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Feature #12430

open

Crunch2 limit output collection to glob patterns

Added by Peter Amstutz over 6 years ago. Updated 9 days ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
Crunch
Start date:
Due date:
% Done:

0%

Estimated time:
(Total: 0.00 h)
Story points:
-

Description

The current behavior for crunch-run is to upload all files in the output directory. This sometimes results in temporary files being uploaded that are not intended to be part of the output. Propose adding an "output_glob" field which is an array of filenames or glob patterns specifying which files and directories should be uploaded.

Specifically:

  • output_glob takes an array of strings.
  • If empty, fall back to default behavior (capture entire output).
  • Only basic Unix globs with ? and * wildcards only.
  • The output only includes paths that match at least one pattern in output_glob.
  • Patterns match both files and directories.
  • Directory match means capture the directory and everything inside it.
  • Pattern can include slashes to capture items in subdirectories. This means parent directories in the path are included in output but should only contain pattern matched items
  • Items are captured in place, this feature does not include rearranging files.
  • output_glob affects container reuse. output_glob must match for container reuse. Although, if we wanted to be clever, we could reuse containers where the output_glob pattern is a superset of the output_glob that we are asking for (maybe a simple version like empty [] for default behavior, or matches all ["*"]).

This feature should work for local output directory (by controlling which files are uploaded) and for the temporary collection directory (by controlling which files are propagated to the final collection). The output_glob should also apply when deciding whether to include items pre-populated in the output directory that are specified in 'mounts'.

I'm pretty sure we don't support updating an existing collection in "mounts" so we don't have to worry about that. Crunch always creates a new collection as output. We should confirm/test for that.

Examples:

Directory listing:

foo
bar
baz/quux
baz/parent1/item1

output_glob: ["foo"]
Captures:
foo

output_glob: ["f*"]
Captures:
foo

output_glob: ["f*", "b*"]
Captures:
foo
bar
baz/quux
baz/parent1/item1

output_glob: ["ba?"]
Captures:
bar
baz/quux
baz/parent1/item1

output_glob: ["ba*"]
Captures:
bar
baz/quux
baz/parent1/item1

output_glob: ["baz"]
Captures:
baz/quux
baz/parent1/item1

output_glob: ["baz/*"]
Captures:
baz/quux
baz/parent1/item1

output_glob: ["baz/parent1"]
Captures:
baz/parent1/item1

output_glob: ["baz/p*"]
Captures:
baz/parent1/item1

output_glob: ["baz/parent1/item1"]
Captures:
baz/parent1/item1

output_glob: ["quux"]
Captures:

output_glob: ["*/quux"]
Captures:
baz/quux


Subtasks 1 (1 open0 closed)

Task #21343: ReviewNewPeter Amstutz

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Related issues

Blocks Arvados - Feature #9964: arvados-cwl-runner limits output data to keep using output_globNew09/07/2016

Actions
Actions #1

Updated by Peter Amstutz over 6 years ago

  • Description updated (diff)
Actions #2

Updated by Tom Clegg over 6 years ago

I'm not keen on this feature. It seems to creep in an awkward direction:
  1. output everything in this dir
  2. output everything in this dir that matches this glob
  3. output everything in this dir that matches any of these globs
  4. output everything in this dir that matches any of these globs, but not this glob
  5. output everything in this dir that matches any of these globs, and apply this path translation

Ideally this can all be done inside the container instead, using the shell or some other programming language of your choice. You could also add a subsequent step to the workflow that rearranges/extracts the desired files (a useful pattern for other situations too, like improving container reuse in downstream work that doesn't need to see the entire output).

Actions #3

Updated by Peter Amstutz over 6 years ago

Tom Clegg wrote:

I'm not keen on this feature. It seems to creep in an awkward direction:
  1. output everything in this dir
  2. output everything in this dir that matches this glob
  3. output everything in this dir that matches any of these globs
  4. output everything in this dir that matches any of these globs, but not this glob
  5. output everything in this dir that matches any of these globs, and apply this path translation

Nobody is asking for 4 and 5.

