lutefish

Glad you got it working - I rely on this workflow, and have seen so many people generously give their time and expertise to keep it working.

Have you installed better bibtex for Zotero? https://retorque.re/zotero-better-bibtex/installation/index.html

(never mind - reinstalling was required for all workflows, to sort out an exciting variety of permissions issues.)

Hello! I've moved to a new computer, and as I get everything migrated over, a small hiccup. (Well, some big hiccups as Box.com moved everything around, but that's a different question) Zothero works, broadly (it loads the database, searches it, and can open files and open items in Zotero). But, when I go to copy citations,I'm encountering a permissions error. Looking at the log file, the text is all there from Zotero, but it's failing to copy. 8:22:05 workflow.py:2114 ERROR [Errno 13] Permission denied: '/Users/USERNAME/Library/CloudStorage/Box-Box/AlfredSync/Alfred.alfredpreferences/workflows/user.workflow.3181B68E-1DF7-497C-B4A8-A4EF8190FFA8/lib/cite/cite' Traceback (most recent call last): File "/Users/USERNAME/Library/CloudStorage/Box-Box/AlfredSync/Alfred.alfredpreferences/workflows/user.workflow.3181B68E-1DF7-497C-B4A8-A4EF8190FFA8/lib/workflow/workflow.py", line 2107, in run func(self) Any thoughts? I've checked and Alfred has Automation, Accessibility, and Full Disk access. Thanks.

In case anyone is using this, the workflow needs updating to work with the Hook -> Hookmark rebranding. Editing the script filter in the workflow and changing to fixes it.

FYI, this stopped working (again) after updating to Mac OS 13. Looking at the debugger gave the following error: Code 1: xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Re-loading the Command Line Developer Tools (terminal, xcode-select --install) fixed the issue.

OK, that was helpful to know. Thanks. Using the "save to Obsidian" option at least let me specify a finder destination, which resolved the write error which was stopping the workflow. I had tried posting on GitHub, but the issue was closed there, with the dev saying "use the bug report form", which I had thought was here. All good - thanks, as always, for the assistance.

Trying to get this up and working - have installed homebrew and pdfannots2json, re-exported a Zotero library via BetterBibTex, and am getting a mkdir error after choosing a PDF and pasting in the citekey manually. I'm not sure quite where the read-only directory is becomming an issue. My Zotero library is stored locally, but as "linked" files, not in the Zotero file structure. Running: Alfred 5.0.3 PDF Annotation Extractor 7.0.6 MacOS 12.6 pdfannots2json version 1.0.12 Thanks. Trying to get this up and working - have installed homebrew and pdfannots2json, re-exported a Zotero library via BetterBibTex, and am getting a mkdir error after choosing a PDF and pasting in the citekey manually. I'm not sure quite where the read-only directory is becomming an issue. My Zotero library is stored locally, but as "linked" files, not in the Zotero file structure. [12:04:17.409] Logging Started... [12:04:21.628] PDF Annotation Extractor[File Filter] Processing complete [12:04:21.630] PDF Annotation Extractor[File Filter] Passing output '/Users/REDACTED/Box Sync/2022/Garnett - 2020 - The Preservation of the Sources for English Mediev.pdf' to Arg and Vars [12:04:21.631] PDF Annotation Extractor[Arg and Vars] Processing complete [12:04:21.632] PDF Annotation Extractor[Arg and Vars] Passing output '/Users/REDACTED/Box Sync/2022/Garnett - 2020 - The Preservation of the Sources for English Mediev.pdf' to Conditional [12:04:21.632] PDF Annotation Extractor[Conditional] Processing complete [12:04:21.633] PDF Annotation Extractor[Conditional] Passing output '/Users/REDACTED/Box Sync/2022/Garnett - 2020 - The Preservation of the Sources for English Mediev.pdf' to Arg and Vars [12:04:21.633] PDF Annotation Extractor[Arg and Vars] Processing complete [12:04:21.634] PDF Annotation Extractor[Arg and Vars] Passing output '' to Keyword [12:04:24.625] PDF Annotation Extractor[Keyword] Processing complete [12:04:24.626] PDF Annotation Extractor[Keyword] Passing output 'garnettPreservationSourcesEnglish2020' to Replace [12:04:24.630] PDF Annotation Extractor[Replace] Processing complete [12:04:24.631] PDF Annotation Extractor[Replace] Passing output 'garnettPreservationSourcesEnglish2020' to Arg and Vars [12:04:24.631] PDF Annotation Extractor[Arg and Vars] Processing complete [12:04:24.632] PDF Annotation Extractor[Arg and Vars] Passing output '/Users/matthew/Box Sync/2022/Garnett - 2020 - The Preservation of the Sources for English Mediev.pdf' to Run Script [12:04:24.888] PDF Annotation Extractor[Run Script] Processing complete [12:04:24.889] PDF Annotation Extractor[Run Script] Passing output '286;;The Preservation of the Sources for English Medieval History in the Sixteenth Century;;;;Garnett, George;;2020;;inbook;;https://doi.org/10.1093/oso/9780198726166.003.0009 ' to Conditional [12:04:24.890] PDF Annotation Extractor[Conditional] Processing complete [12:04:24.890] PDF Annotation Extractor[Conditional] Passing output '286;;The Preservation of the Sources for English Medieval History in the Sixteenth Century;;;;Garnett, George;;2020;;inbook;;https://doi.org/10.1093/oso/9780198726166.003.0009 ' to Split Arg [12:04:24.891] PDF Annotation Extractor[Split Arg] Processing complete [12:04:24.891] PDF Annotation Extractor[Split Arg] Passing output '286;;The Preservation of the Sources for English Medieval History in the Sixteenth Century;;;;Garnett, George;;2020;;inbook;;https://doi.org/10.1093/oso/9780198726166.003.0009 ' to Arg and Vars [12:04:24.892] PDF Annotation Extractor[Arg and Vars] Processing complete [12:04:24.892] PDF Annotation Extractor[Arg and Vars] Passing output '286' to Conditional [12:04:24.893] PDF Annotation Extractor[Conditional] Processing complete [12:04:24.893] PDF Annotation Extractor[Conditional] Passing output '286' to Arg and Vars [12:04:24.894] PDF Annotation Extractor[Arg and Vars] Processing complete [12:04:24.894] PDF Annotation Extractor[Arg and Vars] Passing output '286' to Post Notification [12:04:24.895] PDF Annotation Extractor Processing complete [12:04:24.895] PDF Annotation Extractor Passing output '286' to Hide Alfred [12:04:24.909] PDF Annotation Extractor[Arg and Vars] Passing output '286' to Run Script [12:04:24.910] ERROR: PDF Annotation Extractor[Run Script] mkdir: /attachments: Read-only file system [12:04:24.910] PDF Annotation Extractor[Run Script] Processing complete [12:04:24.911] PDF Annotation Extractor[Run Script] Passing output '' to Conditional [12:04:24.911] PDF Annotation Extractor[Conditional] Processing complete [12:04:24.912] PDF Annotation Extractor[Conditional] Passing output '' to Post Notification [12:04:24.913] PDF Annotation Extractor Processing complete [12:04:24.913] PDF Annotation Extractor Passing output '' to Play Sound

