[jira] [Created] (MATH-1618) Change in Existing Design

2021-07-31 Thread AVIJIT BASAK (Jira)
AVIJIT BASAK created MATH-1618:
--

 Summary: Change in Existing Design
 Key: MATH-1618
 URL: https://issues.apache.org/jira/browse/MATH-1618
 Project: Commons Math
  Issue Type: Sub-task
Affects Versions: 3.6.1
Reporter: AVIJIT BASAK


*1) Creation of abstraction for GeneticAlgorithm*: In order to have different 
types of implementation for Genetic Algorithm like adaptive GA along with the 
existing one, we need to introduce an abstraction and a hierarchy of algorithm. 
AbstracttGeneticAlgorithm class needs to be implemented which would be extended 
by all other Algorithm class. This would also ease any future extension.

Removed Components: None

New Components: AbstractGeneticAlgorithm

Affected Components: GeneticAlgorithm

*2) Delegation of fitness calculation*: As per the current design Fitness 
interface is implemented by chromosome class, which forces implementation of 
fitness() method for any concrete chromosome. However this restricts the use of 
same concrete chromosome implementation to be reused for different problem 
domain. This inheritance based implementation should be replaced by 
composition. A new interface FitnessCalculator would be introduced. An instance 
of FitnessCalculator will be provided during creation of every concrete 
chromosome. This will enable reuse of concrete chromosome classes in different 
problem domain and hence improve extensibility and re-usability. This will 
require addition of an argument for each factory method and constructors.

Removed Components: Fitness 

New Components: FitnessCalculator

Affected Components: Chromosome, AbstractListChromosome, BinaryChromosome, 
RandomKey 

*3) Introducing Elitism interface*: In current design ElitisticListPopulation 
introduces couple of new operations related to elitism without declaring them 
in any abstraction. Elitism interface would be introduced, which would be 
implemented by ElitisticListPopulation. 

Removed Components: None

New Components: Elitism

Affected Components: ElitisticListPopulation

*4) Change of Indirect encoding chromosome hierarchy*: The hierarchy of 
chromosome having indirect encoding would be changed. Currently the design only 
considers permutation chromosome for combinatorial optimization. The base 
interface is PermutationChromosome which is implemented by RandomKey 
chromosome. A more appropriate name(like IndirectEncoding) of 
PermutationChromosome can be used which will declare the decode() method. This 
interface will be implemented by RandomKey chromosome. Tt would be more 
meaningful for any other new indirectly encoded chromosome representing 
different domain to implement the new interface.

Removed Components: PermutationChromosome

New Components: IndirectEncoding

Affected Components: RandomKey

 *5) Enable finer control for mutation and crossover probability*: Current 
design uses the crossover and mutation probability at the chromosome level. For 
finer control of mutation and crossover process the probability would be 
managed within MutationPolicy and CrossoverPolicy implementations. Probability 
would be passed as an argument to the respective operations. This way the 
corresponding operations will be responsible for managing probability and apply 
in convenient way. I have seen the controlling the mutation probability at the 
allele(gene) level improves the exploring capability of the optimization 
process and hence improves robustness.

Removed Components: None

New Components: None

Affected Components: MutationPolicy, CrossoverPolicy and all other 
implementation classes

*6) Addition of new Simulation Stopping conditions*: New simulation stopping 
conditions would be added based on population statistical characteristics. The 
simulation can be stopped based on variations of population average fitness or 
best fitness. These parameters are much better to represent nature of 
convergence. This will improve robustness to a considerable extent.



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[jira] [Commented] (GEOMETRY-139) Share code between GeometryInput and GeometryOutput

2021-07-31 Thread Matt Juntunen (Jira)


[ 
https://issues.apache.org/jira/browse/GEOMETRY-139?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17391070#comment-17391070
 ] 

Matt Juntunen commented on GEOMETRY-139:


PR: https://github.com/apache/commons-geometry/pull/179

> Share code between GeometryInput and GeometryOutput
> ---
>
> Key: GEOMETRY-139
> URL: https://issues.apache.org/jira/browse/GEOMETRY-139
> Project: Apache Commons Geometry
>  Issue Type: Improvement
>Reporter: Matt Juntunen
>Priority: Major
>
> {{GeometryInput}} and {{GeometryOutput}} both have {{getFileName()}} and 
> {{getCharset()}} methods. These methods should be extracted into a 
> {{GeometryIOMetadata}} interface and corresponding abstract class so that 
> code can be shared.