Ideally this can all be done inside the container instead, using the shell or some other programming language of your choice. You could also add a subsequent step to the workflow that rearranges/extracts the desired files (a useful pattern for other situations too, like improving container reuse in downstream work that doesn't need to see the entire output).

The client for this feature is arvados-cwl-runner (because output globs defined in the tool wrapper), not individual tools. The specific problem is intended to solve is programs that produce extra output that we don't want to upload, but gets uploaded anyway. The obvious solution is to have some way to specify what should and should not be uploaded.

Actions #4

Updated by Tom Clegg about 6 years ago

I agree arvados-cwl-runner's needs are important but I would still prefer to find a way to accommodate them without feeding the "container request includes a mini-language for munging inputs and outputs in various ways" pattern.

Actions #5

Updated by Peter Amstutz about 1 year ago

  • Release set to 60
Actions #6

Updated by Peter Amstutz 9 months ago

  • Release deleted (60)
  • Target version set to To be groomed
Actions #7

Updated by Peter Amstutz 9 months ago

  • Category set to Crunch

5 years later, this is still a problem. Users write code that leaves a bunch of stuff in the working directory and expect that only the 1 file that the want for output should be uploaded. We need to meet people where they are.

The proposed feature is to only capture output that matches any item in a list of specified glob patterns, aligned with how CWL output patterns work.

Actions #8

Updated by Peter Amstutz 9 months ago

  • Related to deleted (Feature #9964: arvados-cwl-runner limits output data to keep using output_glob)
Actions #9

Updated by Peter Amstutz 9 months ago

  • Blocks Feature #9964: arvados-cwl-runner limits output data to keep using output_glob added
Actions #10

Updated by Peter Amstutz 4 months ago

  • Target version changed from To be groomed to Development 2024-01-17 sprint
Actions #11

Updated by Peter Amstutz 4 months ago

  • Target version changed from Development 2024-01-17 sprint to Development 2024-01-03 sprint
Actions #12

Updated by Tom Clegg 3 months ago

I think this is fine if we can draw the line at "list of globs to include" (e.g., no "exclude" feature) and specify the globs we accept (e.g., gitignore style).

Feature should come with a test confirming that the following situation can't happen:
  1. cr mounts an existing collection in read+write mode at "/mnt/foo"
  2. cr output directory is "/mnt/foo" or /mnt/foo/bar"
  3. cr output glob is "*.txt"
  4. crunch-run removes files from the original collection
Actions #13

Updated by Peter Amstutz 3 months ago

  • Description updated (diff)
Actions #14

Updated by Peter Amstutz 3 months ago

  • Description updated (diff)
Actions #15

Updated by Peter Amstutz 3 months ago

  • Description updated (diff)
Actions #16

Updated by Peter Amstutz 3 months ago

  • Description updated (diff)
Actions #17

Updated by Peter Amstutz 3 months ago

  • Target version changed from Development 2024-01-03 sprint to Development 2024-01-17 sprint
Actions #18

Updated by Peter Amstutz 2 months ago

  • Description updated (diff)
Actions #19

Updated by Peter Amstutz 2 months ago

  • Target version changed from Development 2024-01-17 sprint to Development 2024-01-31 sprint
Actions #20

Updated by Peter Amstutz about 2 months ago

  • Target version changed from Development 2024-01-31 sprint to Development 2024-01-17 sprint
Actions #21

Updated by Peter Amstutz about 2 months ago

  • Assigned To set to Alex Coleman
Actions #22

Updated by Peter Amstutz about 1 month ago

  • Target version changed from Development 2024-01-17 sprint to Development 2024-01-31 sprint
Actions #23

Updated by Peter Amstutz 22 days ago

  • Target version changed from Development 2024-01-31 sprint to Development 2024-02-14 sprint
  • Assigned To deleted (Alex Coleman)
Actions #24

Updated by Peter Amstutz 22 days ago

  • Target version changed from Development 2024-02-14 sprint to Development 2024-02-28 sprint
Actions #25

Updated by Peter Amstutz 9 days ago

  • Target version changed from Development 2024-02-28 sprint to Development 2024-03-13 sprint
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