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

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I haven’t gotten to make the schema changes yet, got derailed on other
things, but still hope to get to it tonight. I would also advocate the
first option. I think we have a general policy for PSI formats “xxxxxList
elements shall not be empty”. I don’t know if it’s engraved anywhere, but
was a policy we tried to carry through. If there’s a xxxxxList element,
there better be something in it, or else, leave it out. So I would rather
implement it with an empty <index>. Clearly not an obvious conclusion, but
at least a precedent to guide the decision.

Additional comments?

Thanks,

Eric

*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Tuesday, December 18, 2012 10:11 AM
*To:* pro...@li...
*Cc:* Mass spectrometry standard development
*Subject:* Re: [Psidev-ms-dev] [proteowizard-developer] Empty mzML files

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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