Add 'verdi node repo dump' command. #3623

greschd · 2019-12-09T17:22:11Z

The command takes a node pk / uuid, zero or more file names, and an output directory as arguments. By default, it will create a sub-directory with the node uuid in the output directory, and copy the files with the given names from the repository to that directory. If no file names are given, all objects in the repository are copied.

The command has two optional flags:

--no-uuid: copies the files directly into the output directory, without
uuid prefix
--force: Copy files even if they already exist at the target destination

Changed from the discussion with @ltalirz: For specifying the source file names, I am now not using a separate flag, since that mimics how regular cp works. For example:

verdi node repo cp 2323 _scheduler-stderr.txt _scheduler-stdout.txt output_dir

Click help:

Usage: verdi node repo cp [OPTIONS] NODE [SRC_FILES]... OUTPUT_DIRECTORY

  Copy the repository files of a node to an output directory.

Options:
  --no-uuid    Do not prefix the output paths with the node uuid.
  -f, --force  Do not ask for confirmation.
  -h, --help   Show this message and exit.

The command takes a node pk / uuid, zero or more file names, and an ouput directory as arguments. By default, it will create a sub-directory with the node uuid in the output directory, and copy the files with the given names from the repository to that directory. If no file names are given, all objects in the repository are copied. The command has two optional flags: --no-uuid: copies the files directly into the output directory, without uuid prefix --force: Copy files even if they already exist at the target destination

giovannipizzi

Probably this misses proper dealing with folders

The command is renamed to 'verdi node repo dump'. The option of specifying specific file names to be copied is removed. The output paths no longer prefixed with a UUID. When a file or directory exists already, the command prompts to either abort, skip the current file / directory, overwrite the file / directory, or (in the case of directories only) merge the contents. A 'force' option can be given to always overwrite files / directories. Tests are not yet updated to the changed interface, since we want to get feedback on that first.

greschd · 2019-12-10T11:53:28Z

Following the feedback session, made the following changes:

Changed the name of the command to verdi node repo dump.
The option to pass specific file names is removed
The UUID prefix is removed (might be added later as an option, if need arises)
When a file or directory exists already, prompt the user with the following options:
- [a] abort the command
- [s] skip the current file / directory
- [m] (for directories only) merge contents
- [r] replace content - in the case of directories removing the existing content
A --force option can be passed to always replace.

Current click help:

Usage: verdi node repo dump [OPTIONS] NODE OUTPUT_DIRECTORY

  Copy the repository files of a node to an output directory.

Options:
  -f, --force  Overwrite existing directories and files without prompting for
               confirmation.
  -h, --help   Show this message and exit.

greschd · 2019-12-10T11:53:50Z

Mentioning @giovannipizzi @ltalirz for feedback.

giovannipizzi · 2019-12-10T13:15:10Z

The described behaviour looks fine to me thanks!

ltalirz

thanks @greschd
I tried it out locally - some suggestions on the wording to make the prompts less long

aiida/cmdline/commands/cmd_node.py

greschd · 2019-12-10T14:47:57Z

Since there was quite some discussion, maybe we should show the updated interface again?

Apply suggestions for simplified wording of the prompts that ask if a file / directory should be replaced / merged / skipped, or the operation should be aborted. Co-Authored-By: Leopold Talirz <leopold.talirz@gmail.com>

ltalirz · 2019-12-10T15:09:59Z

Sure, we can do it briefly this evening. I think the others will approve.

The command takes a node pk / uuid, zero or more file names, and an ouput directory as arguments. By default, it will create a sub-directory with the node uuid in the output directory, and copy the files with the given names from the repository to that directory. If no file names are given, all objects in the repository are copied. The command has two optional flags: --no-uuid: copies the files directly into the output directory, without uuid prefix --force: Copy files even if they already exist at the target destination

The command is renamed to 'verdi node repo dump'. The option of specifying specific file names to be copied is removed. The output paths no longer prefixed with a UUID. When a file or directory exists already, the command prompts to either abort, skip the current file / directory, overwrite the file / directory, or (in the case of directories only) merge the contents. A 'force' option can be given to always overwrite files / directories. Tests are not yet updated to the changed interface, since we want to get feedback on that first.

Apply suggestions for simplified wording of the prompts that ask if a file / directory should be replaced / merged / skipped, or the operation should be aborted. Co-Authored-By: Leopold Talirz <leopold.talirz@gmail.com>

…ore into add_node_repo_cp_command

The code was currently broken because not all flags were changed from 'o' to 'r' (in the rename from 'overwrite' to 'replace'). Adds a test which runs with '--force' where a single file is replaced.

