Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422024-03-25T16:52:07ZArvados
Redmine Arvados - Bug #21618 (New): cloudtest should give up if test instance disappears from listing bef...https://dev.arvados.org/issues/216182024-03-25T16:52:07ZTom Cleggtom@curii.com
<p>Currently, if an instance/image has a problem that causes it to shutdown before responding to a boot probe, cloudtest keeps probing after it disappears, which is clearly futile.</p> Arvados - Bug #21319 (New): Avoid waiting/deadlock when a controller handler performs subrequests...https://dev.arvados.org/issues/213192023-12-27T23:26:44ZTom Cleggtom@curii.comArvados - Bug #21314 (New): a-d-c should cancel a container if it can't be loadedhttps://dev.arvados.org/issues/213142023-12-21T16:55:13ZTom Cleggtom@curii.com
<p>If a container's "mounts" field is invalid, a-d-c logs this, and keeps trying.</p>
<code class="json syntaxhl"><span class="p">{</span><span class="nl">"ClusterID"</span><span class="p">:</span><span class="s2">"irdev"</span><span class="p">,</span><span class="nl">"ContainerUUID"</span><span class="p">:</span><span class="s2">"<a href="https://arvadosapi.com/xxxxx-dz642-xxxxxxxxxxxxxxx">xxxxx-dz642-xxxxxxxxxxxxxxx</a>"</span><span class="p">,</span><span class="nl">"PID"</span><span class="p">:</span><span class="mi">2037423</span><span class="p">,</span><span class="nl">"error"</span><span class="p">:</span><span class="s2">"json: cannot unmarshal array into Go struct field Container.mounts of type arvados.Mount"</span><span class="p">,</span><span class="nl">"level"</span><span class="p">:</span><span class="s2">"warning"</span><span class="p">,</span><span class="nl">"msg"</span><span class="p">:</span><span class="s2">"error getting mounts"</span><span class="p">,</span><span class="nl">"time"</span><span class="p">:</span><span class="s2">"2023-12-13T20:34:41.064140517Z"</span><span class="p">}</span><span class="w">
</span></code>
<p>In this situation, the offending container should be cancelled.</p> Arvados - Bug #21187 (New): a-c-r should detect and warn when arv:IntermediateOutput outputTTL is...https://dev.arvados.org/issues/211872023-11-09T19:31:33ZTom Cleggtom@curii.com
<p>Currently, if outputTTL is set too low and a workflow tries to use intermediate data after it has already been trashed, a-c-r may read a intermediate collection manifest successfully (before trash time) but then fail to save it later (after trash time) in a combined collection. In that case the user ends up getting a python stack trace ending in a 403 error (invalid blob signature).</p>
<p>a-c-r should warn the user when the duration the current workflow has been running exceeds outputTTL (this is probably a good indicator the user should increase outputTTL even if it hasn't actually broken anything yet)</p>
<p>a-c-r should also report a more helpful error message when it fails to create a collection due to expired blob signatures. This could be done by checking for a 403 error from the create call and/or checking the expiry times (given as hexadecimal unix times) on the blob signatures in the manifest text.</p> Arvados - Bug #21184 (Resolved): Fix build pipeline for debian 11https://dev.arvados.org/issues/211842023-11-08T20:19:52ZTom Cleggtom@curii.comArvados - Bug #21134 (New): Fix proxy error logging in controller's container log handlerhttps://dev.arvados.org/issues/211342023-10-20T15:25:18ZTom Cleggtom@curii.com
<p>Currently, when controller gets a non-HTTP error while trying to proxy a request to keep-web, the error gets logged using stdlib <code>log.Print()</code> instead of structured logs:</p>
<pre>
{"ClusterID":"2xpu4","PID":22503,"RequestID":"req-1bqnt5n2ozwpcscdjc94","level":"info","msg":"request","remoteAddr":"127.0.0.1:38144","reqBytes":0,"reqForwardedFor":"XXX","reqHost":"2xpu4.arvadosapi.com","reqMethod":"PROPFIND","reqPath":"arvados/v1/container_requests/XXX/log/XXX","reqQuery":"","time":"2023-10-20T14:56:54.866512957Z"}
2023/10/20 14:56:54 http: proxy error: dial tcp 127.0.0.1:9002: connect: connection refused
{"ClusterID":"2xpu4","PID":22503,"RequestID":"req-1bqnt5n2ozwpcscdjc94","level":"info","msg":"response","priority":1,"remoteAddr":"127.0.0.1:38144","reqBytes":0,"reqForwardedFor":"XXX","reqHost":"2xpu4.arvadosapi.com","reqMethod":"PROPFIND","reqPath":"arvados/v1/container_requests/XXX/log/XXX","reqQuery":"","respBody":"","respBytes":0,"respStatus":"Bad Gateway","respStatusCode":502,"time":"2023-10-20T14:56:54.881886673Z","timeToStatus":0.015358,"timeTotal":0.015365,"timeWriteBody":0.000007,"tokenUUIDs":["XXX"]}
</pre>
<p>The error should be returned to the client in the 502 response body and, ideally, in a field in the "response" log entry.</p> Arvados - Bug #3047 (Resolved): UrlGenerationError in projects#showhttps://dev.arvados.org/issues/30472014-06-18T13:43:51ZTom Cleggtom@curii.com
<p><a class="external" href="https://workbench.local/projects/qr1hi-j7d0g-it30l961gq3t0oi">https://workbench.local/projects/qr1hi-j7d0g-it30l961gq3t0oi</a></p>
<pre>
...
