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run: Use 'datalad add' in failure instructions #3080

merged 5 commits into from Dec 10, 2018


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@kyleam kyleam commented Dec 8, 2018

  • Minor improvments saves --message-file handling

  • Update add to support --message-file

  • Update runs failure instructions to use datalad add (closes #3072)

kyleam added 5 commits Dec 8, 2018
Under Python 2, we pass a bytestring to commit(), but the intention
was to pass a unicode string, like we do under Python 3.  Passing a
bytestring as the message doesn't seem to cause any issues, at least
according to test_save_message_file, but we should still do so for
consistency across Python versions.
When save is called from the command line with both --message and
--message-file but without -d<dataset>, we get two error messages, the
intentional error message as well as one about a key error:

  [ERROR  ] Both a message and message file were specified
  [ERROR  ] 'path' [] (KeyError)

This is because we pass refds_path as the path to get_status_dict(),
but refds_path is None in the above scenario.

Instead of worrying about properly populating the status dict info,
which isn't particularly relevant for the --message/--message-file
conflict, just raise a plain exception.  Doing so is in line with
what's done in other interfaces (e.g., aggregate raises a ValueError
when it receives an unknown update mode).
This will be used in `add` as well.
`save` learned to accept a --message-file argument in da8d235 (ENH:
save: Add -F/--message-file option, 2018-03-28).  Teach `add` to do
the same.
If a run command has a non-zero exit, we don't save the outputs and
instead instruct the user how to save the outputs given the failure is
expected.  The instructions say to use 'datalad save -r .', but there
are cases where this is not sufficient to add an output file (e.g., if
a file is added to subdataset).  Update the instructions to use 'add'
instead of 'save', which is what run actually uses (by default)

Also add '-d .' to the instructions to match run's dataset.add(),
reducing the possibility of discrepancies like the one that cropped up
in dataladgh-2276.  There are still cases where run's dataset.add() is not
sufficient (a known one is dataladgh-2454, which is addressed in
datalad-revolution), but at least the command in the instructions will
match run's behavior.

Closes datalad#3072.
@kyleam kyleam force-pushed the run-fail-msg-add branch from ab6bd6a to 67ce0e3 Dec 8, 2018
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@codecov codecov bot commented Dec 8, 2018

Codecov Report

Merging #3080 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3080      +/-   ##
+ Coverage   90.24%   90.24%   +<.01%     
  Files         248      248              
  Lines       32571    32589      +18     
+ Hits        29393    29411      +18     
  Misses       3178     3178
Impacted Files Coverage Δ
datalad/interface/ 100% <ø> (ø) ⬆️
datalad/interface/tests/ 100% <100%> (ø) ⬆️
datalad/interface/tests/ 99.83% <100%> (ø) ⬆️
datalad/distribution/tests/ 82.95% <100%> (+0.53%) ⬆️
datalad/distribution/ 96.25% <100%> (+0.14%) ⬆️
datalad/interface/ 88.88% <100%> (+0.07%) ⬆️
datalad/interface/ 100% <100%> (ø) ⬆️

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@@ -611,7 +611,7 @@ def run_command(cmd, dataset=None, inputs=None, outputs=None, expand=None,
ofh.write(assure_bytes(msg))"The command had a non-zero exit code. "
"If this is expected, you can save the changes with "
"'datalad save -r -F %s .'",
"'datalad add -d . -r -F %s .'",
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@yarikoptic yarikoptic Dec 9, 2018

Now thinking about it, this wouldn't be a correct instruction in case of --explicit run... Not sure what would be a sensible cross platform and concise way though, besides add (may be adding it as a feature for all datalad API functions getting a list of files) getting an option of taking a file with filenames to add, and then is preparing that file alongside with the message file to be given here.
I will leave it for you to decide to move that into a new issue/PR and here for explicit mode may be just say that it might add too much or listing all outputs?

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@kyleam kyleam Dec 9, 2018

this wouldn't be a correct instruction in case of --explicit run

When I've thought about it in the past, I've decided it's not worth worrying about --explicit here. If you feel strongly that we should tailor the message, please open a separate PR tweaking the message as you see fit.

