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 - 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 #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 - Task #20437 (New): Reviewhttps://dev.arvados.org/issues/204372023-04-26T16:06:51ZTom Cleggtom@curii.comArvados - Task #19946 (New): Reviewhttps://dev.arvados.org/issues/199462023-01-18T17:40:03ZTom Cleggtom@curii.comArvados - Feature #17751 (New): [arvados-dispatch-cloud] expose rate-limiting condition in metricshttps://dev.arvados.org/issues/177512021-06-02T20:01:54ZTom Cleggtom@curii.com
<p>a-d-c's behavior will seem a bit strange if the sysadmin doesn't realize API calls are being rate-limited (especially "destroy instance" and "update tags"). Suggest adding a metric like arvados_dispatchcloud_ratelimit{api="ListInstances"}=1 when limited, 0 when not.</p> Arvados - Bug #5560 (New): [DRAFT] [API] Good API for accessing the old_ and new_attributes in Lo...https://dev.arvados.org/issues/55602015-03-25T05:31:43ZTom Cleggtom@curii.com
Problems with the <code>old_attributes</code> and <code>new_attributes</code> hashes in the properties hash:
<ul>
<li>They don't look quite close enough to "what the API response to GET would have looked like at the time" for clients to reuse code to interpret/display them (e.g., timestamp formats can be different, computed properties are not present, locators in manifests are not signed).</li>
<li>The <code>*_attributes</code> hashes can be huge (notably for collection updates, where there are two copies of the manifest). This uses a lot of database space, and (worse) makes it very slow for clients to retrieve logs (unless they use <code>select</code> to avoid retrieving <em>any</em> properties).</li>
<li>Even the associated <code>old_etag</code> and <code>new_etag</code> fields are not indexable or searchable.</li>
</ul>
<p>Possible approach:</p>
<p>Add a version table (either a single one, or a table per model type), indexed by etag. Store the attributes in the version table. In the logs table, just store the old and new etags. Provide a distinct API for retrieving a specific version of an object (in the usual API response format for that object type) by giving its etag. Optionally, provide an API for retrieving the logs <em>and</em> the object versions referenced by the logs in one request (this would be as complete as the current behavior -- but that isn't necessarily important).</p> Tapestry - Bug #1471 (New): Researcher > Kits table content loads very slowlyhttps://dev.arvados.org/issues/14712013-05-07T12:07:39ZTom Cleggtom@curii.comGET-Evidence - Bug #1104 (New): Division by zero warning when computing progress percentagehttps://dev.arvados.org/issues/11042012-08-18T18:45:20ZTom Cleggtom@curii.com
<p>JSON::ParserError: 743: unexpected token at '<br /><br /><b>Warning</b>: Division by zero in <b>/home/get-evidence/public_html/lib/genome_display.php</b> on line <b>289</b><br />
{"status":{"progress":0,"status":"map <a class="issue tracker-1 status-3 priority-4 priority-default closed" title="Bug: [SDKs] arv pipeline_instance --help should work even if api server is not running / reachable. (Resolved)" href="https://dev.arvados.org/issues/4041">#4041</a> - 0(+0)\/0","logfilename":false,"result_url":"http:\/\/evidence.personalgenomes.org\/genomes?display_genome_id=c5a9e34e0e82e7c362218954d3160ffb82dc2171"}}'</p> longupload - Bug #451 (New): handle xmlhttprequest timeouts gracefullyhttps://dev.arvados.org/issues/4512011-01-13T19:04:50ZTom Cleggtom@curii.com
<p>Currently, browser may stall for a long time if a "send block to server" operation fails. Perhaps some browsers won't even call the onreadystatechange handler. The "send block" code should use a timer to detect this sort of thing and retry, like it does now after receiving a "fail" message from the server.</p> GET-Evidence - Bug #518 (New): Handle "data set is no longer public" during import_genomeshttps://dev.arvados.org/issues/5182010-06-18T18:08:49ZTom Cleggtom@curii.com
<p>example:</p>
<p><a class="external" href="http://evidence.personalgenomes.org/AGAP7-Thr362Asn">http://evidence.personalgenomes.org/AGAP7-Thr362Asn</a></p>
<p>should not have a "genome" entry for NA19240 since no current data set supports that variant call.</p> GET-Evidence - Bug #509 (New): Clean up runt variants imported by PharmGKBhttps://dev.arvados.org/issues/5092010-05-30T01:04:06ZTom Cleggtom@curii.com
<p>The <a class="wiki-page new" href="https://dev.arvados.org/projects/get-evidence/wiki/PharmGKB">PharmGKB</a> importing robot has managed to create several variants that show up in reports as "CETP 1" (gene='CETP', aa_pos=1, aa_from=!_, aa_to is null), and a couple with stuff like gene='SLC1A1', aa_pos=3780412, aa_from=!_, aa_to='Ala'.</p>
<pre>
mysql> select distinct fullname from variants v
left join edits e on v.variant_id=e.variant_id
left join eb_users on oid=edit_oid
where variant_aa_from=_;
+--------------------------+
| fullname |
+--------------------------+
| [[PharmGKB]] Importing Robot |
+--------------------------+
1 row in set (0.10 sec)
</pre>
<pre>
mysql> select * from variants where variant_aa_from=_ and variant_rsid is null;
</pre> GET-Evidence - Bug #500 (New): Trait-o-matic GET-E importer "AttributeError: 'tuple' object has n...https://dev.arvados.org/issues/5002010-05-17T18:09:59ZTom Cleggtom@curii.com
<p>Some input files cause gff_get-evidence_map.py to crash:</p>
<pre>
==> /scratch/tmp/811786ad1ae74adfdd20dd0372abaaebc6246e343aebd01da0bfc4c02bf0106c-out/lock <==
Traceback (most recent call last):
File "/home/trait/core/gff_get-evidence_map.py", line 295, in <module>
main()
File "/home/trait/core/gff_get-evidence_map.py", line 242, in main
leftover_alleles.remove(ref_allele)
[[AttributeError]]: 'tuple' object has no attribute 'remove'
</pre> GET-Evidence - Bug #479 (New): NSF-Lys702Asn shows wrong hapmap frequencyhttps://dev.arvados.org/issues/4792010-05-07T18:48:33ZTom Cleggtom@curii.com
<p>NSF-Lys702Asn shows wrong hapmap frequency</p> GET-Evidence - Bug #478 (New): Keep "overall odds ratio" updated when editing individual sets of ...https://dev.arvados.org/issues/4782010-05-07T18:47:29ZTom Cleggtom@curii.com
<p>Keep "overall odds ratio" updated when editing individual sets of OR figures</p>