what is best method to move library & preserve citation links (word'06)?

danioore

i am using standalone on a mac (at least, as far as i can tell it is not sync'ed with firefox). my library is approaching 8gigs and i want to move it to a new external harddrive. i am also using citation plugins for word (2006).

what is the best way to move my entire zotero library so that i can work off a hard drive and so that the citations in my documents continue to be connected to my library?

thanks to all the developers and techs who make this program run.

d

adamsmith

generally speaking, all this entails is moving the zotero data folder to wherever you want it to be and then pointing Zotero to that location under Advanced-->Files and Folders in the preferences.
https://www.zotero.org/support/zotero_data

Note, though, that we get a number of error reports from people using external harddisks for their Zotero data folder. People do have it working and there is nothing systematic that should fail (and it won't do any damage to you database for sure), but if you see weird things happening after moving the database folder, that'd likely be the cause.

danioore

Hi again, transferring my zotero library to an external hard drive had seemed to work, as you instructed.
but by fluke, i just now noticed that at some point (maybe after about a month?) zotero switched the library destination back to the old library (which i hadn't deleted) on my computer hardrive. (i don't know how this happened.)
i have added and annotated a substantial number of files over this time, so i don't want to lose any of my work that may currently be distributed across two library locations. i want to streamline everything to the external library so that i can make redundant backups.

how do i fix this?

thank you

danioore

Hi there, any thoughts on this?

Thank you!

fbennett

Here are some step-by-step instructions to rebuild a library from citations contained in a document:

1. From the Juris-M site, install JM Standalone, a variant of Zotero. You may need to stop or disable Zotero to run it, but it will make a copy of your Zotero database at startup, and your existing Zotero database will not be affected.

2. Configure Juris-M to sync to your Zotero account.

3. In Juris-M, create a group library to hold the recovered citations (recovery to My Library is not supported).

4. Sync Juris-M to show the group library in the client.

5. With Juris-M running, open a document, and in the word processor open Document Preferences (same as for Zotero). Open the tab for "Project Name." Set a nickname for the project (anything will do), and hit Enter, then tick the box next to "release for editing" and select the group library you have created.

6. When you close Document Preferences, Juris-M may hang briefly while creating items for citations in the document. When it returns, click "Refresh" to pick up any items that it missed on the first pass.

7. Save the document (which is now linked to the group library items exclusively). Use it as your new working copy.

8. Sync Juris-M to push the newly created items to the group library in your Zotero account.

9. You can now stop Juris-M (or remove it from your system entirely).

10. Open Zotero and sync. The group library should appear in your client, and the document should be linked to the items it contains.

adamsmith

(I don't think fbennett's instructions apply here, but I may misunderstand).

My guess would be that the external HD wasn't available at some point when Zotero started up, so it reverted back to its default location. If you look back up at my original instructions, I warned that you might experience issues like this.

fbennett

(@adamsmith: Since all I have is a hammer ... :)

fbennett

(Aside to @adamsmith: Right. So if each of the library copies is hooked up and synced to the Zotero account, @danioore should be in good shape ... yes?)

adamsmith

yes, I think so, but they'd have the library in two different places, including on their local HD, which I think is exactly what they hoped to avoid.

fbennett

Oh I see - the original library is 8gigs, and not yet synced, hence the desire to make the move offline. Got it.

Thinking out loud ... That is a problem then - but if pushing the library cite data to the cloud is acceptable, it could be synced with attachment-sync disabled, which would be less of a burden. That would at least solve part of the problem.

danioore

Hi thanks.

I am not aware of either library being synced to online account.

I have no idea how many new files were added to the library on the external drive, before zotero switched back to my local drive. but would it be possible to simply look at that one month period during which the external library was used (by checking date added/modified) and import those files to my local drive (and if necessary, merge those items).

and would my citations still work?

thanks!

fbennett

You could export the files added after a certain date from one database, and import them to the other, but with that alone, the citation links to those items would break. (When you import items to the database, they are assigned fresh IDs, and document citations are keyed to the IDs.)

