make ontologies and go-apply-xslt problem

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make ontologies and go-apply-xslt problem

greg gime
Dear All,

I am struggling with the CHADO install more precisely I am fighting with the population of the CV part.
Basically, I have the script  go-apply-xslt that do not generate anything.

I first followed the instruction in the INSTALL file: 

make ontologies it works for Relationship Ontology.
But when I tried to load the SO ([2]) then I got the following error:

which ontologies would you like to load (Comma delimited)? [0]  2
fetching files for Sequence Ontology
  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
    updated
    loading...DBI connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...) failed: fe_sendauth: no password supplied at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81

Could not connect to database: "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"

EITHER   The required DBD driver "Pg" is not installed
    OR   There is no such database as "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"

Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user greg_superuser  tmp/song/so.oboxml' failed: 65280
Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
make: *** [ontologies] Error 255


Then I tried to do it 'manually' by using the script:
 go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt oboxml_to_chadoxml -  > foo.chadoxml

The foo.chadoxml is empty.
So, I checked the first script:go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.

The xlm is generated normally so I also tried to go-apply-xslt oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....

So don't know what I can do. Any ideas or helps will be really appreciated ;-)

All the best,

Greg


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Re: make ontologies and go-apply-xslt problem

Scott Cain
Hi Greg,

Sorry I missed this email when you sent it last week.  There are a few
things I can suggest that you check:

1. You have sufficient disk space.

2. That you have a complete sequence.obo file; if it got truncated
when it was downloaded, I could see that causing a problem.

3. If neither of those things help, I suggest contacting the GO help
desk, since this is GO software:

  http://www.geneontology.org/GO.contacts.shtml

Thanks,
Scott


On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]> wrote:

> Dear All,
>
> I am struggling with the CHADO install more precisely I am fighting with the
> population of the CV part.
> Basically, I have the script  go-apply-xslt that do not generate anything.
>
> I first followed the instruction in the INSTALL file:
> make ontologies it works for Relationship Ontology.
> But when I tried to load the SO ([2]) then I got the following error:
>
> which ontologies would you like to load (Comma delimited)? [0]  2
> fetching files for Sequence Ontology
>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>     updated
>     loading...DBI
> connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
> failed: fe_sendauth: no password supplied at
> /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
>
> Could not connect to database:
> "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>
> EITHER   The required DBD driver "Pg" is not installed
>     OR   There is no such database as
> "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>
> Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
> System call 'stag-storenode.pl -d
> 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
> greg_superuser  tmp/song/so.oboxml' failed: 65280
> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> make: *** [ontologies] Error 255
>
>
> Then I tried to do it 'manually' by using the script:
>  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt
> oboxml_to_chadoxml -  > foo.chadoxml
>
> The foo.chadoxml is empty.
> So, I checked the first script:go2fmt.pl -p obo_text -w xml
> tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
>
> The xlm is generated normally so I also tried to go-apply-xslt
> oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
>
> So don't know what I can do. Any ideas or helps will be really appreciated
> ;-)
>
> All the best,
>
> Greg
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: make ontologies and go-apply-xslt problem

greg gime
Hi Scott,

Thanks for your reply. I checked my disk space and it's ok for that (more than 100Go available..)
So I took the time to reinstall CHADO from scratch again.
And basically now I got the following problem with the make ontologies (Note that all went well since make ontologies step)

make ontologies                                   
./Build ontologies                                                                           
Available ontologies:                                                                        
[1] Relationship Ontology                                                                    
[2] Sequence Ontology                                                                        
[3] Gene Ontology                                                                            
[4] Chado Feature Properties                                                                 
[5] Cell Ontology                                                                            
[6] Plant Ontology                                                                           

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
fetching files for Relationship Ontology
    ./tmp/obo/OBO_REL/ro.obo is up to date
fetching files for Sequence Ontology
    updated
    loading...Use of uninitialized value $str in scalar chomp at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
Use of uninitialized value $fmt in pattern match (m//) at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
Use of uninitialized value $fmt in string eq at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
Use of uninitialized value $fmt in string eq at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
Use of uninitialized value $fmt in string eq at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
Use of uninitialized value $fmt in string eq at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
Use of uninitialized value $fmt in string eq at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
Use of uninitialized value $fmt in concatenation (.) or string at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
Use of uninitialized value $_[1] in join or string at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml -handler Data::Stag::BaseHandler=HASH(0x282d388) at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
        Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-format', undef, '-file', 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)') called at /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
        Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file', 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)') called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
        Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)') called at /usr/local/bin/stag-storenode.pl line 143
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user greg_superuser  --password pass  tmp/song/so.oboxml' failed: 65280
Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
make: *** [ontologies] Error 255


I check the SO file under OBO is present under the ./tmp/song/ directory. but the file tmp/song/so.oboxml is empty.

Do you where I should dig?

Thanks a lot for your help.

Best regards,

Greg



2010/6/4 Scott Cain <[hidden email]>
Hi Greg,

Sorry I missed this email when you sent it last week.  There are a few
things I can suggest that you check:

1. You have sufficient disk space.

2. That you have a complete sequence.obo file; if it got truncated
when it was downloaded, I could see that causing a problem.

3. If neither of those things help, I suggest contacting the GO help
desk, since this is GO software:

 http://www.geneontology.org/GO.contacts.shtml

Thanks,
Scott


On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]> wrote:
> Dear All,
>
> I am struggling with the CHADO install more precisely I am fighting with the
> population of the CV part.
> Basically, I have the script  go-apply-xslt that do not generate anything.
>
> I first followed the instruction in the INSTALL file:
> make ontologies it works for Relationship Ontology.
> But when I tried to load the SO ([2]) then I got the following error:
>
> which ontologies would you like to load (Comma delimited)? [0]  2
> fetching files for Sequence Ontology
>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>     updated
>     loading...DBI
> connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
> failed: fe_sendauth: no password supplied at
> /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
>
> Could not connect to database:
> "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>
> EITHER   The required DBD driver "Pg" is not installed
>     OR   There is no such database as
> "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>
> Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
> System call 'stag-storenode.pl -d
> 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
> greg_superuser  tmp/song/so.oboxml' failed: 65280
> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> make: *** [ontologies] Error 255
>
>
> Then I tried to do it 'manually' by using the script:
>  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt
> oboxml_to_chadoxml -  > foo.chadoxml
>
> The foo.chadoxml is empty.
> So, I checked the first script:go2fmt.pl -p obo_text -w xml
> tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
>
> The xlm is generated normally so I also tried to go-apply-xslt
> oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
>
> So don't know what I can do. Any ideas or helps will be really appreciated
> ;-)
>
> All the best,
>
> Greg
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: make ontologies and go-apply-xslt problem

Scott Cain
Hi Greg,

This is very strange.  The fact the so.oboxml file is empty rather
strongly implies that go2fmt.pl is failing, but it worked just fine
with the relationship ontology, so there isn't a "system-wide" problem
with go2fmt.pl.  I just downloaded so.obo and converted it with this
command:

  go2fmt.pl -p obo_text -w xml so.obo | go-apply-xslt
oboxml_to_chadoxml - > obo_text.xml

and that worked for me; can you check that it works for you on the
command line as well?  If that works, but the oboxml file in the tmp
directory is empty, it is very perplexing, since they are executing
the same command, presumably with the same permissions (right?).

