gmane.text.xml.sedna

Sedna space requirements

Sojma, Zdenek — 2013-05-22T10:48:13

Hello,

I have a question about memory management. I have performed some space evaluation when I periodically stored one document into a collection (document size was approximately 3MB). When I looked at a statistical information about the document, total size of the document in the database was roughly 1MB, so I suppose that compression was in ratio 3:1. Weird thing was, that size of a *.sedata file raised, while the document was periodically stored into the database, in ratio more than 2:1. When 1000 documents (3GB) were successfully stored, size of the *.sedata file was approximately 7.5GB.

I want to ask you if this is a normal behaviour or if it is possible that I have some wrong settings? Or is there a some way how to decrease these space requirements? I have to admit that this is not so critical issue in these days but it would be nice to know that it can be decreased somehow.

Thank you for your answer.

Best regards,

Zdenek Sojma
Software Application Engineer I - Test Systems
Engineering Test Services

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Help me please

iman ghali — 2013-05-05T23:16:53

hello
please i need some help
i am using sedna-php-api-ffa
and there is some missing file
i need "error_codes.h"  file and i couldn't find it ..so i couldn't debug
the program
Can you help me please ?
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Problem using SEDNA ruby client

Matteo Faralli — 2013-04-15T14:59:13

Hi,
i'm working on WIN7 64bit, i've installed Sedna Ruby Client (
http://sedna.rubyforge.org/) with external c drvier using binary downloaded
from Sedna official site.

I've installed the gem in this way:

% gem install sedna -- --with-sedna-dir=c:/sedna

gem has been installed correctly (no errors found)


now i'm trying on IRB to load the gem doing:

require "sedna"


the result is bad:

irb(main):008:0> require "sedna"
LoadError: 126: The specified module could not be found.   - C:/Ruby193/lib/ruby
/gems/1.9.1/gems/sedna-0.6.0/lib/sedna.so
        from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:i
n `require'
        from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:i
n `require'
        from (irb):8
        from C:/Ruby193/bin/irb:12:in `<main>'

if i open the path location i can find sedna.so file, so i can't
understand the problem.

Coould you help me please?

Thank you,
Matteo
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Is read-only supported by XQJ

Ivan Lagunov — 2013-04-15T10:43:30

Hi Charles,

 

I couldn't find the answer on my own so decided to ask. Does XQJ
implementation allow running read-only transactions on Sedna? I mean this:

http://www.sedna.org/javadoc/ru/ispras/sedna/driver/SednaConnection.html#set
ReadonlyMode(boolean)

http://www.mail-archive.com/sedna-discussion-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org/msg01364.
html

 

Best regards,

Ivan Lagunov

 

 

 

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How to calculate hash in XQuery

Ivan Lagunov — 2013-04-12T17:23:00

Hello,

 

Is there a way to calculate hash in XQuery for Sedna? Ideally I'd like to
have something like this module for BaseX:

http://docs.basex.org/wiki/Hashing_Module

 

Best regards,

Ivan Lagunov

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How to locate XQuery errors

Ivan Lagunov — 2013-04-12T16:10:21

Hello,

 

We extensively use XQuery modules in Sedna. When an error happens, what we
see is something like this:

 

ERROR 12/04/2013 17:53:48 (TRN nxp pid=32721 sid=45 trid=37)
[PPSeqChecker.cpp:do_next:75]: (XPTY0019) It is a type error if the result
of a step (other than the last step) in a path expression contains an atomic
value. Details: at (45:25), filter step contains atomic in position 1

 

This is a good message showing (row:column) information that helps a lot.
However, it misses the module name that is really uncomfortable. It'd be
really nice to see the module name and preferably the function name if it's
available. Is it something easy to implement?

