I have downloaded 5.0 and I find the Word connector is not working. When I try to import a citation it tells me that it no longer exists in my Zotero database but it clearly does. Is there a bug here?
Can you please post a new thread with an Error Report ID for an attempt that gives that error, as well as a specific description of the steps needed to reproduce the problem? Importantly, please see whether the problem exists in a new empty document.
There is no error ID given. The steps are as follows: In Word doc, go to Zotero plug in menu and click on insert citation, enters Zotero library find citation, press enter and then, instead of loading the details into Word it gives a dialogue box saying:
'The highlighted citation no long exists in your Zotero database. Do you want a substitute item?
Clicking 'No' will delete the field codes for citations containing this item, preserving the citation text but deleting it from your bibliogrppahy'
I've checked and the record details are clearly present in Zotero still.
You're misunderstanding the message (though it's a little confusing). When you insert a citation for some citation styles, Zotero needs to update all other citations in the document. So it's referring to — and hopefully highlighting — a different, previously entered citation in the document, not the one you're inserting now.
It may be clearer to click the Refresh button, which should update all citations and show that message for any affected citations.
Thanks, that makes sense although the message is very confusing. I am updating an old document and so the previous citations are probably causing the issue. I just tried to insert a citation into a new doc and it worked fine. Thanks for your help!
I'm having a problem that produces the same error message, but I have a different question. I had been editing a (long) document on my desktop at home, and now I'm editing it on my laptop while traveling. The document itself is saved in Dropbox, so I'm working on the same document on both computers.
Many of the citations that I added while working on my desktop now generate the error message any time I try to add a new citation, or edit an existing citation. The items referenced in those citations definitely DO exist in the standalone app on my desktop, so my only guess is that the standalone app on my desktop never synced with my online account, since when I log in to zotero.org, the items do not show up there.
The practical problem I'm faced with is this:
1. I'm trying to edit my document, and that involves adding new citations. 2. Zotero will not permit me to add a new citation until I first reconcile all of my pre-existing citations. 3. In order to do that, I have to either (a) remove the field codes, which means that item will not be included when I generate a bibliography, or (b) create new items in my database, which is a big waste of time, since many of these items are old journal articles that I would have to track down again using Google Book to get the right volume number, issue number, page numbers, etc.
If there were simply a way to get Zotero NOT to check every single goddamn citation in my entire document each time I insert a new citation, then I could insert citations now, and when I get back to my desktop at home, the older citations that currently produce the error message would presumably start working again, since the items they refer to are saved to the standalone app on my computer. But as far as I can tell, Zotero is set up in a way that makes this impossible.
My question is: is there any workaround? Is there any way that I can add citations to the document while working on my laptop, without either deleting all the field codes from the existing citations, or recreating database items that already exist on my desktop? I feel like Zotero is blackmailing me into choosing one of two bad options, just so that I can be allowed to add new citations to my own document.
Zotero embeds the citation data for items into your Word document, so you shouldn’t normally get this error. What version of Zotero are you using on both computers?
What is likely happening is that you have one or a few very old citations from before Zotero embedded the citation data regularly (years ago). You should follow the debugging steps I listed above, particularly step 8, to find and replace/remove just the few problematic citations.
Also, please avoid profanity. It makes helping a lot less pleasant for everyone involved.
What is likely happening is that you have one or a few very old citations from before Zotero embedded the citation data regularly (years ago). You should follow the debugging steps I listed above, particularly step 8, to find and replace/remove just the few problematic citations.
