[REVIEW]: Reiz: Structural Source Code Search at Scale

[whedon]

Submitting author: @isidentical (Batuhan Taskaya)
Repository: https://github.com/reizio/reiz.io
Version: v1.0.0
Editor: @mjsottile
Reviewer: @lutzhamel, @yuhc
Archive: 10.5281/zenodo.5029255

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Reviewers and authors:

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@lutzhamel & @yuhc, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @lutzhamel

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 (@isidentical) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @yuhc

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 (@isidentical) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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. @lutzhamel, @yuhc it looks like you're currently assigned to review this paper 🎉.

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (755.4 files/s, 55795.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          80           1346            173           4098
Markdown                         8            215              0            919
JSON                             4              0              0            901
YAML                             7             13              2            130
TeX                              1              9              0             81
Bourne Shell                     4             14             13             43
DOS Batch                        1              8              1             26
Dockerfile                       2              8              0             17
TOML                             1              2              0             12
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           109           1619            196           6236
-------------------------------------------------------------------------------


Statistical information for the repository '768d7180239c666227fd7a05' was
gathered on 2021/05/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Batuhan Taskaya                177         11703           6086          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Batuhan Taskaya            5617           48.0          3.6                2.99

[whedon]

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

OK DOIs

- 10.1016/j.scico.2012.04.008 is OK
- 10.5281/zenodo.4657163 is OK
- 10.1007/s10664-017-9514-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[yuhc]

Hi @mjsottile, I've tried to run the software within the latest docker on Ubuntu 20.04, but it requires a subtle change and doesn't return search results as expected. Shall I contact the author to resolve this issue? (The document doesn't state enough about the environment settings.)

[isidentical]

Please let me know about any problems you experience to build / run the Reiz on the bug tracker @yuhc. Thanks!

[yuhc]

Please let me know about any problems you experience to build / run the Reiz on the bug tracker @yuhc. Thanks!

Hi @isidentical, I'm running Ubuntu 20.04, Docker 19.03.13, docker-compose 1.26.2.
I had to change docker-compose's version from 3.9 to 3.8 to build and start the container.

The build instruction is usually expected to contain the system environment.

I didn't see API is running on ... on the server end, but I could access the search engine from 8080 port (remotely, as I don't have a desktop environment) and tried to search Call(Name("len")). However, the loading icon never disappeared, and no results was ever returned.

Could you explain more about what the dataset is built on top of ("~75 files from 10 different projects") and help check what's going wrong here?
Also, it'll be great to know the use cases of reiz.io.

[isidentical]

Hi @isidentical, I'm running Ubuntu 20.04, Docker 19.03.13, docker-compose 1.26.2.
I had to change docker-compose's version from 3.9 to 3.8 to build and start the container.

Interesting, I can successfully spin the instances with 3.9 though will definitely investigate (would you mind opening an issue on the tracker).

I didn't see API is running on ... on the server end, but I could access the search engine from 8080 port (remotely, as I don't have a desktop environment) and tried to search Call(Name("len"))

You should wait the API to start before accessing, since without it the web ui will just wait and timeout eventually. Would you mind sending me the logs (btw it would be better if you could create an issue on the repo itself!)

Thanks!

[yuhc]

Interesting, I can successfully spin the instances with 3.9 though will definitely investigate (would you mind opening an issue on the tracker).

Created reizio/reiz.io#51.

You should wait the API to start before accessing, since without it the web ui will just wait and timeout eventually. Would you mind sending me the logs (btw it would be better if you could create an issue on the repo itself!)

Created reizio/reiz.io#52.

[lutzhamel]

Hi @isidentical, perhaps I missed it, but I don't see any instructions in the repo on how to run this software. Could you point me to the spot where it tells me how to install and run the software?

Thanks.

[lutzhamel]

@isidentical, never mind just found it under the docs link....

[lutzhamel]

@isidentical, docker-compose does not run on the given files...

ubuntu@ip-172-31-94-52:~$ git clone https://github.com/reizio/reiz.io
Cloning into 'reiz.io'...
remote: Enumerating objects: 1884, done.
remote: Counting objects: 100% (362/362), done.
remote: Compressing objects: 100% (225/225), done.
remote: Total 1884 (delta 206), reused 264 (delta 132), pack-reused 1522
Receiving objects: 100% (1884/1884), 586.58 KiB | 24.44 MiB/s, done.
Resolving deltas: 100% (1098/1098), done.
ubuntu@ip-172-31-94-52:~$ ls
reiz.io
ubuntu@ip-172-31-94-52:~$ cd reiz.io/
ubuntu@ip-172-31-94-52:~/reiz.io$ docker-compose up --build --remove-orphans
ERROR: Version in "./docker-compose.yml" is unsupported. You might be seeing this error because you're using the wrong Compose file version. Either specify a supported version (e.g "2.2" or "3.3") and place your service definitions under the `services` key, or omit the `version` key and place your service definitions at the root of the file to use version 1.
For more on the Compose file format versions, see https://docs.docker.com/compose/compose-file/
ubuntu@ip-172-31-94-52:~/reiz.io$ 

[isidentical]

What docker version are you using @lutzhamel? Please ensure you are using a newer one, something like 19.03.13.

