gusdev-gusdev

[Gusdev-gusdev] GUS 3.0 schema creation scripts

[Jonathan C. <cra...@sn...>]

I've tested the GUS 3.0 schema creation scripts and have tagged the
current release in CVS as 'schema30-code10' (i.e., GUS schema version
3.0, code version 1.0.)  Here's the install process in a nutshell:

 1. Install the GUS code as described on the gusdb.org web site
    (at <http://www.gusdb.org/BuildSystemSetup.html>)  During the
    installation the build system should tell you to create the
    properties file $GUS_HOME/config/schema.prop;  this file
    should be edited in order to customize the schema installation
    scripts to your site and Oracle database instance.

    (As an aside, if you don't want to place the Oracle SYS password
    in this file, you can instead choose to run the schema creation
    scripts manually, since only of the scripts must be run with
    SYS/DBA privileges.  In fact, now that I think of it, the script
    in question could be run by any user with the ability to create
    user accounts.  I'll put changing this on the to-do list.)

 2. Once the install is complete, cd to $GUS_HOME/schema/oracle
 3. Make sure that the Oracle utility 'sqlplus' is in your $PATH.
 4. Make sure that $GUS_HOME/bin is in your path and that you can
    execute the scripts therein.

    (Another aside; not all of the scripts have been updated to
    the new Perl package structure, but the only one we care
    about for this step is grantPermissions.pl and you can try
    running it on the command line--it should display a short
    usage message if successful.)

 5. Review $GUS_HOME/schema/oracle/create-db.sh to make sure that
    it's not going to do anything that you're unhappy with...
 6. Run ./create-db.sh (Or, if you're using the manual install method,
    run the commands contained in this file in the order given.)
 7. Check that all of the scripts and/or commands in create-db.sh
    ran successfully.

    (This step still needs to be automated.  For now you can either
    query the Oracle system tables to check that the correct number
    of uses/tables/etc. were created, or grep the .log files for the
    same information.  At the end of each .sql file is a line stating
    how many CREATE statements are in that file, which can be compared
    to the query or grep results.)

I won't be in the lab. tomorrow/today (Friday) but people in the lab.
should be able to reach me by mobile phone if there are any questions
or problems.

Jonathan

[Gusdev-gusdev] Gus 3.0

[Chetna W. <ch...@ar...>]

Hi,

I am trying to do:

1) [chetna@mango install]$ build GUS install -append

ant -f /home/projects/install/build.xml install -Dproj=GUS
-DtargetDir=/home/gus_home -Dcomp= -DprojectsDir=/home/projects
-Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']'

BUILD FAILED

/home/projects/install/build.xml:64: Class
org.apache.tools.ant.taskdefs.condition.And doesn't support the nested
"isfalse" element.

2) The ant version I am using is:

[chetna@mango install]$ ant -version
Ant version 1.4.1 compiled on July 31 2002
[chetna@mango install]$

Please let me know which ant version you guys are using. 

Chetna  

Re: [Gusdev-gusdev] Gus 3.0

[Arnaud K. <ax...@sa...>]

Hi

I've been using ant 1.5 to install GUS and it's been working fine.

ant -version
Apache Ant version 1.5 compiled on July 9 2002

Arnaud

Chetna Warade wrote:

>Hi,
>
>I am trying to do:
>
>1) [chetna@mango install]$ build GUS install -append
>
>ant -f /home/projects/install/build.xml install -Dproj=GUS
>-DtargetDir=/home/gus_home -Dcomp= -DprojectsDir=/home/projects
>-Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']'
>
>BUILD FAILED
>
>/home/projects/install/build.xml:64: Class
>org.apache.tools.ant.taskdefs.condition.And doesn't support the nested
>"isfalse" element.
>
>2) The ant version I am using is:
>
>[chetna@mango install]$ ant -version
>Ant version 1.4.1 compiled on July 31 2002
>[chetna@mango install]$
>
>Please let me know which ant version you guys are using. 
>
>Chetna  
>
>
>
>
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Re: [Gusdev-gusdev] Gus 3.0

[Jonathan C. <cra...@sn...>]

Chetna-

> Please let me know which ant version you guys are using.

I've been using Ant version 1.5.1.  Steve, can you confirm that the
following error--

> BUILD FAILED
>
> /home/projects/install/build.xml:64: Class
> org.apache.tools.ant.taskdefs.condition.And doesn't support the nested
> "isfalse" element.

--is due to the Ant version mismatch?  It certainly looks like it might be
complaining about a feature that was only added in version 1.5.  We should
update the documentation to require a recent (1.5+) Ant.

Jonathan

[Gusdev-gusdev] schema.prop

[Chetna W. <ch...@ar...>]

Hi,

I installed Ant 1.5.1 and the isfalse problem seems to disappear. 
What are the changes in the install.prop? It would be great if someone can
give insight.
I am pasting the following:

[chetna@mango install]$ build GUS install -append

ant -f /home/projects/install/build.xml install -Dproj=GUS
-DtargetDir=/home/gus_home -Dcomp= -DprojectsDir=/home/projects
-Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']'


BUILD FAILED
file:/home/projects/install/build.xml:228:
      Error: You must configure the file
/home/gus_home/config/install.prop.  To create it, copy
/home/gus_home/config/install.prop.sample to
/home/gus_home/config/install.prop and edit
/home/gus_home/config/install.prop, giving it the proper values for your
installation.


Total time: 1 second
[chetna@mango install]$

Hope to hear from you
Chetna


> I've tested the GUS 3.0 schema creation scripts and have tagged the
> current release in CVS as 'schema30-code10' (i.e., GUS schema version
> 3.0, code version 1.0.)  Here's the install process in a nutshell:
> 
>  1. Install the GUS code as described on the gusdb.org web site
>     (at <http://www.gusdb.org/BuildSystemSetup.html>)  During the
>     installation the build system should tell you to create the
>     properties file $GUS_HOME/config/schema.prop;  this file
>     should be edited in order to customize the schema installation
>     scripts to your site and Oracle database instance.
> 
>     (As an aside, if you don't want to place the Oracle SYS password
>     in this file, you can instead choose to run the schema creation
>     scripts manually, since only of the scripts must be run with
>     SYS/DBA privileges.  In fact, now that I think of it, the script
>     in question could be run by any user with the ability to create
>     user accounts.  I'll put changing this on the to-do list.)
> 
>  2. Once the install is complete, cd to $GUS_HOME/schema/oracle
>  3. Make sure that the Oracle utility 'sqlplus' is in your $PATH.
>  4. Make sure that $GUS_HOME/bin is in your path and that you can
>     execute the scripts therein.
> 
>     (Another aside; not all of the scripts have been updated to
>     the new Perl package structure, but the only one we care
>     about for this step is grantPermissions.pl and you can try
>     running it on the command line--it should display a short
>     usage message if successful.)
> 
>  5. Review $GUS_HOME/schema/oracle/create-db.sh to make sure that
>     it's not going to do anything that you're unhappy with...
>  6. Run ./create-db.sh (Or, if you're using the manual install method,
>     run the commands contained in this file in the order given.)
>  7. Check that all of the scripts and/or commands in create-db.sh
>     ran successfully.
> 
>     (This step still needs to be automated.  For now you can either
>     query the Oracle system tables to check that the correct number
>     of uses/tables/etc. were created, or grep the .log files for the
>     same information.  At the end of each .sql file is a line stating
>     how many CREATE statements are in that file, which can be compared
>     to the query or grep results.)
> 
> I won't be in the lab. tomorrow/today (Friday) but people in the lab.
> should be able to reach me by mobile phone if there are any questions
> or problems.
> 
> Jonathan
> 
> 

[Gusdev-gusdev] install.prop

[Chetna W. <ch...@ar...>]

Hi,

Sorry guys I gave a mistmatched subject line and email matter. I copied
install.prop in /home/gus_home/config.

