#12341: Empty (full) cremona database in Sage 4.8 causes tests to fail
-------------------------------+--------------------------------------------
Reporter: swenson | Owner: cremona
Type: defect | Status: needs_review
Priority: critical | Milestone: sage-5.0
Component: elliptic curves | Keywords:
Work_issues: | Upstream: N/A
Reviewer: John Cremona | Author: R. Andrew Ohana
Merged: | Dependencies:
-------------------------------+--------------------------------------------
Old description:
> I am on Ubuntu 11.10, and noticed that a fresh install of Sage 4.8 fails
> a bunch of tests because the full cremona database is an empty file by
> default.
>
> {{{
> [swenson@harry 10:18:14] sage-4.8 :) $ ./sage -t /home/swenson/sage-
> src/sage-4.8/devel/sage-main/sage/misc/functional.py
> (hg)-[default]-
> sage -t "devel/sage-main/sage/misc/functional.py"
> #0: simplify_sum(expr='sum(q^k,k,0,inf))
> #1: simplify_sum(expr=a*'sum(q^k,k,0,inf))
> **********************************************************************
> File "/home/swenson/sage-src/sage-4.8/devel/sage-
> main/sage/misc/functional.py", line 1360:
> sage: regulator(EllipticCurve('11a'))
> Exception raised:
> Traceback (most recent call last):
> File "/home/swenson/sage-src/sage-4.8/local/bin/ncadoctest.py",
> line 1231, in run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/swenson/sage-src/sage-4.8/local/bin/sagedoctest.py",
> line 38, in run_one_example
> OrigDocTestRunner.run_one_example(self, test, example, filename,
> compileflags)
> File "/home/swenson/sage-src/sage-4.8/local/bin/ncadoctest.py",
> line 1172, in run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_54[3]>", line 1, in <module>
> regulator(EllipticCurve('11a'))###line 1360:
> sage: regulator(EllipticCurve('11a'))
> File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
> packages/sage/schemes/elliptic_curves/constructor.py", line 295, in
> EllipticCurve
> return ell_rational_field.EllipticCurve_rational_field(x)
> File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
> packages/sage/schemes/elliptic_curves/ell_rational_field.py", line 198,
> in __init__
> X = sage.databases.cremona.CremonaDatabase()[label]
> File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
> packages/sage/databases/cremona.py", line 1363, in CremonaDatabase
> _db = LargeCremonaDatabase(name)
> File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
> packages/sage/databases/cremona.py", line 1119, in __init__
> + 'not appear to be a valid SQL Cremona database.')
> RuntimeError: Database at /home/swenson/sage-
> src/sage-4.8/data//cremona/cremona.db does not appear to be a valid SQL
> Cremona database.
> **********************************************************************
> 1 items had failures:
> 1 of 5 in __main__.example_54
> ***Test Failed*** 1 failures.
> For whitespace errors, see the file
> /home/swenson/.sage//tmp/functional_29532.py
> [4.3 s]
>
> ----------------------------------------------------------------------
> The following tests failed:
>
> sage -t "devel/sage-main/sage/misc/functional.py"
> Total time for all tests: 4.3 seconds
> [swenson@harry 10:18:22] sage-4.8 :( $ rm /home/swenson/sage-
> src/sage-4.8/data/cremona/cremona.db
> (hg)-[default]-
> [swenson@harry 10:18:25] sage-4.8 :) $ ./sage -t /home/swenson/sage-
> src/sage-4.8/devel/sage-main/sage/misc/functional.py
> (hg)-[default]-
> sage -t "devel/sage-main/sage/misc/functional.py"
> [4.3 s]
>
> ----------------------------------------------------------------------
> All tests passed!
> Total time for all tests: 4.3 seconds
> }}}
New description:
I am on Ubuntu 11.10, and noticed that a fresh install of Sage 4.8 fails a
bunch of tests because the full cremona database is an empty file by
default.
