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Workflow for Papers3


Not sure how many Papers3 users there are here, but I found myself frustrated with the opaque nature of the new Papers library structure.


This workflow is designed to allow for quick searches within your existing Papers3 library. With this workflow, you can search for publications by title, author names, publication year, or keyword. The script filter returns a list of publications matching the entered query, which allows you to open the paper in the Papers3 reader window.


To search your Papers library, enter 'pp', followed by the query. The searches are keyword-based: e.g., any word entered into the text field will be searched for in the title, author names, or keywords of your library. The results are returned as titles with the year and shortened author lists (e.g. Griffin C. et al).


Pressing return will open the selected paper in Papers3; command+return will export the paper as a PDF (this requires that the folder be designated within the workflow).


There are also keyword-triggered actions in this workflow:


-expp: Exports the currently-selected publication in Papers3 (e.g., if you are currently reading a paper and trigger this action, the publication will be exported to the designated folder as a PDF- again, this requires that the folder be designated within the workflow).


-opp: Opens the current webpage in Papers3 (thanks to Vitor's bookmarklet workflow!); this is currently configured for Safari, but should work if you were to copy and paste the Chrome bookmarklet into the workflow (or, it may do so without any changes).


-mpp: Matches the currently-selected publication in Papers3, without replacement of metadata.


I hope you enjoy. Download here: https://app.box.com/s/nxyqwx2iib2imxa6jdu1



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I'm not a Papers3 user, but this seems like a great idea. I wrote the ZotQuery workflow and the BibQuery workflow, and I think that Alfred workflows are perfect for bibliography searching. I'm happy that you've now added Papers3 to the fold.

I know from my extended development of ZotQuery that these types of workflows can be a bit tricky. I'm not certain about your data structure on the backend (how Papers3 stores its information, how you read it, how you parse it), but I have been thinking about these issues with Zotero for a long time. If you are interested, you could check out my GitHub repo or shoot me some questions about speeding things up and adding more search features.

Anyways, sounds like a great workflow.


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Also, I've just tested it, and there is a bug. If you have an article with ' in the title, it will break the XML output. If you want to stay with AppleScript, you should really check out qWorkflow as a backend. This will ensure clean XML no matter what. Your current setup is highly susceptible to bugs.

Thank you for the insight, smarg19. Given that I am teaching myself to script as I go, I will definitely have a look at your workflows. I definitely appreciate your suggestions.

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Wow. This is timely.


Papers has almost always been a great application, and it's what I always used instead of Zotero (from Papers1 - 3). It's always been aesthetically pleasing and intuitive in ways that Zotero never was. And it integrates so nicely with its iOS companions.


Unfortunately, Papers3 seems to be lacking for in a couple of ways:


1: I've been fighting with it for the last 18 hours because it doesn't play well with the Yosemite Beta in that it keeps crashing on opening each fucking time. I would chalk that up to me using beta software, but at this point most other software has started playing nice with it, and it should be out, officially, in five days. So, I'm legitimately annoyed with developers who used to be pretty damn on top of things. (I needed a rant).


2: Whatever happened to its ability to search EBSCOhost and Project Muse? I mean, why do they keep taking these things out?


3: Everything was so much easier to merge in Papers2. They seem to have lost a lot of the great things from Papers2...


4: Scripting support is lacking. Well, it's there, and it's easy enough to add certain things to selected papers, but it's not easy to manipulate the DB the way that @smargh has figured out with Zotero, although it might be possible if you dig into the DB itself. It is a sqlite3 database (find it in Library.papers3/Database.papersdb). So you might be able to play with it that way.


But, part of what ZotQuery does so wonderfully well with Zotero isn't needed with Papers because it has the equivalent functionality of searching and inserting citations natively in a pseudo-alfred way.


The matching could be nice.


What I'd love to see this workflow be able to do is to help me clean and maintain the Papers3 library: batch matching from outside the application, batch merging, batch other things. I haven't put any thought into how this would work exactly...


The other possibility that could be great would be for it, somehow, to fit into a sort of workflow that would combine it with Pandoc so as to be able to write a dissertation in markdown that I can still send to my advisor in .docx format.

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You're probably right, Stephen. It should be able to insert the citekey. I think I got overly excited that someone else around here was using Papers3, especially after I had been fighting with it for so long (and submitted six bug reports just before I saw this thread).


@nosatellite: Papers 2 implemented an auto-citation thingie. It's in Papers 3 as well. It runs in the background and can be invoked by a hotkey. If you go into Papers' preferences, you can click on the "Citations" tab, and you'll see that you can activate a hotkey. When you use the hotkey, it'll pull up a little window for you to search. You have the option of using it to insert a Pandoc citekey, which is like a Bibtex citekey. In other words, it's just a unique identifier for the paper that other programs know how to use. Pandoc is an amazing utility that converts pretty much any document format to another document format, and it can turn citekeys in plaintext documents into footnotes in Word.

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I do like Papers3, but it just tries to do too much for my tastes. As you can tell from my Skimmer workflow, I really only want to use Skim for reading and annotating my PDFs. My biblio manager should be only that. Plus, I like Zotero's setup better. But I do agree, Papers3 looks infinitely better.

And, the Citations helper was my primary inspiration for ZotQuery's core functionality actually.

Edited by smarg19
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