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Implementing prefix and type search for workspace.ls #93

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b3c60ac
gexf type for graph viewing
aswarren Nov 6, 2020
f23e4d8
Merge branch 'master' of github.com:BV-BRC/Workspace
aswarren Jun 2, 2025
e1161ad
name_search and type parameters for workspace.ls
aswarren Jun 3, 2025
6b3d739
Merge branch 'BV-BRC:master' into search
aswarren Jul 15, 2025
95585c5
minimum diff of term search from previous solution
aswarren Sep 2, 2025
1b2522b
Merge branch 'master' of github.com:BV-BRC/Workspace into search
aswarren Sep 2, 2025
55033e8
Merge branch 'search' of github.com:aswarren/Workspace into search
aswarren Sep 2, 2025
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24 changes: 16 additions & 8 deletions lib/Bio/P3/Workspace/WorkspaceImpl.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -1251,7 +1251,7 @@ sub _compute_mongo_regex_for_path
}
}

#List all objects matching input query**
#List all objects matching input query** accept the pre-processed $search_filters from ls
sub _list_objects {
my ($self,$fullpath,$query,$excludeDirectories,$excludeObjects,$recursive) = @_;
my $hint;
Expand Down Expand Up @@ -1281,8 +1281,12 @@ sub _list_objects {
#
my %bad_ws = ('942D0C20-D8CF-11EA-A092-E9C4682E0674' => 1,
'7E50286E-C07E-11EB-954E-D6FC682E0674' => 1);
my $perform_recursive_search = $recursive;
if ($recursive == 1 && $bad_ws{$wsobj->{uuid}} && !defined($query->{name}) && !defined($query->{type})) {
$perform_recursive_search = 0;
}

if ($recursive == 1 && !$bad_ws{$wsobj->{uuid}})
if ($perform_recursive_search == 1)
{

if (length($path) > 0) {
Expand Down Expand Up @@ -3301,20 +3305,25 @@ sub ls

$output = {};
$input = $self->_validateargs($input,["paths"],{
excludeDirectories => 0,
excludeDirectories => 0,
excludeObjects => 0,
recursive => 0,
fullHierachicalOutput => 0,
query => {}
});
foreach my $fullpath (@{$input->{paths}}) {
my $objs = [];
my $objs = [];
my $query = $input->{query};
if (defined($query->{name_search})) {
$query->{name} = qr/$query->{name_search}/i;
delete $query->{name_search};
}
if ($fullpath eq "" || $fullpath eq "/") {
$objs = $self->_list_workspaces(undef,$self->_formatQuery($input->{query},1));
$objs = $self->_list_workspaces(undef,$self->_formatQuery($query,1));
} elsif ($fullpath =~ m/^\/([^\/]+)\/*$/) {
$objs = $self->_list_workspaces($1,$self->_formatQuery($input->{query},1));
$objs = $self->_list_workspaces($1,$self->_formatQuery($query,1));
} else {
$objs = $self->_list_objects($fullpath,$self->_formatQuery($input->{query},0),$input->{excludeDirectories},$input->{excludeObjects},$input->{recursive});
$objs = $self->_list_objects($fullpath,$self->_formatQuery($query,0),$input->{excludeDirectories},$input->{excludeObjects},$input->{recursive});
}
for (my $i=0; $i < @{$objs}; $i++) {
my $meta = $self->_generate_object_meta($objs->[$i]);
Expand All @@ -3337,7 +3346,6 @@ sub ls
return($output);
}


=head2 copy

$output = $obj->copy($input)
Expand Down
1 change: 1 addition & 0 deletions typeslist.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ genome
genome_annotation_result
genome_comparison_table
genome_group
gexf
gff
gif
hdf
Expand Down