[lutzhamel]

@isidentical, here is what I am using:

ubuntu@ip-172-31-94-52:~/reiz.io$ docker --version
Docker version 20.10.6, build 370c289
ubuntu@ip-172-31-94-52:~/reiz.io$ docker-compose --version
docker-compose version 1.25.0, build unknown
ubuntu@ip-172-31-94-52:~/reiz.io$ 

[yuhc]

Hi @isidentical , I just uploaded a screenshot of the 8000 page to reizio/reiz.io#52, and hope it would be helpful for your debugging. While I don't think the review is going in the right direction and I think I should state it clearly in case you may not know:

1. The repo, website or article proof should contain the running environment of your software. You should either support the code for multiple environments, or state the supported environments clearly.
   1. I'm using AWS c4.4xlarge instance, Ubuntu 20.04 and the latest packages you can get on 20.04 by default to run the code. IDK what settings @lutzhamel is using, but the expected testing environment should be provided by you.
   2. Otherwise, you should get a c4 instance and fix your code to work there. You can rent a c4.xlarge for a few hours and it will just cost you a buck.
2. The reviewers aren't responsible for helping with the debug.
   1. This is a basic criterion for any peer-review journal or conference, and I believe it also applies to JOSS.
   2. From now on I'll wait for the setup results from @lutzhamel and updated setting instructions from you, otherwise the process will be a Pandora's box for the reviewers.

[isidentical]

Thanks for your comment @yuhc! It is a bit of a block box situation for myself too, since everything is simply reproducible on my environment. I'll try to get everything setup on an AWS machine this weekend and let you both know about the exact environment. Thanks for your patience.

[lutzhamel]

@isidentical, have you considered setting up a working instance on a web based virtual machine like https://replit.com/ eliminating set up issues all together?

@yuhc, thanks for your comments. I agree, as reviewers we should not be wrangling software, we should be just verifying that it works as advertised. I too will be waiting for a working instance before continuing the review.

[isidentical]

@isidentical, have you considered setting up a working instance on a web based virtual machine like https://replit.com/ eliminating set up issues all together?

That is a great idea! i'll create an open instance as well as the instructions on a clear aws machine. Sorry for all the inconvenience i caused!

[isidentical]

@yuhc @lutzhamel I've deployed a public instance on the web address: https://reiz.io. Unfortunately, I wasn't able to give exact instructions for an AWS instance since they still haven't approved my personal account though as you stated, if any of you want to have access to the environment the server is running I can give access (it is running on a digital ocean VPS right now). Please let me know if this method works for you or not, thanks!

[whedon]

👋 @yuhc, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @lutzhamel, please update us on how your review is going (this is an automated reminder).

[yuhc]

Thanks for setting up reiz.io. It works for me.
Could you update the docs to include your exact setup steps on DigitalOcean? I don't think it really matters which cloud service you choose. The main reason why we asked you to install reiz.io on a clean VM is that we want a reproducible instruction.

BTW, registering an AWS account should just take a few minutes. I guess something went wrong, and you may need to contact the support.

[isidentical]

@mjsottile all points are checked out

Please create an archive on zenodo or figshare for the submission

https://zenodo.org/record/5029255 (with the DOI 10.5281/zenodo.5029255)

Ensure that the version for the JOSS submission is correct.

The 1.0.0 version is correct

Ensure that the author list in the paper and archive are correct.

The list is correct.

[mjsottile]

@whedon set 10.5281/zenodo.5029255 as archive

[whedon]

OK. 10.5281/zenodo.5029255 is the archive.

[mjsottile]

@whedon recommend-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.scico.2012.04.008 is OK
- 10.5281/zenodo.4657163 is OK
- 10.1007/s10664-017-9514-4 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#2416

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2416, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

Hi @isidentical, I am doing some final checks for publishing your article.

It looks like most/all of your in-text citations are not using the appropriate citation command. Instead of using \[ and \] to wrap the citations, you should just use [@author:year] to let our parser handle the display. The available commands are

- `@author:2001`  ->  "Author et al. (2001)"
- `[@author:2001]` -> "(Author et al., 2001)"
- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"

I also see some issues with the references at the end to GitHub packages. Could you add the authors for those? It also looks like the "Github code search" reference does not have the correct URL, since it is the same as for "Grep.app".

[yuhc]

Cool, good work @isidentical !

BTW I'd recommend you to read "Cross-Language Code Search using Static and Dynamic Analyses" (which appears to be the latest work in the AST-based code search area). You'll get some knowledge of the state of the art from it and its citations.

[isidentical]

@whedon generate pdf

[whedon]

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

[isidentical]

@whedon generate pdf

[whedon]

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

[isidentical]

@whedon check references

[whedon]

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

OK DOIs

- 10.1016/j.scico.2012.04.008 is OK
- 10.5281/zenodo.4657163 is OK
- 10.1007/s10664-017-9514-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[isidentical]

Thanks @kyleniemeyer, all references should have been fixed now.

[arfon]

@whedon recommend-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.scico.2012.04.008 is OK
- 10.5281/zenodo.4657163 is OK
- 10.1007/s10664-017-9514-4 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#2421

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2421, 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.03296 joss-papers#2422
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03296
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]

@lutzhamel, @yuhc – many thanks for your reviews here and to @mjsottile for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@isidentical – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

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