Add missing commit when building large Cremona database

[jamesjer]

📚 Description

Building the large Cremona database fails like this on an x86_64 Fedora Rawhide machine. (I captured the output from an old sagemath 9.6 build, but the same error occurs with sagemath 9.7.)

Inserting allgens.90000-99999
Committing...
Traceback (most recent call last):
  File "/builddir/build/BUILD/sage-9.6/cremona.sage.py", line 10, in <module>
    c._init_from_ftpdata('ecdata-2019-10-29')
  File "/builddir/build/BUILDROOT/sagemath-9.6-4.fc38.x86_64/usr/lib64/python3.11/site-packages/sage/databases/cremona.py", line 1397, in _init_from_ftpdata
    self.vacuum()
  File "/builddir/build/BUILDROOT/sagemath-9.6-4.fc38.x86_64/usr/lib64/python3.11/site-packages/sage/databases/sql_db.py", line 2180, in vacuum
    self.__connection__.execute('VACUUM')
sqlite3.OperationalError: cannot VACUUM from within a transaction

The issue is a missing database commit, which this PR adds.

📝 Checklist

• I have made sure that the title is self-explanatory and the description concisely explains the PR.
• I have linked an issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation accordingly.

⌛ Dependencies

[github-actions]

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[vincentmacri]

@jamesjer If you're still willing to contribute this I'm willing to review it. Can you merge the latest develop branch and also let me know where you got the Cremona database file to build from?

[jamesjer]

Okay, I have rebased on top of git head. I got the Cremona database file here, specifically from one of the tags. The last one I tried was 2019-10-29.

[vincentmacri]

I'm having difficulty trying to build the database on 10.4 in order to make sure I can replicate your issue.

Can you explain your process for trying to build the database?

This is what I'm doing that doesn't work:

I'm attempting to use sage.databases.cremona.build and I'm running into errors with extracting the tar file because the name of the tar file isn't ecdata. I get:

Extracting files from /home/[username]/Downloads/ecdata.tar.gz...
tar: ecdata/allcurves: Not found in archive
tar: ecdata/allbsd: Not found in archive
tar: ecdata/degphi: Not found in archive
tar: ecdata/allgens: Not found in archive
tar: Exiting with failure status due to previous errors

Renaming the tar file doesn't work, but extracting it then making a new tarfile called ecdata.tar.gz fixes this problem. Then it complains that I already have a cremona database file so I deleted the database file and now it complains that I don't have a cremona database file.

[jamesjer]

I haven't done this for awhile. Looking back through my notes, this seems to be the process. First, run touch /usr/share/sagemath/cremona/cremona.db (replace /usr/share/sagemath with wherever your sagemath installation is). That addresses the problem you are having where it complains that there is no Cremona database file. Then create a file named cremona.sage with these contents:

import sage.databases.cremona
c = sage.databases.cremona.LargeCremonaDatabase('cremona', False, True)
c._init_from_ftpdata('ecdata-2019-10-29')

Replace the ecdata version on that last line with whatever you have. Then run sage cremona.sage.

[vincentmacri]

I've tested locally and everything seems to be working. Thanks for the contribution!