Corrupted database

Hi all,


I'm trying to recover a database in Sedna 3.1.175 in a CentOS 4.3 system (Linux 2.6.18) .  
A days ago, there was a power loss and when the server rebooted the Sedna service didn't started.
We start the service manually:

se_gov
se_sm sampelims

The first command executed correctly, but the second one, fails with a message:

Starting database recovery or hot-backup restoration...
Database recovery in progress...
SEDNA Message: FATAL ERROR
in process [11883] se_sm samplelims
System error. This error means system malfunction.
Details: Offset is out of range

The messages reported in the log files are these:

LOG   09/07/2010 15:01:45 (SM samplelims pid=11860) [sm.cpp:main:547]: Event log is ready
SYS   09/07/2010 15:01:45 (SM samplelims pid=11860) [usocket.c:uconnect_tcp:192]: connect (code = 111): Failed to obtain error message
SYS   09/07/2010 15:02:00 (GOV pid=4035) [usocket.c:uconnect_tcp:192]: connect (code = 111): Failed to obtain error message
INFO  09/07/2010 15:02:05 (GOV pid=11867) [gov.cpp:main:231]: SEDNA version is 3.1.175
INFO  09/07/2010 15:02:05 (GOV pid=11867) [gov_functions.cpp:log_out_system_information:81]: System: Linux 2.6.18-92.1.1.el5.028stab057.2 i686
INFO  09/07/2010 15:02:05 (GOV pid=11867) [gmm.cpp:create_global_memory_mapping:129]: Layer address space start addr = 0x60010000
INFO  09/07/2010 15:02:05 (GOV pid=11867) [gmm.cpp:create_global_memory_mapping:130]: Layer address space boundary   = 0xa0010000
INFO  09/07/2010 15:02:05 (GOV pid=11867) [gmm.cpp:create_global_memory_mapping:131]: Persistent heap start addr     = 0x59c10000
LOG   09/07/2010 15:02:05 (GOV pid=11867) [gov.cpp:main:240]: Process ping server is ready
LOG   09/07/2010 15:02:05 (GOV pid=11867) [listener.cpp:client_listener:67]: GOVERNOR is ready
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:main:547]: Event log is ready
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:main:560]: Ping client has been started
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:main:566]: VMM region values determined
SYS   09/07/2010 15:02:55 (SM samplelims pid=11878) [uprocess.c:uGetEnvironmentVariable:76]: getenv (code = 4): Failed to obtain error message
SYS   09/07/2010 15:02:55 (SM samplelims pid=11878) [uprocess.c:uGetEnvironmentVariable:76]: getenv (code = 4): Failed to obtain error message
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:830]: Event log in recovery procedure is ready
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:834]: init_transaction_ids_table done
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:838]: init_checkpoint_sems done
LOG   09/07/2010 15:02:55 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:844]: Logical log is started
LOG   09/07/2010 15:02:57 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:859]: Persistent heap has been recovered
LOG   09/07/2010 15:02:57 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:864]: start_chekpoint_thread done
LOG   09/07/2010 15:02:57 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:886]: Buffer manager is started
LOG   09/07/2010 15:03:05 (SM samplelims pid=11878) [blk_mngmt.cpp:extend_tmp_file:619]: Temp file has been extended, size: 6400000
LOG   09/07/2010 15:03:05 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:893]: Database has been recovered by physical log successfully
LOG   09/07/2010 15:03:05 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:898]: Checkpoints are disabled
LOG   09/07/2010 15:03:05 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:902]: lm_table.init_lock_table done
LOG   09/07/2010 15:03:05 (SM samplelims pid=11878) [sm.cpp:recover_database_by_physical_and_logical_log:925]: Wu is initialized
LOG   09/07/2010 15:03:05 (UNK samplelims pid=11884) [rcv_db.cpp:TRmain:81]: recovery process by logical log started
LOG   09/07/2010 15:03:15 (SM samplelims pid=11878) [blk_mngmt.cpp:extend_data_file:593]: Data file has been extended, size: 12c10000
LOG   09/07/2010 15:03:24 (SM samplelims pid=11878) [blk_mngmt.cpp:extend_data_file:593]: Data file has been extended, size: 19010000
FATAL 09/07/2010 15:03:28 (SM samplelims pid=11878) [bm_core.cpp:calculate_offset_and_file_handler:162]: Offset is out of range

There are messages before these, but are related to xquery execution before the crash, nothing anormal here.

