[REVIEW]: Nuclear Morphology Analysis 2.0.0: Improved image analysis software for measuring nuclear shape

[editorialbot]

Submitting author: @bmskinner (Ben Skinner)
Repository: https://bitbucket.org/bmskinner/nuclear_morphology
Branch with paper.md (empty if default branch): paper
Version: 2.0.0
Editor: @jmschrei
Reviewers: @petebankhead, @suyashkumar
Archive: 10.5281/zenodo.7303498

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2866df86983e63e6bc8a90113c099fb7"><img src="https://joss.theoj.org/papers/2866df86983e63e6bc8a90113c099fb7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2866df86983e63e6bc8a90113c099fb7/status.svg)](https://joss.theoj.org/papers/2866df86983e63e6bc8a90113c099fb7)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@petebankhead & @suyashkumar, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jmschrei know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @petebankhead

📝 Checklist for @suyashkumar

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.15 s (356.9 files/s, 102561.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              1              1          79242
Java                           746          23599          36591          77680
Maven                            1             30             35            463
Rmd                              5            821           1478            204
TeX                              2             10              0            144
CSS                              2              0              0            141
Markdown                         4             59              0            115
DOS Batch                        3             10             10             13
Bourne Shell                     2              7              9             10
YAML                             1              0              0              5
JSON                             1              0              0              4
-------------------------------------------------------------------------------
SUM:                           768          24537          38124         158021
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1040

[editorialbot]

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

OK DOIs

- 10.1093/biolre/ioz013 is OK
- 10.3390/genes10020109 is OK
- 10.1007/s00412-016-0614-5 is OK
- 10.1016/j.cub.2019.09.031 is OK
- 10.1038/s41598-022-12433-9 is OK
- 10.7554/eLife.75373 is OK
- 10.1095/biolreprod.115.138008 is OK

MISSING DOIs

- 10.1109/tc.1972.5008949 may be a valid DOI for title: Fourier descriptors for plane closed curves

INVALID DOIs

- None

[editorialbot]

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

[jmschrei]

Howdy @petebankhead and @suyashkumar!

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html

Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

[petebankhead]

Review checklist for @petebankhead

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 https://bitbucket.org/bmskinner/nuclear_morphology?
• 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 (@bmskinner) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[suyashkumar]

Review checklist for @suyashkumar

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 https://bitbucket.org/bmskinner/nuclear_morphology?
• 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 (@bmskinner) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[petebankhead]

I had no problems running the software, and the documentation seems very clear and extensive.

Some minor points, relevant to the checklist above:

• I didn't see information about the source of the test/sample images, to check off the 'Human and animal research' box

• I tried the software on macOS, so no installer was available. Installation instructions do work, but the need for Java 16+ complicates things for people who have another Java version installed as the default (I have 17 installed, but 11 is my default). This meant that the 'simple' approach of launching from the terminal was not possible unless I forced a different Java version to use.
  Double-clicking the jar 'solved' this, and made it much easier to launch the program successfully. To do this, it is necessary to right-click the jar and select 'Open' the first time only, to bypass the security flag that otherwise stops double-click from working. Then the double-click seems to successfully locate the appropriate Java version.

• It's relatively hard to infer the dependencies, because they do not seem to be listed and the distributions use fat jars. I can check pom.xml, but it would help to make this information easier to access.

• I didn't see any community guidelines, or information for potential contributors (if external contributions are welcome)

• There are missing images at https://bitbucket.org/bmskinner/nuclear_morphology/wiki/data/Angle_profiles.md

• There are automated tests, but I didn't see instructions for how to run them. I guessed mvn test should do it, but that gave me an error getting dependencies

[ERROR] Failed to execute goal on project nma: Could not resolve dependencies for project com.bmskinner:nma:jar:2.0.0: The following artifacts could not be resolved: fr.inra.ijpb:MorphoLibJ_:jar:1.3.2, jebl:jebl:jar:0.4: Could not find artifact fr.inra.ijpb:MorphoLibJ_:jar:1.3.2 in jitpack.io (https://jitpack.io) -> [Help 1]

• The main information about the 'state of the field' seems to be the second sentence. Another sentence or two would be helpful to understand which other software tools people in the field use, and whether any comparable software exists.