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[GitHub] [commons-geometry] darkma773r opened a new pull request #179: GEOMETRY-139: Abstract GeometryInput/Output duplicated code

2021-07-31 Thread GitBox


darkma773r opened a new pull request #179:
URL: https://github.com/apache/commons-geometry/pull/179


   Abstracting GeometryInput and GeometryOutput commons fields into 
GeometryIOMetadata.


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[jira] [Commented] (GEOMETRY-139) Share code between GeometryInput and GeometryOutput

2021-07-31 Thread Matt Juntunen (Jira)


[ 
https://issues.apache.org/jira/browse/GEOMETRY-139?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17391065#comment-17391065
 ] 

Matt Juntunen commented on GEOMETRY-139:


Duplication is also reported by Sonar Cloud: 
https://sonarcloud.io/project/issues?id=commons-geometry=AXioS5kU1auxhZiRMwW4=AXioS5kU1auxhZiRMwW4

> Share code between GeometryInput and GeometryOutput
> ---
>
> Key: GEOMETRY-139
> URL: https://issues.apache.org/jira/browse/GEOMETRY-139
> Project: Apache Commons Geometry
>  Issue Type: Improvement
>Reporter: Matt Juntunen
>Priority: Major
>
> {{GeometryInput}} and {{GeometryOutput}} both have {{getFileName()}} and 
> {{getCharset()}} methods. These methods should be extracted into a 
> {{GeometryIOMetadata}} interface and corresponding abstract class so that 
> code can be shared.



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[jira] [Created] (GEOMETRY-139) Share code between GeometryInput and GeometryOutput

2021-07-31 Thread Matt Juntunen (Jira)
Matt Juntunen created GEOMETRY-139:
--

 Summary: Share code between GeometryInput and GeometryOutput
 Key: GEOMETRY-139
 URL: https://issues.apache.org/jira/browse/GEOMETRY-139
 Project: Apache Commons Geometry
  Issue Type: Improvement
Reporter: Matt Juntunen


{{GeometryInput}} and {{GeometryOutput}} both have {{getFileName()}} and 
{{getCharset()}} methods. These methods should be extracted into a 
{{GeometryIOMetadata}} interface and corresponding abstract class so that code 
can be shared.



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[jira] [Resolved] (GEOMETRY-138) Use unchecked exceptions in IO modules

2021-07-31 Thread Matt Juntunen (Jira)


 [ 
https://issues.apache.org/jira/browse/GEOMETRY-138?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Matt Juntunen resolved GEOMETRY-138.

Resolution: Fixed

> Use unchecked exceptions in IO modules
> --
>
> Key: GEOMETRY-138
> URL: https://issues.apache.org/jira/browse/GEOMETRY-138
> Project: Apache Commons Geometry
>  Issue Type: Improvement
>Reporter: Matt Juntunen
>Priority: Major
>
> The IO modules should not throw checked exceptions, e.g. {{IOException}}. 
> Instead, a new unchecked {{GeometryIOException}} class should be created to 
> represent all IO and parsing failures.



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[jira] [Commented] (GEOMETRY-138) Use unchecked exceptions in IO modules

2021-07-31 Thread Matt Juntunen (Jira)


[ 
https://issues.apache.org/jira/browse/GEOMETRY-138?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17391064#comment-17391064
 ] 

Matt Juntunen commented on GEOMETRY-138:


Done in commit eddfd0823e36ac29044ee5eac371da62fda0957b

> Use unchecked exceptions in IO modules
> --
>
> Key: GEOMETRY-138
> URL: https://issues.apache.org/jira/browse/GEOMETRY-138
> Project: Apache Commons Geometry
>  Issue Type: Improvement
>Reporter: Matt Juntunen
>Priority: Major
>
> The IO modules should not throw checked exceptions, e.g. {{IOException}}. 
> Instead, a new unchecked {{GeometryIOException}} class should be created to 
> represent all IO and parsing failures.