If the oboxml file gets generated properly, then you should be able to
load it via the command line too, using this command:

  stag-storenode.pl -d
'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
--user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml

which is annoying, but not the end of the world--it's not like you'll
be loading ontologies everyday, so if the convenience methods in the
make file aren't working for you, you'll survive.

Scott


On Tue, Jun 8, 2010 at 9:17 AM, greg gime <[hidden email]> wrote:

> Hi Scott,
> Thanks for your reply. I checked my disk space and it's ok for that (more
> than 100Go available..)
> So I took the time to reinstall CHADO from scratch again.
> And basically now I got the following problem with the make ontologies (Note
> that all went well since make ontologies step)
> make ontologies
> ./Build ontologies
>
> Available ontologies:
>
> [1] Relationship Ontology
>
> [2] Sequence Ontology
>
> [3] Gene Ontology
>
> [4] Chado Feature Properties
>
> [5] Cell Ontology
>
> [6] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
> fetching files for Relationship Ontology
>   +http://www.obofoundry.org/ro/ro.obo
>     ./tmp/obo/OBO_REL/ro.obo is up to date
> fetching files for Sequence Ontology
>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>     updated
>     loading...Use of uninitialized value $str in scalar chomp at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
> Use of uninitialized value $fmt in pattern match (m//) at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in concatenation (.) or string at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> Use of uninitialized value $_[1] in join or string at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml -handler
> Data::Stag::BaseHandler=HASH(0x282d388) at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
>         Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-format', undef,
> '-file', 'tmp/song/so.oboxml', '-handler',
> 'Data::Stag::BaseHandler=HASH(0x282d388)') called at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
>         Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file',
> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)')
> called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
>         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file',
> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)')
> called at /usr/local/bin/stag-storenode.pl line 143
> System call 'stag-storenode.pl -d
> 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user greg_superuser
>  --password pass  tmp/song/so.oboxml' failed: 65280
> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> make: *** [ontologies] Error 255
>
> I check the SO file under OBO is present under the ./tmp/song/ directory.
> but the file tmp/song/so.oboxml is empty.
> Do you where I should dig?
> Thanks a lot for your help.
> Best regards,
>
> Greg
>
>
> 2010/6/4 Scott Cain <[hidden email]>
>>
>> Hi Greg,
>>
>> Sorry I missed this email when you sent it last week.  There are a few
>> things I can suggest that you check:
>>
>> 1. You have sufficient disk space.
>>
>> 2. That you have a complete sequence.obo file; if it got truncated
>> when it was downloaded, I could see that causing a problem.
>>
>> 3. If neither of those things help, I suggest contacting the GO help
>> desk, since this is GO software:
>>
>>  http://www.geneontology.org/GO.contacts.shtml
>>
>> Thanks,
>> Scott
>>
>>
>> On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]> wrote:
>> > Dear All,
>> >
>> > I am struggling with the CHADO install more precisely I am fighting with
>> > the
>> > population of the CV part.
>> > Basically, I have the script  go-apply-xslt that do not generate
>> > anything.
>> >
>> > I first followed the instruction in the INSTALL file:
>> > make ontologies it works for Relationship Ontology.
>> > But when I tried to load the SO ([2]) then I got the following error:
>> >
>> > which ontologies would you like to load (Comma delimited)? [0]  2
>> > fetching files for Sequence Ontology
>> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> >     updated
>> >     loading...DBI
>> >
>> > connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
>> > failed: fe_sendauth: no password supplied at
>> > /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
>> >
>> > Could not connect to database:
>> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >
>> > EITHER   The required DBD driver "Pg" is not installed
>> >     OR   There is no such database as
>> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >
>> > Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
>> > System call 'stag-storenode.pl -d
>> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
>> > greg_superuser  tmp/song/so.oboxml' failed: 65280
>> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
>> > make: *** [ontologies] Error 255
>> >
>> >
>> > Then I tried to do it 'manually' by using the script:
>> >  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt
>> > oboxml_to_chadoxml -  > foo.chadoxml
>> >
>> > The foo.chadoxml is empty.
>> > So, I checked the first script:go2fmt.pl -p obo_text -w xml
>> > tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
>> >
>> > The xlm is generated normally so I also tried to go-apply-xslt
>> > oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
>> >
>> > So don't know what I can do. Any ideas or helps will be really
>> > appreciated
>> > ;-)
>> >
>> > All the best,
>> >
>> > Greg
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> >
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: make ontologies and go-apply-xslt problem

greg gime
Hi Scott,

I tried as us suggested: 

go2fmt.pl -p obo_text -w xml tmp/song/so.obo | go-apply-xslt oboxml_to_chadoxml - > obo_text.xml

and again the obo_text.xml is empty. I split the job in two parts:
1-  go2fmt.pl -p obo_text -w xml tmp/song/so.obo > foo.xml 
This worked perfectly a normal xml file.

2- go-apply-xslt oboxml_to_chadoxml foo.xml
Then nothing at the STN nor at STDR.

So I guess the problem comes from the conversion using the XSLT but since I don't have any error it is quite hard to debug.

Have you any clues where I should dig?

Thanks for your help.

Best regards,

Greg

2010/6/8 Scott Cain <[hidden email]>
Hi Greg,

This is very strange.  The fact the so.oboxml file is empty rather
strongly implies that go2fmt.pl is failing, but it worked just fine
with the relationship ontology, so there isn't a "system-wide" problem
with go2fmt.pl.  I just downloaded so.obo and converted it with this
command:

 go2fmt.pl -p obo_text -w xml so.obo | go-apply-xslt
oboxml_to_chadoxml - > obo_text.xml

and that worked for me; can you check that it works for you on the
command line as well?  If that works, but the oboxml file in the tmp
directory is empty, it is very perplexing, since they are executing
the same command, presumably with the same permissions (right?).

If the oboxml file gets generated properly, then you should be able to
load it via the command line too, using this command:

 stag-storenode.pl -d
'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
--user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml

which is annoying, but not the end of the world--it's not like you'll
be loading ontologies everyday, so if the convenience methods in the
make file aren't working for you, you'll survive.

