[Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi all,

Eric has re-generated the schema documentation for us. This is getting fairly
close to a version I can cut and paste into the spec doc. Let me know if you
have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated HTML
documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in the
subelement listing, any subelements that are double-tall nested substitution
grouped elements do not have their definition visible. If one clicks on the
subelement, the main element does have a definition. So it’s there, but my
program is stymied by the various levels. This is fixable, but probably not
before submission.

 

If you send me screen-capture images to embed in some elements, that can be done
if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We’re aiming
to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest schema
and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get back to
you.

 

Sorry I’ve missed the calls. That time is very awkward for me and I’ve
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs? There’s
a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited attributes
does not appear in the table (e.g. see Specificity rule, no docs for cvRef,
unitName etc.) – unless we were missing documentation for these attributes when
it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light schema
which are completely empty, no attributes or documentation e.g. Organization or
Person.

 

We’re aiming to submit the specs to the PSI process by the end of month (i.e. a
week on Monday), so if you would be able to look at this fairly soon it would be
very much appreciated! Also, any chance that you can get someone to generate the
TPP and SpectraST examples at your end. It’s no disaster if we submit to the
process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the
mapping information for SearchType and it seemed to pull it out of the CV
nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to automatically
pull examples out of?

 

Regards,

Eric

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

-          Finish section on use cases when we have finally agreed the list
online and made all the example files.

-          Import some parts of the example files to demonstrate a few specific
points

-          Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

-          CV - looking through the CV there is still a fair bit of work to do,
there’s quite a few terms with missing or incorrect documentation

-          Mapping file

-          Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the CV
into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy