Tag: PDF

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Cleaning up Zotero’s “The attached file could not be found at the following path”

After an upgrade to one of the machines linked to my Zotero account, I got errors that some of the attached filed could not be found. Now, I attach most of my files, so I was pretty sure that the files were there. I also double-checked that the base directory was set correctly, and that it was set to relative paths (moreover, only some of the attached PDF were affected, so I knew that the basic setup was OK).

Using Zutilo (a plugin for Zotero), I could figure out that the problem of those attached files was that an absolute path was set. In fact, on the Windows machine (i.e. the machine that was upgraded and where Zotero was set up afresh), I could simply choose to select the file again to resolve the issue, but there were more than a handful of attachments involved.

So I used the Zotero Storage Scanner (another plugin for Zotero). I was useful to read the instructions, as the scanner plugin has no GUI and works in the background to tag broken attachments. On my machine, I got around 1 entry tagged per second, so adjust your expectations accordingly.

Because the scanner plugin tags the attachments/PDF and not the articles, I then created a new collection in Zotero. Selecting the #broken_attachments tag, pressing minus (to collapse all items), I then added all the items to that collection. This way, I was sure to select the entries for the next step.

Selecting all articles with broken attachments, enter Zutilo for the second time. This time, I needed to “Modify attachment paths”. There are two boxes, one after the other. So in the first one, I entered that part of the absolute path, that wasn’t needed (I copied this from Zutilo’s “show attachment paths”), like “D:\ZoteroPDF\” (without quotes). In the second one, I added “attachments:” (without quotes, but including the colon). On my machine, this took around 3 seconds for 2k items.

Because I did the fixes on the GNU/Linux machine (this will also apply to Mac), I used Zutilo once again to modify attachment paths: In the first box, I entered the backslash (“\” without quotes), and made sure to tick “change all instances”, and then in the second box I entered the forward slash (“/” without quotes).

Getting everything synced on the Zotero servers took a while, but all my attachments work again as they should.

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Dear journals…

…can we please universally start accepting tables and figures as part of the manuscript during review (i.e., not at the end)? It’s a pain to either scroll up and down, or open a second instance of the PDF just so that I can actually understand what I’m reading. Yes, I understand that there are historical reasons for this, and it facilitates production, but at the time of writing and reviewing, we have different concerns (plus: production gets paid, I don’t). Journals have managed to move from printed copies to digital copies of the manuscript, so there is no reason we cannot do the next step…

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Zotero!

If you aren’t, you should be using Zotero. It amazes me to see researchers ‘managing’ their references manually these days. It’s complicated, takes time, is prone to errors, and simply unnecessary. There are many options out there to manage your references, but you should look at the free and open Zotero. You can install it on all your devices, you’re not limited in the number of citations you can use, you can take it with you when you change workplace, and in fact you’re not even restricted to the feature of Zotero because you can use plugins. Seamless integration in word processors isn’t going to stand out from the competition, but getting stuff into Zotero takes no effort at all — it’s unparalleled easy with just one click in your web browser. You get free syncing, too. There really is no reason not to keep notes of what you are reading.

After grabbing Zotero, you probably want Zotfile, too. Zotfile manages your PDF versions of research articles. In my view, the most useful feature is the ability to extract highlighted text from the PDF. It’s so practical that I sometimes even don’t take proper notes (for the main points, you should store them in your brain anyway).

Image credit: Zotero, Zotfile

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Zotero and Zotfile

Apparently there are still researchers out there (no, I won’t name you) who have not heard of Zotero and Zotfile. Zotfile takes Zotero to another level by managing PDF files, including the ability to extract highlights and comments from PDF files. Try them.

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Use MS Word to Convert PDF Files

Recently we had to convert a PDF file to MS Word so that we could benefit from the Track Changes feature in MS Word. The proofreader did not want to use the commenting tools in Adobe/Acrobat because he found them inefficient to propose changes in the text. (Yes, he could make direct changes, but it takes much more time.) We had a LaTeX source file and faced the common challenge of turning this into a Word file. I remembered that Adobe/Acrobat can export PDF to Word files, but as I have experienced many times, the output did not satisfy me at all. I also tried pandoc, but it turned out that we used bits of LaTeX pandoc cannot (yet) handle. When checking the output, I discovered that Word can open PDF files. We quite liked the output and had to tidy up only a few bits and pieces to have an acceptable Word file.

We could have avoided this challenge by using markdown and pandoc to start with… my usual approach these days.