+9
Fixed

Only small part of Zotero group library is displayed

Антон Морковин 6 years ago updated by Danya 2 months ago 38
I've tried to display the list of publications from my group and also from my private library in Zotero. In both cases only a small part of this collections is displayed by BibBase script.

Answer

+1
Answer
Fixed

Chris, Everyone:


Thanks for your patience. This issue has now been fixed and the fix has been activated on bibbase.org, e.g.:

https://bibbase.org/show?bib=http%3A%2F%2Fbibbase.org%2Fzotero-group%2Figw-hci/411247&msg=embed


This uses the newly created route:

   https://bibbase.org/zotero-group/:userID/:groupID

which returns a bibtex file that can be used with BibBase as usual.


The userID is required in order to look up the API credentials to use. I believe that by using that user's API access credentials, the Zotero API will thereby also grant you access to non-public groups. The ID of any user with access to the Zotero group and who has previously given BibBase an API key for their Zotero account, should do -- by using the Generate BibBase page from your Zotero "Library", collections, or groups link, found on our homepage.


Please let me know if this works for you as expected.


+1
Under review
Could you point me to the page in question so I can investigate what's happening?

Here is my Zotero library which includes more than 1000 papers: https://www.zotero.org/groups/birds_of_russia/items/
And here is this library embedded with javascript on my homepage: http://odd-bird.do.am/

I would be very grateful if you could help me with this problem.
Here is my Zotero library which includes more than 1000 papers: https://www.zotero.org/groups/birds_of_russia/items/
And here is this library embedded with javascript on my homepage: http://odd-bird.do.am/

I would be very grateful if you could help me with this problem.

Has there been any progress with this? We have a zotero library with some strange behavior.


http://bibbase.org/show?bib=https%3A%2F%2Fapi.zotero.org%2Fgroups%2F32374%2Fitems%3Fkey%3D4DiDrqPNwu15c2WuBuqbvMMZ%26format%3Dbibtex%26limit=5


This should at least show 5, yet it only shows 3. The zotero library has around 200+ items, yet we cannot get them to all display.

Not a bug

Hi Peter,


This seems to be a problem on Zotero's side. If you open the link to the bibtex directly (https://api.zotero.org/groups/32374/items?key=4DiDrqPNwu15c2WuBuqbvMMZ&format=bibtex) you will see that you will only get a list of 18 items (not 200 or more).



Hi Christian,


It seems that the Zotero bibtex export is limited to 100 entries. When greater than 100, a new url is required that forces the export from a certain starting point. I fear this is not going to work with bibbase. We may have to categorise the contents in our zotero library into seperate groups.


That is correct, and you are right that BibBase does not yet implement that pulling of subsequent pages correctly for groups, but it does work for a user's library. So if that's an option you can also create a new Zotero account that is shared. That's what others have done.


Hi Christian,

we have the same problem, these two pages have the same bibliography as source:

once in a group:

http://bibbase.org/show?bib=https%3A%2F%2Fapi.zotero.org%2Fgroups%2F411247%2Fitems%3Fkey%3DfAa8lomlYW6ijtQJ5R5rgKmb%26format%3Dbibtex%26limit%3D100

once in a separate account, displaying the whole user lib:

http://bibbase.org/show?bib=http%3A%2F%2Fbibbase.org%2Fzotero%2Figw-hci&msg=embed


The one for the user lib is showing all items, the one in the group is limited to 100. Any idea why and if it is possible to fix it for groups too?


Sharing an account is a lot more inconvenient for an institute than just having a group that everyone can contribute through their own account.


Thanks

Chris

Planned

Thanks for elaborating, Chris. We'll try to get to this in the next couple of weeks.

+1
Answer
Fixed

Chris, Everyone:


Thanks for your patience. This issue has now been fixed and the fix has been activated on bibbase.org, e.g.:

https://bibbase.org/show?bib=http%3A%2F%2Fbibbase.org%2Fzotero-group%2Figw-hci/411247&msg=embed


This uses the newly created route:

   https://bibbase.org/zotero-group/:userID/:groupID

which returns a bibtex file that can be used with BibBase as usual.


The userID is required in order to look up the API credentials to use. I believe that by using that user's API access credentials, the Zotero API will thereby also grant you access to non-public groups. The ID of any user with access to the Zotero group and who has previously given BibBase an API key for their Zotero account, should do -- by using the Generate BibBase page from your Zotero "Library", collections, or groups link, found on our homepage.


Please let me know if this works for you as expected.


Wonderful - many thanks Christian!!

Hello! I'm using the new URL as instructed–https://bibbase.org/show?bib=http%3A%2F%2Fbibbase.org%2Fzotero-group%2Fodellcampbell/1132825&msg=embed#–and it seems like the source bibtex file isn't updating (when I make changes to keywords, for example, in the group library in Zotero, it doesn't update in the bibbase.org output). 


