Show HN: Scholarref tools – never deal with journal webpages again | Hacker News Reader

Show HN: Scholarref tools – never deal with journal webpages again

adamsgaard.dk

127 pointsadmsg18 comments

> clicking the "Download PDF" link should redirect the user to an unusable in-browser PDF viewer

Pro tip: in Elsevier's case, middle-click the "Download PDF" link so it opens in a new tab. Briefly avoid switching to that tab until it does some redirects. Voilà, you get the actual PDF instead of the stupid viewer.

This looks like fantastic software btw, I wish more people would release their tools as old school POSIX-style shell scripts instead of asking for hundreds of MBs of dependencies or fancy electron GUIs.

Which browser are you using for the Elsevier trick? This doesn't work for me in Firefox.

Edit: Middle click doesn't work for me in Firefox, but opening in a new tab via the right-click menu does.

Very neat, when I was writing my thesis I used zotero and its firefox downloader plugin which was a heck of a lot better than dealing with the biography process manually but still fairly manual (then again, so is the process of finding references... I don't understand why, in 2019, people don't include a DOI in their references) but this seems better still. That said, this implementation in particular would not have worked well for me since, at least for the journals I frequent, availability on scihub is patchy and even for the journals which do have good coverage it takes a while for articles to show up. Zotero has connectors for those journals and the auto-downloader works pretty well until the journal rate limits you and requires a captcha for each download.

I'm a refugee from the late, lamented CiteULike.

I have tried to like zotero and mendeley, but neither of them grab me like C-U-L did.

Dinosaur that I am, I am currently using JabRef to maintain a BibTeX database, semi-manually.

Now I'm going to have to play around with the ScholarRef scripts to see if they replace/augment my current somewhat clunky method.

What have any other C-U-L refugees settled on?

I am also a CUL refugee who is using JabRef after trying Zotero. Would be interested to know if there are any other options.

This is great! I did something similar for myself that also renames the input pdf file based on metadata from CrossRef. Hopefully I can get around to contributing code to this project.

That’s a great idea. Please do contribute if you get around to it.

I’m pleased to see this as I have been working on some shell scripts for managing a collection of research PDFs myself. But I think the headline’s a little misleading. The scripts don’t do much more to help you avoid journal webpages than feed a DOI into Sci-Hub. If the material you’re collecting isn’t on Sci-Hub, or breaching the publisher’s copyright is likely to cause problems for you at work, then these tools aren’t useful.

I really love the idea of ditching reference managers. The utility of these three scripts (or something like them) really is demonstrated when on mobile.

RSS feeds, Twitter (or emails from colleagues) give me a raw list of papers to read. Using the url of whatever journal webpage as a basis it then gets converted to a doi by the Zotero translation server (hosted as a lambda on AWS). From there its the crossref API to generate a filename for the PDF, and then Elbakyan's resource to download the actual file (even though I'm usually on an academic network that has full access, the scihub api is cleaner). All this gets launched from the share sheet from the browser, and deposits files in a cloud drive.

A little bit off topic, but could anyone explain to me the actual utility of a reference manager if all your references have dois? I don't get what it provides over a folder of PDFs with annotations?

I use Zotero for references but keep the files in a separate organized directory structure, where the filenames match the citation key in Zotero. Each approach has its own advantages and disadvantages.

The largest advantage of the directories is speed. I don't need to wait for Zotero to launch, and Zotero has gotten much clunkier over the years. (I think they need to do an entire rewrite at this point.) I also have some bash aliases to, for example, open a PDF file I have in my reference folder given only the citation key.

Zotero is better for annotations, and other information associated with a citation. I make very heavy use of the related documents pane. I also often put citations in multiple folders in Zotero. That's a bit more complicated in the directories as I need to add links and then maintain the links. (I have a few shell scripts to help with the creation and maintenance of the links.)

Zotero also makes generating bibliographies in different formats easy. I normally use BibLaTeX format, but a journal I'm submitting some things to requires BibTeX. The conversion was dead simple in Zotero. If you manually curate your bibliography file then this would be a pain.

Also, I have many citations in Zotero where I don't have a copy of the document. Not all documents have DOIs, and not all documents have been digitized. I use Zotero extensively when visiting the library so I can keep track of which documents to scan.

> I use Zotero for references but keep the files in a separate organized directory structure, where the filenames match the citation key in Zotero. Each approach has its own advantages and disadvantages.

Why not install the Zotfile plugin [1]? You can configure it to do exactly that, and point it to a Dropbox folder to get better synchronisation between devices.

[1]: http://zotfile.com/

I wasn't aware of Zotfile. I'll take a look. Thanks. Hopefully it has some way to automatically associate with ~10,000 files...

Well, I do use Zotero for automating the bibliography making (including re-submitting a paper to another journal which uses a different citation style) and it's availability for MS Word and LO Writer users, which let's me send my manuscripts to my PI without a bigger hassle.

I'm trying to establish convention in our lab that bibliography generation is the last step before submission. It always ends up that the bibliography (ie field codes with ref info in Word) is the most fragile part of the document, and everyone that isn't the person that generated the bib is terrified of changing anything in it for fear of ruining the references.

It seems a lot more sane to use nicknames for references and then format references right at the end when you know it's not going to be edited any further. It still seems like it's an unsolved problem in the process.

Thanks, it looks really helpful. I made an AUR package here: https://aur.archlinux.org/packages/scholarref-git/

This looks useful but one thing I've found is that with papers with multiple meta-data sources, some sources are much better than others. That and chasing down references without DOI, probably leads me back to zotero pretty quickly.

Yes, I frequently encounter references which have no DOI and often aren't even online. A system which is based entirely around DOIs is going to be of limited utility to me.

FYI Elsevier doesn’t like people linking to Sci-Hub: https://boingboing.net/2019/08/02/publicsphere-v-elsevier.ht...

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