Re: [GUSDEV] ga +meta --commit

[<mro...@cs...>]

Steve,

Thanks, it worked, but I got new problems, this is what I did:

found
at:http://genomics.upenn.edu/~dillo/research/theileria/gus-on-postgres-ho=
wto.html

At postgres:

insert into core.databaseversion (
        database_version_id,
        version,
        modification_date,
        user_read,
        user_write,
        group_read,
        group_write,
        other_read,
        other_write,
        row_user_id,
        row_group_id,
        row_project_id,
        row_alg_invocation_id
    ) values (
        nextval('core.databaseversion_sq'),
        3.5,
        now(),
        1, 0, 1, 0, 1, 0,
        1, 1, 1, 1
    );

I checked the values in the core.databaseversion table and they are OK

then: ga +meta --commit, and got NO ERRORS

  <Core::Algorithm>
    <description>GUS application framework for plugins</description>
    <name>GA-Plugin</name>
    <Core::AlgorithmImplementation>
      <executable_md5>f9522ed43f9da502107387a274948971</executable_md5>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <cvs_revision>2974</cvs_revision>
      <Core::AlgorithmInvocation>
        <result>meta</result>
        <end_time>now()</end_time>
        <start_time>now()</start_time>
        <cpus_used>1</cpus_used>
      </Core::AlgorithmInvocation>
    </Core::AlgorithmImplementation>
  </Core::Algorithm>
  <Core::Algorithm>
    <description>GUS application framework for plugins</description>
    <name>GA-Plugin</name>
    <modification_date>now()</modification_date>
    <row_alg_invocation_id>1</row_alg_invocation_id>
    <row_project_id>1</row_project_id>
    <row_group_id>1</row_group_id>
    <row_user_id>1</row_user_id>
    <other_write>0</other_write>
    <other_read>1</other_read>
    <group_write>1</group_write>
    <group_read>1</group_read>
    <user_write>1</user_write>
    <Core::AlgorithmImplementation>
      <executable_md5>f9522ed43f9da502107387a274948971</executable_md5>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <cvs_revision>2974</cvs_revision>
      <modification_date>now()</modification_date>
      <row_alg_invocation_id>1</row_alg_invocation_id>
      <row_project_id>1</row_project_id>
      <row_group_id>1</row_group_id>
      <row_user_id>1</row_user_id>
      <other_write>0</other_write>
      <other_read>1</other_read>
      <group_write>1</group_write>
      <group_read>1</group_read>
      <user_write>1</user_write>
      <Core::AlgorithmInvocation>
        <result>meta</result>
        <modification_date>now()</modification_date>
        <end_time>now()</end_time>
        <start_time>now()</start_time>
        <row_alg_invocation_id>1</row_alg_invocation_id>
        <row_project_id>1</row_project_id>
        <row_group_id>1</row_group_id>
        <row_user_id>1</row_user_id>
        <other_write>0</other_write>
        <other_read>1</other_read>
        <group_write>1</group_write>
        <group_read>1</group_read>
        <user_write>1</user_write>
        <user_read>1</user_read>
        <cpus_used>1</cpus_used>
        <algorithm_implementation_id>2</algorithm_implementation_id>
        <algorithm_invocation_id>2</algorithm_invocation_id>
      </Core::AlgorithmInvocation>
      <user_read>1</user_read>
      <algorithm_id>2</algorithm_id>
      <algorithm_implementation_id>2</algorithm_implementation_id>
    </Core::AlgorithmImplementation>
    <user_read>1</user_read>
    <algorithm_id>2</algorithm_id>
  </Core::Algorithm>


I started registering the plugins UNFORTUNATELY I got only 2 correct
and the next 5 with errors so I stopped to send this email, because maybe
I need to follow some strict sequence???

  ga +create GUS::Supported::Plugin::LoadTaxon --commit
  Fri Oct 20 13:06:59 2006        INFO    Plugin
  GUS::Supported::Plugin::LoadTaxon registered with cvs revision '2943'

  ga +create GUS::Supported::Plugin::InsertExternalDatabase --commit
  Fri Oct 20 13:13:59 2006        INFO    Plugin
  GUS::Supported::Plugin::InsertExternalDatabase registered with cvs
  revision '2942'

ERRORS:
  =3D=3D=3D=3D=3D=3D=3D=3D
  ga +create GUS::Supported::Plugin::InsertSequenceFeatures.pm --commit
  Warning: Use of "require" without parens is ambiguous at (eval 8) line =
1.

  Bareword "pm" not allowed while "strict subs" in use at (eval 8) line 1=
.
  Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
  while "strict subs" in use at (eval 8) line 1.
  =3D=3D=3D=3D=3D=3D=3D

  ga +create GUS::Supported::Plugin::LoadRow.pm --commit
  Warning: Use of "require" without parens is ambiguous at (eval 8) line =
1.

  Bareword "pm" not allowed while "strict subs" in use at (eval 8) line 1=
.
  Bareword "GUS::Supported::Plugin::LoadRow" not allowed while "strict
  subs" in use at (eval 8) line 1.
  =3D=3D=3D=3D=3D=3D=3D

In the meantime I will continue registering the other plugins

Thanks

Michael


> michael-
>
> the 3.5 ga looks in the new table Core.DatabaseVersion in the version
> column to find out what version of the schema you have.
>
> i don't know how that value is supposed to be set, but, you can set it
> manually to 3.5
>
> steve
>
> mro...@cs... wrote:
>
>>Hello GUS group,
>>
>>I need some help.
>>
>>I have been trying to use the ISF plugin in GUS, and to make a long sto=
ry
>>short, it appeared that we had a bad GUS 3.5 installed, so we
>>re-installed, the SVN version of GUS 3.5.
>>
>>I am using postgres and the data that was there was erased. Now that I
>>need to start new, I run the following:
>>
>>   ga +meta --commit
>>
>>and got:
>>
>>   Database version does not match required version for Plugin.
>>   Database Version:     Plugin Version: 3.5
>>
>>
>>I have looked all over the place in gus...@li...
>>for an answer but no luck.
>>
>>
>>Your help will be very much appreciated
>>
>>
>>Michael
>>
>>
>>
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>