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 #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 - Bug #21598 (In Progress): Local keepstore invoked by crunch-run should never do EmptyTr...https://dev.arvados.org/issues/215982024-03-15T18:32:48ZTom Cleggtom@curii.com
<p>We don't want N compute nodes periodically checking expiry times on all of the trashed blocks on all backend volumes.</p> Arvados - Bug #21417 (Resolved): Stop trying to read image timestamp from docker metadata in arv-...https://dev.arvados.org/issues/214172024-01-25T16:44:16ZTom Cleggtom@curii.com
<p>This part of <a class="source" href="https://dev.arvados.org/projects/arvados/repository/arvados/entry/sdk/python/arvados/commands/keepdocker.py">source:sdk/python/arvados/commands/keepdocker.py</a> should go away so it doesn't crash on new image tarball formats:</p>
<pre>
json_file = image_tar.extractfile(image_tar.getmember(json_filename))
image_metadata = json.loads(json_file.read().decode('utf-8'))
json_file.close()
image_tar.close()
link_base = {'head_uuid': coll_uuid, 'properties': {}}
if 'created' in image_metadata:
link_base['properties']['image_timestamp'] = image_metadata['created']
</pre>
<p>See <a class="issue tracker-6 status-3 priority-4 priority-default closed" title="Idea: test-provision-debian11 fails loading workflow Docker image (Resolved)" href="https://dev.arvados.org/issues/21408">#21408</a> for example.</p>
<p>(Tom & Peter discussed offline, came to the conclusion that saving the image timestamp is not important enough to justify maintaining the code.)</p> Arvados - Bug #21379 (Resolved): arv-user-activity crashes on file_download event for remote coll...https://dev.arvados.org/issues/213792024-01-12T19:37:43ZTom Cleggtom@curii.com
<pre>
User activity on pirca between 2024-01-11 05:00 and 2024-01-12 05:00
Traceback (most recent call last):
File "/usr/bin/arv-user-activity", line 8, in <module>
sys.exit(main())
File "/usr/share/python3/dist/python3-arvados-user-activity/lib/python3.7/site-packages/arvados_user_activity/main.py", line 214, in main
getCollectionName(arv, e["properties"].get("collection_uuid"), e["properties"].get("portable_data_hash")),
File "/usr/share/python3/dist/python3-arvados-user-activity/lib/python3.7/site-packages/arvados_user_activity/main.py", line 111, in getCollectionName
u = arv.collections().list(filters=filters, order="created_at", limit=1).execute().get("items")
File "/usr/share/python3/dist/python3-arvados-user-activity/lib/python3.7/site-packages/googleapiclient/_helpers.py", line 130, in positional_wrapper
return wrapped(*args, **kwargs)
File "/usr/share/python3/dist/python3-arvados-user-activity/lib/python3.7/site-packages/googleapiclient/http.py", line 938, in execute
raise HttpError(resp, content, uri=self.uri)
arvados.errors.ApiError: <HttpError 400 when requesting https://pirca.arvadosapi.com/arvados/v1/collections?filters=%5B%5B%22uuid%22%2C+%22%3D%22%2C+%22<a href="https://arvadosapi.com/tordo-4zz18-kaaj8hjcnqb8i0p">tordo-4zz18-kaaj8hjcnqb8i0p</a>%22%5D%5D&order=created_at&limit=1&alt=json returned "cannot execute federated list query unless count=="none"">
</pre>
<pre>
User activity on tordo between 2024-01-11 19:33 and 2024-01-12 19:33
Traceback (most recent call last):
File "/tmp/venv/bin/arv-user-activity", line 8, in <module>
sys.exit(main())
File "/tmp/venv/lib/python3.9/site-packages/arvados_user_activity/main.py", line 214, in main
getCollectionName(arv, e["properties"].get("collection_uuid"), e["properties"].get("portable_data_hash")),
File "/tmp/venv/lib/python3.9/site-packages/arvados_user_activity/main.py", line 111, in getCollectionName
u = arv.collections().list(filters=filters, order="created_at", limit=1, count="none").execute().get("items")
File "/tmp/venv/lib/python3.9/site-packages/googleapiclient/_helpers.py", line 130, in positional_wrapper
return wrapped(*args, **kwargs)
File "/tmp/venv/lib/python3.9/site-packages/googleapiclient/http.py", line 938, in execute
raise HttpError(resp, content, uri=self.uri)
arvados.errors.ApiError: <HttpError 400 when requesting https://tordo.arvadosapi.com/arvados/v1/collections?filters=%5B%5B%22uuid%22%2C+%22%3D%22%2C+%22<a href="https://arvadosapi.com/pirca-4zz18-tsiyvmfkr2gub8w">pirca-4zz18-tsiyvmfkr2gub8w</a>%22%5D%5D&order=created_at&limit=1&count=none&alt=json returned "cannot execute federated list query with limit (1) < nUUIDs (1), offset (0) > 0, or order ([created_at]) parameter">
</pre> 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>
...
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>