Thanks for any help you can give me with this problem, 

Regards,

Carlos Andrés Muñoz Bolaños

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Ivan Shcheklein | 9 Jul 2010 23:44
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Re: Corrupted database

Hi Carlos,


Unfortunately, seems that database is completely corrupted.

Either you should recover from the backup (please, use the latest Sedna and update it regularly, 3.1.175 is very old Sedna, many serious bugs are fixed now). If you don't have backups (please, do backups!) you can parse event logs to get all updates and repeat them. Use logparser utility to get all updates:

http://modis.ispras.ru/FTPContent/sedna/tools/logparser.py


Ivan Shcheklein,
Sedna Team


I'm trying to recover a database in Sedna 3.1.175 in a CentOS 4.3 system (Linux 2.6.18) .  
A days ago, there was a power loss and when the server rebooted the Sedna service didn't started.
We start the service manually:

se_gov
se_sm sampelims

The first command executed correctly, but the second one, fails with a message:

Starting database recovery or hot-backup restoration...
Database recovery in progress...
SEDNA Message: FATAL ERROR
in process [11883] se_sm samplelims
System error. This error means system malfunction.
Details: Offset is out of range


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François | 12 Jul 2010 14:29
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Web hosting with Sedna ?

Hi,

I am new to Sedna and it looks promising to me.

I was wondering if anybody knows of a web hosting company offering ready to use
servers with some combination of PHP and Sedna.

Many thanks in advance.

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Ivan Shcheklein | 12 Jul 2010 22:08
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Re: Web hosting with Sedna ?

Hi François,

No. As far as we know, there are no Sedna hostings available.

Ivan Shcheklein,
Sedna Team

On Mon, Jul 12, 2010 at 4:29 PM, François <> wrote:
Hi,

I am new to Sedna and it looks promising to me.

I was wondering if anybody knows of a web hosting company offering ready to use
servers with some combination of PHP and Sedna.

Many thanks in advance.


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Maciej | 15 Jul 2010 15:33
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Results ranking

Hello,

I'm a newbie to Sedna and before I start playing with the look I would 
like whethere it can support me in realizing the following task.

I have a collection of XML documents (WSDLs---Web service definitions) 
formated with respected to a pre-defined stable schema. I need to 
execute (from PHP) search over XML documents. Search process includes:

  - full-text search over chosen XML elements
  - substring search over values of attributes of chosen XML elements

 From what I've read on your site this can be done with Sedna.

I wonder whether it also:
(1) scores relevance of matching XML documents and ranks them (in any way)
(2) allows navigating to identify (in matching document) XML elements 
with matched query terms and than navigating to parental/children nodes 
in XML structure
(3) provides a way to give more weight to some XML element types during 
relevance scoring.

Best regards,
Maciej

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Roman Pastukhov | 15 Jul 2010 16:13
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Re: Results ranking

Hello Maciej,

Sedna supports full-text search using dtSearch engine, so you will
need dtSearch license to use full-text search in Sedna.

dtSearch supports relevance ranking and giving more weight to some XML
elements. Note that ftindex-scan function returns matching elements in
arbitrary order (i.e. not sorted by relevance score), while
ftwindex-scan returns elements orderer by their score. Currently
there is no way to access relevance score values from XQuery in Sedna.

Since, ftindex-scan function returns a sequence of elements you can
easily add structural predicated to these results.

Substring search is supported, though there's no way to speed it up
with indexes (unless it's prefix search).

Also note that ftindex-scan and similar functions are Sedna-specific
and are not defined in XQuery standard. Currently Sedna doesn't support XQuery
full-text search extensions or automatic use of indexes in queries.

Thursday, July 15, 2010, 5:33:20 PM, you wrote:

> Hello,

> I'm a newbie to Sedna and before I start playing with the look I would
> like whethere it can support me in realizing the following task.

> I have a collection of XML documents (WSDLs---Web service definitions)
> formated with respected to a pre-defined stable schema. I need to 
> execute (from PHP) search over XML documents. Search process includes:

>   - full-text search over chosen XML elements
>   - substring search over values of attributes of chosen XML elements

>  From what I've read on your site this can be done with Sedna.

> I wonder whether it also:
> (1) scores relevance of matching XML documents and ranks them (in any way)
> (2) allows navigating to identify (in matching document) XML elements 
> with matched query terms and than navigating to parental/children nodes
> in XML structure
> (3) provides a way to give more weight to some XML element types during
> relevance scoring.