 

Best regards,

Ivan Lagunov

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XML:DB API performance issue - fn:doc-available

Ivan Lagunov — 2013-04-12T15:29:33

Hi Charles,

 

We're having serious performance issues, probably reached the critical
number of documents in the database. According to Ivan Shcheklein, it is
likely to be caused by using doc("documents") function that actually locks
all collections in the database, thus, drastically decreasing performance.
Your implementation of XML:DB API works great for small datasets but
according to event.log it uses doc("documents") quite a lot. So it may
indeed result in bad performance I'm facing. As an improvement, there have
been implemented a function fn:doc-available that checks if a document is
available in the given collection. It locks only one collection. This is an
example of usage:

 

doc-available("collection", "document")

 

Could you please update the Sedna XML:DB API implementation using this
function? I understand it's recommended to migrate to XQJ implementation but
it's really hard to rewrite all the code we have. Nevertheless, I've planned
to investigate required efforts for this migration but we need some solution
on short notice. Thanks a lot!

 

Best regards,

Ivan Lagunov

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Deadlock resolved

Jocelyn Raymond — 2013-03-22T15:20:30

Hi Sedna Team,
Just few weeks ago I sent the sedna Team an issue regarding
deadlocks occurrence in sedna when we were having high volume.  We were
able to resolve the deadlock issue and was able to get some interesting
result which will lead to a question at the end.
First, here is the code that caused the deadlock:

...
        this.cn.begin();
 SednaStatement st1 = this.cn.createStatement();

for (XmlDocument4Sedna xmlDocument : xmlDocuments) {
  try{
    if (this.exists(xmlDocument)) { // THIS CAUSE DEADLOCK
 st1.execute("DROP DOCUMENT '" + xmlDocument.getDocumentname() + "' IN
COLLECTION '" + xmlDocument.getCollectionName() + "'");
    }
    InputStream in = new
ByteArrayInputStream(xmlDocument.getXmlDocument().getBytes("UTF-8"));
    st1.loadDocument(in,xmlDocument.getDocumentname(),
xmlDocument.getCollectionName());
  }catch (Exception es){
              ...
    }
  }
}
this.cn.commit();
 this.cn.close();
        ...

As shown in the java comment above, when we have the line to check if a
document exist, it caused the deadlock.  If we removed the exist line (and
we knew that during our test all document existed), it did not cause the
deadlock.  Our test simulated 50 concurrent users.  Our architecture is
simply that we drop the document if it exist and insert the full new
document with the new data.

SOLUTION:
Our solution was to make the "save" method static synchronized such that
only one user would be able to "drop"/"load" document.  Surprisingly, this
serialization was faster than if we remove the line that caused the
deadlock.  I believe (but I may be wrong) that there are more lock handling
during concurrency than serialization and hence making it slower.  Our
result show:
Serialization: ~4.1 document saved per second.
Concurrent: ~2.8 document saved per second.
Note: 50 users simulation saved a total of 402 documents.

Some of my questions are (I am asking just in case you know an efficient
way of doing this):
Is it a good idea/solution to "DROP" and "LOAD" the new document to replace
the old one each time it need to be persisted?
Should we use "UPDATE replace ..." statement instead i.e. replacing the
entire document from the root of the document? (still require to see if
document exist).
Should the app keep track if a document is new or not (hence would not have
to check if exists on sedna)?
Which way do you usually use?

Thanks you for your support; always appreciated.
Jocelyn Raymond


FYI: our exists(xmlDocument) call above does the following:

  private boolean exists(String documentName, String collectionName) throws
Exception {
    boolean doesExists = false;

    SednaStatement st1 = this.cn.createStatement();
    boolean hasResult =
st1.execute("exists(doc('$documents')/documents/collection[< at >name='" +
collectionName + "']/document[< at >name='" + documentName + "'])");
    if (hasResult) {
SednaSerializedResult result = st1.getSerializedResult();
 String exists = result.next();
doesExists = (exists != null && exists.equals("true")) ? true : false;
    }
    return doesExists;
  }

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document-uri() & doc-available()

Anju — 2013-03-21T17:26:12

Does the current version of Sedna support document-uri() and doc-available() for
documents in a collection?

I ran a test like this:

for $i in collection('dashboard')
 let $uri := document-uri($i)
 let $avail := doc-available($uri)
return <data><uri>{$uri}</uri><available>{$avail}</available></data>

And the output shows the uri as the document ID of the documents with
doc-available() returning false for every document. Is there a way to get
doc-available() working with collections? Thank you!

Anju
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Can not upgrade from 3.4 to 3.5

Adolfho Lopes — 2013-03-20T16:57:41

Hi All,
I have an sedna xml 3.4 instance installed and when I try se_exp restore/import
path "/path" to my new 3.5 instance I got the following error:
ERROR: failed to execute query:

declare boundary-space preserve; LOAD "62.xml" "sdh-dados-violacao-ddh.xsd"
"acao-schemas"

Details:

SEDNA Message: ERROR SE2023
[nid_assign] The length of prefix exceeds PSTRMAXSIZE.

And when I get into se_term in the 3.5 instance and create the collection
"acao-schemas" and run LOAD "62.xml" "sdh-dados-violacao-ddh.xsd" "acao-schemas"
I get NO ERRORS.

Is there any idea where should I check what exactly is happening??

Thanks in Advance

Adolfho




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finding duplicates in sequence

Robby Pelssers — 2013-03-15T12:08:02

Hi guys,

Just wanted to share a little test I did yesterday. And I was pretty surprised by some findings. Maybe interesting for you to see what exactly is causing the slow performance.  That it can be improved dramatically is proved by competition so to say :)

Ps. This is in no way intended negatively but as a little trigger to even make Sedna faster.

http://www.robbypelssers.blogspot.nl/2013/03/finding-duplicate-values-with-xquery.html

Cheers,
Robby
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hot copy

aku — 2013-03-14T22:19:23

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sednaDriver and readOnlyMode

Olli — 2013-03-10T14:26:38

Hi,

I have difficulties to get query result with SednaDriver from java, if I 
try to set readOnlyMode to true:

conn.setReadonlyMode(true);
conn.conn.begin();

The result is allways [], but if I set readOnlyMode to false, then I get 
results normally.
I tried to put "conn.setReadonlyMode(true)" after "conn.conn.begin()", 
but then it is no effect at all (=updates function normally).

Could you help? What I am missing?

Regards,
Olli Santanen


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is XML database a good fit

Malcolm G. Davis — 2013-03-10T05:29:15

Maybe Jonathan is trying to learn XML using a simple example.

Avoiding the normal XML to RDBMS design and translation might be reason
enough if there is there are large amounts of data.


-----Original Message-----
From: sedna-discussion-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org
[mailto:sedna-discussion-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org] 
Sent: Saturday, March 09, 2013 10:39 AM
To: sedna-discussion-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org
Subject: Sedna-discussion Digest, Vol 79, Issue 3

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Today's Topics:

   1. Which database is best [for me] (Silver, Jonathan)
   2. Re: Which database is best [for me] (A. P. Garcia)
   3. The transaction is a victim of deadlockresolution procedure.
      (Jocelyn Raymond)


----------------------------------------------------------------------
Message: 2
Date: Fri, 8 Mar 2013 18:40:18 -0600
From: "A. P. Garcia" <a.phillip.garcia-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org>
Subject: Re: [Sedna-discussion] Which database is best [for me]
To: "Silver, Jonathan" <jonathan.silver-gtF/dg1N09I9ruZUYCyO/yPlML9JkKWw< at >public.gmane.org>
Cc: "sedna-discussion-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org"
<sedna-discussion-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org>
Message-ID:
<CAFCBnZtDYERkycJDCqsScyJ7zZ3k5nd7E1BpCT1884x75Amaeg-JsoAwUIsXosN+BqQ9rBEUg< at >public.gmane.org>
Content-Type: text/plain; charset="windows-1252"

Hi,

It doesn't sound like an XML database is a good fit for this purpose. You
can make it work, but it sounds like you're just using XML to transfer some
data where the schema is really simple and doesn't look like it will change
much (xml's flexibility is one of the things that makes XML dbs so
appealing; you don't even have to know the schema ahead of time, and it can
change pretty much any time you want). Another cool thing you can do with
XML is map complex objects to it, which can be difficult with relational
databases. Your data, on the other hand, can trivially map to an ordinary
rdbms.

