zothero: malformed database schema error

Untested but this should work:

diff --git a/src/lib/zothero/betterbibtex.py b/src/lib/zothero/betterbibtex.py
index df9f23a..eee83ec 100644
--- a/src/lib/zothero/betterbibtex.py
+++ b/src/lib/zothero/betterbibtex.py
@@ -16,9 +16,6 @@ from .util import timed
 log = logging.getLogger(__name__)
 
 
-SQL = "SELECT data FROM `better-bibtex` WHERE name = 'better-bibtex.citekey';"
-
-
 class BetterBibTex(object):
     """Read citkeys from BetterBibTex database.
 
@@ -47,15 +44,14 @@ class BetterBibTex(object):
             
             return
 
-        conn = sqlite3.connect(dbpath)
+        conn = sqlite3.connect(':memory:')
+        conn.execute('ATTACH DATABASE ? AS betterbibtex', dbpath)
         
         with timed('load Better Bibtex data'):
             
-            row = conn.execute(SQL).fetchone()
-            data = json.loads(row[0])['data']
             self._refkeys = {
-                str(ck['libraryID']) + '_' + ck['itemKey']: ck['citekey']
-                for ck in data
+                str(ck['libraryID']) + '_' + ck['itemKey']: ck['citationKey']
+                for c in conn.execute('select * from betterbibtex.citationkey')
             }
         self.exists = True
 

You issue

SELECT COUNT(*) FROM betterbibtex.sqlite_master WHERE type='table' AND name = 'citationkey'

If that returns 1, you have the new database (get the keys from betterbibtex.citationkey), if it returns 0 you have the old database (get the keys from betterbibtex."better-bibtex").

Thanks! I will give it a try.

Untested but this should work:

diff --git a/src/lib/zothero/betterbibtex.py b/src/lib/zothero/betterbibtex.py
index df9f23a..eee83ec 100644
--- a/src/lib/zothero/betterbibtex.py
+++ b/src/lib/zothero/betterbibtex.py
@@ -16,9 +16,6 @@ from .util import timed
 log = logging.getLogger(__name__)
 
 
-SQL = "SELECT data FROM `better-bibtex` WHERE name = 'better-bibtex.citekey';"
-
-
 class BetterBibTex(object):
     """Read citkeys from BetterBibTex database.
 
@@ -47,15 +44,14 @@ class BetterBibTex(object):
             
             return
 
-        conn = sqlite3.connect(dbpath)
+        conn = sqlite3.connect(':memory:')
+        conn.execute('ATTACH DATABASE ? AS betterbibtex', dbpath)
         
         with timed('load Better Bibtex data'):
             
-            row = conn.execute(SQL).fetchone()
-            data = json.loads(row[0])['data']
             self._refkeys = {
-                str(ck['libraryID']) + '_' + ck['itemKey']: ck['citekey']
-                for ck in data
+                str(ck['libraryID']) + '_' + ck['itemKey']: ck['citationKey']
+                for c in conn.execute('select * from betterbibtex.citationkey')
             }
         self.exists = True
 

Thank you so much for the solution!

I have to do a bit adjustments to make it work:

1. Add an additional conn.row_factory = sqlite3.Row to access the data in row using str as indices. Iterating conn.execute(‘select …’) would return tuples otherwise.
2. Wrap dbpath with parentheses and a comma (like (dbpath, )) to expand the argument correctly into the sql command.
3. Use for ck in conn.execute('select * from betterbibtex.citationkey') instead of for c in .... This might be a typo.

The whole __init__ method now looks like this:

    def __init__(self, datadir):
        """Load Better Bibtex database from Zotero data directory.

        Args:
            datadir (unicode, optional): Zotero's data directory.

        Raises:
            RuntimeError: Raised if Better Bibtex database doesn't exist.

        """
        
        self._refkeys = {}
        self.exists = False
        #dbpath = os.path.join(datadir, 'better-bibtex.sqlite')
        dbpath = datadir
        
        if not os.path.exists(dbpath):
            
            return

        conn = sqlite3.connect(':memory:')
        conn.row_factory = sqlite3.Row
        conn.execute('ATTACH DATABASE ? AS betterbibtex', (dbpath, ))
        
        with timed('load Better Bibtex data'):
            
            # for ck in conn.execute('select * from betterbibtex.citationkey'):
            #     print(ck)
            self._refkeys = {
                str(ck['libraryID']) + '_' + ck['itemKey']: ck['citationKey']
                for ck in conn.execute('select * from betterbibtex.citationkey')
            }
        self.exists = True

Now everything works like a charm.

Hope this can help you guys.

No, those are targeted changes, you can’t replace the whole file. The author of this program will have to get involved.

Hi, all - just FYI, if you haven’t updated to Zotero 7, it’s possible to just downgrade to BBT (I used 6.7.71 via Zotero tools/addons/install add on from file). There’s a “corrupt database” error message, but reloading Zotero data via zotconf seems to have resolved all issues with the workflow for now.

Which Zotero will undo within 48 hours by finding a newer BBT and installing that automatically. Please apply the patch to Zothero.

The database schema for auto-exports did change, and another change is slated for the citation key database.