Scott


On Tue, Jun 8, 2010 at 9:17 AM, greg gime <[hidden email]> wrote:
> Hi Scott,
> Thanks for your reply. I checked my disk space and it's ok for that (more
> than 100Go available..)
> So I took the time to reinstall CHADO from scratch again.
> And basically now I got the following problem with the make ontologies (Note
> that all went well since make ontologies step)
> make ontologies
> ./Build ontologies
>
> Available ontologies:
>
> [1] Relationship Ontology
>
> [2] Sequence Ontology
>
> [3] Gene Ontology
>
> [4] Chado Feature Properties
>
> [5] Cell Ontology
>
> [6] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
> fetching files for Relationship Ontology
>   +http://www.obofoundry.org/ro/ro.obo
>     ./tmp/obo/OBO_REL/ro.obo is up to date
> fetching files for Sequence Ontology
>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>     updated
>     loading...Use of uninitialized value $str in scalar chomp at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
> Use of uninitialized value $fmt in pattern match (m//) at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in concatenation (.) or string at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> Use of uninitialized value $_[1] in join or string at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml -handler
> Data::Stag::BaseHandler=HASH(0x282d388) at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
>         Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-format', undef,
> '-file', 'tmp/song/so.oboxml', '-handler',
> 'Data::Stag::BaseHandler=HASH(0x282d388)') called at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
>         Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file',
> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)')
> called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
>         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file',
> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)')
> called at /usr/local/bin/stag-storenode.pl line 143
> System call 'stag-storenode.pl -d
> 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user greg_superuser
>  --password pass  tmp/song/so.oboxml' failed: 65280
> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> make: *** [ontologies] Error 255
>
> I check the SO file under OBO is present under the ./tmp/song/ directory.
> but the file tmp/song/so.oboxml is empty.
> Do you where I should dig?
> Thanks a lot for your help.
> Best regards,
>
> Greg
>
>
> 2010/6/4 Scott Cain <[hidden email]>
>>
>> Hi Greg,
>>
>> Sorry I missed this email when you sent it last week.  There are a few
>> things I can suggest that you check:
>>
>> 1. You have sufficient disk space.
>>
>> 2. That you have a complete sequence.obo file; if it got truncated
>> when it was downloaded, I could see that causing a problem.
>>
>> 3. If neither of those things help, I suggest contacting the GO help
>> desk, since this is GO software:
>>
>>  http://www.geneontology.org/GO.contacts.shtml
>>
>> Thanks,
>> Scott
>>
>>
>> On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]> wrote:
>> > Dear All,
>> >
>> > I am struggling with the CHADO install more precisely I am fighting with
>> > the
>> > population of the CV part.
>> > Basically, I have the script  go-apply-xslt that do not generate
>> > anything.
>> >
>> > I first followed the instruction in the INSTALL file:
>> > make ontologies it works for Relationship Ontology.
>> > But when I tried to load the SO ([2]) then I got the following error:
>> >
>> > which ontologies would you like to load (Comma delimited)? [0]  2
>> > fetching files for Sequence Ontology
>> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> >     updated
>> >     loading...DBI
>> >
>> > connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
>> > failed: fe_sendauth: no password supplied at
>> > /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
>> >
>> > Could not connect to database:
>> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >
>> > EITHER   The required DBD driver "Pg" is not installed
>> >     OR   There is no such database as
>> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >
>> > Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
>> > System call 'stag-storenode.pl -d
>> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
>> > greg_superuser  tmp/song/so.oboxml' failed: 65280
>> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
>> > make: *** [ontologies] Error 255
>> >
>> >
>> > Then I tried to do it 'manually' by using the script:
>> >  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt
>> > oboxml_to_chadoxml -  > foo.chadoxml
>> >
>> > The foo.chadoxml is empty.
>> > So, I checked the first script:go2fmt.pl -p obo_text -w xml
>> > tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
>> >
>> > The xlm is generated normally so I also tried to go-apply-xslt
>> > oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
>> >
>> > So don't know what I can do. Any ideas or helps will be really
>> > appreciated
>> > ;-)
>> >
>> > All the best,
>> >
>> > Greg
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> >
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: make ontologies and go-apply-xslt problem

Scott Cain
Hi Greg,

I have no idea, so I cc'ed Chris Mungall in hopes that he will have a
suggestion.  The script go-apply-xslt is just a wrapper around
xsltproc, and since you aparently have that installed (the script
would have complained, and processing the relationship ontology
wouldn't have worked if you didn't), I don't know what else can be
done.  Perhaps you could send the foo.xml output from the first step
to the list so we can try it on our end to see if something is going
wrong with the xml production.

Scott


On Tue, Jun 8, 2010 at 10:38 AM, greg gime <[hidden email]> wrote:

