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Changed kill qc jobs command to use HTGT API as VMs dont have qc inst…
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…alled.
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Alex Hodgkins committed Feb 5, 2013
1 parent c64bcfd commit cb47821
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Showing 4 changed files with 130 additions and 50 deletions.
101 changes: 59 additions & 42 deletions lib/LIMS2/WebApp/Controller/User/QC.pm
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Original file line number Original file line Diff line number Diff line change
Expand Up @@ -170,7 +170,7 @@ sub view_qc_alignment :Path('/user/view_qc_alignment') :Args(0) {
} }


sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) { sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
my ($self, $c) = @_; my ( $self, $c ) = @_;


$c->assert_user_roles( 'edit' ); $c->assert_user_roles( 'edit' );


Expand All @@ -189,14 +189,14 @@ sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
$c->stash->{profile} = $c->req->param('profile'); $c->stash->{profile} = $c->req->param('profile');


my $run_id; my $run_id;
if ( $c->req->param('submit_initial_info')){ if ( $c->req->param( 'submit_initial_info' ) ){
try{ try{
# validate input params before doing anything else # validate input params before doing anything else
$c->model('Golgi')->check_params($c->req->params, $requirements); $c->model( 'Golgi' )->check_params( $c->req->params, $requirements );


my $plate_map = create_suggested_plate_map( my $plate_map = create_suggested_plate_map(
$c->stash->{sequencing_project}, $c->stash->{sequencing_project},
$c->model('Golgi')->schema, $c->model( 'Golgi' )->schema,
"Plate", "Plate",
); );
$c->stash->{plate_map} = $plate_map; $c->stash->{plate_map} = $plate_map;
Expand All @@ -218,7 +218,7 @@ sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
return; return;
} }


if ( $run_id = $self->_launch_qc($c, $validated_plate_map) ){ if ( $run_id = $self->_launch_qc( $c, $validated_plate_map ) ){
$c->stash->{run_id} = $run_id; $c->stash->{run_id} = $run_id;
$c->stash->{success_msg} = "Your QC job has been submitted with ID $run_id. " $c->stash->{success_msg} = "Your QC job has been submitted with ID $run_id. "
."Go to <a href=\"".$c->uri_for('/user/latest_runs')."\">Latest Runs</a>" ."Go to <a href=\"".$c->uri_for('/user/latest_runs')."\">Latest Runs</a>"
Expand All @@ -229,53 +229,67 @@ sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
} }


sub _launch_qc{ sub _launch_qc{
my ($self, $c, $plate_map) = @_; my ($self, $c, $plate_map ) = @_;

my $ua = LWP::UserAgent->new();
my $qc_conf = Config::Tiny->new();
$qc_conf = Config::Tiny->read($ENV{LIMS2_QC_CONFIG});

unless ($qc_conf){
die "No QC submission service has been configured. Cannot submit QC job.";
}


$plate_map ||= {}; $plate_map ||= {};


my $params = { my $params = {
profile => $c->stash->{profile}, profile => $c->stash->{ profile },
template_plate => $c->stash->{template_plate}, template_plate => $c->stash->{ template_plate },
sequencing_projects => $c->stash->{sequencing_project}, sequencing_projects => $c->stash->{ sequencing_project },
plate_map => $plate_map, plate_map => $plate_map,
username => $qc_conf->{_}->{username}, created_by => $c->user->name,
password => $qc_conf->{_}->{password}, species => $c->session->{ selected_species },
created_by => $c->user->name,
species => $c->session->{selected_species},
}; };


my $uri = $qc_conf->{_}->{submit_uri}; my $content = $self->_htgt_api_call( $c, $params, 'submit_uri' );

return $content->{ qc_run_id };
}

#generic function to make a htgt api call, accepting a hashref of user parameters,
#and returning the decoded json content provided by the api page.
sub _htgt_api_call {
my ( $self, $c, $params, $conf_uri_key ) = @_;


my $content; my $content;


try{ #do everythign in a try because if it fails there's no template and you get a useless error
my $req = HTTP::Request->new(POST => $uri); try {
$req->content_type('application/json'); die "No URI specified." unless $conf_uri_key;

my $ua = LWP::UserAgent->new();
my $qc_conf = Config::Tiny->new();
$qc_conf = Config::Tiny->read( $ENV{ LIMS2_QC_CONFIG } );

#add authentication information
$params->{ username } = $qc_conf->{_}->{ username };
$params->{ password } = $qc_conf->{_}->{ password };

my $uri = $qc_conf->{_}->{ $conf_uri_key }; #kill_uri or submit_uri

die "No QC submission service has been configured. Cannot submit QC job."
unless $qc_conf;

#create a http request object sending json
my $req = HTTP::Request->new( POST => $uri );
$req->content_type( 'application/json' );
$req->content( encode_json( $params ) ); $req->content( encode_json( $params ) );


my $response = $ua->request($req); #make the actual request
my $response = $ua->request( $req );


unless ($response->is_success){ die "Request to $uri was not successful. Response: " . $response->status_line
die "Request to $uri was not successful. Response: ".$response->status_line; unless $response->is_success;
}


