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Changed kill qc jobs command to use HTGT API as VMs dont have qc inst…

…alled.
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commit cb4782195401e00d2ff73d6129751f4b81355823 1 parent c64bcfd
ah19 ah19 authored
101 lib/LIMS2/WebApp/Controller/User/QC.pm
@@ -170,7 +170,7 @@ sub view_qc_alignment :Path('/user/view_qc_alignment') :Args(0) {
170 170 }
171 171
172 172 sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
173   - my ($self, $c) = @_;
  173 + my ( $self, $c ) = @_;
174 174
175 175 $c->assert_user_roles( 'edit' );
176 176
@@ -189,14 +189,14 @@ sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
189 189 $c->stash->{profile} = $c->req->param('profile');
190 190
191 191 my $run_id;
192   - if ( $c->req->param('submit_initial_info')){
  192 + if ( $c->req->param( 'submit_initial_info' ) ){
193 193 try{
194 194 # validate input params before doing anything else
195   - $c->model('Golgi')->check_params($c->req->params, $requirements);
  195 + $c->model( 'Golgi' )->check_params( $c->req->params, $requirements );
196 196
197 197 my $plate_map = create_suggested_plate_map(
198 198 $c->stash->{sequencing_project},
199   - $c->model('Golgi')->schema,
  199 + $c->model( 'Golgi' )->schema,
200 200 "Plate",
201 201 );
202 202 $c->stash->{plate_map} = $plate_map;
@@ -218,7 +218,7 @@ sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
218 218 return;
219 219 }
220 220
221   - if ( $run_id = $self->_launch_qc($c, $validated_plate_map) ){
  221 + if ( $run_id = $self->_launch_qc( $c, $validated_plate_map ) ){
222 222 $c->stash->{run_id} = $run_id;
223 223 $c->stash->{success_msg} = "Your QC job has been submitted with ID $run_id. "
224 224 ."Go to <a href=\"".$c->uri_for('/user/latest_runs')."\">Latest Runs</a>"
@@ -229,53 +229,67 @@ sub submit_new_qc :Path('/user/submit_new_qc') :Args(0) {
229 229 }
230 230
231 231 sub _launch_qc{
232   - my ($self, $c, $plate_map) = @_;
233   -
234   - my $ua = LWP::UserAgent->new();
235   - my $qc_conf = Config::Tiny->new();
236   - $qc_conf = Config::Tiny->read($ENV{LIMS2_QC_CONFIG});
237   -
238   - unless ($qc_conf){
239   - die "No QC submission service has been configured. Cannot submit QC job.";
240   - }
  232 + my ($self, $c, $plate_map ) = @_;
241 233
242 234 $plate_map ||= {};
243 235
244 236 my $params = {
245   - profile => $c->stash->{profile},
246   - template_plate => $c->stash->{template_plate},
247   - sequencing_projects => $c->stash->{sequencing_project},
248   - plate_map => $plate_map,
249   - username => $qc_conf->{_}->{username},
250   - password => $qc_conf->{_}->{password},
251   - created_by => $c->user->name,
252   - species => $c->session->{selected_species},
  237 + profile => $c->stash->{ profile },
  238 + template_plate => $c->stash->{ template_plate },
  239 + sequencing_projects => $c->stash->{ sequencing_project },
  240 + plate_map => $plate_map,
  241 + created_by => $c->user->name,
  242 + species => $c->session->{ selected_species },
253 243 };
254 244
255   - my $uri = $qc_conf->{_}->{submit_uri};
  245 + my $content = $self->_htgt_api_call( $c, $params, 'submit_uri' );
  246 +
  247 + return $content->{ qc_run_id };
  248 +}
  249 +
  250 +#generic function to make a htgt api call, accepting a hashref of user parameters,
  251 +#and returning the decoded json content provided by the api page.
