Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422024-03-26T14:10:39ZArvados
Redmine Arvados - Task #21619 (In Progress): Review 21617-fed-contenthttps://dev.arvados.org/issues/216192024-03-26T14:10:39ZTom Cleggtom@curii.comArvados - 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 #21617 (In Progress): Timeout error reading content from collection on a remote clu...https://dev.arvados.org/issues/216172024-03-25T14:43:50ZTom Cleggtom@curii.com
In a 3-way federation with login cluster z1111:
<ul>
<li>a collection stored on z1111 can be read from z2222 (e.g., workbench.z2222/collections/z1111-4zz18-...)</li>
<li>a collection stored on z2222 cannot be read from z1111 (timeout)</li>
<li>a collection stored on z2222 cannot be read from z3333 (timeout)</li>
</ul>
<p>It looks like the intermediate cluster's keepstore process cannot retrieve the list of keep services from the cluster where the data is stored ("failed to validate remote token") -- this auto-retries in the background for a while, then eventually blockReadRemote gives up.</p>
<p>Manual testing, with jutro/tordo/pirca playing the roles of z1111/z2222/z3333, indicates the same problem existed before and after <a class="issue tracker-2 status-2 priority-4 priority-default parent" title="Feature: Keepstore can stream GET and PUT requests using keep-gateway API (In Progress)" href="https://dev.arvados.org/issues/2960">#2960</a> was merged and deployed to tordo.</p> Arvados - Feature #21606 (In Progress): configurable keep-web output buffer to reduce delay betwe...https://dev.arvados.org/issues/216062024-03-19T03:59:41ZTom Cleggtom@curii.com
<p>According to <a class="issue tracker-2 status-5 priority-4 priority-default closed" title="Feature: Go FileSystem / FUSE mount supports block prefetch (Closed)" href="https://dev.arvados.org/issues/18961">#18961</a>, now that <a class="issue tracker-2 status-2 priority-4 priority-default parent" title="Feature: Keepstore can stream GET and PUT requests using keep-gateway API (In Progress)" href="https://dev.arvados.org/issues/2960">#2960</a> has reduced the TTFB for fetching a block, predicting and pre-fetching the next block appears to be more complex than it's worth.</p>
<p>Instead, in a typical scenario where the backend (keepstore→keep-web) bandwidth is faster than the frontend (keep-web→client), keep-web can reduce or eliminate the between-block delay by writing to an asynchronous output buffer. While keep-web is waiting a few milliseconds for the next block to start arriving from the backend, the client continues to receive the data that has accumulated in the output buffer.</p>
<p>The size of the output buffer should be configurable.</p> Arvados - Feature #21599 (New): _inspect/requests endpoint should reveal whether each request is ...https://dev.arvados.org/issues/215992024-03-15T18:45:20ZTom Cleggtom@curii.com
<p>This is a little inconvenient because the queue decision happens lower in the handler stack than the inspector (and we don't want to change that).</p>
<p>We can do something similar to responseLogFieldsContextKey in <a class="source" href="https://dev.arvados.org/projects/arvados/repository/arvados/entry/sdk/go/httpserver/logger.go">source:sdk/go/httpserver/logger.go</a> -- attach an atomic.Value to the request context as it passes through the Inspect handler, then have RequestLimiter Store() queue status there (queue label, time the request was released for processing), and Load() when generating the _inspect/requests report.</p> Arvados - Bug #21184 (Resolved): Fix build pipeline for debian 11https://dev.arvados.org/issues/211842023-11-08T20:19:52ZTom Cleggtom@curii.comArvados - 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>
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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)
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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>