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Bug #14984
closed
Display command line, inputs with links to collections
Status:
Resolved
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
Start date:
Due date:
% Done:
0%
Estimated time:
Story points:
-
Description
- The "inputs" link/menu item gives an error:
https://workbench.c97qk.arvadosapi.com/container_requests/c97qk-xvhdp-s5ha6v4vd3thq6y
https://workbench2.c97qk.arvadosapi.com/processes/c97qk-xvhdp-s5ha6v4vd3thq6y -- this yells at you saying "there are no inputs" instead of disabling it entirely.
- The "/var/lib/cwl/cwl.input.json" under "mounts" is generally only present for workflow runner containers, not running individual tools, so it is normal if it is not present and shouldn't result in any errors.
- Something is mangling keys. In the "advanced" view, the key {"mounts": {"/var/lib/cwl/cwl.input.json": ...}} is rendered as "varLibCwlCwlInputJson". I have noticed this bug appearing in other places as well, such as in the "info" sidebar. (#15407)
- I recommend making "inputs" and "command line" additional cards on the "process" page that are always visible (instead of a popup)
- "inputs" and "command line" should be annotated with hyperlinks to collections and individual files (see https://workbench.c97qk.arvadosapi.com/container_requests/c97qk-xvhdp-s5ha6v4vd3thq6y and https://workbench.c97qk.arvadosapi.com/container_requests/c97qk-xvhdp-5spabnjx530kf7n)
The existing implementation of this can be found at https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/apps/workbench/app/views/application/_show_text_with_locators.html.erb and https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/apps/workbench/app/helpers/application_helper.rb#L681
The approach is: start by format the content as pretty-printed JSON, with one item per line, then apply the regular expression to identify collection hashes and UUIDs and file within them.
Updated by 
Updated by 
Updated by Tom Morris
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