gusdev-gusdev — Topics concerning GUS development

[GUSDEV] GUS Config Changes

[Michael S. <msa...@pc...>]

All,

I've finally fixed the long standing and often confusion generating  
issue of properly configuring GUS.  This change should be relatively  
minor, and full details are below, but I wanted to make sure everyone  
was clear.

Short Version:

******    All GUS configuration* now comes from $GUS_HOME/config/ 
gus.config.  $GUS_CONFIG_FILE is no longer used anywhere in the  
codebase.

$GUS_HOME/config/gus.config is created at build time from  
$PROJECT_HOME/install/gus.config.  Thus, you should make changes  
there and do a build to move them to $GUS_HOME if you need to make  
config changes.

Long Version:

In 3.5, we had the gus.config file as well as the $GUS_HOME_CONFIG  
file.  The latter was generated by the former, and some components  
used one while other components used the other.  It thus became  
confusion to know what configuration you were actually using, and  
there was of course redundancy.  This resolves that issue.  An  
outstanding issue remains how to provide functionality to easily  
switch between multiple configurations.

*  (except when otherwise overridden on the command line)

Re: [GUSDEV] Gus build and DBD::Oracle

[Michael S. <msa...@pc...>]

No, we've never been able to install DBD::Oracle without a force.  It  
requires a lot of setup (i.e. a database with the scott/tiger user).

--Mike

On Oct 27, 2005, at 1:24 PM, Juan Carlos Perin wrote:

> Yes, that was my mistake, I was looking at 'orcl', 'sys'.  Orcl is  
> the db
> name.  Although, You are right.  My gus.config had the right user  
> that I had
> created with DBA privileges, but the gus.properties was still the  
> older
> version with sys as the user.  I changed this and it appears to be  
> building
> just fine.  Thanks Mike!
>
> Do you forsee any potential problems from having forced DBD::Oracle to
> install.  I'm not sure why it would ever need to login as 'scott',  
> but I
> don't know if that's a fundamental component of DBD in general.
>
> Juan
>
>
> On 10/27/05 12:59 PM, "Michael Saffitz" <msa...@pc...>  
> wrote:
>
>
>>
>> Hi Juan
>>
>> You should not install using the sys or system users.  Instead,
>> create a new user, grant that user DBA privileges, and then install
>> using that user.  After the install you may revoke the DBA privileges
>> from that user if you'd like.
>>
>> It doesn't look like it's trying to connect as orcl... where is that
>> coming from?
>>
>> --Mike
>>
>> On Oct 27, 2005, at 11:43 AM, Juan Carlos Perin wrote:
>>
>>
>>> I was encountering errors when installing DBD::Oracle for perl
>>> where while
>>> using MCPAN to install I kept seeing connect errors for (scott/
>>> tiger).  A
>>> resident Oracle expert confirmed all our oracle settings were fine,
>>> and that
>>> connection was perfectly fine through all other connect methods.
>>> So, I
>>> decided to force install DBD::Oracle and hope it was just a
>>> localized error
>>> with MCPAN.
>>>
>>> BUT.. When attempting to finally build, the system has trouble
>>> connecting
>>> once again, with a different user (maybe unrelated to the above
>>> problem, but
>>> is a DBD issue) and gives the following error:
>>>
>>> [InstallSchema] INFO: Writing Database
>>>      [echo] .
>>>      [echo] Installing GUS/ObjRelP
>>>      [echo] generating Perl Objects
>>>      [exec] GUS::ObjRelP::DbiDbHandle connect('orcl','sys',...)
>>> failed:
>>> ORA-28009: connection as SYS should be as SYSDBA or SYSOPER (DBD
>>> ERROR:
>>> OCISessionBegin) at
>>> /home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm  
>>> line 165
>>>      [exec] Can't bless non-reference value at
>>> /home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm  
>>> line 21.
>>>
>>> BUILD FAILED
>>> /home/oracle/GUS/project_home/install/build.xml:28: The following
>>> error
>>> occurred while executing this line:
>>> /home/oracle/GUS/project_home/GUS/build.xml:225: exec returned: -1
>>>
>>> Total time: 2 minutes 4 seconds
>>>
>>> This time its having trouble as orcl.  The user doesn't even exist
>>> when I
>>> look into the user list.  I'm not sure if I should create the user,
>>> or if
>>> there is a bigger problem.  I'm learning oracle as I go, so I have
>>> a lot to
>>> learn, any suggestions will help.  Thanks all!
>>>
>>> Juan Perin
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by the JBoss Inc.
>>> Get Certified Today * Register for a JBoss Training Course
>>> Free Certification Exam for All Training Attendees Through End of  
>>> 2005
>>> Visit http://www.jboss.com/services/certification for more  
>>> information
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.
>> Get Certified Today * Register for a JBoss Training Course
>> Free Certification Exam for All Training Attendees Through End of  
>> 2005
>> Visit http://www.jboss.com/services/certification for more  
>> information
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>

[GUSDEV] WDK error

[<hen...@gm...>]

Hi.

Thanks for the attention again =3D)

I got this error while trying to create a toyModel (I guess this is
the last version):

$ wdkTestDb -model toyModel -create
Loading table usertest.WDKTestEst to database from file

ERROR: column "row_project_id" is of type numeric but expression is of
type character varying
java.sql.SQLException: ERROR: column "row_project_id" is of type
numeric but expression is of type character varying
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(Qu=
eryExecutorImpl.java:1471)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExe=
cutorImpl.java:1256)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorIm=
pl.java:175)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc=
2Statement.java:392)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(Abs=
tractJdbc2Statement.java:330)
        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(Abstra=
ctJdbc2Statement.java:282)
        at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdat=
e(DelegatingPreparedStatement.java:233)
        at org.gusdb.wdk.model.implementation.SqlUtils.getResultSet(SqlUtil=
s.java:51)
        at org.gusdb.wdk.model.test.TestDBManager.main(TestDBManager.java:1=
17)




Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] Re: Unraveling the mistery of SVN

[Steve F. <sfi...@pc...>]

see below

-steve

Henrique Juc=E1 wrote:

>Dear "GUSers",
>
>
>After cracking my hard skull a bit, I managed to install GUS from SVN.
>I will describe the steps I took, to check with you guys if what I did
>was unnecessary and/or incorrect:
>
>1) I created a folder named GUS, and inside it two folders:
>project_home/ and gus_home/;
>
>2) Inside project_home, I downloaded via 'svn checkout' CBIL/,
>GusSchema/, GusAppFramework/,  (this folder I renamed GUS/), install/,
>and SchemaBrowser/;
>
>3) I did the rest of the configuration as usual (gus.config, etc.);
>
>4) I built using 'build install GUS -append -installDBSchema';
>
>And it built as it should (I guess). Now, here comes the questions:
>
>1) What does that Djob/ folder in SVN repos stands for?
> =20
>
distributed job controller that runs on a compute cluster.  this is in=20
production use at CBIL and at UGA, but, we don't really have the=20
resources to support it for others use.  You're welcome to use it, but,=20
we just won't be able to help too much.

>2) From the structure I created, will I be able to use 'svn update'
>pointing to the project_home/ folder, or would it be wiser to update
>each branch (GUS/, GusSchema/, and so on) at a time?
> =20
>
each branch

>3) What does the webinstall option in build stands for?
> =20
>
to install a website.  it copies stuff to both gus_home and also to the=20
specified directory in a web site

>4) Can (or should) I install WDK/ and WDKToySite/ separately?
>
> =20
>
i think separately would probably be good.   then, you'd need to change=20
your $GUS_HOME when you change between loading gus application software=20
and using the wdk

>
>Thanks for your attention guys, and sorry for bothering ...
>(and sorry about the silly jokes.....)
>
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
> =20
>

Re: [GUSDEV] Gus build and DBD::Oracle

[Michael S. <msa...@pc...>]

Hi Juan

You should not install using the sys or system users.  Instead,  
create a new user, grant that user DBA privileges, and then install  
using that user.  After the install you may revoke the DBA privileges  
from that user if you'd like.

It doesn't look like it's trying to connect as orcl... where is that  
coming from?