Odd. It's working for me with 5.0 GM1

@iandol - thanks for drawing attention to that workflow. A quick tinker with it wasn't working for me (I don't actively use Bibtex, even though I've installed the Zotero/Bibtex plugin, so even configuring the workflow to point to my base Zotero directory wasn't finding my library), but I'll definitely keep an eye on it. On the other hand, this Zotero workflow has started working again, after i changed the Zotero export type back to BetterBibText (I had changed it to a particular style when the workflow stopped working, but changing it back to BBT seems to have resolved the error I was seeing).

I'm suddenly getting a new error that precludes all use (with Alfred 5, so perhaps I should post it over there?) "NoneType object is not subscriptable" Let me know if you need more to figure out what's changed.

I manually downloaded them.

Cheers - deleting/reinstalling resolved the issue. I'm not sure why updating it (two versions ago) introduced the error, but no worries. Thank you so much for your work on this workflow.

@Giovanni - The last two versions have given me errors, but the version before that worked. Not sure where things are going wrong - seeing this in the logs: 10:51:42 workflow.py:2114 ERROR UNIQUE constraint failed: data.id Traceback (most recent call last): File "lib/workflow/workflow.py", line 2107, in run func(self) File "zh.py", line 754, in main return do_search(query) File "zh.py", line 135, in do_search if app.stale and not running: File "lib/zothero/core.py", line 159, in stale if self.index.empty: File "lib/zothero/core.py", line 152, in index self._index.update(self.zotero) File "lib/zothero/index.py", line 277, in update if not self._update(zot, force): File "lib/zothero/index.py", line 405, in _update c.execute('INSERT INTO data VALUES (?, ?)', sqlite3.IntegrityError: UNIQUE constraint failed: data.id 10:51:42 workflow.py:2116

First I got a "database locked" error, so I closed Zotero. Now I'm getting a "name 'unicode' is not defined" error. 16:07:51 workflow.py:2114 ERROR name 'unicode' is not defined Traceback (most recent call last): File "lib/workflow/workflow.py", line 2107, in run func(self) File "zh.py", line 721, in main return do_search(query) File "zh.py", line 131, in do_search if app.stale and not running: File "lib/zothero/core.py", line 159, in stale if self.index.empty: File "lib/zothero/core.py", line 152, in index self._index.update(self.zotero) File "lib/zothero/index.py", line 277, in update if not self._update(zot, force): File "lib/zothero/index.py", line 325, in _update for e in it: File "lib/zothero/zotero.py", line 268, in all_entries yield self._load_entry(row) File "lib/zothero/zotero.py", line 320, in _load_entry e.citekey = self.bbt.citekey('{}_{}'.format(e.library, e.key)) File "lib/zothero/zotero.py", line 195, in bbt self._bbt = BetterBibTex(self.datadir) File "lib/zothero/betterbibtex.py", line 50, in __init__ self._refkeys = { File "lib/zothero/betterbibtex.py", line 51, in <dictcomp> unicode(ck['libraryID']) + '_' + ck['itemKey']: ck['citekey'] NameError: name 'unicode' is not defined 16:07:51 workflow.py:2116 INFO for assistance, see: https://github.com/deanishe/zothero/issues 16:07:51 workflow.py:2136 DEBUG ---------- finished in 0.185s ---------- [16:07:51.785] ZotHero[Script Filter] { "items": [