Recently, the Mendeley bibliography-management and paper-archive tool started encrypting users’ databases of bibliographic data.
Each such database includes annotations and is the product of a user’s careful, hard manual work.
Previously, users were able to access their valuable data using standard tools. Now, that access has been removed.
I have used Mendeley for almost a decade, now, and I value my database and my data very highly.
Therefore, I looked into what exactly Mendeley has done to prevent me accessing my data, and figured out an awkward manual technique for rescuing enough of it to let me switch to a new bibliography management system.
The reasons for the change are unclear, but it’s possible that this user-hostile encryption was put into the product in retaliation for a competing product, Zotero, adding support for importing records from a Mendeley database. Zotero discusses the problem here, stating that
“Mendeley 1.19 and later have begun encrypting the local database, making it unreadable by Zotero and other standard database tools.”
and the project has also tweeted that
“The latest version of Mendeley prevents you from getting all of your data out of the app.”
Certainly, the old technique for accessing the database no longer works:
$ sqlite3 email@example.com@www.mendeley.com.sqlite SQLite version 3.23.1 2018-04-10 17:39:29 Enter ".help" for usage hints. sqlite> .tables Error: file is not a database sqlite>
The new encryption definitely prevents me from getting all of my data from the database I have so carefully constructed.
The encryption Mendeley is using
Mendeley is using the SQLite Encryption Extension (“SEE”) with a hidden key.
The SEE library is closed-source and very proprietary. Its API is documented, but its on-disk structures are not (publicly) documented, and the source code is not publicly available. Applications using SEE are required to make it impossible to access SEE functionality from outside the application.
For a while, I had hoped that they might have used the open-source sqlcipher library. Unfortunately, they did not. Even more unfortunately, while tooling exists for sqlcipher, and while SEE and sqlcipher are API-compatible, the resulting files are neither binary- nor tooling-compatible.
It is not clear where the key material is coming from—whether the key is per-database, or whether it is a hard-coded key that is part of the Mendeley application binary, or whether it is a key that is retrieved from the Mendeley online API.
The question is ultimately moot, given the closedness of the SEE format and library. Even if I had the key, there is no tooling for making use of it in any other context than the Mendeley application itself.
How to rescue your data
Here’s the technique I used to rescue my data for long enough to allow a Zotero import to work.
Unfortunately, it’s not easy. It works only on Linux, and relies on
being able to run
gdb to call an internal SQLite SEE routine,
In the instructions below, modify file paths etc. to line up with your own Mendeley and Unix usernames etc.
Quit Mendeley. You don’t want it running while you’re fiddling with its database.
BACK UP YOUR DATABASE. You will want to put things back the way they were after you’re done so you can use Mendeley again. THE REST OF THIS PROCEDURE MODIFIES THE DATABASE FILE ON DISK in ways that I do not know whether the Mendeley application can handle.
cd ~/.local/share/data/Mendeley\ Ltd./Mendeley\ Desktop/ cp firstname.lastname@example.org@www.mendeley.com.sqlite ~/backup-encrypted.sqlite
Start Mendeley under the control of
Add a breakpoint that captures the moment a SQLite database is opened.
(gdb) b sqlite3_open_v2
Start the program.
The program will stop at the breakpoint several times. Keep continuing the program until the string pointed to by
$rdinames the file you backed up in the step above.
Thread 1 "mendeleydesktop" hit Breakpoint 1, 0x000000000101b1b0 in sqlite3_open_v2 () (gdb) x/s $rdi 0x1dca928: "/home/tonyg/.local/share/data/Mendeley Ltd./Mendeley Desktop/Settings.sqlite" (gdb) c Continuing. Thread 1 "mendeleydesktop" hit Breakpoint 1, 0x000000000101b1b0 in sqlite3_open_v2 () (gdb) x/s $rdi 0x1dcb318: "/home/tonyg/.local/share/data/Mendeley Ltd./Mendeley Desktop/Settings.sqlite" (gdb) c
(… repeats a few times …)
Thread 1 "mendeleydesktop" hit Breakpoint 1, 0x000000000101b1b0 in sqlite3_open_v2 () (gdb) x/s $rdi 0x25f1818: "/home/tonyg/.local/share/data/Mendeley Ltd./Mendeley Desktopemail@example.com@www.mendeley.com.sqlite"
Now, set a breakpoint for the moment the key is supplied to SEE. We don’t care about the key itself (for reasons discussed above), but we do care to find the moment just after
(gdb) b sqlite3_key Breakpoint 2 at 0x101b2c0 (gdb) c Continuing. Thread 1 "mendeleydesktop" hit Breakpoint 2, 0x000000000101b2c0 in sqlite3_key () (gdb) info registers rax 0x7fffffffc6b0 140737488340656 rbx 0x25f0590 39781776 rcx 0x7fffea9a0c40 140737129352256 rdx 0x20 32 rsi 0x260fd68 39910760 rdi 0x25ef4e8 39777512 rbp 0x7fffffffc730 0x7fffffffc730 rsp 0x7fffffffc688 0x7fffffffc688 r8 0xc1 193 r9 0x7fffea9a0cc0 140737129352384 r10 0x0 0 r11 0x1 1 r12 0x7fffffffc6b0 140737488340656 r13 0x7fffffffc6a0 140737488340640 r14 0x7fffffffc790 140737488340880 r15 0x7fffffffc790 140737488340880 rip 0x101b2c0 0x101b2c0 <sqlite3_key> eflags 0x202 [ IF ] cs 0x33 51 ss 0x2b 43 ds 0x0 0 es 0x0 0 fs 0x0 0 gs 0x0 0
Copy down the value of
info registersoutput. It is the pointer to the open SQLite database handle. Then, finish execution of
(gdb) fin Run till exit from #0 0x000000000101b2c0 in sqlite3_key () 0x0000000000f94e54 in SqliteDatabase::openInternal(QString const&, SqlDatabaseKey*) ()
gdb’s ability to call C functions to rekey the database to the null key, thereby decrypting it in-place and allowing Zotero import to do its work.