> Best regards,
> Maciej

--

-- 
Best regards,
 Roman                            mailto:ignatich@...

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SourceForge.net | 19 Jul 2010 11:58
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[ sedna-Bugs-3031529 ] Error SE4211 under path with 2 bytes characters

Bugs item #3031529, was opened at 2010-07-19 10:58
Message generated for change (Tracker Item Submitted) made by goodluckfish
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=713730&aid=3031529&group_id=129076

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: General
Group: Sedna (development)
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: chun chen (goodluckfish)
Assigned to: Nobody/Anonymous (nobody)
Summary: Error SE4211 under path with 2 bytes characters

Initial Comment:
version of Sedna - 3.3.55
operating system version - Windows 5.1.2600 (SP3.0) x86

When trying to create a database under path with 2 bytes characters, I got the ERROR SE4211.
2 bytes characters means Chinese or Japanese characters. Command lines :

  E:\publish\版本发布\sedna\bin>se_gov
GOVERNOR has been started in the background mode

E:\publish\版本发布\sedna\bin>se_cdb aaa
Creating a data base (it can take a few minutes)...
SEDNA Message: ERROR SE4211
Failed to create the database
Details: aaa

Cannot complete cleanup. Please stop Sedna and remove the following:
file   -  /cfg/aaa_cfg.xml
folder -  /data/aaa_files
Sorry for inconvenience.

E:\publish\版本发布\sedna\bin>

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SourceForge.net | 19 Jul 2010 14:55
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[ sedna-Bugs-3031529 ] Error SE4211 under path with 2 bytes characters

Bugs item #3031529, was opened at 2010-07-19 13:58
Message generated for change (Settings changed) made by shcheklein
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=713730&aid=3031529&group_id=129076

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: General
Group: Sedna (development)
Status: Open
>Resolution: Accepted
>Priority: 3
Private: No
Submitted By: chun chen (goodluckfish)
>Assigned to: Ivan Shcheklein (shcheklein)
Summary: Error SE4211 under path with 2 bytes characters

Initial Comment:
version of Sedna - 3.3.55
operating system version - Windows 5.1.2600 (SP3.0) x86

When trying to create a database under path with 2 bytes characters, I got the ERROR SE4211.
2 bytes characters means Chinese or Japanese characters. Command lines :

  E:\publish\版本发布\sedna\bin>se_gov
GOVERNOR has been started in the background mode

E:\publish\版本发布\sedna\bin>se_cdb aaa
Creating a data base (it can take a few minutes)...
SEDNA Message: ERROR SE4211
Failed to create the database
Details: aaa

Cannot complete cleanup. Please stop Sedna and remove the following:
file   -  /cfg/aaa_cfg.xml
folder -  /data/aaa_files
Sorry for inconvenience.

E:\publish\版本发布\sedna\bin>

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

>Comment By: Ivan Shcheklein (shcheklein)
Date: 2010-07-19 16:55

Message:
Hi Chun,

This is a known limitation of Sedna. For the moment the only workaround is
to use ASCII chars in path.

Technical comments for developers for further work on this issue:

1. On windows seems we have to define UNICODE (see MSND, Conventions for
Function Prototypes) and use wchar* for all system calls. Everywhere we
need we should translate Sedna's UTF-8 strings (like SEDNA_DATA) -> wchar
and backward.

2. On windows we should also explicitly use _wfopen instead of fopen, etc
... 

3. On Linux there is no "wfopen()" (just plain old "fopen()" will
suffice), but there *are* Unicode equivalents for each of the file read and
write APIs. Should we use them?

4. We should also check other supported platforms - OS X, Solaris, BSD.

5. As a temporary fix probably we may raise some exception on se_gov if
there are non ASCII chars?

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Brett Zamir | 19 Jul 2010 16:36
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Sedna in Firefox

Hello all!

I've just added an add-on for Firefox which uses Sedna; I'm calling it 
"XDIB" or "XML Database In a Browser". See 
https://addons.mozilla.org/en-US/firefox/addon/199900/ .

Basically, this lets any web developer, who is given permission by the 
user, to add XML content to Sedna (databases stored in Firefox's Profile 
folder by default, so that the data will not be lost whenever the 
extension may get updated) and then query it, update it, etc..

Actually, we've basically wrapped every command there is in Sedna 
(though removing "Sedna" from the methods in case this could become 
abstracted--sorry, no XQJ at the moment), though I haven't really tested 
anything besides loading XML and doing XQueries against data in a 
collection.