--Mike

On Oct 27, 2005, at 11:43 AM, Juan Carlos Perin wrote:

> I was encountering errors when installing DBD::Oracle for perl  
> where while
> using MCPAN to install I kept seeing connect errors for (scott/ 
> tiger).  A
> resident Oracle expert confirmed all our oracle settings were fine,  
> and that
> connection was perfectly fine through all other connect methods.   
> So, I
> decided to force install DBD::Oracle and hope it was just a  
> localized error
> with MCPAN.
>
> BUT.. When attempting to finally build, the system has trouble  
> connecting
> once again, with a different user (maybe unrelated to the above  
> problem, but
> is a DBD issue) and gives the following error:
>
> [InstallSchema] INFO: Writing Database
>      [echo] .
>      [echo] Installing GUS/ObjRelP
>      [echo] generating Perl Objects
>      [exec] GUS::ObjRelP::DbiDbHandle connect('orcl','sys',...)  
> failed:
> ORA-28009: connection as SYS should be as SYSDBA or SYSOPER (DBD  
> ERROR:
> OCISessionBegin) at
> /home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 165
>      [exec] Can't bless non-reference value at
> /home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
>
> BUILD FAILED
> /home/oracle/GUS/project_home/install/build.xml:28: The following  
> error
> occurred while executing this line:
> /home/oracle/GUS/project_home/GUS/build.xml:225: exec returned: -1
>
> Total time: 2 minutes 4 seconds
>
> This time its having trouble as orcl.  The user doesn't even exist  
> when I
> look into the user list.  I'm not sure if I should create the user,  
> or if
> there is a bigger problem.  I'm learning oracle as I go, so I have  
> a lot to
> learn, any suggestions will help.  Thanks all!
>
> Juan Perin
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] Unraveling the mistery of SVN

[<hen...@gm...>]

Dear "GUSers",


After cracking my hard skull a bit, I managed to install GUS from SVN.
I will describe the steps I took, to check with you guys if what I did
was unnecessary and/or incorrect:

1) I created a folder named GUS, and inside it two folders:
project_home/ and gus_home/;

2) Inside project_home, I downloaded via 'svn checkout' CBIL/,
GusSchema/, GusAppFramework/,  (this folder I renamed GUS/), install/,
and SchemaBrowser/;

3) I did the rest of the configuration as usual (gus.config, etc.);

4) I built using 'build install GUS -append -installDBSchema';

And it built as it should (I guess). Now, here comes the questions:

1) What does that Djob/ folder in SVN repos stands for?
2) From the structure I created, will I be able to use 'svn update'
pointing to the project_home/ folder, or would it be wiser to update
each branch (GUS/, GusSchema/, and so on) at a time?
3) What does the webinstall option in build stands for?
4) Can (or should) I install WDK/ and WDKToySite/ separately?



Thanks for your attention guys, and sorry for bothering ...
(and sorry about the silly jokes.....)



Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] Gus build and DBD::Oracle

[Juan C. P. <bi...@ge...>]

I was encountering errors when installing DBD::Oracle for perl where while
using MCPAN to install I kept seeing connect errors for (scott/tiger).  A
resident Oracle expert confirmed all our oracle settings were fine, and that
connection was perfectly fine through all other connect methods.  So, I
decided to force install DBD::Oracle and hope it was just a localized error
with MCPAN.  

BUT.. When attempting to finally build, the system has trouble connecting
once again, with a different user (maybe unrelated to the above problem, but
is a DBD issue) and gives the following error:

[InstallSchema] INFO: Writing Database
     [echo] .
     [echo] Installing GUS/ObjRelP
     [echo] generating Perl Objects
     [exec] GUS::ObjRelP::DbiDbHandle connect('orcl','sys',...) failed:
ORA-28009: connection as SYS should be as SYSDBA or SYSOPER (DBD ERROR:
OCISessionBegin) at
/home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 165
     [exec] Can't bless non-reference value at
/home/oracle/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.

BUILD FAILED
/home/oracle/GUS/project_home/install/build.xml:28: The following error
occurred while executing this line:
/home/oracle/GUS/project_home/GUS/build.xml:225: exec returned: -1

Total time: 2 minutes 4 seconds

This time its having trouble as orcl.  The user doesn't even exist when I
look into the user list.  I'm not sure if I should create the user, or if
there is a bigger problem.  I'm learning oracle as I go, so I have a lot to
learn, any suggestions will help.  Thanks all!

Juan Perin

Re: [GUSDEV] PK constraints for version tables

[Michael S. <msa...@pc...>]

Ok-- I'm not hearing any major opposition to the easy fix-- dropping  
all primary key constraints for version tables-- so I'm going to push  
this into the trunk.  If you're really opposed to this, and you've  
been waiting to object, now's the time!

--Mike

On Oct 24, 2005, at 9:29 AM, Angel Pizarro wrote:

> OK, let's collect our knowledge:
>
> DB throughput is high enough to cause conflicts in version tables.
> Version tables are rarely used.
> Indexes/constraints of any type reduce transaction throughput.
>
> Given these three items, I think that steve's suggestion of using a  
> sequence to order inserted rows, and debbies request for dropping  
> any PKs in the version tables are a good way to keep track of data  
> provenance and not make version tables a limitting factor on  
> database population.
>
> -angel
>
> Michael Saffitz wrote:
>
>
>> What does the VERSION_TRANSACTION_ID column track?  Perhaps we  
>> could take
>> advantage of this for a composite PK, although I suppose that it  
>> may not
>> work if there are multiple edits to a given row within a  
>> transaction (which
>> is not well defined here).
>>
>> --Mike
>>
>>
>>
>> On 10/24/05 7:32 AM, "pi...@pc..."  
>> <pi...@pc...> wrote:
>>
>>
>>
>>> The date format was modified (precision increased) and the  
>>> problem persisted).
>>>
>>> The version tables are useful for a few reasons:
>>> 1) Rows can be restored that were updated or deleted in error.
>>> 2) There is a record of who, when, and how a row was updated or  
>>> deleted.
>>>
>>> Restoration can be accomplished using the alg_inv_id and as long  
>>> as the
>>> user_id
>>> and version modification and original modification date are  
>>> available, the
>>> modifications can be tracked.
>>>
>>> I'd like to point out that the version tables are rarely used.
>>>
>>> Quoting Steve Fischer <sfi...@pc...>:
>>>
>>>
>>>
>>>> the "race" condition we have is that a single process is rapidly
>>>> updating a row in time that is less than the resolution of our
>>>> current date stamp.  we won't be able to distinguish them by
>>>> row_alg_invocation_id as they are done by the same process.  it it
>>>> likely but not assured that an increase in resolution will solve  
>>>> the
>>>> problem. i propose that we:
>>>> 1. increase the precision
>>>> 2. drop the constraint
>>>> 3. don't really care too much
>>>>
>>>> if we want to care, then, i suppose, we would have to add another
>>>> column to the version tables that was an increasing sequence.
>>>>
>>>> steve
>>>>
>>>>
>>>> Chris Sarnowski wrote:
>>>>
>>>>
>>>>
>>>>> I was going to suggest (2) below, but will nitpick and point out
>>>>> that  it would make the problem 1000 times less likely to  
>>>>> occur, but
>>>>> that  it's still possible to have collisions, especially if,  
>>>>> say, 2
>>>>> processes are simultaneously working on overlapping data.
>>>>> With (1), the problem is that with any collision, there is the
>>>>> possibility that you won't be able to determine in what order
>>>>> changes  were made to data (which could, for example, break an
>>>>> automated  "rollback" system). Given that collisions are probably
>>>>> already rare,  and that algorithm_invocation_id helps distinguish
>>>>> simultaneous  processes, this just may not be an important  
>>>>> problem.
>>>>> So (1) is still the easiest workaround, and I'd guess "good  
>>>>> enough".
>>>>> -Chris
>>>>>
>>>>>
>>>>> On Oct 21, 2005, at 3:44 PM, Angel Pizarro wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Debbie's point is that uniqueness in version tables doesn't  
>>>>>> really
>>>>>> matter and it is getting in the way of fast inserts. The only  
>>>>>> ways
>>>>>> to fix this are:
>>>>>>
>>>>>> 1) drop the constraints
>>>>>> 2) increase the precision of row_modification_date to  
>>>>>> milliseconds.
>>>>>>
>>>>>> -angel
>>>>>>
>>>>>> msa...@pc... wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> The problem with that is that the ID alone isn't necessarily
>>>>>>> unique-- a row that
>>>>>>> has been edited multiple times will end up in the version table
>>>>>>> multiple times,
>>>>>>> hence the addition of the modification_date to (attempt to)  
>>>>>>> ensure
>>>>>>> uniqueness.
>>>>>>>
>>>>>>> --Mike
>>>>>>>
>>>>>>> Quoting Steve Fischer <sfi...@pc...>:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> yes, i guess so.
>>>>>>>>
>>>>>>>> steve
>>>>>>>>
>>>>>>>> Deborah Pinney wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> You mean drop the uniqueness constraint for the original PK
>>>>>>>>> +modification_date?
>>>>>>>>> Steve Fischer wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> how about just dropping the uniqueness constraint of the
>>>>>>>>>> modification date?
>>>>>>>>>>
>>>>>>>>>> steve
>>>>>>>>>>
>>>>>>>>>> Chris Sarnowski wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> I can't speak for GUS needs in this particular case, but  
>>>>>>>>>>> I've
>>>>>>>>>>> had the  same issue in other systems. Deborah is correct in
>>>>>>>>>>> that these fields  are not right for PK. The question is how
>>>>>>>>>>> important it is to preserve  exact order of the changes  
>>>>>>>>>>> to the
>>>>>>>>>>> data. If it's not critical you  could just drop the PK.  
>>>>>>>>>>> If it
>>>>>>>>>>> is (or even if it's not but you believe  in the rule "every
>>>>>>>>>>> table must have a PK"), then you should use a  surrogate key
>>>>>>>>>>> from a sequence. In practice, at least, the sequence  values
>>>>>>>>>>> increase monotonically so changes to a record that occur
>>>>>>>>>>> multiple times with the same modification date can still be
>>>>>>>>>>> ordered  correctly.
>>>>>>>>>>> I prefer the latter, in general, but I suppose adding a new
>>>>>>>>>>> surrogate  key field to all version tables in GUS would be a
>>>>>>>>>>> pretty big deal.
>>>>>>>>>>>
>>>>>>>>>>> Just my thoughts.
>>>>>>>>>>> -Chris Sarnowski
>>>>>>>>>>>
>>>>>>>>>>> On Oct 21, 2005, at 11:07 AM, Deborah Pinney wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> I suggest that we drop the uniqueness constraint for PKs of
>>>>>>>>>>>> version  tables. PKs for these tables consist of the  
>>>>>>>>>>>> original
>>>>>>>>>>>> PK and the  modification date. Rapid computation can result
>>>>>>>>>>>> in uniqueness  copnstraint violations that are not remedied
>>>>>>>>>>>> by date format  changes. There doesn't seem to be a purpose
>>>>>>>>>>>> in having these  constraints for any of the version tables
>>>>>>>>>>>> and dropping the  constraints would not result in the  
>>>>>>>>>>>> loss of
>>>>>>>>>>>> information or change  query results. I don't know if there
>>>>>>>>>>>> is implicit indexing on these  keys but I wonder if this
>>>>>>>>>>>> could be handled using explicit indexing.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by:
>>>>> Power Architecture Resource Center: Free content, downloads,  
>>>>> discussions,
>>>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by:
>>>> Power Architecture Resource Center: Free content, downloads,  
>>>> discussions,
>>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by the JBoss Inc.
>>> Get Certified Today * Register for a JBoss Training Course
>>> Free Certification Exam for All Training Attendees Through End of  
>>> 2005
>>> Visit http://www.jboss.com/services/certification for more  
>>> information
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.
>> Get Certified Today * Register for a JBoss Training Course
>> Free Certification Exam for All Training Attendees Through End of  
>> 2005
>> Visit http://www.jboss.com/services/certification for more  
>> information
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] ISO error