@yarikoptic yarikoptic merged commit c47a37a into datalad:master Dec 10, 2018
6 of 8 checks passed
@kyleam kyleam deleted the run-fail-msg-add branch Dec 10, 2018
yarikoptic added a commit that referenced this issue Feb 8, 2019
 A variety of bugfixes and enhancements

 ### Major refactoring and deprecations

 - All extracted metadata is now placed under git-annex by default.
   Previously files smaller than 20 kb were stored in git. ([#3109])
 - TODO: get_runner #3104 and pending #3131

 ### Fixes

 - Improved handling of long commands:
   - The code that inspected `SC_ARG_MAX` didn't check that the
     reported value was a sensible, positive number. ([#3025])
   - More commands that invoke `git` and `git-annex` with file
     arguments learned to split up the command calls when it is likely
     that the command would fail due to exceeding the maximum supported
     length. ([#3138])
 - The `setup_yoda_dataset` procedure created a malformed
   .gitattributes line. ([#3057])
 - [download-url] unnecessarily tried to infer the dataset when
   `--no-save` was given. ([#3029])
 - [rerun] aborted too late and with a confusing message when a ref
   specified via `--onto` didn't exist. ([#3019])
 - [run]:
   - `run` didn't preserve the current directory prefix ("./") on
      inputs and outputs, which is problematic if the caller relies on
      this representation when formatting the command. ([#3037])
   - Fixed a number of unicode py2-compatibility issues. ([#3035]) ([#3046])
   - To proceed with a failed command, the user was confusingly
     instructed to use `save` instead of `add` even though `run` uses
     `add` underneath. ([#3080])
 - Fixed a case where the helper class for checking external modules
   incorrectly reported a module as unknown. ([#3051])
 - [add-archive-content] mishandled the archive path when the leading
   path contained a symlink. ([#3058])
 - Following denied access, the credential code failed to consider a
   scenario, leading to a type error rather than an appropriate error
   message. ([#3091])
 - Some tests failed when executed from a `git worktree` checkout of the
   source repository. ([#3129])
 - During metadata extraction, batched annex processes weren't properly
   terminated, leading to issues on Windows. ([#3137])
 - [add] incorrectly handled an "invalid repository" exception when
   trying to add a submodule. ([#3141])
 - Pass `GIT_SSH_VARIANT=ssh` to git processes to be able to specify
   alternative ports in SSH urls

 ### Enhancements and new features

 - [search] learned to suggest closely matching keys if there are no
   hits. ([#3089])
 - [create-sibling] gained a `--group` option so that the caller can
   specify the file system group for the repository. ([#3098])
 - Interface classes can now override the default renderer for
   summarizing results. ([#3061])
 - [run]:
   - `--input` and `--output` can now be shortened to `-i` and `-o`.
   - Placeholders such as "{inputs}" are now expanded in the command
     that is shown in the commit message subject. ([#3065])
   - `` gained an `extra_inputs` argument so
     that wrappers like [datalad-container] can specify additional inputs
     that aren't considered when formatting the command string. ([#3038])
   - "--" can now be used to separate options for `run` and those for
     the command in ambiguous cases. ([#3119])
 - The utilities `create_tree` and `ok_file_has_content` now support
   ".gz" files. ([#3049])
 - The Singularity container for 0.11.1 now uses [nd_freeze] to make
   its builds reproducible.
 - A [publications] page has been added to the documentation. ([#3099])
 - `GitRepo.set_gitattributes` now accepts a `mode` argument that
   controls whether the .gitattributes file is appended to (default) or
   overwritten. ([#3115])
 - `datalad --help` now avoids using `man` so that the list of
   subcommands is shown.  ([#3124])

* tag '0.11.2': (124 commits)
  Changelog entry for GIT_SSH_VARIANT change
  BF: sshconnector: Don't use ssh's port flag as scp's
  RF: sshconnector: Simplify shlex quote import
  CHANGELOG(0.11.2): Fix some typos
  [DATALAD RUNCMD] CHANGELOG: Linkify 0.11.2 entries
  CHANGELOG: Do first pass for 0.11.2
  CHANGELOG: Add missing link target for download-url
  Start cooking the 0.11.2 release
  RF: appveyor - move test_install tests to be ran the last
  RF: text_type instead of str
  ENH(TST): provide my timing for the slow test
  BF(TST): adjust the test for the fact that AnnexRepo.add does not blow on nonexisting files
  ENH(TST): two tests which test quick or thorough for add failing with too long list of files
  BF: get stderr if present, otherwise just use str(e)
  BF: append out/err only if not empty/None
  Centrlize handling running commands with long files list in _run_command_files_split
  RF: remove minor duplication of -- handling, place all files handling closer to the call
  RF: move unrelated to try/except handling outside
  ENH+DOC: Report actual process handle, not just PID
@yarikoptic yarikoptic added this to the Release 0.11.2 milestone Feb 10, 2019
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