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[GitHub] [commons-geometry] asfgit merged pull request #178: GEOMETRY-138: switching to unchecked exceptions in IO modules

2021-07-31 Thread GitBox


asfgit merged pull request #178:
URL: https://github.com/apache/commons-geometry/pull/178


   


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[jira] [Commented] (DBCP-579) Performance of DelegatingConnection.prepareStatement(String) regressed enormously in 2.8.0 compared to 1.4

2021-07-31 Thread Gary D. Gregory (Jira)


[ 
https://issues.apache.org/jira/browse/DBCP-579?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17391062#comment-17391062
 ] 

Gary D. Gregory commented on DBCP-579:
--

[~sjhala]

FYI, a release candidate for 2.9.0 is up for review, please see the developer 
mailing list for details. 

 

> Performance of DelegatingConnection.prepareStatement(String) regressed 
> enormously in 2.8.0 compared to 1.4
> --
>
> Key: DBCP-579
> URL: https://issues.apache.org/jira/browse/DBCP-579
> Project: Commons DBCP
>  Issue Type: Bug
>Affects Versions: 2.8.0
> Environment: OS: Windows Server 2008 R2 Enterprise 
> Java: Open JDK 12.0.1
> DB: Microsoft SQL Server 2012 - 11.0.5058.0 (X64)
>Reporter: Shaktisinh Jhala
>Priority: Major
> Attachments: DBCP_v1.4.jpg, DBCP_v2.8.0.jpg, 
> WithPrivateJarFrom2.9.0.jpg
>
>
> We recently upgraded the commons DBCP from version 1.4 to latest version 
> 2.8.0. After the upgrade, we observed significant degradation in our use 
> case. After the analysis it was found that the performance of 
> DelegatingConnection.prepareStatement(String) is regressed in version 2.8.0 
> enormously compared to 1.4 where the approx time taken in 2.8.0 is 7400 
> seconds compared to approx 183 sec in 1.4.
> Looking at the Yourkit snapshot, it is observed that the newly added call 
> PoolingConnection.createKey(String) in the method 
> PoolingConnection.prepareStatement(String) is the major contributor for this 
> regression.
>  
> We took multiple snapshot and in all these snapshot we observed the 
> regression. So it was not intermittent. Also, we observed this with both the 
> our DBs (MS SQL server and PostgreSQL)
>  
> Please find attached the screenshot of YourKit Snapshot showing the Merged 
> Callees of DelegatingConnection.prepareStatement(String) taken for MS SQL 
> server with commons DBCP version 1.4 and version 2.8 for further details.



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[jira] [Commented] (GEOMETRY-138) Use unchecked exceptions in IO modules

2021-07-31 Thread Gilles Sadowski (Jira)


[ 
https://issues.apache.org/jira/browse/GEOMETRY-138?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17391022#comment-17391022
 ] 

Gilles Sadowski commented on GEOMETRY-138:
--

+1

> Use unchecked exceptions in IO modules
> --
>
> Key: GEOMETRY-138
> URL: https://issues.apache.org/jira/browse/GEOMETRY-138
> Project: Apache Commons Geometry
>  Issue Type: Improvement
>Reporter: Matt Juntunen
>Priority: Major
>
> The IO modules should not throw checked exceptions, e.g. {{IOException}}. 
> Instead, a new unchecked {{GeometryIOException}} class should be created to 
> represent all IO and parsing failures.



