[REVIEW]: DASF: A data analytics software framework for distributed environments

[whedon]

Submitting author: @d-eggert (Daniel Eggert)
Repository: https://git.geomar.de/digital-earth/dasf/dasf-messaging-python
Branch with paper.md (empty if default branch): joss-submission
Version: v0.3.0
Editor: @martinfleis
Reviewers: @cjwu, @pritchardn
Archive: 10.5880/GFZ.1.4.2021.008

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@sk1p & @cjwu, 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 @cjwu

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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.

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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 (@d-eggert) 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. @uellue, @sk1p, @cjwu it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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@whedon commands

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

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.15 s (314.2 files/s, 50747.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          33           1351           1802           4003
Jinja Template                   3             19              0            118
JSON                             6              0              0             89
Markdown                         1             33              0             80
YAML                             2              5              4             57
INI                              1              3              0             17
TOML                             1              1              0              9
-------------------------------------------------------------------------------
SUM:                            47           1412           1806           4373
-------------------------------------------------------------------------------


Statistical information for the repository 'd1bde33bfa14f5f95cc8e19e' was
gathered on 2022/01/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Daniel Eggert                   34          1369            299           11.07
Daniela Rabe                     2            27              9            0.24
Peter Morstein                   5            53             20            0.48
Philipp S. Sommer               44          6048           2999           60.02
Philipp Sommer                  13          3616            631           28.17
Stefan Lüdtke                    1             3              0            0.02

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
Daniel Eggert               672           49.1          9.7               16.22
Daniela Rabe                 19           70.4         23.9               31.58
Peter Morstein               17           32.1         15.2                0.00
Philipp S. Sommer          5232           86.5         13.8               12.02
Philipp Sommer             1216           33.6          1.9                3.78

[whedon]

PDF failed to compile for issue #4052 with the following error:

 Can't find any papers to compile :-(

[martinfleis]

👋🏼 @d-eggert, @uellue, @sk1p, @cjwu this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #4052 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks but considering upcoming holidays, feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

[martinfleis]

@whedon generate pdf from branch joss-submission

[whedon]

Attempting PDF compilation from custom branch joss-submission. Reticulating splines etc...

[whedon]

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

[martinfleis]

@uellue, @sk1p, @cjwu Please note, that this review should look at the whole DASF ecosystem composed of 4 packages stored at https://git.geomar.de/digital-earth/dasf, not just the dasf-messaging-python linked above. Thanks!

[uellue]

@martinfleis would it be possible to link to that also in the paper instead of an individual repository? Otherwise this is confusing for readers. Alternatively one could include several repository links. Since there are also other projects that are spread over several repositories, linking to several repositories or a project could make sense as an option for JOSS.

[uellue]

State of the field

Right now this seems to be entirely missing in the paper. It should compare DASF with other software to build web applications and do RPC, and point out what the unique selling points of DASF are. From my own experience I know that interactive visualization of large amounts of data is not solved ideally in the "standard" frameworks for web applications, so this could be a strong point of DASF. If that is the case, it should be fleshed out through a more detailed comparison. Probably that should be included in the DASF documentation and referenced from the paper. This relates to the general documentation issue that I created there. Unfortunately https://git.geomar.de seems to be down at the moment, I'll try to add a link later.

[uellue]

Service desk feature

Referring to my previous comment, the Issue that I tried to create via Service Desk seems to be missing. I sent to and received the message Thank you for your support request! We are tracking your request as ticket #41, and will respond as soon as we can. However, it doesn't appear in https://git.geomar.de/groups/digital-earth/dasf/-/issues?scope=all&state=opened

Creating pull requests

https://git.geomar.de/digital-earth/dasf/dasf-messaging-python#contributing does describe how to set up for local development. However, it should also include instructions on how to make improvements available upstream, in particular since 3rd parties can't create an account on https://git.geomar.de, apparently.

[uellue]

Reliability of https://git.geomar.de

The repository is "on and off" at this time. This makes reviewing very hard. Is this a temporary issue or more persistent? A reliable hosting platform would be an absolute "must", and with all the previous discussions in #4009 and the issues with the Service Desk feature (my comment above), perhaps a better hosting platform for a public OSS project should be selected?

[uellue]

@d-eggert I'll halt my review for now. Please let me know when I can reliably access the repository and create Issues so that I can continue with the review.

[uellue]

@d-eggert is it possible that https://git.geomar.de uses some form of IP blacklisting or rate limiting? Sometimes it is unreachable from my home IP, sometimes from my institutional IP at FZ Jülich. So apparently the server is not down, but the traffic doesn't reach it. How is it from your internal network?

[d-eggert]

@uellue thanks for starting the review this quickly.

Regarding your service desk issue, it is there. For privacy reasons service desk issues are flagged confidential, so only registered users can see them. As soon as there is some activity going on regarding your issue, you will get a notification via email.

Regarding the reliability of the server, i didn't experience them. But there was some maintenance downtime scheduled recently. Maybe they aren't finished yet. Maybe @cfgmr can elaborate on that.

[uellue]

Regarding your service desk issue, it is there. For privacy reasons service desk issues are flagged confidential, so only registered users can see them. As soon as there is some activity going on regarding your issue, you will get a notification via email.

