Thread: [GUSDEV] Re: [Bug 257] The rules had not been created

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[GUSDEV] Re: [Bug 257] The rules had not been created

From: Ricardo B. <rb...@gm...> - 2006-01-10 17:29:26

Mike / Steve,
  We would like to know if you already had created the rules of the version
tables.
  We believe that with these rules we will go to obtain the loads, using th=
e
ISF.
  In case that you have some position, you he could inform to me, please.

thanks in advance,
Ricardo

2006/1/3, bug...@pc... <bug...@pc...>:
>
> https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D257
>
>
> msa...@pc... changed:
>
>            What    |Removed                     |Added
>
> -------------------------------------------------------------------------=
---
>              Status|RESOLVED                    |REOPENED
>          Resolution|INVALID                     |
>
>
>
>
> ------- Comment #4 from msa...@pc...  2006-01-03 12:05 -------
> version table rules are indeed not being created.  this should be
> relatively
> straight forward to fix.
>
>
> --
> Configure bugmail:
> https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=3Demail
> ------- You are receiving this mail because: -------
> You reported the bug, or are watching the reporter.
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

From: Angel P. <an...@ma...> - 2006-01-17 16:24:54

Attachments: DBAdmin.diff

Hi Ricardo,

The error did not stem from my patch, but rather from another class that 
failed to add the none-default columns to the version view objects. I 
have edited a few files, so you will need to revert to current SVN 
version of the repository for this patch to work:
<copy attached file to project home>
cd $PROJECT_HOME
svn revert GUS/DBAdmin
patch -p0 <DBAdmin.diff

Then you should be able to rebuild GUS/DBAdmin and run dbaDump schema as 
before.

An example of the output view and rule follows
-angel


CREATE VIEW DoTSVer.AAFeatureVer AS
SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, 
NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, 
PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, 
EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID, 
IS_PREDICTED, REVIEW_STATUS_ID , 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, 
VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID FROM 
DoTSVer.AAFeatureImpVer;

CREATE RULE AAFeatureVer_32675 AS ON INSERT TO DoTSVer.AAFeatureVer DO 
INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( AA_FEATURE_ID, 
AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID, 
SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID, 
MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID, 
SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID, 
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, VERSION_ALG_INVOCATION_ID, VERSION_DATE, 
VERSION_TRANSACTION_ID ) VALUES ( new.AA_FEATURE_ID, new.AA_SEQUENCE_ID, 
new.FEATURE_NAME_ID, new.PARENT_ID, new.NA_FEATURE_ID, 
new.SUBCLASS_VIEW, new.SEQUENCE_ONTOLOGY_ID, new.DESCRIPTION, 
new.PFAM_ENTRY_ID, new.MOTIF_AA_SEQUENCE_ID, new.REPEAT_TYPE_ID, 
new.EXTERNAL_DATABASE_RELEASE_ID, new.SOURCE_ID, 
new.PREDICTION_ALGORITHM_ID, new.IS_PREDICTED, new.REVIEW_STATUS_ID, 
new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ, 
new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, 
new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, 
new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, 
new.VERSION_TRANSACTION_ID );

Angel Pizarro wrote:

> Yes, I have an idea of what is going on ... sloppy copy-paste coding 
> on my part :(
>
> I'll add the other columns to the method and get you another patch.
>
> -angel
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

From: Ricardo B. <rb...@gm...> - 2006-01-17 19:36:33

Hi Angel,

  It is all right now with versioning tables.
  Now I passed to a next error.
  It follows below the error that happened.

  I am using the revision 4422

  Do you have any idea ?

ERROR:
In feature map XML file '/GUS/gus_home/config/genbank2gus.xml' <feature
name=3D"mRNA"> does not have a <qualifier> for 'transcript_id', which is fo=
und
in the input at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm
line 106, <GEN30> line 569.

STACK TRACE:
 at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 106

GUS::Supported::BioperlFeatMapper::_checkTagExists('GUS::Supported::Bioperl=
FeatMapper=3DHASH(0xa7d23cc)',
'transcript_id') called at
/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 30

GUS::Supported::BioperlFeatMapper::sortTags('GUS::Supported::BioperlFeatMap=
per=3DHASH(0xa7d23cc)',
'db_xref', 'locus_tag', 'product', 'transcript_id') called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
800

GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::SeqFeature::Generic=3DHASH(0xab16364)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
750

GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported=
::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::SeqFeature::Generic=3DHASH(0xab16364)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
758

GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported=
::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::SeqFeature::Generic=3DHASH(0xabaf3ac)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
727

GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::Seq::RichSeq=3DHASH(0xa95e35c)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330

GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'HASH(0xa49ac04)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
    eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541

GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9538c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9538c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9538c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9538c20)',
'ARRAY(0x954c728)') called at /GUS/gus_home/bin/ga line 11