> Hi Scott,
> I tried as us suggested:
> go2fmt.pl -p obo_text -w xml tmp/song/so.obo | go-apply-xslt
> oboxml_to_chadoxml - > obo_text.xml
> and again the obo_text.xml is empty. I split the job in two parts:
> 1-  go2fmt.pl -p obo_text -w xml tmp/song/so.obo > foo.xml
> This worked perfectly a normal xml file.
> 2- go-apply-xslt oboxml_to_chadoxml foo.xml
> Then nothing at the STN nor at STDR.
> So I guess the problem comes from the conversion using the XSLT but since I
> don't have any error it is quite hard to debug.
> Have you any clues where I should dig?
> Thanks for your help.
> Best regards,
> Greg
> 2010/6/8 Scott Cain <[hidden email]>
>>
>> Hi Greg,
>>
>> This is very strange.  The fact the so.oboxml file is empty rather
>> strongly implies that go2fmt.pl is failing, but it worked just fine
>> with the relationship ontology, so there isn't a "system-wide" problem
>> with go2fmt.pl.  I just downloaded so.obo and converted it with this
>> command:
>>
>>  go2fmt.pl -p obo_text -w xml so.obo | go-apply-xslt
>> oboxml_to_chadoxml - > obo_text.xml
>>
>> and that worked for me; can you check that it works for you on the
>> command line as well?  If that works, but the oboxml file in the tmp
>> directory is empty, it is very perplexing, since they are executing
>> the same command, presumably with the same permissions (right?).
>>
>> If the oboxml file gets generated properly, then you should be able to
>> load it via the command line too, using this command:
>>
>>  stag-storenode.pl -d
>> 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
>> --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml
>>
>> which is annoying, but not the end of the world--it's not like you'll
>> be loading ontologies everyday, so if the convenience methods in the
>> make file aren't working for you, you'll survive.
>>
>> Scott
>>
>>
>> On Tue, Jun 8, 2010 at 9:17 AM, greg gime <[hidden email]> wrote:
>> > Hi Scott,
>> > Thanks for your reply. I checked my disk space and it's ok for that
>> > (more
>> > than 100Go available..)
>> > So I took the time to reinstall CHADO from scratch again.
>> > And basically now I got the following problem with the make ontologies
>> > (Note
>> > that all went well since make ontologies step)
>> > make ontologies
>> > ./Build ontologies
>> >
>> > Available ontologies:
>> >
>> > [1] Relationship Ontology
>> >
>> > [2] Sequence Ontology
>> >
>> > [3] Gene Ontology
>> >
>> > [4] Chado Feature Properties
>> >
>> > [5] Cell Ontology
>> >
>> > [6] Plant Ontology
>> >
>> > Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
>> > fetching files for Relationship Ontology
>> >   +http://www.obofoundry.org/ro/ro.obo
>> >     ./tmp/obo/OBO_REL/ro.obo is up to date
>> > fetching files for Sequence Ontology
>> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> >     updated
>> >     loading...Use of uninitialized value $str in scalar chomp at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
>> > Use of uninitialized value $fmt in pattern match (m//) at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
>> > Use of uninitialized value $fmt in string eq at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
>> > Use of uninitialized value $fmt in string eq at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
>> > Use of uninitialized value $fmt in string eq at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
>> > Use of uninitialized value $fmt in string eq at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
>> > Use of uninitialized value $fmt in string eq at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
>> > Use of uninitialized value $fmt in concatenation (.) or string at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
>> > Use of uninitialized value $_[1] in join or string at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
>> > cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml
>> > -handler
>> > Data::Stag::BaseHandler=HASH(0x282d388) at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
>> >         Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-format',
>> > undef,
>> > '-file', 'tmp/song/so.oboxml', '-handler',
>> > 'Data::Stag::BaseHandler=HASH(0x282d388)') called at
>> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
>> >         Data::Stag::StagImpl::parse('Data::Stag', '-format', undef,
>> > '-file',
>> > 'tmp/song/so.oboxml', '-handler',
>> > 'Data::Stag::BaseHandler=HASH(0x282d388)')
>> > called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
>> >         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file',
>> > 'tmp/song/so.oboxml', '-handler',
>> > 'Data::Stag::BaseHandler=HASH(0x282d388)')
>> > called at /usr/local/bin/stag-storenode.pl line 143
>> > System call 'stag-storenode.pl -d
>> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
>> > greg_superuser
>> >  --password pass  tmp/song/so.oboxml' failed: 65280
>> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
>> > make: *** [ontologies] Error 255
>> >
>> > I check the SO file under OBO is present under the ./tmp/song/
>> > directory.
>> > but the file tmp/song/so.oboxml is empty.
>> > Do you where I should dig?
>> > Thanks a lot for your help.
>> > Best regards,
>> >
>> > Greg
>> >
>> >
>> > 2010/6/4 Scott Cain <[hidden email]>
>> >>
>> >> Hi Greg,
>> >>
>> >> Sorry I missed this email when you sent it last week.  There are a few
>> >> things I can suggest that you check:
>> >>
>> >> 1. You have sufficient disk space.
>> >>
>> >> 2. That you have a complete sequence.obo file; if it got truncated
>> >> when it was downloaded, I could see that causing a problem.
>> >>
>> >> 3. If neither of those things help, I suggest contacting the GO help
>> >> desk, since this is GO software:
>> >>
>> >>  http://www.geneontology.org/GO.contacts.shtml
>> >>
>> >> Thanks,
>> >> Scott
>> >>
>> >>
>> >> On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]> wrote:
>> >> > Dear All,
>> >> >
>> >> > I am struggling with the CHADO install more precisely I am fighting
>> >> > with
>> >> > the
>> >> > population of the CV part.
>> >> > Basically, I have the script  go-apply-xslt that do not generate
>> >> > anything.
>> >> >
>> >> > I first followed the instruction in the INSTALL file:
>> >> > make ontologies it works for Relationship Ontology.
>> >> > But when I tried to load the SO ([2]) then I got the following error:
>> >> >
>> >> > which ontologies would you like to load (Comma delimited)? [0]  2
>> >> > fetching files for Sequence Ontology
>> >> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> >> >     updated
>> >> >     loading...DBI
>> >> >
>> >> >
>> >> > connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
>> >> > failed: fe_sendauth: no password supplied at
>> >> > /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
>> >> >
>> >> > Could not connect to database:
>> >> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >> >
>> >> > EITHER   The required DBD driver "Pg" is not installed
>> >> >     OR   There is no such database as
>> >> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >> >
>> >> > Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
>> >> > System call 'stag-storenode.pl -d
>> >> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
>> >> > greg_superuser  tmp/song/so.oboxml' failed: 65280
>> >> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
>> >> > make: *** [ontologies] Error 255
>> >> >
>> >> >
>> >> > Then I tried to do it 'manually' by using the script:
>> >> >  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt
>> >> > oboxml_to_chadoxml -  > foo.chadoxml
>> >> >
>> >> > The foo.chadoxml is empty.
>> >> > So, I checked the first script:go2fmt.pl -p obo_text -w xml
>> >> > tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
>> >> >
>> >> > The xlm is generated normally so I also tried to go-apply-xslt
>> >> > oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
>> >> >
>> >> > So don't know what I can do. Any ideas or helps will be really
>> >> > appreciated
>> >> > ;-)
>> >> >
>> >> > All the best,
>> >> >
>> >> > Greg
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Gmod-schema mailing list
>> >> > [hidden email]
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: make ontologies and go-apply-xslt problem

Chris Mungall-3
In reply to this post by greg gime

On Jun 8, 2010, at 7:38 AM, greg gime wrote:

> Hi Scott,
>
> I tried as us suggested:
>
> go2fmt.pl -p obo_text -w xml tmp/song/so.obo | go-apply-xslt  
> oboxml_to_chadoxml - > obo_text.xml
>
> and again the obo_text.xml is empty. I split the job in two parts:
> 1-  go2fmt.pl -p obo_text -w xml tmp/song/so.obo > foo.xml
> This worked perfectly a normal xml file.
>
> 2- go-apply-xslt oboxml_to_chadoxml foo.xml
> Then nothing at the STN nor at STDR.
>
> So I guess the problem comes from the conversion using the XSLT but  
> since I don't have any error it is quite hard to debug.

Let's try running xsltproc manually and see what happens

I presume you installed go-perl from CPAN? If so, the xslt file should  
be installed alongside the perl modules. The location will be system  
dependent

for me it would be this:
xsltproc /Library/Perl/5.8.8/GO/xsl/oboxml_to_chadoxml.xsl foo.xml

I'm not aware of any versioning issues with xsltproc, but you might  
want to have a look at the version anyway. I have:

  $ xsltproc  -V
Using libxml 20616, libxslt 10112 and libexslt 810
xsltproc was compiled against libxml 20616, libxslt 10112 and libexslt  
810
libxslt 10112 was compiled against libxml 20616
libexslt 810 was compiled against libxml 20616

Email me foo.xml just so I can check it's as expected.