{{{
[swenson@harry 10:18:14] sage-4.8 :) $ ./sage -t /home/swenson/sage-
src/sage-4.8/devel/sage-main/sage/misc/functional.py
(hg)-[default]-
sage -t "devel/sage-main/sage/misc/functional.py"
#0: simplify_sum(expr='sum(q^k,k,0,inf))
#1: simplify_sum(expr=a*'sum(q^k,k,0,inf))
**********************************************************************
File "/home/swenson/sage-src/sage-4.8/devel/sage-
main/sage/misc/functional.py", line 1360:
sage: regulator(EllipticCurve('11a'))
Exception raised:
Traceback (most recent call last):
File "/home/swenson/sage-src/sage-4.8/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/swenson/sage-src/sage-4.8/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File "/home/swenson/sage-src/sage-4.8/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_54[3]>", line 1, in <module>
regulator(EllipticCurve('11a'))###line 1360:
sage: regulator(EllipticCurve('11a'))
File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
packages/sage/schemes/elliptic_curves/constructor.py", line 295, in
EllipticCurve
return ell_rational_field.EllipticCurve_rational_field(x)
File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
packages/sage/schemes/elliptic_curves/ell_rational_field.py", line 198, in
__init__
X = sage.databases.cremona.CremonaDatabase()[label]
File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
packages/sage/databases/cremona.py", line 1363, in CremonaDatabase
_db = LargeCremonaDatabase(name)
File "/home/swenson/sage-src/sage-4.8/local/lib/python/site-
packages/sage/databases/cremona.py", line 1119, in __init__
+ 'not appear to be a valid SQL Cremona database.')
RuntimeError: Database at /home/swenson/sage-
src/sage-4.8/data//cremona/cremona.db does not appear to be a valid SQL
Cremona database.
**********************************************************************
1 items had failures:
1 of 5 in __main__.example_54
***Test Failed*** 1 failures.
For whitespace errors, see the file
/home/swenson/.sage//tmp/functional_29532.py
[4.3 s]
----------------------------------------------------------------------
The following tests failed:
sage -t "devel/sage-main/sage/misc/functional.py"
Total time for all tests: 4.3 seconds
[swenson@harry 10:18:22] sage-4.8 :( $ rm /home/swenson/sage-
src/sage-4.8/data/cremona/cremona.db
(hg)-[default]-
[swenson@harry 10:18:25] sage-4.8 :) $ ./sage -t /home/swenson/sage-
src/sage-4.8/devel/sage-main/sage/misc/functional.py
(hg)-[default]-
sage -t "devel/sage-main/sage/misc/functional.py"
[4.3 s]
----------------------------------------------------------------------
All tests passed!
Total time for all tests: 4.3 seconds
}}}
----
See comment:14 for an explanation of the issues causing this.
----
Apply attachment:trac12341.patch to the Sage Library.
--
Comment(by rohana):
Replying to [comment:13 cremona]:
> I have not checked all the logic in the revised code.
I don't think I have explained the issue that this ticket fixes very
clearly (which was exposed when running one of the optional doctests
without having the optional spkg installed). There are 2 main issues that
caused this:
* When calling `CremonaDatabase('name')` the file
`SAGE_ROOT/data/cremona/name.db` was being touched, something that is bad
in general if the file wasn't there to start with.
* When calling `CremonaDatabase()`, to determine if the full database is
installed, it would check for the existence of
`SAGE_ROOT/data/cremona/cremona.db` rather than use one of the functions
in `sage.misc` for this purpose.
With these combined, running the optional doctests would break the cremona
database: it would run `CremonaDatabase('cremona')`, which would touch
`SAGE_ROOT/data/cremona/cremona.db` and thus later calls of
`CremonaDatabase()` would break since it would think the full cremona
database was installed and try to use the touched file.
> I was puzzled by the remark about testing with flag --optional since I
thought that only made sense with some sensible string after the word
"optional", e.g. "magma".
Unless you want to test all optional packages (which could be useful for a
giant system install -- unfortunately there are a few optional packages
that don't want to build properly at the moment).
> But it seems that there are doctest lines which are tagged "# optional"
with no mention of which optional package is relevant.
I consider this a bug and something that should be required for any
optional tags.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12341#comment:14>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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