The changes are reflected in the "old" link, from "generate BibBase page" (although of course this has the old problem of not returning the whole library). 


Thank you!

Under review

One thing to note is that the update will take two page loads (with a pause in-between). The first one will trigger the refresh from Zotero. If that completes then the second page load will show the refreshed results. This is done for speed: Zotero is not super fast in responding and your page should not be delayed in loading.


If that doesn't explain and resolve your issue, then please point us at the Zotero page where the updates are happening, so we can debug.


Thanks.

Hi Christian, thank you for elaborating the issue! Unfortunately, I haven't noticed any differences yet: most part of the library is still invisible. Even more, now I don't see the green panel with embedding suggestion when I choose my zotero group for generating (here is the link: bibbase.org/show?bib=https%3A%2F%2Fapi.zotero.org%2Fgroups%2F326590%2Fitems%3Fkey%3DaeNBZCKSTCeK3MEV89bpsb9v%26format%3Dbibtex%26limit%3D100 ).

Anton,


That is still the old URL. You need to use the new one (see my previous post). If you want the green panel, then you need to add &msg=embed to the URL.



I don't know what goes wrong... I createad a bibase key with default permissions, than typed https://bibbase.org/zotero-group/a_marko/birds_of_russia&msg=embed Than I recieved a message "Your Zotero collection could not be retrieved. Please try requesting a new Zotero key using the link on the BibBase homepage" and nothing else...

Yes, that error message seems to be saying the truth. Your Zotero API key doesn't seem to work, because https://bibbase.org/zotero/a_marko doesn't work either. Could re-grant BibBase access to your Zotero account by click "Generate BibBase page from your Zotero "Library", collections, or groups" on the homepage and accepting the defaults?

Well, that's strange because there is a key called bibase in my Feeds/API list in Zotero Settings. I've tried to revoke it and create again several times, without any effect. Can the problem be caused by underlyings in my nickname or group name?

Hi Christian,

Here is the Zotero collection I would like to display withe bibbase (if possible in an embedded frame) :

https://www.zotero.org/groups/1340424/scienceigno/items/collectionKey/WRU9JA9J

It contains 495 items.

When I try with "Generate BibBase page from your Zotero "Library", collection, grouves, it gives me the following code :

https://bibbase.org/show?bib=https%3A%2F%2Fapi.zotero.org%2Fgroups%2F1340424%2Fitems%3Fkey%3DcRN9nOxfOS9RcEg6ioSHlbD8%26format%3Dbibtex%26limit%3D100

The display is wonderfull ! But unfortunatly only about 60 bibliographical references appears. I understand very well that this coudn't be a success at the first try. But have you got any idea of the reason ?
The result on my website (in construction) : https://ignostudies.hypotheses.org/ressources-et-medias/bibliographie-science-et-ignorance

Hi Julie,

I have the same problem (my Zotero bibliography is not fully displayed with Bibbase) and I just saw on your website that you managed to present your whole bibliography: did you find a solution in order to solve the sync problem ? Thank you !


Jenny

Hello,

I would like to use BibBase to display my bibliography hosted on Zotero (as a public close group). I try to use the newly created route but it didn't work at all. As has already been mentioned the function "generate BibBase page from your Zotero Library" is limited to very few references.

Is there any (new) solution ?


Thank you so much for your help,

Alexandra

Hi Alexandra,

As has already been mentioned the function "generate BibBase page from your Zotero Library" is limited to very few references.

Can you elaborate? I don't think anyone has said anything about the page generated from their library yet. That one should not be limited, and at least for me, I see my entire library. The limitation has always been with collection and in the past also with groups. How many items do you have in your library and how many are displayed? If possible, could you also send me a link to the page/URL where you see things missing?

Thanks.

Hi Christian,

Thank you for your work and for your quick reply. I have 1636 items in my group CIAO (a public close group) : https://www.zotero.org/groups/2349776/ciao_-_ceramica_della_magna_grecia/library

When I generate BibBase page from my Zotero group, only 78 are displayed, but I don't understand why : https://bibbase.org/show?bib=https%3A%2F%2Fapi.zotero.org%2Fgroups%2F2349776%2Fitems%3Fkey%3D3orkNRACP4HBEuZmFHISBDOW%26format%3Dbibtex%26limit%3D100&msg=embed#

Is there something I did wrong ?


Thank you for your help,

Alexandra


Fixed

You are using the old format, which is the one that had the limitation for groups. As indicated in this comment, you need to use

https://bibbase.org/zotero-group/:userID/:groupID

to get the whole group content.