>
> Have you any clues where I should dig?
>
> Thanks for your help.
>
> Best regards,
>
> Greg
>
> 2010/6/8 Scott Cain <[hidden email]>
> Hi Greg,
>
> This is very strange.  The fact the so.oboxml file is empty rather
> strongly implies that go2fmt.pl is failing, but it worked just fine
> with the relationship ontology, so there isn't a "system-wide" problem
> with go2fmt.pl.  I just downloaded so.obo and converted it with this
> command:
>
>  go2fmt.pl -p obo_text -w xml so.obo | go-apply-xslt
> oboxml_to_chadoxml - > obo_text.xml
>
> and that worked for me; can you check that it works for you on the
> command line as well?  If that works, but the oboxml file in the tmp
> directory is empty, it is very perplexing, since they are executing
> the same command, presumably with the same permissions (right?).
>
> If the oboxml file gets generated properly, then you should be able to
> load it via the command line too, using this command:
>
>  stag-storenode.pl -d
> 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
> --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml
>
> which is annoying, but not the end of the world--it's not like you'll
> be loading ontologies everyday, so if the convenience methods in the
> make file aren't working for you, you'll survive.
>
> Scott
>
>
> On Tue, Jun 8, 2010 at 9:17 AM, greg gime <[hidden email]> wrote:
> > Hi Scott,
> > Thanks for your reply. I checked my disk space and it's ok for  
> that (more
> > than 100Go available..)
> > So I took the time to reinstall CHADO from scratch again.
> > And basically now I got the following problem with the make  
> ontologies (Note
> > that all went well since make ontologies step)
> > make ontologies
> > ./Build ontologies
> >
> > Available ontologies:
> >
> > [1] Relationship Ontology
> >
> > [2] Sequence Ontology
> >
> > [3] Gene Ontology
> >
> > [4] Chado Feature Properties
> >
> > [5] Cell Ontology
> >
> > [6] Plant Ontology
> >
> > Which ontologies would you like to load (Comma delimited)? [0]  
> 1,2,3,4
> > fetching files for Relationship Ontology
> >   +http://www.obofoundry.org/ro/ro.obo
> >     ./tmp/obo/OBO_REL/ro.obo is up to date
> > fetching files for Sequence Ontology
> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
> >     updated
> >     loading...Use of uninitialized value $str in scalar chomp at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
> > Use of uninitialized value $fmt in pattern match (m//) at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in concatenation (.) or string at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> > Use of uninitialized value $_[1] in join or string at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> > cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml -
> handler
> > Data::Stag::BaseHandler=HASH(0x282d388) at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
> >         Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-
> format', undef,
> > '-file', 'tmp/song/so.oboxml', '-handler',
> > 'Data::Stag::BaseHandler=HASH(0x282d388)') called at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
> >         Data::Stag::StagImpl::parse('Data::Stag', '-format',  
> undef, '-file',
> > 'tmp/song/so.oboxml', '-handler',  
> 'Data::Stag::BaseHandler=HASH(0x282d388)')
> > called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
> >         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-
> file',
> > 'tmp/song/so.oboxml', '-handler',  
> 'Data::Stag::BaseHandler=HASH(0x282d388)')
> > called at /usr/local/bin/stag-storenode.pl line 143
> > System call 'stag-storenode.pl -d
> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user  
> greg_superuser
> >  --password pass  tmp/song/so.oboxml' failed: 65280
> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> > make: *** [ontologies] Error 255
> >
> > I check the SO file under OBO is present under the ./tmp/song/  
> directory.
> > but the file tmp/song/so.oboxml is empty.
> > Do you where I should dig?
> > Thanks a lot for your help.
> > Best regards,
> >
> > Greg
> >
> >
> > 2010/6/4 Scott Cain <[hidden email]>
> >>
> >> Hi Greg,
> >>
> >> Sorry I missed this email when you sent it last week.  There are  
> a few
> >> things I can suggest that you check:
> >>
> >> 1. You have sufficient disk space.
> >>
> >> 2. That you have a complete sequence.obo file; if it got truncated
> >> when it was downloaded, I could see that causing a problem.
> >>
> >> 3. If neither of those things help, I suggest contacting the GO  
> help
> >> desk, since this is GO software:
> >>
> >>  http://www.geneontology.org/GO.contacts.shtml
> >>
> >> Thanks,
> >> Scott
> >>
> >>
> >> On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]>  
> wrote:
> >> > Dear All,
> >> >
> >> > I am struggling with the CHADO install more precisely I am  
> fighting with
> >> > the
> >> > population of the CV part.
> >> > Basically, I have the script  go-apply-xslt that do not generate
> >> > anything.
> >> >
> >> > I first followed the instruction in the INSTALL file:
> >> > make ontologies it works for Relationship Ontology.
> >> > But when I tried to load the SO ([2]) then I got the following  
> error:
> >> >
> >> > which ontologies would you like to load (Comma delimited)? [0]  2
> >> > fetching files for Sequence Ontology
> >> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/ 
> so.obo
> >> >     updated
> >> >     loading...DBI
> >> >
> >> >  
> connect
> ('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
> >> > failed: fe_sendauth: no password supplied at
> >> > /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
> >> >
> >> > Could not connect to database:
> >> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
> >> >
> >> > EITHER   The required DBD driver "Pg" is not installed
> >> >     OR   There is no such database as
> >> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
> >> >
> >> > Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
> >> > System call 'stag-storenode.pl -d
> >> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
> >> > greg_superuser  tmp/song/so.oboxml' failed: 65280
> >> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> >> > make: *** [ontologies] Error 255
> >> >
> >> >
> >> > Then I tried to do it 'manually' by using the script:
> >> >  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-
> apply-xslt
> >> > oboxml_to_chadoxml -  > foo.chadoxml
> >> >
> >> > The foo.chadoxml is empty.
> >> > So, I checked the first script:go2fmt.pl -p obo_text -w xml
> >> > tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
> >> >
> >> > The xlm is generated normally so I also tried to go-apply-xslt
> >> > oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
> >> >
> >> > So don't know what I can do. Any ideas or helps will be really
> >> > appreciated
> >> > ;-)
> >> >
> >> > All the best,
> >> >
> >> > Greg
> >> >
> >> >
> >> >
> >> >  
> ------------------------------------------------------------------------------
> >> >
> >> >
> >> > _______________________________________________
> >> > Gmod-schema mailing list
> >> > [hidden email]
> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >>  
> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at  
> scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                      
> 216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo_______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
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Re: make ontologies and go-apply-xslt problem

greg gime
Hi Chris and Scott,

Thanks for your quick reply.
So it starts to make more sense. I just did what you advice:

xsltproc /usr/local/share/perl/5.10.0/GO/xsl/oboxml_to_chadoxml.xsl foo.xml
And I got a  "beautiful " Segmentation fault !!

I did then a versioning:

xsltproc -V
Using libxml 20632, libxslt 10124 and libexslt 813
xsltproc was compiled against libxml 20632, libxslt 10124 and libexslt 813
libxslt 10124 was compiled against libxml 20632
libexslt 813 was compiled against libxml 20632

My Linux box is a AMD 64 under Ubuntu 9.10 server edition with KDE Version 4.3.2.

Have you ever heard about the same kind of error? I guess I would need probably need to reinstall some packages.

I also joined my foo.xml if you have time to have a look.

Thanks for your help,

Best regards,

Greg

 



2010/6/8 Chris Mungall <[hidden email]>

On Jun 8, 2010, at 7:38 AM, greg gime wrote:

Hi Scott,

I tried as us suggested:

go2fmt.pl -p obo_text -w xml tmp/song/so.obo | go-apply-xslt oboxml_to_chadoxml - > obo_text.xml

and again the obo_text.xml is empty. I split the job in two parts:
1-  go2fmt.pl -p obo_text -w xml tmp/song/so.obo > foo.xml
This worked perfectly a normal xml file.

2- go-apply-xslt oboxml_to_chadoxml foo.xml
Then nothing at the STN nor at STDR.

So I guess the problem comes from the conversion using the XSLT but since I don't have any error it is quite hard to debug.

Let's try running xsltproc manually and see what happens

I presume you installed go-perl from CPAN? If so, the xslt file should be installed alongside the perl modules. The location will be system dependent

for me it would be this:
xsltproc /Library/Perl/5.8.8/GO/xsl/oboxml_to_chadoxml.xsl foo.xml

I'm not aware of any versioning issues with xsltproc, but you might want to have a look at the version anyway. I have:

 $ xsltproc  -V
Using libxml 20616, libxslt 10112 and libexslt 810
xsltproc was compiled against libxml 20616, libxslt 10112 and libexslt 810
libxslt 10112 was compiled against libxml 20616
libexslt 810 was compiled against libxml 20616

Email me foo.xml just so I can check it's as expected.


Have you any clues where I should dig?

Thanks for your help.

