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[PRE REVIEW]: LCIA Formatter #3304

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @WesIngwersen (Wesley Ingwersen) Repository: https://github.com/USEPA/LCIAformatter Version: v1.0.0 Editor: @csoneson Reviewers: @tngTUDOR, @mfastudillo Managing EiC: Kyle Niemeyer

: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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/2903a4c2b79558927543544f5b01819a/status.svg)](https://joss.theoj.org/papers/2903a4c2b79558927543544f5b01819a)

Author instructions

Thanks for submitting your paper to JOSS @WesIngwersen. Currently, there isn't an JOSS editor assigned to your paper.

@WesIngwersen if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 3 years ago

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.

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

@whedon commands

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

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (549.7 files/s, 51708.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            354            229           1507
TeX                              1             24              0            183
Markdown                         4             29              0            136
JSON                             1              1              0             54
YAML                             1              7              0             16
-------------------------------------------------------------------------------
SUM:                            27            415            229           1896
-------------------------------------------------------------------------------

Statistical information for the repository '80f8d7b86b1552caf619554c' was
gathered on 2021/05/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
BMorelli                         8           264             44            6.55
Ben Young                      114          1329            655           42.19
TAHottle                         3            45             22            1.42
WesIngwersen                    22           130             66            4.17
hottleta                         1             5              1            0.13
msrocka                         30          1619            523           45.55

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
BMorelli                    124           47.0          3.2               10.48
Ben Young                   915           68.8          5.2               13.11
WesIngwersen                 78           60.0         16.9                6.41
hottleta                     26          520.0         14.2               11.54
msrocka                     947           58.5         21.0                4.01
whedon commented 3 years ago

PDF failed to compile for issue #3304 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/orcid_validator.rb:12:in `initialize': undefined method `strip' for nil:NilClass (NoMethodError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in `block in check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.ecolecon.2008.01.019 is OK
- 10.1007/s11367-017-1354-3 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK

MISSING DOIs

- 10.1007/s10098-010-0338-9 may be a valid DOI for title: TRACI 2.0: the tool for the reduction and assessment of chemical and other environmental impacts 2.0

INVALID DOIs

- 10.23719/1522445 is INVALID
- 10.23719/1522444 is INVALID
- 10.23719/1522413 is INVALID
- 10.23719/1522414 is INVALID
kyleniemeyer commented 3 years ago

Hi @WesIngwersen, thanks for your interest in JOSS. Due to low editor availability in this area, I am placing your submission on a waitlist for now; once an appropriate editor becomes available, we will get this assigned and move the process forward.

In the meantime, you could address the issues with the references raised above, and also provide reviewer suggestions. Thanks!

kyleniemeyer commented 3 years ago

@WesIngwersen regarding the paper generation error, I think you cannot have an empty orcid field for an author, so you should just remove that for someone that does not have an ORCID.

Also, I am not sure that the corresponding author footnote will work. @openjournals/dev is that correct?

WesIngwersen commented 3 years ago

FYI co-author @bl-young

WesIngwersen commented 3 years ago

@kyleniemeyer, I removed the empty orcid field for Michael Srocka with this commit and removed the corresponding author note with this commit

danielskatz commented 3 years ago

You can use the command @whedon check references to check the references, and the command @whedon generate pdf to make a new PDF. Whedon commands need to be the first entry in a new comment.

danielskatz commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 3 years ago

Note that there are some potential reference problems flagged above too...

WesIngwersen commented 3 years ago

Recommended reviewers:

  1. Chris Mutel, author of Brightway: An open source framework for Life Cycle Assessment and two other JOSS articles
  2. James Joyce, author of Lcopt - An interactive tool for creating fully parameterised Life Cycle Assessment (LCA) foreground models
  3. Konstantin Stadler, author of The country converter coco - a Python package for converting country names between different classification schemes

All 3 recommended reviewers are PhD level domain experts (in life cycle assessment), Python developers, and have published in JOSS

WesIngwersen commented 3 years ago

Note that there are some potential reference problems flagged above too...