Use the value for
$rdiyou noted down in the previous step as the first argument to
sqlite3_rekey_v2, and zero for the other three arguments.
(gdb) p sqlite3_rekey_v2(0x25ef4e8, 0, 0, 0) $1 = 0
If you see
$1 = 0from the rekey command, all is well, and you may now use Zotero to import your Mendeley database. (Update: See below if you don’t see
$1 = 0; for example, you might see
$1 = 8.)
While this is happening, leave
gdbrunning and don’t touch it! DO NOT QUIT GDB OR RUN MENDELEY while the import is proceeding. Who knows what might happen to your carefully decrypted database if you do!
In fact, before you start Zotero, you might like to copy your decrypted database to somewhere safe, so you don’t have to do this again:
cd ~/.local/share/data/Mendeley\ Ltd./Mendeley\ Desktop/ cp firstname.lastname@example.org@www.mendeley.com.sqlite ~/backup-decrypted.sqlite
Once the import is complete, quit
gdband terminate the associated partially-initialised Mendeley process.
(gdb) quit A debugging session is active. Inferior 1 [process 32750] will be killed. Quit anyway? (y or n) y [322:322:0100/000000.491674:ERROR:broker_posix.cc(43)] Invalid node channel message
Finally, restore your backed-up copy of the encrypted database, so that Mendeley will continue to run OK.
cd ~/.local/share/data/Mendeley\ Ltd./Mendeley\ Desktop/ cp ~/backup-encrypted.sqlite email@example.com@www.mendeley.com.sqlite
You can now, if you like, in addition to using your new Zotero database as normal, access the raw contents of your decrypted Mendeley database using the standard SQLite tools, like you could in previous Mendeley versions:
$ sqlite3 ~/backup-decrypted.sqlite SQLite version 3.23.1 2018-04-10 17:39:29 Enter ".help" for usage hints. sqlite> .tables CanonicalDocuments DocumentZotero NotDuplicates DataCleaner Documents Profiles DocumentCanonicalIds EventAttributes RemoteDocumentNotes DocumentContributors EventLog RemoteDocuments DocumentDetailsBase FileHighlightRects RemoteFileHighlights DocumentFields FileHighlights RemoteFileNotes DocumentFiles FileNotes RemoteFolders DocumentFolders FileReferenceCountsView Resources DocumentFoldersBase FileViewStates RunsSinceLastCleanup DocumentKeywords Files SchemaVersion DocumentNotes Folders Settings DocumentReferences Groups Stats DocumentTags HtmlLocalStorage SyncTokens DocumentUrls ImportHistory ZoteroLastSync DocumentVersion LastReadStates sqlite>
No user should have to do this to access their data. I’m lucky I have the skills to do it at all.
I’m sad that Mendeley violated my trust this way, but glad I have an exit strategy now.
Update: what to do if you see
$1 = 8
p sqlite3_rekey_v2(...) attempt fails, with (say)
$1 = 8
as the outcome, then you may have been victim of an unfortunate thread
interleaving, or you might have caught a “spurious” opening of the
database. It seems that the program sometimes opens the main database
at least once in some odd way, before opening it properly for
If you think it’s threading, you could try abandoning the procedure
and restarting from the beginning: just quit
gdb and restart the
To deal with the “spurious” openings, experiment to see if the program
opens the main database a second time. Run the procedure all the way
up to the
p sqlite3_rekey_v2(...) step, but do not run
sqlite3_rekey_v2. Instead, just type
c to continue, returning to
the step where you inspect each call to
sqlite3_open_v2, waiting for
$rdi pointing to a string with the right database filename.
When you see it come round again, then try the
step. If you see
$1 = 0 this time, you’re all set, and can proceed
as described above for a successful call to
If you’re still having problems with this procedure, do feel free to email me, and I’ll try to help if I can.