P3 workspace changes

LICENSE → LICENSE.md

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

Makefile

@@ -42,7 +42,7 @@ TPAGE_ARGS = --define kb_top=$(TARGET) \
 
 TESTS = $(wildcard t/client-tests/*.t)
 
-all: bin service
+all: bin compile-typespec service
 
 jarfile:
 	gen_java_client $(SERVER_SPEC) org.patricbrc.Workspace java
@@ -84,7 +84,7 @@ bin: $(BIN_PERL) $(BIN_SERVICE_PERL)
 
 deploy: deploy-client deploy-service
 deploy-all: deploy-client deploy-service
-deploy-client: deploy-libs deploy-scripts 
+deploy-client: compile-typespec deploy-docs deploy-libs deploy-scripts 
 
 deploy-service: deploy-dir deploy-monit deploy-libs deploy-service-scripts
 	$(TPAGE) $(TPAGE_ARGS) service/start_service.tt > $(TARGET)/services/$(SERVICE)/start_service

Workspace.spec

@@ -110,7 +110,7 @@ typedef structure {
 		bool metadata_only;
 		bool adminmode;
 } get_params;
-funcdef get(get_params input) returns (list<tuple<ObjectMeta,ObjectData>> output) authentication required;
+funcdef get(get_params input) returns (list<tuple<ObjectMeta,ObjectData>> output) authentication optional;
 
 /* "update_shock_meta" command
 	Description:
@@ -138,7 +138,7 @@ funcdef update_auto_meta(update_auto_meta_params input) returns (list<ObjectMeta
 typedef structure {
 	list<FullObjectPath> objects;
 } get_download_url_params;
-funcdef get_download_url(get_download_url_params input) returns (list<string> urls) authentication required;
+funcdef get_download_url(get_download_url_params input) returns (list<string> urls) authentication optional;
 
 /* "get_archive_url" command
 	Description:
@@ -158,7 +158,7 @@ typedef structure {
 	string archive_name;
 	string archive_type;
 } get_archive_url_params;
-funcdef get_archive_url(get_archive_url_params input) returns (string url);
+funcdef get_archive_url(get_archive_url_params input) returns (string url)  authentication optional;
 
 /* "list" command
 	Description: 
@@ -182,7 +182,7 @@ typedef structure {
 		mapping<string,list<string>> query;
 		bool adminmode;
 } list_params;
-funcdef ls(list_params input) returns (mapping<FullObjectPath,list<ObjectMeta>> output) authentication required;
+funcdef ls(list_params input) returns (mapping<FullObjectPath,list<ObjectMeta>> output)  authentication optional;
 
 /********** REORGANIZATION FUNCTIONS *******************/
 
@@ -244,7 +244,7 @@ typedef structure {
 	WorkspacePerm new_global_permission;
 	bool adminmode;
 } set_permissions_params;
-funcdef set_permissions(set_permissions_params input) returns (ObjectMeta output) authentication required;
+funcdef set_permissions(set_permissions_params input) returns (list<tuple<Username,WorkspacePerm> > output) authentication required;
 
 /* "list_permissions" command
 	Description: 
@@ -258,6 +258,6 @@ typedef structure {
 	list<FullObjectPath> objects;
 	bool adminmode;
 } list_permissions_params;
-funcdef list_permissions(list_permissions_params input) returns (mapping<string,list<tuple<Username,WorkspacePerm> > > output) authentication required;
+funcdef list_permissions(list_permissions_params input) returns (mapping<string,list<tuple<Username,WorkspacePerm> > > output) authentication optional;
 
 };

lib/Bio/P3/Workspace/ScriptHelpers.pm

@@ -9,7 +9,13 @@ use HTTP::Request::Common;
 use LWP::UserAgent;
 use Bio::P3::Workspace::WorkspaceClient;
 use Bio::P3::Workspace::WorkspaceClientExt;
-use Bio::ModelSEED::ProbModelSEED::ProbModelSEEDClient;
+
+our $have_kb_auth = 0;
+eval
+{
+    require Bio::KBase::Auth;
+    $have_kb_auth = 1;
+};
 