When passing a pathlib.Path to 'shutil', it needs to be explicitly cast to 'str'. The compatibility of 'os' and 'shutil' with pathlib objects was added only in Python 3.6.

ltalirz

thanks a lot @greschd
to me this looks ready to be merged

greschd · 2019-12-17T11:57:53Z

@giovannipizzi, do you want to have a final look?

giovannipizzi · 2019-12-17T12:34:36Z

Thanks @greschd ! @sphuber was a bit doubtful on whether to keep the complex logic for merging, or just limit the possibility to create a new folder, specified on the cmd line by the user. Did you already discuss with him?

greschd · 2019-12-17T12:39:24Z

I did not, but I would be ok with removing the "merge" option and only leave abort / skip / overwrite.

sphuber · 2019-12-17T12:50:30Z

Sorry, I did not take this up yet with @greschd . Apologies for coming with this after you have already implemented it but I was wondering if it is not a simpler/safer to make the target directory into which the files should be dumped a required argument and require that it cannot exist. If the goal of the command is to be as simple as possible and just dump the entire content of a node's repo this seems in line with that goal. I think for the same reason we decided not to provide flags to include/exclude certain paths. @ltalirz pointed out that it prevents one from dumping in the current directory, but my argument would be that doing mkdir some_folder just before is a lot easier then potentially responding to a bunch of prompts. I am afraid that the current solution provides unnecessary functionality that introduces quite some code complexity which is difficult to fully test and may provide surprising behavior. @giovannipizzi agreed with my suggestion to simplify the code/interface when we discussed this on Friday @fiesch. I realize that you have already invested quite some time in writing the code and it would be unfortunate if we decide not to include it. Let me know what you think about simplifying the command

greschd · 2019-12-17T13:04:04Z

[...] I was wondering if it is not a simpler/safer to make the target directory into which the files should be dumped a required argument and require that it cannot exist.

So the proposed syntax would be verdi node repo dump <ID> <PATH> where PATH does not exist, but its parent does, correct? Or would you also auto-create the parents?

[...] that doing mkdir some_folder

which means the user wouldn't have to mkdir the folder, right?

I realize that you have already invested quite some time in writing the code and it would be unfortunate if we decide not to include it. Let me know what you think about simplifying the command

No worries, I'm not particularly attached to my code - that also doesn't make a particularly strong technical argument 😄 I'm fine with making this as simple as possible.

sphuber · 2019-12-17T13:09:07Z

I think it is fine to automatically create a nested folder, as long as the leaf folder does not already exist. This is just to prevent copying files by accident into an already existing folder. So interface:

verdi node repo dump <ID> <PATH>

with <ID> and <PATH> both required and <PATH> can be a relative nested path where the leaf folder should not exist but any sub paths can exist and if not will be created on the fly. The contents of the node repository are then copied wholesale into the leaf folder of <PATH> (omitting the still present but soon to be removed path or raw_input sub paths in the node repo).

But before we go ahead, lets get an OK on this proposal from @giovannipizzi and @ltalirz and yourself :)

greschd · 2019-12-17T13:12:34Z

Good for me. The path and raw_input are omitted by virtue of going through the list_objects interface, I think.

giovannipizzi · 2019-12-17T13:14:22Z

I would not have created intermediate paths, but I do not see a major problem with this, so I'm ok with Sebastiaan's proposal.
Just to be clear, I agree that the simplest is to stop if the provided path already exists.

…o add_node_repo_cp_command

greschd · 2019-12-17T18:57:33Z

Just to be clear, I agree that the simplest is to stop if the provided path already exists.

Yes, that's the intended behavior. In principle this could be handled by click, by setting type=click.Path(exists=False, file_okay=False, dir_okay=False). However, the resulting error message

Usage: verdi node repo dump [OPTIONS] NODE OUTPUT_DIRECTORY
Try "verdi node repo dump -h" for help.

Error: Invalid value for "OUTPUT_DIRECTORY": Path "." is a directory.

is not very clear IMO, so I'll instead handle it directly and write

Error: Invalid value for "OUTPUT_DIRECTORY": Path "." exists.
Aborted!

Instead of prompting when a file / directory exists, we now only allow specifying an OUTPUT_DIRECTORY that does not exist, and simply abort the command if it does.

ltalirz

thanks @greschd , looks good to me!

sphuber

Two minor final changes and then its good to go, I promise :)

sphuber · 2019-12-19T09:52:07Z

aiida/cmdline/commands/cmd_node.py

+)
+@with_dbenv()
+def repo_dump(node, output_directory):
+    """Copy the repository files of a node to an output directory."""


Can you write a note saying that the output directory should not exist

Done! I did notice though that this doesn't appear anywhere in the documentation, only the top-level command help is shown. That should probably be improved, we could show the help for all command groups.

sphuber · 2019-12-19T09:52:21Z

aiida/cmdline/commands/cmd_node.py

+    try:
+        output_directory.mkdir(parents=True, exist_ok=False)
+    except FileExistsError:
+        click.echo('Error: Invalid value for "OUTPUT_DIRECTORY": Path "{}" exists.'.format(output_directory))


can you please use aiida.cmdline.utils.echo.echo_critical here

sphuber · 2019-12-19T10:00:53Z

aiida/cmdline/commands/cmd_node.py

+        for file in node.list_objects(key=key):
+            # Not using os.path.join here, because this is the "path"
+            # in the AiiDA node, not an actual OS - level path.
+            file_key = file.name if not key else key + '/' + file.name


This is a good point and I now start to wonder whether we actually handle this correctly and consistently everywhere in the repositiory interface. Anyhow, this is good for now.