Hope this helps,
A. P. Garcia

On Mar 8, 2013 3:36 PM, "Silver, Jonathan" <
jonathan.silver-gtF/dg1N09I9ruZUYCyO/yPlML9JkKWw< at >public.gmane.org> wrote:
and Sedona documentation trying to figure out which addresses my application
needs and have not been able to figure it out. Any advise is appreciated.
copiesSoldLastMonth from each doc)
if any database has facilities to support this kind of thing.


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xml options

Malcolm G. Davis — 2013-03-10T05:29:15

Hello Jonathan,

I looked at BaseX, eXist, and Sedna prior to selecting Sedna.  (You may want
to consider the free version of DB2 also.  There are other FOSS solutions.)

BaseX and eXist have changed a great deal since I originally reviewed them
several years ago.  The following is based on previous experience that may
not apply anymore:

* BaseX was just too immature at the time, I had issues setting up as a
server, connection problems etc.  

* eXist performed well on small data sets, but totally fell apart on larger
data sets.  eXist had index corruption issues and could not support multiple
databases.  

I use Senda on Amazon micro-instances (500 MB of available memory, with
databases of 1G-5G). 

If you are a JavaBot, then BaseX or eXist may work for you.  If you are not
into Java, then I recommend considering Sedna first.

XQuery has sum and sort features, so you can sum items, sort, and then pull
the first item out of list (I do this a lot).

I don't know how to handle which items have been added or removed other than
keeping up with the transaction history.

Malcolm
-----Original Message-----
From: sedna-discussion-request-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org
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Sent: Saturday, March 09, 2013 10:39 AM
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Subject: Sedna-discussion Digest, Vol 79, Issue 3

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Today's Topics:

   1. Which database is best [for me] (Silver, Jonathan)
   2. Re: Which database is best [for me] (A. P. Garcia)
   3. The transaction is a victim of deadlockresolution procedure.
      (Jocelyn Raymond)


----------------------------------------------------------------------

Message: 1
Date: Fri, 8 Mar 2013 16:47:15 +0000
From: "Silver, Jonathan" <jonathan.silver-gtF/dg1N09I9ruZUYCyO/yPlML9JkKWw< at >public.gmane.org>
Subject: [Sedna-discussion] Which database is best [for me]
To: "sedna-discussion-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org"
<sedna-discussion-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org>
Message-ID:
<6034286D166E324CB91B35AFEB348A680B8186-9J7noYBq+MGGPL2mZxYKzCvx6IqKIQag< at >public.gmane.org>
Content-Type: text/plain; charset="us-ascii"

I am new to xml base databases and I've been reading through baseX, eXist
and Sedona documentation trying to figure out which addresses my application
needs and have not been able to figure it out. Any advise is appreciated.

I have a set of documents like:
   <booklist>
     <listDate>  date  </listDate>
      <Book>
         <title>title 1 </Title>
         <LastPublishDate> date </>
         <copiesSoldLastMonth> 213 </>
     </Book>
                   ......
  </booklist>

I will get this xml doc each month and I'd like query for things like
            Which books sold the most last month
            Which Book has the most sold copies (need to add
copiesSoldLastMonth from each doc)
            Which books have been added to the list
            Which books have been removed from this list

I've also been reading through Xquery and I do not see how to do this or if
any database has facilities to support this kind of thing.

Thanks for any pointers,
jonathan


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The transaction is a victim of deadlockresolution procedure.

Jocelyn Raymond — 2013-03-09T16:09:41

Hi Sedna Team,
Sorry for the long email.
We have been having some serious problem in our production database with
"(SE4703) The transaction is a victim of deadlock resolution procedure."
We have the latest sedna release on Linux Red Hat.