At the moment, the databases are accessible to any site which requests 
permission, as I wanted this to be the default behavior, since I think 
it should be up to users how they want their data shared, and not have 
their own data be locked in by a particular site, even if that site 
originated the storage of the data. The access is granted depending on 
whether read permissions, insert permissions, etc., are desired, and I 
really need to add the ability to specify which database one has 
permission to access, since for now, it is any one! (though it does ask 
permission at least).

I also hope to make the API available as special protocol links, so a 
link could trigger the view of certain content, and if my other add-on, 
Open URIs (at https://addons.mozilla.org/en-US/firefox/addon/162154/ ) 
is used together with this, one could link to locally stored by default, 
but fallback to an online site in case the user is visiting the site 
without this add-on installed. I like the idea of bookmarks that work 
offline, and which could do fancy queries, and trigger a download of the 
data (and subsequent auto-updates) if the data had not yet been 
downloaded. But that's not implemented at the moment...

I paid a friend to implement the C++ code which as part of an XPCOM 
component for Mozilla's Cross-Platform Component Object Model, among 
other things, lets JavaScript communicate with C++ so that people like 
me who do not know C++ can still write Firefox extensions or the like 
which interact with cool tools or libraries like Sedna, so my apologies 
if anything has been lost in translation as far as how the API is to be 
used (though I know it is working for XQueries at least--though I do 
need help on figuring out how Sedna can support UTF-8 if it uses "const 
char" as I understand that to be ASCII only; the component may need to 
be updated to support multi-byte strings).

And since my friend is a Windows guy, we've only compiled so far in 
Windows, but since this is supposed to be cross-platform, hopefully we 
can get this working on other systems as well.

As I mention on the add-on site, the API is of course very much new (not 
to mention there may well be problems in our code), so while we are 
whole-heartedly encouraging experimentation, please do not use this for 
critical content, nor depend on the API remaining frozen.

I have the off-hope that we could get XML databases to be part of HTML5; 
e.g., see the debate at 
http://hacks.mozilla.org/2010/06/beyond-html5-database-apis-and-the-road-to-indexeddb/ 
or

http://hacks.mozilla.org/2010/06/comparing-indexeddb-and-webdatabase/comment-page-1/#comment-95595 
. My energy is fairly limited as far as what I can contribute, but I do 
hope to make piecemeal progress on this, and fully welcome anyone 
interested to offer their feedback, improvements, or whatever...  :) 
(I've cc'd myself if you wish to get in touch off-list to indicate you 
wish to be kept informed.)

best wishes,
Brett

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N. Zavaritsky | 20 Jul 2010 10:47
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Re: Sedna in Firefox

Hi Brett,

First of all let me express appreciation of your great work!

It sounds sort of fantastik (wow, Firefox! everyone use Firefox these
days!). Unfortunately Sedna was never designed to be an embedable
database. Sedna launches and manages it's own processes (one master +
one process per db + one process per query session). Though I'd prefer
for a database that Firefox is using internally to be nicely wrapped
inside Firefox itself (no external processes, just a dll/so/dylib loaded
into Firefox process, database code sharing threads with the browser) a
bunch of external processes is just a minor inconvenience. However there
is more to come.

Embedable database must be lean. For the standalone database it is ok to
consume 90% of avalible memory. Anyway the entire computer may be
dedicated to the task of running that particular database. Obviously
embedable database is not the main task running on the computer, but
just the oposite!

Sedna memory usage is configurable but if given less than 100Mb RAM
Sedna slows down considerably. Of course the amount of RAM neccessary to
achieve adequite performance depends on the complexity of the queries
used. It is quite reasonable to expect that queries executed against the
XML database embeded inside Firefox won't be complex ones so probably we
could use less memory.

Finally there are issues with the data file. Well, just one ISSUE. The
data file size. It starts at 100Mb and grows in 100Mb increments. These
numbers are configurable as well. But don't expect to tune it down to
1Mb or so :)  The data representation used internally was not designed
to be space-efficient. Basically Sedna manages storage in 64Kb blocks.
By design distinct named XML elements must live in distinct blocks (it
makes queries like doc("aaa")/foo/bar really fast). So even not so
complex XML document can easily consume hundreds of blocks. There are
certain techniques that helps to reduce the number of blocks used ([a]
redesigning data to utilize fewer distinct named elements or [b] storing
documents with similar structure together) but I doubt that end users
will be willing to learn and apply these techniques.