Ricardo

2006/1/17, Angel Pizarro <an...@ma...>:
>
> Hi Ricardo,
>
> The error did not stem from my patch, but rather from another class that
> failed to add the none-default columns to the version view objects. I
> have edited a few files, so you will need to revert to current SVN
> version of the repository for this patch to work:
> <copy attached file to project home>
> cd $PROJECT_HOME
> svn revert GUS/DBAdmin
> patch -p0 <DBAdmin.diff
>
> Then you should be able to rebuild GUS/DBAdmin and run dbaDump schema as
> before.
>
> An example of the output view and rule follows
> -angel
>
>
> CREATE VIEW DoTSVer.AAFeatureVer AS
> SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID,
> NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION,
> PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID,
> EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID,
> IS_PREDICTED, REVIEW_STATUS_ID , 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,
> VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID FROM
> DoTSVer.AAFeatureImpVer;
>
> CREATE RULE AAFeatureVer_32675 AS ON INSERT TO DoTSVer.AAFeatureVer DO
> INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( AA_FEATURE_ID,
> AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID,
> SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID,
> MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID,
> SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID,
> 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, VERSION_ALG_INVOCATION_ID, VERSION_DATE,
> VERSION_TRANSACTION_ID ) VALUES ( new.AA_FEATURE_ID, new.AA_SEQUENCE_ID,
> new.FEATURE_NAME_ID, new.PARENT_ID, new.NA_FEATURE_ID,
> new.SUBCLASS_VIEW, new.SEQUENCE_ONTOLOGY_ID, new.DESCRIPTION,
> new.PFAM_ENTRY_ID, new.MOTIF_AA_SEQUENCE_ID, new.REPEAT_TYPE_ID,
> new.EXTERNAL_DATABASE_RELEASE_ID, new.SOURCE_ID,
> new.PREDICTION_ALGORITHM_ID, new.IS_PREDICTED, new.REVIEW_STATUS_ID,
> new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
> new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
> new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE,
> new.VERSION_TRANSACTION_ID );
>
> Angel Pizarro wrote:
>
> > Yes, I have an idea of what is going on ... sloppy copy-paste coding
> > on my part :(
> >
> > I'll add the other columns to the method and get you another patch.
> >
> > -angel
> >
>
>
>
> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (revision
> 4068)
> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (working
> copy)
> @@ -48,6 +48,10 @@
>          return column;
>      }
>
> +    public void setColumns( ArrayList<ColumnPair> colpair) {
> +        column =3D colpair;
> +    }
> +
>      public void addColumn( ColumnPair columnPair ) {
>          if ( !this.column.contains( columnPair ) ) {
>              this.column.add( columnPair );
> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (revision 4068)
> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (working copy)
> @@ -12,6 +12,7 @@
> import org.gusdb.dbadmin.model.GusSchema;
> import org.gusdb.dbadmin.model.GusTable;
> import org.gusdb.dbadmin.model.GusView;
> +import org.gusdb.dbadmin.model.VersionView;
> import org.gusdb.dbadmin.model.Schema;
> import org.gusdb.dbadmin.model.Sequence;
> import org.gusdb.dbadmin.model.Table;
> @@ -105,6 +106,8 @@
>          super.writeView( view );
>          if ( view instanceof GusView ) {
>              writeViewRules( (GusView) view );
> +        }else if ( view instanceof VersionView ) {
> +            writeVersionViewRules( (VersionView) view );
>          }
>      }
>
> @@ -112,8 +115,6 @@
>       * Since PostgreSQL doesn't support updatable views, this is a hack
> that
>       * uses rules to mimick the updatable view functionality.
>       *
> -     * TODO: Note that this means version views are now not updatable
> since they
> -     * don't have a PK.
>       *
>       * @param view DOCUMENT ME!
>       * @throws IOException DOCUMENT ME!
> @@ -174,7 +175,47 @@
>          oStream.flush( );
>      }
>
> +
>      /**
> +     * Since PostgreSQL doesn't support updatable views, this is a hack
> that
> +     * uses rules to mimick the updatable view functionality.
> +     *
> +     * Version views are now not updatable since they
> +     * don't have a PK, so we limit rules to insertion
> +     *
> +     * @param view DOCUMENT ME!
> +     * @throws IOException DOCUMENT ME!
> +     */
> +    private void writeVersionViewRules( VersionView view ) throws
> IOException {
> +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
> random.nextInt( 100000 ) + " AS ON INSERT TO "
> +                + view.getSchema( ).getName( ) + "." + view.getName( ) +
> " DO INSTEAD INSERT INTO  "
> +                + view.getTable( ).getSchema( ).getName( ) + "." +
> view.getTable( ).getName( ) + " ( " );
> +
> +        boolean first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( columnPair.getTableName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " ) VALUES ( " );
> +
> +        first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( "new." + columnPair.getViewName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " );\n\n" );
> +
> +    }
> +
> +    /**
>       * DOCUMENT ME!
>       *
>       * @param type DOCUMENT ME!
> Index:
> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.ja=
va
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> ---
> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.ja=
va
> (revision 4068)
> +++
> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.ja=
va
> (working copy)
> @@ -363,6 +363,9 @@
>              superClassView.setVersioned( true );
>              verSql =3D sql.concat( " " );
>
> +           // We need to add the superclass columns to the version view.
> +           superClassView.getVersionView(
> ).setColumns((ArrayList<ColumnPair>) superClassView.getColumns().clone())=
;
> +
>              for ( Column column : verHousekeepingColumns ) {
>                  verSql =3D verSql.concat( ", " + column.getName( ) );
>                  superClassView.getVersionView( ).addColumn( new
> ColumnPair( column.getName( ), column.getName( ) ) );
> @@ -448,7 +451,8 @@
>          if ( impTable.isVersioned( ) ) {
>              subClass.setVersioned( true );
>              verSql =3D sql.concat( " " );
> -
> +           // We need to add the subclass_view's columns
> +           subClass.getVersionView( ).setColumns((ArrayList<ColumnPair>)
> subClass.getColumns().clone());
>              for ( Column column : verHousekeepingColumns ) {
>                  verSql =3D verSql.concat( ", " + column.getName( ) );
>                  subClass.getVersionView( ).addColumn( new ColumnPair(
> column.getName( ), column.getName( ) ) );
>
>
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