$content = decode_json( $response->content ); $content = decode_json( $response->content );
} }
catch{ catch {
$c->stash( error_msg => "Sorry, your QC job submission failed with error $_" ); $c->stash( error_msg => "Sorry, your HTGT API submission failed with error: $_" );
return;
}; };


my $run_id = $content->{'qc_run_id'}; return $content;

return $run_id;
} }


sub latest_runs :Path('/user/latest_runs') :Args(0) { sub latest_runs :Path('/user/latest_runs') :Args(0) {
Expand Down Expand Up @@ -313,14 +327,17 @@ sub kill_farm_jobs :Path('/user/kill_farm_jobs') :Args(1) {


$c->assert_user_roles( 'edit' ); $c->assert_user_roles( 'edit' );


my $kill_jobs = HTGT::QC::Util::KillQCFarmJobs->new( my $content = $self->_htgt_api_call( $c, { qc_run_id => $qc_run_id }, 'kill_uri' );
{
qc_run_id => $qc_run_id, if ( $content ) {
config => $self->qc_config, my @jobs_killed = @{ $content->{ job_ids } };
} ); $c->stash( info_msg => "Killing farm jobs (" . join( ' ', @jobs_killed ) . ") from QC run $qc_run_id" );
}
else {
my $error = $c->stash->{ error_msg } . "<br/>Failed to kill farm jobs."; #dont overwrite other error
$c->stash( error_msg => $error );
}


my $jobs_killed = $kill_jobs->kill_unfinished_farm_jobs();
$c->stash( info_msg => 'Killing farm jobs (' . join( ' ', @{$jobs_killed} ) . ') from QC run '.$qc_run_id );
$c->go( 'latest_runs' ); $c->go( 'latest_runs' );


return; return;
Expand Down
76 changes: 68 additions & 8 deletions root/site/user/qc/latest_runs.tt
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Original file line number Original file line Diff line number Diff line change
Expand Up @@ -2,6 +2,35 @@


[% INCLUDE 'pagination.tt' pageset = pageset %] [% INCLUDE 'pagination.tt' pageset = pageset %]


<link href="[% c.uri_for( '/static/css/jquery.qtip.min.css' ) %]" rel="stylesheet">

<style type="text/css">
.table-striped tbody tr td.failed { background-color: #FF8080; }
.table-striped tbody tr td.successful { background-color: #80FF80; }
</style>
<script type="text/javascript" src="[% c.uri_for( "/static/js/jquery.qtip.min.js" ) %]"></script>
<script type="text/javascript">
//load tooltips for all last stage links
$(document).ready(function() {
$('.laststage').qtip({
content: {
attr: 'title',
},
position: {
my: 'top left',
at: 'bottom center'
},
hide: {
fixed: true,
delay: 500
},
style: {
classes: 'qtip-blue'
}
});
});
</script>

<table class="table table-striped"> <table class="table table-striped">
<thead> <thead>
<tr> <tr>
Expand All @@ -17,18 +46,49 @@
</thead> </thead>
<tbody> <tbody>
[% FOREACH l IN latest -%] [% FOREACH l IN latest -%]
[% IF l.failed %]
[% td_class = "class='failed'" %]
[% ELSIF l.ended %]
[% td_class = "class='successful'" %]
[% ELSE %]
[% td_class = "" %]
[% END %]
<tr> <tr>
<td>[% l.qc_run_id %]</td> <td [% td_class %]>[% l.qc_run_id %]</td>
<td>[% l.created %]</td> <td [% td_class %]>[% l.created %]</td>
<td>[% l.profile %]</td> <td [% td_class %]>[% l.profile %]</td>
<td>[% l.seq_projects %]</td> <td [% td_class %]>[% l.seq_projects %]</td>
<td>[% l.template_plate %]</td> <td [% td_class %]>[% l.template_plate %]</td>
<td><a href="[%c.uri_for( "/user/qc_farm_error_rpt/${l.qc_run_id}___${l.last_stage}" ) %]">[% l.last_stage %]</td> <td [% td_class %]>
<td>[% l.last_stage_time %]</td> [%# the code below stores text in the title attribute of each link,
<td align="center"><a href="[%c.uri_for( "/user/kill_farm_jobs/${l.qc_run_id}" ) %]" class="button link">Kill Farm Jobs</a></td> to create the tooltips on the page. (I'm sorry) %]
<a
href="[%c.uri_for( "/user/qc_farm_error_rpt/${l.qc_run_id}___${l.last_stage}" ) %]"
class="laststage"
title='
[% IF l.previous_stages && l.previous_stages.size %]
[% FOREACH stage IN l.previous_stages -%]
<a href="[%c.uri_for( "/user/qc_farm_error_rpt/${l.qc_run_id}___${stage}" ) %]">[% stage %]</a><br/>
[% END -%]
[% ELSE %]
No previous stages.
[% END %]
'
>[% l.last_stage %]</a><br/>
</td>
<td [% td_class %]>[% l.last_stage_time %]</td>
<td align="center" [% td_class %]>
[% IF l.ended %]
Finished
[% ELSE %]
<a href="[%c.uri_for( "/user/kill_farm_jobs/${l.qc_run_id}" ) %]" class="button link">Kill Farm Jobs</a>
[% END %]
</td>
</tr> </tr>
[% END -%] [% END -%]
</tbody> </tbody>
</table> </table>


</div> </div>


1 change: 1 addition & 0 deletions root/static/css/jquery.qtip.min.css
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