  252 +sub _htgt_api_call {
  253 + my ( $self, $c, $params, $conf_uri_key ) = @_;
256 254
257 255 my $content;
258 256
259   - try{
260   - my $req = HTTP::Request->new(POST => $uri);
261   - $req->content_type('application/json');
  257 + #do everythign in a try because if it fails there's no template and you get a useless error
  258 + try {
  259 + die "No URI specified." unless $conf_uri_key;
  260 +
  261 + my $ua = LWP::UserAgent->new();
  262 + my $qc_conf = Config::Tiny->new();
  263 + $qc_conf = Config::Tiny->read( $ENV{ LIMS2_QC_CONFIG } );
  264 +
  265 + #add authentication information
  266 + $params->{ username } = $qc_conf->{_}->{ username };
  267 + $params->{ password } = $qc_conf->{_}->{ password };
  268 +
  269 + my $uri = $qc_conf->{_}->{ $conf_uri_key }; #kill_uri or submit_uri
  270 +
  271 + die "No QC submission service has been configured. Cannot submit QC job."
  272 + unless $qc_conf;
  273 +
  274 + #create a http request object sending json
  275 + my $req = HTTP::Request->new( POST => $uri );
  276 + $req->content_type( 'application/json' );
262 277 $req->content( encode_json( $params ) );
263 278
264   - my $response = $ua->request($req);
  279 + #make the actual request
  280 + my $response = $ua->request( $req );
265 281
266   - unless ($response->is_success){
267   - die "Request to $uri was not successful. Response: ".$response->status_line;
268   - }
  282 + die "Request to $uri was not successful. Response: " . $response->status_line
  283 + unless $response->is_success;
269 284
270 285 $content = decode_json( $response->content );
271 286 }
272   - catch{
273   - $c->stash( error_msg => "Sorry, your QC job submission failed with error $_" );
  287 + catch {
  288 + $c->stash( error_msg => "Sorry, your HTGT API submission failed with error: $_" );
  289 + return;
274 290 };
275 291
276   - my $run_id = $content->{'qc_run_id'};
277   -
278   - return $run_id;
  292 + return $content;
279 293 }
280 294
281 295 sub latest_runs :Path('/user/latest_runs') :Args(0) {
@@ -313,14 +327,17 @@ sub kill_farm_jobs :Path('/user/kill_farm_jobs') :Args(1) {
313 327
314 328 $c->assert_user_roles( 'edit' );
315 329
316   - my $kill_jobs = HTGT::QC::Util::KillQCFarmJobs->new(
317   - {
318   - qc_run_id => $qc_run_id,
319   - config => $self->qc_config,
320   - } );
  330 + my $content = $self->_htgt_api_call( $c, { qc_run_id => $qc_run_id }, 'kill_uri' );
  331 +
  332 + if ( $content ) {
  333 + my @jobs_killed = @{ $content->{ job_ids } };
  334 + $c->stash( info_msg => "Killing farm jobs (" . join( ' ', @jobs_killed ) . ") from QC run $qc_run_id" );
  335 + }
  336 + else {
  337 + my $error = $c->stash->{ error_msg } . "<br/>Failed to kill farm jobs."; #dont overwrite other error
  338 + $c->stash( error_msg => $error );
  339 + }
321 340
322   - my $jobs_killed = $kill_jobs->kill_unfinished_farm_jobs();
323   - $c->stash( info_msg => 'Killing farm jobs (' . join( ' ', @{$jobs_killed} ) . ') from QC run '.$qc_run_id );
324 341 $c->go( 'latest_runs' );
325 342
326 343 return;
76 root/site/user/qc/latest_runs.tt