From: <jld...@pc...> - 2006-01-17 19:48:31

Ricardo,

The error you received simply means that your mapping file is incomplete.  So,
in your mapping file, under the mRNA feature, you will need to add a qualifier
with the name 'transcript_id' that tells the plugin what to do with transcript
IDs.  There should be examples of qualifiers for you to follow already in the
mapping file.

I hope this helps.

Jennifer

Quoting Ricardo Balbi <rb...@gm...>:

> Hi Angel,
>
>  It is all right now with versioning tables.
>  Now I passed to a next error.
>  It follows below the error that happened.
>
>  I am using the revision 4422
>
>  Do you have any idea ?
>
> ERROR:
> In feature map XML file '/GUS/gus_home/config/genbank2gus.xml' <feature
> name="mRNA"> does not have a <qualifier> for 'transcript_id', which is found
> in the input at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm
> line 106, <GEN30> line 569.
>
> STACK TRACE:
> at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 106
>
> GUS::Supported::BioperlFeatMapper::_checkTagExists('GUS::Supported::BioperlFeatMapper=HASH(0xa7d23cc)',
> 'transcript_id') called at
> /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 30
>
> GUS::Supported::BioperlFeatMapper::sortTags('GUS::Supported::BioperlFeatMapper=HASH(0xa7d23cc)',
> 'db_xref', 'locus_tag', 'product', 'transcript_id') called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 800
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::SeqFeature::Generic=HASH(0xab16364)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 750
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::SeqFeature::Generic=HASH(0xab16364)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 758
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::SeqFeature::Generic=HASH(0xabaf3ac)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 727
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::Seq::RichSeq=HASH(0xa95e35c)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 330
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'HASH(0xa49ac04)') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
>    eval {...} called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'ARRAY(0x954c728)') called at /GUS/gus_home/bin/ga line 11
>
>
> Ricardo
>
> 2006/1/17, Angel Pizarro <an...@ma...>:
>>
>> Hi Ricardo,
>>
>> The error did not stem from my patch, but rather from another class that
>> failed to add the none-default columns to the version view objects. I
>> have edited a few files, so you will need to revert to current SVN
>> version of the repository for this patch to work:
>> <copy attached file to project home>
>> cd $PROJECT_HOME
>> svn revert GUS/DBAdmin
>> patch -p0 <DBAdmin.diff
>>
>> Then you should be able to rebuild GUS/DBAdmin and run dbaDump schema as
>> before.
>>
>> An example of the output view and rule follows
>> -angel
>>
>>
>> CREATE VIEW DoTSVer.AAFeatureVer AS
>> SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID,
>> NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION,
>> PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID,
>> EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID,
>> IS_PREDICTED, REVIEW_STATUS_ID , 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,
>> VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID FROM
>> DoTSVer.AAFeatureImpVer;
>>
>> CREATE RULE AAFeatureVer_32675 AS ON INSERT TO DoTSVer.AAFeatureVer DO
>> INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( AA_FEATURE_ID,
>> AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID,
>> SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID,
>> MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID,
>> SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID,
>> 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, VERSION_ALG_INVOCATION_ID, VERSION_DATE,
>> VERSION_TRANSACTION_ID ) VALUES ( new.AA_FEATURE_ID, new.AA_SEQUENCE_ID,
>> new.FEATURE_NAME_ID, new.PARENT_ID, new.NA_FEATURE_ID,
>> new.SUBCLASS_VIEW, new.SEQUENCE_ONTOLOGY_ID, new.DESCRIPTION,
>> new.PFAM_ENTRY_ID, new.MOTIF_AA_SEQUENCE_ID, new.REPEAT_TYPE_ID,
>> new.EXTERNAL_DATABASE_RELEASE_ID, new.SOURCE_ID,
>> new.PREDICTION_ALGORITHM_ID, new.IS_PREDICTED, new.REVIEW_STATUS_ID,
>> new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
>> new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
>> new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
>> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE,
>> new.VERSION_TRANSACTION_ID );
>>
>> Angel Pizarro wrote:
>>
>> > Yes, I have an idea of what is going on ... sloppy copy-paste coding
>> > on my part :(
>> >
>> > I'll add the other columns to the method and get you another patch.
>> >
>> > -angel
>> >
>>
>>
>>
>> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java
>> ===================================================================
>> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (revision
>> 4068)
>> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (working
>> copy)
>> @@ -48,6 +48,10 @@
>>          return column;
>>      }
>>
>> +    public void setColumns( ArrayList<ColumnPair> colpair) {
>> +        column = colpair;
>> +    }
>> +
>>      public void addColumn( ColumnPair columnPair ) {
>>          if ( !this.column.contains( columnPair ) ) {
>>              this.column.add( columnPair );
>> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>> ===================================================================
>> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>> (revision 4068)
>> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>> (working copy)
>> @@ -12,6 +12,7 @@
>> import org.gusdb.dbadmin.model.GusSchema;
>> import org.gusdb.dbadmin.model.GusTable;
>> import org.gusdb.dbadmin.model.GusView;
>> +import org.gusdb.dbadmin.model.VersionView;
>> import org.gusdb.dbadmin.model.Schema;
>> import org.gusdb.dbadmin.model.Sequence;
>> import org.gusdb.dbadmin.model.Table;
>> @@ -105,6 +106,8 @@
>>          super.writeView( view );
>>          if ( view instanceof GusView ) {
>>              writeViewRules( (GusView) view );
>> +        }else if ( view instanceof VersionView ) {
>> +            writeVersionViewRules( (VersionView) view );
>>          }
>>      }
>>
>> @@ -112,8 +115,6 @@
>>       * Since PostgreSQL doesn't support updatable views, this is a hack
>> that
>>       * uses rules to mimick the updatable view functionality.
>>       *
>> -     * TODO: Note that this means version views are now not updatable
>> since they
>> -     * don't have a PK.
>>       *
>>       * @param view DOCUMENT ME!
>>       * @throws IOException DOCUMENT ME!
>> @@ -174,7 +175,47 @@
>>          oStream.flush( );
>>      }
>>
>> +
>>      /**
>> +     * Since PostgreSQL doesn't support updatable views, this is a hack
>> that
>> +     * uses rules to mimick the updatable view functionality.
>> +     *
>> +     * Version views are now not updatable since they
>> +     * don't have a PK, so we limit rules to insertion
>> +     *
>> +     * @param view DOCUMENT ME!
>> +     * @throws IOException DOCUMENT ME!
>> +     */
>> +    private void writeVersionViewRules( VersionView view ) throws
>> IOException {
>> +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
>> random.nextInt( 100000 ) + " AS ON INSERT TO "
>> +                + view.getSchema( ).getName( ) + "." + view.getName( ) +
>> " DO INSTEAD INSERT INTO  "
>> +                + view.getTable( ).getSchema( ).getName( ) + "." +
>> view.getTable( ).getName( ) + " ( " );
>> +
>> +        boolean first = true;
>> +        for ( ColumnPair columnPair : view.getColumns() ) {
>> +            if ( !first ) {
>> +                oStream.write( ", " );
>> +            }
>> +            oStream.write( columnPair.getTableName( ) );
>> +            first = false;
>> +        }
>> +
>> +        oStream.write( " ) VALUES ( " );
>> +
>> +        first = true;
>> +        for ( ColumnPair columnPair : view.getColumns() ) {
>> +            if ( !first ) {
>> +                oStream.write( ", " );
>> +            }
>> +            oStream.write( "new." + columnPair.getViewName( ) );
>> +            first = false;
>> +        }
>> +
>> +        oStream.write( " );\n\n" );
>> +
>> +    }
>> +
>> +    /**
>>       * DOCUMENT ME!
>>       *
>>       * @param type DOCUMENT ME!
>> Index:
>> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.java
>> ===================================================================
>> ---
>> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.java
>> (revision 4068)
>> +++
>> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.java
>> (working copy)
>> @@ -363,6 +363,9 @@
>>              superClassView.setVersioned( true );
>>              verSql = sql.concat( " " );
>>
>> +           // We need to add the superclass columns to the version view.
>> +           superClassView.getVersionView(
>> ).setColumns((ArrayList<ColumnPair>) superClassView.getColumns().clone());
>> +
>>              for ( Column column : verHousekeepingColumns ) {
>>                  verSql = verSql.concat( ", " + column.getName( ) );
>>                  superClassView.getVersionView( ).addColumn( new
>> ColumnPair( column.getName( ), column.getName( ) ) );
>> @@ -448,7 +451,8 @@
>>          if ( impTable.isVersioned( ) ) {
>>              subClass.setVersioned( true );
>>              verSql = sql.concat( " " );
>> -
>> +           // We need to add the subclass_view's columns
>> +           subClass.getVersionView( ).setColumns((ArrayList<ColumnPair>)
>> subClass.getColumns().clone());
>>              for ( Column column : verHousekeepingColumns ) {
>>                  verSql = verSql.concat( ", " + column.getName( ) );
>>                  subClass.getVersionView( ).addColumn( new ColumnPair(
>> column.getName( ), column.getName( ) ) );
>>
>>
>>
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

