[REVIEW]: EndoMineR for the extraction of endoscopic and associated pathology data from medical reports #701

whedon · 2018-04-25T16:29:33Z

Submitting author: @sebastiz (Sebastian Zeki)
Repository: https://github.com/ropensci/EndoMineR
Version: v1.0.0
Editor: @arfon
Reviewer: @arfon
Archive: 10.5281/zenodo.1232059

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6daff9a9c80c03f1e3c32552b5a7e4f8"><img src="http://joss.theoj.org/papers/6daff9a9c80c03f1e3c32552b5a7e4f8/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/6daff9a9c80c03f1e3c32552b5a7e4f8/status.svg)](http://joss.theoj.org/papers/6daff9a9c80c03f1e3c32552b5a7e4f8)

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) 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

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Review checklist for @arfon

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
Version: Does the release version given match the GitHub release (v1.0.0)?
Authorship: Has the submitting author (@sebastiz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

The text was updated successfully, but these errors were encountered:

whedon · 2018-04-25T16:29:35Z

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @arfon it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

whedon · 2018-04-25T16:29:36Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-25T16:29:41Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 252 0 --:--:-- --:--:-- --:--:-- 254
Error reading bibliography ./paper.bib (line 2, column 10):
unexpected "="
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

arfon · 2018-04-25T16:32:29Z

Accepting because of ropensci/software-review#153

arfon · 2018-04-25T16:39:02Z

@sebastiz - a couple of things:

Could you please take a look at the PDF compilation errors above? If you push changes to https://github.com/ropensci/EndoMineR then you can ask Whedon to try and compile the paper with @whedon generate pdf
Once the paper compiles properly, please make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive?

sebastiz · 2018-04-25T17:23:44Z

@whedon generate pdf

whedon · 2018-04-25T17:23:46Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-25T17:23:54Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 160 0 --:--:-- --:--:-- --:--:-- 160
100 13 0 13 0 0 159 0 --:--:-- --:--:-- --:--:-- 158
Error reading bibliography ./paper.bib (line 2, column 10):
unexpected "="
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

sebastiz · 2018-04-25T17:27:18Z

@whedon generate pdf

whedon · 2018-04-25T17:27:20Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-25T17:27:25Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 147 0 --:--:-- --:--:-- --:--:-- 149
Error reading bibliography ./paper.bib (line 2, column 12):
unexpected "="
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

sebastiz · 2018-04-25T17:29:12Z

@whedon generate pdf

whedon · 2018-04-25T17:29:14Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-25T17:29:21Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 176 0 --:--:-- --:--:-- --:--:-- 178
Error reading bibliography ./paper.bib (line 2, column 12):
unexpected "="
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

sebastiz · 2018-04-25T17:30:41Z

@whedon generate pdf

whedon · 2018-04-25T17:30:43Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-25T17:30:49Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 116 0 --:--:-- --:--:-- --:--:-- 117
Error reading bibliography ./paper.bib (line 2, column 12):
unexpected "="
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

sebastiz · 2018-04-26T13:46:51Z

@whedon generate pdf

whedon · 2018-04-26T13:46:54Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-26T13:47:00Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 87 0 --:--:-- --:--:-- --:--:-- 87
Error reading bibliography ./paper.bib (line 21, column 1):
unexpected end of input
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

sebastiz · 2018-04-26T13:48:27Z

@whedon generate pdf

whedon · 2018-04-26T13:48:29Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-26T13:48:47Z

--> Check article proof 📄 <--

sebastiz · 2018-04-26T13:55:39Z

@whedon generate pdf

whedon · 2018-04-26T13:55:41Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-26T13:55:58Z

--> Check article proof 📄 <--

sebastiz · 2018-04-26T14:03:01Z

@whedon generate pdf

whedon · 2018-04-26T14:03:03Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-26T14:03:29Z

--> Check article proof 📄 <--

sebastiz · 2018-04-26T14:05:11Z

@whedon generate pdf

whedon · 2018-04-26T14:05:13Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-26T14:05:37Z

--> Check article proof 📄 <--

sebastiz · 2018-04-26T15:36:28Z

@whedon generate pdf

whedon · 2018-04-26T15:36:30Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-26T15:37:01Z

--> Check article proof 📄 <--

sebastiz · 2018-04-27T07:57:30Z

@whedon generate pdf

whedon · 2018-04-27T07:57:33Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-27T07:57:42Z

PDF failed to compile for issue #701 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 13 0 13 0 0 91 0 --:--:-- --:--:-- --:--:-- 91
Error reading bibliography ./paper.bib (line 19, column 25):
unexpected "."
expecting letter, digit, white space or "="
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

sebastiz · 2018-04-27T08:06:35Z

@whedon generate pdf

whedon · 2018-04-27T08:06:37Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-27T08:06:57Z

--> Check article proof 📄 <--

sebastiz · 2018-04-27T08:56:44Z

@arfon I have now proofed the pdf and uploaded to zenodo. Two questions: Do I put the DOI on the ReadMe for the package I uploaded a copy of the software from a forked version in my repository as the software is now under rOpenSci and zenodo wouldnt link to that. Is that the correct way to do it? The DOI is: doi.org/10.5281/zenodo.1232059