@@ -2,6 +2,35 @@
2 2
3 3 [% INCLUDE 'pagination.tt' pageset = pageset %]
4 4
  5 +<link href="[% c.uri_for( '/static/css/jquery.qtip.min.css' ) %]" rel="stylesheet">
  6 +
  7 +<style type="text/css">
  8 + .table-striped tbody tr td.failed { background-color: #FF8080; }
  9 + .table-striped tbody tr td.successful { background-color: #80FF80; }
  10 +</style>
  11 +<script type="text/javascript" src="[% c.uri_for( "/static/js/jquery.qtip.min.js" ) %]"></script>
  12 +<script type="text/javascript">
  13 + //load tooltips for all last stage links
  14 + $(document).ready(function() {
  15 + $('.laststage').qtip({
  16 + content: {
  17 + attr: 'title',
  18 + },
  19 + position: {
  20 + my: 'top left',
  21 + at: 'bottom center'
  22 + },
  23 + hide: {
  24 + fixed: true,
  25 + delay: 500
  26 + },
  27 + style: {
  28 + classes: 'qtip-blue'
  29 + }
  30 + });
  31 + });
  32 +</script>
  33 +
5 34 <table class="table table-striped">
6 35 <thead>
7 36 <tr>
@@ -17,18 +46,49 @@
17 46 </thead>
18 47 <tbody>
19 48 [% FOREACH l IN latest -%]
  49 + [% IF l.failed %]
  50 + [% td_class = "class='failed'" %]
  51 + [% ELSIF l.ended %]
  52 + [% td_class = "class='successful'" %]
  53 + [% ELSE %]
  54 + [% td_class = "" %]
  55 + [% END %]
20 56 <tr>
21   - <td>[% l.qc_run_id %]</td>
22   - <td>[% l.created %]</td>
23   - <td>[% l.profile %]</td>
24   - <td>[% l.seq_projects %]</td>
25   - <td>[% l.template_plate %]</td>
26   - <td><a href="[%c.uri_for( "/user/qc_farm_error_rpt/${l.qc_run_id}___${l.last_stage}" ) %]">[% l.last_stage %]</td>
27   - <td>[% l.last_stage_time %]</td>
28   - <td align="center"><a href="[%c.uri_for( "/user/kill_farm_jobs/${l.qc_run_id}" ) %]" class="button link">Kill Farm Jobs</a></td>
  57 + <td [% td_class %]>[% l.qc_run_id %]</td>
  58 + <td [% td_class %]>[% l.created %]</td>
  59 + <td [% td_class %]>[% l.profile %]</td>
  60 + <td [% td_class %]>[% l.seq_projects %]</td>
  61 + <td [% td_class %]>[% l.template_plate %]</td>
  62 + <td [% td_class %]>
  63 + [%# the code below stores text in the title attribute of each link,
  64 + to create the tooltips on the page. (I'm sorry) %]
  65 + <a
  66 + href="[%c.uri_for( "/user/qc_farm_error_rpt/${l.qc_run_id}___${l.last_stage}" ) %]"
  67 + class="laststage"
  68 + title='
  69 + [% IF l.previous_stages && l.previous_stages.size %]
  70 + [% FOREACH stage IN l.previous_stages -%]
  71 + <a href="[%c.uri_for( "/user/qc_farm_error_rpt/${l.qc_run_id}___${stage}" ) %]">[% stage %]</a><br/>
  72 + [% END -%]
  73 + [% ELSE %]
  74 + No previous stages.
  75 + [% END %]
  76 + '
  77 + >[% l.last_stage %]</a><br/>
  78 + </td>
  79 + <td [% td_class %]>[% l.last_stage_time %]</td>
  80 + <td align="center" [% td_class %]>
  81 + [% IF l.ended %]
  82 + Finished
  83 + [% ELSE %]
  84 + <a href="[%c.uri_for( "/user/kill_farm_jobs/${l.qc_run_id}" ) %]" class="button link">Kill Farm Jobs</a>
  85 + [% END %]
  86 + </td>
29 87 </tr>
30 88 [% END -%]
31 89 </tbody>
32 90 </table>
33 91
34 92 </div>
  93 +
  94 +
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