OK, I have a pretty big problem here.
I just opened my ref database and found that 400-500 of them were completely blank, all that was left was the unique ID, everything else was gone...
I tried to re-index and rebuild the database but that just crashed Bookends.
I really don't know what might have caused this, I closed the program when I left work yesterday and today it opened like this. I did perform some global find/replace actions yesterday, that's the only thing I can think of really.
Luckily I had a backup from the day before that I could go back to, but this was pretty scary. I had just started to feel happy about Bookends and really appreciate some of its features (groups, live searches, PDF archiving, developer support...) but this makes me consider moving back to endnote again. As much as I have come to dislike it, it has never ever lost any data for me. And with a program like this, stability and reliability is really the main feature.
So, I wonder, was this a freak occurence, or is it something that happens occasionally? Has enyone else seen this? I did see that someone else lost the journal names when upgrading to 8.01. In my case the upgrade shouldn't be the cause though.
By the way, these database maintenence options... How often should one run them, should it be done regularily or only in case of a problem? And the defragment & compact option... what does that do? I noticed that my bookends library takes up almost 16 MB, while the same library in endnote is only 2 MB. That's a 8-fold increase in size... is that normal?
Many questions... sorry for that, but I am a little frustrated... I will keep updating my endnote library in parallell for a while, but I really would like to continue with Bookends.
Best regards, Niklas
Blank records
Hi niklas,
Sorry about this problem, but I'm glad you have good backups.
I am getting sporadic reports (rare, fortunately) of data being lost for no obvious reason. If you can send me your database (stuffed, please) I'll see if there is anything to be learned from it. And importantly, if you can reproduce this it would be of tremendous help -- if we can reproduce a bug, we can fix it.
As for frequency of maintenance operations:
1. Reindex/rebuild -- I would run these only if you are having unexplained problems (e.g. a Find that fails when it should work could be due to a bad index).
2. Defragment and compact -- only after deleting a lot of references. Otherwise it has little effect.
As far as the size of databases, every field is indexed by word, and that adds a lot. Furthermore, the db engine is optimized for speed, and the compromise is that some space saving is sacrificed. I'm surprised that a 2 MB db in EndNote is 16 in Bookends -- the ratio is usually much less. But Bookends databases do tend to be larger. You will find, though, that they compress to much smaller sizes when you zip or stuff them.
Anyway, once again, although 8.0.1 fixed many of the initial problems people encountered, there are still things we are finding and fixing. If you can possibly reproduce a problem we would be grateful if you reported it to us.
Jon
Sonny Software
Sorry about this problem, but I'm glad you have good backups.
I am getting sporadic reports (rare, fortunately) of data being lost for no obvious reason. If you can send me your database (stuffed, please) I'll see if there is anything to be learned from it. And importantly, if you can reproduce this it would be of tremendous help -- if we can reproduce a bug, we can fix it.
As for frequency of maintenance operations:
1. Reindex/rebuild -- I would run these only if you are having unexplained problems (e.g. a Find that fails when it should work could be due to a bad index).
2. Defragment and compact -- only after deleting a lot of references. Otherwise it has little effect.
As far as the size of databases, every field is indexed by word, and that adds a lot. Furthermore, the db engine is optimized for speed, and the compromise is that some space saving is sacrificed. I'm surprised that a 2 MB db in EndNote is 16 in Bookends -- the ratio is usually much less. But Bookends databases do tend to be larger. You will find, though, that they compress to much smaller sizes when you zip or stuff them.
Anyway, once again, although 8.0.1 fixed many of the initial problems people encountered, there are still things we are finding and fixing. If you can possibly reproduce a problem we would be grateful if you reported it to us.
Jon
Sonny Software
Hi Jon, and thanks for your response.
This kind of quick and helpful developer feedback is perhaps my main incentive to stay with Bookends. It is very much appreciated. Thanks also for your explanation of DB sizes. For what it's worth, I just recreated my database from scratch, by first importing my new Bookends records from the previous database and then my old Endnote records, and now the size of the database was just 6.4 MB...
Anyway, I will send you a copy of my corrupt database, and I will keep an eye out and will tell you if it happens again.
Best regards, Niklas
This kind of quick and helpful developer feedback is perhaps my main incentive to stay with Bookends. It is very much appreciated. Thanks also for your explanation of DB sizes. For what it's worth, I just recreated my database from scratch, by first importing my new Bookends records from the previous database and then my old Endnote records, and now the size of the database was just 6.4 MB...
Anyway, I will send you a copy of my corrupt database, and I will keep an eye out and will tell you if it happens again.
Best regards, Niklas
Abstract field information missing
I didn't lose all my data, but once again it seems fairly certain that the 505a field that is set up to occupy the abstract field is getting lost. Now I will track this by not including any reference with 505 information in the hit list. I like having this (505) information available, especially since it's useful for knowing what is in edited volumes.
Another minor problem discovered today: one item cannot be opened as a reference. Clicking on the item always opens the item above it. I have tried different ways of opening the item; result is always the same (title above it).
Another minor problem discovered today: one item cannot be opened as a reference. Clicking on the item always opens the item above it. I have tried different ways of opening the item; result is always the same (title above it).
Re: Abstract field information missing
For this sort of technical issue, please contact me directly. I'll need the db (stuffed, please) to reproduce the problem with opening the wrong reference, as well as explicit directions for how to reproduce the 505a problem.spd wrote:...but once again it seems fairly certain that the 505a field that is set up to occupy the abstract field is getting lost. Now I will track this by not including any reference with 505 information in the hit list. I like having this (505) information available, especially since it's useful for knowing what is in edited volumes.
Another minor problem discovered today: one item cannot be opened as a reference. Clicking on the item always opens the item above it. I have tried different ways of opening the item; result is always the same (title above it).
Jon
Sonny Software
related to library size mentioned above...
Hello,
a comment about the large size of libraries in Bookends: I have noticed that after adding several (10-20-30?) new references to my library and assigning them to groups, the library often increases in size considerably, by about 2 MB or so.
To fix this I now rebuild the library after adding new references. That brings the size down again.
A question about groups: is it possible to assign one of the "User" fields to show which group(s) a reference belongs to? Or: what's the easiest way to find out whether a reference is part any group(s)?
stef
a comment about the large size of libraries in Bookends: I have noticed that after adding several (10-20-30?) new references to my library and assigning them to groups, the library often increases in size considerably, by about 2 MB or so.
To fix this I now rebuild the library after adding new references. That brings the size down again.
A question about groups: is it possible to assign one of the "User" fields to show which group(s) a reference belongs to? Or: what's the easiest way to find out whether a reference is part any group(s)?
stef
Hi,
1. DB size. This is a function of the db engine, Valentina, which uses a lot of real estate to optimize performance. Note that if you compress a database (stuffit or zip) it gets pretty small. It is also partially due to the fact that in Bookends all fields are indexed. The indexes can account for 30-40% of the size of a database. Finally, the data are stored as UTF-16 (2 bytes per char). When UTF-8 storage is implemented, there should be substantial (not twofold, though) reduction in db size.
2. How to know if a reference is in a (presumably static) group? You can click on the group and see if the reference is there, of course. But other than that there is now way to know, unless you place that info in the reference itself (e.g. put the name of the group in Keywords or a User field). And of course one reference could belong to many groups. FWIW, if you add a reference to a group in which it is already a member, Bookends is smart enough to not put it in twice.
Jon
Sonny Software
1. DB size. This is a function of the db engine, Valentina, which uses a lot of real estate to optimize performance. Note that if you compress a database (stuffit or zip) it gets pretty small. It is also partially due to the fact that in Bookends all fields are indexed. The indexes can account for 30-40% of the size of a database. Finally, the data are stored as UTF-16 (2 bytes per char). When UTF-8 storage is implemented, there should be substantial (not twofold, though) reduction in db size.