@danielskatz @kyleniemeyer Regarding DOI issues. I will address the missing DOI (actually others can be added). The invalid DOIs are for 4 datasets that are data products of the LCIA formatter software and currently in the cue in the EPA data review/publication system. They should be through that process and registered within a week. I will report back on them once they are registered.

WesIngwersen commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s10098-010-0338-9 is OK
- 10.1007/s11367-016-1246-y is OK
- 10.1007/s11367-019-01583-0 is OK
- 10.1016/j.ecolecon.2008.01.019 is OK
- 10.1007/s11367-017-1354-3 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK

MISSING DOIs

- None

INVALID DOIs

- 10.23719/1522445 is INVALID
- 10.23719/1522444 is INVALID
- 10.23719/1522413 is INVALID
- 10.23719/1522414 is INVALID
WesIngwersen commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s10098-010-0338-9 is OK
- 10.1007/s11367-016-1246-y is OK
- 10.1007/s11367-019-01583-0 is OK
- 10.1016/j.ecolecon.2008.01.019 is OK
- 10.1007/s11367-017-1354-3 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.23719/1522445 is OK
- 10.23719/1522444 is OK
- 10.23719/1522413 is OK
- 10.23719/1522414 is OK

MISSING DOIs

- None

INVALID DOIs

- None
WesIngwersen commented 3 years ago

@danielskatz All DOIs are now active so reference issues are resolved. FYI co-author @bl-young

danielskatz commented 3 years ago

@whedon generate pdf

danielskatz commented 3 years ago

👋 @csoneson - Would you be able to edit this submission?

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 3 years ago

@whedon invite @csoneson as editor

whedon commented 3 years ago

@csoneson has been invited to edit this submission.

csoneson commented 3 years ago

@whedon assign @csoneson as editor

whedon commented 3 years ago

OK, the editor is @csoneson

csoneson commented 3 years ago

👋🏻 @cmutel, @pjamesjoyce, @konstantinstadler - would (two of) you be willing to review this submission for JOSS?

LCIA Formatter This paper describes a USEPA LCA ecosystem tool 'LCIA formatter' that extracts LCIA information from original source methods and converts the data for interoperability with the rest of the USEPA LCA ecosystem tools.

konstantinstadler commented 3 years ago

@csoneson : I am on my last days before my vacation so I can not commit to this now. However, it is a very interesting piece of software. If you struggle to find reviewers you can ping me again on the 26th July and I would be happy to do a review then.

csoneson commented 3 years ago

@konstantinstadler - thank you! Enjoy your holidays and thanks for the offer - I'll keep you posted!

cmutel commented 3 years ago

@csoneson I have a conflict of interest, so don't feel comfortable being a reviewer here.

Here are some possible alternatives: @mfastudillo @tngTUDOR @aleksandra-kim

csoneson commented 3 years ago

@cmutel - no problem, thanks for the quick response!

@mfastudillo @tngTUDOR @aleksandra-kim - would one or two of you be up for reviewing this submission for JOSS?

LCIA Formatter This paper describes a USEPA LCA ecosystem tool 'LCIA formatter' that extracts LCIA information from original source methods and converts the data for interoperability with the rest of the USEPA LCA ecosystem tools.

tngTUDOR commented 3 years ago

I'm available and willing to review.

csoneson commented 3 years ago

Excellent, thank you @tngTUDOR! Once we have secured one more reviewer I will open the actual review issue where you'll find more information, review check list etc.

mfastudillo commented 3 years ago

I am available too

csoneson commented 3 years ago

Brilliant, thanks @mfastudillo! So this means that we have our two reviewers - I'll assign you now and open the review issue.

csoneson commented 3 years ago

@whedon assign @tngTUDOR as reviewer

whedon commented 3 years ago

OK, @tngTUDOR is now a reviewer

csoneson commented 3 years ago

@whedon add @mfastudillo as reviewer

whedon commented 3 years ago

OK, @mfastudillo is now a reviewer

csoneson commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3392.