• The citation for ImageJ (Abramoff, 2004) differs from that suggested at https://imagej.net/contribute/citing#imagej-and-variants and does not include ImageJ's creator in the author list.
  It is mentioned as an option at https://imagej.net/contribute/citing but I would suggest considering one of the more recent papers, since I think the current citation alone risks creating the wrong idea of who wrote the software.

[jmschrei]

Thanks for the review @petebankhead! @bmskinner, let me know if there are any challenges addressing these points.

[bmskinner]

Thanks @petebankhead for these comments! I have addressed them as follows:

Some minor points, relevant to the checklist above:

I didn't see information about the source of the test/sample images, to check off the 'Human and animal research' box

The testing image zip file now has a readme file included with full details of the animals, suppliers, the licence under which they were collected, and the experimental protocol.

I tried the software on macOS, so no installer was available. Installation instructions do work, but the need for Java 16+ complicates things for people who have another Java version installed as the default (I have 17 installed, but 11 is my default). This meant that the 'simple' approach of launching from the terminal was not possible unless I forced a different Java version to use.
Double-clicking the jar 'solved' this, and made it much easier to launch the program successfully. To do this, it is necessary to right-click the jar and select 'Open' the first time only, to bypass the security flag that otherwise stops double-click from working. Then the double-click seems to successfully locate the appropriate Java version.

Thank you for this - the wiki has been updated, and the instructions will be included in the internal user guide in the next release.

It's relatively hard to infer the dependencies, because they do not seem to be listed and the distributions use fat jars. I can check pom.xml, but it would help to make this information easier to access.

Information on all dependencies have been added to a new wiki page (https://bitbucket.org/bmskinner/nuclear_morphology/wiki/Building_from_source.md)

I didn't see any community guidelines, or information for potential contributors (if external contributions are welcome)

There is no formal process at the moment, since it's just been me working on the code. I've added a note that external contributions are welcome though to the new build page and the FAQ, and potential contributors should contact me directly to discuss further.

There are missing images at https://bitbucket.org/bmskinner/nuclear_morphology/wiki/data/Angle_profiles.md

Missing images have been added to the wiki. The internal user guide was not affected by this.

There are automated tests, but I didn't see instructions for how to run them. I guessed mvn test should do it, but that gave me an error getting dependencies

[ERROR] Failed to execute goal on project nma: Could not resolve dependencies for project com.bmskinner:nma:jar:2.0.0: The following artifacts could not be resolved: fr.inra.ijpb:MorphoLibJ_:jar:1.3.2, jebl:jebl:jar:0.4: Could not find artifact fr.inra.ijpb:MorphoLibJ_:jar:1.3.2 in jitpack.io (https://jitpack.io) -> [Help 1]

One of the dependencies is not in Maven Central, and this was only mentioned within the POM. I've added a new wiki page explaining the build process, and prerequisites (https://bitbucket.org/bmskinner/nuclear_morphology/wiki/Building_from_source.md). The build process has been checked on Windows and Linux; on MacOs, the jar with bundled dependencies should be generated, but I've not been able to test this.

The main information about the 'state of the field' seems to be the second sentence. Another sentence or two would be helpful to understand which other software tools people in the field use, and whether any comparable software exists.

The section has been expanded to give examples of existing software, and explain the methods in some more detail.

The citation for ImageJ (Abramoff, 2004) differs from that suggested at https://imagej.net/contribute/citing#imagej-and-variants and does not include ImageJ's creator in the author list.
It is mentioned as an option at https://imagej.net/contribute/citing but I would suggest considering one of the more recent papers, since I think the current citation alone risks creating the wrong idea of who wrote the software.

The citation has been updated as suggested.

[petebankhead]

Thanks @bmskinner ! I can confirm the tests now run on macOS.

The section has been expanded to give examples of existing software, and explain the methods in some more detail.

Do you know how I can access the updated version?

[bmskinner]

@editorialbot generate pdf

[bmskinner]

@petebankhead it should have triggered now!

