[PRE REVIEW]: Bloatectomy: A python package for the identification and removal of duplicate text in the bloated notes of electronic health records and other documents

[whedon]

Submitting author: @1fmusic (Summer Rankin) Repository: https://github.com/MIT-LCP/bloatectomy Version: v0.0.12 Editor: Pending Reviewer: Pending Managing EiC: Arfon Smith

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[whedon]

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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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 1.84  T=0.11 s (128.0 files/s, 15557.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2            138              0            466
TeX                              1             16              0            256
Python                           4             35             70            216
Jupyter Notebook                 2              0            408             90
HTML                             3              0              0              3
DOS Batch                        1              0              0              2
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                            14            189            478           1034
-------------------------------------------------------------------------------

Statistical information for the repository '2370' was gathered on 2020/06/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alistair Johnson                 1           319              0           96.96
Rankin_summer                    3             5              4            2.74
Summer K. Rankin                 1             1              0            0.30

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
Alistair Johnson            315           98.7          0.0               14.29
Rankin_summer                 5          100.0          0.0               20.00
Summer K. Rankin              1          100.0          0.0                0.00

[whedon]

Reference check summary:

OK DOIs

- 10.4300/JGME-D-15-00201.1 is OK
- 10.4338/ACI-2016-09-R-0150 is OK
- 10.1097/01.CCM.0000104112.34142.79 is OK
- 10.1186/1471-2105-14-10 is OK
- 10.1371/journal.pone.0087555 is OK
- 10.7326/0003-4819-157-1-201206190-00429 is OK
- 10.1016/S0022-2836(05)80360-2 is OK
- 10.13026/C2XW26 is OK
- 10.1103/PhysRevX.5.011007 is OK
- 10.1016/j.ijmedinf.2006.06.004 is OK
- 10.1197/jamia.M3390 is OK

MISSING DOIs

- https://doi.org/10.1038/sdata.2016.35 may be missing for title: MIMIC-III, a freely accessible critical care database
- https://doi.org/10.25080/majora-92bf1922-00a may be missing for title: Data structures for statistical computing in python
- https://doi.org/10.1055/s-0038-1638592 may be missing for title: Extracting information from textual documents in the electronic health record: a review of recent research
- https://doi.org/10.1109/icicic.2008.422 may be missing for title: Plagiarism Detection Using the Levenshtein Distance and Smith-Waterman Algorithm
- https://doi.org/10.1109/mc.1984.1659158 may be missing for title: A Technique for High-Performance Data Compression

INVALID DOIs

- 10.5555/1593511 is INVALID

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[1fmusic]

potential reviewer: Darthpathos

[1fmusic]

potential reviewer username: jkanche email: jayaram.kancherla@gmail.com

[1fmusic]

INVALID DOIs

• 10.5555/1593511 is INVALID

I'm not sure why this is invalid? it's the python reference manual... http://citebay.com/how-to-cite/python/

@book{10.5555/1593511, author = {Van Rossum, Guido and Drake, Fred L.}, title = {Python 3 Reference Manual}, year = {2009}, isbn = {1441412697}, publisher = {CreateSpace}, address = {Scotts Valley, CA} }

[arfon]

...well https://doi.org/10.5555/1593511 doesn't resolve so whatever this DOI is, it's not a valid one 😄

[1fmusic]

ok, took it out

[1fmusic]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[1fmusic]

@whedon generate pdf

[1fmusic]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[1fmusic]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.4300/JGME-D-15-00201.1 is OK
- 10.4338/ACI-2016-09-R-0150 is OK
- 10.1097/01.CCM.0000104112.34142.79 is OK
- 10.1186/1471-2105-14-10 is OK
- 10.1371/journal.pone.0087555 is OK
- 10.7326/0003-4819-157-1-201206190-00429 is OK
- 10.1016/S0022-2836(05)80360-2 is OK
- 10.1038/sdata.2016.35 is OK
- 10.13026/C2XW26 is OK
- 10.1103/PhysRevX.5.011007 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1055/s-0038-1638592 is OK
- 10.1109/icicic.2008.422 is OK
- 10.1016/j.ijmedinf.2006.06.004 is OK
- 10.1109/mc.1984.1659158 is OK
- 10.1197/jamia.M3390 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

:wave: @1fmusic - thanks for your submission to JOSS. After consulting with the JOSS editorial team, we've determined that this work is out of scope for JOSS as it falls into our minor utility category.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[arfon]

@whedon reject

[whedon]

Paper rejected.