 our $defaultWSURL   = "http://p3.theseed.org/services/Workspace";
 our $defaultAPPURL = "http://p3.theseed.org/services/app_service";
@@ -227,9 +233,12 @@ sub appurl {
 sub process_paths {
 	my $paths = shift;
 	for (my $i=0; $i < @{$paths}; $i++) {
-		if ($paths->[$i] !~ /^\// && $paths->[$i] !~ /^PATRICSOLR/) {
+		if ($paths->[$i] !~ /^\// && $paths->[$i] !~ /^PATRIC:/ && $paths->[$i] !~ /^PUBSEED:/ && $paths->[$i] !~ /^RAST:/ && $paths->[$i] !~ /^REFSEQ:/) {
 			$paths->[$i] = Bio::P3::Workspace::ScriptHelpers::directory().$paths->[$i];
 		}
+		while ($paths->[$i] =~ m/[^\/]+\/\.\.\/*/) {
+			$paths->[$i] =~ s/[^\/]+\/\.\.\/*//g;
+		}
 	}
 	return $paths;
 }
@@ -303,15 +312,33 @@ sub login {
 			user_id => $params->{user_id},
 			password => undef
 		});
+		#
+		# Update the KBase .kbase_config file as well.
+		#
+		if ($have_kb_auth)
+		{
+		    Bio::KBase::Auth::SetConfigs(token => $token,
+						 user_id => $params->{user_id},
+						 password => undef);
+		}
 	}
 	return $token;
 }
 
 sub logout {
-	Bio::P3::Workspace::ScriptHelpers::SetConfig({
-		token => undef,
-		user_id => undef
+    Bio::P3::Workspace::ScriptHelpers::SetConfig({
+	token => undef,
+	user_id => undef
 	});
+    #
+    # Update the KBase .kbase_config file as well.
+    #
+    if ($have_kb_auth)
+    {
+	Bio::KBase::Auth::SetConfigs(token => undef,
+				     user_id => undef,
+				     password => undef);
+    }
 }
 
 sub msClient {
@@ -321,14 +348,35 @@ sub msClient {
 	}
 	if ($url eq "impl") {
 		require "Bio/ModelSEED/ProbModelSEED/ProbModelSEEDImpl.pm";
-		$ENV{KB_DEPLOYMENT_CONFIG} = "/Users/chenry/code/ProbModelSEED/configs/test.cfg";
 		$Bio::ModelSEED::ProbModelSEED::Service::CallContext = Bio::ModelSEED::ProbModelSEED::Service::CallContext->new(Bio::P3::Workspace::ScriptHelpers::token(),"unknown",Bio::P3::Workspace::ScriptHelpers::user());
 		my $client = Bio::ModelSEED::ProbModelSEED::ProbModelSEEDImpl->new();
 		return $client;
 	}
+	require "Bio/ModelSEED/ProbModelSEED/ProbModelSEEDClient.pm";
 	return Bio::ModelSEED::ProbModelSEED::ProbModelSEEDClient->new($url,token => Bio::P3::Workspace::ScriptHelpers::token());
 }
 
+sub get_workspace_object {
+	my $ref = shift;
+	my $options = shift;
+	my $input = {objects => [$ref]};
+	if ($options->{adminmode}) {
+		$input->{adminmode} = $options->{adminmode};
+	}
+	if ($options->{metadata_only}) {
+		$input->{metadata_only} = $options->{metadata_only};
+	}
+	my $wc = wsClient();
+	my $output = $wc->get($input);
+	if (defined($output->[0]->[11])) {
+		my $ua = LWP::UserAgent->new();
+		$ua->default_header( "Authorization" => $options->{token} );
+		my $res = $ua->get($options->{url});
+		$output->[1] = $res->{content};
+	}
+	return $output;
+}
+
 sub wsClient {
 	my $url = shift;
 	if (!defined($url)) {

lib/Bio/P3/Workspace/Service.pm

@@ -6,6 +6,7 @@ use Moose;
 use POSIX;
 use JSON;
 use Bio::KBase::Log;
+use Class::Load qw();
 use Config::Simple;
 my $get_time = sub { time, 0 };
 eval {
@@ -44,15 +45,15 @@ our %return_counts = (
 our %method_authentication = (
         'create' => 'required',
         'update_metadata' => 'required',
-        'get' => 'required',
+        'get' => 'optional',
         'update_auto_meta' => 'required',
-        'get_download_url' => 'required',
-        'get_archive_url' => 'none',
-        'ls' => 'required',
+        'get_download_url' => 'optional',
+        'get_archive_url' => 'optional',
+        'ls' => 'optional',
         'copy' => 'required',
         'delete' => 'required',
         'set_permissions' => 'required',
-        'list_permissions' => 'required',
+        'list_permissions' => 'optional',
 );
 
 
@@ -149,6 +150,23 @@ sub _build_loggers
     return $loggers;
 }
 
+#
+# Override method from RPC::Any::Server::JSONRPC 
+# to eliminate the deprecation warning for Class::MOP::load_class.
+#
+sub _default_error {
+    my ($self, %params) = @_;
+    my $version = $self->default_version;
+    $version =~ s/\./_/g;
+    my $error_class = "JSON::RPC::Common::Procedure::Return::Version_${version}::Error";
+    Class::Load::load_class($error_class);
+    my $error = $error_class->new(%params);
+    my $return_class = "JSON::RPC::Common::Procedure::Return::Version_$version";
+    Class::Load::load_class($return_class);
+    return $return_class->new(error => $error);
+}
+
+
 #override of RPC::Any::Server
 sub handle_error {
     my ($self, $error) = @_;
@@ -396,7 +414,7 @@ sub get_method
 			     "There is no method package named '$package'.");
 	}
 
