Re: [Psidev-ms-dev] [proteowizard-developer] Empty mzML files

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So is this what the tail end of such a file would look like?
   ....
    </run>
  </mzML>
  <indexList count="2">
    <index name="spectrum">
    </index>
    <index name="chromatogram">
    </index>
  </indexList>
  <indexListOffset>3960</indexListOffset>
  <fileChecksum>03a9be216becb05f58b9bd967ff521f5b9883154</fileChecksum>
</indexedmzML>

or would it be
   ....
    </run>
  </mzML>
  <indexList count="0">
  </indexList>
  <indexListOffset>3902</indexListOffset>
  <fileChecksum>e216bec03a9bb67ff521f5b98805f58b9bd93154</fileChecksum>
</indexedmzML>

?

I lean toward the former, but what would the revised schema dictate?.

Brian

On Mon, Dec 17, 2012 at 4:14 PM, Eric Deutsch
<ede...@sy...>wrote:

> So it sounds like there is consensus that we update the index wrapper
> schema to allow an empty index at version 1.1.2. I agree that this is the
> best solution. Are there any objections to this?
>
>
>
> If no objections emerge, I would propose to update the mzML wrapper schema
> to 1.1.2 tomorrow (Tuesday). The primary mzML schema will remain unchanged
> at 1.1. I will also update the documentation to reflect this update as well
> as another pending documentation update.
>
>
>
> Objections?  Comments?
>
>
>
> Thanks,
>
> Eric
>
>
>
>
>
> *From:* Brian Pratt [mailto:bri...@in...]
> *Sent:* Monday, December 17, 2012 1:03 PM
> *To:* Mass spectrometry standard development;
> pro...@li...
> *Subject:* Re: [Psidev-ms-dev] Empty mzML files
>
>
>
> So the right thing to do is write an empty index with warning for schema <
> 1.1.2, and without warning thereafter.
>
> On Mon, Dec 17, 2012 at 12:59 PM, Fredrik Levander <
> fre...@im...> wrote:
>
> I just tried, and it actually worked fine to send an indexed file with
> mzML1.1.1_idx changed to mzML1.1.2_idx in the <indexedzmML> element
> through Mascot. There is no version attribute in the index, only in the
> mzML itself. So my worries were exaggerated, and it should probably be
> smooth to update the index schema to 1.1.2 and use it for all files.
>
> Fredrik
>
> Matt Chambers skrev 2012-12-17 21:28:
>
> > Can a 1.1.1 validating parser accept a non-empty 1.1.2 file? Then it
> would only fail on the empty
> > files (which will actually be valid, but won't appear so until the
> parser is updated). I definitely
> > prefer a long-term solution of consistent schema emptiness requirements.
> >
> > -Matt
> >
> >
> > On 12/17/2012 2:21 PM, Fredrik Levander wrote:
> >> Hi,
> >>
> >> I agree there is certainly good use cases for mzML files without
> >> spectra, and yes, it makes sense to allow for empty index as well.
> >> However, schema updates are likely to cause problems and should be
> >> avoided if possible.  I am a bit concerned that updating the index
> >> schema will cause validating tools to fail if they are not updated to
> >> support index version 1.1.2. It would maybe cause less problems if
> >> Proteowizard continues to produce 1.1.1 for files with spectra and 1.1.2
> >> for empty ones, but that is maybe not such a great solution either. But
> >> on a an index schema update, all Mascot servers will need an update to
> >> support new indexed mzML files (also those with spectra). So, actually
> >> it might even be better from a practical point of view to allow pwiz to
> >> produce invalid 1.1.1 files with empty index, as Brian suggests, than
> >> updating to schema version 1.1.2 only. A validating tool would protest
> >> on receiving the file, but it could probably not use it either, so that
> >> could still be OK if the error message tells what's wrong.
> >>
> >> Fredrik
> >>
> >> Matt Chambers skrev 2012-12-17 20:09:
> >>> Hi Brian,
> >>>
> >>> I'm moving this back to psidev-ms-dev because I want to wait and see
> how the specification
> >>> discussion works out. I'm inclined to agree with John that there isn't
> a strong reason to disallow
> >>> empty indexed mzML files. After a schema change, a 1.1.2 empty indexed
> mzML file submitted to a
> >>> 1.1.1 validator would fail. But it's only going to happen on an empty
> file, so it's not a big deal.
> >>>
> >
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