If the items in both copies of the database are synced to a Zotero account, your document links would be preserved (because sync transfers the IDs along with the rest of the item metadata). It is not necessary to sync the attachments---they could be recovered by exporting the recent items and importing (as above), and then merging duplicates. (Merge, like sync, preserves item IDs.)

There isn't a feasible solution to the dilemma that does not involve either syncing the metadata from both libraries, or relinking citations in the documents by hand. (You don't need the solution I posted above, but it also would require a sync of your library.)

danioore

i would like to do this (sync or merge). however...

currently i only use my online zotero account for its 'save to zotero' function (that lets me grab citation data from certain online sources and export it to my stand alone zotero library. in other words, i don't need any of my online items... because i imported whatever i want to my stand alone.)

how do i delete my online library so that i have a 'clean slate' when i sync up my stand alone libraries?

after that... do i simply sync both my external drive and local drive libraries to one single library online?

...and once that is complete, do i manually find the files and click and drag, based on 'date modified' info, or...?

sorry if i am complicating this.

thank you for your help

fbennett

No, this all makes sense. One thing to clarify, though: I'm not sure what you mean by "online zotero account" and "stand alone zotero library." Do you mean that you have a local Standalone Zotero client that you sync to your online library, and that your research library (now residing on separate machines in slightly versions) is completely separate from the synced one?

If that is the case, you can just create a separate Zotero account, and use that to sync your research library. (Be sure to turn off attachment uploads before syncing, though, to save time and bandwidth.)

fbennett

And yes, you should be able to sync both copies of the research library to the same account, without generating duplicates. The sync should complete (possibly after some conflict resolution queries) with all content from both in a single place.

danioore

ok, by 'online zotero account' i mean the one i am using to post these comments, and which also has an associated library whose 'save to zotero' function i use regularly to import items to what i call my (perhaps incorectly) my 'stand alone libraries' which are on my computer and external hard drives.
(am i confusing the library terminology: 'online'/'stand alone'?)

once the 'online library' has synced the two stand alone libraries, how do i then merge the items on my hard drive? will the system automatically prompt me about each file or batch?

i feel like i have many unknowns in the syncing process. and just want to ensure i don't compromise any of my work in the process.

thanks for your patience.

fbennett

I'm still a little confused. "Save to Zotero" is the hint you see when you roll over the Zotero download icon in your browser. That message isn't coming from the online site; the button is part of your local Zotero setup (either the Standalone client plus a browser plugin, or the Zotero-for-Firefox plugin). Clicking on the button will download the item to your local Zotero database if possible.

If you do not use Firefox for browsing, but instead browse with Chrome or Safari, and use Standalone Zotero to manage your local library, then when Standalone is not running, clicking on the icon will send the item to your online library. The only way to get items from the online copy of your library to the local copy of it (the library that you view with Standalone Zotero or the Zotero for Firefox plugin) is via sync.

Two questions will help us understand your setup:

First, when you click on the gear menu, then Preferences, then the Sync tab, is there a user name and ID entered there?

Second, when you are viewing this forum, and you click on the My Library tab at the top of the page, does it show any items in the (online) library?

(It's late here in Japan and I'll be off to sleep soon, but others may pick up the conversation. Once we are clear about how you have been managing your content, we'll have some clear advice for how to proceed.)

danioore

really appreciate your time...

1. when i look at preferences there is no user name or id (and neither 'sync auto' nor 'sync full-text content' are selected).

2. yes, when i click the 'my library' tab, i have 517 items. these are the items that are imported whenever i select the 'save to zotero'—it always saves to what i call the 'online library', and then i export these to the library stored on my computer. this is why all my 'online library' items are redundant, and can be deleted.

if i can't simply clear my online account, i need to create a new one as you suggested. then, in order to sync, i guess i will need to enter the username and password of the new account into the preference window. but to do this for the external library, will i need to reset the destination library?


also...
all my zotero citations exist in one single document (my dissertation), and i haven't had any cues that any of my citation links have 'died.' (would i have discovered dead links when rebuilding my bibliography?)
so i wonder if all my zotero citations are all only connected to items in one single library. and the items i added to my external drive (over the course of a single month), could be moved without any reprecussions.

the only curious thing with my citations is that it usually takes a few minutes to add a citation (occasionally its quicker). it used to be fast. is this slowness related to the increasing size of my bibliography, or the size of my stand alone library (2.5k items), or is it because zotero is pulling citation info from multiple libraries?

thank you!

fbennett

Okay, that's all very clear now! I'm off to bed, unfortunately, but we can outline clear steps now.

danioore

ok, thank you and good night!!

fbennett

Good morning.