1) I still want to know what are the changes in the install.prop

2) [chetna@mango install]$ build GUS install -append

ant -f /home/projects/install/build.xml install -Dproj=GUS
-DtargetDir=/home/gus_home -Dcomp= -DprojectsDir=/home/projects
-Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']'


BUILD FAILED
file:/home/projects/install/build.xml:24: java.io.FileNotFoundException:
/home/projects/GUS/build.xml (No such file or directory)

Total time: 1 second
[chetna@mango install]$

I am wondering if the changes in (1) is related to (2)?

Chetna

Re: [Gusdev-gusdev] schema.prop

[Jonathan C. <cra...@sn...>]

Chetna-

On Mon, 17 Feb 2003, Chetna Warade wrote:
>
> BUILD FAILED
> file:/home/projects/install/build.xml:228:
>       Error: You must configure the file
> /home/gus_home/config/install.prop.  To create it, copy
> /home/gus_home/config/install.prop.sample to
> /home/gus_home/config/install.prop and edit
> /home/gus_home/config/install.prop, giving it the proper values for your
> installation.
>

Did you follow these instructions?  The reason that you're getting a
FileNotFoundException is that the build system is looking for a file
called $GUS_HOME/config/install.prop.  As the above directions indicate,
you're supposed to copy "install.prop.sample" (which is in the same
directory) to "install.prop" and then edit "install.prop" to match your
site's configuration.  Maybe we should change the message to say "You must
create the file ..." instead of "You must configure the file ...", since
the latter suggests that the file exists already.

This file is there to let you configure things that might be different
between different installations of GUS.  At the moment it only contains a
single property, which is the location of the Perl interpreter.  If your
Perl interpreter is /usr/bin/perl then you can simply use the default
file (although you still have to copy it into install.prop)  Let me know
if this makes sense, and, if so, how you think we could make the
directions clearer.  Thanks,

Jonathan

[Gusdev-gusdev] grantPermissions.pl

[Chetna W. <ch...@ar...>]

Hi,

1) The FileNotFoundException occured because java was not able to find
build.xml located in the GUS project (point 8 in Build System set up html
page at gusdb.org). Point 8 in the Build System setup document says 
"At a minimum you need the CBIL project because GUS depends upon it..  You
may also get other CBIL projects as needed." Thats why I downloaded only
CBIL project as there were many projects and I found that confusing. In
order to solve this problem then I downloaded the GUS project from
cvsweb.sanger.ac.uk as that was the latest and GUS project at gusdb.org
was older. This solved my problem of FileNotFoundException.

- In summary the BuildSystemsetup should mention to download both CBIL and
GUS projects.

2) I tried running grantPermissions.pl (standlone with perl) and here's
the problem. The GUS project that I downloaded from cvsweb has the
directory structure: /home/projects/GUS/DBAdmin/lib/perl/*.pm

and the grantPremissions.pl has:

use GUS::DBAdmin::Database;
use GUS::DBAdmin::Schema;
 
which is why it fails. I am not quite sure if the build creates this
grantPermissions.pl but I dont know how to fix the discrepancy in the
directory structure (I could make changes though). Thats why I havent run
the create-db.sh script. Also permission of grantPermission.pl is not set
as executable. Maybe it should.

Chetna

Re: [Gusdev-gusdev] grantPermissions.pl

[Jonathan C. <cra...@sn...>]

Hi Chetna-

On Mon, 17 Feb 2003, Chetna Warade wrote:
> 1) The FileNotFoundException occured because java was not able to find
> build.xml located in the GUS project (point 8 in Build System set up html

OK, my mistake; I didn't realize that you hadn't downloaded the GUS
project.

> - In summary the BuildSystemsetup should mention to download both CBIL and
> GUS projects.

