Upgrade StorageZotero file management and storage
Hello,
been using Zotero for years now and always refrained from using Zotero for saving pdfs and syncing full text due to the storage limits and other personal preferences.
I have recently decided to reconsider my position and read a few guidelines and posts here. Yet I have a number of questions I would like to ask:
1) I use one folder for storing all my documents (mostly pdfs), which I manually rename as author year title. I would like to keep this folder as main storage for my files. Is this possible without moving all the Zotero settings into the folder?
2) I would now like to start attaching pdf to Zotero for note-taking and more efficient workflow. However:
2a) I do not want to save all pdf for items saved in Zotero. I routinely save in Zotero papers I have just quickly skimmed or just read the abstract just for future searches and tags. I would normally not need these pdfs. Is there a way to avoid attaching all pdfs? It looks the only option is to manually attach the file or the link to file, correct?
2b) I would like the pdfs I decide to download to be stored in my main folder under 1) and not in the Zotero hard-to-read folder. Should I set my main folder as as "Data Directory Location" for Zotero? Would this create additional folders and move all the Zotero settings into the main folder? Is there a way just to move the storage folders while keeping the setting-files in the User/Zotero folder? Is it possible only through the link to file option? Currently, with Zotfile, I download the pdf on, say, the desktop, attach it to a Zotero item, clic on the pop up and have Zotfile rename and move it to the main folder under 1) as a link. It looks quite efficient, but I was just wondering whether there is a better way to go?
2c) I would like to use Zotero in-build pdf reader/notes for more efficient reading. Is there a way to have highlights/notes/comments added in the pdf integrated in the pdf in the folder (i.e. available if you open the pdf with any reader such as acrobat reader)? The only way I found was to "Save as" in Zotero. Again, sounds quite efficient (not sure I want my notes permanently in the pdf) but maybe there is a better way to go.
Thanks for any suggestion and feedback.
been using Zotero for years now and always refrained from using Zotero for saving pdfs and syncing full text due to the storage limits and other personal preferences.
I have recently decided to reconsider my position and read a few guidelines and posts here. Yet I have a number of questions I would like to ask:
1) I use one folder for storing all my documents (mostly pdfs), which I manually rename as author year title. I would like to keep this folder as main storage for my files. Is this possible without moving all the Zotero settings into the folder?
2) I would now like to start attaching pdf to Zotero for note-taking and more efficient workflow. However:
2a) I do not want to save all pdf for items saved in Zotero. I routinely save in Zotero papers I have just quickly skimmed or just read the abstract just for future searches and tags. I would normally not need these pdfs. Is there a way to avoid attaching all pdfs? It looks the only option is to manually attach the file or the link to file, correct?
2b) I would like the pdfs I decide to download to be stored in my main folder under 1) and not in the Zotero hard-to-read folder. Should I set my main folder as as "Data Directory Location" for Zotero? Would this create additional folders and move all the Zotero settings into the main folder? Is there a way just to move the storage folders while keeping the setting-files in the User/Zotero folder? Is it possible only through the link to file option? Currently, with Zotfile, I download the pdf on, say, the desktop, attach it to a Zotero item, clic on the pop up and have Zotfile rename and move it to the main folder under 1) as a link. It looks quite efficient, but I was just wondering whether there is a better way to go?
2c) I would like to use Zotero in-build pdf reader/notes for more efficient reading. Is there a way to have highlights/notes/comments added in the pdf integrated in the pdf in the folder (i.e. available if you open the pdf with any reader such as acrobat reader)? The only way I found was to "Save as" in Zotero. Again, sounds quite efficient (not sure I want my notes permanently in the pdf) but maybe there is a better way to go.
Thanks for any suggestion and feedback.
If having all your files stored in a single, 'physical' folder is a non-negotiable feature, Zotero storage is not for you. You can set up a saved search/virtual folder for PDFs in Zotero storage to mirror that effect (i.e. show all PDFs from within Zotero storage in said virtual folder), but if that's not sufficient for you, using Zotero's "store file" won't work for you.
Also, you should absolutely not move your data directory into any folder you're using otherwise. That will not help with anything -- it will just add the various setting files as well as the storage folder and alphanumeric subfolders into an already existing folder with files, causing nothing but chaos.
2) You can use notes/annotations on linked files, so no need to store files for that
2a) You can either turn off automatic PDF attachment (and then download & attach files individually) or turn it on (and then delete attached PDFs) but you can't toggle this for individual imports, no.
2b) For the first part, see above. ZotFile is the way to go, but not that with what should normally be the standard way of adding items to Zotero, i.e. via the web connector, ZotFile will automatically move files into the specified custom folder. It's only when you save the PDF directly -- either from your file system or the browser -- and rely on Zotero's retrieve metadata that you then need to manually trigger ZotFile's rename&move. That's just a limitation of ZotFile: I suspect it could be addressed if the tool was more actively developed.
2c) No. See https://www.zotero.org/support/kb/annotations_in_database for details on this. Zotero's annotations allow for easy bulk export to PDF annotations to avoid lock in, but the reader is not designed to be used simultaneously with other PDF readers. It's either/or for any reasonably efficient workflow.
Regarding 1) (the main folder approach) this is non negotiable at least for the costs of transitioning from a one-classic-folder to Zotero storage. Is there any way to automate the process? If not, I do not think I have time to manually migrate about 4000 files ...
Now I get that the data directory should not be moved (and see reasons for this).
2a) ok thanks. I can probably turn it off and download & attach manually.
2b) not sure I understand ZotFile's limitation. I have made some trials: after I have captured the item through web-connector, manually downloaded the pdf, I attach the pdf as a link file. Zot file asks me (or I can access the option in a menu) whether I want to rename & move the file. This works smoothly and the final result is quite efficient: correctly renamed files are quickly moved to the main folder and linked to the Zotero item. No need to use Z's retrieve metadata from pdf...
2c) All clear here, thanks. The link is very useful. I can easily keep annotations and notes within Zotero and the pdf file clean. If needed the annotated pdf can be saved as or exported.
Thanks again
Any thoughts on point 1) above, especially on whether "Is there any way to automate the process? If not, I do not think I have time to manually migrate about 4000 files ..."
If so, Tools (in the top menu) --> Manage Attachments --> Convert Linked Files to Stored Files can be run in batch. If you go this way, I'd suggest moving slowly at the beginning -- i.e. move ~20 PDFs first to make sure stored files are working the way you want to, then move 100-200 to make sure the process works smoothly, then do the rest in a couple of large batches.
You could add them all to Zotero, let it retrieve metadata as best as possible, and then use the Duplicate Items view to merge the items with the existing ones, but merging currently has to be done one at a time, so it'd be a bit tedious with that many items. In a future update it will be possible to merge all duplicates, so it might be worth revisiting at that point.
We could also consider having Zotero automatically attach an added PDF to an existing item if it detects the same identifier (DOI, ISBN, etc.), instead of retrieving metadata and creating a new item. It's never worked that way, but as much as we encourage saving via the Connector, it's fairly common for people to add metadata some way (Add by Identifier, RIS/BibTeX import, etc.) and then later seek out the PDF and add it, and ending up with a duplicate item at that point is kind of dumb. We'd need to have a way to undo that and create a new item based on the metadata, similar to the Undo Retrieve Metadata option we already have after metadata retrieval runs.
(Of course, either way, any PDFs that couldn't be recognized would just remain as separate standalone attachments, so how useful these would be for you would depend on the files.)