[REVIEW]: s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques

[whedon]

Submitting author: @tobias-dv-lnu (Tobias Olsson)
Repository: https://github.com/tobias-dv-lnu/s4rdm3x
Version: v1.3
Editor: @gkthiruvathukal
Reviewer: @kinow, @xirdneh
Archive: 10.5281/zenodo.4475664

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Review checklist for @kinow

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• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tobias-dv-lnu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @xirdneh

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tobias-dv-lnu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @kinow, @xirdneh it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2791 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - 241d63aa7177374e42894fdd (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:66:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:53:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
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from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[kinow]

@gkthiruvathukal hi, do you have karma to re-generate the article? I think the bot failed to do so, and I think I need it to complete the review checklist items for the paper. Please.

Thank you!

[arfon]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kinow]

Thanks!

[gkthiruvathukal]

@gkthiruvathukal Sorry I didn't get to your request as fast as @arfon, @kinow. Looks like we're good now.

[whedon]

👋 @kinow, please update us on how your review is going.

[whedon]

👋 @xirdneh, please update us on how your review is going.

[kinow]

My review is complete @gkthiruvathukal ✔️

Even managed to test s4rdm3x with Apache Commons Imaging. I was going to use Apache Commons Lang, but I am currently working on Imaging. I didn't add all the relationships between packages, and the tool correctly highlighted the failed clusterings.

Didn't get fully familiar with the rest of the interface and metrics, but looks really useful for developers inspecting code bases, and getting familiar with new architectures.

I used IntelliJ's diagram builder to remind me of some of the relationships, but in the past I used Stan4J that would be a good tool to help users to create sysmdl files.

commons-imaging.sysmdl

# name Apache Commons Imaging

jar

commons-imaging-1.0-alpha2.jar

root-packages

org/apache/commons/imaging/

metrics file

#commons-imaging-file-metrics.csv

modules

base
color
common
bmp
dcx
gif
icns
ico
jpeg
pcx
png
pnm
psd
rgbe
tiff
wbmp
xbm
xpm
icc
internal
palette

mapping

<high_level_module> <regular_expression>

base org.apache.commons.imaging.color.[^.]*
color org.apache.commons.imaging.color.*
common org.apache.commons.imaging.common.*
bmp org.apache.commons.imaging.formats.bmp.*
dcx org.apache.commons.imaging.formats.dcx.*
gif org.apache.commons.imaging.formats.gif.*
icns org.apache.commons.imaging.formats.icns.*
ico org.apache.commons.imaging.formats.ico.*
jpeg org.apache.commons.imaging.formats.jpeg.*
pcx org.apache.commons.imaging.formats.pcx.*
png org.apache.commons.imaging.formats.png.*
pnm org.apache.commons.imaging.formats.pnm.*
psd org.apache.commons.imaging.formats.psd.*
rgbe org.apache.commons.imaging.formats.rgbe.*
tiff org.apache.commons.imaging.formats.tiff.*
wbmp org.apache.commons.imaging.formats.wbmp.*
xbm org.apache.commons.imaging.formats.xbm.*
xpm org.apache.commons.imaging.formats.xpm.*
icc org.apache.commons.imaging.formats.icc.*
internal org.apache.commons.imaging.formats.internal.*
palette org.apache.commons.imaging.formats.palette.*

relations

<source_module> <target_module>

base icc
base common
common base
common internal
icc common
jpeg common
palette base
palette internal
color internal

Thank you for your patience and help with the issues found during the review @tobias-dv-lnu!

[h0bb3]

Awesome! @kinow: Do you consider the sysmdl for commons imaging to be "correct"? If so would can I include it in the repo as an available system (always on the lookout for more data :) )

And thank you for the feedback and found problems!

[kinow]

Awesome! @kinow: Do you consider the sysmdl for commons imaging to be "correct"? If so would can I include it in the repo as an available system (always on the lookout for more data :) )

Not yet, but I will open a draft pull request. We can discuss how to improve it. I didn't understand how to use all the options and settings, and for the experiment.xml I simply used the same one from JebRef modifying the system loaded.

I've created a draft PR: h0bb3/s4rdm3x#14

[xirdneh]

Having some trouble testing a couple of things on the paper. I think it has to do with my local setup, I am currently tweaking some thing and will try to finish this over the weekend.
Sorry for the delay.

[h0bb3]

@xirdneh: just let me know if I can help :)

[gkthiruvathukal]

@xirdneh Just checking on how things are coming along with your review. I'm definitely not trying to rush you but would like to see if we are getting closer.

@kinow Am I correct in interpreting your review as being complete and ready to recommend acceptance, or are their still issues requiring attention?

[kyleniemeyer]

@whedon set v1.3 as version

[whedon]

OK. v1.3 is the version.

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2077

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2077, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/3241403.3241456 is OK

MISSING DOIs

- 10.1016/j.infsof.2006.10.015 may be a valid DOI for title: Automated clustering to support the reflexion method
- 10.1109/wcre.2010.26 may be a valid DOI for title: Improving automated mapping in reflexion models using information retrieval techniques
- 10.1145/3344948.3344984 may be a valid DOI for title: Semi-automatic mapping of source code using naive Bayes
- 10.1145/3344948.3344997 may be a valid DOI for title: An exploration and experiment tool suite for code to architecture mapping techniques
- 10.1007/s11219-018-9404-z may be a valid DOI for title: Exploring the suitability of source code metrics for indicating architectural inconsistencies
- 10.1109/wcre.2012.35 may be a valid DOI for title: On the evolutionary nature of architectural violations

INVALID DOIs

- None

[kyleniemeyer]

@tobias-dv-lnu, it looks like DOIs may be available but missing for a number of your references. Can you please check these, and add if appropriate? I will then be able to accept the submission. Thanks!

[gkthiruvathukal]

Thanks, @kyleniemeyer for helping to bring this to closure! :)

[h0bb3]

@kyleniemeyer Thanks! Just added the missing DOIs in the paper.bib file (whedon had made the correct guesses on the DOIs), everything should be ok now I hope :)

[arfon]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.infsof.2006.10.015 is OK
- 10.1109/WCRE.2010.26 is OK
- 10.1145/3344948.3344984 is OK
- 10.1145/3344948.3344997 is OK
- 10.1145/3241403.3241456 is OK
- 10.1007/s11219-018-9404-z is OK
- 10.1109/wcre.2012.35 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.infsof.2006.10.015 is OK
- 10.1109/WCRE.2010.26 is OK
- 10.1145/3344948.3344984 is OK
- 10.1145/3344948.3344997 is OK
- 10.1145/3241403.3241456 is OK
- 10.1007/s11219-018-9404-z is OK
- 10.1109/wcre.2012.35 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2078

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2078, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02791 joss-papers#2081
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02791
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@kinow, @xirdneh - many thanks for your reviews here and to @gkthiruvathukal for editing this submission. JOSS relies upon the volunteer efforts of folks like yourselves and we simply wouldn't be able to do this without you! ✨

@tobias-dv-lnu - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[h0bb3]

@kinow, @xirdneh, @gkthiruvathukal, @arfon : Thank you all for making this happen!

[kinow]

Thank you for writing the article and having patience with the review process @tobias-dv-lnu . And thanks to all involved too 💐 !