Point 7 does say that you should check out the GUS and install projects
from the Sanger CVS repository (and provides the command for doing so,
lest you should misconstrue "check out" to mean "look at.")  However, we
could reword point 8 so that it says something like this:

"At a minimum you will need to get the CBIL project (in addition to the
GUS and install projects, which you should have downloaded in step 7.)"

> 2) I tried running grantPermissions.pl (standlone with perl) and here's
> the problem. The GUS project that I downloaded from cvsweb has the
> directory structure: /home/projects/GUS/DBAdmin/lib/perl/*.pm
>
> and the grantPremissions.pl has:
>
> use GUS::DBAdmin::Database;
> use GUS::DBAdmin::Schema;
>
> which is why it fails. I am not quite sure if the build creates this
> grantPermissions.pl but I dont know how to fix the discrepancy in the
> directory structure (I could make changes though). Thats why I havent run
> the create-db.sh script. Also permission of grantPermission.pl is not set
> as executable. Maybe it should.

The build process creates a new copy of this script in your $GUS_HOME,
and makes it executable.  It will also copy the library (.pm) files to a
location in your $GUS_HOME, where they *will* conform to the directory
structure that you would expect from the package names.  If you follow
all of the setup directions (including setting your PATH and other
environment variables as indicated), then you should end up with the
grantPermissions.pl in your PATH (i.e. you should be able to just say
'rehash; grantPermissions.pl' and have it find and run the script
correctly.)  I'll try to improve the documentation to explain some of
these things a little more thoroughly.

Jonathan

[Gusdev-gusdev] grantPermissions.pl

[Chetna W. <ch...@ar...>]

Hi,

I ran the create-db.sh script and the grantPermissions.pl fails and
thats why the constraints script fails. All the users and tables are
correctly created. 

I have strictly followed all the steps and setting up the env variables as
the Build System Set up doc says except the point 7 (steve recommended
that choice as I could download stuff from cvsweb too)

[chetna@mango chetna]$ grantPermissions.pl
Can't locate GUS/DBAdmin/Database.pm in @INC (@INC contains:
/home/projects/GUS/DBAdmin/lib/perl /home/projects/lib
/usr/lib/perl5/5.6.1/i386-linux /usr/lib/perl5/5.6.1
/usr/lib/perl5/site_perl/5.6.1/i386-linux /usr/lib/perl5/site_perl/5.6.1
/usr/lib/perl5/site_perl/5.6.0/i386-linux /usr/lib/perl5/site_perl/5.6.0
/usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.6.1/i386-linux
/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at
/home/gus_home/bin/grantPermissions.pl line 15.
BEGIN failed--compilation aborted at
/home/gus_home/bin/grantPermissions.pl line 15.
[chetna@mango chetna]$

I am observing that the @INC stuff is actually using PERL5LIB env variable
from my .bash_profile and the Build System doesnt talk about this var.

Please let me know how to debug the grantPermissions.pl.

Thanks
Chetna

Re: [Gusdev-gusdev] grantPermissions.pl

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

chetna-

step 5. of the build system setup tells you what to do with PERL5LIB. 
 (we added this about a week ago, so you might have missed it).

you need to add $GUS_HOME/lib/perl to the front of PERL5LIB.  I suspect 
that much of the rest of the stuff in there is unneeded. (it might have 
been from the the old gus)

in any case, the first element in your @INC shouldn't be there.  maybe 
you put it there to try to solve the problem?

steve

Chetna Warade wrote:

>Hi,
>
>I ran the create-db.sh script and the grantPermissions.pl fails and
>thats why the constraints script fails. All the users and tables are
>correctly created. 
>
>I have strictly followed all the steps and setting up the env variables as
>the Build System Set up doc says except the point 7 (steve recommended
>that choice as I could download stuff from cvsweb too)
>
>[chetna@mango chetna]$ grantPermissions.pl
>Can't locate GUS/DBAdmin/Database.pm in @INC (@INC contains:
>/home/projects/GUS/DBAdmin/lib/perl /home/projects/lib
>/usr/lib/perl5/5.6.1/i386-linux /usr/lib/perl5/5.6.1
>/usr/lib/perl5/site_perl/5.6.1/i386-linux /usr/lib/perl5/site_perl/5.6.1
>/usr/lib/perl5/site_perl/5.6.0/i386-linux /usr/lib/perl5/site_perl/5.6.0
>/usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.6.1/i386-linux
>/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at
>/home/gus_home/bin/grantPermissions.pl line 15.
>BEGIN failed--compilation aborted at
>/home/gus_home/bin/grantPermissions.pl line 15.
>[chetna@mango chetna]$
>
>I am observing that the @INC stuff is actually using PERL5LIB env variable
>from my .bash_profile and the Build System doesnt talk about this var.
>
>Please let me know how to debug the grantPermissions.pl.
>
>Thanks
>Chetna
>
>
>
>
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[Gusdev-gusdev] grantP ...

[Chetna W. <ch...@ar...>]

Hi,

There is a conflict with the DBI version:

[chetna@mango chetna]$ grantPermissions.pl
DBI 1.2 required--this is only version 1.18
(/usr/lib/perl5/site_perl/5.6.1/i386-linux/DBI.pm) at
/home/gus_home/lib/perl/GUS/DBAdmin/Util.pm line 18 Compilation failed in
require at
/home/gus_home/lib/perl/GUS/DBAdmin/Util.pm line 18.
BEGIN failed--compilation aborted at
/home/gus_home/lib/perl/GUS/DBAdmin/Util.pm line 18.
Compilation failed in require at
/home/gus_home/lib/perl/GUS/DBAdmin/Tablespace.pm line 17.
BEGIN failed--compilation aborted at
/home/gus_home/lib/perl/GUS/DBAdmin/Tablespace.pm line 17.
Compilation failed in require at
/home/gus_home/lib/perl/GUS/DBAdmin/Database.pm line 17.
BEGIN failed--compilation aborted at
/home/gus_home/lib/perl/GUS/DBAdmin/Database.pm line 17.
Compilation failed in require at /home/gus_home/bin/grantPermissions.pl
line 15.
BEGIN failed--compilation aborted at
/home/gus_home/bin/grantPermissions.pl line 15.
[chetna@mango chetna]$

I have 1.18 here which version do you guys recommend.

Chetna

Re: [Gusdev-gusdev] grantP ...

[Jonathan C. <cra...@pc...>]

Hi Chetna-

Chetna Warade wrote:
> There is a conflict with the DBI version:

I don't believe that our code requires a particularly recent version
of DBI, so my guess is that the incompatibility is between your DBD::Oracle
and DBI.  Can you try creating the following trivial Perl script and tell me
whether it will run:

-----------------------------begin test.pl---------------------------
#!/usr/bin/perl
use DBI;
use DBD::Oracle;

print "Test successful!\n";

-----------------------------end test.pl-----------------------------

If you get the same error message from this test script then it's likely
that your copy of DBD::Oracle is not compatible with your copy of DBI.

> I have 1.18 here which version do you guys recommend.

We're using DBD-Oracle-1.12 and DBI-1.28 on our test machine, and so I know
that these versions are definitely compatible.  Let me know whether the above
test works.

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115

Re: [Gusdev-gusdev] grantP ...

[Chetna W. <ch...@ar...>]

Hi,

Thanks for the mail.
I'm getting the same error msg for the test pl.