If that's the case, there are two alternatives to step 8 that might be faster:
* Switch the document to show field codes (Alt + F9 on Windows), and check if any any of the citations lack embedded metadata. This wouldn't be as easy to check if you have multi-item citations for which only a subset is missing metadata, though. E.g. a (single-item) citation field without metadata looks like:
{ ADDIN ZOTERO_ITEM {"citationID":"a2htojki1l6","properties":{"formattedCitation":"(Aach et al., 2014)","plainCitation":"(Aach et al., 2014)"},"citationItems":[{"id":952,"uris":["http://zotero.org/users/1031436/items/38U5R36M"],"uri":["http://zotero.org/users/1031436/items/38U5R36M"]}]} }
Whereas the same citation field with embedded metadata looks like:
{ ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"a2htojki1l6","properties":{"formattedCitation":"(Aach et al., 2014)","plainCitation":"(Aach et al., 2014)"},"citationItems":[{"id":952,"uris":["http://zotero.org/users/1031436/items/38U5R36M"],"uri":["http://zotero.org/users/1031436/items/38U5R36M"],"itemData":{"id":952,"type":"article-journal","title":"CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes","container-title":"bioRxiv","page":"005074","source":"www.biorxiv.org","abstract":"CRISPR/Cas9 systems enable many molecular activities to be efficiently directed in vivo to user-specifiable DNA sequences of interest, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems being developed and deployed in more and more organisms, there is now strong need for a flexible and rational method for finding Cas9 sites with low off-targeting potential. We address this through the CasFinder system, which we demonstrate by generating human and mouse exome-wide catalogs of specific sites for three varieties of Cas9 - S. pyogenes, S. thermophilus (ST1), and N. meningitidis - that each target 56-74% of all exons. We also generate reduced sets of up to 3 targets per gene for use in high-throughput Cas9-based gene knockout screens that target 75-80% of all genes.","URL":"http://www.biorxiv.org/content/early/2014/05/12/005074","DOI":"10.1101/005074","note":"CRISPR/Cas9 systems enable many molecular activities to be efficiently directed in vivo to user-specifiable DNA sequences of interest, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems being developed and deployed in more and more organisms, there is now strong need for a flexible and rational method for finding Cas9 sites with low off-targeting potential. We address this through the CasFinder system, which we demonstrate by generating human and mouse exome-wide catalogs of specific sites for three varieties of Cas9 - S. pyogenes, S. thermophilus (ST1), and N. meningitidis - that each target 56-74% of all exons. We also generate reduced sets of up to 3 targets per gene for use in high-throughput Cas9-based gene knockout screens that target 75-80% of all genes.","shortTitle":"CasFinder","language":"en","author":[{"family":"Aach","given":"John"},{"family":"Mali","given":"Prashant"},{"family":"Church","given":"George M."}],"issued":{"date-parts":[["2014",5,12]]},"accessed":{"date-parts":[["2015",2,18]]}}}],"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"} }
* Option two is to run your document through http://rintze.zelle.me/ref-extractor/, and check first whether the number of extracted references matches the number of references in your document. If there is disagreement, identify the missing ones.
Thanks for your replies. I checked the field codes, and the metadata are not embedded. Is there a way to change that? I know it's possible to remove the field codes entirely so that the endnotes are just text, but since I'm still adding to the document I don't want to do that.
Re. bwiernik's reply, actually these aren't old citations, they're the ones I added most recently. I know that the items are in the Zotero database on my desktop at home, because that's what I used to add them, but they're not in the database on my laptop or on zotero.org. So the only explanation I can think of is that the Zotero app on my desktop somehow failed to sync. The version of Zotero I'm using on my laptop is 5.0.11, but I don't know which version is on my desktop.
Ideally I would like to find a work-around so that I can continue adding new citations to the document while traveling, without Zotero prompting me to reconcile all of the existing citations that do not correspond to items in the database -- of course I could do that, but it's a big waste of time since I know those items are already in the database on my computer at home.
I checked the field codes, and the metadata are not embedded.
So you are seeing something like my top example, correct?
It's my understanding that this only could have happened if you were using Zotero 4.0.x on your desktop at home and unchecked the "Store references in document" Zotero option for your document, which I believe is enabled by default. Zotero 5.0 always embeds citation metadata.
If it's a relatively small number of references, you could just convert those to plain text, and reinsert them later at home (and make sure to then re-check the preference, or upgrade to Zotero 5.0).
Yes, that's correct. I'll have to update the version of Zotero on my desktop when I get home. For now I think the best workaround for me will be to just enter the info for new citations manually, and use Zotero to replace those with real citations when I get home. I was hoping there was a way to temporarily prevent Zotero from checking every citation each time I enter a new one, but it seems like there isn't.
You could also enter new citations into a different document, then cut and paste into your real one. This will let you enter live citations without the document trying to update.
Upgrade Storage
'The highlighted citation no long exists in your Zotero database. Do you want a substitute item?
Clicking 'No' will delete the field codes for citations containing this item, preserving the citation text but deleting it from your bibliogrppahy'
I've checked and the record details are clearly present in Zotero still.
It may be clearer to click the Refresh button, which should update all citations and show that message for any affected citations.
https://www.zotero.org/support/word_processor_plugin_troubleshooting
Many of the citations that I added while working on my desktop now generate the error message any time I try to add a new citation, or edit an existing citation. The items referenced in those citations definitely DO exist in the standalone app on my desktop, so my only guess is that the standalone app on my desktop never synced with my online account, since when I log in to zotero.org, the items do not show up there.
The practical problem I'm faced with is this:
1. I'm trying to edit my document, and that involves adding new citations.
2. Zotero will not permit me to add a new citation until I first reconcile all of my pre-existing citations.
3. In order to do that, I have to either (a) remove the field codes, which means that item will not be included when I generate a bibliography, or (b) create new items in my database, which is a big waste of time, since many of these items are old journal articles that I would have to track down again using Google Book to get the right volume number, issue number, page numbers, etc.
