Re: [XMLPipeDB-developer] attempt to import entire UniProt xml failed

[John D. N. D. <do...@lm...>]

Hi Kam,

No problem, I remember about jury duty from last week...as for the fix, there are two items involved:

(a) The original reported error (problem with the 'molecule' element)---this has been fixed, and was fixed by the usual XSD update

(b) When I was testing the fix in (a), I encountered another problem with importing---this is the issue that I haven't isolated yet.  I've tried a few approaches at getting a handle on this latter bug, but have come up short.

So the issue in (b) remains, but it does not appear to be content-specific, so I decided to release this new version anyway to see what happens on your end.

Let me know if that clarifies things.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Jun 24, 2014, at 10:57 AM, Dahlquist, Kam D. <Kam...@lm...> wrote:

> Hi,
> 
> I'm at jury duty today, so I'll try the import when I get back to the office.  I'll keep you posted as to whether I'll be there for Thursday's meeting. I'm not sure I understand your description of the fix below, what specifically does that mean?
> 
> Thanks,
> Kam
> 
> ________________________________________
> From: John David N. Dionisio [do...@lm...]
> Sent: Tuesday, June 24, 2014 9:55 AM
> To: xml...@li...
> Subject: Re: [XMLPipeDB-developer] attempt to import entire UniProt xml failed
> 
> Hi Kam,
> 
> I've gone ahead and released GenMAPP Builder 2.0b79.  This updates UniProt code and SQL to the latest XSD libraries, but may still harbor a latent bug regarding something completely different, but which I have been unable to isolate yet.  In particular, just changing the file (but retaining the data where the original XML import failed) seems to avoid the problem.  Let me know what happens with your import.
> 
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
> 
> 
> 
> On Jun 23, 2014, at 1:27 AM, John David N. Dionisio <do...@lm...> wrote:
> 
>> Greetings,
>> 
>> The direct error reported turned out to be an XSD update, and that went fine upon testing, but then I encountered another error that has turned out to be less straightforward to resolve.  So this issue is still in progress; I added the gory details as a follow-up to the entry in your narrative page:
>> 
>>      http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-22
>> 
>> I will look at this fresh on Monday and report back on how things go.
>> 
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Associate Director, University Honors Program
>> Loyola Marymount University
>> 
>> 
>> 
>> On Jun 19, 2014, at 3:02 PM, Dahlquist, Kam D. <Kam...@lm...> wrote:
>> 
>>> Hi,
>>> 
>>> I attempted to import the entire UniProt XML, downloaed from here: http://www.uniprot.org/downloads using gmb2b78.  The import failed after just a few seconds upon encountering an unexpected element, molecule, (as far as I can tell).  Screenshots of the console window with messages are on my narrative page here:
>>> 
>>> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-19
>>> 
>>> Note that the individual Vibrio and Helicobacter pylori proteome XML files from this release imported just fine.
>>> 
>>> Best,
>>> Kam
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> 
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> Quickly connect people, data, and systems into organized workflows
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