From: Angel P. <an...@ma...> - 2006-01-10 18:18:56

Attachments: PostgresWriter.diff

Hi Ricardo,
I imagine that Mike has not had a chance to get to this, so I took a 
stab at fixing this problem. Could you test out the attached patch? Copy 
the file to $PROJECT_HOME then:

cd $PROJECT_HOME
patch -p0 <PostgresWriter.diff

Then rebuild the GUS/DBAdmin project and redump the schema from the XML 
schema file:

build GUS/DBAdmin install -append
dbaDumpSchema -sourceType xml -source  
GusSchema/Definition/config/gus_schema.xml -targetType postgres -target 
gus.pg.ddl

That should produce the proper PostgreSQL ddl from which you can grep 
the version views and test the loads. If your tests are successful, I'll 
commit the file and post the patch on the bug.

-angel

Ricardo Balbi wrote:

> Mike / Steve,
>   We would like to know if you already had created the rules of the 
> version tables. 
>   We believe that with these rules we will go to obtain the loads, 
> using the ISF. 
>   In case that you have some position, you he could inform to me, please.
>
> thanks in advance,
> Ricardo
>
> 2006/1/3, bug...@pc... 
> <mailto:bug...@pc...> 
> <bug...@pc... <mailto:bug...@pc...>>:
>
>     https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257
>     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257>
>
>
>     msa...@pc... <mailto:msa...@pc...> changed:
>
>                What    |Removed                     |Added
>     ----------------------------------------------------------------------------
>                  Status|RESOLVED                    |REOPENED
>              Resolution|INVALID                     |
>
>
>
>
>     ------- Comment #4 from msa...@pc...
>     <mailto:msa...@pc...>  2006-01-03 12:05 -------
>     version table rules are indeed not being created.  this should be
>     relatively
>     straight forward to fix.
>
>
>     --
>     Configure bugmail:
>     https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=email
>     ------- You are receiving this mail because: -------
>     You reported the bug, or are watching the reporter.
>
>

-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

From: Ricardo B. <rb...@gm...> - 2006-01-17 12:05:40

Angel,
  I followed all the steps that you indicated me.
  I saved the PostgresWriter.diff file that you sent in $PROJECT_HOME.
  I executed the commands
    1. patch - p0 < PostgresWriter.diff
    2. build GUS/DBAdmin install - append
    3. dbaDumpSchema - sourceType xml - source
GusSchema/Definition/config/gus_schema.xml - targetType postgres - target
gus.pg.ddl,
  that generated the gus.pg.ddl file with all the creation of the database.

  However, the rules of table versioning had not been created correctly
because only some common fields  are involved in the rules
(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, version_alg_invocation_id, version_date,
version_transaction_id).
  If the other fields will no be created, errors in the execution of ISF
plugin occur when trying to insert null fields.

  It follows the example of three bred rules:

CREATE RULE AAFeatureVer_5159 AS ON INSERT TO DoTSVer.AAFeatureVer DO
INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( 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,
VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID ) VALUES (
new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, new.VERSION_TRANSACTION_ID=
);

CREATE RULE AffymetrixCELVer_10403 AS ON INSERT TO
RADVer.AffymetrixCELVerDO INSTEAD INSERT INTO
RADVer.ElementResultImpVer ( 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, VERSION_ALG_INVOCATION_ID,
VERSION_DATE, VERSION_TRANSACTION_ID ) VALUES ( new.MODIFICATION_DATE,
new.USER_READ, new.USER_WRITE, new.GROUP_READ, new.GROUP_WRITE,
new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, new.ROW_GROUP_ID,
new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, new.VERSION_ALG_INVOCATION_I=
D,
new.VERSION_DATE, new.VERSION_TRANSACTION_ID );

CREATE RULE BioSourceVer_45682 AS ON INSERT TO StudyVer.BioSourceVer DO
INSTEAD INSERT INTO  StudyVer.BioMaterialImpVer ( 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,
VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID ) VALUES (
new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, new.VERSION_TRANSACTION_ID=
);

  Do you have any idea why this is happening ?

