Add support for setting per-task user_metadata

Author: olsonanl

.gitignore

@@ -2,3 +2,4 @@
 *.pm.bak-201*
 *.py.bak-201*
 lib/Bio/KBase/AppService/AppConfig.pm
+lib/javascript/AppService/Client.js

AppService.spec

@@ -73,6 +73,7 @@ module AppService
 	workspace_id workspace;
 	string base_url;
 	string container_id;
+	string user_metaata;
     } StartParams;
     funcdef start_app2(app_id, task_parameters params, StartParams start_params)
 	returns (Task task);

lib/Bio/KBase/AppService/SchedulerDB.pm

@@ -183,6 +183,7 @@ sub create_task
 	req_runtime => $preflight->{runtime},
 	req_policy_data => $self->json->encode($preflight->{policy_data} // {}),
 	req_is_control_task => ($preflight->{is_control_task} ? 1 : 0),
+	user_metadata => $start_parameters->{user_metadata},    
 	(defined($container_id) ? (container_id => $container_id) : ()),
 	};
 

lib/Bio/KBase/AppService/Schema.sql

@@ -134,6 +134,7 @@ CREATE TABLE Task
 	hidden BOOLEAN default FALSE,
 	container_id VARCHAR(255),
 	base_url VARCHAR(255),
+	user_metadata TEXT,
 	FOREIGN KEY (owner) REFERENCES ServiceUser(id),
 	FOREIGN KEY (state_code) REFERENCES TaskState(code),
 	FOREIGN KEY (application_id) REFERENCES Application(id),

lib/Bio/KBase/AppService/Schema/Result/SiteDefaultContainer.pm

@@ -48,13 +48,27 @@ __PACKAGE__->table("SiteDefaultContainer");
   is_nullable: 1
   size: 255
 
+=head2 last_modified
+
+  data_type: 'timestamp'
+  datetime_undef_if_invalid: 1
+  default_value: current_timestamp
+  is_nullable: 0
+
 =cut
 
 __PACKAGE__->add_columns(
   "base_url",
   { data_type => "varchar", is_nullable => 0, size => 255 },
   "default_container_id",
   { data_type => "varchar", is_foreign_key => 1, is_nullable => 1, size => 255 },
+  "last_modified",
+  {
+    data_type => "timestamp",
+    datetime_undef_if_invalid => 1,
+    default_value => \"current_timestamp",
+    is_nullable => 0,
+  },
 );
 
 =head1 PRIMARY KEY
@@ -92,8 +106,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-03-10 14:48:58
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:V6EqtIbT76SwZFjX+kEb4A
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-03-25 13:44:04
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QMwEFGWcM+UY+LiYNXFGmw
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

lib/Bio/KBase/AppService/Schema/Result/Task.pm

@@ -165,6 +165,11 @@ __PACKAGE__->table("Task");
   is_nullable: 1
   size: 255
 
+=head2 user_metadata
+
+  data_type: 'text'
+  is_nullable: 1
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -227,6 +232,8 @@ __PACKAGE__->add_columns(
   { data_type => "varchar", is_foreign_key => 1, is_nullable => 1, size => 255 },
   "base_url",
   { data_type => "varchar", is_nullable => 1, size => 255 },
+  "user_metadata",
+  { data_type => "text", is_nullable => 1 },
 );
 
 =head1 PRIMARY KEY
@@ -389,8 +396,8 @@ __PACKAGE__->has_many(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-03-10 14:48:59
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:IF9bnr/uurQeFeJEocy84g
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-03-25 13:44:04
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:3855e9g3LybZorgM6ul/nA
 
 __PACKAGE__->many_to_many(cluster_jobs => 'task_executions', 'cluster_job');
 

lib/javascript/AppService/Client.js

@@ -18,7 +18,7 @@ function AppService(url, auth, auth_cb) {
     }
 
     if (typeof(_url) != "string" || _url.length == 0) {
-        _url = "https://p3.theseed.org/services/app_service";
+        _url = "https://p3.theseed.org/services_test/app_service_test";
     }
     var _auth = auth ? auth : { 'token' : '', 'user_id' : ''};
     var _auth_cb = auth_cb;

scripts/appserv-start-app.pl

@@ -10,6 +10,8 @@
 				    ["output-file|f=s", "Change the output file"],
 				    ["container-id|c=s", "Use the specified container"],
 				    ["base-url|b=s", "Submit with the chosen base URL"],
+				    ["user-metadata=s", "Tag the job with the given metadata"],
+				    ["user-metadata-file=s", "Tag the job with the given metadata from this file"],
 				    ["verbose|v", "Show verbose output"],
 				    ["url|u=s", "Service URL"],
 				    ["help|h", "Show this help message"]);
@@ -25,10 +27,18 @@
 
 my $params = decode_json(scalar read_file($params_data));
 
+my $user_metadata = $opt->user_metadata;
+if ($opt->user_metadata_file)
+{
+    $user_metadata = read_file($opt->user_metadata);
+}
+
+
 my $start_params = {
     defined($workspace) ? (workspace => $workspace) : (),
     $opt->container_id ? (container_id => $opt->container_id) : (),
     $opt->base_url ? (base_url => $opt->base_url) : (),
+    defined($user_metadata) ? (user_metadata => $user_metadata) : (),
 };
 
 if ($params->{output_path} && $opt->output_path)

service-scripts/p3x-run-qa.pl

@@ -21,6 +21,7 @@
 				    ["submit|s" => "Submit the job to the scheduler"],
 				    ["base|b=s" => "Use this directory as the deployment base for the run (not for use with --submit)"],
 				    ["app|a=s" => "Application name"],
+				    ["user-metadata=s" => "User metadata for this run"],
 				    ['override=s@' => "Override other parameter settings in app parameter file", { default => [] }],
 				    ["out|o=s" => "Use this workspace path as the output base",
 				 { default => '/olson@patricbrc.org/PATRIC-QA/applications' }],
@@ -189,6 +190,7 @@ sub run_in_container
     my $exitcode = $?;
     write_file("$out_dir/exitcode", "$exitcode\n");
     write_file("$out_dir/hostname", "$hostname\n");
+    write_file("$out_dir/user_metadata", $opt->user_metadata) if $opt->user_metadata;
     $ok or die "Error running @cmd\n";
 
 }
@@ -212,6 +214,7 @@ sub run_locally
     my $exitcode = $?;
     write_file("$out_dir/exitcode", "$exitcode\n");
     write_file("$out_dir/hostname", "$hostname\n");
+    write_file("$out_dir/user_metadata", $opt->user_metadata) if $opt->user_metadata;
     $ok or die "Error running @cmd\n";
 
 }
@@ -221,6 +224,7 @@ sub submit_job
     my($app, $params, $out_dir, $container) = @_;
     my @cmd = ('appserv-start-app');
     push(@cmd, '-c', $container) if $container;
+    push(@cmd, "--user-metadata", $opt->user_metadata) if $opt->user_metadata;
     push(@cmd, $app, $params);
 
     my $out;