Best regards,

Greg

2010/6/8 Scott Cain <[hidden email]>
Hi Greg,

This is very strange.  The fact the so.oboxml file is empty rather
strongly implies that go2fmt.pl is failing, but it worked just fine
with the relationship ontology, so there isn't a "system-wide" problem
with go2fmt.pl.  I just downloaded so.obo and converted it with this
command:

 go2fmt.pl -p obo_text -w xml so.obo | go-apply-xslt
oboxml_to_chadoxml - > obo_text.xml

and that worked for me; can you check that it works for you on the
command line as well?  If that works, but the oboxml file in the tmp
directory is empty, it is very perplexing, since they are executing
the same command, presumably with the same permissions (right?).

If the oboxml file gets generated properly, then you should be able to
load it via the command line too, using this command:

 stag-storenode.pl -d
'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
--user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml

which is annoying, but not the end of the world--it's not like you'll
be loading ontologies everyday, so if the convenience methods in the
make file aren't working for you, you'll survive.

Scott


On Tue, Jun 8, 2010 at 9:17 AM, greg gime <[hidden email]> wrote:
> Hi Scott,
> Thanks for your reply. I checked my disk space and it's ok for that (more
> than 100Go available..)
> So I took the time to reinstall CHADO from scratch again.
> And basically now I got the following problem with the make ontologies (Note
> that all went well since make ontologies step)
> make ontologies
> ./Build ontologies
>
> Available ontologies:
>
> [1] Relationship Ontology
>
> [2] Sequence Ontology
>
> [3] Gene Ontology
>
> [4] Chado Feature Properties
>
> [5] Cell Ontology
>
> [6] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
> fetching files for Relationship Ontology
>   +http://www.obofoundry.org/ro/ro.obo
>     ./tmp/obo/OBO_REL/ro.obo is up to date
> fetching files for Sequence Ontology
>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>     updated
>     loading...Use of uninitialized value $str in scalar chomp at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
> Use of uninitialized value $fmt in pattern match (m//) at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in string eq at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> Use of uninitialized value $fmt in concatenation (.) or string at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> Use of uninitialized value $_[1] in join or string at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml -handler
> Data::Stag::BaseHandler=HASH(0x282d388) at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
>         Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-format', undef,
> '-file', 'tmp/song/so.oboxml', '-handler',
> 'Data::Stag::BaseHandler=HASH(0x282d388)') called at
> /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
>         Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file',
> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)')
> called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
>         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file',
> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x282d388)')
> called at /usr/local/bin/stag-storenode.pl line 143
> System call 'stag-storenode.pl -d
> 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user greg_superuser
>  --password pass  tmp/song/so.oboxml' failed: 65280
> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> make: *** [ontologies] Error 255
>
> I check the SO file under OBO is present under the ./tmp/song/ directory.
> but the file tmp/song/so.oboxml is empty.
> Do you where I should dig?
> Thanks a lot for your help.
> Best regards,
>
> Greg
>
>
> 2010/6/4 Scott Cain <[hidden email]>
>>
>> Hi Greg,
>>
>> Sorry I missed this email when you sent it last week.  There are a few
>> things I can suggest that you check:
>>
>> 1. You have sufficient disk space.
>>
>> 2. That you have a complete sequence.obo file; if it got truncated
>> when it was downloaded, I could see that causing a problem.
>>
>> 3. If neither of those things help, I suggest contacting the GO help
>> desk, since this is GO software:
>>
>>  http://www.geneontology.org/GO.contacts.shtml
>>
>> Thanks,
>> Scott
>>
>>
>> On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]> wrote:
>> > Dear All,
>> >
>> > I am struggling with the CHADO install more precisely I am fighting with
>> > the
>> > population of the CV part.
>> > Basically, I have the script  go-apply-xslt that do not generate
>> > anything.
>> >
>> > I first followed the instruction in the INSTALL file:
>> > make ontologies it works for Relationship Ontology.
>> > But when I tried to load the SO ([2]) then I got the following error:
>> >
>> > which ontologies would you like to load (Comma delimited)? [0]  2
>> > fetching files for Sequence Ontology
>> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> >     updated
>> >     loading...DBI
>> >
>> > connect('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
>> > failed: fe_sendauth: no password supplied at
>> > /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
>> >
>> > Could not connect to database:
>> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >
>> > EITHER   The required DBD driver "Pg" is not installed
>> >     OR   There is no such database as
>> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
>> >
>> > Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
>> > System call 'stag-storenode.pl -d
>> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
>> > greg_superuser  tmp/song/so.oboxml' failed: 65280
>> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
>> > make: *** [ontologies] Error 255
>> >
>> >
>> > Then I tried to do it 'manually' by using the script:
>> >  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-apply-xslt
>> > oboxml_to_chadoxml -  > foo.chadoxml
>> >
>> > The foo.chadoxml is empty.
>> > So, I checked the first script:go2fmt.pl -p obo_text -w xml
>> > tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
>> >
>> > The xlm is generated normally so I also tried to go-apply-xslt
>> > oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
>> >
>> > So don't know what I can do. Any ideas or helps will be really
>> > appreciated
>> > ;-)
>> >
>> > All the best,
>> >
>> > Greg
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> >
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo_______________________________________________



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: make ontologies and go-apply-xslt problem

Chris Mungall-3

On Jun 9, 2010, at 1:47 AM, greg gime wrote:

> Hi Chris and Scott,
>
> Thanks for your quick reply.
> So it starts to make more sense. I just did what you advice:
>
> xsltproc /usr/local/share/perl/5.10.0/GO/xsl/oboxml_to_chadoxml.xsl  
> foo.xml
> And I got a  "beautiful " Segmentation fault !!

Aha!

sorry, I'll make the wrapper script report these things

> I did then a versioning:
>
> xsltproc -V
> Using libxml 20632, libxslt 10124 and libexslt 813
> xsltproc was compiled against libxml 20632, libxslt 10124 and  
> libexslt 813
> libxslt 10124 was compiled against libxml 20632
> libexslt 813 was compiled against libxml 20632

don't see anything amiss there.

> My Linux box is a AMD 64 under Ubuntu 9.10 server edition with KDE  
> Version 4.3.2.
>
> Have you ever heard about the same kind of error? I guess I would  
> need probably need to reinstall some packages.

No, I haven't. I'm afraid I don't have any specific suggestions. You  
might want to see if you have problems with upstream dependencies,  
e.g. libxml.

In theory it's possible to swap in some other xslt processor, such as  
xalan (100% java). But I'd persevere a bit with xsltproc.