If there were simply a way to get Zotero NOT to check every single goddamn citation in my entire document each time I insert a new citation, then I could insert citations now, and when I get back to my desktop at home, the older citations that currently produce the error message would presumably start working again, since the items they refer to are saved to the standalone app on my computer. But as far as I can tell, Zotero is set up in a way that makes this impossible.
My question is: is there any workaround? Is there any way that I can add citations to the document while working on my laptop, without either deleting all the field codes from the existing citations, or recreating database items that already exist on my desktop? I feel like Zotero is blackmailing me into choosing one of two bad options, just so that I can be allowed to add new citations to my own document.
What is likely happening is that you have one or a few very old citations from before Zotero embedded the citation data regularly (years ago). You should follow the debugging steps I listed above, particularly step 8, to find and replace/remove just the few problematic citations.
Also, please avoid profanity. It makes helping a lot less pleasant for everyone involved.
* Switch the document to show field codes (Alt + F9 on Windows), and check if any any of the citations lack embedded metadata. This wouldn't be as easy to check if you have multi-item citations for which only a subset is missing metadata, though. E.g. a (single-item) citation field without metadata looks like:
{ ADDIN ZOTERO_ITEM {"citationID":"a2htojki1l6","properties":{"formattedCitation":"(Aach et al., 2014)","plainCitation":"(Aach et al., 2014)"},"citationItems":[{"id":952,"uris":["http://zotero.org/users/1031436/items/38U5R36M"],"uri":["http://zotero.org/users/1031436/items/38U5R36M"]}]} }Whereas the same citation field with embedded metadata looks like:
{ ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"a2htojki1l6","properties":{"formattedCitation":"(Aach et al., 2014)","plainCitation":"(Aach et al., 2014)"},"citationItems":[{"id":952,"uris":["http://zotero.org/users/1031436/items/38U5R36M"],"uri":["http://zotero.org/users/1031436/items/38U5R36M"],"itemData":{"id":952,"type":"article-journal","title":"CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes","container-title":"bioRxiv","page":"005074","source":"www.biorxiv.org","abstract":"CRISPR/Cas9 systems enable many molecular activities to be efficiently directed in vivo to user-specifiable DNA sequences of interest, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems being developed and deployed in more and more organisms, there is now strong need for a flexible and rational method for finding Cas9 sites with low off-targeting potential. We address this through the CasFinder system, which we demonstrate by generating human and mouse exome-wide catalogs of specific sites for three varieties of Cas9 - S. pyogenes, S. thermophilus (ST1), and N. meningitidis - that each target 56-74% of all exons. We also generate reduced sets of up to 3 targets per gene for use in high-throughput Cas9-based gene knockout screens that target 75-80% of all genes.","URL":"http://www.biorxiv.org/content/early/2014/05/12/005074","DOI":"10.1101/005074","note":"CRISPR/Cas9 systems enable many molecular activities to be efficiently directed in vivo to user-specifiable DNA sequences of interest, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems being developed and deployed in more and more organisms, there is now strong need for a flexible and rational method for finding Cas9 sites with low off-targeting potential. We address this through the CasFinder system, which we demonstrate by generating human and mouse exome-wide catalogs of specific sites for three varieties of Cas9 - S. pyogenes, S. thermophilus (ST1), and N. meningitidis - that each target 56-74% of all exons. We also generate reduced sets of up to 3 targets per gene for use in high-throughput Cas9-based gene knockout screens that target 75-80% of all genes.","shortTitle":"CasFinder","language":"en","author":[{"family":"Aach","given":"John"},{"family":"Mali","given":"Prashant"},{"family":"Church","given":"George M."}],"issued":{"date-parts":[["2014",5,12]]},"accessed":{"date-parts":[["2015",2,18]]}}}],"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"} }* Option two is to run your document through http://rintze.zelle.me/ref-extractor/, and check first whether the number of extracted references matches the number of references in your document. If there is disagreement, identify the missing ones.
Re. bwiernik's reply, actually these aren't old citations, they're the ones I added most recently. I know that the items are in the Zotero database on my desktop at home, because that's what I used to add them, but they're not in the database on my laptop or on zotero.org. So the only explanation I can think of is that the Zotero app on my desktop somehow failed to sync. The version of Zotero I'm using on my laptop is 5.0.11, but I don't know which version is on my desktop.
Ideally I would like to find a work-around so that I can continue adding new citations to the document while traveling, without Zotero prompting me to reconcile all of the existing citations that do not correspond to items in the database -- of course I could do that, but it's a big waste of time since I know those items are already in the database on my computer at home.
It's my understanding that this only could have happened if you were using Zotero 4.0.x on your desktop at home and unchecked the "Store references in document" Zotero option for your document, which I believe is enabled by default. Zotero 5.0 always embeds citation metadata.
If it's a relatively small number of references, you could just convert those to plain text, and reinsert them later at home (and make sure to then re-check the preference, or upgrade to Zotero 5.0).