Thanks in advance,
Ricardo

2006/1/10, Angel Pizarro <an...@ma...>:
>
> Hi Ricardo,
> I imagine that Mike has not had a chance to get to this, so I took a
> stab at fixing this problem. Could you test out the attached patch? Copy
> the file to $PROJECT_HOME then:
>
> cd $PROJECT_HOME
> patch -p0 <PostgresWriter.diff
>
> Then rebuild the GUS/DBAdmin project and redump the schema from the XML
> schema file:
>
> build GUS/DBAdmin install -append
> dbaDumpSchema -sourceType xml -source
> GusSchema/Definition/config/gus_schema.xml -targetType postgres -target
> gus.pg.ddl
>
> That should produce the proper PostgreSQL ddl from which you can grep
> the version views and test the loads. If your tests are successful, I'll
> commit the file and post the patch on the bug.
>
> -angel
>
> Ricardo Balbi wrote:
>
> > Mike / Steve,
> >   We would like to know if you already had created the rules of the
> > version tables.
> >   We believe that with these rules we will go to obtain the loads,
> > using the ISF.
> >   In case that you have some position, you he could inform to me,
> please.
> >
> > thanks in advance,
> > Ricardo
> >
> > 2006/1/3, bug...@pc...
> > <mailto:bug...@pc...>
> > <bug...@pc... <mailto:bug...@pc...
> >>:
> >
> >     https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D257
> >     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D257>
> >
> >
> >     msa...@pc... <mailto:msa...@pc...> changed:
> >
> >                What    |Removed                     |Added
> >
> -------------------------------------------------------------------------=
---
> >                  Status|RESOLVED                    |REOPENED
> >              Resolution|INVALID                     |
> >
> >
> >
> >
> >     ------- Comment #4 from msa...@pc...
> >     <mailto:msa...@pc...>  2006-01-03 12:05 -------
> >     version table rules are indeed not being created.  this should be
> >     relatively
> >     straight forward to fix.
> >
> >
> >     --
> >     Configure bugmail:
> >     https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=3Demail
> >     ------- You are receiving this mail because: -------
> >     You reported the bug, or are watching the reporter.
> >
> >
>
>
> --
>
> Angel Pizarro
> Director, Bioinformatics Facility
> Institute for Translational Medicine and Therapeutics
> University of Pennsylvania
> 806 BRB II/III
> 421 Curie Blvd.
> Philadelphia, PA 19104-6160
>
> P: 215-573-3736
> F: 215-573-9004
>
>
>
> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (revision 4068)
> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (working copy)
> @@ -12,6 +12,7 @@
> import org.gusdb.dbadmin.model.GusSchema;
> import org.gusdb.dbadmin.model.GusTable;
> import org.gusdb.dbadmin.model.GusView;
> +import org.gusdb.dbadmin.model.VersionView;
> import org.gusdb.dbadmin.model.Schema;
> import org.gusdb.dbadmin.model.Sequence;
> import org.gusdb.dbadmin.model.Table;
> @@ -105,6 +106,8 @@
>          super.writeView( view );
>          if ( view instanceof GusView ) {
>              writeViewRules( (GusView) view );
> +        }else if ( view instanceof VersionView ) {
> +            writeVersionViewRules( (VersionView) view );
>          }
>      }
>
> @@ -112,8 +115,6 @@
>       * Since PostgreSQL doesn't support updatable views, this is a hack
> that
>       * uses rules to mimick the updatable view functionality.
>       *
> -     * TODO: Note that this means version views are now not updatable
> since they
> -     * don't have a PK.
>       *
>       * @param view DOCUMENT ME!
>       * @throws IOException DOCUMENT ME!
> @@ -174,7 +175,47 @@
>          oStream.flush( );
>      }
>
> +
>      /**
> +     * Since PostgreSQL doesn't support updatable views, this is a hack
> that
> +     * uses rules to mimick the updatable view functionality.
> +     *
> +     * Version views are now not updatable since they
> +     * don't have a PK, so we limit rules to insertion
> +     *
> +     * @param view DOCUMENT ME!
> +     * @throws IOException DOCUMENT ME!
> +     */
> +    private void writeVersionViewRules( VersionView view ) throws
> IOException {
> +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
> random.nextInt( 100000 ) + " AS ON INSERT TO "
> +                + view.getSchema( ).getName( ) + "." + view.getName( ) +
> " DO INSTEAD INSERT INTO  "
> +                + view.getTable( ).getSchema( ).getName( ) + "." +
> view.getTable( ).getName( ) + " ( " );
> +
> +        boolean first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( columnPair.getTableName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " ) VALUES ( " );
> +
> +        first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( "new." + columnPair.getViewName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " );\n\n" );
> +
> +    }
> +
> +    /**
>       * DOCUMENT ME!
>       *
>       * @param type DOCUMENT ME!
>
>
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

From: Angel P. <an...@ma...> - 2006-01-17 14:26:59

Yes, I have an idea of what is going on ... sloppy copy-paste coding on 
my part :(

I'll add the other columns to the method and get you another patch.

