https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422014-11-14T01:44:41ZArvadosArvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=178742014-11-14T01:44:41ZRadhika Chippadaradhika@curoverse.com
<ul><li><strong>Category</strong> set to <i>Workbench</i></li></ul><p>Run pipeline with File input (pipeline_templates/qr1hi-p5p6p-xt9iw6rmhvm93q5) -> Select a file (selected into a clippy before hand) -> Run it -> Pipeline failing with 404 (pipeline_instances/qr1hi-d1hrv-udkzowfb2qr65nb)</p>
<p>stderr arvados.errors.ApiError: <HttpError 404 when requesting <a class="external" href="https://qr1hi.arvadosapi.com/arvados/v1/collections/qr1hi-4zz18-pudu13a9iuwvgwg%2Ffile1_in_main.txt?alt=json">https://qr1hi.arvadosapi.com/arvados/v1/collections/qr1hi-4zz18-pudu13a9iuwvgwg%2Ffile1_in_main.txt?alt=json</a> returned "Path not found”</p> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=178892014-11-14T15:56:33ZTim Piercetwp@curoverse.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/17889/diff?detail_id=16815">diff</a>)</li></ul><p>The URL makes this look like the problem could be excessive URL-encoding. Is this a problem specific to Clippy? If so I'm inclined to call this a nice-to-have until we either retire Clippy or decided that we're not going to.</p> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=179442014-11-14T20:07:23ZWard Vandewegeward@curii.com
<ul><li><strong>Target version</strong> changed from <i>Bug Triage</i> to <i>Arvados Future Sprints</i></li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=179452014-11-14T20:08:24ZWard Vandewegeward@curii.com
<ul><li><strong>Story points</strong> set to <i>0.5</i></li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=182832014-11-19T20:26:19ZTom Cleggtom@curii.com
<ul><li><strong>Target version</strong> changed from <i>Arvados Future Sprints</i> to <i>2014-12-10 sprint</i></li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=182862014-11-19T20:38:32ZRadhika Chippadaradhika@curoverse.com
<ul><li><strong>Assigned To</strong> set to <i>Radhika Chippada</i></li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=183202014-11-19T21:09:31ZRadhika Chippadaradhika@curoverse.com
<ul><li><strong>Assigned To</strong> deleted (<del><i>Radhika Chippada</i></del>)</li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=183252014-11-19T21:16:11ZBrett Smithbrett.smith@curii.com
<ul><li><strong>Assigned To</strong> set to <i>Brett Smith</i></li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=186882014-12-02T16:23:26ZBrett Smithbrett.smith@curii.com
<ul><li><strong>Status</strong> changed from <i>New</i> to <i>In Progress</i></li></ul> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=186892014-12-02T16:35:03ZBrett Smithbrett.smith@curii.com
<ul><li><strong>Status</strong> changed from <i>In Progress</i> to <i>Closed</i></li></ul><p>This is not an Arvados bug. This error is happening because of a mistake in the pipeline template: it says that the <code>input</code> parameter to the <code>do_hash</code> script is a File, but <code>do_hash</code> is actually expecting a Collection—it calls one_task_per_input_file to work iteratively over each file in the Collection. Ultimately <code>do_hash</code> crashes trying to treat the File spec as a Collection.</p>
<p>There's lots of discussion to be had about ways we might prevent this or make it clearer to the user—CollectionReader could support path syntax, or Arvados could have more information about how scripts expect their inputs to be formatted—but those need further discussion and speccing out as stories. Since I expect those to be handled separately, I'm closing this.</p> Arvados - Bug #4524: [Workbench] Error running pipeline with File input data type.https://dev.arvados.org/issues/4524?journal_id=186902014-12-02T16:38:09ZBrett Smithbrett.smith@curii.com
<ul></ul><p>I just double-checked our documentation and confirmed that it doesn't suggest using <code>do_hash</code> with a File dataclass.</p>