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Re: [GUSDEV] Re: [Bug 257] The rules had not been created
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From: Ricardo B. <rb...@gm...> - 2006-01-17 19:36:33
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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( ) ) );
>
>
>
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