-angel

Ricardo Balbi wrote:

> Angel,
>   I followed all the steps that you indicated me. 
>   I saved the PostgresWriter.diff file that you sent in $PROJECT_HOME.
>   I executed the commands
>     1. patch - p0 < PostgresWriter.diff
>     2. build GUS/DBAdmin install - append
>     3. dbaDumpSchema - sourceType xml - source 
> GusSchema/Definition/config/gus_schema.xml - targetType postgres - 
> target gus.pg.ddl,
>   that generated the gus.pg.ddl file with all the creation of the 
> database. 
>   However, the rules of table versioning had not been created 
> correctly because only some common fields  are involved in the rules 
> (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, version_alg_invocation_id, version_date, 
> version_transaction_id). 
>   If the other fields will no be created, errors in the execution of 
> ISF plugin occur when trying to insert null fields. 
>  
>   It follows the example of three bred rules:
>
> CREATE RULE AAFeatureVer_5159 AS ON INSERT TO DoTSVer.AAFeatureVer DO 
> INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( 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, VERSION_ALG_INVOCATION_ID, VERSION_DATE, 
> VERSION_TRANSACTION_ID ) VALUES ( new.MODIFICATION_DATE, 
> new.USER_READ, new.USER_WRITE, new.GROUP_READ, new.GROUP_WRITE, 
> new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, new.ROW_GROUP_ID, 
> new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, 
> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, 
> new.VERSION_TRANSACTION_ID );
>
> CREATE RULE AffymetrixCELVer_10403 AS ON INSERT TO 
> RADVer.AffymetrixCELVer DO INSTEAD INSERT INTO  
> RADVer.ElementResultImpVer ( 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, 
> VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID ) 
> VALUES ( new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, 
> new.GROUP_READ, new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, 
> new.ROW_USER_ID, new.ROW_GROUP_ID, new.ROW_PROJECT_ID, 
> new.ROW_ALG_INVOCATION_ID, new.VERSION_ALG_INVOCATION_ID, 
> new.VERSION_DATE, new.VERSION_TRANSACTION_ID );
>
> CREATE RULE BioSourceVer_45682 AS ON INSERT TO StudyVer.BioSourceVer 
> DO INSTEAD INSERT INTO  StudyVer.BioMaterialImpVer ( 
> 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, VERSION_ALG_INVOCATION_ID, VERSION_DATE, 
> VERSION_TRANSACTION_ID ) VALUES ( new.MODIFICATION_DATE, 
> new.USER_READ, new.USER_WRITE, new.GROUP_READ, new.GROUP_WRITE, 
> new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, new.ROW_GROUP_ID, 
> new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, 
> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, 
> new.VERSION_TRANSACTION_ID );
>
>   Do you have any idea why this is happening ?
>
> Thanks in advance,
> Ricardo
>
> 2006/1/10, Angel Pizarro <an...@ma... 
> <mailto:an...@ma...>>:
>
>     Hi Ricardo,
>     I imagine that Mike has not had a chance to get to this, so I took a
>     stab at fixing this problem. Could you test out the attached
>     patch? Copy
>     the file to $PROJECT_HOME then:
>
>     cd $PROJECT_HOME
>     patch -p0 <PostgresWriter.diff
>
>     Then rebuild the GUS/DBAdmin project and redump the schema from
>     the XML
>     schema file:
>
>     build GUS/DBAdmin install -append
>     dbaDumpSchema -sourceType xml -source
>     GusSchema/Definition/config/gus_schema.xml -targetType postgres
>     -target
>     gus.pg.ddl
>
>     That should produce the proper PostgreSQL ddl from which you can grep
>     the version views and test the loads. If your tests are
>     successful, I'll
>     commit the file and post the patch on the bug.
>
>     -angel
>
>     Ricardo Balbi wrote:
>
>     > Mike / Steve,
>     >   We would like to know if you already had created the rules of the
>     > version tables.
>     >   We believe that with these rules we will go to obtain the loads,
>     > using the ISF.
>     >   In case that you have some position, you he could inform to
>     me, please.
>     >
>     > thanks in advance,
>     > Ricardo
>     >
>     > 2006/1/3, bug...@pc...
>     <mailto:bug...@pc...>
>     > <mailto:bug...@pc...
>     <mailto:bug...@pc...>>
>     > <bug...@pc...
>     <mailto:bug...@pc...>
>     <mailto:bug...@pc...
>     <mailto:bug...@pc...>>>:
>     >
>     >     https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257
>     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257>
>     >     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257>
>     >
>     >
>     >     msa...@pc... <mailto:msa...@pc...>
