katie

I don't need the fancy things - just importing citation information into BibDesk. @giovanni, you've made my day/week/year!!!! This is amazing; works for me. Thank you!!

Thanks, @vitor. I've just downloaded the Supercharged Citation Picker, but it's for inserting citations into writing - not adding citation information to a reference manager (BibDesk) so that it can then be cited. I'm doing it manually now; I just miss this workflow!

I've installed the workflow from @emraher in issue #17 (https://github.com/andrewning/alfred-workflows-scientific/issues/17#issuecomment-912063594). The debugger shows that the workflow is looking for python 2, which doesn't exist on my device - I'm on a institution-managed computer that has python 3, but I don't have the ability/permissions to install a previous version of python. I tried changing the workflow to call python 3, hoping it was an easy fix, but that did not work. Debugger output is here: [15:19:32.856] Reference Importer[Script Filter] Queuing argument 'l' [15:19:32.969] Reference Importer[Script Filter] Script with argv '(null)' finished [15:19:32.973] ERROR: Reference Importer[Script Filter] Code 1: Traceback (most recent call last): File "/Users/ejq413/Dropbox/Alfred/Alfred.alfredpreferences/workflows/user.workflow.6C06FC8C-1824-405B-9086-C3BDD31E925E/crossref.py", line 6, in <module> from workflow import Workflow File "/Users/ejq413/Dropbox/Alfred/Alfred.alfredpreferences/workflows/user.workflow.6C06FC8C-1824-405B-9086-C3BDD31E925E/workflow/__init__.py", line 16, in <module> from .workflow import Workflow, manager File "/Users/ejq413/Dropbox/Alfred/Alfred.alfredpreferences/workflows/user.workflow.6C06FC8C-1824-405B-9086-C3BDD31E925E/workflow/workflow.py", line 25, in <module> import cPickle ModuleNotFoundError: No module named 'cPickle' Any help would be appreciated! Katie

That must be it. I've run it, and I will be sure to give it some time!

I downloaded 2.0.1 and it seems to work, but the emoji icons don't appear in Alfred - just the emoji names.

@xilopaint I can help with testing - but only as a user with pdfs to manage, not an expert in programming.

Wow, thank you. I can't believe you found it! I will start looking through Rob Trew's posts on all of those platforms. Thank you, also, for the advice. I will pursue the AppleScript path. In fact, I think I should regardless of whether I find a working script for this so that I won't be so stuck again in the future if something breaks. I don't use TeX at all, either. I just love how quick, accessible, and open BibDesk is. My goal is to move everything to plain text, stored in my university-provided cloud, and indexed/processed in DT. I couldn't find a suitable alternative for DT; it's just so good at what it does. At least it's easy to keep your files where they are or get them out, if necessary.