> I also joined my foo.xml if you have time to have a look.

this looks fine

> Thanks for your help,
>
> Best regards,
>
> Greg
>
>
>
> 2010/6/8 Chris Mungall <[hidden email]>
>
> On Jun 8, 2010, at 7:38 AM, greg gime wrote:
>
> Hi Scott,
>
> I tried as us suggested:
>
> go2fmt.pl -p obo_text -w xml tmp/song/so.obo | go-apply-xslt  
> oboxml_to_chadoxml - > obo_text.xml
>
> and again the obo_text.xml is empty. I split the job in two parts:
> 1-  go2fmt.pl -p obo_text -w xml tmp/song/so.obo > foo.xml
> This worked perfectly a normal xml file.
>
> 2- go-apply-xslt oboxml_to_chadoxml foo.xml
> Then nothing at the STN nor at STDR.
>
> So I guess the problem comes from the conversion using the XSLT but  
> since I don't have any error it is quite hard to debug.
>
> Let's try running xsltproc manually and see what happens
>
> I presume you installed go-perl from CPAN? If so, the xslt file  
> should be installed alongside the perl modules. The location will be  
> system dependent
>
> for me it would be this:
> xsltproc /Library/Perl/5.8.8/GO/xsl/oboxml_to_chadoxml.xsl foo.xml
>
> I'm not aware of any versioning issues with xsltproc, but you might  
> want to have a look at the version anyway. I have:
>
>  $ xsltproc  -V
> Using libxml 20616, libxslt 10112 and libexslt 810
> xsltproc was compiled against libxml 20616, libxslt 10112 and  
> libexslt 810
> libxslt 10112 was compiled against libxml 20616
> libexslt 810 was compiled against libxml 20616
>
> Email me foo.xml just so I can check it's as expected.
>
>
> Have you any clues where I should dig?
>
> Thanks for your help.
>
> Best regards,
>
> Greg
>
> 2010/6/8 Scott Cain <[hidden email]>
> Hi Greg,
>
> This is very strange.  The fact the so.oboxml file is empty rather
> strongly implies that go2fmt.pl is failing, but it worked just fine
> with the relationship ontology, so there isn't a "system-wide" problem
> with go2fmt.pl.  I just downloaded so.obo and converted it with this
> command:
>
>  go2fmt.pl -p obo_text -w xml so.obo | go-apply-xslt
> oboxml_to_chadoxml - > obo_text.xml
>
> and that worked for me; can you check that it works for you on the
> command line as well?  If that works, but the oboxml file in the tmp
> directory is empty, it is very perplexing, since they are executing
> the same command, presumably with the same permissions (right?).
>
> If the oboxml file gets generated properly, then you should be able to
> load it via the command line too, using this command:
>
>  stag-storenode.pl -d
> 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
> --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml
>
> which is annoying, but not the end of the world--it's not like you'll
> be loading ontologies everyday, so if the convenience methods in the
> make file aren't working for you, you'll survive.
>
> Scott
>
>
> On Tue, Jun 8, 2010 at 9:17 AM, greg gime <[hidden email]> wrote:
> > Hi Scott,
> > Thanks for your reply. I checked my disk space and it's ok for  
> that (more
> > than 100Go available..)
> > So I took the time to reinstall CHADO from scratch again.
> > And basically now I got the following problem with the make  
> ontologies (Note
> > that all went well since make ontologies step)
> > make ontologies
> > ./Build ontologies
> >
> > Available ontologies:
> >
> > [1] Relationship Ontology
> >
> > [2] Sequence Ontology
> >
> > [3] Gene Ontology
> >
> > [4] Chado Feature Properties
> >
> > [5] Cell Ontology
> >
> > [6] Plant Ontology
> >
> > Which ontologies would you like to load (Comma delimited)? [0]  
> 1,2,3,4
> > fetching files for Relationship Ontology
> >   +http://www.obofoundry.org/ro/ro.obo
> >     ./tmp/obo/OBO_REL/ro.obo is up to date
> > fetching files for Sequence Ontology
> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
> >     updated
> >     loading...Use of uninitialized value $str in scalar chomp at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 186.
> > Use of uninitialized value $fmt in pattern match (m//) at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 223.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in string eq at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 228.
> > Use of uninitialized value $fmt in concatenation (.) or string at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> > Use of uninitialized value $_[1] in join or string at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247.
> > cannot guess parser from fmt="" -format  -file tmp/song/so.oboxml -
> handler
> > Data::Stag::BaseHandler=HASH(0x282d388) at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 247
> >         Data::Stag::StagImpl::parser('ARRAY(0x282d5f8)', '-
> format', undef,
> > '-file', 'tmp/song/so.oboxml', '-handler',
> > 'Data::Stag::BaseHandler=HASH(0x282d388)') called at
> > /usr/local/share/perl/5.10.0/Data/Stag/StagImpl.pm line 267
> >         Data::Stag::StagImpl::parse('Data::Stag', '-format',  
> undef, '-file',
> > 'tmp/song/so.oboxml', '-handler',  
> 'Data::Stag::BaseHandler=HASH(0x282d388)')
> > called at /usr/local/share/perl/5.10.0/Data/Stag.pm line 181
> >         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-
> file',
> > 'tmp/song/so.oboxml', '-handler',  
> 'Data::Stag::BaseHandler=HASH(0x282d388)')
> > called at /usr/local/bin/stag-storenode.pl line 143
> > System call 'stag-storenode.pl -d
> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user  
> greg_superuser
> >  --password pass  tmp/song/so.oboxml' failed: 65280
> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> > make: *** [ontologies] Error 255
> >
> > I check the SO file under OBO is present under the ./tmp/song/  
> directory.
> > but the file tmp/song/so.oboxml is empty.
> > Do you where I should dig?
> > Thanks a lot for your help.
> > Best regards,
> >
> > Greg
> >
> >
> > 2010/6/4 Scott Cain <[hidden email]>
> >>
> >> Hi Greg,
> >>
> >> Sorry I missed this email when you sent it last week.  There are  
> a few
> >> things I can suggest that you check:
> >>
> >> 1. You have sufficient disk space.
> >>
> >> 2. That you have a complete sequence.obo file; if it got truncated
> >> when it was downloaded, I could see that causing a problem.
> >>
> >> 3. If neither of those things help, I suggest contacting the GO  
> help
> >> desk, since this is GO software:
> >>
> >>  http://www.geneontology.org/GO.contacts.shtml
> >>
> >> Thanks,
> >> Scott
> >>
> >>
> >> On Fri, May 28, 2010 at 5:51 AM, greg gime <[hidden email]>  
> wrote:
> >> > Dear All,
> >> >
> >> > I am struggling with the CHADO install more precisely I am  
> fighting with
> >> > the
> >> > population of the CV part.
> >> > Basically, I have the script  go-apply-xslt that do not generate
> >> > anything.
> >> >
> >> > I first followed the instruction in the INSTALL file:
> >> > make ontologies it works for Relationship Ontology.
> >> > But when I tried to load the SO ([2]) then I got the following  
> error:
> >> >
> >> > which ontologies would you like to load (Comma delimited)? [0]  2
> >> > fetching files for Sequence Ontology
> >> >   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/ 
> so.obo
> >> >     updated
> >> >     loading...DBI
> >> >
> >> >  
> connect
> ('dbname=annotation_db;host=localhost;port=5432','greg_superuser',...)
> >> > failed: fe_sendauth: no password supplied at
> >> > /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 81
> >> >
> >> > Could not connect to database:
> >> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
> >> >
> >> > EITHER   The required DBD driver "Pg" is not installed
> >> >     OR   There is no such database as
> >> > "dbi:Pg:dbname=annotation_db;host=localhost;port=5432"
> >> >
> >> > Died at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 120.
> >> > System call 'stag-storenode.pl -d
> >> > 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user
> >> > greg_superuser  tmp/song/so.oboxml' failed: 65280
> >> > Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
> >> > make: *** [ontologies] Error 255
> >> >
> >> >
> >> > Then I tried to do it 'manually' by using the script:
> >> >  go2fmt.pl -p obo_text -w xml tmp/obo/OBO_REL/ro.obo |  go-
> apply-xslt
> >> > oboxml_to_chadoxml -  > foo.chadoxml
> >> >
> >> > The foo.chadoxml is empty.
> >> > So, I checked the first script:go2fmt.pl -p obo_text -w xml
> >> > tmp/obo/OBO_REL/ro.obo > foo.oboxml is working.
> >> >
> >> > The xlm is generated normally so I also tried to go-apply-xslt
> >> > oboxml_to_chadoxml foo.oboxml but again nothing on the prompt....
> >> >
> >> > So don't know what I can do. Any ideas or helps will be really
> >> > appreciated
> >> > ;-)
> >> >
> >> > All the best,
> >> >
> >> > Greg
> >> >
> >> >
> >> >
> >> >  
> ------------------------------------------------------------------------------
> >> >
> >> >
> >> > _______________________________________________
> >> > Gmod-schema mailing list
> >> > [hidden email]
> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >>  
> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at  
> scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                      
> 216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
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>
>
> <foo.xml>


