db_demo remove does not work

[redbluewater]

[joefutrelle]

Looks like other parts of the CLI are out of sync with the same ORM changes:

ubuntu@dashboard-v28:~/domdb$ python db_demo.py 
18215 metabolites in database
Hi Krista
(Cmd) count tps4
Traceback (most recent call last):
  File "db_demo.py", line 122, in <module>
    shell.cmdloop('Hi Krista')
  File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
    stop = self.onecmd(line)
  File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
    return func(arg)
  File "db_demo.py", line 68, in do_count
    n = mtab_count(session, exp)
  File "db_demo.py", line 43, in mtab_count
    q = q.filter(Mtab.exp_name == exp)
AttributeError: type object 'Mtab' has no attribute 'exp_name'

[joefutrelle]

Aha, doesn't work to write

session.query(Mtab).filter(Mtab.exp.name==exp)

Instead, in SQLAlchemy, one has to write

session.query(Mtab).filter(Mtab.exp.has(name=exp))

That fixed the "count" query but I'm getting an unfamiliar error when I try to fix the "remove" command the same way:

ubuntu@dashboard-v28:~/domdb$ python db_demo.py 
18215 metabolites in database
Hi Krista
(Cmd) remove tps4
Removing all tps4 data ...
Traceback (most recent call last):
  File "db_demo.py", line 122, in <module>
    shell.cmdloop('Hi Krista')
  File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
    stop = self.onecmd(line)
  File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
    return func(arg)
  File "db_demo.py", line 107, in do_remove
    session.query(Mtab).filter(Mtab.exp.has(name=exp)).delete()
  File "/usr/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2603, in delete
    delete_op.exec_()
  File "/usr/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 815, in exec_
    self._do_pre_synchronize()
  File "/usr/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 866, in _do_pre_synchronize
    "Could not evaluate current criteria in Python. "
sqlalchemy.exc.InvalidRequestError: Could not evaluate current criteria in Python. Specify 'fetch' or False for the synchronize_session parameter.

[joefutrelle]

That's because the query, which used to be a simple one, is now a join, and so SQLAlchemy needs a synchronization strategy parameter. Works like a charm.

http://stackoverflow.com/questions/7892618/sqlalchemy-delete-subquery

Chasing down more out of date references before I close this out. More than just the remove command is affected.

[joefutrelle]

Fixed, but not pushing yet until I fix a related issue, which I'll open momentarily.

[redbluewater]

As an aside (since we are both learning here)...I think I figured out why GitHub ignored my changes yesterday about notifications. There is clearly a delay between 'changing your notification options' and 'something actually getting changed'.

Krista

On 10/9/2014 4:45 PM, Joe Futrelle wrote:

Fixed, but not pushing yet until I fix a related issue, which I'll open momentarily.

— Reply to this email directly or view it on GitHub https://github.com/joefutrelle/domdb/issues/5#issuecomment-58574821.

Krista Longnecker Woods Hole Oceanographic Institution Marine Chemistry and Geochemistry Fye 112, MS#4 360 Woods Hole Road Woods Hole, MA 02543-1541 http://www.whoi.edu/people/klongnecker/

klongnecker@whoi.edu 508 289 2824

[joefutrelle]

fixed