[Steve F. <sfi...@pc...>]

henrique-

i am confused.  no, GO.defs does not sound like the right file.  where=20
did you get it?  that sounds like Gene Ontology not Sequence Ontology.

steve

Henrique Juc=E1 wrote:

>Hi Michael,
>
>Thanks for the attention. Steve's suggestion solved my problem. Sorry
>about that resumed error I printed, I'll paste the whole message next
>time. Now, I'm facing a problem w/ InsertSequenceOntology.  We're
>using Postgres here, and when I tried to upload GO.defs (is that the
>right file? - i checked so.definitions and it seems to have just
>changed its name), and I received this message:
>
>[juca1@kineto3 GUS]$ ga GUS::Supported::Plugin::InsertSequenceOntology
>--inputFile /gus/GUS-Files/GO/GO.defs --soCvsVersion '1.419'
>--soVersion '3.3.48' --user juca --group TESTE --commit
>Wed Oct 26 15:01:05 2005        ARGS    algoinvo        1
>Wed Oct 26 15:01:05 2005        ARGS    comment
>Wed Oct 26 15:01:05 2005        ARGS    commit  1
>Wed Oct 26 15:01:05 2005        ARGS    debug   0
>Wed Oct 26 15:01:05 2005        ARGS    group   TESTE
>Wed Oct 26 15:01:05 2005        ARGS    gusconfigfile   /gus/GUS/gus.pro=
perties
>Wed Oct 26 15:01:05 2005        ARGS    help
>Wed Oct 26 15:01:05 2005        ARGS    helpHTML
>Wed Oct 26 15:01:05 2005        ARGS    inputFile     =20
>/gus/GUS-Files/GO/GO.defs
>Wed Oct 26 15:01:05 2005        ARGS    project
>Wed Oct 26 15:01:05 2005        ARGS    soCvsVersion    1.419
>Wed Oct 26 15:01:05 2005        ARGS    soVersion       3.3.48
>Wed Oct 26 15:01:05 2005        ARGS    sqlVerbose      0
>Wed Oct 26 15:01:05 2005        ARGS    user    juca
>Wed Oct 26 15:01:05 2005        ARGS    verbose 0
>Wed Oct 26 15:01:05 2005        ARGS    veryVerbose     0
>Wed Oct 26 15:01:05 2005        COMMIT  commit on
>Wed Oct 26 15:01:05 2005        ALGINVID        10
>
>ERROR:
>You have exceeded the maximum number of allowable objects in memory:
>  You must use the method 'undefPointerCache()' in each loop
>    to clear the cache and allow garbage collection!!
> If you need > 10000 objects at one time,
>   then increase the default number with the method
>'setMaximumNumberOfObjects(<number>)' at
>/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 467
>        GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiD=
atabase=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb=
469c84)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
>        GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HA=
SH(0x96a2b08)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence=
Ontology.pm
>line 159
>        GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOnto=
logy('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','=
GO:0050834','molybdenum
>incorporation via L-cysteinyl copper sulfido molyb...','The
>incorporation of molybdenum into a protein by L-cysteinyl...') called
>at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOntolog=
y.pm
>line 137
>        GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Suppor=
ted::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','HASH(0x99b9a48)')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 469
>        eval {...} called at
>/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
>        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Pl=
uginMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::Inser=
tSequenceOntology',1)
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
>        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:=
:GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenc=
eOntology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
>        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnt=
ology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
>        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','ARRAY(0x91e0668)')
>called at /gus/GUS/gus_home/bin/ga line 11
>
>STACK TRACE:
> at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 467
>        GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiD=
atabase=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb=
469c84)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
>        GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HA=
SH(0x96a2b08)')
>called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence=
Ontology.pm
>line 159
>        GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOnto=
logy('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','=
GO:0050834','molybdenum
>incorporation via L-cysteinyl copper sulfido molyb...','The
>incorporation of molybdenum into a protein by L-cysteinyl...') called
>at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOntolog=
y.pm
>line 137
>        GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Suppor=
ted::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','HASH(0x99b9a48)')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 469
>        eval {...} called at
>/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
>        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Pl=
uginMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::Inser=
tSequenceOntology',1)
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
>        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:=
:GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenc=
eOntology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
>        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnt=
ology')
>called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
>        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::Gus=
Application=3DHASH(0x91ccc18)','ARRAY(0x91e0668)')
>called at /gus/GUS/gus_home/bin/ga line 11
>
>
>Thanks for the time,
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by the JBoss Inc.
>Get Certified Today * Register for a JBoss Training Course
>Free Certification Exam for All Training Attendees Through End of 2005
>Visit http://www.jboss.com/services/certification for more information
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

[GUSDEV] Re: ISO error

[Trish W. <wh...@pc...>]

Hi Henrique,

Actually, the InsertSequenceOntology file uses the SequenceOntology.obo 
file as the input.  I believe there is another plugin that loads the GO 
module of tables.  The file can be obtained from:
http://cvs.sourceforge.net/viewcvs.py/*checkout*/song/ontology/so.obo?rev=1.35