[chetna@mango chetna]$ ./test.pl
DBI 1.2 required--this is only version 1.18
(/usr/lib/perl5/site_perl/5.6.1/i386-linux/DBI.pm) at ./test.pl line 3
Compilation failed in require at ./test.pl line 3.
BEGIN failed--compilation aborted at ./test.pl line 3.
[chetna@mango chetna]$

I am getting DBI-2.28 for mango and the DBD-Oracle that I use is 1.12

chetna



> I don't believe that our code requires a particularly recent version
> of DBI, so my guess is that the incompatibility is between your DBD::Oracle
> and DBI.  Can you try creating the following trivial Perl script and tell me
> whether it will run:
> 
> -----------------------------begin test.pl---------------------------
> #!/usr/bin/perl
> use DBI;
> use DBD::Oracle;
> 
> print "Test successful!\n";
> 
> -----------------------------end test.pl-----------------------------
> 
> If you get the same error message from this test script then it's likely
> that your copy of DBD::Oracle is not compatible with your copy of DBI.
> 
> > I have 1.18 here which version do you guys recommend.
> 
> We're using DBD-Oracle-1.12 and DBI-1.28 on our test machine, and so I know
> that these versions are definitely compatible.  Let me know whether the above
> test works.
> 
> Jonathan
> 
> -- 
> Jonathan Crabtree
> Center for Bioinformatics, University of Pennsylvania
> 1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
> 215-573-3115
> 
> 

Re: [Gusdev-gusdev] grantP ...

[Jonathan C. <cra...@pc...>]

Chetna-

> I'm getting the same error msg for the test pl.
> 
> [chetna@mango chetna]$ ./test.pl
> DBI 1.2 required--this is only version 1.18
> (/usr/lib/perl5/site_perl/5.6.1/i386-linux/DBI.pm) at ./test.pl line 3
> Compilation failed in require at ./test.pl line 3.
> BEGIN failed--compilation aborted at ./test.pl line 3.
> [chetna@mango chetna]$
> 
> I am getting DBI-2.28 for mango and the DBD-Oracle that I use is 1.12

OK, sounds good; once you've installed the newer version of DBI I think
the test script should work.  And once the test script works, the GUS
scripts should also be OK.  Let me know if this is not the case,

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115

[Gusdev-gusdev] DBI 1.28

[Chetna W. <ch...@ar...>]

Hi,

I was wondering from which site to get the perl DBI 1.28 module. I thought
it should be obvious to reach there but I am not able to find it. Is ti
possible for you guys to tell me where to look for the DBI 1.28 module 

chetna

Re: [Gusdev-gusdev] DBI 1.28

[Jonathan C. <cra...@sn...>]

Chetna-

On Thu, 20 Feb 2003, Chetna Warade wrote:
> I was wondering from which site to get the perl DBI 1.28 module. I thought
> it should be obvious to reach there but I am not able to find it. Is ti
> possible for you guys to tell me where to look for the DBI 1.28 module

Depending on what operating system you're running, you may be able to
download modules either in the form of packages (for example, RedHat
Linux supports this through 'rpm') or as gzipped tar files.  We use
RedHat but I installed both DBI and DBD::Oracle without using .rpm files.
It's often easier to get the latest versions of software in .tar.gz, which
is the main reason for doing this.

Anyway, the best place to look for any Perl module is the site CPAN.org;
all kinds of Perl modules are indexed there, and there's a good search
interface.  Here are the DBI and DBD modules in .tar.gz form:

http://www.cpan.org/modules/by-module/DBI/
http://www.cpan.org/modules/by-module/DBD/

Jonathan

[Gusdev-gusdev] gus schema 3.0 is done

[Chetna W. <ch...@ar...>]

Hi,

Just wanted to let you know that the 3.0 schema is done now. Will be
looking for the 3.0 plugins and object layer matter.

Thanks
Chetna

Re: [Gusdev-gusdev] grantPermissions.pl

[Jonathan C. <cra...@pc...>]

Hi Chetna-

Chetna Warade wrote:
> Hi,
> 
> I ran the create-db.sh script and the grantPermissions.pl fails and
> thats why the constraints script fails. All the users and tables are
> correctly created. 

That's why I recommended (I think!) testing grantPermissions.pl and sqlplus
*before* running the create-db.sh script.  I'm writing up the schema install
documentation later today, so I'll be sure to include a warning about this.

Jonathan

-- 
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115