It is normal that you are not getting errors on the missing items. Zotero embeds citation metadata in the document, and will use it as a fallback when the item is not available.

The speed issue is indeed related to document size. If you split your project into multiple files for drafting, updates will be faster.

I understand your workflow now. That's not the most efficient way to go at it—if the local library were synced to the online account, the items would be pulled into your local library automatically, without need for the secondary "save to Zotero" step. But what you are doing there will work.

Getting the two versions of the local library into one online account is simply a matter of setting your Zotero account ID and password in the Sync preferences panel and clicking the green sync icon in the upper right corner of the Zotero window. After one copy of the library has finished syncing, go to gear menu -> Preferences -> Advanced -> Files and Folders, and point Zotero at the other data directory. Then click the sync icon again -- don't use the Reset settings, they would only break things in this case. The sync process will handle everything.

As for whether to sync to your existing account, or to a new one, that's your call—it will work either way. If all of the items in the online account have been downloaded, then they will turn up in the Duplicates folder when you sync, and it would be (tedious but) easy to merge them. (One library is simpler to handle than two, so that's probably what I would do.)

danioore

Okay, this seems clear.

Is there a quick way to batch delete all the items on my online account? (i.e. to avoid having to pick through and do it one by one, once ive synced my local libraries..)

Do you think i should deal with existing duplicates in my local library before i sync and merge the two libraries?

Also, when it comes time to sync and merge, will i be picking one duplicate by one, or batch duplicates, or something else, and will i be doing this in the online library, or in my stand alone local library?

Thank you very much.

fbennett

Just checked that. You can select all items in a view, and delete them as a batch. With a few iterations, you can remove all of them. Do that before the sync, obviously—once the online and local libraries are joined by sync, deleting in one location will also delete in the other.

I would leave duplicate merging to the last, after everything is in one place. During sync you will receive popup messages only if an item has been modified in both libraries and the changes conflict; from the sound of it, that won't be an issue in this case.

You would handle the merging of duplicates after sync is done, working in the local (stand alone) library. It's very simple: one of the last folders in your My Library will be a folder called "Duplicate Items." If it's not there, click on My Library, then right-click and select "Show Duplicates" from the menu. That will reveal the folder. When you enter the folder, clicking on any item will highlight that item plus its duplicates, with a panel to control the merge to the right.

danioore

Okay, great, this is clear.

Just one clarification: i currently already have about 40 pairs of items in my duplicate folder. are you are suggesting i deal with these after the sync? (i just wonder if it might slow down my one by one evaluation of these, as i try to remember which version is correct.)

fbennett

You can merge before, but I would probably wait, since merging in both libraries might trigger sync conflicts. If you remove the content of the online library before the sync, the number of duplicates shouldn't increase much when the two copies of the library are schmooshed together.

danioore

super. thanks so much!

(i'll be back on here to post the results.)

fbennett

Good luck, hope it all goes smoothly. Do be sure to turn off attachment uploads before the sync, that will make things go much faster.

danioore

ohh, another q:

do i deselect these two *file* sync option boxes:
'sync attachment files'?
'sync attachment files in group libraries using zotero storage?'

(my library is too much memory to upload..)

fbennett

Yep, unselect both of those. You don't need to sync attachments. (If you run into snags with the sync itself, the devs may need to chime in, but so far, so good.)

danioore

sorry.. more:
do i select 'sync automatically' and 'sync full-text content'?

(not sure if this is related/relevant, but i have extracted annotations on a number of items.)

fbennett

I would untick both of those also, for the initial sync. You can always select them later, once the content is all in place.