Our situation is as follow:
1. Our main entity is an "Award Competition" which is split into several
smaller entities kept into separate sedna collections.
2. Our smaller entities are: collection('personal-info'),
collection('student-payload'), collection('activity') and so on.  Each
entities are quite small (average of 10-20 tags with fairly short text
nodes).
3. So one person applying to one "Award Competition" will need to do a
"write" to all those collections.
4. We also need to "write" all those xml documents in one transaction
(write all or rollback).
5. We know that, in order to write to sedna, the transaction need to
acquire a lock on the "collection" and not the "document".
6. We have thousands of people applying and what we think is happening is
that one person gets the lock for the collection('personal-info') and
another person gets the lock for collection('student-payload') which result
in the deadlock i.e. the first person having the lock for
collection('personal-info'), in the same transaction, is trying to acquire
the lock for collection('student-payload') but can't because it is used by
the second person transaction and vice versa.

The questions are:
1. Is it possible to have sedna locking on document instead of collection?
 (probably not but worth to ask).
2. We tried to make our transaction as small as possible but need to "save"
to several collections in one transactions.
3. Any suggestions?

We are in the process to try the XQJ driver but we don't think it will
resolve our deadlock situation.  Let me know if you think XQJ may give us
better result.
As such, I have a question in regard using XQJ:
Would this be valid xquery with sedna (we want to "LOAD" a new document):
XQPreparedExpression expression = conn.prepareExpression("declare variable
$collection external; " +
                                                         "declare variable
$docname external; " +
                                                         "declare variable
$xmldoc external; " +
                                                         "UPDATE insert
$xmldoc INTO doc($docname,$collection)";
//
String collection = "activity";
String docname    = "unique_name_goes_here";
String xmldoc     = "<activity>...</activity>";
// Or Document xmldoc = builder.newDocument()...;
expression.bindDocument(new QName("xmldoc"), xmldoc, null, null); // not
sure of the last two parameters
expression.bindString(new QName("docname"), docname, null, null);
expression.bindString(new QName("collection"), collection, null, null);

The question is "expression.bindDocument(...)"  Is it the right thing to do
to LOAD new document or should we use "expression.bindItem(...)" or
"expression.bindSequence(...)" or
"expression.bindNode(...)" or
"expression.bindObject(...)"

Note:  We use JAXB.  Can we pass JAXB as a "bind???" method?



Entities:
Here is an example of entity model we have for collection('activity')
<activity type="university" id="1360861690701">
  <organization-name>female basketball team</organization-name>
  <position-title>player</position-title>
  <date attending="" end="2012-10-25" start="2012-05-03"/>
  <time-commitment-per-week>120</time-commitment-per-week>
  <description>This is a sample description that can contain up to 300
words.</description>
</activity>

Thank you very much for your input,
Jocelyn Raymond
--
Data Architect / Development Manager
Information Systems
Office of the Registrar
University of Alberta
780.492.3874

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Which database is best [for me]

Silver, Jonathan — 2013-03-08T16:47:15

I am new to xml base databases and I've been reading through baseX, eXist and Sedona documentation trying to figure out which addresses my application needs and have not been able to figure it out. Any advise is appreciated.

I have a set of documents like:
   <booklist>
     <listDate>  date  </listDate>
      <Book>
         <title>title 1 </Title>
         <LastPublishDate> date </>
         <copiesSoldLastMonth> 213 </>
     </Book>
                   ......
  </booklist>

I will get this xml doc each month and I'd like query for things like
            Which books sold the most last month
            Which Book has the most sold copies (need to add copiesSoldLastMonth from each doc)
            Which books have been added to the list
            Which books have been removed from this list

I've also been reading through Xquery and I do not see how to do this or if any database has facilities to support this kind of thing.

Thanks for any pointers,
jonathan
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The transaction is a victim of deadlockresolution procedure.

Jocelyn Raymond — 2013-02-28T22:08:56

Hi Sedna Team,
We are running sedna (Sedna Governor Version 3.5.161) on RedHat Enterprise
(Linux  2.6.32-279.2.1.el6.x86_64 #1 SMP Thu Jul 5 21:08:58 EDT 2012 x86_64
x86_64 x86_64 GNU/Linux).

