Re: [proteowizard-developer] Closing Files

[Brendan M. <bre...@pr...>]

Ack!  Apparently the act of stepping through the C# code impacts the
outcome.  Removing the breakpoint on run.chromatogramList causes everything
to behave as expected.

So, it really was just the missing ChromatogramList.Dispose() call all
along...  and unfortunately, I am 2 hours of debugging past realizing that.
Also apparently that Dispose() method can be triggered with a using ()
block, despite not implementing IDisposable...

Oh, well, at least it works now, and I certainly have a much better
understanding of the inner workings of the MSData.Run. :-)

--Brendan

On Fri, Aug 7, 2009 at 6:07 AM, Brendan MacLean <bre...@pr...>wrote:

> Hi Matt,
> My kingdom for a data breakpoint!  Apparently you can't set them in C#
> debugging, even with native debugging enabled.
>
> But, I have gotten a bit further.  All the interesting add_ref calls seem
> to happen executing the line of C# code:
>
> run.chromatogramList
>
> I can watch the ref count in the memory window, and it gets incremented 3
> times:
>
>    - Before the actual C++ code for Run::chromatogramList::get()
>    - As expected in the code for Run::chromatogramList::get(), and I can
>    break on the add_ref_copy() call that does it.
>    - After the debugger has returned to the C# code, during the step to
>    the next line
>
> My code appears to add no further references to the chromatogramList, and
> when I Dispose() it, the count drops to 2.  And, when the CLI
> ChromatogramList object is actually destroyed in garbage collection, the
> destructor for the C++ ChromatogramList fires.
>
> Sure wish I could figure out where to put the breakpoint in
> shared_count.hpp to catch the two bounding add_ref calls.  And, of course, a
> data breakpoint would make this so much easier.
>
> Anyway, moving forward still....
>
> --Brendan
>
>
> On Fri, Aug 7, 2009 at 5:50 AM, Matt Chambers <
> mat...@va...> wrote:
>
>> It might be some ChromatogramIdentity objects that haven't been
>> disposed. Those hold references to their parent list because in the
>> native code they are destroyed when the list is destroyed.
>>
>> We discussed having an explicit close function for MSData but it hasn't
>> been done yet. The distasteful thing is that the function would have no
>> meaning for the base MSData class, only for MSDataFile. And what do you
>> do with MSData objects from WIFF files which share their WiffFilePtr
>> with other MSData objects from the same WIFF?
>>
>> Also, have you tried a using(MSData blah bla) {} block?
>>
>> -Matt
>>
>>
>> Brendan MacLean wrote:
>> > Well, the root cause appears to be the CLI binding for
>> > ChromatogramList is holding onto the ChromatogramList_mzML, which in
>> > turn has a shared_pointer on the file.  I thought I was home free when
>> > I noticed that both ChromatogramList and SpectrumList have Dispose()
>> > methods (though not implementing IDisposable).  But, I have tried
>> > calling ChromatogramList.Dispose() to no avail, and stepping into it,
>> > it does release a shared pointer, but the reference count appears to
>> > be 3 before the release and 2 after.  The C++ version of
>> > ChromatogramList doesn't have its destructor called until the GC
>> > thread gets a turn at the end of my test.  Though the C++ MSData and
>> > SpectrumList (which I am not using) get destroyed when I call
>> > MSData.Dispose().
>> >
>> > Quite a tangled web, but PWiz really does need to support
>> > deterministic file closing from the CLI binding...
>> >
>> > --Brendan
>> >
>> > On Thu, Aug 6, 2009 at 4:24 PM, Brendan MacLean
>> > <bre...@pr... <mailto:bre...@pr...>> wrote:
>> >
>> >     I had been assuming MSData.Dispose() would close any open file
>> >     handles, but as I am writing regression tests, it appears that I
>> >     was mistaken.  And on a simple mzML file no less.  I'll dig into
>> >     this further, but if anyone would like to offer a solution, I'd be
>> >     happy to hear of it...
>> >
>> >     --Brendan
>> >
>> >
>>
>>
>>
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