Trish

> Thanks for the attention. Steve's suggestion solved my problem. Sorry
> about that resumed error I printed, I'll paste the whole message next
> time. Now, I'm facing a problem w/ InsertSequenceOntology.  We're
> using Postgres here, and when I tried to upload GO.defs (is that the
> right file? - i checked so.definitions and it seems to have just
> changed its name), and I received this message:
>
> [juca1@kineto3 GUS]$ ga GUS::Supported::Plugin::InsertSequenceOntology
> --inputFile /gus/GUS-Files/GO/GO.defs --soCvsVersion '1.419'
> --soVersion '3.3.48' --user juca --group TESTE --commit
> Wed Oct 26 15:01:05 2005        ARGS    algoinvo        1
> Wed Oct 26 15:01:05 2005        ARGS    comment
> Wed Oct 26 15:01:05 2005        ARGS    commit  1
> Wed Oct 26 15:01:05 2005        ARGS    debug   0
> Wed Oct 26 15:01:05 2005        ARGS    group   TESTE
> Wed Oct 26 15:01:05 2005        ARGS    gusconfigfile   /gus/GUS/gus.proper=
> ties
> Wed Oct 26 15:01:05 2005        ARGS    help
> Wed Oct 26 15:01:05 2005        ARGS    helpHTML
> Wed Oct 26 15:01:05 2005        ARGS    inputFile     =20
> /gus/GUS-Files/GO/GO.defs
> Wed Oct 26 15:01:05 2005        ARGS    project
> Wed Oct 26 15:01:05 2005        ARGS    soCvsVersion    1.419
> Wed Oct 26 15:01:05 2005        ARGS    soVersion       3.3.48
> Wed Oct 26 15:01:05 2005        ARGS    sqlVerbose      0
> Wed Oct 26 15:01:05 2005        ARGS    user    juca
> Wed Oct 26 15:01:05 2005        ARGS    verbose 0
> Wed Oct 26 15:01:05 2005        ARGS    veryVerbose     0
> Wed Oct 26 15:01:05 2005        COMMIT  commit on
> Wed Oct 26 15:01:05 2005        ALGINVID        10

Re: [GUSDEV] GUS Java Requirements?

[Mark S. H. <mh...@ug...>]

We switched to 1.5 to meet the WDK's requirements. The switch has  
been a fairly painless and trivial process.

On Oct 26, 2005, at 3:22 PM, Michael Saffitz wrote:

>
> I'm curious what folks are using for Java?  If GUS were to begin  
> requiring 1.5/5.0, how much trouble would this create for the  
> community?  All of CBIL at this point is using 1.5/5.0
>
> Note:  The WDK already makes this requirement.
>
> --Mike
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] GUS Java Requirements?

[Michael S. <msa...@pc...>]

I'm curious what folks are using for Java?  If GUS were to begin  
requiring 1.5/5.0, how much trouble would this create for the  
community?  All of CBIL at this point is using 1.5/5.0

Note:  The WDK already makes this requirement.

--Mike

[GUSDEV] ISO error

[<hen...@gm...>]

Hi Michael,

Thanks for the attention. Steve's suggestion solved my problem. Sorry
about that resumed error I printed, I'll paste the whole message next
time. Now, I'm facing a problem w/ InsertSequenceOntology.  We're
using Postgres here, and when I tried to upload GO.defs (is that the
right file? - i checked so.definitions and it seems to have just
changed its name), and I received this message:

[juca1@kineto3 GUS]$ ga GUS::Supported::Plugin::InsertSequenceOntology
--inputFile /gus/GUS-Files/GO/GO.defs --soCvsVersion '1.419'
--soVersion '3.3.48' --user juca --group TESTE --commit
Wed Oct 26 15:01:05 2005        ARGS    algoinvo        1
Wed Oct 26 15:01:05 2005        ARGS    comment
Wed Oct 26 15:01:05 2005        ARGS    commit  1
Wed Oct 26 15:01:05 2005        ARGS    debug   0
Wed Oct 26 15:01:05 2005        ARGS    group   TESTE
Wed Oct 26 15:01:05 2005        ARGS    gusconfigfile   /gus/GUS/gus.proper=
ties
Wed Oct 26 15:01:05 2005        ARGS    help
Wed Oct 26 15:01:05 2005        ARGS    helpHTML
Wed Oct 26 15:01:05 2005        ARGS    inputFile     =20
/gus/GUS-Files/GO/GO.defs
Wed Oct 26 15:01:05 2005        ARGS    project
Wed Oct 26 15:01:05 2005        ARGS    soCvsVersion    1.419
Wed Oct 26 15:01:05 2005        ARGS    soVersion       3.3.48
Wed Oct 26 15:01:05 2005        ARGS    sqlVerbose      0
Wed Oct 26 15:01:05 2005        ARGS    user    juca
Wed Oct 26 15:01:05 2005        ARGS    verbose 0
Wed Oct 26 15:01:05 2005        ARGS    veryVerbose     0
Wed Oct 26 15:01:05 2005        COMMIT  commit on
Wed Oct 26 15:01:05 2005        ALGINVID        10

ERROR:
You have exceeded the maximum number of allowable objects in memory:
  You must use the method 'undefPointerCache()' in each loop
    to clear the cache and allow garbage collection!!
 If you need > 10000 objects at one time,
   then increase the default number with the method
'setMaximumNumberOfObjects(<number>)' at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 467
        GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiData=
base=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb469c8=
4)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
        GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HASH(=
0x96a2b08)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOnt=
ology.pm
line 159
        GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOntolog=
y('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','GO:00=
50834','molybdenum
incorporation via L-cysteinyl copper sulfido molyb...','The
incorporation of molybdenum into a protein by L-cysteinyl...') called
at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOntology.p=
m
line 137
        GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Supported=
::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','HASH(0x99b9a48)')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 469
        eval {...} called at
/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequ=
enceOntology',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnto=
logy')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOntology=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x91ccc18)','ARRAY(0x91e0668)')
called at /gus/GUS/gus_home/bin/ga line 11

STACK TRACE:
 at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 467
        GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiData=
base=3DHASH(0x91e5560)','GUS::Model::SRes::SequenceOntology=3DHASH(0xb469c8=
4)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
        GUS::Model::GusRow::new('GUS::Model::SRes::SequenceOntology','HASH(=
0x96a2b08)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOnt=
ology.pm
line 159
        GUS::Supported::Plugin::InsertSequenceOntology::makeSequenceOntolog=
y('GUS::Supported::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','GO:00=
50834','molybdenum
incorporation via L-cysteinyl copper sulfido molyb...','The
incorporation of molybdenum into a protein by L-cysteinyl...') called
at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceOntology.p=
m
line 137
        GUS::Supported::Plugin::InsertSequenceOntology::run('GUS::Supported=
::Plugin::InsertSequenceOntology=3DHASH(0x97544f0)','HASH(0x99b9a48)')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 469
        eval {...} called at
/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequ=
enceOntology',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOnto=
logy')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x91ccc18)','GUS::Supported::Plugin::InsertSequenceOntology=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x91ccc18)','ARRAY(0x91e0668)')
called at /gus/GUS/gus_home/bin/ga line 11


Thanks for the time,


Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] GUS build error

[Steve F. <sfi...@pc...>]

actually, henrique, i thought about this again.   my response below is=20
wrong.

mike will follow with a mail instructing you on what to do.

steve

Steve Fischer wrote:

> henrique-
>
> are you using postgres?
> if so, try using the -skipJavaCompiling flag to the build command
>
> steve
>
> Henrique Juc=E1 wrote:
>
>> Hello everyone,
>>
>> While I was trying to build GUS, I received this error message:
>>
>>
>>  [echo] .
>>     [echo] Installing GUS/ObjRelJ
>>     [copy] Copying 2 files to
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS
>>     [copy] Copying 1 file to
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes
>>     [echo] Starting target: JavaModel
>>     [echo] .
>>     [echo] Installing GUS/Model
>>    [javac] Compiling 1260 source files to
>> /gus/GUS/project_home/GUS/Model/classes
>>    [javac]=20
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorith=
m_Row.java:86:=20
>>
>> cannot find symbol
>>    [javac] symbol  : class notdefyet
>>    [javac] location: class org.gusdb.model.Core.Algorithm_Row
>>    [javac]     public void setModificationDate (notdefyet value)
>>    [javac]                                      ^
>>    [javac]=20
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorith=
m_Row.java:91:=20
>>
>> cannot find symbol
>>    [javac] symbol  : class notdefyet
>>    [javac] location: class org.gusdb.model.Core.Algorithm_Row
>>    [javac]     public notdefyet getModificationDate () { return
>> (notdefyet)get_Attribute("modification_date"); }
>>    [javac]            ^
>>    [javac]=20
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorith=
mInvocation_Row.java:54:=20
>>
>> cannot find symbol    [javac] symbol  : class notdefyet
>>    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Ro=
w
>>    [javac]     public void setStartTime (notdefyet value)
>>    [javac]                               ^
>>    [javac]=20
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorith=
mInvocation_Row.java:59:=20
>>
>> cannot find symbol    [javac] symbol  : class notdefyet
>>    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Ro=
w
>>    [javac]     public notdefyet getStartTime () { return
>> (notdefyet)get_Attribute("start_time"); }
>>    [javac]            ^
>>    [javac]=20
>> /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorith=
mInvocation_Row.java:86:=20
>>
>> cannot find symbol    [javac] symbol  : class notdefyet
>>    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Ro=
w
>>    [javac]     public void setEndTime (notdefyet value)
>> (.. i resumed the error for it repeats itself a lot ..)
>> [javac] Note: Some input files use unchecked or unsafe operations.
>>    [javac] Note: Recompile with -Xlint:unchecked for details.
>>    [javac] 100 errors
>>
>> BUILD FAILED
>> /gus/GUS/project_home/install/build.xml:28: The following error
>> occurred while executing this line:
>> /gus/GUS/project_home/GUS/build.xml:99: The following error occurred
>> while executing this line:
>> /gus/GUS/project_home/install/build.xml:259: The following error
>> occurred while executing this line:
>> /gus/GUS/project_home/install/build.xml:278: Compile failed; see the
>> compiler error output for details.
>>
>> Total time: 2 minutes 26 seconds
>>
>> What did I miss?
>>
>>
>> Thanks for the attention,
>>
>>
>> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>>
>> "As soon as you concern yourself with the "good" and "bad" of your=20
>> fellows,
>> you create an opening in your heart for maliciousness to enter. Testin=
g,
>> competing with, and criticizing others weaken and defeat you."
>>
>> Morihei Ueshiba, O-Sensei (1883-1969)
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.
>> Get Certified Today * Register for a JBoss Training Course
>> Free Certification Exam for All Training Attendees Through End of 2005
>> Visit http://www.jboss.com/services/certification for more information
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> =20
>>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

FW: [GUSDEV] GUS DB Level Permissions

[Michael S. <msa...@pc...>]

cc:ing the list.

------ Forwarded Message
> From: Ed Robinson <ero...@ug...>
> Date: Wed, 26 Oct 2005 09:23:08 -0400
> To: Michael Saffitz <msa...@pc...>
> Subject: Re: [GUSDEV] GUS DB Level Permissions
> 
> I think GUSR and GUSW should be enough.  I think you're asking
> for real management nightmares trying to decide and manage
> permissions at an install level.  Just my two cents, but I
> think you're create far more headaches then they're worth.
> 
> -ed
> 
> 
> 
> ---- Original message ----
>> Date: Wed, 26 Oct 2005 08:54:41 -0400
>> From: Michael Saffitz <msa...@pc...>
>> Subject: [GUSDEV] GUS DB Level Permissions
>> To: Gusdev gusdev-gusdev <gus...@li...>
>> 
>> 
>> I'm curious how other groups are addressing database level
>> permissions/privileges, especially within Oracle.  The
> motivation for this
>> is to see if there are a set of base privileges that are
> common enough that
>> we could have the installer automatically apply for all sites.
>> 
>> Here at CBIL, we use two roles, GUS_R and GUS_W (read and
> write) that are
>> given select on all tables/views and
> update/insert/delete/select on all
>> tables/views/sequences (respectively).  Users are then
> granted the roles as
>> appropriate.
>> 
>> Does anyone have any strong objections for including these
> grants as part of
>> the install process?  What other privilege models are folks
> using that may
>> be a better approach?  One option is to use a cascading role
> system and have
>> GUS_W (for example) be granted RAD_W, DOTS_W, ..., which are
> then granted
>> the individual schema level privileges.
>> 
>> --Mike
>> 
>> 
>> 
>> 
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.
>> Get Certified Today * Register for a JBoss Training Course
>> Free Certification Exam for All Training Attendees Through
> End of 2005
>> Visit http://www.jboss.com/services/certification for more
> information
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883

------ End of Forwarded Message

Re: [GUSDEV] problems compiling GUS java object layer

[Mark S. H. <mh...@ug...>]

I discovered late last night that our entire set of prot and rad  
schema tables are missing. They are listed in core.tableinfo though,  
so I guess that's where the generator is getting the notion that it  
should generate a layer for them.

Thanks,
Mark

On Oct 26, 2005, at 7:50 AM, Steve Fischer wrote:

> this looks like there is a foreign key attribute defined against a  
> table that does not exist.
>
> mark, on line 407 of $GUS_HOME/lib/perl/GUS/OblRelP/Generator/ 
> JavaRowGenerator, add:
>
>  $parentTableName || die "Can't find parentTableName for foreign  
> key attribute '$fkAtt' of table '$self->{schemaName}::$self-> 
> {tableName}'";
>
> steve
>
> Mark S. Heiges wrote:
>
>
>> I'm unable to fully build the java object layer for a GUS 3.5.1   
>> schema. The perl layer builds fine, and the java layer builds  
>> until  it hits the PROT schema.
>> Below is the stack trace. I'm using a fresh checkout of the   
>> GusApplicationFramework svn trunk and building into an empty   
>> gus_home. Anyone know the problem off hand?
>>
>>      [exec] generating java object for DoTS::UTRFeature
>>      [exec] generating java object for DoTS::VirtualSequence
>>      [exec] generating java object for PROT::Acquisition
>>      [exec] Warning: No JavaType found for '', type: ''
>>      [exec] Warning: No JavaType found for '', type: ''
>>      [exec] Error:  Package Table Name '' is not in the form of   
>> org.gusdb.model.SCHEMA.NAME at /home/mheiges/GUS35/gus_home/lib/ 
>> perl/ GUS/ObjRelP/Generator/RowGenerator.pm line 91
>>      [exec]       
>> GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName  
>> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',   
>> 'undef') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ 
>> ObjRelP/ Generator/JavaRowGenerator.pm line 413
>>      [exec]       
>> GUS::ObjRelP::Generator::JavaRowGenerator::_createParentAccessors  
>> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',  
>> 'HASH (0x8b22bb8)') called at /home/mheiges/GUS35/gus_home/lib/ 
>> perl/GUS/ ObjRelP/Generator/JavaRowGenerator.pm line 130
>>      [exec]       
>> GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors  
>> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)')  
>> called  at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/ 
>> Generator/ JavaRowGenerator.pm line 33
>>      [exec]      
>> GUS::ObjRelP::Generator::JavaRowGenerator::generate  
>> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',   
>> 'undef') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ 
>> ObjRelP/ Generator/Generator.pm line 109
>>      [exec]     GUS::ObjRelP::Generator::Generator::generate  
>> ('GUS::ObjRelP::Generator::Generator=HASH(0x83da534)', 'undef')   
>> called at /home/mheiges/GUS35/gus_home/bin/generateGusObjects line 67
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.
>> Get Certified Today * Register for a JBoss Training Course
>> Free Certification Exam for All Training Attendees Through End of  
>> 2005
>> Visit http://www.jboss.com/services/certification for more  
>> information
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>

[GUSDEV] GUS DB Level Permissions

[Michael S. <msa...@pc...>]

I'm curious how other groups are addressing database level
permissions/privileges, especially within Oracle.  The motivation for this
is to see if there are a set of base privileges that are common enough that
we could have the installer automatically apply for all sites.

Here at CBIL, we use two roles, GUS_R and GUS_W (read and write) that are
given select on all tables/views and update/insert/delete/select on all
tables/views/sequences (respectively).  Users are then granted the roles as
appropriate.

Does anyone have any strong objections for including these grants as part of
the install process?  What other privilege models are folks using that may
be a better approach?  One option is to use a cascading role system and have
GUS_W (for example) be granted RAD_W, DOTS_W, ..., which are then granted
the individual schema level privileges.