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[jira] [Resolved] (VFS-807) LocalFile migration to NIO is not done correctly

2021-07-31 Thread Gary D. Gregory (Jira)


 [ 
https://issues.apache.org/jira/browse/VFS-807?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Gary D. Gregory resolved VFS-807.
-
Fix Version/s: 2.9.1
   Resolution: Fixed

> LocalFile migration to NIO is not done correctly
> 
>
> Key: VFS-807
> URL: https://issues.apache.org/jira/browse/VFS-807
> Project: Commons VFS
>  Issue Type: Bug
>Affects Versions: 2.9.0
>Reporter: L
>Priority: Blocker
> Fix For: 2.9.1
>
> Attachments: TestJdkWriteFile.java
>
>
> According to release notes 
> ([https://archive.apache.org/dist/commons/vfs/RELEASE-NOTES.txt),] version 
> 2.9.0 includes the following change:
> Replace construction of FileInputStream and FileOutputStream objects with 
> Files NIO APIs. #164. Thanks to Arturo Bernal.
> Strangely, it was not completed: LocalFlie.java has the following now, even 
> in master: 
> {code:java}
> /**
>  * Creates an input stream to read the content from.
>  */
>  @Override
>  protected InputStream doGetInputStream(final int bufferSize) throws 
> Exception {
> return new FileInputStream(file);
>  } 
> {code}
>  
> But what is worse, doGetOutputStream is *completely* broken: 
> {code:java}
> /**
>  * Creates an output stream to write the file content to.
>  */
> @Override
> protected OutputStream doGetOutputStream(final boolean bAppend) throws 
> Exception {
> return Files.newOutputStream(file.toPath(), bAppend ? 
> StandardOpenOption.APPEND : StandardOpenOption.CREATE);
> } {code}
>  
> This can be demonstrated with a small java program, see attachment. The 
> program just tries to write to a local file (into the same directory), using 
> different ways to do it:
>  # Java IO, how it was done before VFS 2.9.0
>  # Java NIO the way VFS 2.9.0 does it
>  # Java NIO the way it must be done
> What is important, the program also verifies the result.
> VFS 2.9.0 fails in 2 cases: 
>  # When the file does not exist and append must be performed:  
> java.nio.file.NoSuchFileException is thrown in this case.
>  # When the file exists and no append must be performed: the file is not 
> truncated, so whatever is written overwrites the beginning of the file, 
> keeping the rest.
>  
>  
>  



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[jira] [Commented] (GEOMETRY-138) Use unchecked exceptions in IO modules

2021-07-31 Thread Matt Juntunen (Jira)


[ 
https://issues.apache.org/jira/browse/GEOMETRY-138?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17390960#comment-17390960
 ] 

Matt Juntunen commented on GEOMETRY-138:


PR is in: https://github.com/apache/commons-geometry/pull/178

[~erans], please let me know what you think.

> Use unchecked exceptions in IO modules
> --
>
> Key: GEOMETRY-138
> URL: https://issues.apache.org/jira/browse/GEOMETRY-138
> Project: Apache Commons Geometry
>  Issue Type: Improvement
>Reporter: Matt Juntunen
>Priority: Major
>
> The IO modules should not throw checked exceptions, e.g. {{IOException}}. 
> Instead, a new unchecked {{GeometryIOException}} class should be created to 
> represent all IO and parsing failures.



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[GitHub] [commons-geometry] darkma773r opened a new pull request #178: GEOMETRY-138: switching to unchecked exceptions in IO modules

2021-07-31 Thread GitBox


darkma773r opened a new pull request #178:
URL: https://github.com/apache/commons-geometry/pull/178


   


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[GitHub] [commons-bcel] arturobernalg opened a new pull request #99: Minor Changes:

2021-07-31 Thread GitBox


arturobernalg opened a new pull request #99:
URL: https://github.com/apache/commons-bcel/pull/99


   * fix javadoc
   * Use constant array
   * Simplify conditions
   * inline variable


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[GitHub] [commons-pool] coveralls commented on pull request #91: Fix worng javadoc.

