Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422014-07-20T10:12:58ZArvados
Redmine Arvados - Task #3309 (New): [Documentation] Present an efficient pattern for developing a Python ...https://dev.arvados.org/issues/33092014-07-20T10:12:58ZTom Cleggtom@curii.com
Approximate outline:
<ul>
<li>Find/make a small test dataset and put it in Keep</li>
<li>Clone git repository to shell VM (or start a new one)</li>
<li>Put crunch wrapper in <code>/crunch_scripts/foobar</code></li>
<li>Run on VM in terminal using crunch-job</li>
<li>Repeat until this works</li>
<li>Commit and push</li>
<li>Run as a real job using small test dataset</li>
<li>Repeat until this works</li>
<li>Run as a real job using real data</li>
</ul>
Simplifying assumptions:
<ul>
<li>One task per job</li>
</ul>
<p>Here, just present the minimum feature set. Refer to appropriate doc sections for related features, something like "Learn more about what scripts are expected to see/do/output on the {foobar doc page}" (link to outcome of <a class="issue tracker-6 status-5 priority-4 priority-default closed" title="Idea: [Documentation] Improve documentation for authoring crunch scripts (Closed)" href="https://dev.arvados.org/issues/3044">#3044</a>)</p> Arvados - Idea #3304 (New): [Workbench] Add checkboxes to multi-type chooser modal to filter by o...https://dev.arvados.org/issues/33042014-07-18T21:04:07ZTom Cleggtom@curii.comArvados - Bug #3257 (In Progress): [Workbench] Hard to find user agreement after it has been signedhttps://dev.arvados.org/issues/32572014-07-16T14:33:47ZPjotr Prins
<p>After logging in the user agreement should be available in a straightforward way. Add an item to one of the dropdown menus at the top right.</p>
<p>There's a plan to consolidate these menus based on feedback from our UX/UI person. Tom can tell you more about that.</p>
<p>The user agreement is just a collection stored in Keep. Users can actually see it if they go to their 'Links' page and look for the entry with link class 'Signature'. But of course that's not user friendly.</p> Arvados - Idea #3199 (New): [SDK] Keep clients (e.g., arv-put and crunch-job) ask API to refresh ...https://dev.arvados.org/issues/31992014-07-07T10:45:02ZTom Cleggtom@curii.comArvados - Task #3192 (New): Clarify requirements/implementationhttps://dev.arvados.org/issues/31922014-07-04T15:53:06ZTom Cleggtom@curii.comArvados - Task #3189 (New): [Blocker] Clarify design/requirementshttps://dev.arvados.org/issues/31892014-07-04T15:20:47ZTom Cleggtom@curii.comArvados - Idea #3180 (New): [Crunch] When a job fails in a pipeline instance, should the other qu...https://dev.arvados.org/issues/31802014-07-03T15:12:02ZTom Cleggtom@curii.comArvados - Feature #3162 (New): [API] Client can request signed locators for specific blobs from A...https://dev.arvados.org/issues/31622014-07-02T21:10:51ZPeter Amstutzpeter.amstutz@curii.com
<p>For uploading or future "synchronize" operations where some data may already be present on the remote Keep instance, it would be very useful if the client can ask the API server directly for signed locators from a list of blobs. The server will check if the blobs exist and are readable by the user and then returns signed locators suitable for submitting a manifest.</p>
<p>This depends on the client already having permission to read the blobs in question, which means they are already referenced by a collection. Currently we expect clients to know the relevant collection UUID in any situation where it's appropriate to read a blob -- in that case the client can already retrieve fresh signatures via <code>collections.get</code>. If a future situation makes this particularly difficult for a client, this feature would simplify client behavior at the cost of maintaining a cross-reference of blob→collection in the API server's database.</p> Arvados - Idea #3094 (New): No UI to edit runtime constraints for draft container requestshttps://dev.arvados.org/issues/30942014-06-26T09:08:47ZPeter Amstutzpeter.amstutz@curii.comArvados - Idea #3093 (New): [Crunch] Pipeline can use other pipelines templates as componentshttps://dev.arvados.org/issues/30932014-06-26T09:07:19ZPeter Amstutzpeter.amstutz@curii.comArvados - Feature #2960 (In Progress): Keepstore can stream GET and PUT requests using keep-gatew...https://dev.arvados.org/issues/29602014-06-04T10:48:26ZTim Piercetwp@curoverse.comArvados - Task #2889 (New): Make other users' shared instances accessible via dashboard/homehttps://dev.arvados.org/issues/28892014-05-27T20:27:02ZTom Cleggtom@curii.comArvados - Feature #2706 (New): [SDKs] Python SDK Keep client can enable "HEAD before PUT" mode wh...https://dev.arvados.org/issues/27062014-04-29T11:17:19ZTom Cleggtom@curii.comArvados - Idea #2679 (New): [API] If enabled by user via "preferences" checkbox in Workbench, not...https://dev.arvados.org/issues/26792014-04-22T17:04:20ZTom Cleggtom@curii.com
<ul>
<li>Concepts
<ul>
<li>Per-user preference to enable emails notifications:
<ul>
<li>On completion</li>
<li>On failure of a child job (avoiding multiple notifications if more than one child fails)</li>
</ul>
</li>
<li>Only toplevel jobs should send notifications, so in the case of a "will fail" state, only one is sent.</li>
<li>For now, only the project owner will be notified and not any other user that has access to it</li>
<li>The email address that will be used to send the notifications to is the one being used for login, and not the one provided on the user's profile</li>
</ul>
</li>
<li>Implementation
<ul>
<li>API Server
<ul>
<li>A server setting establishing the default behavior for users that don't have the preference explicitly set</li>
<li>A server setting establishing if emails notifications are enabled or not.</li>
<li>Add a new mailer like <code>services/api/app/mailers/admin_notifier.rb</code></li>
<li>Add necessary callbacks on containers/pipelines updates to call the mailer when needed</li>
</ul>
</li>
<li>Workbench
<ul>
<li>New UI element to show & change user preference on the user’s profile page, under a new "Preferences" section.</li>
</ul>
</li>
<li>Documentation updates</li>
</ul></li>
</ul> Arvados - Task #2152 (New): Set appropriate permissions on an instance of the GATK exome pipeline...https://dev.arvados.org/issues/21522014-02-12T16:29:58ZPeter Amstutzpeter.amstutz@curii.com