…

________________________________ From: Arfon Smith <[email protected]> Sent: 25 April 2018 16:39 To: openjournals/joss-reviews Cc: Gastroenterology Data Science; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: EndoMineR for the extraction of endoscopic and associated pathology data from medical reports (#701) @sebastiz<https://github.com/sebastiz> - a couple of things: 1. Could you please take a look at the PDF compilation errors above? If you push changes to https://github.com/ropensci/EndoMineR then you can ask Whedon to try and compile the paper with @whedon generate pdf 2. Once the paper compiles properly, please make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#701 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AJHXPaN06wz4_Eb3OIavEOhPZrMC9dRZks5tsKangaJpZM4Tjwmr>.

sebastiz · 2018-04-27T08:57:36Z

@arfon Sorry.... My last question is how do I get the paper registered on pubmed? Thanks Sebastian Zeki

…

________________________________ From: Arfon Smith <[email protected]> Sent: 25 April 2018 16:39 To: openjournals/joss-reviews Cc: Gastroenterology Data Science; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: EndoMineR for the extraction of endoscopic and associated pathology data from medical reports (#701) @sebastiz<https://github.com/sebastiz> - a couple of things: 1. Could you please take a look at the PDF compilation errors above? If you push changes to https://github.com/ropensci/EndoMineR then you can ask Whedon to try and compile the paper with @whedon generate pdf 2. Once the paper compiles properly, please make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#701 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AJHXPaN06wz4_Eb3OIavEOhPZrMC9dRZks5tsKangaJpZM4Tjwmr>.

arfon · 2018-04-27T10:12:35Z

@whedon set 10.5281/zenodo.1232059 as archive

whedon · 2018-04-27T10:12:38Z

OK. 10.5281/zenodo.1232059 is the archive.

arfon · 2018-04-27T10:16:01Z

@sebastiz - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00701 ⚡️:rocket: :boom:

arfon · 2018-04-27T10:16:54Z

Sorry.... My last question is how do I get the paper registered on pubmed?

I'm not sure what the current status of this. I know some of our editors were working on this over in openjournals/joss#153

whedon · 2018-04-27T10:16:57Z

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

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00701/status.svg)](https://doi.org/10.21105/joss.00701)

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=

whedon assigned arfon Apr 25, 2018

whedon added the review label Apr 25, 2018

whedon mentioned this issue Apr 25, 2018

[PRE REVIEW]: EndoMineR for the extraction of endoscopic and associated pathology data from medical reports #700

Closed

arfon added the accepted label Apr 25, 2018

arfon closed this as completed Apr 27, 2018

arfon added the rOpenSci Submissions associated with rOpenSci label Feb 6, 2020

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

[REVIEW]: EndoMineR for the extraction of endoscopic and associated pathology data from medical reports #701

[REVIEW]: EndoMineR for the extraction of endoscopic and associated pathology data from medical reports #701

Comments

whedon commented Apr 25, 2018 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @arfon

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Apr 25, 2018

whedon commented Apr 25, 2018

whedon commented Apr 25, 2018

arfon commented Apr 25, 2018

arfon commented Apr 25, 2018

sebastiz commented Apr 25, 2018

whedon commented Apr 25, 2018

whedon commented Apr 25, 2018

sebastiz commented Apr 25, 2018

whedon commented Apr 25, 2018

whedon commented Apr 25, 2018

sebastiz commented Apr 25, 2018

whedon commented Apr 25, 2018

whedon commented Apr 25, 2018

sebastiz commented Apr 25, 2018

whedon commented Apr 25, 2018

whedon commented Apr 25, 2018

sebastiz commented Apr 26, 2018

whedon commented Apr 26, 2018

whedon commented Apr 26, 2018

sebastiz commented Apr 26, 2018

whedon commented Apr 26, 2018

whedon commented Apr 26, 2018

sebastiz commented Apr 26, 2018

whedon commented Apr 26, 2018

whedon commented Apr 26, 2018

sebastiz commented Apr 26, 2018

whedon commented Apr 26, 2018

whedon commented Apr 26, 2018

sebastiz commented Apr 26, 2018

whedon commented Apr 26, 2018

whedon commented Apr 26, 2018

sebastiz commented Apr 26, 2018

whedon commented Apr 26, 2018

whedon commented Apr 26, 2018

sebastiz commented Apr 27, 2018

whedon commented Apr 27, 2018

whedon commented Apr 27, 2018

sebastiz commented Apr 27, 2018

whedon commented Apr 27, 2018

whedon commented Apr 27, 2018

sebastiz commented Apr 27, 2018 via email

sebastiz commented Apr 27, 2018 via email

arfon commented Apr 27, 2018

whedon commented Apr 27, 2018

arfon commented Apr 27, 2018

arfon commented Apr 27, 2018

whedon commented Apr 27, 2018

whedon commented Apr 25, 2018 •

edited

Loading