Thank you for the working script for exporting to markdown, @dfay. I'm wondering how difficult it would be to change this script for my own workflow. My goal is the following: Export into separate markdown files for each annotation. Ideally, these would be named automatically, for e.g., using the first 5 words of the contents, and placed in a folder named by the pdf name. Include the name of the colour of the highlight from Skim in each file (so it can be used to filter/process them). Edit: ✓ I couldn't figure out how to capture and name colours, but, I've managed the important part of indicating the colour of the highlight. As a plus, it should work with any used colour, not just set values. Include the link back to the PDF in each file. I know it was mentioned that this could be done by adding back in that functionality, but I could not figure this out. This one is just a perk though. Edit: ✓ Essentially, I am in this situation because my original workflow relied on a script that did exactly this. It would take a Skim pdf, export all annotations as separate files to DevonThink (but to .rtf, not markdown). I cannot find it anywhere - all links to it are broken (e.g. https://wippp.com/home/writing-workflows-processing-annotations-all-roads-lead-to-skim). My workflow was based around the idea the zettelkasten information management - so preparing little chunks of information that can be further processed and filtered and summarized, etc. From what I can tell, this could potentially be accomplished in two ways: (1) starting with this script for exporting to markdown, but instead parsing the clipboard to create different files and adding colour information (2) using a Skim export template, which can apparently identify colour (https://sourceforge.net/p/skim-app/feature-requests/1417/) and include a link to specific annotations in the pdf (https://sourceforge.net/p/skim-app/feature-requests/1520/). I found a template that exports to markdown (https://github.com/semicolonsnet/skim-templates), but I'm really new to this and couldn't get it to function. It's not clear to me whether separate files can be created. For those of you who are experts in coding - would you be familiar enough with this to know which approach (applescript or template) I should attempt? And how future-proof would it be? I'm kicking myself for getting used to this workflow. Once it broke, I procrastinated on trying to fix it and now I have a bunch of read pdf's that are just stuck. I'm not sure if I should give up on this entirely and just figure out a new academic workflow. I'm definitely not expecting or asking anyone to do this for me. I'm just hoping that someone might have an opinion on which approach would be more sustainable and a worthwhile use of my time to pursue. Or if there's another simpler approach that would work best. I've also found that it is surprisingly difficult to try to change my method of reading/highlighting, so I'm open to hearing about other people's academic workflows! Thank you for reading! Katie Edit: I forgot to mention that I found a similar script (https://github.com/achamess/skim_to_md_script) but it relies on the user having Papers3.app and I use BibDesk. Update (2021-01-09): You can add a link back to the specific page in Skim, by adding the following in the appropriate sections of the script: set tURL to "<$skimURL?><$skimURL/></$skimURL?>" -- not sure if only the middle tag is necessary but it works like this set skimURL to format n using template tURL -- convert template text to actual url -- Then add " [" & correctedPage & "](" & skimURL & ")" to format as a markdown link under each type of supported highlight Update (2021-03-06 ): You can add the colour of the highlight, by adding the following in the appropriate sections of the script: set tColour to "<$color.hexString?><$color.hexString/></$color.hexString?>" -- then add this to the export part: set noteString to noteString & "> " & "<mark style=\"background-color: " & noteColour & "\">" & formattedNote & "</mark>" & " (p. [" & correctedPage & "](" & skimURL & "))" & LF & LF

Thank you; I will try that! Just spent a good chunk of time doing this manually. Edit: And it works! I must have missed an update. This is literally the best day ever.

I really miss this workflow. Has anyone been able to find a workaround or alternative solution?

It's amazing!! Works great!! Thank you so much!!

Hello, I just found out that this workflow doesn't work if you use brackets () in the filename. I get this error in debug mode: [2017-01-30 12:59:29][ERROR: action.script] 15:16: syntax error: Expected “"” but found unknown token. (-2741) It's definitely a minor issue, and not necessary. But if somebody knows what's going on, I'd like to fix it if I can. Thanks

Hi @robwalton! Thanks for getting back to me. I have tried the 'uo <search term>' option and it works - as long as Ulysses is already open. If Ulysses isn't open, then I get two "something went wrong beeps" (as I call them), and Ulysses opens but the open dialogue doesn't. Because of this, I deactivated that keyword because a lot of times I don't want to open Ulysses, especially if it doesn't have what I'm looking for. I guess my computer is slow enough that waiting for a program (even one as light as Ulysses) to open so I can re-do a search, and (potentially) close it, is frustrating. I only use the 'us' and 'ug' keywords! I have a pretty formalized grouping system that 'ug' works great with and I can drill down to the group I need (amazing job on this). The downside of my system, as I mentioned, is that many sheet names are pretty useless or I don't really remember them (e.g. a sheet named "syllabus" in every course admin group). This is why a content search is so appealing to me - so I can check if something is in Ulysses before opening it up (and head right to the sheet, e.g. psy311) or make sure I've made a note of something without opening up Ulysses. And some sheet names are useful. What I'm trying to say is that I think there's a clear distinction between group and sheet searches (at least for me) so I think a new keyword 'uf' would be the best idea (and not to mix in sheet searches with groups as a 'u' search). If it's possible. And if you think it would be useful, too. As it is, I'm really happy with the workflow just so I can open the groups I need! It's what was missing for me to make the most of Ulysses (I used to use nvalt and there are some great workflows for it). Thank you for expending time and effort to build it!

I love this workflow! I've been waiting for something like this! Would it be possible to include a search of the contents of sheets (like ⌘O in Ulysses)? I don't always remember the title of my sheets

I will admit to scanning documentation and being herded effectively by big scary warnings