>     <mailto:msa...@pc... <mailto:msa...@pc...>>
>     changed:
>     >
>     >                What    |Removed                     |Added
>     >    
>     ----------------------------------------------------------------------------
>     >                  Status|RESOLVED                    |REOPENED
>     >              Resolution|INVALID                     |
>     >
>     >
>     >
>     >
>     >     ------- Comment #4 from msa...@pc...
>     <mailto:msa...@pc...>
>     >     <mailto:msa...@pc...
>     <mailto:msa...@pc...>>  2006-01-03 12:05 -------
>     >     version table rules are indeed not being created.  this
>     should be
>     >     relatively
>     >     straight forward to fix.
>     >
>     >
>     >     --
>     >     Configure bugmail:
>     >     https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=email
>     >     ------- You are receiving this mail because: -------
>     >     You reported the bug, or are watching the reporter.
>     >
>     >
>
>
>     --
>
>     Angel Pizarro
>     Director, Bioinformatics Facility
>     Institute for Translational Medicine and Therapeutics
>     University of Pennsylvania
>     806 BRB II/III
>     421 Curie Blvd.
>     Philadelphia, PA 19104-6160
>
>     P: 215-573-3736
>     F: 215-573-9004
>
>
>
>     Index:
>     GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>     ===================================================================
>     ---
>     GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java  
>     (revision 4068)
>     +++
>     GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java  
>     (working copy)
>     @@ -12,6 +12,7 @@
>     import org.gusdb.dbadmin.model.GusSchema;
>     import org.gusdb.dbadmin.model.GusTable;
>     import org.gusdb.dbadmin.model.GusView ;
>     +import org.gusdb.dbadmin.model.VersionView;
>     import org.gusdb.dbadmin.model.Schema;
>     import org.gusdb.dbadmin.model.Sequence;
>     import org.gusdb.dbadmin.model.Table;
>     @@ -105,6 +106,8 @@
>              super.writeView ( view );
>              if ( view instanceof GusView ) {
>                  writeViewRules( (GusView) view );
>     +        }else if ( view instanceof VersionView ) {
>     +            writeVersionViewRules( (VersionView) view );
>              }
>          }
>
>     @@ -112,8 +115,6 @@
>           * Since PostgreSQL doesn't support updatable views, this is
>     a hack that
>           * uses rules to mimick the updatable view functionality.
>           *
>     -     * TODO: Note that this means version views are now not
>     updatable since they
>     -     * don't have a PK.
>           *
>           * @param view DOCUMENT ME!
>           * @throws IOException DOCUMENT ME!
>     @@ -174,7 +175,47 @@
>              oStream.flush( );
>          }
>
>     +
>          /**
>     +     * Since PostgreSQL doesn't support updatable views, this is
>     a hack that
>     +     * uses rules to mimick the updatable view functionality.
>     +     *
>     +     * Version views are now not updatable since they
>     +     * don't have a PK, so we limit rules to insertion
>     +     *
>     +     * @param view DOCUMENT ME!
>     +     * @throws IOException DOCUMENT ME!
>     +     */
>     +    private void writeVersionViewRules( VersionView view ) throws
>     IOException {
>     +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
>     random.nextInt( 100000 ) + " AS ON INSERT TO "
>     +                + view.getSchema( ).getName( ) + "." +
>     view.getName( ) + " DO INSTEAD INSERT INTO  "
>     +                + view.getTable( ).getSchema( ).getName( ) + "."
>     + view.getTable( ).getName( ) + " ( " );
>     +
>     +        boolean first = true;
>     +        for ( ColumnPair columnPair : view.getColumns() ) {
>     +            if ( !first ) {
>     +                oStream.write( ", " );
>     +            }
>     +            oStream.write( columnPair.getTableName( ) );
>     +            first = false;
>     +        }
>     +
>     +        oStream.write( " ) VALUES ( " );
>     +
>     +        first = true;
>     +        for ( ColumnPair columnPair : view.getColumns() ) {
>     +            if ( !first ) {
>     +                oStream.write( ", " );
>     +            }
>     +            oStream.write( "new." + columnPair.getViewName( ) );
>     +            first = false;
>     +        }
>     +
>     +        oStream.write( " );\n\n" );
>     +
>     +    }
>     +
>     +    /**
>           * DOCUMENT ME!
>           *
>           * @param type DOCUMENT ME!
>
>
>