[editorialbot]

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

[jmschrei]

@suyashkumar how is the review coming?

[suyashkumar]

Hi @jmschrei thanks for following up--I expect to complete the rest of the review in the next 2 days. Apologies for the delay!

[suyashkumar]

Overall this looks good to me! I was able to run the prebuilt Linux software according to the installation instructions, run a test analysis, and run the full test suite successfully. I had only one very minor rubric-based recommendation, and a couple optional ones that are non-blocking suggestions.

Minor Rubric-based recommendations

• A minor point: I think documentation around “reporting issues” or “seeking support” could be more clear (as this is a noted entry on the review rubric). While the FAQ mentions a way to get in touch, I didn’t see an obvious recommendation on how you prefer folks to report issues (e.g. should they just report on Bitbucket, reach out to you first, check a troubleshooting page first, etc).

Optional General/Future Suggestions:

• It could be helpful to add links to the additional list of required programs in the building from source list here: https://bitbucket.org/bmskinner/nuclear_morphology/wiki/Building_from_source.
• It may be helpful to link to the “building from source” page from the installation page for those who wish to install from source (for security or development reasons)
• You may consider a shell script or Dockerfile that also gathers the additional non-maven dependencies to streamline the install process for those looking to contribute or build from source. (Docker may be complicated for this project, but can support X11 GUI applications).
• I’m less familiar with bitbucket, but on GitHub and other platforms it is standard to have contributing guidelines and recommendations in a CONTRIBUTING file in the root of the repository (this may be what prospective contributors look for first). Seems that having such a file can also trigger other features in bitbucket server too if that interests you: https://confluence.atlassian.com/bitbucketserver/creating-a-contributions-guidelines-file-938025885.html
• Having the test suite run automatically on commits or pull requests could be helpful, particularly if you start to get more community contributions in the future! It appears bitbucket has a free tier for this (but with not a lot of build minutes) but there are other providers like circleci and GitHub actions that offer more expansive build time for free.

[jmschrei]

Thanks for the review @suyashkumar! @bmskinner, let me know if there are any challenges addressing these points.

[bmskinner]

Thank you @suyashkumar for the feedback and suggestions!

Overall this looks good to me! I was able to run the prebuilt Linux software according to the installation instructions, run a test analysis, and run the full test suite successfully. I had only one very minor rubric-based recommendation, and a couple optional ones that are non-blocking suggestions.

Minor Rubric-based recommendations

• A minor point: I think documentation around “reporting issues” or “seeking support” could be more clear (as this is a noted entry on the review rubric). While the FAQ mentions a way to get in touch, I didn’t see an obvious recommendation on how you prefer folks to report issues (e.g. should they just report on Bitbucket, reach out to you first, check a troubleshooting page first, etc).

I have added this to the FAQ, and to the internal user guide for future versions.

Optional Suggestions:

• It could be helpful to add links to the additional list of required programs in the building from source list here: https://bitbucket.org/bmskinner/nuclear_morphology/wiki/Building_from_source.

Links have been added as suggested

• It may be helpful to link to the “building from source” page from the installation page for those who wish to install from source (for security or development reasons)

I have added a link to the installation page as suggested

• You may consider a shell script or Dockerfile that also gathers the additional non-maven dependencies to streamline the install process for those looking to contribute or build from source. (Docker may be complicated for this project, but can support X11 GUI applications).

This is a good suggestion, I've added a script to download and install the non-Maven dependency. The manual instructions are still on the wiki for those with non-standard local Maven repo paths.

• I’m less familiar with bitbucket, but on GitHub and other platforms it is standard to have contributing guidelines and recommendations in a CONTRIBUTING file in the root of the repository (this may be what prospective contributors look for first). Seems that having such a file can also trigger other features in bitbucket server too if that interests you: https://confluence.atlassian.com/bitbucketserver/creating-a-contributions-guidelines-file-938025885.html

Thanks for this - there is no formal process at the moment, since I'm the only developer, but I have added a contributions file to welcome prospective collaborators and get them to contact me directly.

