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

[<jld...@pc...>]

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( ) ) );
>>
>>
>>
>