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Re: make ontologies and go-apply-xslt problem

Don Gilbert-2-3
In reply to this post by greg gime


Greg & Chris,

I've used this java replacement in the past for go-apply-xslt
instead of the binary xsltproc/libxml that some of my computers did not have.
This uses standard java libaries.  I've not tried it for a few years.

- Don

// xsltproc.java
/** basic java xslt transformer
  * should work with current Java runtime libraries without additional software installs
  * GMOD need: current CV loaders use GO perl tools with xsltproc requirement.
  * alternate to c-code xsltproc used by GO perl tools:
  *   $gobin/go-apply-xslt: " ... you will need an xslt processor. I use
  *   xsltproc, which comes as part of libxml and libxml2."
  *
  *  compile: javac -classpath . xsltproc.java
  *  use: java -cp . xsltproc xsl-source xml-source > output
  *  author: d. gilbert; 2006
  */

import java.io.*;
import java.util.*;
import java.net.*;
import org.w3c.dom.*;
import javax.xml.transform.*;
import javax.xml.transform.dom.*;
import javax.xml.transform.stream.*;

public class xsltproc {

public static void main(String[] args)
{
  if (args.length < 2) {
    System.err.println("# xsltproc transform xml with xsl stylesheet");
    System.err.println("# usage: xsltproc xsl-source xml-source1 .. xml-sourceN");
    System.err.println("#   source can be file, url, string-value");
    }
  else
    xtransforms( new PrintWriter(System.out), args[0], args, 1, args.length-1);
}

static void xtransforms( Writer sout, String xsl, String[] xmls, int first, int last )
{
  try {
        StreamSource trsource= getSource(xsl);
        TransformerFactory factory = TransformerFactory.newInstance();
        Transformer processor = factory.newTransformer( trsource );
        StreamResult result = new StreamResult( sout );

  for (int i= first; i<= last; i++) {
          StreamSource xsource=  getSource(xmls[i]);
          processor.transform( xsource, result );
          }
        }
        catch (Exception ex) {
          System.err.println("# xslt-Error: "+ex.getMessage()+"\n");
          ex.printStackTrace();
          }
}
       
static StreamSource getSource(String x) throws Exception
{
        Reader rdr= null;
        if ( "-".equals(x) )  
          rdr= new InputStreamReader(System.in);
        else if ( x.indexOf("<?xml")>=0 )
          rdr =  new StringReader(x);
        else if ( x.indexOf("://")>0 )
                rdr = new InputStreamReader( new URL(x).openStream() );
        else {
          File f= null;
          if ( x.length()<255 && (f= new File(x)).exists() )
                  rdr = new FileReader(f);  
                else if ( x.indexOf('<')>=0 )
            rdr = new StringReader(x);
                }
  StreamSource ssrc= new StreamSource( rdr );
  return ssrc;
}


}


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Re: make ontologies and go-apply-xslt problem

greg gime
Hi Don and Chris,

Sorry for the late answer but I was out of the office. Don's script worked perfectly! Thanks a lot for that.
Basically, I just followed Don advices and ran:

java -cp . xsltproc /home/greg/perl_modules/go-perl-0.11/GO/xsl/oboxml_to_chadoxml.xsl foo.xml > foo.chadoxml
Then the loading into POSGRESQL:
stag-storenode.pl -d 'dbi:Pg:dbname=annotation_db;host=localhost;port=5432' --user user --password pass foo.chadoxml

And no complain for SO ontologies loading.
So I ll load all ontologies with this scripts.

Again thanks a lot for your help,

All the best,


Greg





2010/6/9 Don Gilbert <[hidden email]>


Greg & Chris,

I've used this java replacement in the past for go-apply-xslt
instead of the binary xsltproc/libxml that some of my computers did not have.
This uses standard java libaries.  I've not tried it for a few years.

- Don

// xsltproc.java
/** basic java xslt transformer
 * should work with current Java runtime libraries without additional software installs
 * GMOD need: current CV loaders use GO perl tools with xsltproc requirement.
 * alternate to c-code xsltproc used by GO perl tools:
 *   $gobin/go-apply-xslt: " ... you will need an xslt processor. I use
 *   xsltproc, which comes as part of libxml and libxml2."
 *
 *  compile: javac -classpath . xsltproc.java
 *  use: java -cp . xsltproc xsl-source xml-source > output
 *  author: d. gilbert; 2006
 */

import java.io.*;
import java.util.*;
import java.net.*;
import org.w3c.dom.*;
import javax.xml.transform.*;
import javax.xml.transform.dom.*;
import javax.xml.transform.stream.*;

public class xsltproc {

public static void main(String[] args)
{
 if (args.length < 2) {
   System.err.println("# xsltproc transform xml with xsl stylesheet");
   System.err.println("# usage: xsltproc xsl-source xml-source1 .. xml-sourceN");
   System.err.println("#   source can be file, url, string-value");
   }
 else
   xtransforms( new PrintWriter(System.out), args[0], args, 1, args.length-1);
}

static void xtransforms( Writer sout, String xsl, String[] xmls, int first, int last )
{
 try {
       StreamSource trsource= getSource(xsl);
       TransformerFactory factory = TransformerFactory.newInstance();
       Transformer processor = factory.newTransformer( trsource );
       StreamResult result = new StreamResult( sout );

 for (int i= first; i<= last; i++) {
         StreamSource xsource=  getSource(xmls[i]);
         processor.transform( xsource, result );
         }
       }
       catch (Exception ex) {
         System.err.println("# xslt-Error: "+ex.getMessage()+"\n");
         ex.printStackTrace();
         }
}

static StreamSource getSource(String x) throws Exception
{
       Reader rdr= null;
       if ( "-".equals(x) )
         rdr= new InputStreamReader(System.in);
       else if ( x.indexOf("<?xml")>=0 )
         rdr =  new StringReader(x);
       else if ( x.indexOf("://")>0 )
               rdr = new InputStreamReader( new URL(x).openStream() );
       else {
         File f= null;
         if ( x.length()<255 && (f= new File(x)).exists() )
                 rdr = new FileReader(f);
               else if ( x.indexOf('<')>=0 )
           rdr = new StringReader(x);
               }
 StreamSource ssrc= new StreamSource( rdr );
 return ssrc;
}


}



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