• Having the test suite run automatically on commits or pull requests could be helpful, particularly if you start to get more community contributions in the future! It appears bitbucket has a free tier for this (but with not a lot of build minutes) but there are other providers like circleci and GitHub actions that offer more expansive build time for free.

This is also very useful to know and I will implement this if more developers join the project.

[suyashkumar]

Thanks @bmskinner! Looks good from my end 👍🏽 !

[jmschrei]

Great, thanks for the reviews!

[jmschrei]

@editorialbot check references

[editorialbot]

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

[bmskinner]

@jmschrei Sorry, I blatted the paper files when merging the changes back into the paper branch. All back now.

[jmschrei]

Great. Do you have a DOI and a software version to tag this submission with?

[bmskinner]

@jmschrei The repo is now on Zenodo:
Version: 2.0.0
DOI: https://doi.org/10.5281/zenodo.7303498

[jmschrei]

@editorialbot set 10.5281/zenodo.7303498 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7303498

[jmschrei]

@editorialbot set 2.0.0 as version

[editorialbot]

Done! version is now 2.0.0

[jmschrei]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1093/biolre/ioz013 is OK
- 10.3390/genes10020109 is OK
- 10.1109/tc.1972.5008949 is OK
- 10.1007/s00412-016-0614-5 is OK
- 10.1016/j.cub.2019.09.031 is OK
- 10.1038/s41598-022-12433-9 is OK
- 10.7554/eLife.75373 is OK
- 10.1038/nmeth.2089 is OK
- 10.1095/biolreprod.115.138008 is OK
- 10.7717/peerj.3913 is OK
- 10.1186/s12859-021-04344-9 is OK
- 10.1093/jhered/93.5.384 is OK
- 10.1111/j.1755-0998.2010.02924.x is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1002/j.1939-4640.2001.tb02218.x is INVALID

[editorialbot]

👋 @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#3699, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[jmschrei]

@Kevin-Mattheus-Moerman just pinging you about this.

[Kevin-Mattheus-Moerman]

@bmskinner I am the AEiC for this track and here to help process acceptance of this work in JOSS. I have just read your paper and inspected the archive and have the below remaining issues to address:

• Please manually edit the ZENODO archive such that the title matches that of the paper. (@jmschrei in the future the handling editor can check this too).
• I recommend that you also edit the License listed on the ZENODO archive to match your project's open source license.
• I recommend that you spell out United Kingdom in your affiliation.
• In ....simpler and higher throughput..., would it be better to say something like ....simpler and allow for high-throughput analysis...? Perhaps I am misunderstanding this but higher throughput sounds awkward.
• The text says: Left: Landmark editing on mouse sperm dataset in v1.20.0 showing landmarks as vertical lines on the angle profile. Right: improved editing shows the landmarks as diamonds on the consensus nucleus outline, with the name shown on mouseover (here the tip of the hook)., this sounds like it is describing a figure. Is a figure missing? I do not see one in the paper.

Let me know when you've worked on these.

[bmskinner]

@editorialbot generate pdf

[editorialbot]

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

[bmskinner]

@Kevin-Mattheus-Moerman I've made the following changes as requested:

Please manually edit the ZENODO archive such that the title matches that of the paper.

The Zenodo title has been updated to match the paper title

I recommend that you also edit the License listed on the ZENODO archive to match your project's open source license

The Zenodo license has been updated to GPL3

I recommend that you spell out United Kingdom in your affiliation.

United Kingdom is now given in the affiliation

....simpler and higher throughput...

The sentence has been revised to Decomposing nuclear outlines into elliptic fourier descriptors is simpler and allows high-throughput analysis

Is a figure missing? I do not see one in the paper.

Apologies, the missing figure file has been added back to the repository

[Kevin-Mattheus-Moerman]

@bmskinner great, all looks good now and we shall proceed with the acceptance process.

[Kevin-Mattheus-Moerman]

@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.04767 joss-papers#3725
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04767
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...

[Kevin-Mattheus-Moerman]

@bmskinner congratulations on this publication in JOSS!!

Thanks for editing @jmschrei! And special thanks to @petebankhead and @suyashkumar for your review efforts!!!!!!!!!!

[editorialbot]

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

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