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Remove path_prefix property from the runner and TES model #367

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giventocode opened this issue Aug 22, 2023 · 1 comment · Fixed by #375
Closed

Remove path_prefix property from the runner and TES model #367

giventocode opened this issue Aug 22, 2023 · 1 comment · Fixed by #375
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@giventocode
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giventocode commented Aug 22, 2023

Overview:

The node task definition has an outputs field that contains a list of output files or directories. If an output has a path_prefix property, the runner uses the value in the path as relative path pattern. The runner uploads the matching files to the storage system. The TES server maps this property to the path_prefix field in the TES task model (v 1.1). In addition, the TES server uses this functionality to upload log files after the task is completed.

However, this property is no longer part of the TES task spec in the latest proposal. Therefore, we need to remove it from the node task definition as well as the TES model on the server. This property makes the implementation of #364 more complex.

AC:

  • The runner should assume that the path value is an absolute path pattern and upload the matching files if the output type is FILE or not set.
  • Modify the TES server to use the new functionality instead of path_prefix when creating additional outputs.
@giventocode giventocode added this to the 4.5.0 milestone Aug 22, 2023
@giventocode giventocode self-assigned this Aug 22, 2023
@BMurri
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BMurri commented Aug 22, 2023

It appears that ga4gh/task-execution-schemas#194 isn't entirely settled. This should be deferred until the final resolution is determined.

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