[FEATURE] Allow overwrite existing files, add flags for permission handling #2009

Irallia · 2020-08-06T10:45:59Z

Please do not merge before the naming discussion of the enum on gitter has ended.

Existing Ideas:

enum output_file_open_mode
{
   overwritable / rewritable,
   exclusive
};

There is something in system.io from Microsoft that sounds good: https://docs.microsoft.com/de-de/dotnet/api/system.io.filemode?view=netcore-3.1 :

enum FileMode
{
    open_or_create,
    create_new
};

enum accept_existing_file
{
    true / yes,
    false / no
};

Rust:

enum OpenOptions
{
    create,
    create_new
};

2020-08-31

Discussion result:

enum output_file_open_options
{
    open_or_create,
    create_new
};

You call this validator like:

seqan3::output_file_validator{seqan3::output_file_open_options::open_or_create});

codecov · 2020-08-10T10:20:59Z

Codecov Report

Merging #2009 into master will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master    #2009   +/-   ##
=======================================
  Coverage   97.95%   97.96%           
=======================================
  Files         264      264           
  Lines       10045    10050    +5     
=======================================
+ Hits         9840     9845    +5     
  Misses        205      205

Impacted Files	Coverage Δ
include/seqan3/argument_parser/validators.hpp	`89.20% <100.00%> (+0.31%)`	⬆️

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joergi-w

Thank you for this draft PR! I agree with the implementation and the tests are actually good (they cover all combinations of file formats and the boolean flag). I think after cleaning up the comments you can switch it to a "real" PR.

joergi-w · 2020-08-14T06:13:33Z

include/seqan3/argument_parser/validators.hpp

@@ -600,10 +600,16 @@ template <typename file_t = void>
 class output_file_validator : public file_validator_base
 {
 public:
+    //!\brief Stores, if it is valid to overwrite the output file.
+    bool allow_overwrite = false; // ToDo: bool oder enum? Für jedes File einzeln entscheiden, also zum Pfad dazugeben? Oder als Vektor angeben?


append cannot be implemented with the argument parser, as the user receives the file name and opens the file themself (with or without append flag). So I suggest to only focus on the binary distinction of the output file "may exist or not".

Note: If we would not handle it at all, the decision (of throwing an error if the file exists) could be still be made by the app developer after obtaining the filename.

include/seqan3/argument_parser/validators.hpp

joergi-w

Mostly documentation ideas...

doc/tutorial/argument_parser/index.md

CHANGELOG.md

include/seqan3/argument_parser/validators.hpp

joergi-w · 2020-08-28T11:54:44Z

include/seqan3/argument_parser/validators.hpp

@@ -575,6 +574,15 @@ class input_file_validator : public file_validator_base
    }
 };

+//!\brief Stores, if it is valid to overwrite the output file.
+enum output_file_open_mode


Question (no need to change, just an opinion):
How about naming it accept_existing_file?
Because mode expresses nothing useful about the function of this enum.

include/seqan3/argument_parser/validators.hpp

test/unit/argument_parser/format_parse_validators_test.cpp

joergi-w

Thanks! 👍

marehr

Waiting on naming

eseiler · 2020-08-31T09:35:31Z

https://doc.rust-lang.org/std/fs/struct.OpenOptions.html#implementations

include/seqan3/argument_parser/validators.hpp

marehr

first round :)

include/seqan3/argument_parser/validators.hpp

test/snippet/argument_parser/validators_output_file.cpp

test/unit/argument_parser/format_parse_validators_test.cpp

include/seqan3/argument_parser/validators.hpp

test/unit/argument_parser/format_parse_validators_test.cpp

marehr · 2020-09-08T08:32:00Z

Core-Meeting 2020-09-08

We want semi-regularity (that means default constructible) and as default case is conservative with seqan3::output_file_open_options::create_new.

marehr

I didn't go through all test cases. Thank you!

include/seqan3/argument_parser/validators.hpp

test/snippet/argument_parser/validators_output_file.cpp

test/unit/argument_parser/format_parse_validators_test.cpp

include/seqan3/argument_parser/validators.hpp

marehr

Sorry for being late; This is just some nail polish :)

include/seqan3/argument_parser/validators.hpp

test/snippet/argument_parser/validators_output_file.cpp

test/unit/argument_parser/format_parse_validators_test.cpp

…ermission [TEST] Update validator test [DOC] Update changelog, update (tutorial) documentation and code documentation Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

joergi-w · 2020-09-28T09:28:17Z

@seqan/core Can we still include this in the current 3.0.2 release or do we have to wait for the next one? I think many applications can already benefit from this.

marehr · 2020-09-28T09:49:03Z

@joergi-w We didn't plan it for this release and I think we shouldn't do last minute changes.

@Irallia We noticed that you put the changelog entry in the 3.0.2 section, can you create a new PR that moves that in the 3.0.3 section?

…gs for permission handling' PR (seqan#2009) Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Irallia · 2020-09-28T14:15:18Z

@Irallia We noticed that you put the changelog entry in the 3.0.2 section, can you create a new PR that moves that in the 3.0.3 section?

Done in: #2177

Irallia self-assigned this Aug 6, 2020

Irallia force-pushed the feature/argument_parser/allow_overwrite_existing_files branch 3 times, most recently from 497ff94 to b4ad152 Compare August 7, 2020 14:16

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Irallia force-pushed the feature/argument_parser/allow_overwrite_existing_files branch 2 times, most recently from 3fc5b0a to 85ee726 Compare August 31, 2020 10:45

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Irallia force-pushed the feature/argument_parser/allow_overwrite_existing_files branch from 171f5e5 to a85540b Compare September 22, 2020 13:39

[FEATURE] Use enum output_file_open_options to handle overwriting p…

c94d251

…ermission [TEST] Update validator test [DOC] Update changelog, update (tutorial) documentation and code documentation Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Irallia force-pushed the feature/argument_parser/allow_overwrite_existing_files branch from a85540b to c94d251 Compare September 22, 2020 13:56

Irallia requested a review from marehr September 23, 2020 08:38

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marehr merged commit bc5e30a into seqan:master Sep 28, 2020

eseiler mentioned this pull request Sep 28, 2020

3.0.2 Release #2001

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Irallia added a commit to Irallia/seqan3 that referenced this pull request Sep 28, 2020

[DOC] fix changelog entry of 'Allow overwrite existing files, add fla…

523aff1

…gs for permission handling' PR (seqan#2009) Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Irallia mentioned this pull request Sep 28, 2020

[DOC] fix changelog entry of 'Allow overwrite existing files...' #2177

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eseiler mentioned this pull request Mar 15, 2022

out_file extensions doesn't work seqan/sharg-parser#63

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[FEATURE] Allow overwrite existing files, add flags for permission handling #2009

[FEATURE] Allow overwrite existing files, add flags for permission handling #2009

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[FEATURE] Allow overwrite existing files, add flags for permission handling #2009

[FEATURE] Allow overwrite existing files, add flags for permission handling #2009

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