Rendered application/_selection_checkbox.html.erb (3.8ms)
Rendered projects/_show_contents_rows.html.erb (25.5ms)
Rendered projects/_show_contents.html.erb (89.8ms)
Rendered application/_content.html.erb (127.9ms)
Rendered application/show.html.erb within layouts/application (133.7ms)
#<ActionController::UrlGenerationError: No route matches {:action=>"show", :controller=>"links", :id=>nil}>
Rendered application/error.html.erb within layouts/application (0.6ms)
Rendered notifications/_ssh_key_notification.html.erb (42.5ms)
API client: 0.000286336 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups/qr1hi-tpzed-tpj2ff66551eyym
API client: 0.008911487 API transaction
</pre> Arvados - Bug #2892 (Resolved): Error page when signing user agreementhttps://dev.arvados.org/issues/28922014-05-28T09:25:40ZTom Cleggtom@curii.com
<p><a class="external" href="https://workbench.qr1hi.arvadosapi.com/user_agreements/sign">https://workbench.qr1hi.arvadosapi.com/user_agreements/sign</a><br />→ undefined method `keys' for nil:NilClass<br />[28/May/2014:13:24:45 +0000] "POST /user_agreements/sign HTTP/1.1" 422 3367</p> GET-Evidence - Bug #725 (Resolved): evidence.personalgenomes.org/NKX2-5-Glu21Gln has PHP warnings...https://dev.arvados.org/issues/7252011-09-28T13:20:41ZTom Cleggtom@curii.comGET-Evidence - Feature #489 (Closed): Fix PharmGKB analysis so it matches against all SNPs, not j...https://dev.arvados.org/issues/4892010-05-08T16:03:10ZTom Cleggtom@curii.com
<p>Fix <a class="wiki-page new" href="https://dev.arvados.org/projects/get-evidence/wiki/PharmGKB">PharmGKB</a> analysis so it matches against all SNPs, not just the nsSNPs</p> GET-Evidence - Feature #487 (Closed): Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/4872010-05-08T15:44:07ZTom Cleggtom@curii.com
<p>"I'd like to have PGP9 & PGP12 genomes processed and visible on snp.med and get-evidence sites as soon as possible, so we can review them. It's not blocking me from working on the paper, but I want to have as much time as possible for us to look over them and evaluate new variants as needed." (Madeleine)</p> GET-Evidence - Bug #480 (Closed): NA12878 has no chr:pos on CYP2C9-R144Chttps://dev.arvados.org/issues/4802010-05-07T18:48:44ZTom Cleggtom@curii.com
<p>NA12878 has no chr:pos on CYP2C9-R144C</p> GET-Evidence - Feature #477 (Closed): Integrate trait-o-matic functionality into GET-Evidencehttps://dev.arvados.org/issues/4772010-05-07T18:45:48ZTom Cleggtom@curii.com
GET-Evidence should subsume:
<ul>
<li>Directory of public genomes (like Trait-o-matic front page <a class="external" href="http://snp.med.harvard.edu">http://snp.med.harvard.edu</a>)</li>
<li>Genome report page (like Trait-o-matic "view results")</li>
</ul>
<p>PGP genome data should be imported directly/automatically from the "PGP profiles" site, rather than uploaded from a web form.</p>
<p>Trait-o-matic core (dbsnp lookups, nsSNP calls, and external variant db xrefs) should be ported to a warehouse mr-function to improve throughput and allow many genomes to be processed in parallel.</p>
Trait-o-matic's "manual processing" features should be accessed through the data processing system using warehouse processing facilities:
<ul>
<li>Upload GFF (or provide warehouse locator, etc.)</li>
<li>View job status/results</li>
<li>Reprocess job</li>
</ul> GET-Evidence - Feature #474 (Closed): Move todo's from http://evidence.personalgenomes.org/status...https://dev.arvados.org/issues/4742010-05-07T14:39:00ZTom Cleggtom@curii.com
<p>Move todo's from <a class="external" href="http://evidence.personalgenomes.org/status">http://evidence.personalgenomes.org/status</a> to trac</p> GET-Evidence - Feature #473 (Closed): Implement auto-scoring mechanismhttps://dev.arvados.org/issues/4732010-05-07T14:24:29ZTom Cleggtom@curii.com
<p>Remaining to do:</p>
<ul>
<li>"within 1 base of a splice site" test</li>
<li>"indel in a coding region" and "...with frame shift" tests</li>
</ul>