Hi Christian,

Thank you. I tried with the newly created route you mentioned. But I probably made some mistake because all my tries failed. I haven't received any bibtex files but it only indicates "server error". What did I wrong ? 

https://bibbase.org/zotero-group/alexandra_attia/2349776

or "Error retrieving bibtex file" with

https://bibbase.org/show?bib=http%3A%2F%2Fbibbase.org%2Fzotero-group%2Falexandra_attia/2349776&msg=embed#

I'm pretty sure the API key is ok because I use the link "Generate BibBase page from your Zotero "Library", collections, or groups".

I'm so sorry to insist but it makes me crazy...

Sorry for the lack of detail in the error message, that could definitely be improved. The server log shows "The Zotero user you specified could not be found". It turns out that your Zotero username is "Alexandra ATTIA" (at least in the Zotero API). Using that gets rid of the error you saw and BibBase goes to fetch the data from Zotero, but unfortunately your group collection seems to be too big, because the request times out before BibBase was able to fetch all data from Zotero:

https://bibbase.org/zotero-group/Alexandra%20ATTIA/2349776. Zotero's API does not allow fetching more than 100 items at a time, so this has to be sent in 16 consecutive requests and each one of them can take a couple of seconds. So I'm afraid this may not work with such a large collection.


Would it be an option for you to export the collection from Zotero into a bibtex file manually and then use that to render your page?

Thank you Christian for your explainations that make me feel better even if it's not possible to generate my bibliography by this way. Is is to possible to choose only specific years (for example 2017-2019) using Zotero's API or the newly created route ? Or maybe it will be easier to create a specific collection...

I have a bibtex file but I'm note sure I can use it directly in my blog (https://ciao.hypotheses.org/) Hypothese.org recommand to use BibBase. I saw we could generate also generate a bibliography via Bibtex on BibBase but I don't know how to proceed

Is your bibtex file somewhere on the web? If so, then you can just use https://bibbase.org/show?bib=https://URL-TO-YOUR-BIBTEX-FILE instead of the zotero-group URL above. If you con't yet have a place to host your bibtex file, then I recommend setting up a free page using Github Pages (see our example).

A specific, smaller collection on Zotero would probably work, too, but might be a little slower.

Hi Christian,

Thank you for your help. I created my own Github page to host my bibtex file https://github.com/AlexandraAttia

Github told me that my page https://alexandraattia.github.io/CIAO.github.io/ is published but when I click on the link, I have a message saying Error 404 / File not Found.

The same problem when I try to use the url 

https://bibbase.org/show?bib=https://alexandraattia.github.io/CIAO.github.io/

Have you an idea of what is going wrong ? Thank you

Github pages require you to call your repository exactly like your username, so in your case it has to be named alexandraattia.github.io (instead of CIAO.github.io).

Thank you so much it finally worked !

Hi Christian, 

I have the same problem when I try to embed this: 

<script src="https://bibbase.org/zotero-group/andrea_bertino/2358901"></script>

What I am doing wrong?

Thank you for you help,

Andrea

Andrea, your userId seems to be "Andrea Bertino". When you use that, it works: https://bibbase.org/zotero-group/Andrea%20Bertino/2358901. Note that this give you the bibtex file that is exported from the Zotero API. What you want to embed in your page is:

<script src="https://bibbase.org/show?bib=https://bibbase.org/zotero-group/Andrea%20Bertino/2358901&jsonp=1"></script>

Hope this helps.

Sorry, but then I don't understand why this other group doesn't work: 

<script src="https://bibbase.org/show?bib=https://bibbase.org/zotero-group/Andrea%20Bertino/2358893&jsonp=1"></script>

It works for me: https://bibbase.org/show?bib=https://bibbase.org/zotero-group/Andrea%20Bertino/2358893, so the embedding should work, too. Does it not? Can you send me the URL of the page where you are working on it?

+1

It works! thank you very much!

Hi Christian,

Just found this thread and it was quite helpful, I'm wondering if there is a shortcut like the URL format you posted for generating my own URL of just a collection within my Zotero library.

Background: I'm trying to make a workaround because when I try to log into bib base with my zotero account and click 'Allow Access' nothing happens, but when I go to the  URL you provided, I see an up-to-date bibtex file, so I figured if I could just specify in that link that I only want the Bibtex of one collection then that would work just as well. 

Hi Christian,

Sorry for repeating the question after it's been discussed for so long, but I'm having the same problem and nothing seems to work... When I'm using the new method to create a link for my group it just says "504 Gateway Time-out." I tried creating a new account and embed it as a personal library but then the same error occurred. Can it be because the library is too large (over a 1000 items)? But then even if I try to embed only one collection from my personal library (around 500 items) I only have a minuscule part of it displayed... Is there some sort of new solution I might have overlooked?

Thanks a lot for your work!