--Mike

Re: [GUSDEV] problems compiling GUS java object layer

[Steve F. <sfi...@pc...>]

this looks like there is a foreign key attribute defined against a table 
that does not exist.

mark, on line 407 of 
$GUS_HOME/lib/perl/GUS/OblRelP/Generator/JavaRowGenerator, add:

  $parentTableName || die "Can't find parentTableName for foreign key 
attribute '$fkAtt' of table '$self->{schemaName}::$self->{tableName}'";

steve

Mark S. Heiges wrote:

> I'm unable to fully build the java object layer for a GUS 3.5.1  
> schema. The perl layer builds fine, and the java layer builds until  
> it hits the PROT schema.
> Below is the stack trace. I'm using a fresh checkout of the  
> GusApplicationFramework svn trunk and building into an empty  
> gus_home. Anyone know the problem off hand?
>
>      [exec] generating java object for DoTS::UTRFeature
>      [exec] generating java object for DoTS::VirtualSequence
>      [exec] generating java object for PROT::Acquisition
>      [exec] Warning: No JavaType found for '', type: ''
>      [exec] Warning: No JavaType found for '', type: ''
>      [exec] Error:  Package Table Name '' is not in the form of  
> org.gusdb.model.SCHEMA.NAME at /home/mheiges/GUS35/gus_home/lib/perl/ 
> GUS/ObjRelP/Generator/RowGenerator.pm line 91
>      [exec]      
> GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName 
> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',  
> 'undef') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/ 
> Generator/JavaRowGenerator.pm line 413
>      [exec]      
> GUS::ObjRelP::Generator::JavaRowGenerator::_createParentAccessors 
> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)', 'HASH 
> (0x8b22bb8)') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ 
> ObjRelP/Generator/JavaRowGenerator.pm line 130
>      [exec]      
> GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors 
> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)') called  
> at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/Generator/ 
> JavaRowGenerator.pm line 33
>      [exec]     GUS::ObjRelP::Generator::JavaRowGenerator::generate 
> ('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',  
> 'undef') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/ 
> Generator/Generator.pm line 109
>      [exec]     GUS::ObjRelP::Generator::Generator::generate 
> ('GUS::ObjRelP::Generator::Generator=HASH(0x83da534)', 'undef')  
> called at /home/mheiges/GUS35/gus_home/bin/generateGusObjects line 67
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GUS build error

[Steve F. <sfi...@pc...>]

henrique-

are you using postgres?=20

if so, try using the -skipJavaCompiling flag to the build command

steve

Henrique Juc=E1 wrote:

>Hello everyone,
>
>While I was trying to build GUS, I received this error message:
>
>
>  [echo] .
>     [echo] Installing GUS/ObjRelJ
>     [copy] Copying 2 files to
>/gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS
>     [copy] Copying 1 file to
>/gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes
>     [echo] Starting target: JavaModel
>     [echo] .
>     [echo] Installing GUS/Model
>    [javac] Compiling 1260 source files to
>/gus/GUS/project_home/GUS/Model/classes
>    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Cor=
e/Algorithm_Row.java:86:
>cannot find symbol
>    [javac] symbol  : class notdefyet
>    [javac] location: class org.gusdb.model.Core.Algorithm_Row
>    [javac]     public void setModificationDate (notdefyet value)
>    [javac]                                      ^
>    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Cor=
e/Algorithm_Row.java:91:
>cannot find symbol
>    [javac] symbol  : class notdefyet
>    [javac] location: class org.gusdb.model.Core.Algorithm_Row
>    [javac]     public notdefyet getModificationDate () { return
>(notdefyet)get_Attribute("modification_date"); }
>    [javac]            ^
>    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Cor=
e/AlgorithmInvocation_Row.java:54:
>cannot find symbol    [javac] symbol  : class notdefyet
>    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>    [javac]     public void setStartTime (notdefyet value)
>    [javac]                               ^
>    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Cor=
e/AlgorithmInvocation_Row.java:59:
>cannot find symbol    [javac] symbol  : class notdefyet
>    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>    [javac]     public notdefyet getStartTime () { return
>(notdefyet)get_Attribute("start_time"); }
>    [javac]            ^
>    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Cor=
e/AlgorithmInvocation_Row.java:86:
>cannot find symbol    [javac] symbol  : class notdefyet
>    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>    [javac]     public void setEndTime (notdefyet value)
>(.. i resumed the error for it repeats itself a lot ..)
>[javac] Note: Some input files use unchecked or unsafe operations.
>    [javac] Note: Recompile with -Xlint:unchecked for details.
>    [javac] 100 errors
>
>BUILD FAILED
>/gus/GUS/project_home/install/build.xml:28: The following error
>occurred while executing this line:
>/gus/GUS/project_home/GUS/build.xml:99: The following error occurred
>while executing this line:
>/gus/GUS/project_home/install/build.xml:259: The following error
>occurred while executing this line:
>/gus/GUS/project_home/install/build.xml:278: Compile failed; see the
>compiler error output for details.
>
>Total time: 2 minutes 26 seconds
>
>What did I miss?
>
>
>Thanks for the attention,
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by the JBoss Inc.
>Get Certified Today * Register for a JBoss Training Course
>Free Certification Exam for All Training Attendees Through End of 2005
>Visit http://www.jboss.com/services/certification for more information
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

[GUSDEV] GUS build error

[<hen...@gm...>]

Hello everyone,

While I was trying to build GUS, I received this error message:


  [echo] .
     [echo] Installing GUS/ObjRelJ
     [copy] Copying 2 files to
/gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS
     [copy] Copying 1 file to
/gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes
     [echo] Starting target: JavaModel
     [echo] .
     [echo] Installing GUS/Model
    [javac] Compiling 1260 source files to
/gus/GUS/project_home/GUS/Model/classes
    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/A=
lgorithm_Row.java:86:
cannot find symbol
    [javac] symbol  : class notdefyet
    [javac] location: class org.gusdb.model.Core.Algorithm_Row
    [javac]     public void setModificationDate (notdefyet value)
    [javac]                                      ^
    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/A=
lgorithm_Row.java:91:
cannot find symbol
    [javac] symbol  : class notdefyet
    [javac] location: class org.gusdb.model.Core.Algorithm_Row
    [javac]     public notdefyet getModificationDate () { return
(notdefyet)get_Attribute("modification_date"); }
    [javac]            ^
    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/A=
lgorithmInvocation_Row.java:54:
cannot find symbol    [javac] symbol  : class notdefyet
    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
    [javac]     public void setStartTime (notdefyet value)
    [javac]                               ^
    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/A=
lgorithmInvocation_Row.java:59:
cannot find symbol    [javac] symbol  : class notdefyet
    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
    [javac]     public notdefyet getStartTime () { return
(notdefyet)get_Attribute("start_time"); }
    [javac]            ^
    [javac] /gus/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/A=
lgorithmInvocation_Row.java:86:
cannot find symbol    [javac] symbol  : class notdefyet
    [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
    [javac]     public void setEndTime (notdefyet value)
(.. i resumed the error for it repeats itself a lot ..)
[javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 100 errors

BUILD FAILED
/gus/GUS/project_home/install/build.xml:28: The following error
occurred while executing this line:
/gus/GUS/project_home/GUS/build.xml:99: The following error occurred
while executing this line:
/gus/GUS/project_home/install/build.xml:259: The following error
occurred while executing this line:
/gus/GUS/project_home/install/build.xml:278: Compile failed; see the
compiler error output for details.

Total time: 2 minutes 26 seconds

What did I miss?


Thanks for the attention,


Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] problems compiling GUS java object layer

[Mark S. H. <mh...@ug...>]

I'm unable to fully build the java object layer for a GUS 3.5.1  
schema. The perl layer builds fine, and the java layer builds until  
it hits the PROT schema.
Below is the stack trace. I'm using a fresh checkout of the  
GusApplicationFramework svn trunk and building into an empty  
gus_home. Anyone know the problem off hand?