Well, that's only going to be a problem if os.sep is a backslash.. not the trickiest part for Windows support, I suppose 😄

Add a note that the output directory should not exist to the doc- string. When it does, abort with the 'echo_critical' provided by AiiDA instead of the click default.

sphuber

Thanks a lot @greschd and especially for your patience

greschd requested review from ltalirz and giovannipizzi December 9, 2019 17:22

giovannipizzi reviewed Dec 9, 2019

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greschd changed the title ~~Add 'verdi node repo cp' command.~~ [WIP] Add 'verdi node repo cp' command. Dec 9, 2019

ltalirz suggested changes Dec 10, 2019

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greschd changed the title ~~[WIP] Add 'verdi node repo cp' command.~~ [WIP] Add 'verdi node repo dump' command. Dec 10, 2019

greschd force-pushed the add_node_repo_cp_command branch from 2626e56 to 71f1b26 Compare December 10, 2019 14:51

Apply suggestions for simplified prompt wording.

6bd8b2a

Apply suggestions for simplified wording of the prompts that ask if a file / directory should be replaced / merged / skipped, or the operation should be aborted. Co-Authored-By: Leopold Talirz <leopold.talirz@gmail.com>

greschd force-pushed the add_node_repo_cp_command branch from 71f1b26 to 6bd8b2a Compare December 10, 2019 14:56

Dominik Gresch and others added 5 commits December 10, 2019 22:27

Apply suggestions for simplified prompt wording.

b63281e

Apply suggestions for simplified wording of the prompts that ask if a file / directory should be replaced / merged / skipped, or the operation should be aborted. Co-Authored-By: Leopold Talirz <leopold.talirz@gmail.com>

Adapt test cases to modified interface of the dump command.

e616d7e

Merge branch 'add_node_repo_cp_command' of github.com:greschd/aiida_c…

29ece24

…ore into add_node_repo_cp_command

greschd changed the title ~~[WIP] Add 'verdi node repo dump' command.~~ Add 'verdi node repo dump' command. Dec 10, 2019

greschd and others added 2 commits December 10, 2019 23:18

Merge branch 'develop' into add_node_repo_cp_command

ddf3048

Add check that stderr is empty in 'node repo dump' tests.

8829b46

greschd force-pushed the add_node_repo_cp_command branch from e71a17e to 8829b46 Compare December 11, 2019 16:16

Dominik Gresch added 3 commits December 11, 2019 17:45

Fix and simplify '--force' handling, add test.

d9ff8ac

The code was currently broken because not all flags were changed from 'o' to 'r' (in the rename from 'overwrite' to 'replace'). Adds a test which runs with '--force' where a single file is replaced.

Do not catch exceptions when running commands through click runner.

da7ab3f

Fix compatibility with Python 3.5

445880a

When passing a pathlib.Path to 'shutil', it needs to be explicitly cast to 'str'. The compatibility of 'os' and 'shutil' with pathlib objects was added only in Python 3.6.

greschd requested review from ltalirz and giovannipizzi December 11, 2019 17:29

ltalirz self-requested a review December 12, 2019 10:02

ltalirz previously approved these changes Dec 12, 2019

View reviewed changes

greschd added 2 commits December 12, 2019 12:52

Merge branch 'develop' into add_node_repo_cp_command

f32d03c

Merge branch 'develop' into add_node_repo_cp_command

290d5ac

Merge branch 'develop' into add_node_repo_cp_command

340fa3e

Merge branch 'develop' of https://github.com/aiidateam/aiida-core int…

39f0800

…o add_node_repo_cp_command

Simplify 'verdi node repo dump' command.

00e0d63

Instead of prompting when a file / directory exists, we now only allow specifying an OUTPUT_DIRECTORY that does not exist, and simply abort the command if it does.

greschd dismissed ltalirz’s stale review via 00e0d63 December 17, 2019 19:06

Merge branch 'develop' into add_node_repo_cp_command

10a9583

greschd requested a review from ltalirz December 18, 2019 18:12

ltalirz previously approved these changes Dec 19, 2019

View reviewed changes

Merge branch 'develop' into add_node_repo_cp_command

7e60feb

sphuber requested changes Dec 19, 2019

View reviewed changes

Improve docstring and abort message of 'verdi node repo dump'

ef4a659

Add a note that the output directory should not exist to the doc- string. When it does, abort with the 'echo_critical' provided by AiiDA instead of the click default.

greschd dismissed ltalirz’s stale review via ef4a659 December 19, 2019 11:40

greschd requested review from sphuber and ltalirz December 19, 2019 11:42

sphuber approved these changes Dec 19, 2019

View reviewed changes

sphuber merged commit d3e05c3 into aiidateam:develop Dec 19, 2019

greschd deleted the add_node_repo_cp_command branch December 19, 2019 14:32

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Add 'verdi node repo dump' command. #3623

Add 'verdi node repo dump' command. #3623

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