And lastly the concept of "distinctly named XML elements living in
distinct blocks" was an oversimplification. It is not just the element
name that counts but the complete path from the document root. For
instance book/section/title and book/section/figure/title occupy
distinct blocks. You may see Sedna is not great at storing XML markup
(count the number of say <a>-s in average HTML page; how many <a>-s
share the same path from the document root?).

Over are the bad news.

Now comes some good ones.

Sedna is continually developed. The idea to refine data storage hovered
for a long time. I guess we can address the abovementioned issues in
some time.

And I must say the opportunity to get Sedna into Firefox is pretty
exciting! Achieving the really WIDE adoption of XML database is so much
important for the XML database community.

wbr,
mejedi

On Mon, 2010-07-19 at 22:36 +0800, Brett Zamir wrote:
> Hello all!
> 
> I've just added an add-on for Firefox which uses Sedna; I'm calling it 
> "XDIB" or "XML Database In a Browser". See 
> https://addons.mozilla.org/en-US/firefox/addon/199900/ .
> 
> Basically, this lets any web developer, who is given permission by the 
> user, to add XML content to Sedna (databases stored in Firefox's Profile 
> folder by default, so that the data will not be lost whenever the 
> extension may get updated) and then query it, update it, etc..
> 
> Actually, we've basically wrapped every command there is in Sedna 
> (though removing "Sedna" from the methods in case this could become 
> abstracted--sorry, no XQJ at the moment), though I haven't really tested 
> anything besides loading XML and doing XQueries against data in a 
> collection.
> 
> At the moment, the databases are accessible to any site which requests 
> permission, as I wanted this to be the default behavior, since I think 
> it should be up to users how they want their data shared, and not have 
> their own data be locked in by a particular site, even if that site 
> originated the storage of the data. The access is granted depending on 
> whether read permissions, insert permissions, etc., are desired, and I 
> really need to add the ability to specify which database one has 
> permission to access, since for now, it is any one! (though it does ask 
> permission at least).
> 
> I also hope to make the API available as special protocol links, so a 
> link could trigger the view of certain content, and if my other add-on, 
> Open URIs (at https://addons.mozilla.org/en-US/firefox/addon/162154/ ) 
> is used together with this, one could link to locally stored by default, 
> but fallback to an online site in case the user is visiting the site 
> without this add-on installed. I like the idea of bookmarks that work 
> offline, and which could do fancy queries, and trigger a download of the 
> data (and subsequent auto-updates) if the data had not yet been 
> downloaded. But that's not implemented at the moment...
> 
> I paid a friend to implement the C++ code which as part of an XPCOM 
> component for Mozilla's Cross-Platform Component Object Model, among 
> other things, lets JavaScript communicate with C++ so that people like 
> me who do not know C++ can still write Firefox extensions or the like 
> which interact with cool tools or libraries like Sedna, so my apologies 
> if anything has been lost in translation as far as how the API is to be 
> used (though I know it is working for XQueries at least--though I do 
> need help on figuring out how Sedna can support UTF-8 if it uses "const 
> char" as I understand that to be ASCII only; the component may need to 
> be updated to support multi-byte strings).
> 
> And since my friend is a Windows guy, we've only compiled so far in 
> Windows, but since this is supposed to be cross-platform, hopefully we 
> can get this working on other systems as well.
> 
> As I mention on the add-on site, the API is of course very much new (not 
> to mention there may well be problems in our code), so while we are 
> whole-heartedly encouraging experimentation, please do not use this for 
> critical content, nor depend on the API remaining frozen.
> 
> I have the off-hope that we could get XML databases to be part of HTML5; 
> e.g., see the debate at 
> http://hacks.mozilla.org/2010/06/beyond-html5-database-apis-and-the-road-to-indexeddb/ 
> or 
>
http://hacks.mozilla.org/2010/06/comparing-indexeddb-and-webdatabase/comment-page-1/#comment-95595 
> . My energy is fairly limited as far as what I can contribute, but I do 
> hope to make piecemeal progress on this, and fully welcome anyone 
> interested to offer their feedback, improvements, or whatever...  :) 
> (I've cc'd myself if you wish to get in touch off-list to indicate you 
> wish to be kept informed.)
> 
> best wishes,
> Brett
> 
> 
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What will you do first with EVO, the first 4G phone?
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Gmane