }
 
 1;

diff --git a/t/RemoteDB/SeqVersion.t b/t/RemoteDB/SeqVersion.t
@@ -26,20 +26,25 @@ SKIP: {
 
     my $latest_gi = $query->get_recent(2);
     is($latest_gi, 2, 'get_recent');
+    is($query->get_status(2), 'live');
 
     my @all_gis = $query->get_all(2);
     cmp_ok(@all_gis, '>=', 8, 'get_all');
+    is($query->get_status(2), 'live');
 
     $latest_gi = $query->get_recent('A00002');
     is($latest_gi, 2, 'get_recent, string');
+    is($query->get_status('A00002'), 'live');
 
     $latest_gi = $query->get_recent(27478738);
     is($latest_gi, 42659163, 'get_recent, integer');
+    is($query->get_status(27478738), 'dead');
 
     # check that default type is "gi"
     ok $query = Bio::DB::SeqVersion->new();
     ok my $ref = $query->get_history(3245);
     is($ref->[0]->[0], 578167, 'get_history');
+    is($query->get_status('3245'), 'dead');
 }
 
 done_testing();