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[REVIEW]: Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration. #6837
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👋🏼 @birm, @flekschas, @sebastian-raubach - this is the review thread for the submission. All of our communications will happen here from now on. As a reviewer, the first step is to create a checklist for your review by entering
as the top of a new comment in this thread. These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier 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. Please let me know if any of you require some more time. We can also use EditorialBot (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 (@csoneson) if you have any questions or concerns. Thanks! |
Review checklist for @sebastian-raubachConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@birm Would you be able to clarify the author contribution for me please? Looking at the contribution graphs (https://github.com/sharmalab/eaglescope/graphs/contributors) I can see major code contributions from yourself, Nan Li (with two separate accounts?) and Yahia Zakaria. I can, however, not identify Tony Pan's contribution. Additionally, there are smaller code contributions from other individuals who aren't included in the author list. If you could shine some light on those two items, that'd be great. @csoneson As this is my first JOSS review, could you let me know if questions of this nature are best posted on this thread or (as the initial comment suggests) on the software's main repository? Cheers. |
Hi @sebastian-raubach - I'd say that this type of question, which is not strictly related to the functionality or implementation of the software, but rather to the JOSS submission, are better posed in this thread. But there is no strict boundary, and as long as you mention the issues posted in the software repository here, we can keep track of them. Also, in case it's useful re: your question above, here is a link to the JOSS authorship policy. |
Added an issue asking about documentation of the tool sharmalab/eaglescope#118 |
I don't know why Nan used two different accounts, but that's accurate. |
@csoneson I noticed this section on web-applications in the JOSS guidelines and I'm not convinced this tool fulfils either of the two requirements. Having said that, just because they used web-technologies, this doesn't necessarily make it a web-application as it doesn't need to be hosted on the web somewhere, you can just run it locally. So I'm a bit unsure about how to proceed. This is further complicated by the fact that I cannot see any form of automated testing in place for this tool which is one of the other checkboxes to tick in the list. @birm would you be able to confirm whether or not there are automated tests for Eaglescope? |
The automated tests exist but are currently quite basic (triggered https://github.com/sharmalab/eaglescope/blob/main/.github/workflows/smoke_test.yml, which currently just checks if the code builds properly, and there's also a code style check. |
Review checklist for @flekschasConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Just to update everyone, I'm still working on addressing the comments/issues from @sebastian-raubach but have not had much time lately. I haven't fallen asleep on these suggestions. |
Thanks for putting together this tool @birm. It looks really promising! However, I have several remarks:
In summary, this truly looks like a neat tool but it (primarily) needs documentation and the exact use case its supports should be worked out more in the paper. PS: After digging around in the code I found out how one can change the config. The wine, demo, and collection-vis configs work but it seems that |
We've added community guidelines, improved the documentation, and added (slightly) better testing for eaglescope. I think we still need to address points 2 and 5 @flekschas |
@sebastian-raubach thanks for your comment and sorry for the delayed response, I was out of office for a few days. We have discussed it in the editor team and we do feel that this is technically in scope - however, as you (and @flekschas) have pointed out, implementing sufficient testing to be able to catch unexpected behaviour in a way that is as automated and comprehensive as possible will be essential. @birm - I would also suggest providing direct links to tests, contribution guidelines and similar in the README, so that they are easy to find. |
I've added some more links/instructions to the readme! Thank you for the continued suggestions! |
I think this is fair. We're more interested in the flexibility of deployment than we are about optimizing for large data in the current form. Larger scale data via a series of data summary APIs has been on our roadmap for a but, but we have not yet taken much action to make this happen. I've changed the paper writeup to focus a little more on the tabular/cohort than claiming "large". |
👋🏻 Just wanted to check in to see where things are at here. Let me know if you have any questions. Thanks! |
Hi Charlotte, for me things are kind of stuck on the automated testing criterion. I can see that there has been a little work done on that front but ultimately, only the smoke test (does it even compile and run?) and some very limited other test (does it show the correct page title and show one visualization element) are included. There are no tests that look into the functionality of the application, e.g. is the input data loaded correctly? does the filtering work? are interactions with the charts working as expected? is the exported configuration correct? None of these are covered. Since you mentioned in one of your earlier replies the editorial team wanted to ensure that things like this are covered, which at this point they aren't. There is also more that could be done on the documentation front. I am happy to see that the format and structure of the configuration files has been added as documentation, but there is no user-facing documentation when it comes to the use of the interface. Finally, there is no "state of the field" section to speak of where the tool would be compared and evaluated against other tools in the area. |
@editorialbot generate pdf |
And once more to fix the corresponding author: |
@editorialbot generate pdf |
Thank you @birm! For the Zenodo archive, could you link it directly to the GitHub repository (see here), so that all the files are visible in the archive as well (not just the compressed repo)? Also, please make sure that the title and author list of the archive agree with those of the paper. Thanks! |
Ok, it went and made a new DOI at https://zenodo.org/records/14040758 |
@editorialbot set 10.5281/zenodo.14040758 as archive |
Done! archive is now 10.5281/zenodo.14040758 |
@editorialbot set 1.1.1 as version |
Done! version is now 1.1.1 |
Great, thanks @birm! Final detail: could you swap the order of the authors in the Zenodo archive to agree with the order in the paper? In the meanwhile I will pass the submission to the Associate EiC for the final steps. |
@editorialbot recommend-accept |
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👋 @openjournals/bcm-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#6091, then you can now move forward with accepting the submission by compiling again with the command |
@birm as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. These are some final checks: Checks on repository
Checks on review issue
Checks on archive
Checks on paper
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@editorialbot accept |
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@birm one this I could not see is contributing guidelines. Can you point me to them or can you add them if missing? (see here for some examples: https://contributing.md/example/). |
Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository. If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file. You can copy the contents for your CITATION.cff file here: CITATION.cff
If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation. |
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@birm congratulations on this JOSS publication! Thanks for editing @csoneson ! And a special thank you to the reviewers: @flekschas, @sebastian-raubach !! |
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Submitting author: @birm (Ryan Birmingham)
Repository: https://github.com/sharmalab/eaglescope
Branch with paper.md (empty if default branch):
Version: 1.1.1
Editor: @csoneson
Reviewers: @flekschas, @sebastian-raubach
Archive: 10.5281/zenodo.14040758
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