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Old 02-08-2019, 03:12 AM   #166
dzgarza
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Quote:
Originally Posted by DaltonST View Post
The Original Post, its attachments, and the ZMI plug-in's ToolTips contain the only up-to-date information that needs to be read. All old posts should be ignored as they often are deprecated or obsolete, add no value, and are a waste of time to peruse. To answer any questions you may have, simply download and carefully review the image attachments to the Original Post, then create a test Library, install ZMI, read the ToolTips (they are the documentation), and use it. It is all self-explanatory.


DaltonST
Thanks for the response!

I should have been more clear - I've already installed the plugin and have used it successfully, no real issues there.

The issue is that I noticed that my annotations to PDFs opened via Calibre were not appearing in when opening the corresponding Zotero entry imported via ZMI (and vice versa), and also that all of my references within Zotero seemed to break when my /tmp directory was cleaned.

I did follow most of the steps outlined in original post and tooltips, but it appears that it is still using the workaround of copying the entire library to "safe" names under /tmp and pointing to those files, instead of linking to the PDF in Calibre's library folder.

My question is mainly whether or not this is intentional, and if there is a workaround or fix that avoids this and links directly.
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Old 02-08-2019, 08:30 AM   #167
DaltonST
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Quote:
Originally Posted by dzgarza View Post
Thanks for the response!

I should have been more clear - I've already installed the plugin and have used it successfully, no real issues there.

The issue is that I noticed that my annotations to PDFs opened via Calibre were not appearing in when opening the corresponding Zotero entry imported via ZMI (and vice versa), and also that all of my references within Zotero seemed to break when my /tmp directory was cleaned.

I did follow most of the steps outlined in original post and tooltips, but it appears that it is still using the workaround of copying the entire library to "safe" names under /tmp and pointing to those files, instead of linking to the PDF in Calibre's library folder.

My question is mainly whether or not this is intentional, and if there is a workaround or fix that avoids this and links directly.

ZMI uses no "workaround". I do not know where you are getting that unless it is from some old, obsolete post from when ZMI was being first developed.

Zotero is Zotero, Calibre is Calibre, and they do not "link" to each other.

When exporting from Calibre, all of the PDFs are temporarily stored in a temp folder until you open Zotero and import them into Zotero. Then, you have the PDFs in both Zotero and Calibre, separately and independently. The temporary folder is just that: a temporary place to keep the PDFs in the middle of the whole process, and is purged later like any other "trash" would be in your OS.

When you open a PDF in Zotero that originally came from Calibre, Zotero uses the Zotero copy of the PDF that it put in your Zotero database's "storage" folder.

Likewise, when you export from Zotero and import your PDFs into Calibre, Calibre has a copy of the original Zotero PDF along with the Zotero metadata. When you open your PDF in Calibre, it uses only the PDF in the Calibre Library.

You should be using the "embed metadata" tool in Calibre to update the PDF's internal metadata before you export them and then import them into Zotero. Otherwise, when you open the PDF in Zotero, it will not have all of the internal PDF metadata otherwise available in Calibre's metadata.db because it was not first embedded from metadata.db into the .pdf book format prior to exporting.

To reiterate, a Calibre PDF uses only Calibre, and a Zotero PDF uses only Zotero, and they do not "link" to each other once the Zotero import of the RIS file has completed.


Attached is an image from the Original Post that shows what in Zotero came from Calibre. Everything shown in Zotero is entirely stored within Zotero. You could then delete your entire Calibre Library with no impact whatsoever on Zotero once it has finished importing the RIS file.


Added: ZMI was designed to be used with Zotero installed on the same computer system as Calibre. If you are using some "cloud" version of Zotero, then it will probably not work. I tested with Zotero using the latest version for Windows 10 as of the latest release 1.0.59 of ZMI in April 2018. My Zotero database and storage folder were on my SSD.


Added: You mentioned "annotations". If you use the "embed metadata" tool in Calibre, all metadata, including Comments and any Custom Columns containing anything, including "annotations", will be embedded. How the "annotations" got there in the first place (manually or via another plug-in) does not matter. Everything in metadata.db (what you see in the Calibre "Library View" of its GUI) gets embedded. I believe there is a ToolTip in ZMI that says to always "embed metadata" prior to exporting to Zotero. That is true whether you have "annotations" or not. Also, your ZMI configuration for mapping Calibre metadata to the RIS export file must include the source of "annotations" in Calibre that you want in Zotero. Refer to the ZMI RIS Configuration ToolTips and also the images attached to the Original Post.



DaltonST
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Last edited by DaltonST; 02-08-2019 at 01:00 PM. Reason: Comments about Zotero Cloud & "Annotations"
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