Quite frankly, that is not very user-friendly. It feels like sending feedback to /dev/null. Most other OSS projects allow more interaction. To the very least the created Issues should be public so that users can send follow-up and 3rd parties can participate. IMO the current setup is not acceptable for a JOSS paper, but perhaps the editors can pitch in on that.

[uellue]

@d-eggert is it possible that https://git.geomar.de uses some form of IP blacklisting or rate limiting? Sometimes it is unreachable from my home IP, sometimes from my institutional IP at FZ Jülich. So apparently the server is not down, but the traffic doesn't reach it. How is it from your internal network?

Now I can confirm that an external IP is apparently blacklisted after only a few clicks in the repo web interface. It can be triggered reliably by looking at the commit history a few times, and is apparently per IP. This should be resolved before I can continue reviewing.

[d-eggert]

In general I agree with your view. We already discussed the service desk option to some extend with @martinfleis in the pre-review. I just looked at the service desk configuration and there is unfortunately no option to disable this behavior.

What's possible is, that I remove the confidential flag, once I read the issue, so I can make sure that it does not contain sensible information, e.g. since you didn't remove your email signature, there are some addresses and phone numbers in there. This might be fine for you, but maybe not for everyone.

Btw. you can send a follow-up by replying to the corresponding notification emails

[uellue]

Btw. you can send a follow-up by replying to the corresponding notification emails

Ah OK. That would be very important information for the user that should be contained in the response e-mail.

What's possible is, that I remove the confidential flag, once I read the issue, so I can make sure that it does not contain sensible information, e.g. since you didn't remove your email signature, there are some addresses and phone numbers in there. This might be fine for you, but maybe not for everyone.

That should also be described in the response e-mail. Also, that puts a permanent burden on your team to do this quickly. Quite frankly, why not just host the project on github.com?

[d-eggert]

Ah OK. That would be very important information for the user that should be contained in the response e-mail.

I simply used the default template. I will have a look at how to change this and add the corresponding information.

That should also be described in the response e-mail. Also, that puts a permanent burden on your team to do this quickly. Quite frankly, why not just host the project on github.com?

You are absolutely right, if I had a say in this, I would consider it. But I have to follow certain rules from my institution, so it's not me to decide this.

[d-eggert]

I removed your email signature from the issue and removed the confidential flag.

https://git.geomar.de/digital-earth/dasf/dasf-messaging-python/-/issues/41

[d-eggert]

Now I can confirm that an external IP is apparently blacklisted after only a few clicks in the repo web interface. It can be triggered reliably by looking at the commit history a few times, and is apparently per IP. This should be resolved before I can continue reviewing.

@cfgmr can you confirm this?

I also access the Geomar git from home and have no such issues.

[uellue]

You are absolutely right, if I had a say in this, I would consider it. But I have to follow certain rules from my institution, so it's not me to decide this

Yes, I've also heard these data protection discussions in other context. Fortunately that's not an issue here at FZ Jülich. Since Geomar is also Helmholtz like FZ Jülich and also operates in Germany, perhaps the policies at Geomar could be improved? The information in public OSS projects is generally public. The closest thing to personal information are names and e-mail addresses as part of Git commits, and this is publicly available independent if it is hosted on premise or externally. That means I don't see an issue to have this hosted by 3rd parties -- they could access everything anyway. If it was confidential or private information (technology to be patented or patient data, for example), it would be a different story, of course.

At least here in Jülich there's a strong push to do both innovation and data science, the Helmholtz mission is large scale research infrastructure, and developing and maintaining software like DASF fits that mission perfectly. That means policies that make it difficult to do that successfully should be reviewed carefully. The limits of https://git.geomar.de/ look like a real burden for the success of DASF, and perhaps this could be taken higher up at Geomar for that reason.

[uellue]

Also, feel free to quote me on that and/or include me in the discussions. Maybe it helps to show that this is a larger concern and not just users complaining. :-)

[d-eggert]

@martinfleis do you have everything to wrap this up, or is still something missing?

[martinfleis]

@editorialbot set v0.3.0 as version

[editorialbot]

Done! version is now v0.3.0

[martinfleis]

@editorialbot set 10.5880/GFZ.1.4.2021.008 as archive

[editorialbot]

Done! Archive is now 10.5880/GFZ.1.4.2021.008

[martinfleis]

@editorialbot generate pdf

[editorialbot]

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

[martinfleis]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/978-3-030-99546-1 is OK
- 10.1093/nar/gky379 is OK
- 10.5880/GFZ.1.4.2022.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[martinfleis]

Thank you @d-eggert! I'm going to hand this over now to the associate EiC for the final steps.

[martinfleis]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3614, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1007/978-3-030-99546-1 is OK
- 10.1093/nar/gky379 is OK
- 10.5880/GFZ.1.4.2022.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kthyng]

Everything looks good to me!

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.04052 joss-papers#3617
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04052
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...

[kthyng]

Congratulations on your new publication @d-eggert! Many thanks to editor @martinfleis and reviewers @cjwu and @pritchardn for your time, hard work, and expertise!!

[editorialbot]

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

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