2021-07-31 Thread GitBox


coveralls commented on pull request #91:
URL: https://github.com/apache/commons-pool/pull/91#issuecomment-890305683


   
   [![Coverage 
Status](https://coveralls.io/builds/41800364/badge)](https://coveralls.io/builds/41800364)
   
   Coverage increased (+0.1%) to 84.702% when pulling 
**3d0b598e76719d4c7b7dfd4d429add7afad211fb on arturobernalg:feature/javadoc** 
into **74516b59cc36b69847ae0f60ff00e02ea5423e6a on apache:master**.
   


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[GitHub] [commons-csv] coveralls commented on pull request #172: Minor changes:

2021-07-31 Thread GitBox


coveralls commented on pull request #172:
URL: https://github.com/apache/commons-csv/pull/172#issuecomment-890305735


   
   [![Coverage 
Status](https://coveralls.io/builds/41800366/badge)](https://coveralls.io/builds/41800366)
   
   Coverage remained the same at 98.323% when pulling 
**df7bc5243a934dbbded1cff9cdabba36300844c6 on arturobernalg:feature/changes** 
into **9482924309bdc585d4f49c740626f292640c9500 on apache:master**.
   


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[GitHub] [commons-csv] arturobernalg opened a new pull request #172: Minor changes:

2021-07-31 Thread GitBox


arturobernalg opened a new pull request #172:
URL: https://github.com/apache/commons-csv/pull/172


   * Use diamond type <>
   * Extract commons expressions
   * Replace For loop with map.forEach


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[GitHub] [commons-pool] coveralls commented on pull request #90: Remove explicitly initialized.

2021-07-31 Thread GitBox


coveralls commented on pull request #90:
URL: https://github.com/apache/commons-pool/pull/90#issuecomment-890305244


   
   [![Coverage 
Status](https://coveralls.io/builds/41800355/badge)](https://coveralls.io/builds/41800355)
   
   Coverage increased (+0.06%) to 84.667% when pulling 
**156bfe2d67035993784bf534c612ef6317ff127b on arturobernalg:feature/redundant** 
into **74516b59cc36b69847ae0f60ff00e02ea5423e6a on apache:master**.
   


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[GitHub] [commons-pool] coveralls commented on pull request #89: Minors Changes:

2021-07-31 Thread GitBox


coveralls commented on pull request #89:
URL: https://github.com/apache/commons-pool/pull/89#issuecomment-890305072


   
   [![Coverage 
Status](https://coveralls.io/builds/41800353/badge)](https://coveralls.io/builds/41800353)
   
   Coverage increased (+0.3%) to 84.88% when pulling 
**e5b5ac016f04eb662e29f759ccf98ef97fde6c0a on arturobernalg:feature/changes** 
into **74516b59cc36b69847ae0f60ff00e02ea5423e6a on apache:master**.
   


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[GitHub] [commons-pool] arturobernalg opened a new pull request #91: Fix worng javadoc.

2021-07-31 Thread GitBox


arturobernalg opened a new pull request #91:
URL: https://github.com/apache/commons-pool/pull/91


   


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[GitHub] [commons-pool] arturobernalg opened a new pull request #90: Remove explicitly initialized.

2021-07-31 Thread GitBox


arturobernalg opened a new pull request #90:
URL: https://github.com/apache/commons-pool/pull/90


   


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[GitHub] [commons-pool] arturobernalg opened a new pull request #89: Minors Changes:

2021-07-31 Thread GitBox


arturobernalg opened a new pull request #89:
URL: https://github.com/apache/commons-pool/pull/89


   * Replace For loop with map.forEach
   * Inline variable
   * Chain Stream


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[GitHub] [commons-daemon] arturobernalg commented on pull request #31: MInor Changes:

2021-07-31 Thread GitBox


arturobernalg commented on pull request #31:
URL: https://github.com/apache/commons-daemon/pull/31#issuecomment-890301895


   > @arturobernalg
   > May you please rebase on master?
   > TY.
   
   HI @garydgregory 
   Done


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[jira] [Comment Edited] (COMPRESS-583) 1.21 generates different output binaries compared to older versions as well as on different OSes

2021-07-31 Thread Peter Lee (Jira)


[ 
https://issues.apache.org/jira/browse/COMPRESS-583?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=17390837#comment-17390837
 ] 

Peter Lee edited comment on COMPRESS-583 at 7/31/21, 6:50 AM:
--

I pushed a commit 
[d57b8e9|https://github.com/apache/commons-compress/commit/d57b8e9068bc0184b783aa488e613f4fcf2140d6]
 to add this in changelog. Please have a look.