-	Class::MOP::load_class($module);
+	Class::Load::load_class($module);
     }
 
     if (!$module->can($method)) {

lib/Bio/P3/Workspace/WorkspaceClient.pm

@@ -35,10 +35,6 @@ sub new
 {
     my($class, $url, @args) = @_;
 
-    if (!defined($url))
-    {
-	$url = 'http://p3.theseed.org/services/Workspace';
-    }
 
     my $self = {
 	client => Bio::P3::Workspace::WorkspaceClient::RpcClient->new,
@@ -511,7 +507,7 @@ sub get
 {
     my($self, @args) = @_;
 
-# Authentication: required
+# Authentication: optional
 
     if ((my $n = @args) != 1)
     {
@@ -733,7 +729,7 @@ sub get_download_url
 {
     my($self, @args) = @_;
 
-# Authentication: required
+# Authentication: optional
 
     if ((my $n = @args) != 1)
     {
@@ -828,7 +824,7 @@ sub get_archive_url
 {
     my($self, @args) = @_;
 
-# Authentication: none
+# Authentication: optional
 
     if ((my $n = @args) != 1)
     {
@@ -973,7 +969,7 @@ sub ls
 {
     my($self, @args) = @_;
 
-# Authentication: required
+# Authentication: optional
 
     if ((my $n = @args) != 1)
     {
@@ -1314,7 +1310,9 @@ sub delete
 
 <pre>
 $input is a set_permissions_params
-$output is an ObjectMeta
+$output is a reference to a list where each element is a reference to a list containing 2 items:
+	0: a Username
+	1: a WorkspacePerm
 set_permissions_params is a reference to a hash where the following keys are defined:
 	path has a value which is a FullObjectPath
 	permissions has a value which is a reference to a list where each element is a reference to a list containing 2 items:
@@ -1327,26 +1325,6 @@ FullObjectPath is a string
 Username is a string
 WorkspacePerm is a string
 bool is an int
-ObjectMeta is a reference to a list containing 12 items:
-	0: an ObjectName
-	1: an ObjectType
-	2: a FullObjectPath
-	3: (creation_time) a Timestamp
-	4: an ObjectID
-	5: (object_owner) a Username
-	6: an ObjectSize
-	7: a UserMetadata
-	8: an AutoMetadata
-	9: (user_permission) a WorkspacePerm
-	10: (global_permission) a WorkspacePerm
-	11: (shockurl) a string
-ObjectName is a string
-ObjectType is a string
-Timestamp is a string
-ObjectID is a string
-ObjectSize is an int
-UserMetadata is a reference to a hash where the key is a string and the value is a string
-AutoMetadata is a reference to a hash where the key is a string and the value is a string
 
 </pre>
 
@@ -1355,7 +1333,9 @@ AutoMetadata is a reference to a hash where the key is a string and the value is
 =begin text
 
 $input is a set_permissions_params
-$output is an ObjectMeta
+$output is a reference to a list where each element is a reference to a list containing 2 items:
+	0: a Username
+	1: a WorkspacePerm
 set_permissions_params is a reference to a hash where the following keys are defined:
 	path has a value which is a FullObjectPath
 	permissions has a value which is a reference to a list where each element is a reference to a list containing 2 items:
@@ -1368,26 +1348,6 @@ FullObjectPath is a string
 Username is a string
 WorkspacePerm is a string
 bool is an int
-ObjectMeta is a reference to a list containing 12 items:
-	0: an ObjectName
-	1: an ObjectType
-	2: a FullObjectPath
-	3: (creation_time) a Timestamp
-	4: an ObjectID
-	5: (object_owner) a Username
-	6: an ObjectSize
-	7: a UserMetadata
-	8: an AutoMetadata
-	9: (user_permission) a WorkspacePerm
-	10: (global_permission) a WorkspacePerm
-	11: (shockurl) a string
-ObjectName is a string
-ObjectType is a string
-Timestamp is a string
-ObjectID is a string
-ObjectSize is an int
-UserMetadata is a reference to a hash where the key is a string and the value is a string
-AutoMetadata is a reference to a hash where the key is a string and the value is a string
 
 
 =end text
@@ -1503,7 +1463,7 @@ sub list_permissions
 {
     my($self, @args) = @_;
 
-# Authentication: required
+# Authentication: optional
 
     if ((my $n = @args) != 1)
     {