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Bug #14984
closed
Display command line, inputs with links to collections
Status:
Resolved
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
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.
Related issues
Updated by 
Updated by 
Updated by Tom Morris
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