      [exec] generating java object for DoTS::UTRFeature
      [exec] generating java object for DoTS::VirtualSequence
      [exec] generating java object for PROT::Acquisition
      [exec] Warning: No JavaType found for '', type: ''
      [exec] Warning: No JavaType found for '', type: ''
      [exec] Error:  Package Table Name '' is not in the form of  
org.gusdb.model.SCHEMA.NAME at /home/mheiges/GUS35/gus_home/lib/perl/ 
GUS/ObjRelP/Generator/RowGenerator.pm line 91
      [exec]      
GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName 
('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',  
'undef') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/ 
Generator/JavaRowGenerator.pm line 413
      [exec]      
GUS::ObjRelP::Generator::JavaRowGenerator::_createParentAccessors 
('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)', 'HASH 
(0x8b22bb8)') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ 
ObjRelP/Generator/JavaRowGenerator.pm line 130
      [exec]      
GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors 
('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)') called  
at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/Generator/ 
JavaRowGenerator.pm line 33
      [exec]     GUS::ObjRelP::Generator::JavaRowGenerator::generate 
('GUS::ObjRelP::Generator::JavaRowGenerator=HASH(0x8b22b94)',  
'undef') called at /home/mheiges/GUS35/gus_home/lib/perl/GUS/ObjRelP/ 
Generator/Generator.pm line 109
      [exec]     GUS::ObjRelP::Generator::Generator::generate 
('GUS::ObjRelP::Generator::Generator=HASH(0x83da534)', 'undef')  
called at /home/mheiges/GUS35/gus_home/bin/generateGusObjects line 67

Re: [GUSDEV] XML::Simple in BioperlFeatMapper.pm

[Ed R. <ero...@ug...>]

XML::Simple refers to the XML::Simple package available from
CPan.  It is not a BioPerl module.

-ed



---- Original message ----
>Date: Mon, 24 Oct 2005 16:40:47 -0400
>From: "Weichen Wu" <we...@se...>  
>Subject: [GUSDEV] XML::Simple in BioperlFeatMapper.pm  
>To: <gus...@li...>
>
>In program BioperlFeatMapper.pm, there is a line
>use XML::Simple;
> I think the Simple.pm is the one from Bioperl package. Since
in Bioperl, 
>the Simple.pm is under directory Bio/Location/ rather than
XML/, I made a 
>sub-directory XML in gus_home/lib/perl/ and copy the
Simple.pm to the XML 
>sub-directory. Is it right?
>That I ask this is because I have compilation error when run
Insert 
>SequenceFeatures.pm
>
>[wewu@noodle import_ipi_zebrafish]$ ga 
>GUS::Supported::Plugin::InsertSequenceFeatures --mapFile 
>genbank2gus.xml --inputFileOrDir embl.dat --fileFormat EMBL
--extDbName 
>embl --extDbRlsVer 2.2
>
>ERROR:
>Can't locate object method "new" via package "XML::Simple"
(perhaps you 
>forgot to load "XML::Simple"?) at 
>/home/wewu/work/6_gus/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm

>line 67.
>STACK TRACE:
> at 
>/home/wewu/work/6_gus/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm

>line 67
>       
GUS::Supported::BioperlFeatMapperSet::_parseMapFile('GUS::Supported::BioperlFeatMapperSet=HASH(0x1e08420)',

>'ipi2gus.xml',
>
>Thanks,
>Weichen
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by the JBoss Inc.
>Get Certified Today * Register for a JBoss Training Course
>Free Certification Exam for All Training Attendees Through
End of 2005
>Visit http://www.jboss.com/services/certification for more
information
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

[GUSDEV] XML::Simple in BioperlFeatMapper.pm

[Weichen W. <we...@se...>]

In program BioperlFeatMapper.pm, there is a line
use XML::Simple;
 I think the Simple.pm is the one from Bioperl package. Since in Bioperl, 
the Simple.pm is under directory Bio/Location/ rather than XML/, I made a 
sub-directory XML in gus_home/lib/perl/ and copy the Simple.pm to the XML 
sub-directory. Is it right?
That I ask this is because I have compilation error when run Insert 
SequenceFeatures.pm

[wewu@noodle import_ipi_zebrafish]$ ga 
GUS::Supported::Plugin::InsertSequenceFeatures --mapFile 
genbank2gus.xml --inputFileOrDir embl.dat --fileFormat EMBL --extDbName 
embl --extDbRlsVer 2.2

ERROR:
Can't locate object method "new" via package "XML::Simple" (perhaps you 
forgot to load "XML::Simple"?) at 
/home/wewu/work/6_gus/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm 
line 67.
STACK TRACE:
 at 
/home/wewu/work/6_gus/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm 
line 67
        GUS::Supported::BioperlFeatMapperSet::_parseMapFile('GUS::Supported::BioperlFeatMapperSet=HASH(0x1e08420)', 
'ipi2gus.xml',

Thanks,
Weichen

Re: [GUSDEV] PK constraints for version tables

[Angel P. <an...@ma...>]

OK, let's collect our knowledge:

DB throughput is high enough to cause conflicts in version tables.
Version tables are rarely used.
Indexes/constraints of any type reduce transaction throughput.

Given these three items, I think that steve's suggestion of using a 
sequence to order inserted rows, and debbies request for dropping any 
PKs in the version tables are a good way to keep track of data 
provenance and not make version tables a limitting factor on database 
population.

-angel

Michael Saffitz wrote:

>What does the VERSION_TRANSACTION_ID column track?  Perhaps we could take
>advantage of this for a composite PK, although I suppose that it may not
>work if there are multiple edits to a given row within a transaction (which
>is not well defined here).
>
>--Mike
>
>
>
>On 10/24/05 7:32 AM, "pi...@pc..." <pi...@pc...> wrote:
>
>  
>
>>The date format was modified (precision increased) and the problem persisted).
>>
>>The version tables are useful for a few reasons:
>>1) Rows can be restored that were updated or deleted in error.
>>2) There is a record of who, when, and how a row was updated or deleted.
>>
>>Restoration can be accomplished using the alg_inv_id and as long as the
>>user_id
>>and version modification and original modification date are available, the
>>modifications can be tracked.
>>
>>I'd like to point out that the version tables are rarely used.
>>
>>Quoting Steve Fischer <sfi...@pc...>:
>>
>>    
>>
>>>the "race" condition we have is that a single process is rapidly
>>>updating a row in time that is less than the resolution of our
>>>current date stamp.  we won't be able to distinguish them by
>>>row_alg_invocation_id as they are done by the same process.  it it
>>>likely but not assured that an increase in resolution will solve the
>>>problem. i propose that we:
>>> 1. increase the precision
>>> 2. drop the constraint
>>> 3. don't really care too much
>>>
>>>if we want to care, then, i suppose, we would have to add another
>>>column to the version tables that was an increasing sequence.
>>>
>>>steve
>>>
>>>
>>>Chris Sarnowski wrote:
>>>
>>>      
>>>
>>>>I was going to suggest (2) below, but will nitpick and point out
>>>>that  it would make the problem 1000 times less likely to occur, but
>>>>that  it's still possible to have collisions, especially if, say, 2
>>>>processes are simultaneously working on overlapping data.
>>>>With (1), the problem is that with any collision, there is the
>>>>possibility that you won't be able to determine in what order
>>>>changes  were made to data (which could, for example, break an
>>>>automated  "rollback" system). Given that collisions are probably
>>>>already rare,  and that algorithm_invocation_id helps distinguish
>>>>simultaneous  processes, this just may not be an important problem.
>>>>So (1) is still the easiest workaround, and I'd guess "good enough".
>>>>-Chris
>>>>
>>>>
>>>>On Oct 21, 2005, at 3:44 PM, Angel Pizarro wrote:
>>>>
>>>>        
>>>>
>>>>>Debbie's point is that uniqueness in version tables doesn't really
>>>>>matter and it is getting in the way of fast inserts. The only ways
>>>>>to fix this are:
>>>>>
>>>>>1) drop the constraints
>>>>>2) increase the precision of row_modification_date to milliseconds.
>>>>>
>>>>>-angel
>>>>>
>>>>>msa...@pc... wrote:
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>>>The problem with that is that the ID alone isn't necessarily
>>>>>>unique-- a row that
>>>>>>has been edited multiple times will end up in the version table
>>>>>>multiple times,
>>>>>>hence the addition of the modification_date to (attempt to) ensure
>>>>>> uniqueness.
>>>>>>
>>>>>>--Mike
>>>>>>
>>>>>>Quoting Steve Fischer <sfi...@pc...>:
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>yes, i guess so.
>>>>>>>
>>>>>>>steve
>>>>>>>
>>>>>>>Deborah Pinney wrote:
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>You mean drop the uniqueness constraint for the original PK
>>>>>>>>+modification_date?
>>>>>>>>Steve Fischer wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>>>
>>>>>>>>>how about just dropping the uniqueness constraint of the
>>>>>>>>>modification date?
>>>>>>>>>
>>>>>>>>>steve
>>>>>>>>>
>>>>>>>>>Chris Sarnowski wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                  
>>>>>>>>>
>>>>>>>>>>I can't speak for GUS needs in this particular case, but I've
>>>>>>>>>>had the  same issue in other systems. Deborah is correct in
>>>>>>>>>>that these fields  are not right for PK. The question is how
>>>>>>>>>>important it is to preserve  exact order of the changes to the
>>>>>>>>>> data. If it's not critical you  could just drop the PK. If it
>>>>>>>>>> is (or even if it's not but you believe  in the rule "every
>>>>>>>>>>table must have a PK"), then you should use a  surrogate key
>>>>>>>>>>from a sequence. In practice, at least, the sequence  values
>>>>>>>>>>increase monotonically so changes to a record that occur
>>>>>>>>>>multiple times with the same modification date can still be
>>>>>>>>>>ordered  correctly.
>>>>>>>>>>I prefer the latter, in general, but I suppose adding a new
>>>>>>>>>>surrogate  key field to all version tables in GUS would be a
>>>>>>>>>>pretty big deal.
>>>>>>>>>>
>>>>>>>>>>Just my thoughts.
>>>>>>>>>>-Chris Sarnowski
>>>>>>>>>>
>>>>>>>>>>On Oct 21, 2005, at 11:07 AM, Deborah Pinney wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                    
>>>>>>>>>>
>>>>>>>>>>>I suggest that we drop the uniqueness constraint for PKs of
>>>>>>>>>>>version  tables. PKs for these tables consist of the original
>>>>>>>>>>> PK and the  modification date. Rapid computation can result
>>>>>>>>>>>in uniqueness  copnstraint violations that are not remedied
>>>>>>>>>>>by date format  changes. There doesn't seem to be a purpose
>>>>>>>>>>>in having these  constraints for any of the version tables
>>>>>>>>>>>and dropping the  constraints would not result in the loss of
>>>>>>>>>>> information or change  query results. I don't know if there
>>>>>>>>>>>is implicit indexing on these  keys but I wonder if this
>>>>>>>>>>>could be handled using explicit indexing.
>>>>>>>>>>>                      
>>>>>>>>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by:
>>>>Power Architecture Resource Center: Free content, downloads, discussions,
>>>>and more. http://solutions.newsforge.com/ibmarch.tmpl
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>        
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by:
>>>Power Architecture Resource Center: Free content, downloads, discussions,
>>>and more. http://solutions.newsforge.com/ibmarch.tmpl
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>      
>>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by the JBoss Inc.
>>Get Certified Today * Register for a JBoss Training Course
>>Free Certification Exam for All Training Attendees Through End of 2005
>>Visit http://www.jboss.com/services/certification for more information
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>    
>>
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by the JBoss Inc.
>Get Certified Today * Register for a JBoss Training Course
>Free Certification Exam for All Training Attendees Through End of 2005
>Visit http://www.jboss.com/services/certification for more information
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [GUSDEV] PK constraints for version tables

