Apps now relay stdout/stderr and status to the app service.

Add query_task_details to retrieve this data. Stdout/stderr are retrieved
via REST URLs.

Author: olsonanl

AppService.spec

@@ -67,6 +67,15 @@ module AppService
 
     funcdef query_task_summary() returns (mapping<task_status status, int count> status);
 
+    typedef structure {
+	string stdout_url;
+	string stderr_url;
+	int pid;
+	string hostname;
+	int exitcode;
+    } TaskDetails;
+    funcdef query_task_details(task_id) returns (TaskDetails details);
+
     funcdef enumerate_tasks(int offset, int count)
 	returns (list<Task>);
 };

Makefile

@@ -61,7 +61,6 @@ compile-typespec: Makefile
 	touch lib/biokbase/$(SERVICE_NAME_PY)/__init__.py 
 	mkdir -p lib/javascript/$(SERVICE_NAME)
 	compile_typespec \
-		--psgi $(SERVICE_PSGI_FILE) \
 		--impl Bio::KBase::$(SERVICE_NAME)::%sImpl \
 		--service Bio::KBase::$(SERVICE_NAME)::Service \
 		--client Bio::KBase::$(SERVICE_NAME)::Client \

deploy.cfg

@@ -4,6 +4,19 @@
 awe-server = http://redwood.mcs.anl.gov:7080
 shock-server = http://redwood.mcs.anl.gov:7078
 app-directory = app_specs
+
+;
+; Directory into which task status (stdout/err etc) are written
+;
+
+; task-status-dir =
+
+;
+; AWE client group to submit jobs iwth
+;
+; awe-clientgroup =
+
+
 ; service-url = 
 ; service-host =
 ; service-port =
@@ -13,6 +26,19 @@ app-directory = app_specs
 awe-server = http://redwood.mcs.anl.gov:7080
 shock-server = http://redwood.mcs.anl.gov:7078
 app-directory = app_specs
+
+;
+; Directory into which task status (stdout/err etc) are written
+;
+
+; task-status-dir =
+
+;
+; AWE client group to submit jobs iwth
+;
+; awe-clientgroup =
+
+
 ; service-url = 
 ; service-host =
 ; service-port =

lib/AppService.psgi

@@ -8,11 +8,8 @@ use Plack::Builder;
 
 my @dispatch;
 
-{
-    my $obj = Bio::KBase::AppService::AppServiceImpl->new;
-    push(@dispatch, 'AppService' => $obj);
-}
-
+my $obj = Bio::KBase::AppService::AppServiceImpl->new;
+push(@dispatch, 'AppService' => $obj);
 
 my $server = Bio::KBase::AppService::Service->new(instance_dispatch => { @dispatch },
 				allow_get => 0,
@@ -23,6 +20,7 @@ my $rpc_handler = sub { $server->handle_input(@_) };
 $handler = builder {
     mount "/ping" => sub { $server->ping(@_); };
     mount "/auth_ping" => sub { $server->auth_ping(@_); };
+    mount "/task_info" => sub { $obj->_task_info(@_); };
     mount "/" => $rpc_handler;
 };
 

lib/Bio/KBase/AppService/AppScript.pm

@@ -6,10 +6,14 @@ use strict;
 use JSON::XS;
 use File::Slurp;
 use IO::File;
+use IO::Pipe;
+use IO::Select;
 use Capture::Tiny 'capture';
 use Bio::P3::Workspace::WorkspaceClientExt;
 use Bio::KBase::AuthToken;
 use Time::HiRes 'gettimeofday';
+use LWP::UserAgent;
+use REST::Client;
 
 use base 'Class::Accessor';
 
@@ -27,7 +31,107 @@ sub new
     return bless $self, $class;
 }
 
+#
+# Run the script.
+#
+# We wish the script to always succeed (from the point of view of the execution environment)
+# so we will run the script itself as a forked child, and monitor its execution. We create
+# pipes from stdout and stderr and push their output to the app service URL provided as the first argument to
+# the script.
+#
 sub run
+{
+    my($self, $args) = @_;
+
+    #
+    # Hack to finding task id.
+    #
+    my $task_id = 'TBD';
+    if ($ENV{PWD} =~ /([0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})_\d+_\d+$/i)
+    {
+	$task_id = $1;
+    }
+    else
+    {
+	$task_id = "UNK-$$";
+    }
+
+    my $appserv_url = shift @$args;
+
+    my $ua = LWP::UserAgent->new();
+    my $rest = REST::Client->new();
+    $rest->setHost("$appserv_url/$task_id");
+    $self->{rest} = $rest;
+
+    my $sel = IO::Select->new();
+
+    my $stdout_pipe = IO::Pipe->new();
+    my $stderr_pipe = IO::Pipe->new();
+
+    my $pid = fork();
+
+    if ($pid == 0)
+    {
+	$stdout_pipe->writer();
+	$stderr_pipe->writer();
+
+	open(STDOUT, ">&", $stdout_pipe);
+	open(STDERR, ">&", $stderr_pipe);
+
+	$self->subproc_run($args);
+	exit(0);
+    }
+
+    my $host = `hostname -f`;
+    $host = `hostname` if !$host;
+    chomp $host;
+
+    $self->write_block("pid", $pid);
+    $self->write_block("hostname", $host);
+    
+    $stdout_pipe->reader();
+    $stderr_pipe->reader();
+
+    $sel->add($stdout_pipe);
+    $sel->add($stderr_pipe);
+
+    while ($sel->count() > 0)
+    {
+	my @ready = $sel->can_read();
+	for my $r (@ready)
+	{
+	    my $which = ($r == $stdout_pipe) ? 'stdout' : 'stderr';
+	    my $block;
+	    my $n = $r->read($block, 1_000_000);
+	    if (!defined($n))
+	    {
+		die "error reading $which $r: $!";
+	    }
+	    elsif ($n == 0)
+	    {
+		print STDERR "EOF on $r\n";
+		$self->write_block("$which/eof");
+		$sel->remove($r);
+	    }
+	    else
+	    {
+		$self->write_block("$which/data", $block);
+	    }
+	}
+    }
+
+    my $x = waitpid($pid, 0);
+    $self->write_block("exitcode",$?);
+}
+
+sub write_block
+{
+    my($self, $path, $data) = @_;
+    print "Write to $path: $data\n";
+    $self->{rest}->POST($path, $data);
+}
+
+sub subproc_run
 {
     my($self, $args) = @_;