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olsonanlolsonanl
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Add awe debugging support.
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‎Makefile

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@@ -71,6 +71,12 @@ compile-typespec: Makefile
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bin: $(BIN_PERL) $(BIN_SERVICE_PERL)
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#
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# Manually run this to update the AweEvents module.
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#
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log-events:
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perl make-log-events-data.pl > lib/Bio/KBase/AppService/AweEvents.pm
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deploy: deploy-client deploy-service
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deploy-all: deploy-client deploy-service
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deploy-client: compile-typespec deploy-docs deploy-libs deploy-scripts

‎lib/Bio/KBase/AppService/AweEvents.pm

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package Bio::KBase::AppService::AweEvents;
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use strict;
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our %events = (
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CR => ['CLIENT_REGISTRATION', 'client registered (for the first time)'],
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CA => ['CLIENT_AUTO_REREGI', 'client automatically re-registered'],
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CU => ['CLIENT_UNREGISTER', 'client unregistered'],
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WC => ['WORK_CHECKOUT', 'workunit checkout'],
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WF => ['WORK_FAIL', 'workunit fails running'],
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SS => ['SERVER_START', 'awe-server start'],
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SR => ['SERVER_RECOVER', 'awe-server start with recover option (-recover)'],
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JQ => ['JOB_SUBMISSION', 'job submitted'],
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TQ => ['TASK_ENQUEUE', 'task parsed and enqueue'],
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WD => ['WORK_DONE', 'workunit received successful feedback from client'],
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WR => ['WORK_REQUEUE', 'workunit requeue after receive failed feedback from client'],
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WP => ['WORK_SUSPEND', 'workunit suspend after failing for conf.Max_Failure times'],
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TD => ['TASK_DONE', 'task done (all the workunits in the task have finished)'],
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TS => ['TASK_SKIPPED', 'task skipped (skip option > 0)'],
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JD => ['JOB_DONE', 'job done (all the tasks in the job have finished)'],
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JP => ['JOB_SUSPEND', 'job suspended'],
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JL => ['JOB_DELETED', 'job deleted'],
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WS => ['WORK_START', 'workunit command start running'],
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WE => ['WORK_END', 'workunit command finish running'],
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WR => ['WORK_RETURN', 'send back failed workunit to server'],
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WI => ['WORK_DISCARD', 'workunit discarded after receiving discard signal from server'],
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PS => ['PRE_WORK_START', 'workunit command start running'],
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PE => ['PRE_WORK_END', 'workunit command finish running'],
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FI => ['FILE_IN', 'start fetching input file from shock'],
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FR => ['FILE_READY', 'finish fetching input file from shock'],
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FO => ['FILE_OUT', 'start pushing output file to shock'],
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FD => ['FILE_DONE', 'finish pushing output file to shock'],
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AI => ['ATTR_IN', 'start fetching input attributes from shock'],
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AR => ['ATTR_READY', 'finish fetching input attributes from shock'],
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WQ => ['WORK_QUEUED', 'workunit queued at proxy'],
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);
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1;

‎lib/Bio/KBase/AppService/Shock.pm

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@@ -55,6 +55,23 @@ sub get_file
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return $self->rest->responseContent();
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}
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sub get_node
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{
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my($self, $node) = @_;
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if ($node !~ /^http/)
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{
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$node = $self->server . "/node/$node";
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}
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my $res = $self->rest->GET($node);
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if ($self->rest->responseCode != 200)
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{
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die "get_node failed: " . $self->rest->responseContent();
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}
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my $obj = $self->json->decode($self->rest->responseContent());
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return $obj->{data};
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}
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sub put_file
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{
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my($self, $file) = @_;

‎lib/javascript/AppService/Client.js

+1-1
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ function AppService(url, auth, auth_cb) {
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}
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if (typeof(_url) != "string" || _url.length == 0) {
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_url = "https://kbase.us/services/app_service";
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_url = "http://p3.theseed.org/services/app_service";
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}
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var _auth = auth ? auth : { 'token' : '', 'user_id' : ''};
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var _auth_cb = auth_cb;

‎make-log-events-data.pl

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use strict;
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my $url = 'https://raw.githubusercontent.com/MG-RAST/AWE/master/lib/logger/event/event.go';
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open(P, "-|", "curl", $url) or die $!;
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print <<'END';
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package Bio::KBase::AppService::AweEvents;
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use strict;
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our %events = (
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END
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while (<P>)
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{
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if (m,^\s+(\S+)\s+=\s+"([A-Z][A-Z])".*//(.*),)
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{
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print "$2 => ['$1', '$3'],\n";
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}
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}
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print ");\n";
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print "1;\n";

‎scripts/appserv-debug-task.pl

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use Bio::KBase::AppService::Client;
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use Bio::KBase::AppService::Shock;
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use Bio::KBase::AppService::Awe;
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use Bio::KBase::AppService::AweEvents;
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use Bio::KBase::AuthToken;
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use Getopt::Long::Descriptive;
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use strict;
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use Data::Dumper;
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use JSON::XS;
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use File::Slurp;
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my($opt, $usage) = describe_options("%c %o task-id",
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["url|u=s", "Service URL"],
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["help|h", "Show this help message"]);
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print($usage->text), exit if $opt->help;
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print($usage->text), exit 1 if (@ARGV != 1);
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my $token = Bio::KBase::AuthToken->new;
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#
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# TODO get this from configs
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#
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my $awe_server = "http://redwood.mcs.anl.gov:7080";
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my $awe_root = "/disks/awe";
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my $awe_logs = "$awe_root/logs";
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my $json = JSON::XS->new->pretty(1);
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my $shock = Bio::KBase::AppService::Shock->new(undef, $token->token);
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my $awe = Bio::KBase::AppService::Awe->new($awe_server, $token->token);
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my $client = Bio::KBase::AppService::Client->new($opt->url);
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my $task_id = shift;
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my @tasks = ($task_id);
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my $res = $client->query_tasks(\@tasks);
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my $task_info = $res->{$task_id};
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print Dumper($task_info);
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my $stderr_node = $shock->get_node($task_info->{stderr_shock_node});
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print "Stderr: " . $json->encode($stderr_node);
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print '-' x 40 . "\n";
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my $stdout_node = $shock->get_node($task_info->{stdout_shock_node});
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print "Stdout: " . $json->encode($stdout_node);
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print '-' x 40 . "\n";
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my $awe_job = $awe->job($task_id);
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print "AWE job: " . $json->encode($awe_job);
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print '-' x 40 . "\n";
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#
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# Find the relevant events.
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#
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for my $log (<$awe_logs/*/event.log>)
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{
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open(E, "<", $log) or warn "Cannot open $log: $!";
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my $printed = 0;
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my $qtask_id = quotemeta($task_id);
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while (<E>)
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{
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if (/$qtask_id/)
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{
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if (!$printed)
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{
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print "\n$log\n";
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$printed = 1;
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}
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my($date, $level, $code, $rest) = parse_event($_);
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my $event_info = $Bio::KBase::AppService::AweEvents::events{$code};
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my @details = map { s/=/\t/; $_ } split(/;/, $rest);
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print "$event_info->[0]\t$date\n";
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print "\t$_\n" foreach @details;
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}
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}
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}
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sub parse_event
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{
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my ($x) = @_;
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return $x =~ /^\[([^]]+)\]\s+\[([^]]+)\]\s+([A-Z][A-Z]);(.*)/
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}
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