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[PRE REVIEW]: Translational Informatics Management System (TIMS): Towards OMICS based clinical data management for long term curation of clinical studies #1512

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @absd@bii.a-star.edu.sg (Wing-Cheong Wong) Repository: https://github.com/bii-absd/tims Version: v1.0 Editor: @csoneson Reviewers: @rabdill, @andreysmelter

Author instructions

Thanks for submitting your paper to JOSS @absd@bii.a-star.edu.sg. The JOSS editor @lpantano, will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@absd@bii.a-star.edu.sg if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lpantano it looks like you're currently assigned as the editor for this paper :tada:

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

@whedon commands

What happens now?

This submission is currently in a pre-review state which means we are waiting for the assigned editor (@lpantano) to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1512 with the following error:

Error reading bibliography ./TIMSpaper.bib (line 10, column 20): 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

danielskatz commented 5 years ago

👋 @lpantano - The author suggested you as the editor - Are you able to do this? Or can someone else from the bioinformatics team (@mgymrek, @brainstorm, @csoneson)?

danielskatz commented 5 years ago

👋 @absd@bii.a-star.edu.sg - there's a problem with your .bib file line 10, now volume = 36(4):336-353, should be

volume = {36},
number={4},
pages={336--353},

you will need to make similar changes for other entries.

Once you have made these changes, enter @whedon generate pdf as a new comment in this issue, and whedon will try to generate the pdf again.

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1512 with the following error:

Error reading bibliography ./TIMSpaper.bib (line 28, column 9): unexpected "p" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

Dear Editor, The pdf article seems alright in general except for the missing captions from the figure. I have referred to the pandoc references and made several attempts to fix it but to no avail. Can you kindly advise? Many thanks

danielskatz commented 5 years ago

I've made a bunch of suggested edits, including attempts to fix the caption issue, in https://github.com/bii-absd/tims/pull/1

lpantano commented 5 years ago

sorry, I don't think I can take this one right now.

danielskatz commented 5 years ago

👋 bioinformatics editors (@mgymrek, @brainstorm, @csoneson) - Can someone else besides @lpantano edit this submission?

danielskatz commented 5 years ago

@whedon unset editor

danielskatz commented 5 years ago

@arfon - I feel like this should have worked, but don't think it did ... Maybe an addition for @whedon?

arfon commented 5 years ago

@arfon - I feel like this should have worked, but don't think it did ...

Yeah, Whedon doesn't know how to do this. It can only replace an editor with another one...

danielskatz commented 5 years ago

Can we teach Whedon this new trick?

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@danielskatz - Greatly appreciate your fixes. The generated pdf looks good.

danielskatz commented 5 years ago

@bii-absd - there are clearly still some problems with the fact that the figure numbers are automatically generated, and the text references to them do not match, but this should be easy for you to fix by changing the text mentions to match the autogenerated names/numbers.

danielskatz commented 5 years ago

👋 bioinformatics editors (@mgymrek, @brainstorm, @csoneson) - Can someone else besides @lpantano edit this submission?

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

bii-absd commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

csoneson commented 5 years ago

👋 bioinformatics editors (@mgymrek, @brainstorm, @csoneson) - Can someone else besides @lpantano edit this submission?

I can do it.