2. How to know if a reference is in a (presumably static) group? You can click on the group and see if the reference is there, of course. But other than that there is now way to know, unless you place that info in the reference itself (e.g. put the name of the group in Keywords or a User field). And of course one reference could belong to many groups. FWIW, if you add a reference to a group in which it is already a member, Bookends is smart enough to not put it in twice.
Jon
Sonny Software
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rlanderson
- Posts: 2
- Joined: Tue Mar 22, 2005 3:29 pm
Blank Records
I had the same blank record problem that niklas described. I created a new Bookends database, imported 84 records from an Endnote Refer import file, did some clean up on the imported data, and closed the database. When I opened it again, there were still 84 records in the database, but all the records were blank. Rebuilding the database did nothing.
I have a copy of the corrupted database that I can send your way if that would be helpful.
I have a copy of the corrupted database that I can send your way if that would be helpful.
Hi rlanderson,
Better than a corrupted database would be an email describing exactly what you did, step-by-step. If I can reproduce the problem, I can fix it.
It would be very helpful if you could contact me directly with this information.
suppport@sonnysoftware.com
Thanks,
Jon
Sonny Software
Better than a corrupted database would be an email describing exactly what you did, step-by-step. If I can reproduce the problem, I can fix it.
It would be very helpful if you could contact me directly with this information.
suppport@sonnysoftware.com
Thanks,
Jon
Sonny Software
One additional note. The problem with loss of data is rare and has been difficult to reproduce, but it obviously can occur. This issue is in the hands of the database engine developer, and we are working together to isolate and fix it. I would like to take this opportunity to repeat that the best insurance (for any problem) is backing up databases. When we have more information about this particular problem I'll post it here, and upload any fixes as soon as they are ready.
Jon
Sonny Software
Jon
Sonny Software
No records (twice)
I imported an endnote reference, with the appropriate filter checked. When I was looking at the reference view of the last record imported, I noticed two records instead of one were added. I attempted to delete the extra reference. But the confirmation that usually comes up reminding me that the action is undoable, never came up. Next thing I see are blank references. I go to All on Listview, and there was completely nothing in my database. This is the second time I have tried to import an endnote reference and something weird happened. Fortunately I had a back up.
-Ni
It is not the import that is the problem. There is a combination of events, difficult to reproduce, where importing, creating references, and deleting references, all without closing the database in between, seems to cause this problem. We have been able to create one reproducible scenario, and it has been confirmed by the database engine developer. We hope to have isolated the problem soon, and will post a fix as soon as we do.
Jon
Sonny Software
Jon
Sonny Software
We have isolated and fixed an uncommon bug in the delete function that could result in loss of data in one or more fields in other references (i.e. blank records). The fix has been incorporated into 8.0.3, which is now available for downloading. We urge everyone to obtain this version.
Of course, you should still maintain good backups of your data. And if you encounter problems, please contact us with the steps necessary to reproduce them, if possible. This helps enormously in identifying the underlying cause.
Jon
Sonny Software
Of course, you should still maintain good backups of your data. And if you encounter problems, please contact us with the steps necessary to reproduce them, if possible. This helps enormously in identifying the underlying cause.
Jon
Sonny Software
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Guest
Hi, I closed bookends 8.0.1, installed 8.0.3 and whoops all my references are still there but blank. I really hope this is fixed in 8.0.3. Meanwhile it looks like the data is not completely lost. If I "cat" the database file in a terminal window I can see the text that makes up my references scroll by. So it looks like the info is there, but it's just not visible anymore 
Database maintenance doen't fix it though. I tried going back to 8.0.1, but my DB is still hosed.
Database maintenance doen't fix it though. I tried going back to 8.0.1, but my DB is still hosed.