We are starting to have more demand on our application using sedna as data
store.  We are getting the following error (also see our event.log
attached):

ERROR 28/02/2013 14:08:16 (SM student-awards pid=20818)
[lock_table.cpp:visit:580]: (SE4705) Deadlock is detected.
ERROR 28/02/2013 14:08:16 (TRN student-awards pid=21077 sid=45 trid=48)
[locks.cpp:obtain_lock:204]: (SE4703) The transaction is a victim of
deadlock resolution procedure.


Today our database went down three times and not sure why yet.  We suspect
that it might be caused by either a higher load or the deadlock situation.
I also did:  cat event-2013-02-28* | grep ERROR > errors.log
and attached the "errors.log" to this email.  As you can see, we have been
getting lots of errors today.
My question is: "Is there any ideas/suggestions you could give us to
improve this situation (deadlock, Interupted system call, etc...)?"

Also we want to increase the number of "allowed connections" from 50 to ??.
Do you have any suggestion about the maxmum connections sedna can support?
 We are preparing ourselves to recompile sedna on our RedHat Linux and
would like to change that parameter.  BTW: Are there other parameters you
know that we should "check" that might be useful before we re-compile?

Thank you,
Jocelyn Raymond

--
Data Architect / Development Manager
Information Systems
Office of the Registrar
University of Alberta
780.492.3874

*** Please note: Our unit has moved to SAB-1-26. Other moves will be
happening within the Office of the Registrar over the coming weeks. To keep
updated, please visit our
website<http://www.registrarsoffice.ualberta.ca/Faculty-and-Staff/Office-Move.aspx>.
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serialization options

Robby Pelssers — 2013-02-25T13:12:12

Hi all,

We are generating RDF from our XMLDB and the exported XML gives a few parsing problems while importing into our RDF store:

rapper: Parsing URI http://qa.data.nxp.com/dataset/data_sheet.rdf with parser rdfxml
rapper: Serializing with serializer ntriples
rapper: Warning - URI http://qa.data.nxp.com/dataset/data_sheet.rdf:49486 - Property element 'title' has a string not in Unicode Normal Form C: PSMN1R0-30YLC - N-channel 30 V 1.15 mΩ logic level MOSFET in LFPAK using NextPower technology
rapper: Warning - URI http://qa.data.nxp.com/dataset/data_sheet.rdf:49502 - Property element 'title' has a string not in Unicode Normal Form C: PSMN4R5-30YLC - N-channel 30 V 4.8 mΩ logic level MOSFET in LFPAK using NextPower technology


They are due to Normalization of Unicode characters.  I was checking Sedna documentation 
http://www.sedna.org/progguide/ProgGuidesu5.html#x9-300002.2.1

and noticed I can't use the normalization-form parameter:
http://www.w3.org/TR/xslt-xquery-serialization/#XML_NORMALIZATION-FORM

Will that be supported on short notice? :)

Robby

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Recalculation of descriptive schema

Sojma, Zdenek — 2013-02-25T12:59:01

Hello,

I want to ask you, if there is a way, how to recalculate descriptive schema of a collection. My goal is to remove a document from the database and ensure that elements, which were only in that document, will not remain in the schema.

Thanks a lot.

Best regards,

Zdenek Sojma
Software Application Engineer I - Test Systems
Engineering Test Services

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Using fn:error in XQuery module

Ivan Lagunov — 2013-02-25T10:37:50

Hi all,

 

Is it possible to throw a dynamic error from an XQuery module? I'm referring
to the fn:error function. I get the following error when I try to load my
module:

 

2013/02/25 11:34:29 database query/update failed (SEDNA Message: ERROR
XPST0003

It is a static error if an expression is not a valid instance of the grammar
defined in A.1 EBNF.

Details: at (74:7), syntax error, unexpected QName

         

)

 

This is a function from the module:

 

declare function vp:getMapSubtitle($vp as element(value-proposition)*) as
xs:string? {

    if (count($vp) < 2)

    then data($vp/topicmeta/subtitle)

    else

      let $vp_ids := for $single_vp in $vp return data($single_vp/< at >id)

      error(xs:QName("vp:getMapSubtitle"), "More than one VPs provided",
$vp_ids)

};

 

Any suggestions?

 

Best regards,

Ivan Lagunov

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