zotfile can't move over 200 pdfs to custom file

sky_myl

Hi all,

I'm trying to move my whole library (over 2000 PDFs) using zotfile to the onedrive sync folder. However, I just found each time, if i selected over 200 pdfs (a rough number, not exactly), then the zotfile moving-renaming process will not responding after a short while and those file i selected can't be moved completely. (I guess it stops moving after not responding)

Previously, i didn't move the file but only rename the pdf, the function worked well for the whole library. this problem only appears after i tried to move it to custom file

Hope to get your reply. Thanks!

D1780910880

sky_myl

Also, I used terminal to monitor this process, it showed multiple output like this:
Crash Annotation GraphicsCriticalError: |[0][GFX1-]: Failed to allocate a surface due to invalid size (CDT) Size(510,32787) (t=55.7298) |.......

dstillman

[JavaScript Error: "this is undefined" {file: "resource://gre/modules/osfile/osfile_shared_allthreads.jsm" line: 1262}]

I can't help with ZotFile itself, but it's quite likely a problem with a specific file (filename or path), not the number of files. You should be able to narrow down the list to find the item in question and reproduce it with that item. You can open the Error Console from Tools → Developer to see when the above error appears.

Based on the debug output, I'd guess that it's the item that's select when you run either ZoteroPane.selectItem(19603) or ZoteroPane.selectItem(19604) in Tools → Developer → Run JavaScript.

sky_myl

Hi dstillman,

Thanks for your kind reply! I followed your instructions and i found the single file after Item(19603) that can't be processed by zotfile. But everything looks normal for the file, I have no clue what is wrong.

And I just found a new problem: There're multiple items having this issue, which will interrupt Zotfile relocate process. I'm wondering is there any solution to search through the whole library for the PDF files that are not linked yet? So I can deal with them manually.

Thanks!

this is the debug ID for new items having similar issue: D2101504104

sky_myl

To figure out the problem, I deleted the PDF inside item, and use "find avail PDF" getting a new pdf. Zotfile still can't rename this freshly new PDF.

But after I moving this PDF outside the item and retrieve the metadata to create a new item from it, Zotfile works well with this new item!

So it seems the problem lies in the item itself

dstillman

Yes, it's likely the metadata being used to rename the file.

What's the output of Zotero.Items.get(19603)?

(You can email to support@zotero.org with a link to this thread if you don't want to post it publicly.)

sky_myl

{
"key": "FE4CWEA5",
"version": 1773,
"itemType": "attachment",
"title": "2010_Effects of cleavable PEG-cholesterol derivatives on the accelerated blood clearance of PEGylated liposomes_Biomaterials_Xu et al.pdf",
"parentItem": "GJ8JBVXH",
"linkMode": "linked_file",
"contentType": "application/pdf",
"charset": "",
"path": "attachments:2010_Effects of cleavable PEG-cholesterol derivatives on the accelerated blood clearance of PEGylated liposomes_Biomaterials_Xu et al.pdf",
"note": "<p xmlns=\"http://www.w3.org/1999/xhtml\"; id=\"title\"><strong>Contents</strong></p><ul xmlns=\"http://www.w3.org/1999/xhtml\"; style=\"list-style-type: none; padding-left:0px\" id=\"toc\"><li><a href=\"zotero://open-pdf/0_FE4CWEA5/1\">Introduction</a></li><li style=\"padding-top:8px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/2\">Materials and methods</a><ul style=\"list-style-type: none; padding-left:12px\"><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/2\">Materials</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/2\">Animal</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/2\">Preparation of vesicles and liposomes</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/2\">Pharmacokinetics and tissue distribution of calcein loaded liposomes or vesicles in vivo</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/2\">Analytical procedure</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/3\">Statistical analysis</a></li></ul></li><li style=\"padding-top:8px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/3\">Results</a><ul style=\"list-style-type: none; padding-left:12px\"><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/3\">The characteristics of liposome/vesicles</a></li><li style=\"padding-top:8px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/3\">Effect of repeated injections on biodistribution and pharmacokinetics of PEGylated liposomes/vesicles</a><ul style=\"list-style-type: none; padding-left:24px\"><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/3\">Blood clearance and biodistribution of PEG-lipid modified liposomes in rats after the first and second injections</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/3\">Blood clearance and biodistribution of PEG-lipid modified vesicles in rat after the first and the second injection</a></li></ul></li></ul></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/5\">Discussion</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/6\">Conclusions</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/6\">Supplementary data</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/6\">Appendix</a></li><li style=\"padding-top:4px\"><a href=\"zotero://open-pdf/0_FE4CWEA5/6\">References</a></li></ul>",
"tags": [],
"relations": {},
"dateAdded": "2020-04-24T22:28:55Z",
"dateModified": "2020-04-24T22:28:57Z"
}



This is item 19603, it's fine. Actually it's the item right after 19603 in whole library view that can't be processed by zotfile. I already deleted that item yesterday so i can't provide you the output...

sky_myl

Anyway, I've already finished moviing the whole library by deleting those problematic files manually by your method. Dstillman Thanks for your kind help!

dstillman

Ah, OK — yeah, that output wouldn't help, then. Let us know if you see this again.