Now the changelog of COMPRESS-404 is :

_Update the class of variable file in TarArchiveEntry from_
 _java.io.File to java.nio.file.Path. Corresponding constructors_
 _and methods are also modified/added._
 _NOTE: The userName, groupName, userID and groupID will also be_
 _set if they are available. The userName and groupName was not_
 _set previously, and the previous value of UserID:GroupID was_
 _0:0 by default._
 _Please note this may cause a reproducibility problem._

_Github Pull Request #97._


was (Author: peterlee):
I pushed a commit 
[d57b8e9|https://github.com/apache/commons-compress/commit/d57b8e9068bc0184b783aa488e613f4fcf2140d6]
 to add this in changelog. Please have a look.

Now the changelog of COMPRESS-404 is :
 _Update the class of variable file in TarArchiveEntry from_
 _java.io.File to java.nio.file.Path. Corresponding constructors_
 _and methods are also modified/added._

_NOTE: The UserID and GroupID will also be read if they are_
 _available. The previous default value UserID:GroupdID of was 0:0._
 _This may cause a reproducibility problem._
 _Github Pull Request #97._

> 1.21 generates different output binaries compared to older versions as well 
> as on different OSes
> 
>
> Key: COMPRESS-583
> URL: https://issues.apache.org/jira/browse/COMPRESS-583
> Project: Commons Compress
>  Issue Type: Bug
>Affects Versions: 1.21
>Reporter: Chanseok Oh
>Priority: Major
>
> Upgrading {{commons-compress}} had always been generating the same compressed 
> output byte-to-byte for the same input (i.e., their SHA checksum didn't 
> change between versions). However, starting with 1.21, we noticed it's 
> generating different output than what previous versions are generating.
> We also noticed that the same code generates different binaries on different 
> OSes. For example, 1.21 on Linux is different from 1.21 on Mac.
> However, at least on the same OS, 1.21 seems to reproducibly generate the 
> same output.
> See the context at [https://github.com/GoogleContainerTools/jib/pull/3342]
> 
> *UPDATE*: running diffoscope reveals that 1.21 is picking up the user and 
> group of a local environment.
> (output below manually reformatted slightly for readability)
> {{$ diffoscope 
> 6d2763b0f3940d324ea6b55386429e5b173899608abf7d1bff62e25dd2e4dcea.tar.gz 
> 32258c626498c13412679442e3417811bc7ab801c6928da2c2a97e0bbc380a88.tar.gz}}
> {{--- 
> 6d2763b0f3940d324ea6b55386429e5b173899608abf7d1bff62e25dd2e4dcea.tar.gz}}
> {{+++ 
> 32258c626498c13412679442e3417811bc7ab801c6928da2c2a97e0bbc380a88.tar.gz}}
> {{│ --- 6d2763b0f3940d324ea6b55386429e5b173899608abf7d1bff62e25dd2e4dcea.tar}}
> {{├── +++ 
> 32258c626498c13412679442e3417811bc7ab801c6928da2c2a97e0bbc380a88.tar}}
> {{│ ├── file list}}
> {{│ │ @@ -1,3 +1,3 @@}}
> {{│ │ {color:#de350b}-drwxr-xr-x 0                 0          0 0 1970-01-01 
> 00:00:01.00 app/{color}}}
> {{│ │ {color:#00875a}+drwxr-xr-x 0 chanseok (252384) eng (5000) 0 1970-01-01 
> 00:00:01.00 app/{color}}}
> {{│ │ -rw-r--r--  0                 0          0 0 1970-01-01 00:00:01.00 
> app/fileB.txt}}
> {{│ │ -rw-r--r--  0                 0          0 0 1970-01-01 00:00:01.00 
> app/fileC.txt}}



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