[Michael S. <msa...@pc...>]

What does the VERSION_TRANSACTION_ID column track?  Perhaps we could take
advantage of this for a composite PK, although I suppose that it may not
work if there are multiple edits to a given row within a transaction (which
is not well defined here).

--Mike



On 10/24/05 7:32 AM, "pi...@pc..." <pi...@pc...> wrote:

> The date format was modified (precision increased) and the problem persisted).
> 
> The version tables are useful for a few reasons:
> 1) Rows can be restored that were updated or deleted in error.
> 2) There is a record of who, when, and how a row was updated or deleted.
> 
> Restoration can be accomplished using the alg_inv_id and as long as the
> user_id
> and version modification and original modification date are available, the
> modifications can be tracked.
> 
> I'd like to point out that the version tables are rarely used.
> 
> Quoting Steve Fischer <sfi...@pc...>:
> 
>> the "race" condition we have is that a single process is rapidly
>> updating a row in time that is less than the resolution of our
>> current date stamp.  we won't be able to distinguish them by
>> row_alg_invocation_id as they are done by the same process.  it it
>> likely but not assured that an increase in resolution will solve the
>> problem. i propose that we:
>>  1. increase the precision
>>  2. drop the constraint
>>  3. don't really care too much
>> 
>> if we want to care, then, i suppose, we would have to add another
>> column to the version tables that was an increasing sequence.
>> 
>> steve
>> 
>> 
>> Chris Sarnowski wrote:
>> 
>>> I was going to suggest (2) below, but will nitpick and point out
>>> that  it would make the problem 1000 times less likely to occur, but
>>> that  it's still possible to have collisions, especially if, say, 2
>>> processes are simultaneously working on overlapping data.
>>> With (1), the problem is that with any collision, there is the
>>> possibility that you won't be able to determine in what order
>>> changes  were made to data (which could, for example, break an
>>> automated  "rollback" system). Given that collisions are probably
>>> already rare,  and that algorithm_invocation_id helps distinguish
>>> simultaneous  processes, this just may not be an important problem.
>>> So (1) is still the easiest workaround, and I'd guess "good enough".
>>> -Chris
>>> 
>>> 
>>> On Oct 21, 2005, at 3:44 PM, Angel Pizarro wrote:
>>> 
>>>> Debbie's point is that uniqueness in version tables doesn't really
>>>> matter and it is getting in the way of fast inserts. The only ways
>>>> to fix this are:
>>>> 
>>>> 1) drop the constraints
>>>> 2) increase the precision of row_modification_date to milliseconds.
>>>> 
>>>> -angel
>>>> 
>>>> msa...@pc... wrote:
>>>> 
>>>> 
>>>>> 
>>>>> 
>>>>> The problem with that is that the ID alone isn't necessarily
>>>>> unique-- a row that
>>>>> has been edited multiple times will end up in the version table
>>>>> multiple times,
>>>>> hence the addition of the modification_date to (attempt to) ensure
>>>>>  uniqueness.
>>>>> 
>>>>> --Mike
>>>>> 
>>>>> Quoting Steve Fischer <sfi...@pc...>:
>>>>> 
>>>>> 
>>>>>> yes, i guess so.
>>>>>> 
>>>>>> steve
>>>>>> 
>>>>>> Deborah Pinney wrote:
>>>>>> 
>>>>>> 
>>>>>>> You mean drop the uniqueness constraint for the original PK
>>>>>>> +modification_date?
>>>>>>> Steve Fischer wrote:
>>>>>>> 
>>>>>>> 
>>>>>>>> how about just dropping the uniqueness constraint of the
>>>>>>>> modification date?
>>>>>>>> 
>>>>>>>> steve
>>>>>>>> 
>>>>>>>> Chris Sarnowski wrote:
>>>>>>>> 
>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> I can't speak for GUS needs in this particular case, but I've
>>>>>>>>> had the  same issue in other systems. Deborah is correct in
>>>>>>>>> that these fields  are not right for PK. The question is how
>>>>>>>>> important it is to preserve  exact order of the changes to the
>>>>>>>>>  data. If it's not critical you  could just drop the PK. If it
>>>>>>>>>  is (or even if it's not but you believe  in the rule "every
>>>>>>>>> table must have a PK"), then you should use a  surrogate key
>>>>>>>>> from a sequence. In practice, at least, the sequence  values
>>>>>>>>> increase monotonically so changes to a record that occur
>>>>>>>>> multiple times with the same modification date can still be
>>>>>>>>> ordered  correctly.
>>>>>>>>> I prefer the latter, in general, but I suppose adding a new
>>>>>>>>> surrogate  key field to all version tables in GUS would be a
>>>>>>>>> pretty big deal.
>>>>>>>>> 
>>>>>>>>> Just my thoughts.
>>>>>>>>> -Chris Sarnowski
>>>>>>>>> 
>>>>>>>>> On Oct 21, 2005, at 11:07 AM, Deborah Pinney wrote:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>> I suggest that we drop the uniqueness constraint for PKs of
>>>>>>>>>> version  tables. PKs for these tables consist of the original
>>>>>>>>>>  PK and the  modification date. Rapid computation can result
>>>>>>>>>> in uniqueness  copnstraint violations that are not remedied
>>>>>>>>>> by date format  changes. There doesn't seem to be a purpose
>>>>>>>>>> in having these  constraints for any of the version tables
>>>>>>>>>> and dropping the  constraints would not result in the loss of
>>>>>>>>>>  information or change  query results. I don't know if there
>>>>>>>>>> is implicit indexing on these  keys but I wonder if this
>>>>>>>>>> could be handled using explicit indexing.
>>>>>>>>> 
>>> 
>>> 
>>> 
>>> 
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads, discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> 
>> 
>> 
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads, discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> 
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev